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  • Q1: TVO ILC Student name: Date: SBI3U Assessment #1 for Feedback and Grade Assessment #1 for Feedback and Grade Level/Mark Percentage of term work /10% Instructions: • • Answer the questions for this assessment on a separate piece of paper. Make sure to note the task and question number you are answering for each. (e.g. Task 1, Question #1, etc. Review the rubric for this assessment located on the last pages before answering the questions for an understanding of how the assessment will be graded. • All terms must be included in mindmap. Copyright © 2021 The Ontario Educational Communications Authority. All rights reserved. TVO ILC SBI3U Assessment #1 for Feedback and Grade Task 1: Short answer - 10 Questions 1. In many viral diseases (such as smallpox, mumps, or influenza), illness occurs shortly after exposure to the virus. In others (such as AIDS), the victim may not show symptoms for many years following the initial exposure. How would you explain the difference between these two situations? 2. Various bacteria are normally present in most of our body systems. These “good” bacteria are essential for maintaining health. Describe two risks and two benefits of using antibacterial creams to cure vaginal infections. 3. State and describe two differences between bacteria and viruses. 4. a) State one reason why viruses are considered to be non-living organisms by some biologists. b) State one reason why viruses are considered to be living organisms by some biologists. 5. a) Which major level of classification contains the most closely related species? b) Which major level of classification contains the largest grouping of species? 6. List and describe three ecological roles of fungi OR three ecological roles of protists. 7. State and describe three characteristics of a body plan. 8. List and describe three reasons for habitat loss caused by humans. 9. Why do endothermic animals have far greater energy requirements than ectotherms? 10. Using the shark anatomy pictures and the key provided, classify the 10 sharks labelled 1- 10 in the following diagram: Copyright © 2021 The Ontario Educational Communications Authority. All rights reserved. TVO ILC Shark species 4 6 2 5 7 SBI3U Assessment #1 for Feedback and Grade 3 8 9 10 Shark Anatomy Use these terms related to shark anatomy to help you work through the key below. Key First dorsal fin Anal fin Pelvic fin Pectoral fin Dorsal surface Copyright © 2021 The Ontario Educational Communications Authority. All rights reserved. -Caudal fin TVO ILC SBI3U Assessment #1 for Feedback and Grade 1a. Body, as seen from the top, shaped like a kite...... 1b. Body, as seen from the top, not shaped like a kite.. 2a. Pelvic fin absent......... 2b. Pelvic fin present.. 3a. Six gill slits...... 3b. Five gill slits.. 4a. One dorsal fin.……………………. 4b. Two dorsal fins..... ..go to 12 ..go to 2 ..Pristiophoridae ..go to 3 ..Hexanchidae .go to 4 .Scyliorhinidae 5a. Mouth located at front of snout... .go to 5 Rhincodontidae go to 6 5b. Mouth located on underside of head.... 6a. Head expanded, with eyes located at end of expansion………………………….. ..Sphrynidea 6b. Head not expanded....... 7a. Top half of caudal fin same as bottom half.. 7b. Top half of caudal fin different than bottom half 8a. First dorsal fin extremely short... 8b. First dorsal fin regular length……………….. 9a. Caudal fin extremely long.. 9b. Caudal fin regular length...... 10a. A long point on end of snout… 10b. Snout without long point... 11a. Anal fin absent...... 11b. Anal fin present.... 12a. Small dorsal fin present near tip of tail.. 12b. No dorsal fin near tip of tail….. 13a. Front of animal with two horn-like appendages...... 13b. No horn-like appendages...... .go to 7 ....Isuridae .go to 8 .Pseuodotriakidae .go to 9 ..Alopiidae ..go to 10 ..Scapanorhynchidae go to 11 .Squalidae .Carcharhinidae .Rajidae .go to 13 .Mobulidae .Dasyatidae Copyright © 2021 The Ontario Educational Communications Authority. All rights reserved. TVO ILC SBI3U Assessment #1 for Feedback and Grade Task 2: Mind Map Recall an earlier activity where you created a mind map of the kingdom Animalia. It may have looked something like this one: Kingdom Animalia Invertebrates Simple Invertebrates phylum phylum Porifera Cnidaria (no backbone) Worm-like Invertebrates phylum Nematoda phylum phylum Complex Joint-legged Invertebrates phylum Invertebrates phylum Mollusca Echinodermata Platyhelminthes Annelida phylum Porifera Vertebrates (backbone) phylum Chordata class Arachnida class Crustacea class Insecta class Diplopoda class Chilopoda class Agnatha class Osteichthyes class Amphibia class Reptilia class Aves class Mammalia Now, it is time to put together all the information you learned about the different kingdoms into one concept map. All terms must be included. You may create this concept map however you like. You may use pen and paper or you may choose to use a computer program/digital tool. Another option would be to use index cards to write the terms on them and then organize them on a flat surface and take a picture to submit when complete. This could be done with "sticky notes" on a wall too. There are lots of terms and you must consider how they will be organized together. Notice how, in the example above, the categories or 'groupings' that were not official scientific classifications (for example, simple invertebrates, worm-like invertebrates, complex invertebrates, joint-legged invertebrates, invertebrates, and vertebrates) do not have kingdom, phylum, or class in front of them. They are just classifications that scientists use to help them understand the living world. In your concept map, make sure you can tell which classifications are official phyla and which ones are just groupings scientists make to help their understanding. The reason this is done is because there are so many phyla in each kingdom. In your concept map, aim to incorporate and make connections between all the terms as provided in the table below. Include characteristics and common features in your concept map. Organizing all of this will be difficult, but stick with it. It will help to get the big picture of all the material and terms you have learned throughout this unit. Copyright © 2021 The Ontario Educational Communications Authority. All rights reserved.See Answer
  • Q2: Research The biophysics of the ion channel recordings of stomata under salt stress theory and experimental application. Content about: Stomata ion channel recordings. salt concentration stress the importance of this topic for plants to grow in arid climates. what ion channels are effective in biophysicals according to them? biophysical theory and measurement. experimental technique (experimentation) the model from the Wang paper and from the Hedrich paper as they both involve ion channel recordings. 13 pages at least, references pictures and others do not account. 1.5 line space Times new Roman 12 points. an outline should be in a separate file with references. Supplementary Materials: Comprising Materials and Methods, figures, and tables; should be in a separate file. One Sentence Summary: no more than 110 characters. introductory paragraph, a thesis statement. Abstract: no more 115 words, and organized in this structure: An opening sentence that sets the question that you address and is comprehensible to the general reader, background content specific to this study, results, and a concluding sentence. It should be a single paragraph. References: Followed by a numbered list only a single reference list should be provided for the main text and supplemental information. please add the pictures from the articles I have attachedSee Answer
  • Q3: CHY547 W2024 - February 14/15, 2024 Structure of presentation 1 (10 min + 2-3 min questions) Introductory slide (1-2 slides) Objective of article (1 slide) Materials and methods (2 slides) Summary of research and conclusion (3 slides) Identify the strengths and weaknesses (2 slides) Usefulness and validity of research findings (1 slide) Pointers: Presentation structure makes sense. Show that you have the scientific foundation necessary to discuss your article Practice and be prepared to present ... avoid reading from notes! Structure of your written appraisal (~ 5 pages) (written as a duo) Introduction Objective of article Materials and methods Summary of research and conclusion Identify the strengths and weaknesses Usefulness and validity of research findings The 5 pages exclude the title page and references, should you choose to use some./n ELSEVIER ARTICLE INFO Quality of green beans (Phaseolus vulgaris L.) influenced by microwave and hot water pasteurization Keywords: Microwave pasteurization Frozen green beans Color Food Control 124 (2021) 107936 Zhi Quª, Zhongwei Tangª, Fang Liuª, Shyam S. Sablaniª, Carolyn F. Ross ¹, Sindhuja Sankaranª, Juming Tang a, Chlorophyll Aerobic mesophilic bacteria Ascorbic acid Contents lists available at ScienceDirect a Department of Biological Systems Engineering, Washington State University, Pullman, WA, 99164-6120, USA b School of Food Science, Washington State University, Pullman, WA, 99164-6120, USA 1. Introduction Food Control journal homepage: www.elsevier.com/locate/foodcont Corresponding author. E-mail address: jtang@wsu.edu (J. Tang). ABSTRACT Vegetables are critical components of a healthy diet and account for an essential part of ready-to-eat (RTE) meals. RTE vegetables can be consumed either as recipe dishes intended for the retail market or as pre- cooked ingredients for caterers or other food services (Choma et al., 2000). Thermal processing is a classical method of food preservation that has been widely used in the production of RTE vegetables. In commercial preparation of RTE meals for cold chain distribution, a thermal process that exposes food products at 90 °C for 10 min, or an equivalent lethality, at the cold spot (the spot in the food which receives the least heat) in packages is often used to achieve a 6-log reduction of non-proteolytic Clostridium botulinum. This process would provide the products up to 6 weeks' shelf life at 5 °C (ECFF, 2006). The chill tem- perature storage serves as a prudent second barrier to maintain quality and extend the shelf life of the RTE meals. The process mentioned above is sufficient to inactivate vegetative microbial flora; it may also activate dormant bacterial endospores (Krawczyk et al., 2017; Luu et al., 2015), leading to subsequent germi- nation and outgrowth of nonpathogenic vegetative cells during cold storage. Sonar, Rasco, Tang, & Sablani (2019) reported that the aerobic CONTROL CONTROL FOOD CONTROL CONTROL CONTROL CONTROL CONTROL PELL This research investigated the influence of 915 MHz microwave-assisted thermal pasteurization and conventional hot water pasteurization (F30=10 min) on chlorophylls, greenness (a*), ascorbic acid, and the growth of spoilage microorganisms in green beans in storage at 10, 7, and 2 °C for up to 100 days. Frozen cut green beans were processed in vacuum-sealed containers flushed with N₂. The beans suffered 28.3% and 33.9% losses of chloro- phyll a, 9.2% and 15.3% losses of ascorbic acid during the microwave and hot water processing, respectively. During storage, slower spoilage (21 days at 10 °C, 42 days at 7 °C, and 100 days at 2 °C), superior preservation of chlorophyll (47-50%), ascorbic acid (47-62%), and a lower increase in a* (2.8-5.2) were obtained in samples processed with microwave-assisted thermal pasteurization. Paenibacillus spp. were identified as the predominant bacteria in the spoiled green beans pasteurized with both methods. The results highlighted the potential of microwave pasteurization for producing safe, high-quality vegetable products. Check for updates https://doi.org/10.1016/j.foodcont.2021.107936 Received 29 June 2020; Received in revised form 22 January 2021; Accepted 23 January 2021 Available online 29 January 2021 0956-7135/© 2021 Elsevier Ltd. All rights reserved. of HACCP and Food Safety CONTROL CONTROL mesophilic bacterial growth in pasteurized green pea puree (F=10 min) reached 6 log CFU/g after 80 days at 7 °C. Sous vide processed julienne carrots (85 °C) stored at 8 °C for four weeks had a total plate count of 6.48 log CFU/g (Nyati, 2000). Carlin et al. (2000) also observed that the count of aerobic mesophilic bacteria in pasteurized broccoli, carrot, zucchini, leek, potato, and split pea puree (80 °C, 30 min) increased up to 6–8 log CFU/g after 20-day storage at 10 °C. It has been reported that pasteurized zucchini puree showed the most rapid bacte- rial growth, while cook-chilled soybean sprouts (90 °C, 10 min) had no aerobic bacterial growth when stored at 10 °C for 24 days (Koo, Kim, Lee, Lyu, & Paik, 2008). It is evident from the literature that various vegetables after thermal pasteurization supported different bacterial growth, leading to a wide range of shelf life in cold storage at different temperatures. Thus, it is important to assess bacterial growth at different storage temperatures in studying quality losses and shelf life of RTE vegetables. The thermal processing and storage of vegetables inevitably result in changes in physical characteristics and chemical composition, such as color, bioactive compounds, and antioxidants (Baardseth, Bjerke, Mar- tinsen, & Skrede, 2010; Mazzeo et al., 2011; Peng et al., 2017). Con- sumers' demand for high-quality, fresh-like products has stimulated the Z. Qu et al. development of new technologies aiming at reducing the adverse effects of processing and storage. Microwave heating has shown advantages in reduced heating time and improved heating uniformity when compared with conventional hot water heating (Khan, Tango, Miskeen, Lee, & Oh, 2017). The microwaves penetrate into the food and generate heat throughout the whole volume of food, making thermal conductivity and heat transfer coefficients no longer the limit of heat transfer (Burfoot, Griffin, & James, 1988). Another advantage of microwave heating is the direct conversion of electromagnetic radiation into heat within foods, which could improve energy efficiency (Regier & Schubert, 2001). These advantages over hot water heating often yield an increased pro- duction rate and a reduction in undesirable thermal degradation (Ahmed & Ramaswamy, 2007; Khan et al., 2017). 93.3 Several studies have compared the quality of different RTE foods preserved by microwave with hot water heating that delivered an equivalent level of control of foodborne pathogens. Pérez-Tejeda et al. (2016) reported less color changes in tomato puree after processing using microwaves (950W, F833 = 1 min). Marszałek, Mitek, and Skąpska (2015) concluded that microwave heating better preserved the color and nutrient of strawberry puree than conventional heat pasteurization. Published shelf life studies on pasteurized vegetables have been limited to puree or smoothie (Arjmandi et al., 2017; Benlloch-Tinoco, Igual, Rodrigo, & Martínez-Navarrete, 2015; Klug et al., 2018), which do not represent a typical range of commonly consumed RTE meals. In addition, the studies on microwave pasteurization of vegetables are based on domestic microwave ovens, which do not represent the pro- cessing conditions used in industrial microwave systems for the com- mercial production of RTE meals. The objective of this study was to systematically evaluate the effects of 915 MHz microwave-assisted thermal pasteurization and conventional hot water pasteurization (F30=10 min) on the quality of green beans stored at different temper- atures (10, 7, and 2 °C). The green beans were characterized in terms of aerobic mesophilic bacteria count, pH, chlorophyll, color, and ascorbic acid. 2. Materials and methods 2.1. Sample preparation Since our intention was to simulate industrial processes for year- around operation, we selected frozen green beans for this research. Frozen cut green beans (Phaseolus vulgaris L.), with a size of ~2.5 cm in length and 0.8 cm in diameter, and a moisture content of 90.5%, were purchased from the local market and stored in sealed bags at -18 °C. The green beans were blanched before flash freezing, as indicated by the manufacturer. Before testing, the green beans were defrosted in 4 °C water for 10 min and then drained off for 5 min. Approximately 226 g thawed green beans were filled into each rigid tray (Silgan Plastics, Chesterfield, MO) with a PP/regrind/tie/EVOH/tie/regrind/PP struc- ture and an inner dimension of 140 × 95 × 30 mm. The trays were vacuum sealed with lidding film tal oxide coated PET/biaxial ori- ented PA/PP) with a thickness of 101 ± 1.6 µm (Printpack., Atlanta, GA), using a vacuum sealer (Multivac T-200, Multivac Inc., Kansas City, MO). The sealing conditions were set at 200 °C for 8 s, with a vacuum (6.5 kPa absolute pressure) and nitrogen flushing at 45 kPa (absolute pressure). 2.2. Thermal processing and storage Thermal processing was designed to achieve the lethality of F30 = 10 min at the cold spot in the trays. The lethality value was calculated according to Eq. (1): F= jio 0 T-Tref (1) 2 Food Control 124 (2021) 107936 where T (°C) is the temperature measured at the cold spot at time t (min), Tref is the reference temperature (90 °C), and z represents the temperature sensitivity of the heat tolerance of the target microor- ganism. We selected a z-value of 10 °C for non-proteolytic Clostridium botulinum (ECFF, 2006). The cold spot in the trays during the hot water processing was located at the geometric center of the package. For microwave-assisted thermal pasteurization, a mashed potato model food containing chemical marker precursors was employed for cold spot determination (Bornhorst, Tang, Sablani, & Barbosa-Cánovas, 2017). The heating pattern inside the microwave processed model food, as indicated by the intensity of browning, was analyzed using a computer vision method developed by Pandit, Tang, Liu, and Mikhaylenko (2007). Based on the heating pattern, the cold spot was located off the geometric center and in the middle layer of the trays. Heat penetration studies were carried out by collecting time-temperature data at the cold spot in the food trays to determine the process schedules. The temperatures were recorded every 2 s by a mobile metallic temperature sensor and a TMI data logger workstation (TMI-USA Inc., Reston, VA) (Luan, Tang, Pedrow, Liu, & Tang, 2013, 2015). This measurement method has been validated with fiber optic temperature sensors for developing microwave-assisted pasteurization processes (Tang, 2015). 2.2.1. Microwave-assisted thermal processing The microwave processing was performed in a pilot-scale 915 MHz semi-continuous Microwave-Assisted Pasteurization System (MAPS) developed at Washington State University. The system consisted of four sections (preheating, microwave heating, holding, and cooling), and each section had a separate water circulation system to control the water temperature and flow. The microwave section had four single-mode cavities connected to microwave generators. Approximately 5 kW of power was applied to each of the first two cavities, and the other two cavities equally split 8.7 kW. A metal carrier that could carry eight trays was immersed in the water and moved through the four sections mentioned above. The details of MAPS can be found in Tang, Hong, Inanoglu, and Liu (2018). 2.2.2. Conventional hot water processing Conventional hot water (HW) processing was conducted by immersing the packages in a precision digital circulating water bath (Model 260, Thermo Scientific, Marietta, OH) set at 91 °C. Two trays were processed at a time. 2.2.3. Storage conditions A total of 144 trays were processed and stored with protection from light at 10 ± 1 (a common refrigeration abuse temperature), 7 ± 1 (domestic refrigeration temperature), and 2 ± 0.5 °C (lower chill tem- perature) for 21, 42, and 100 days (Cronin & Wilkinson, 2009; James, Evans, & James, 2008). Three trays were randomly selected for each time point (Day 3, 7, 11, 14, 17, 21 at 10 °C; Day 5, 10, 15, 21, 28, 35, 42 at 7 °C; Day 7, 14, 28, 42, 60, 80, 100 at 2 °C), and each tray was measured in triplicate for quality quantification and microbiological analyses. 2.3. Microbiological analyses Thawed or processed green beans were pureed using a hand blender (KHB100ER1, KitchenAid, Benton Harbor, MI). Before grinding, the blending arm and blade of the blender were sterilized using steam at 121 °C for 15 min, the motor body (holding part) was cleaned with 70% ethanol wipes. Every 30 s grinding followed by 30 s rest to allow ground green beans to cool down. The total grinding/resting time equaled 5 min. The total mesophilic bacteria were examined by diluting the green bean puree in 0.1% (w/v) of sterilized peptone water and plated on Plate Count Agar (PCA) and then incubated at 37 °C for 48 h, both aerobically and anaerobically. Yeast and mold were enumerated by dispensing Z. Qu et al. aliquots onto Potato Dextrose Agar (PDA) following incubation at 25 °C for 5 days. The PDA was acidified by adding 1 mL of tartaric acid per 10 mL of PDA. The aerobic mesophilic bacteria, yeast, and mold were analyzed before and after thermal pasteurization (Day 0), and at the selected sampling points as described in section 2.2.3. The anaerobic mesophilic count was only determined at the end of the storage (Day 21 at 10 °C, Day 42 at 7 °C, Day 100 at 2 °C). The selected dilutions from each green bean sample were plated in triplicate. All microbial counts were reported as log₁0 colony-forming units per gram of green bean (log CFU/g). The isolated colonies were identified by amplification of the 16S rRNA or the rpoB gene by PCR using universal eubacterial primers and comparing the results with sequences in the GenBank Database by the Washington Animal Disease Diagnostic Laboratory (Washington State University, Pullman, WA). 2.4. pH The pH was determined by mixing 3 g of puree with 27 mL of deionized water and measuring at room temperature (23 °C) with a pH meter (Oakton Instruments, Vernon Hills, Il). 2.5. Chlorophyll For chlorophyll determination, 3 g of green bean puree was ho- mogenized with 25 mL of acetone-water (80:20, v/v) for 5 min at 7000 rpm (Polytron PT 10/35 GT, Kinematica AG, Luzern, Switzerland). The mixture was then put in a shaker rotating at 300 rpm at room temper- ature for 30 min and centrifuged at 8870 g for 6 min (Sorvall Biofuge Primo, Thermo Scientific, Waltham, MA). The supernatant was collected and brought up to a volume of 50 mL with acetone-water for spectro- photometric analysis (V-5000, Metash Instruments, Shanghai, China) at the wavelengths of 663 and 647 nm, measured against a blank. Eqs. (2)— (4) were used for calculation (Lichtenthaler, 1987), and the chlorophyll content was expressed as mg per 100 g. Chlorophyll a = 12.25A663 -2.79A647 Chlorophyll b = 21.5A647 - 5.10A663 Total chlorophyll=7.15A663 +18.71A647 2.6. Color (2) (3) (4) The sample color was quantified in CIE L*a*b* color space using image analysis. L* corresponds to lightness/darkness, a* represents red (+) to green (-), and b* represents yellow (+) to blue (−). The green beans from the topmost layer of the trays were taken out for image analysis, which aimed to simulate the first impression of the consumers as they opened the package. A computer vision system described by Zhang, Tang, Liu, Bohnet, and Tang (2014) was used to take photos (resolution: 5184 × 3456). The RGB images were calibrated using a color reference card (QPcard 203, QPcard AB, Helsingborg, Sweden) in Adobe Photoshop CC (Adobe system, Inc., San Jose, CA). Image analysis was performed in MATLAB R2019b (MathWorks, Inc., Natick, MA) by converting RGB to L*a*b*. Thresholding was applied to select the region of interest through background removal. The color value obtained was the average color value of all pixels in the region of interest. The color difference was calculated based on Eq. (5): 2.7. Ascorbic acid 2 AE = √√ (L* − Lö)² + (a* − aj)² + (b* − bő)² where Lo, do, and be correspond to the initial values of L*, a*, and b*. (5) Quantification of ascorbic acid (AA) was determined by HPLC 3 following the method described by Scherer et al. (2012) with modifi- cations. Five grams of green bean puree was homogenized with 10 mL 3% (w/v) meta-phosphoric acid for 1 min at 7000 rpm. The homogenate was incubated at room temperature (23 °C) for 2 h and centrifuged at 8870 g for 6 min. The supernatant was collected and filtered through a 0.45 μm nylon filter. Ten microliters of this filtered aliquot was injected into an Agilent 1100 HPLC system (Agilent Technology, Santa Clara, CA) to chromatographically separate the mixture into its component peaks through an RP18 5-µm 4.6 × 250 mm column (Waters Corporation, Milford, MA) equipped with a diode array detector. The mobile phase was a 0.01 mol/L monopotassium phosphate solution adjusted to a pH of 2.6 with o-phosphoric acid. The separation was accomplished using a 15-min isocratic elution procedure with a flow rate of 0.5 mL/min and a column temperature of 25 °C. The detecting wavelength was 250 nm. Pure L-Ascorbic acid was used to build a standard curve, and the AA content was expressed as mg per 100 g green beans. 2.8. Data analysis Kinetic degradation of quality attributes was analyzed based on the analytical data collected during storage. The zero-order reaction model (Eq. (6)) and the first-order fractional conversion model (Eq. (7)) were found to best fit with the experimental data in this study: C=Co - kt C-Co co Coo Food Control 124 (2021) 107936 -kt (6) (7) where Co is the initial value of the food quality attribute at t = 0 (day), C is the value at time t (day), C… is the final equilibrium value, and k is the reaction rate constant (day¯¹), which is temperature-dependent and follows the Arrhenius relationship (Peleg, Normand, & Corradini, 2012): Ea RT k = koexp( (8) 3. Results and discussion where Ea is the activation energy (kJ/mol), R is the universal gas con- stant (0.008314 kJ/mol K), T is the absolute temperature (K), and ko is the pre-exponential factor. The analysis of variance and Tukey's honestly significant difference test at a 95% confidence level (P < 0.05) were performed to identify the differences among groups using SPSS v25 (IBM Corp., Armonk, NY). Two-tailed Pearson correlation analysis was carried out at the signifi- cance level of 0.01. 3.1. Thermal processing Typical temperature profiles at the cold spots in trays are shown in Fig. 1. MAPS processing included preheating for 35 min at 51 °C, mi- crowave heating for 4.5 min in circulating water set at 91 °C, holding for 7.5 min in circulating water set at 91 °C, and cooling for 5 min at 23 °C. In HW processing, samples were heated for 47 min at 91 °C and cooled for 10 min in ice water. The lethality at the cold spots reached F 14.1 ± 0.3 min and 13.3 ± 0.7 min for MAPS and HW processing, respectively. In MAPS processing, the 35 min preheating step at 51 °C took up almost 60% of the whole processing time. This was to allow the samples to reach a uniform initial temperature before microwave heating. In an industrial process, this can be achieved by heating pre-packaged meals in a water flume at a constant temperature or through hot fill of the beans in packages before sealing. In the microwave heating section, the sample temperature increased from 51 to 89 °C at a heating rate of 8.4 °C/min. In HW processing, the temperature increase was relatively fast in the early part of the 47 min heating, as the temperature difference Z. Qu et al. Temperature (°C) 100 80 60 40 20 0 0 Aerobic mesophilic bacteria (log CFU/g) Temperature-MAPS Temperature-HW Lethality-MAPS Lethality-HW 10 8 20 30 Time (min) 40 20 I 50 I 60 40 60 Time (day) 100 Fig. 1. Temperature profiles and thermal lethality at cold spots of microwave (MAPS) and hot water (HW) processing. 80 between the heating medium and green beans was large. The heating rate gradually decreased as the green bean temperature approached the medium temperature of 91 °C, due to the reducing temperature differ- ence. The average heating rate of HW processing was 1.6 °C/min, about 1/5 of that in the microwave heating section MAPS. higher heating rate in MAPS meant less thermal exposure, which should have positive effects on the quality of food products. 1 80 60 3.2. Microbiological analyses 3.2.1. Shelf life determined by bacterial growth The initial population of aerobic mesophilic bacteria in frozen- thawed green beans before thermal processing was 4.11 ± 0.15 log CFU/g. After processing, no plated colonies were detected in the samples processed by either method (limit of detection was 100 CFU/g), which was shown as 0 at day 0 in Fig. 2. The bacterial population increased dramatically to ~4 log CFU/g in the early part of the storage (day 3 at 10 °C, day 5 at 7 °C, and day 7 at 2 °C). The increase then slowed down to reach 7-8 log CFU/g at the end of the storage (Fig. 2). The initial rapid growth of the spoilage bacteria in the green beans may be explained by the availability of more nutrients for microbial growth from the damaged green bean plant cells and the lack of competing vegetative bacteria cells after the pasteurization. No yeast or mold counts were detected in any of the samples throughout the storage period, and no 40 -- HW-7°C 20 0 -- HW-2°C MAPS-10°C - HW-10°C MAPS-7°C Lethality (min) MAPS-2°C 1 100 Fig. 2. Aerobic mesophilic bacteria count of microwave (MAPS) and hot water (HW) processed green beans during storage at 10, 7, and 2 °C. (For interpre- tation of the references to color in this figure legend, the reader is referred to the Web version of this article.) 4 Food Control 124 (2021) 107936 anaerobic growth was observed in any samples at the end of the storage. Pasteurized RTE meals could be considered as spoiled when the total aerobic microbial counts reach 7 log CFU/g or higher (FSANZ, 2001). In this study, package swelling was the first sign of spoilage, together with the presence of an off-odor that appeared when the package was opened. All swollen packages had aerobic mesophilic bacterial counts larger than 7 log CFU/g. During storage at 10 °C, the population reached 7 log CFU/g on day 17 and day 21 in HW and MAPS processed green beans, respectively (Fig. 2). Reducing the storage temperature from 10 °C to either 7 or 2 °C could delay spoilage by 2.5-4.5 times, as the lower temperatures reduced the growth of microorganisms. The MAPS pro- cessed samples took 42 and 100 days, while HW processed samples took 35 and 80 days, to reach the microbiological quality mark when stored at 7 and 2 °C, respectively. The results suggest that microwave heating had the potential to produce pasteurized green beans with longer shelf life. 3.2.2. Identification of spoilage bacteria in pasteurized green beans Four morphologically different isolates from spoiled samples after 21 days at 10 °C were identified, of which three were classified as Paeni- bacillus spp. (Paenibacillus sp. F, Paenibacillus terrae, and Paenibacillus sp. FSL H7-0357) and one as Bacillus spp. (Bacillus pumilus). Only Paeniba- cillus spp. were identified from samples spoiled at 7 and 2 °C storage. All the bacteria identified are spore formers, which survived the pasteuri- zation process and germinated into metabolically active cells during storage. Similar to our study, Guinebretiere et al. (2001) reported high fre- quencies of the presence of Paenibacillus spp. in pasteurized zucchini puree stored at 10 °C. Helmond, Nierop Groot, and van Bokhorst-van de Veen (2017) isolated P. terrae from rice-vegetable RTE meals stored at 7 °C, and Carlin et al. (2000) isolated B. pumilus from pasteurized vegetable purees stored at 10 °C. Guinebretiere, Girardin, Dargaignar- atz, Carlin, and Nguyen-The (2003) examined the contamination flows of spore-forming aerobic bacteria in a pasteurized zucchini puree pro- cessing line.Paenibacillus spp. and Bacillus spp. are known to be frequent contaminants in the soil, and the spore counts in the soil can be as high as 9 log CFU/g (Ammann, Kölle, & Brandl, 2011). The spore-forming bacteria may enter the plant through the root or attach to the surface of the vegetables by contact with soil or aerosols of soil. Another possible contamination pathway is the processing equipment, such as storage tanks and production lines (Soni, Oey, Silcock, & Bremer, 2016). Both Paenibacillus spp. and Bacillus spp. have been isolated from food pro- cessing plants as they can attach to stainless steel surfaces (Huck, Woodcock, Ralyea, & Boor, 2007; Salustiano et al., 2009). Conse- quently, they could enter the food chain easily. 3.3. pH The initial pH of the green beans was 6.28. Thermal processing reduced the pH to 6.23 and 6.16 when MAPS and HW were employed, respectively. This may be due to the release of organic acids from the food matrix. The pH decreased in all samples during storage (Table 1). This was also demonstrated in other pasteurized vegetable puree during storage at 4-10 °C (Carlin et al., 2000; Sonar et al., 2019b). The pH drop during storage was caused by the growth of microbial flora, as observed in section 3.2. In the current study, the significant pH drop started somewhere around the middle of the shelf life. MAPS processed samples always had similar or higher pH as compared to HW processed ones. Referring to the microbial analysis in section 3.2, a pH value lower than 5.5 may suggest the end of the shelf life of pasteurized green beans due to spoilage. 3.4. Chlorophyll degradation The total chlorophyll content of unheated green beans was 10.46 mg/100 g, out of which 68.0% was chlorophyll a. Both heating methods Z. Qu et al. Table 1 pH of microwave (MAPS) and hot water (HW) processed green beans during storage at 10, 7, and 2 °C. 10 °C 7 °C Day 0 3 7 11 14 17 21 MAPS 6.23 ± 0.01ªA 6.00+ 0.01bCA 6.03 ± 0.01 BA 5.99 ± 0.01 CA 5.95 + 0.01 A 5.81 ± 0.02⁹A 5.47 ± 0.02fA Typical image L* a* b* ΔΕ pH caused significant (P < 0.05) degradation of chlorophyll a and b (Table 2). Compared with HW, MAPS induced less loss in chlorophyll a. Chlorophylls continued to degrade during storage following the first- order fractional conversion model described in Eq. (7) (Fig. 3). The ki- netic parameters of degradation are summarized in Table 3. As expected, the higher the storage temperature, the faster the degradation of chlo- rophylls over time, as indicated by higher degradation rates (k). Reducing the storage temperature from 10 to 2 °C could bring about a threefold reduction in k for both chlorophyll a and b. To better interpret the influence of storage temperature on chlorophyll degradation, chlo- rophyll content in samples after 17 days at 10 °C, 21 days at 7 °C, and 28 days at 2 °C were compared. MAPS processed green beans had total chlorophyll retentions of 49.6%, 53.2%, and 55.4%, while preservation of 45.4%, 49.3%, and 52.2% was obtained in the HW processed samples. Microwave technology provided green beans with greater chlorophyll retention over time, due to the lower k in MAPS processed samples than HW. The chlorophyll content of MAPS processed samples at the end of storage at 7 °C was significantly higher as compared with HW processed ones, and the values of those stored at 10 and 2 °C were still comparable (Fig. 3). HW 6.16 + 0.01 B 5.99 ± 0.02bA 6.04 ± 0.01 DA Schwartz and Von Elbe (1983) suggested that chlorophyll degrada- tion in vegetables is the result of chlorophyll degrade to pheophytin and further to pyropheophytin. First-order degradation kinetics of chloro- phyll were reported for fresh asparagus (Tenorio, Villanueva, & Sagar- doy, 2004), pasteurized green pee puree (Sonar, Rasco, et al., 2019), and frozen green beans (Martins & Silva, 2002) during storage. But Benl- loch-Tinoco et al. (2015b) reported second-order chlorophyll degrada- tion kinetics in microwave and conventionally heated kiwifruit puree; Table 2 Quality attributes of green beans before and after thermal processing. Before processing After processing MAPS 50.51 ± 1.41ª -29.52 ±0.08ª 44.06 ± 1.24ª 5.72 ± 0.01 CB 5.52 ± 0.01 dB 5.27 ± 0.03eB 5.15 + 0.02eB 6.28 ± 0.02² 7.11 0.10² 3.35 ± 0.18a 6.12 ± 0.10² Day 0 5 10 15 21 28 35 42 Values with different superscript letters have a significant difference (P < 0.05). Small superscript letters indicate the results in the same column, and capital su- perscript letters compare rows within the same temperature. 50.55 ± 0.52² -13.94 +0.71b 41.88 0.12ª 15.82 ± 0.44ª 6.23 ± 0.01b 5.10+ 0.12b MAPS 6.23 ± 0.01ªA 6.19 + 0.01 A 6.21 ± 0.02ªA 6.18 ± 0.02ªA 6.17 ± 0.02abA 6.08 ± 0.01 BA 5.92 ± 0.03CA 5.60 ± 0.08dA 1.86 ± 0.13b Chlorophyll a (mg/ 100 g) Chlorophyll b (mg/ 100 g) Ascorbic acid (mg/ 0 g) Means in rows followed by different letters differed significantly (P < 0.05). 5.56 ± 0.08¹ HW 49.63 ± 1.48² -9.39 ± 0.29€ 43.45 ± 0.37a 20.27± 0.52b 6.16 0.01⁹ 4.70 ± 0.13º 1.70 ± 0.16b 5.18± 0.03 HW 6.16 + 0.01 B 6.13 +0.00B 6.14 ± 0.01 B 6.13 ± 0.02aB 6.01 + 0.01 B 5.57 ± 0.02CB 5.39 +0.03dB 5.17 ± 0.03eB 5 2 °C Day 0 7 14 28 42 60 80 100 Food Control 124 (2021) 107936 MAPS 6.23 ± 0.01 A 6.16± 0.02¹A 6.14 ± 0.01 BA 6.12 + 0.01 DA 6.06 ± 0.02CA 6.02 +0.04cdA 5.99 ± 0.02dA 5.69 ± 0.01 A HW 6.16 + 0.01 B 6.06 ± 0.02bB 6.08 ± 0.01 B 6.11 +0.03abA 5.93 0.01 CB 5.26 +0.03dB 5.13 + 0.03eB the degradation rate decreased from 0.031 to 0.007 day-¹ when the storage temperature changed from 22 to 4 °C. Besides storage temper- ature, the kinetic of chlorophyll degradation is also affected by pH and microbial growth. Gunawan and Barringer (2000) showed that micro- bial growth accelerates the color change in broccoli by producing acids. The decrease in pH favors converting chlorophyll to pheophytin by facilitating the replacement of Mg²+ by H+ (Gunawan & Barringer, 2000). Koca, Karadeniz, and Burdurlu (2007) reported that the degra- dation rate of chlorophyll a in green peas at pH 5.5 was twice that at pH 6.5. The higher pH in MAPS processed samples may be another reason that more chlorophyll was preserved. Klug et al. (2018) reported that microwave (30s, 11 kW) caused less loss in chlorophyll in faba bean sauce compared to conventional pasteurization (85 °C, 5 min). Benlloch-Tinoco et al. (2015b) also confirmed the superiority of microwave heating in preserving chloro- phylls and carotenoids in kiwifruit puree stored at 4-22 °C. The observed difference could be explained by the higher heating rate and less exposure time to high temperature in microwave heating. 3.5. Color degradation Both MAPS and HW processing induced considerable changes in color, as indicated by an increase in the a* values (Table 2). No signif- icant changes in L* and b* occurred during processing or storage, so a* was used as the greenness indicator. A larger increase in a* was observed when the green beans were conventionally heated. The more significant change in a* of HW processed samples led to a significantly higher AE. A AE value of 3 is perceptible by most people (Paciulli, Palermo, Chiavaro, & Pellegrini, 2017), and the color changes were visually noticeable as shifting from bright green to olive green, as shown in typical images in Table 2. The increase of a* during storage followed the first-order fractional conversion model (Eq. (7)). Storage temperature showed a considerable effect on the rate of reduction in greenness. A reduction in the storage temperature from 10 to 2 °C could reduce the color degra- dation rate from 0.149 and 0.173 to 0.0359 and 0.0363 day in MAPS and HW processed green beans, respectively (Table 3). As shown in Fig. 4, microwave processed green beans had significantly (P < 0.05) lower a* at each measured time point regardless of storage tempera- tures. The a* of microwave heated green beans at the end of storage at all temperatures was between 2.8 and 5.2, while it was between 5.1 and 6.8 for conventionally processed samples. This suggests that MAPS better preserved the green color of green beans during storage. -1 An increase in a* during thermal processing of green vegetables was observed previously (Aamir, Ovissipour, Rasco, Tang, & Sablani, 2014; Steet & Tong, 1996). Besides the increase of a*, Kotani, Yamauchi, Ueda, Imahori, and Chachin (1999) reported that L* and b* were unchanged in boiled broccoli florets during storage at 10 °C. Several studies compared the effects of microwave and conventional heating on color. Faba bean sauce preserved by microwave had a smaller increase in a* after pro- cessing (Klug et al., 2018). Microwave heated kiwifruit puree had a color change of 6.54 after 123 days storage at 4 °C, while the color change wasSee Answer
  • Q4: Descriptive Epidemiology Report Format for Descriptive Epidemiology Report Objective: investigate HIV using descriptive epidemiology. Definition of the health problem At least 3 references from reliable sources cited in APA format, including in-text citations Description of the nature of the health problem, its extent and its significance • • Description of the agent causing the outbreak • Description of the condition associated with the agent Summary and visual display of data on the health problem by person, place and time 3 visual displays of data such as graphs – these must be original creations not copied from literature. All data sources must be cited. Person - age, sex, race/ethnicity; relevant social, economic, environmental characteristics Place – state/region; explore pockets of greater concentration • Time - any variations that might be cyclic or seasonal Interpretation • What observations/conclusions can be made from the data? You may cite current hypotheses from scientific literature that have been proposed to explain the observations. Be sure to include references in APA format. • How can the information accumulated through descriptive epidemiology on this issue be used to prevent or control the outbreak? • Does your study offer any suggestions for further action or research on this health issue? APA References and IN TEXT CITATIONSSee Answer
  • Q5:/n nature ecology & evolution 8 Article https://doi.org/10.1038/s41559-022-01885-x Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants Received: 8 November 2021 Accepted: 12 August 2022 Published online: 29 September 2022 Check for updates Brogan J. Harris 16, James W. Clark 1,2,6, Dominik Schrempf³, Gergely J. Szöllősi ①3,4,5, Philip C. J. Donoghue 2, Alistair M. Hetherington 1 and Tom A. Williams 1,2 The origin of plants and their colonization of land fundamentally transformed the terrestrial environment. Here we elucidate the basis of this formative episode in Earth history through patterns of lineage, gene and genome evolution. We use new fossil calibrations, a relative clade age calibration (informed by horizontal gene transfer) and new phylogenomic methods for mapping gene family origins. Distinct rooting strategies resolve tracheophytes (vascular plants) and bryophytes (non-vascular plants) as monophyletic sister groups that diverged during the Cambrian, 515-494 million years ago. The embryophyte stem is characterized by a burst of gene innovation, while bryophytes subsequently experienced an equally dramatic episode of reductive genome evolution in which they lost genes associated with the elaboration of vasculature and the stomatal complex. Overall, our analyses reveal that extant tracheophytes and bryophytes are both highly derived from a more complex ancestral land plant. Understanding the origin of land plants requires tracing character evolution across a diversity of modern lineages. The origin and early evolution of land plants (embryophytes) consti- tuted a formative episode in Earth history, transforming the terrestrial landscape, the atmosphere and the carbon cycle¹². Along with bac- teria, algae, lichens and fungi³, land plants were fundamental to the creation of the earliest terrestrial ecosystems, and their subsequent diversification has resulted in more than 370,000 extant species*. Embryophytes form a monophyletic group nested within freshwater streptophyte algae and their move to land, while providing a new eco- logical niche, presented new challenges that required adaptation to water loss and growth against gravity6. Early innovations that evolved in response to these challenges include a thick waxy cuticle, stomata and a means of transporting water from the roots up vertically growing stems 2,5,7,8. Modern land plants comprise two main lineages, vascular plants (tracheophytes) and non-vascular plants (bryophytes), that have responded to these evolutionary challenges in different ways. The evolutionary origins of many gene families, including those of key transcription factors, have been shown to predate the coloniza- tion of land 9,10. However, studies of gene family evolution within land plants have typically been restricted to individual gene families or sets of genes that encode single traits 11-16. A lack of genome-scale data from non-flowering plants has also hindered efforts to reconstruct pat- terns of genome and gene content evolution more broadly across land plants, although this challenge has been mitigated by the publication of large transcriptomic datasets 18. Progress has also been made towards resolving the ambiguous phylogenetic relationships at the root of land plants 15,18-23. The bryophyte fossil record has also undergone a radical ¹School of Biological Sciences, University of Bristol, Bristol, UK. 2Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK. ³Department of Biological Physics, Eötvös Loránd University, Budapest, Hungary. *MTA-ELTE 'Lendület' Evolutionary Genomics Research Group, Budapest, Hungary. 5 Institute of Evolution, Centre for Ecological Research, Budapest, Hungary. These authors contributed equally: Brogan J. Harris, James W. Clark. e-mail: tom.a.williams@bristol.ac.uk Nature Ecology & Evolution | Volume 6 | November 2022 | 1634-1643 1634 Article reinterpretation such that there are now many more records with the potential to constrain the timescale of early land plant evolution²4-26. Finally, new methods have been developed for timetree calibration based on the relative time constraints informed by horizontal gene transfer (HGT) events²7. Here we seek to exploit these advances in elucidating early land plant evolution. We first infer a rooted phylogeny of land plants using outgroup-free rooting methods and both concatenation and coales- cent approaches. We then estimate an updated timescale of land plant evolution incorporating densely sampled fossil calibrations that reflect a revised interpretation of the fossil record. We extend this analysis using gene transfer events to better calibrate the timescale of hornwort evolution, a poorly constrained region of the land plant tree. By build- ing on this dated phylogeny, we reconstruct the gene content evolution of bryophytes, tracheophytes and the ancestral embryophyte, reveal- ing how key genes, pathways and genomes diverged during early land plant evolution. Results Complementary rooting approaches support the monophyly of bryophytes A rooted phylogenetic framework is required to infer the nature of the ancestral embryophyte and to trace changes in gene content during the evolution of land plants. To that end, we compiled a com- prehensive dataset of the published genome and transcriptome data from embryophytes and their algal relatives, and we inferred species trees using concatenation (PhyloBayes and IQ-TREE) and coalescent (ASTRAL) approaches (Supplementary Information). When the tree was rooted with an algal outgroup, we recovered bryophyte mono- phyly and a root between bryophytes and tracheophytes with high support across all analyses (Extended Data Fig. 1), in agreement with recent work 15,18,20,22,23,28. However, rooting phylogenies with an out- group can influence the ingroup topology due to long-branch attraction (LBA)29-31, where distantly related or fast-evolving taxa artifactually branch with the outgroup. LBA resulting from the large evolutionary distance between land plants and their algal relatives has previously been suggested as a possible cause of the difficulty in resolving the land plant phylogeny³32. Indeed, outgroup-rooting analyses using different models 20,33, datasets and molecules (that is, chloroplast, mitochon- drial or nuclear sequences 22,28) have provided support for conflicting hypotheses about the earliest-branching lineages and the nature of the ancestral land plant. LBA is thus a known artefact when recovering the land plant phylogeny. To address the impact of LBA and complement traditional outgroup-rooting analyses, we used two outgroup-free rooting meth- ods-amalgamated likelihood estimation (ALE) and STRIDE 34,35-to infer root placement on a dataset of 24 high-quality embryophyte genomes without the inclusion of an algal outgroup (Fig. 1). ALE calculates gene family likelihoods for a given root position under a model of gene dupli- cation, transfer and loss (DTL)³4; support for candidate root positions can then be evaluated by comparing their summed gene family likeli- hoods. STRIDE first identifies putative gene duplications in unrooted gene trees that can act as synapomorphies for post-duplication clades. The root of the species tree is then estimated using a probabilistic model that accounts for conflict among the inferred duplications³5. Across 18,560 orthogroups, STRIDE recovered three most parsimo- nious roots: between bryophytes and tracheophytes, between liv- erworts and the remaining land plants and between hornworts and the remaining land plants (Fig. 1). Of these, the rooting on hornworts was assigned a 0.2% probability, on liverworts a 59.8% probability and between bryophytes and tracheophytes a 39.9% probability. To estimate root likelihoods using the ALE approach, we first used the divergence time estimates from the molecular clock analysis to convert branch lengths into units of geological time, allowing us to perform time-consistent reconciliations (that is, to prevent reconciliations in Nature Ecology & Evolution | Volume 6 | November 2022 | 1634-1643 https://doi.org/10.1038/s41559-022-01885-x which gene transfers occur into the past). We reconciled 18,560 gene families under the 12 rooted and dated embryophyte trees (Fig. 1a) and used an approximately unbiased (AU) test (Fig. 1b) to evaluate support for the tested root positions. The AU test rejected 9 of 12 roots (P<0.05; Fig. 2b and Supplementary Table 3), resulting in a credible set of three roots: the hornwort stem, the moss stem and a root between bryophytes and tracheophytes. These three credible roots are in close proximity on the tree, and root positions further from this region are rejected with increasing confidence (Fig. 1b and Supplementary Table 1). To evaluate the nature of the root signal for these three branches, we performed a family-filtering analysis in which families with high DTL rates were sequentially removed and the likelihood re-evaluated. The rationale for this analysis is that the evolution of these families may be poorly described by the model, and so they may contribute misleading signals 36. In this case, the root order did not change after the removal of the high-DTL-rate families (Supplementary Fig. 1), suggesting broad support for these root positions from the data and analysis. Note that, in the ALE analysis, the moss and hornwort stems were accorded a higher summed gene family likelihood than was the branch separating bryophytes and tracheophytes, although the difference was not signifi- cant (hornwort stem log-likelihood,-824,522.9, P=0.624; moss stem log-likelihood, -824,606.5, P = 0.475; bryophyte stem log-likelihood, -824709.1, P = 0.277). In a secondary analysis, we also used ALE to compare support for these different root positions in a smaller dataset of 11 genomes that included algal outgroups; in this analysis, all roots were rejected except for a root between tracheophytes and bryophytes (Extended Data Fig. 2, P < 0.05). Finally, we constrained the topology of the tree inferred from the concatenated alignment to be in accordance with the three credible roots and computed the likelihood of sequence data along those trees. Trees with embryophyte roots constrained to hornworts and moss were significantly rejected (P<0.05, AU test; Supplementary Table 2). The agreement between three rooting methods using different sources of information (outgroup placement, gene duplications alone and DTL events more broadly) therefore provides the most compelling support for a root between bryophytes and tracheophytes from our analyses. Taking our analyses together with other recent work 15,20,22,23,28, suggests that a root between monophyletic tracheophytes and bryophytes is the best-supported hypothesis of land plant phylogeny. Bryophyte monophyly is therefore the default hypothesis with which to interpret land plant evolution. Combined fossil and genomic evidence, including an ancient HGT, calibrate the timescale of land plant evolution We estimated divergence times on the resolved land plant phylogeny (Fig. 2). We assembled a set of 68 fossil calibrations, representing every major lineage of land plant and notably sampling more bryophyte fossils than previous studies (Supplementary Methods). Despite this increased sampling, the fossil record of hornworts remains particularly sparse, and no fossils unambiguously calibrate the deepest branches within the clade. To ameliorate the limitations of the fossil record, we implemented a relative node age constraint based on the horizontal transfer of the chimaeric photoreceptor NEOCHROME from hornworts into ferns 37. To account for uncertainty in the timing of the gene transfer, we evaluated the impacts of several possible scenarios on our analy- ses (Extended Data Fig. 3). In the absence of direct fossil calibrations for hornworts, this gene transfer provides a relative constraint that ties the history of hornworts to that of ferns, for which more fossils are available. Our results are congruent with those of previous studies 38 but offer greater precision on many nodes and in some cases greater accuracy (Supplementary Fig. 2). This has been leveraged by a denser sampling of fossil calibrations, improved taxonomic sampling (especially among bryophytes), relative calibration of hornworts using the NEOCHROME HGT, and the ability to condition divergence times on a single topology. 1635 Article a Syntrichia Ceratodon Fontinalis Lineages Algae Bryophytes Physcomitrium 12 Hornworts Moss 8 Liverworts Lycophytes Anthoceros punctatus Anthoceros agrestis 11 9 Ferns 2 Gymnosperms Angiosperms Ceratophyllum Magnolia Cinnamomum Dioscorea Brachypodium Kalanchoe Arabidopsis Selaginella lepidophylla Selaginella moellendorfii Amborella Nymphaea Azolla Salvinia Ginkgo b https://doi.org/10.1038/s41559-022-01885-x Name Root Rank STRIDE AU Rejected Hornwort 9 1 0.2% 0.624 No Moss 12 2 0.0% 0.475 No Monophyletic bryophytes 8 3 39.9% 0.277 No Setaphyte 10 4 0.0% 0.001 Yes Between fern and gymnosperm 4 5 0.0% 9 x 10-50 Yes Lycophyte 7 6 0.0% 0.0001 Yes Liverwort 11 7 59.8% 0.002 Yes Fern 5 8 0.0% 0.055 Yes Angiosperm 2 9 0.0% 7 x 10-10 Yes Between lycophyte and fern 6 10 0.0% 1 x 10-130 Yes Gymnosperm 3 11 0.0% 3 × 10-46 Yes Arabidopsis 1 12 0.0% 3 x 10-9 Yes Gnetum Pinus Pseudotsuga с Monophyletic bryophytes Mosses Hornworts Fig. 1 Investigating the root of embryophytes using outgroup-free rooting. a, An unrooted maximum likelihood tree was inferred from an alignment of 24 species and 249 single-copy orthogroups under the LG + C60+ G4 + F model 69. Twelve candidate root positions for embryophytes were investigated using both ALE and STRIDE. For the ALE analysis, the unrooted tree was rooted in each of the 12 positions and scaled to geological time on the basis of the results of the divergence time analysis, and 18,560 gene clusters were reconciled using the ALEml algorithm88. The green circles highlight supported roots following the ALE analysis, while the red circles denote supported nodes in the STRIDE analysis. b, The likelihood of the 12 embryophyte roots was assessed with an AU test. The AU test significantly rejected 9 of the 12 roots, with roots on hornworts, moss and monophyletic bryophytes (root positions 9, 12 and 8, respectively) comprising the credible set. c, Phylogenetic trees constrained to the credible roots were inferred in IQ-TREE69 under the LG + C60+ G + F model. An AU test was used to evaluate the likelihood of each of the constrained trees⁹0, with the root resulting in monophyletic bryophytes being the only one not to be significantly rejected. The role and influence of fossil calibrations in molecular clock studies, especially maximum age calibrations, remain controver- sial 23,39,40. While the fossil record is an incomplete representation of past diversity, our analyses account for this uncertainty in the form of soft minima and maxima. Morris et al.38 inferred a relatively young age for the embryophyte crown ancestor (515-470 million years ago (Ma)), making use of a maximum age constraint based on the absence of embryophyte spores in strata for which fossilization conditions were such that spores of non-embryophyte algae have been preserved. Hedges et al.39 and Su et al. 2³ argued against the suitability of this maxi- mum age constraint on the basis that calibrations derived from fossil absences are unreliable and that the middle Cambrian maximum age exerts too great an influence on the posterior estimate 8,41. To assess the sensitivity of our approach to the effect of maximum age calibra- tions, we repeated the clock analyses with less informative maximum age calibrations (Supplementary Methods). Removing the maximum age constraint on the embryophyte node produced highly similar estimates to when the maximum is employed (Extended Data Fig. 4). Relaxing all maxima did result in more ancient estimates for the origin of embryophytes, although still considerably younger than recent studies23, extending the possible origin for land plants back to the Edi- acaran (540-597 Ma; Extended Data Fig. 4). The older ages estimated Nature Ecology & Evolution | Volume 6 | November 2022 | 1634-1643 in Su et al. 23 seem to reflect, in part, differences in the phylogenetic assignment of certain fossils (Supplementary Methods), such as the putative algae Proterocladus antiquus and the liverwort Ricardiothallus devonicus, rather than a dependence on the maximum age calibration. Our results reject the possibility that land plants originated during the Neoproterozoic, instead supporting an origin of the land plant crown group during the mid-late Cambrian, 515-493 Ma, with crown tracheophytes and crown bryophytes originating 452-447 Ma (Late Ordovician) and 500-473 Ma (late Cambrian to Early Ordovician), respectively. Within bryophytes, the divergence between Setaphyta (mosses + liverworts) and hornworts occurred by 479-450 Ma (Ordovi- cian), with the radiation of crown mosses by 420-364 Ma (latest Silurian to Late Devonian) and crown liverworts 440-412 Ma (early Silurian to Early Devonian). Among tracheophytes, the crown ancestor of lyco- phytes is dated to the middle Silurian to Early Devonian, 431-411 Ma, coincident with that of euphyllophytes 432-414 Ma. The calibration of hornwort diversification using the NEOCHROME HGT had a substantial impact on inferences of stem and crown group age. In the absence of fossil calibrations on deep nodes, hornworts are characterized by an ancient stem lineage and the youngest crown line- age among land plants 38,42. The effect of the relative age constraint is to make the crown group older (294-214 Ma; Fig. 2) and thus shorten the 1636 Bryophytes Hor. Mosses Liverworts Lyco. Article https://doi.org/10.1038/s41559-022-01885-x Phragmoplastida Embryophyta Ferns Tracheophytes Euphyllophytes Spermatophytes Tu. Cr. Ed. Ca. Or. Si. De. Ca. Pe. Tr. Ju. Cr. Pa. N. 860 720 635 541 485 443 419 359 299 252 201 145 66 23 0 Time (millions of years before present) Fig. 2 The timescale of land plant evolution. Divergence times in millions of years as inferred using a molecular clock model, 68 fossil calibrations and an HGT. The inference that the common ancestor of embryophytes lived during the Cambrian is robust to the choice of maximum age constraints (Supplementary Methods). The divergence times of hornworts are constrained by an HGT into polypod ferns, with the result that the hornwort crown is inferred to have diverged during the Permian-Triassic. The nodes are positioned on the mean age, and the bars represent the 95% highest posterior density. length of the stem, with divergence times within the crown group all moving older. We repeated the analysis with alternative placements for the relative time constraint, with the age of crown hornworts becoming increasingly ancient when the transfer was placed into the ancestor of more inclusive clades, Cyatheales + Polypodiales (258-419 Ma) or before the divergence of Gleicheniales from the Cyatheales + Polypo- diales clade (331-445 Ma), respectively (these scenarios are illustrated in Extended Data Fig. 3). All of these estimates considerably predate the earliest unequivocal fossils assigned to hornworts. However, given the scarcity of hornwort fossils, it seems likely that this clade is older than a literal reading of the fossil record might suggest. Gene content of the embryophyte common ancestor We used gene-tree/species-tree reconciliation to estimate the gene content of the embryophyte common ancestor (Supplementary Tables 3-5). We used the genome dataset from the ALE rooting analysis with the addition of five algal genomes, to better place the origin of families that predate the origin of embryophytes (Supplementary Fig. 3). The tree was dated following the same methodology as the larger dating analysis while using an applicable subset of calibrations, allowing the use of a dated reconciliation algorithm (ALEml) to improve the estima- tion of DTL events (Supplementary Fig. 4). The analysis of ancestral gene content highlighted considerable gene gain along the ancestral embryophyte branch (Fig. 3a and Supple- mentary Table 3). A substantial number of duplications defined this tran- sition, with fewer transfers and losses observed. Our analysis suggests that the common ancestor of embryophytes and Zygnematales had more of the building blocks of plant complexity than extant Zygnematales, which have undergone a loss of 1,442 gene families since their diver- gence, the largest loss observed on the tree (Fig. 3a). Functional charac- terization of the genes lost in the Zygnematales using the KEGG database Nature Ecology & Evolution | Volume 6 | November 2022 | 1634-1643 identified gene families involved in the production of cytoskeletons, exosomes and phenylpropanoid synthesis (Supplementary Table 6). Exosomes and complex cytoskeletons are essential for multicellular organisms to function 43,44, and the inferred loss of these gene families is consistent with the hypothesis that the body plan of the algal ancestor of embryophytes was multicellular³, rather than possessing the single-cell or filamentous architecture observed in extant Zygnematales. The more complex cytoskeleton could be associated with increased rigidity, helping overcome the gravitational and evaporative pressures associ- ated with the transition to land. Interestingly, phenylpropanoids are associated with protection against UV irradiance 45 and homiohydry³, suggesting that the common ancestor may have been better adapted to a terrestrial environment than extant Zygnematales. We also observed greater gene loss along the bryophyte stem line- age (Fig. 3a and Supplementary Tables 3, 7 and 8), with the rate of gene loss (in terms of gene families per year) substantially greater than in all other major clades (Fig. 3b). It is important to note that inferences of gene loss from large-scale analyses are sensitive to the approach used to cluster sequences and define gene families; current approaches are not consummate. We therefore sought to evaluate the robustness of our conclusions using a range of sensitivity analyses (Supplemen- tary Figs. 5-8). These suggested that, while the number of inferred gene losses on the bryophyte stem varies, it remains an event of major gene loss under all conditions tested. We also observed considerable losses along the tracheophyte stem, countered by a greater number of duplications (Supplementary Table 9). This suggests a period of genomic upheaval on both sides of the embryophyte phylogeny. Gene Ontology (GO) term functional annotation of the gene families lost in bryophytes reveals reductions in shoot and root development from the ancestral embryophyte (Supplementary Table 7 and Extended Data Fig. 5). To investigate the evolution of genes underlying morphological 1637 events Number of DTL b Article a 35,000 30,000 25,000 20,000 4,705 Event 6,561 Duplication 7,508 Transfer Loss 500 7,043 https://doi.org/10.1038/s41559-022-01885-x Chlorokybus Klebsormidium Chara. braunii Spirogloea Mesotaenium Anthoceros punctatus Anthoceros agrestis 12,981 M. polymorpha rud. 10,646 M. polymorpha 9,597 8,485 9,712 Physcomitrium Fontinalis 14,601 14,857 Syntrichia 14,980 Ceratodon 10,473 Selaginella moellendorfii 11,287 11,927 14,376 11,755 13,244 Selaginella lepidophylla Salvinia Azolla Ginkgo Gnetum 15,547 15,273 Pseudotsuga 19,282 Pinus 15,000 с 15,109 Embryophyte Liverwort 15,521 10,000 507 6,462 1,031 5,553 5,000 6,642 5,618 2,616 0 Zygnemataceae Embryophyta Bryophyta Tracheophyta Angiosperm 16,752 Amborella Nymphaea Ceratophyllum Magnolia 15,764 15,719 Cinnamomum Kalanchoe 15,186 Arabidopsis 15,881 Dioscorea 14,435 Brachypodium Fig. 3 | Gene content reconstruction of the ancestral embryophyte. a, Ancestral gene content was inferred for the internal branches of the embryophyte tree. A maximum likelihood tree was inferred from an alignment of 30 species of plants and algae, comprising 185 single-copy orthologues and 71,855 sites, under the LG + C60+ G4 + F model in IQ-TREE69, and rooted in accordance with our previous phylogenetic analysis. A timescale for the tree was then calculated using a subset of 18 applicable fossil calibrations in MCMCtree. We reconciled 20,822 gene family clusters, inferred using Markov clustering 87, against the rooted dated species tree using the ALEml algorithm 88. The summed copy number of each gene family (under each branch) was determined using custom Python code (branchwise_number_of_events.py). Branches with reduced copies from the ancestral node are coloured in red. The numbers of DTL events are represented by purple, blue and red circles, respectively. The sizes of the circles are proportional to the summed number of events (the scale is indicated by the grey circle). b, The number of DTL events scaled by time for four clade- defining branches in the embryophyte tree. c, The number of shared gene families between the ancestral embryophyte, liverwort and angiosperm. The ancestral embryophyte shares more gene families with the ancestral angiosperm than with the ancestral liverwort. differences between tracheophytes and bryophytes, we evaluated the evolutionary history of gene families containing key Arabidopsis genes for vasculature and stomata (Supplementary Table 10). Gene families associated with both vasculature and stomatal function exhibited lineage-specific loss in bryophytes (Supplementary Figs. 9 and 10). Specifically, four orthologous gene families that are involved in the determination of the Arabidopsis body plan, containing WOX4, SPCH/ MUTE/FAMA, AP2 and ARR, were inferred to be lost on the bryophyte stem (Supplementary Table 10). To investigate these inferred losses in more detail, we manually curated sequence sets and inferred phyloge- netic trees for these families (Supplementary Methods and Extended Data Fig. 6). These analyses of individual gene families corroborated the pattern of loss along the branch leading to bryophytes. The loss of these orthologous gene families strengthens the hypothesis that Nature Ecology & Evolution | Volume 6 | November 2022 | 1634-1643 ancestral embryophytes had a more complex vasculature system than that of extant bryophytes³. Overall, the loss of gene families (Fig. 3) and the change in GO term frequencies (Extended Data Fig. 5) suggest a widespread reduction in complexity in bryophytes, and the ancestral embryophyte being more complex than previously envisaged. Indeed, gene loss defines the bryophytes early in their evolutionary history, but large numbers of duplication and transfer events are observed follow- ing the divergence of the setaphytes and hornworts (Supplementary Table 3), with (for example) extant mosses boasting a similar gene copy number to tracheophytes (Fig. 3). Discussion We have presented a time-scaled phylogeny for embryophytes, which confirms the growing body of evidence that bryophytes form 1638See Answer
  • Q6: frontiers in Pediatrics REVIEW published: 11 February 2019 doi: 10.3389/fped.2019.00028 Check for updates Severe Asthma and Allergy: A Pediatric Perspective Stefania Arasi 1*, Federica Porcaro², Renato Cutrera² and Alessandro G. Fiocchi¹ 1 Pediatric Allergology Unit, Bambino Gesù Hospital (IRCCS), Rome, Italy, 2 Pediatric Pulmonology & Respiratory Intermediate Care Unit, Sleep and Long-Term Ventilation Unit, Department of Pediatrics, Bambino Gesù Children's Hospital, Rome, Italy OPEN ACCESS Edited by: Milos Jesenak, Comenius University, Slovakia Reviewed by: Vladimir Pohanka, Slovak Medical University, Slovakia Zuzana Rennerova, Pneumo-Alergo Center, Slovakia *Correspondence: Stefania Arasi stefania.arasi@opbg.net Specialty section: This article was submitted to Pediatric Pulmonology, a section of the journal Frontiers in Pediatrics Received: 29 November 2018 Accepted: 23 January 2019 Published: 11 February 2019 Citation: Arasi S, Porcaro F, Cutrera R and Fiocchi AG (2019) Severe Asthma and Allergy: A Pediatric Perspective. Front. Pediatr. 7:28. doi: 10.3389/fped.2019.00028 Severe asthma in children is associated with significant morbidity and lung function decline. It represents a highly heterogeneous disorder with multiple clinical phenotypes. As its management is demanding, the social and economic burden are impressive. Several co-morbidities may contribute to worsen asthma control and complicate diagnostic and therapeutic management of severe asthmatic patients. Allergen sensitization and/or allergy symptoms may predict asthma onset and severity. A better framing of “allergen sensitization" and understanding of mechanisms underlying progression of atopic march could improve the management and the long-term outcomes of pediatric severe asthma. This review focuses on the current knowledge about interactions between severe asthma and allergies. Keywords: allergy, allergic rhinitis, atopic dermatitis, children, difficult-to-treat asthma, food allergy, severe asthma INTRODUCTION Atopic sensitization is a well-established, but not exclusive, risk factor for severe asthma both in children (1, 2) and adults (3), all over the world (1-4). Although its role in determining asthma severity has been considered limited in the past years, some reports confirm that allergy may play a significant role especially in childhood, when early atopic sensitization is crucial to determine the severity of disease. Though most asthmatic children achieve symptoms' control through occasional bronchodilator (BD) use or low to medium dose of inhaled corticosteroids (ICSs), a small but significant subset of patients remains with uncontrolled asthma despite treatment with high-dose inhaled glucocorticoids (Table 1) or requiring such a treatment to remain well-controlled (5). This group of children with chronic symptoms and episodic exacerbation requiring short-acting beta2 agonists (SABA) is defined as affected by “difficult-to-treat asthma.” This definition includes poorly-controlled asthma due to at least one of the following: an incorrect diagnosis; comorbidities; poor adherence to therapy because of adverse psychological or environmental factors (6). “Severe asthma" is considered a specific subset of “difficult-to-treat asthma.” It is characterized by the need of higher intensity therapy in order to maintain symptom control or uncontrolled symptoms despite such therapy (6), proper diagnosis (7), and management of comorbidities and correction of unsuitable behavior for control disease. In 2014, a task force of the European Respiratory Society (ERS) and the American Thoracic Society (ATS) updated the definition of severe asthma in pediatric patients. According to the latter, children affected by severe asthma require treatment with high-dose ICSs and either a long-acting beta-agonist (LABA) or a leukotriene antagonist for the previous year or systemic corticosteroids for at least 50% of the previous year to prevent uncontrolled asthma or asthma that remains uncontrolled despite this therapy (5). Frontiers in Pediatrics | www.frontiersin.org 1 February 2019 | Volume 7 | Article 28 Arasi et al. TABLE 1 | High-dose ICD dosages for children (mcg/d) according to Global Initiative for Asthma (GINA) guidelines. Drug name Beclomethasone dipropionate (HFA) Budesonide (DPI) Budesonide (nebules) Ciclesonide (HFA) Fluticasone propionate (DPI) Fluticasone propionate (HFA) Mometasone furoate (DPI) DPI, dry powder inhalers; HFA, hydrofluoroalkane. Severe Asthma and Allergy TABLE 2 | Characteristics of severe bronchial asthma in children and adults. Characteristics GINA (6-11 y) GINA (>12 y) Pediatric asthma Adult-onset asthma >200 >400 IgE-sensitization +++ + >400 >800 Poly-sensitization +++ + >1,000 High specific IgE levels +++ + >160 >320 >400 >500 >500 >500 Clinical heterogeneity (i.e., multiple phenotypes) Severe non-allergic obese female prevalent phenotype +++ +++ +++ >440 >440 Severe non-allergic eosinophilic phenotype +++ (nasal polyposis, sputum eosinophilia, and aspirin sensitivity) In a birth cohort study, the prevalence of severe asthma has been estimated about 0.5 and 4.5% in all 10-year-olds and current asthmatic children when assessed in 10 year olds, respectively (8). Notwithstanding, it is associated with a significant economic burden related to more and severe symptoms needing of adjunctive medical resource use and higher health costs (9). Furthermore, the increased number of parent's working days lost during child asthma exacerbations is accompanied by less global economic productivity (10). Since only a small percentage of asthmatic patients is affected by severe asthma, this clinical entity is still poorly known even if associated with notable morbidity. Both in children and adults, severe asthma is a heterogeneous disorder with multiple clinical phenotypes (11). However, elegant cluster analyses have shown that the role of atopic sensitization might be more important in the pathogenesis of severe asthma specifically in childhood onset asthma: more than 85% of children with severe asthma are severely atopic (12). In contrast, severe adult-onset asthma is a distinct phenotype that is usually not characterized by atopic sensitization, but often associated with nasal polyposis and sputum eosinophilia (13, 14). A brief overview of characteristics and differences between pediatric and adult-onset severe asthma is provided in Table 2. Though it is well-recognized that atopic sensitization is an important risk factor mainly for pediatric asthma, the role of allergy in children affected by severe asthma is still under debate. This review aims to focus the role of allergy in pediatric severe asthma. THE ATOPIC MARCH Though atopic manifestations may persist for several and years then resolve over time (15), in atopic children, adolescents, and adults allergy manifestations may evolve according to Abbreviations: ABPA, allergic bronchopulmonary aspergillosis; AERD, aspirin exacerbated respiratory disease; AD, atopic dermatitis; AIT, allergen specific immunotherapy; AR, allergic rhinitis; ATS, American Thoracic Society; BD, bronchodilator; ERS, European Respiratory Society; FA, food allergy; HDM, house dust mites; ICS, inhaled corticosteroid; IgE, immunoglobulin E; LABA, long-acting beta2-agonist; MAAS, Manchester Asthma and Allergy Study; MAS, Multicentre Allergy Study; NSAIDs, non-steroidal anti-inflammatory drugs; SABA, short- acting beta2-agonist; SAFS, Severe asthma with fungal sensitization. a predetermined sequence, characterized by the progression from atopic dermatitis (AD) to allergic rhinitis (AR) and asthma (16-18). Therefore, it seems that atopic predisposition represents a major risk factor for developing all atopic diseases in patients for which the progression from AD to asthma defines the well- known "atopic march” (19). However, the temporal presentation of allergic diseases may differ from the usual progression of the atopic march due to genetic influences and environmental factors (20). Foremost, allergens may penetrate easier a defective skin barrier, therefore leading to transcutaneous sensitization and subsequentially initiating the atopic march (21). Indeed, IgE sensitization to food or airborne allergens is a significant cofactor to induce the progression of the atopic march in patients with AD (22-24). Moreover, it is widely described that the risk of developing asthma in patients with AD is strictly related to both the clinical expression of IgE sensitization and the severity of eczema (25-27). It seems that transcutaneous IgE-sensitization may precede airway sensitization (28) and that IgE-associated AD might represent the first step of the atopic march and, therefore, it may predict the upcoming development of allergic diseases, including food allergy, AR, and asthma (please see Figure 1) (28). Since AR is a further major risk factor for bronchial hyper-reactivity and asthma, it can precede asthma onset in the natural history of the atopic march (29-31). ALLERGIC COMORBIDITIES Several factors and co-morbidities may contribute to worsen asthma control and complicate diagnostic and therapeutic management of severe asthmatic patients (Figure 2) (32). Atopic Dermatitis Several studies reported that family history of atopy, early onset AD, higher initial severity of atopic eczema, hens' egg sensitization and male sex are associated with an increased risk of asthma in childhood (33). Furthermore, the percentage of patients with severe asthma and concomitant eczema is greater than expected and close relationship between asthma and atopic dermatitis severity has been reported (34). Frontiers in Pediatrics | www.frontiersin.org 2 February 2019 | Volume 7 | Article 28 Arasi et al. Airborne allergens Food allergens Pollutants Microbes Irritants epithelial damage EPIDERMIS increased epithelial permeability 0000 (tight Junctions, filaggrin, E-cadherin) IL-33, IL-25, TSLP DERMIS DC Mast cell ILC2 Basophil Eosinophil IL-4, IL-5, IL-9, IL-13 Th2 B cell LYMPHOID ORGANS IgE Severe Asthma and Allergy FIGURE 1 | A model of epithelial barrier damage and skin IgE-sensitization. Impaired skin barrier (e.g., eczema) promotes foreign antigen (e.g., airborne and food allergens) penetration and activation of innate and specific immune responses. Epithelial cell-derived cytokines (such as TSLP, IL-33, and IL-25) license antigen presenting cells (i.e., dendritic cells) to drive type 2 immune responses and stimulate several cell types (including basophils, eosinophils, mast cells, and ILCs) to start and maintain allergic inflammation also in regional draining lymph nodes (e.g., B-cell IgE skewing). Furthermore, T cells circulate back to infiltrate the skin or are distributed peripherally to other end organs to initiate diverse atopic disorders. DC, dendritic cells; lg, Immunoglobulin; IL, interleukin; ILC, Innate Lymphoid cells; Th, T helper cells; TSLP, thymic stromal lymphopoietin. Therefore, as AD and the subsequent atopic march mostly present in early infancy, primary, and secondary prevention should be attempted as early as possible to prevent asthma symptoms onset (35). Allergic Rhinitis Allergic rhinitis is almost ubiquitous in children with asthma living in urban areas. The presence of allergic sensitization to inhalant allergens and rhinitis symptoms is typically associated with early onset of severe asthma (36). Patients with AR report poorer asthma control, more exacerbations and emergency visits (37) and have more difficulty in achieving symptom control (38). Perennial allergic rhinitis with seasonal exacerbations is considered the most severe phenotype and most likely to be associated with difficult-to-control asthma (39). This means that treating coexisting allergic rhinitis could improve asthma control and reduce healthcare resource utilization (40). Food Allergy Respiratory symptoms as clinical manifestation of IgE-mediated food allergy (FA), usually, occur immediately after exposure to the offensive food and are accompanied by skin and/or gastrointestinal manifestations. Food allergen exposure occurs usually by ingestion, but the inhalation of food proteins (through dust or aerosolized particles) may also trigger respiratory symptoms (41). Among patients with FA, asthmatic symptoms are more frequent in children, and especially in those with concomitant atopic dermatitis. In addition to respiratory symptoms occurring Frontiers in Pediatrics | www.frontiersin.org 3 February 2019 | Volume 7 | Article 28 Arasi et al. Severe Asthma and Allergy Severe atopic Atopy eczema predisposition Severe food Severe allergy asthma Severe allergic rhinitis Allergic sensitization Viruses Smoking Pollutants FIGURE 2 | Factors contributing to severe asthma development in childhood. as a presentation of FA, patients with FA are at increased risk for developing asthma and often severe asthma as expression of progression of the atopic march. Symptomatic FA and food allergen sensitization are associated with asthma development both in younger and older children: it was reported that this association is stronger among children with multiple or severe FAS (42-44). Moreover, children with FA develop asthma earlier and at a higher prevalence than children without FA. The opposite is also true, as asthma is a risk factor for the persistence of food allergy (45-47). Food allergy and food sensitization can be also considered as important markers to predict asthma severity. Indeed, it is reported that children with FA and sensitization to at least one food (e.g., egg, milk, soy, peanut, wheat, and fish) had worse lung function (48), higher rates of hospitalization, emergency department visits, use of systemic glucocorticoids (49), or need of mechanical ventilation for severe asthma exacerbation (50, 51). Aspirin Sensitization Aspirin-exacerbated respiratory disease (AERD) is a chronic medical condition, usually in adults and adolescents, consisting of three clinical features: sinus disease with recurrent nasal polyps, asthma, and sensitivity to aspirin and other non-steroidal anti-inflammatory drugs (NSAIDs). Even though asthma is not always present in AERD, asthma symptoms develop 1-3 years after the development of rhinitis or later. When present, asthma is severe and difficult to treat and often characterized by increased residual volume and diminished diffusing capacity due to increased airway remodeling (52). ROLE OF ATOPIC SENSITIZATION IN SEVERE ASTHMA Previous studies showed that atopic sensitization is a major risk factor for severe asthma in children (53-55). Overall, the Frontiers in Pediatrics | www.frontiersin.org 4 expression “atopic sensitization” refers to the positivity either of serum allergen-specific IgE (sIgE) or a positive skin prick test (SPT) to allergen extracts. Arbitrary cut-off points have been set: levels of sIgE >0.35 KU/1 (56) and a mean wheal diameter ≥3mm (SPT) (57). Though these tests are highly sensitive, their mere positivity do not mean itself clinical disease. Quantification of atopic sensitization increases the specificity in relation to childhood asthma presence and severity (4), and asthma persistence in adulthood (58-60). The severity of asthma correlates with both sIgE levels and the number of sensitizations, also on the molecular level. The number of component-specific sensitizations correlate with disease severity in grass allergic children (61) as well as in house dust mites allergic (HDM) pediatric patients. In the Multicentre Allergy Study (MAS) cohort, a birth cohort started in 1990 in Germany, the number of HDM-component specific sensitizations increased with disease severity and with age. Sensitization to Der p 1 and Der p 23 before the age of 5 years was predictive of asthma at school age (62). Similarly, in the Manchester Asthma and Allergy Study (MAAS) birth cohort, asthmatic children were characterized by more complex molecular patterns of IgE sensitization to grass and mite molecules (Der p 1 and Der p 2) (63). In a French study, atopic sensitization to Der p 2 and Der f 2 was more common in severe asthma. In a cohort of 300 asthmatic children (age range, 4-12 years), higher levels of Der p 1 and pet allergen [cat (Fel d 1), dog (Can f 1)] were found to be associated with greater asthma severity (64). Similarly, in latex allergy sensitization to 3 (5, 6.01/6.02) of the 12 recombinant natural rubber antigens so far known was strongly linked with asthma (65). Fungal Allergy Fungal allergy drives asthma severity, too (66). Sensitization to molds has been estimated: 7-20% in the general asthma population; 35-75% in severe asthma patients; 54-91% in life-threatening asthma population (67-69). The severity of exacerbation relates to the different fungi species: in particular, Aspergillus or Alternaria or Cladosporium spp. sensitization has been linked to severe asthma (70, 71). Long-term or uncontrolled fungal infections are associated with a poor controlled asthma, bronchiectasis, and chronic allergic bronchopulmonary aspergillosis (ABPA) (71). The term "Severe asthma with fungal sensitization” (SAFS), introduced by Denning et al. (71), describes a specific phenotype in patients with persistent severe asthma (despite standard treatment) and evidence of fungal sensitization, and do not meet the criteria for ABPA. An EAACI Task Force sets the total IgE cut-off at <1,000 IU/ml for SAFS and >1,000 IU/ml for ABPA, a specific endotypes of asthma, with a genetic predisposition. ROLE OF VIRUSES, SMOKING, AND POLLUTANTS In poli-sensitized asthmatics, daily exposure to allergens combined with other enhancing factors, such as viral infections, smoking (even tertiary one), and/or environmental pollution, influences the asthma course and severity (Figure 2). There is robust evidence concerning the synergistic effect of viral February 2019 | Volume 7 | Article 28 Arasi et al. Severe Asthma and Allergy lower respiratory tract infections (LRTI) and IgE sensitization on asthma development, particularly in children predisposed to atopy (72) and asthma exacerbation (73). Increased risks of asthma inception in atopic predisposed children include: the type of virus (more than 10-fold increased risk for asthma development with rhinovirus compared to 5-fold with respiratory syncytial virus); the severity of viral LRTI; and the age during viral LRTI (74). The risk of hospital admission due to asthma exacerbation is increased by the interaction among respiratory viral infections in combination with atopic sensitization and exposure to allergens (75). Cigarette Smoking Cigarette smoking itself may influence asthma severity, through different patho-mechanisms (76). There is evidence that smoking increases itself serum IgE levels, especially in male adults (77), and rises the risk of IgE sensitization, mainly to occupational allergens (78). Nevertheless, in severe asthmatic patients, the complex association between cigarette smoking and allergy remains currently controversial. Data reports that children exposed to air pollution are at major to develop IgE sensitization to inhalant allergens (79, 80). However, the immunological mechanisms underlying this link remain to be better clarified. Notwithstanding, some data suggest that ultrafine carbon black particles may induce maturation of dendritic cells in vitro (81), which might then facilitate sensitization to airborne allergens. On the other side, airborne pollutants may modulate the inflammatory cellular response in the lungs, thereby lowering the threshold for sensitization. PREVENTION STRATEGIES As widely described above and resumed in Table 2, children with early onset atopy, high specific IgE-sensitization and multiple IgE-sensitizations are at increased risk for developing severe asthma in childhood. In addition, it is well-established that severe allergic diseases more frequently coexist (Figure 2). Based on these premises, it is reasonable that prevention strategies and proper treatments of atopic diseases could prevent occurrence of severe asthma and viceversa. However, asthma development depends on complex and still not fully known interception of genes and environment. Therefore, effective primary prevention strategies for asthma, and especially for severe asthma in children, -though highly desirable- might be difficult to be identified both at population and individual level. Primary Prevention Some studies have suggested that maternal consumption of allergenic food (such us cow's milk, peanut, or fish) and vitamin D and E intake during pregnancy could be associated to decreased risk of allergy and wheezing in their offspring, respectively (82-84). Conflicting results have been reported about the beneficial effect of maternal breastfeeding on pediatric asthma development (85). The role of prebiotics, probiotics, and synbiotic interventions (86) and other dietary supplements (such as nucleosides and nucleotides) (87) is under investigation. Overall, the level of evidence remains currently low or even very low because of the risk of bias, heterogeneity among studies, imprecision, and inconsistency of results, as well as indirectness of available research. Instead, there is stronger evidence concerning maternal smoking and tobacco post-natal exposition. They are both associated to increased risk of asthma in offspring (88). Atopic Dermatitis Since the epithelium plays an important role in protecting against the development of allergic diseases and the occurrence of transcutaneous IgE-sensitization may precede airway sensitization (Figure 1), proactive emollient therapy able to make stronger the epithelial barrier may prevent or delay the development of IgE-sensitization in children affected by AD (89). Allergic Rhinitis It is well-known that AR and asthma often coexist. As they share genetic background, chronic airway inflammation pathway and similar triggers (allergen exposure, viral infections, cold air, and air pollution) (90), treatment of rhinitis can be beneficial for preventing severe asthma exacerbations. The role of exposure to airborne allergens on AR and asthma is well-established and strict avoidance of the culprit allergen(s) is desirable though it is often hard or even impossible. Symptomatic drugs for AR, such as H1-antihistamines and intranasal corticosteroids are not recommended for asthma management (40). However, data suggest that the use of H1- antihistamines in AR children is associated with delayed asthma development (91) and improvement of asthma outcomes (92). Similarly, a significant reduction of asthma symptom scores and rescue medication use has been reported for patients with AR and coexisting asthma by using intranasal corticosteroid therapy (93). Moreover, anti-leukotrienes target both upper and lower airways and could be beneficial in patients with asthma and concomitant AR (94). Biological drugs such as anti-IgE therapy (i.e., omalizumab) and antibody against the a-subunit of receptor for IL-4 and IL-13 (i.e., dupilumab)- have been approved for a few specific phenotypes of severe asthmatic patients at different ages (Table 3). They could be beneficial on both diseases: severe asthma and severe AR (95, 96). Notwithstanding, allergen immunotherapy (AIT) is considered the only etiological treatment able to prevent asthma development (97), to improve asthma symptoms in AR affected children (98), and to prevent new sensitizations in already sensitized patients (99). Furthermore, since adverse events are more common during the escalation or build-up phases of AIT, omalizumab has been suggested as "add-on therapy” to AIT (100). Nevertheless, larger studies are needed to identify patients who would benefit the addition of omalizumab to AIT, as well as optimal dosing strategies and duration treatment (101). Food Allergy Strict avoidance of the culprit food(s) represents currently the standard therapeutic option for FA (102). However, accidental exposure is possible and related to severe adverse events. Allergen Frontiers in Pediatrics | www.frontiersin.org 5 February 2019 | Volume 7 | Article 28/nSee Answer
  • Q7:Instructions The data runs for the lab report are already completed along with 5 questions, please answer the remaining questions on the attached "Activity Form". Use the "Reading-Metabolism" document for reference need to do the observations and questions the answers must go under the word "Answer" and be of the same blue font color./n Data Sheet: Activity - Photosynthesis and Respiration It is a serious Violation of Copyright Law to Post or Share this document ANYWHERE except your Classroom. Posting or sharing this document outside of your classroom can result in account termination and legal action. Do not post ANY Table Top Science (TTS) content or questions outside of your classroom. Name Course Date Biol 103 7377 April 14, 2024 Activity Data Code: LCX The Activity Data Code (3 letters) can be found under the Activity Form tab on the TTS site. Screenshot Paste a screenshot of the completed Procedure I data run below. Make sure you know how your computer/device saves screenshots. Follow this link to get details on how to take and save a screenshot. Paste screenshot here: Lab Menu Background Table Top Science - Lab Activity: Metabolism Procedure Activity Activity Form Pick a leaf sample and click "Display Data." Options: adjust illumination using the slider. Sign Out Leaf Samples Sun Adapted Shade Adapted Danielle ONeal is 02 Probe Photosynthesis Display Data CO₂ Probe Illumination: 100 % Time: 40.0 s Data Run Complete! illumination slider Carbon Dioxide Concentration Change Oxygen Concentration Change 30 30 Change (ppm) 505 Change (ppm) 15 0 15 -30 - 30 04/14/2024 12:07 AM LCX 19.78 ppm 02 Change: CO2 Change: -19.78 ppm Table Top Science Copyright 2016-2024 All Rights Reserved Table Top Science - All Rights Reserved Reset 1 Procedure I - Net Photosynthesis Rates - 100% Illumination Complete the tables below using your data and information found under the Background tab (see the Summary of Needed Formulas section) Leaf Illumination Sample Type Level Oxygen Concentration Elapsed Time Oxygen Change Rate Change Data (s) (ppm/s) (ppm) Sun- Adapted 100% 19.78 40.0 0.4945 Shade- Adapted 100% 12.00 40.0 0.30 Leaf Sample Type Illumination Level Carbon Dioxide Concentration Elapsed Time Carbon Dioxide Change Rate Change Data (s) (ppm/s) (ppm) Sun- Adapted 100% -19.78 40.0 -0.4945 Shade- Adapted 100% -12.00 40.0 -0.30 Observations and Questions [1] What is the function of chlorophyll in photosynthesis? Answer: Chlorophyll's main role is to absorb sunlight and transform water and carbon dioxide into glucose and oxygen. [2] What are enzymes? What is their function in biological and chemical reactions? Specifically, what do they do to a chemical reaction's activation energy? 2 Table Top Science - All Rights Reserved Answer: [3] How might enzyme concentration differences affect rates of photosynthesis and respiration? Answer: [4] Show your oxygen change rate calculation for the Sun-Adapted data run. Be sure to include the units of measurement for each step. Calculation: O2 = change rate / time interval 02 19.78 ppm / 40 s 02 0.4945 ppm/s [5] Show your carbon dioxide change rate calculation for the Shade-Adapted data run. Be sure to include the units of measurement for each step. Calculation: CO2 = change rate / time interval CO2 -19.78/40 s CO2 = -0.4945 ppm/s [6] (a) What is the chemical reaction for photosynthesis? Answer (a): 6H2O + 6CO2 → 602 + C6H12O6 (b) Carefully examine your results from Procedure I. Do your results support the relationship between oxygen and carbon dioxide shown in the chemical reaction? Explain and cite your results as part of your explanation. Answer (b): [7] In procedure I, the oxygen concentration changes differed between sun-adapted leaves and shade adapted leaves. Can chlorophyll concentrations alone explain the differences seen between the two leaf types? Explain your answer, citing your results to support this. Answer: Table Top Science - All Rights Reserved 3 [8] What is the difference between photosynthesis rate and net photosynthesis rate? Which rate are you determining in this procedure? Explain. Answer: Photosynthesis rate is the overall rate of carbon fixation while net photosynthesis rate is the carbon fixation rate minus the carbon loss rate in respiration. [9] Can respiration occur when illumination is 100%? Can respiration occur when illumination is 0%? Explain why (or why not) you would expect this? Answer: Procedure II - Respiration Rates -0% Illumination Data Run Complete the tables below using your data and information found under the Background tab (see the Summary of Needed Formulas section) Leaf Illumination Sample Level Oxygen Concentration Elapsed Time Oxygen Change Rate Type Change Data (s) (ppm/s) (ppm) Sun- Adapted 0% -12.97 40.0 -0.3245 Shade- Adapted 0% -7.78 40.0 -0.1945 Leaf Sample Type Illumination Level Carbon Dioxide Concentration Elapsed Time Carbon Dioxide Change Data (s) Change Rate (ppm/s) (ppm) Sun- Adapted 0% 12.97 40.0 0.3245 Shade- Adapted 0% 7.78 40.0 0.1945 4 Table Top Science - All Rights Reserved Observations and Questions [10] What would be the photosynthesis rate if measured at 0% illumination? Explain your answer. Cite your results from Procedure II to assist with your explanation. Answer: [11] Using your results for the change in carbon dioxide concentration in Procedure Il as a reference, compare the rates of cellular respiration for sun-adapted versus shade-adapted leaves. Explain the biological principles/bases underlying this comparison. Answer: Procedure III - Low-Light Net Photosynthesis Rates -15% Illumination Complete the table below using your data and information found under the Background tab (see the Summary of Needed Formulas section) Leaf Illumination Sample Level Oxygen Concentration Elapsed Time Oxygen Change Rate Change Data Type (s) (ppm/s) (ppm) Sun- Adapted 15% 4.42 40.0 0.1105 Shade- Adapted 15% 7.59 40.0 -0.1105 Observations and Questions [12] Based on the data you collected in Procedures I (100% illumination) and III (15% illumination), which system of leaves produces the most oxygen: Sun-adapted or shade- adapted? Is one system (sun- or shade-adapted) more productive than the other in all light levels? Explain how your results support your answer. Table Top Science - All Rights Reserved 5See Answer
  • Q8: TVO ILC Student Name: Unit 2 ● Learning goals ● Unit title ● Plants Unit 02: LA06 Assessment for feedback and grade Level/Mark Date: SBI3U Assessment Grading of Your Learning Percentage of term Work Copyright © 2021 The Ontario Educational Communications Authority. All rights reserved. /15% evaluate the importance of the sustainable use of plants to Canadian society and other cultures; describe and compare the structures and functions of plant tissues evaluate data and draw conclusions about factors affecting plant growth demonstrate an understanding of the diversity of vascular plants, including their structures, internal transport systems, and their role in maintaining biodiversity Complete the eight short answer questions and then attach your Three Sisters research and submit them both for grading by the teacher. TVO ILC Part 1: Eight short answer questions 1. Match the following eight angiosperm structures to their functions. List of Structures Calyx, Sepal, Carpel, Ovule, Seed, Stamen, Anther, and Corolla List of Functions A. This structure produces pollen. B. This structure contains the fertilized zygote. C. This structure attracts pollinators. D. This structure is a collection of sepals. E. This structure is the male sex organ. F. This structure is where meiosis takes place in order to produce eggs. G. This structure contains the stigma, style, and ovary. H. This structure protects the developing flower. SBI3U Assessment Grading of Your Learning 2. List three factors that are contributing to the decline of pollinator populations. 3. From an agricultural perspective, describe two advantages of vegetative propagation. Copyright © 2021 The Ontario Educational Communications Authority. All rights reserved. TVO ILC 4. For a plant colonizing a remote island, describe one advantage and one disadvantage for each of the following methods: self-pollination and cross-pollination. 5. Three factors that affect plant growth are soil health, nitrogen fixation, and sunlight. Explain how each factor works to affect the growth of plants. 6. The following experiment was carried out at ILC laboratories to measure the effects of different nutrient solutions on bean root growth. Three nutrient solutions were made: Nutrient solutions containing: Results: root length, leaf colour all required nutrients 47 mm; deep green Solution 1 Solution 2 Solution 3 SBI3U Assessment Grading of Your Learning all required nutrients except nitrogen distilled water Copyright © 2021 The Ontario Educational Communications Authority. All rights reserved. 17 mm; pale green-yellow 14 mm; pale green-yellow Interpret the results for each solution. In your answer for each, a) explain how the solution ranked in relation to the other two (in terms of growth and health of the plant); TVO ILC b) state the evidence that supports your answer; and c) explain why the plant grew the way it did. 7. A botanist wanted to see if a new strain of corn could germinate in soil that was too salty for regular corn. She conducted a study on the germination success of seeds from the new strain that were exposed to various levels of salty soil, from zero to normal (100 mg/L), high (200 mg/L), very high (400 mg/L), to normally lethal (800 mg/L). The table below shows her data for this study. Petri dish Number of seeds planted label 1 2 3 4 5 Salt concentratio n (mg/L) 0 100 200 400 800 20 20 20 20 20 Number of seeds that germinated Copyright © 2021 The Ontario Educational Communications Authority. All rights reserved. 16 18 18 11 SBI3U Assessment Grading of Your Learning 7 Percentage of seeds that germinated 80% 90% 90% 55% 35% a) Write a formal hypothesis for this study. b) Does her data support or reject the hypothesis? Explain your reasoning. TVO ILC 8. The table shown below represents the number of species growing in an area that was logged using clear-cutting 45 years ago in Temagami, Ontario. Data was collected periodically over 45 years. a) Describe the changes occurring in vegetation type and species diversity over the 45 years. b) What does the pattern of change tell you about what is happening this area? c) Explain how the data supports your conclusion. Type of vegetation Years after clear-cut logging that the area was sampled 1 32 Grasses Shrubs Trees Total species 32 ܘ ܘ 5 28 4 。 32 SBI3U Assessment Grading of Your Learning 15 24 5 29 Copyright © 2021 The Ontario Educational Communications Authority. All rights reserved. 25 31 8 16 55 45 35 18 24 77See Answer
  • Q9:. Page 1 y of 2 Choose a specific endangered species of Strepsirrhine to research for this assignment. I recommend that you review several appropriate species before making your selection. Look up and read at least five different sources about this endangered Strepsirrhine species. o Sources for this assignment must be from .org or .edu or.gov sources (NO.com sources, no encyclopedia or Wikipedia sources). Make sure that your sources are recent (published within the past 10 years, preferably more recent). Create a source page that contains the full source citation in APA format for every source used to research information for your paper. APA Source Citation Format: Family name of author(s), followed by personal name initial(s). (Year of publication). Title of article. Publication, volume number (issue number), page numbers. DOI number (Digital Object Information number) if available. Include the complete URL if your information came from online source(s). Example of APA source format for articles: Smithson, J. and Brittan, G. (2023). Endangered bison bonasus. Bison Weekly, Vol. 12 (issue 16), pp. 45-47. DOI: 12345678910 How to construct your paper: o Introduce your chosen endangered Strepsirrhine species: common name, scientific name, location in the wild, physical and behavioral characteristics o Describe the habitat and environment in which this endangered species is usually found o Discuss the factors that contribute to the endangered status of your chosen species o Review possible ways to mitigate the factors that contribute to the endangered status of your chosen speciesSee Answer
  • Q10:2. Using the "rest ECG" in the assignment page in Canvas, measure the R-R interval and use that to calculate the heart rate. Show the work.See Answer
  • Q11:http://www.personal.rdg.ac.uk/~llsroach/phon2/artic-basics.htm Links to an external site. Oral Motor Therapy (3).pdf Download Oral Motor Therapy (3).pdf Efficacy-of-Using-an-Oral.pdf write a short 2 paragraph summary (minimum of 500 words) explaining the support and opposition to using oral motor therapy. (What are some reasons why some therapists think it is effective and others think it is a waste of time? What is your opinion?)See Answer
  • Q12:water. Q11. Do a brief internet search to determine if there is a relationship between the temperature and volume of a known amount of water. Cite the web pages/sites you use as a reference. Look for credible and accurate sources of information.See Answer
  • Q13:Q9. Janice has a geranium in a flowerpot, and after a while it dies. Janice thinks, "I wonder if it is because of the type of potting soil I used?" So she goes to the store and buys a new geranium and a different type of potting soil to plant it in. She also waters this new geranium every other day and is careful not to forget about it like she did before. After the plant survives for one year, Janice decides that her experiment proved that this new brand of potting soil is excellent and recommends it to all her friends. Use the information in the link above and: Explain why Janice's experiment is actually NOT good enough to make the interpretation that she made? • Help Janice out by designing an experiment for her. Include all steps of the scientific method and the information on the link above. Be sure to specifically list all your variables and which type each is. o Make sure to label from the experiment the independent variable, dependent variable, and control variables. Q10. What is a "control group"? Why does an experiment need to have a control group? (Hint: Look in the blue link above that says scientific experiments.)See Answer
  • Q14:Q7. Come up with your own examples of a falsifiable statement and a non-falsifiable statement. For each one, explain how it can or cannot be proven false. Q8. Find out what is meant by the term pseudo-science and give an example not found in this lesson.See Answer
  • Q15:Q4. Give one example that is not found in the lesson for each: a.) inductive reasoning b.) deductive reasoningSee Answer
  • Q16:The test will either support your hypothesis because the lights do not work or the test will not support your hypothesis because the lights do work, and you will have to modify your hypothesis or come up with a completely new one Q2. Your uncle Jim makes a salad dressing that you really like. After Sunday's dinner he gives you a bottle with some of the dressing to take home to use during the following week. When you take the bottle out of the fridge next day, you see that there are different layers of fluid. Your first instinct is to call uncle Jim and ask him whether the dressing went bad. However, you remember reviewing the scientific method and want to use it to find out what happened to the dressing. Write out each of the 6 steps above applying the scientific method to this observation. 1. observation: 2. question: 3. hypothesis: 4. prediction: 5. test: 6. conclusion: Q3. Your friend, Barbara, tells you she is using a new fertilizer on her roses. She believes this new fertilizer, "Mega Rose", is making her roses grow faster and flower more than your roses. How could you use the scientific method to decide if you should start using "Mega Rose" on your roses, too? Write out each of the 6 steps above applying the scientific method to this observation. 1. observation: 2. question: 3. hypothesis: 4. prediction: 5. test: 6. conclusion:See Answer
  • Q17:write a short 2 paragraph summary (minimum of 500 words) explaining the support and opposition to using oral motor therapy. (What are some reasons why some therapists think it is effective and others think it is a waste of time? What is your opinion?)See Answer
  • Q18:"Facing Death", you came across an elderly woman called Martha and her two daughters. She is 86 years old & has been diagnosed with dementia & so her daughters must decide whether to remove her from the ventilator. Which of the two sisters do you agree with, Nadege or Sherley? Explain why in 100 words and reply to one of your classmates posts.See Answer
  • Q19:What purpose does phenol red serve in this experiment? If there is a colour change in tubes 3 & 4, what is happening in these tubes to drive the colour change?See Answer
  • Q20:Why are bile salts added to tube 2 if there is no pancreatin added?See Answer

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