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Q1: In the Tree Building Challenge exercise, please use the following steps to build a tree. Identify which tree of the options below is the one that you constructed. 1. Start on Peak 1. Reset the simulation until you get to this starting point. 2. Let some time pass. 3. Move a flower from Peak 1 to Peak 3 4. Let some time pass. 5. Move a flower from Peak 3 to Peak 4 6. Let some time pass. 7. Move a flower from Peak 1 to Peak 2. 8. Let some time pass. See Answer
Q2: Consider the three trees below. One of them has different evolutionary relationships among the four peaks than the other two. Which one is it? Tree A Tree BC' Tree CSee Answer
Q3: Question 1.4 in this exercise asks about whether the timing of a trait change (in this case dark petals) differs when you rotate the tree around the nodes (your answer to this should be NO!). What would alter the timing of a trait change? If the simulation was run again and I allowed the columbines to evolve for different numbers of generations before I made the mutation happen If I rotated around the node that joins the columbines on all four peaks If I rotated around the node that joins Peaks 1, 3 and 4 There is no way this can changeSee Answer
Q4: Consider the tree that you are working with (shown here again so you don't have to scroll around!). What is the order that trait change occurred in the group of columbines, starting at the one that happened earliest? anthers petal tips spur colour petal colourSee Answer
Q5: Advanced Cell Biology 2022-23: Coursework 3 Topic: Genome Editing Aim: To demonstrate an ability to explain scientific research to a non-specialist audience. This is a key skill for all scientists and helps clarify our thinking about what is most important about a particular piece of work. Most funding applications for research require a lay summary, and this is considered an essential part of public engagement and scientific accountability. Similarly, many jobs in science involve communication of complex data to non-specialist audiences such as the general public, shareholders, or politicians. For a wider context, see also: https://www.nature.com/articles/d41586-020-00580-w The Task: Write a lay summary of not more than 250 words explaining the research described in the technical abstract below from a controversial scientific paper about genome editing in human embryos. Use the example from class to guide you in structuring the summary. You will be introduced to the scientific concepts described in the abstract in the Genome Editing lectures on the ACB course. For this coursework, your target reader is an engaged year 11 school student (~age 16). This coursework should be submitted in electronic format using Moodle by midnight on 27th January 2023. You must express the summary in your own words - text transcribed from other sources will be excluded from marking. Please include your student number at the start of your document. Correction of a pathogenic gene mutation in human embryos ABSTRACT Genome editing has potential for the targeted correction of germline mutations. Here we describe the correction of the heterozygous MYBPC3 mutation in human preimplantation embryos with precise CRISPR-Cas9-based targeting accuracy and high homology-directed repair efficiency by activating an endogenous, germline-specific DNA repair response. Induced double-strand breaks (DSBs) at the mutant paternal allele were predominantly repaired using the homologous wild-type maternal gene instead of a synthetic DNA template. By modulating the cell cycle stage at which the DSB was induced, we were able to avoid mosaicism in cleaving embryos and achieve a high yield of homozygous embryos carrying the wild-type MYBPC3 gene without evidence of off-target mutations. The efficiency, accuracy and safety of the approach presented suggest that it has potential to be used for the correction of heritable mutations in human embryos by complementing preimplantation genetic diagnosis. However, much remains to be considered before clinical applications, including the reproducibility of the technique with other heterozygous mutations. Nature. 2017 Aug 24;548(7668):413-419. https://www.nature.com/articles/nature23305 Further reading Some of the interpretations in this paper have been questioned by other researchers. Their views are published as Brief Communications Arising in the same journal: https://www.nature.com/articles/s41586-018-0380-z https://www.nature.com/articles/s41586-018-0379-5 The authors of the original study then had the chance to reply: https://www.nature.com/articles/s41586-018-0381-y Reading these associated articles will give a broader perspective on the original study. Plagiarism statement Digital submission of your answer file is equivalent to your explicit declaration that you have adhered to our community expectations of academic integrity and that the work submitted is entirely your own. Answer files will be checked with software designed to detect plagiarism. Answers comprised mainly of text simply copied directly from learning materials will reveal little understanding by the student and hence cannot score highly. Further: markers will be looking for unseemly degrees of similarity in the answers of multiple students; such answers will attract no marks. Assessment Criteria See next page. Grade (Degree Class) A+ (1) D (1) A- (1) B+ B B- (21) C+ tu (2ii) D- (3) F (Fail) Numerical Scale 98 95 92 88 85 82 78 75 72 68 65 62 58 55 52 48 45 40 Pass-Fail Boundary 38 30 20 10 Level 6 Assessment Criteria: ACB Coursework 3 O CRITERIA Exceptional. All the attributes of an A, plus: A highly sophisticated grasp of the topic, with sufficient clarity and originality that the submission could be used without editing for effective communication with non-scientists.. Outstanding. All the positive attributes of an A-, plus: further/deeper outside reading, marshalled effectively in the submission. Minor defects in synthesis may be compensated for by originality and clarity of presentation. Excellent. Clear, complete and logical description of the topic. Appreciation of the wider context underlying key concepts is evident, some of which may have been gained from outside reading. Lucid and original communication of the topic is clearly demonstrated. Very Good. The answer displays a very sound understanding of the main issues and concepts, is generally well-organised, and the quality of writing and the language used is overall very good. Lucid and original communication will be evident, but will be less sophisticated than in a First Class answer. Some errors, minor omissions and/or partial understanding of some aspects of the topic may be tolerated, so long as these do not detract from an otherwise sound answer. Good, but limited. The answer displays a reasonable understanding of the key issues and concepts relevant to the topic, but may go little further than to reword, with little evidence of insight or synthesis, information in the source material. Organisation of the information is adequate for most of the answer. Errors, omissions, poorly expressed ideas, and/or use of technical language -although none too serious-detract from the overall quality. Weak, but passable. The answer demonstrates a partial understanding of at least some of the topic. Writing quality is adequate for at least part of the answer. However, the answer is likely to be poorly organised and some of the basic requirements of the question may not have been met. Errors, omissions, poorly expressed ideas using highly technical language, and/or partial understanding will be too frequent/serious to merit a higher grade. Just passing. The answer must demonstrate a minimal understanding of the topic, but coverage is only partial and superficial. The topic is covered by only the bare minimum of required information, primarily in the form of minimal rephrasing of source material. The minimum mark for a pass is 40%. Borderline Fail. A serious attempt, but of insufficient quality to pass. A structured answer is attempted, but it fails to demonstrate an adequate depth of knowledge and understanding of the topic. This deficiency may be compounded by a disorganised explanation and/or very poor or very technical language. Minimum serious attempt. An attempt has been made to engage with the question, and parts of the answer may have some merit, but there are major errors and/or omissions. May also apply to an answer that is reasonably competent in parts, but for the most part does not address the question set. Clear Fail. A few relevant points show some engagement with the question, but these are outweighed by severe errors and/or omissions. An extremely brief answer, probably with only one or two key words or phrases of any relevance to the subject addressed by the question. Answer given has no merit, or answer is absent.See Answer
Q6:write a journal on this topic: What is genomic information? How can genomics be used to improved patient care? Word limit: 200 Words Format: MLASee Answer
Q7: Advanced Cell Biology 2022-23: Coursework 3 Topic: Genome Editing Aim: To demonstrate an ability to explain scientific research to a non-specialist audience. This is a key skill for all scientists and helps clarify our thinking about what is most important about a particular piece of work. Most funding applications for research require a lay summary, and this is considered an essential part of public engagement and scientific accountability. Similarly, many jobs in science involve communication of complex data to non-specialist audiences such as the general public, shareholders, or politicians. For a wider context, see also: https://www.nature.com/articles/d41586-020-00580-w The Task: Write a lay summary of not more than 250 words explaining the research described in the technical abstract below from a controversial scientific paper about genome editing in human embryos. Use the example from class to guide you in structuring the summary. You will be introduced to the scientific concepts described in the abstract in the Genome Editing lectures on the ACB course. For this coursework, your target reader is an engaged year 11 school student (~age 16). This coursework should be submitted in electronic format using Moodle by midnight on 27th January 2023. You must express the summary in your own words - text transcribed from other sources will be excluded from marking. Please include your student number at the start of your document. Correction of a pathogenic gene mutation in human embryos ABSTRACT Genome editing has potential for the targeted correction of germline mutations. Here we describe the correction of the heterozygous MYBPC3 mutation in human preimplantation embryos with precise CRISPR-Cas9-based targeting accuracy and high homology-directed repair efficiency by activating an endogenous, germline-specific DNA repair response. Induced double-strand breaks (DSBs) at the mutant paternal allele were predominantly repaired using the homologous wild-type maternal gene instead of a synthetic DNA template. By modulating the cell cycle stage at which the DSB was induced, we were able to avoid mosaicism in cleaving embryos and achieve a high yield of homozygous embryos carrying the wild-type MYBPC3 gene without evidence of off-target mutations. The efficiency, accuracy and safety of the approach presented suggest that it has potential to be used for the correction of heritable mutations in human embryos by complementing preimplantation genetic diagnosis. However, much remains to be considered before clinical applications, including the reproducibility of the technique with other heterozygous mutations. Nature. 2017 Aug 24;548(7668):413-419. https://www.nature.com/articles/nature23305 Further reading Some of the interpretations in this paper have been questioned by other researchers. Their views are published as Brief Communications Arising in the same journal: https://www.nature.com/articles/s41586-018-0380-z https://www.nature.com/articles/s41586-018-0379-5 The authors of the original study then had the chance to reply: https://www.nature.com/articles/s41586-018-0381-y Reading these associated articles will give a broader perspective on the original study. Plagiarism statement Digital submission of your answer file is equivalent to your explicit declaration that you have adhered to our community expectations of academic integrity and that the work submitted is entirely your own. Answer files will be checked with software designed to detect plagiarism. Answers comprised mainly of text simply copied directly from learning materials will reveal little understanding by the student and hence cannot score highly. Further: markers will be looking for unseemly degrees of similarity in the answers of multiple students; such answers will attract no marks. Assessment Criteria See next page. Level 6 Assessment Criteria: ACB Coursework 3 CRITERIA Exceptional. All the attributes of an A, plus: A highly sophisticated grasp of the topic, with sufficient clarity and originality that the submission could be used without editing for effective communication with non-scientists.. Outstanding. All the positive attributes of an A-, plus: further/deeper outside reading, marshalled effectively in the submission. Minor defects in synthesis may be compensated for by originality and clarity of presentation. Grade Numerical (Degree Class) Scale A+ 98 (1) 95 92 D 88 (1) 85 82 A- 78 (1) B 812 75 72 B+ 68 B- 65 (2i) 62 8052 C+ 58 C 55 C- (2ii) 52 D+ D 48 45 D- (3) 40 40 Pass-Fail Boundary F 38 (Fail) 30 20 10 Excellent. Clear, complete and logical description of the topic. Appreciation of the wider context underlying key concepts is evident, some of which may have been gained from outside reading. Lucid and original communication of the topic is clearly demonstrated. Very Good. The answer displays a very sound understanding of the main issues and concepts, is generally well-organised, and the quality of writing and the language used is overall very good. Lucid and original communication will be evident, but will be less sophisticated than in a First Class answer. Some errors, minor omissions and/or partial understanding of some aspects of the topic may be tolerated, so long as these do not detract from an otherwise sound answer. Good, but limited. The answer displays a reasonable understanding of the key issues and concepts relevant to the topic, but may go little further than to reword, with little evidence of insight or synthesis, information in the source material. Organisation of the information is adequate for most of the answer. Errors, omissions, poorly expressed ideas, and/or use of technical language -although none too serious-detract from the overall quality. Weak, but passable. The answer demonstrates a partial understanding of at least some of the topic. Writing quality is adequate for at least part of the answer. However, the answer is likely to be poorly organised and some of the basic requirements of the question may not have been met. Errors, omissions, poorly expressed ideas using highly technical language, and/or partial understanding will be too frequent/serious to merit a higher grade. Just passing. The answer must demonstrate a minimal understanding of the topic, but coverage is only partial and superficial. The topic is covered by only the bare minimum of required information, primarily in the form of minimal rephrasing of source material. The minimum mark for a pass is 40%. Borderline Fail. A serious attempt, but of insufficient quality to pass. A structured answer is attempted, but it fails to demonstrate an adequate depth of knowledge and understanding of the topic. This deficiency may be compounded by a disorganised explanation and/or very poor or very technical language. Minimum serious attempt. An attempt has been made to engage with the question, and parts of the answer may have some merit, but there are major errors and/or omissions. May also apply to an answer that is reasonably competent in parts, but for the most part does not address the question set. Clear Fail. A few relevant points show some engagement with the question, but these are outweighed by severe errors and/or omissions. An extremely brief answer, probably with only one or two key words or phrases of any relevance to the subject addressed by the question. Answer given has no merit, or answer is absent. 0See Answer
Q8: Biology Department of Applied a Biotechnology قسم علوم الحياة التطبيقية. University of Sharjah College of Graduate Studies & Sci. Research Department of Applied Biology/Biotechnology Program Paper Critique Format Selected Topics in Biotechnology A (1450592A) جامعة الشارقة UNIVERSITY OF SHARJAH Dear Students, For the paper critique, you are to take 1 paper from the current literature and share the results with the class, evaluate the data, turn in a formal critique for grading. The paper should be different that is going to be presented in the class. The format shall be in 2-3 pages only and can be as follows: Selected Topics in Biotechnology A (1450592A) By For Authors: Title.. Journal. Volume:. Pages: *Corresponding Author:. Background Authors studied Advantage of the technology applied Methodology: Attach a flow chart (describe the method) Narrate about methodology Ex. -This paper did not show.. -did not clarify ..... -Contradiction in the results -Methodology is not clear -Results are not explained well -Discussion is not based on obtained results Biotechnology Article Critique Assignment Title of the article: Suggested Improvements for the Allergenicity Assessment of Genetically Modified Plants Used in Foods. Authors: Richard E. Goodman & Afua O. Tetteh Journal & Date of publishing: Curr Allergy Asthma Rep- 13 April 2011 This is an interesting article, as it targets a very important and common problem faced by millions of people around the world; that is food allergies. As the world population have dramatically increased within the past few centuries, demand on food resources have multiplied, in order to meet the needs of the growing populations. This made scientists opt for other possible resources for food and feed until they reached the golden era of genetically modified (GM) plants and crops. Although this might sound as the brilliant solution to the world's feeding problems, but it also gives rise to a different kind of problems related to the consumers themselves. Food allergies related to those GM plants and crops evolved; therefore, rules and regulations controlling the production, distribution and consumption of these food products have been set. Unfortunately, there are no global testing, approval and registration guidelines; in fact, approvals regarding GM products are country specific. As the title of the article suggests, the authors are trying to find out more efficient criteria and methods that can help lawmakers and stakeholders identify the risks associated with allergic reactions regarding consumption of GM foodstuff. Reading the abstract gives you a general idea about the article and raise lots of questions in the mind of the reader about possible conflicts. The authors discussed their idea efficiently, supporting their arguments with valid literature resources and significant data. I would suggest more elaboration on the techniques and tests used in identifying the allergenicity of proteins, and the rationale behind their usage. For example, on what basis where allergens designated so? According to FASTA and BLAST, an overall sequence identity alignment of proteins sharing less than 50% was unlikely to share IgE cross-reactivity; is “unlikely” a reliable word? Can consumers depend on the decreased likelihood of allergenicity? I strongly believe that this point is debatable. Allergy related issues should not depend on likelihood. It is true that allergies, mostly, are unpredictable, but allergies related to GM plants and crops should be clearly present or absent. As you go through the article, you can notice that the authors opt for results that are biased towards the high safety levels of GM plants and crops. The conclusion paragraph summarizes their findings and their suggestions that consumer's safety comes first; therefore, guidelines need to be regulated and monitored and efficiently implemented under a single umbrella globally.See Answer
Q9:/n IMPACT FACTOR Indexed in: CITESCORE PubMed 6.4 microorganisms 4.5 Article Activation of Secondary Metabolism in Red Soil-Derived Streptomycetes via Co-Culture with Mycolic Acid-Containing Bacteria Kairui Wang, Ning Liu, Fei Shang, Jiao Huang, Bingfa Yan, Minghao Liu and Ying Huang Special Issue Secondary Metabolism of Microorganisms Edited by Dr. Carlos García-Estrada and Dr. Carlos Barreiro MDPI https://doi.org/10.3390/microorganisms9112187 MDPI wwww Article microorganisms Activation of Secondary Metabolism in Red Soil-Derived Streptomycetes via Co-Culture with Mycolic Acid-Containing Bacteria Kairui Wang 1,2, Ning Liu ¹, Fei Shang ³, Jiao Huang 1,2, Bingfa Yan 1,2, Minghao Liu ¹,* and Ying Huang 1 3 1,2,* State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; wangkairui1994@163.com (K.W.); fussliu@126.com (N.L.); huangjiao515665@163.com (J.H.); yanbingfa2014@126.com (B.Y.) 2 College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China 3 Analytical and Testing Center, Beijing University of Chemical Technology, Beijing 100029, China; shangfei@mail.buct.edu.cn * Correspondence: lysf1987313@163.com (M.L.); huangy@im.ac.cn (Y.H.) check for updates Citation: Wang, K.; Liu, N.; Shang, F.; Huang, J.; Yan, B.; Liu, M.; Huang, Y. Activation of Secondary Metabolism in Red Soil-Derived Streptomycetes via Co-Culture with Mycolic Acid-Containing Bacteria. Microorganisms 2021, 9, 2187. https://doi.org/10.3390/ microorganisms9112187 Academic Editors: Carlos García-Estrada and Carlos Barreiro Received: 28 September 2021 Accepted: 15 October 2021 Published: 20 October 2021 Abstract: Our previous research has demonstrated a promising capacity of streptomycetes isolated from red soils to produce novel secondary metabolites, most of which, however, remain to be explored. Co-culturing with mycolic acid-containing bacteria (MACB) has been used successfully in activating the secondary metabolism in Streptomyces. Here, we co-cultured 44 strains of red soil- derived streptomycetes with four MACB of different species in a pairwise manner and analyzed the secondary metabolites. The results revealed that each of the MACB strains induced changes in the metabolite profiles of 35-40 streptomycetes tested, of which 12–14 streptomycetes produced "new" metabolites that were not detected in the pure cultures. Moreover, some of the co-cultures showed additional or enhanced antimicrobial activity compared to the pure cultures, indicating that co-culture may activate the production of bioactive compounds. From the co-culture-induced metabolites, we identified 49 putative new compounds. Taking the co-culture of Streptomyces sp. FXJ1.264 and Mycobacterium sp. HX09-1 as a case, we further explored the underlying mechanism of co-culture activation and found that it most likely relied on direct physical contact between the two living bacteria. Overall, our results verify co-culture with MACB as an effective approach to discover novel natural products from red soil-derived streptomycetes. Keywords: Streptomyces; co-culture; mycolic acid-containing bacteria (MACB); secondary metabolites (SMs); activation of natural products Publisher's Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. CC BY Copyright: 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). 1. Introduction Natural products (NPs), or their semi-synthetic derivatives, are important sources of lead compounds in drug discovery [1,2]. More than 50% of clinically used antibiotics were derived from filamentous Gram-positive bacteria of the genus Streptomyces [3,4]. Analysis of the genome sequences of Streptomyces and related genera revealed that they may contain a great variety of secondary metabolite (SM) biosynthetic gene clusters (BGCs) encoding novel NPs [5,6]. However, most of these BGCs remain silent under laboratory conditions, thus triggering research in the sense of developing activating strategies for the genome mining of microbial NPs [7–9]. Several previous studies reported that microbial cryptic BGCs could be activated by co-culturing the host strains with other species [10–13], partially due to mimicking the in situ microbial interactions in the original environment where microorganisms coexist [14]. However, traditional co-culture methods require large-scale screening to find ideal micro- bial combinations, and thus, is laborious and difficult to apply at scale. In recent years, it has been shown that co-cultures with mycolic acid-containing bacteria (MACB) widely Microorganisms 2021, 9, 2187. https://doi.org/10.3390/microorganisms9112187 https://www.mdpi.com/journal/microorganisms Microorganisms 2021, 9, 2187 2 of 15 activate cryptic SM-BGCs in streptomycetes [15]. Hitherto, around 40 novel NPs have been discovered from Streptomyces, and rare actinobacteria by co-culture with MACB strains. These compounds comprise a variety of chemical scaffolds and bioactivities, validating this SM-BGC activation method of co-culture [16–18]. Red soils are widely distributed in tropic and subtropical areas of southern China. These soils are acidic, oligotrophic, and rich in iron and aluminum oxides, and thus provide ideal habitats for acidophilic actinobacteria [19]. Our recent studies have shown that red soil-derived streptomycetes are prolific NP producers [19], and have identified several NPs with novel scaffolds or modifications from these strains, as exemplified by azolemycins [20], NC-1 [21], and mycemycins [22]. Meanwhile, the in silico genome- mining of red soil-derived streptomycetes also reveals that these strains contain numerous unidentified SM-BGCs, the products of which remain to be unraveled. To activate the silent SM-BGCs of red soil-derived streptomycetes for NPs discovery, we selected 44 bioactive Streptomyces isolates and co-cultured them with four MACB of different species in a pairwise manner. Metabolites of the co-cultures were subjected to multi-spectroscopic analyses and bioactivity assay, which showed that the MACB strains effectively activated secondary metabolism in most of the streptomycetes. We also tried to explore the underlying mechanism of co-culture activation. Results of the study gain a deep insight into the NP biosynthetic potential of red soil-derived streptomycetes. 2. Materials and Methods 2.1. Strains and Media The strains used in this work are listed in Table S1. Eight MACB were isolated from soils collected in Haixi Mongolian and Tibetan Autonomous Prefecture, China [23], and two MACB and all Streptomyces strains were from red soils collected in Jiangxi Province, China [19,24]. All these strains were preliminarily identified by 16S rRNA gene sequencing in our previous studies [19,23,24]. Three indicator strains from different phyla were used for antimicrobial activity assay: Micrococcus luteus CGMCC 1.2567 (Gram-positive bacterium) and Trichoderma viride CGMCC 3.1913 (fungus) were obtained from the China General Microbiological Culture Collection Center (CGMCC), and extended-spectrum ß-lactamase (ESBL)-producing Escherichia coli 4-1 (Gram-negative bacterium) was obtained from the Weifang Medical University, Shandong Province, China. A YGGS medium (glucose 5.0 g, soluble starch 20.0 g, glycerin 20.0 g, yeast extract 3.0 g in 1 L dd-H₂O, pH 7.2) [25] was used for the co-culture and pure culture of strains. A TSB medium (pancreatic digest of casein 17.0 g, papaic digest of soybean 3.0 g, dextrose 2.5 g, NaCl 5.0 g, K₂HPO4 2.5 g in 1 L dd-H₂O, pH 7.1-7.5) was used for seed culture. A GYM agar (yeast extract 4.0 g, malt extract 10.0 g, glucose 4.0 g, CaCO3 2.0 g, agar 15.0 g in 1 L dd-H2O) was used for recovering strains from glycerol stocks. An LB agar (tryptone 10.0 g, yeast extract 5.0 g, NaCl 10.0 g, agar 15.0 g in 1 L dd-H₂O) and PDA (glucose 20.0 g, potato powder 6.0 g, agar 15.0 g in 1 L dd-H2O) were used to culture the indicator bacteria and fungus, respectively. 2.2. Co-Culture and Pure Culture of Strains After the incubation of the strains on a GYM plate for 2-3 days, an agar block of about 1 cm² with bacterial lawn was cut out and transferred into a 250 mL shake flask containing 50 mL of TSB medium for seed culture. The seeds of Streptomyces and MACB were cultured at 28 °C on a rotary shaker at 160 rpm for 3 and 2 days, respectively. Then, 3 mL of Streptomyces and 1 mL of MACB seed cultures were co-transferred into a 250 mL flask containing 100 mL of YGGS medium and fermented at 28 °C, 220 rpm for 7 days. Pure culture controls were performed similarly but with single strains. Each experiment was repeated in triplicate in this study. Microorganisms 2021, 9, 2187 3 of 15 2.3. SM Extraction, Isolation, and Analysis The resulting cultures were collected and extracted three times with an equal volume of ethyl acetate. The extracts were combined and concentrated in vacuo to evaporate the solvent, and the residue was re-dissolved in 1 mL of methanol. An HPLC analysis was carried out with a Shimadzu SPD-M20A HPLC system, using a Waters Xbridge ODS column (4.6 × 150 mm, 5 μm) with a linear gradient of MeOH/H2O (see Table S2). The injection volume of the sample was 20 µL. The Dionex 3000 RS system was used to set the temperature at 30 °C and the flow rate at 1.0 mL/min; the elution curves of metabolites were monitored at 220, 254, and 300 nm, respectively. Differences in the secondary metabolism between the co-cultures and pure cultures were determined by comparing their HPLC profiles based on the retention time and UV absorption spectra of peaks. Metabolites corresponding to the differential HPLC peaks were then collected and subjected to UHPLC-HRMS (Waters Xevo G2 quadrupole time of flight-ultra performance liquid chromatography, and mass spectra scanning from 100 to 2000 atomic mass units) to obtain their accurate molecular weights (MWs). The resultant mass spectrum data were analyzed by the Mass Lynx v 4.1 software system. Compounds were identified by the comparison of MWs, UV spectra, and retention times with published chemical data from standard databases (Dictionary of Natural Prod- ucts [DNP] on DVD, version 22.2 and on web, version 30.1 [http://dnp.chemnetbase.com/, accessed on 1 September 2021]; ChemSpider [http://www.chemspider.com/, accessed on 2 September 2021]) and references. The activated metabolites with characteristic information unmatched with that in the databases were inferred as putative new products. Some of these compounds were subjected to nuclear magnetic resonance (NMR) spectroscopic analysis (Bruker AVIII 500 MHz NMR spectrometer, Bruker, Karlsruhe, Germany) for further structure elucidation. 2.4. Bioactivity Assay Bioactivities of the fermentation extracts were tested against M. luteus, ESBL-producing E. coli, and T. viride using agar-well diffusion assay. Twenty μL of each extract were added into a punched hole (7 mm in diameter) in LB/PDA plates containing indicator strains. The plates were then cultured at 37 °C for 12 h for bacterial indicators or at 28 °C for 48 h for the fungus. Antimicrobial activity was estimated by measuring the diameter of the inhibition zones: positive (7 mm < diameter ≤ 9 mm) and strongly positive (diameter > 9 mm). 2.5. Non-Contact Co-Culture of Streptomyces sp. FXJ1.264 and Mycobacterium sp. HX09-1 The co-culture was carried out in a device of two connected culture compartments separated by a 0.22-µm polyether sulfone (PES) membrane (Figure S1). Each of the com- partments contained 50 mL YGSS medium and were inoculated with 3 mL seed culture of S. sp. FXJ1.264 or 1 mL seed culture of M. sp. HX09-1. The device only allowed substance exchange between the compartments, but the cells of the two strains could not contact each other. For the control groups, only one compartment in the device was inoculated, with either a single strain or two strains mixed. The device was fixed on a shaker and the strains were fermented at 28 °C, 220 rpm for 7 days. The fermentation metabolites from each compartment were analyzed using the method described in Section 2.3. 2.6. Co-Culture of S. sp. FXJ1.264 and Heat-killed M. sp. HX09-1 M. sp. HX09-1 was cultured in 250 mL flasks each containing 50 mL of the YGGS medium for 2 or 7 days. The culture broths were then heated at 121 °C for 20 min to kill the cells. After cooling down to room temperature, the flask was added with 50 mL fresh YGGS medium and 3 mL seed culture of S. sp. FXJ1.264, and the resulting culture was incubated at 28 °C, 220 rpm for 7 days. The fermentation metabolites were analyzed as above. Microorganisms 2021, 9, 2187 4 of 15 3. Results 3.1. Preliminary Evaluation of the Activation Ability of MACB and Selection of Red Soil-Derived Streptomycetes Ten MACB candidates (listed in Table S1) and two known NPs producer strains that were isolated from red soil, Streptomyces spp. FXJ1.172 and FXJ1.264 [19], were used for preliminary co-culture evaluation. The HPLC profiles of metabolites showed that three of the MACB (Mycobacterium sp. HX10-42, Nocardia sp. HX14-21, and Rhodococcus sp. HX10-55) obviously activated S. sp. FXJ1.172 to produce new peaks compared to their individual pure cultures (Figure 1a). Meanwhile, a series of unique peaks were detected in the combined culture of S. sp. FXJ1.264 and Mycobacterium sp. HX09-1 (Figure 1b). The other six MACB did not exhibit activation ability when co-cultured with the two Streptomyces strains. Therefore, the above four strains of MACB were chosen for subsequent co-culture. In addition, based on the antimicrobial activity and 16S rRNA gene similarity of the red soil-derived Streptomyces strains [19,24], 44 bioactive streptomycetes with abundant diversity were preferentially selected for this study (Table S1). The selected MACB and streptomycetes thus formed 176 (4 × 44) co-culture pairs. a. Absorbance units A=316 nm b. 1.5 (vii) (vi) 1.5 1.0 (V) 1.172+HX10-42 HX10-42 1.172+HX14-21 (iv) HX14-21 (iii) 1.172+HX10-55 0.5 (ii) (i) HX10-55 Absorbance units 1.0 (iii) 0.5 (ii) 1.172 (i) Ми A=254 nm 1.264+HX09-1 HX09-1 1.264 0.01 0.01 15.0 17.5 20.0 Retention time (min) 22.5 25.0 15.0 17.5 20.0 Retention time (min) 22.5 25.0 Figure 1. Preliminary evaluation of the activation ability of mycolic acid-containing bacteria (MACB). (a) HPLC analysis of the fermentation extracts of S. sp. FXJ1.172 co-cultured with different MACB and the extracts of their pure cultures; (b) HPLC analysis of the fermentation extracts of S. sp. FXJ1.264, M. sp. HX09-1, and their combined culture. 3.2. Co-Culture with MACB Changed the SM Profiles of Streptomycetes M. HPLC analysis showed changes in SM profiles of most (82.9%, 146/176) of the co- cultures compared to the pure culture counterparts (Figure 2 and Table 1). The differences of metabolites were characterized by four patterns of HPLC peaks: the increase/decrease in metabolite production (the integral area of peaks changed by more than 30%), appearance of new metabolite peaks, loss of original peaks, and no change. The comparison results were mostly a combination of the above patterns due to the complex secondary metabolism in Streptomyces (Figure 2). For example, compared to the pure cultures, co-culture with sp. HX09-1 changed the secondary metabolism of 40 Streptomyces strains. Among them, 30 and 23 strains enhanced and decreased the production of some original metabolites, respectively, 14 strains produced new metabolites that were not found in the pure cultures, and seven strains lost some metabolites (Figure 2a). M. sp. HX10-42, R. sp. HX10-55, and N. sp. HX14-21 exhibited similar activation ability (Figure 2b-d) (Table 1). In summary, 29.5% (52/176) of the co-cultures activated the production of "new" SMs and 60.8% (107/176) of the co-cultures increased the production of original metabolites (Table 1). For all four MACB strains, the proportion of positive impact (increase in production and/or appearance of "new" metabolites) on the secondary metabolism of Streptomyces is significantly higher (p<0.01) than that of negative impact (decrease in production and/or loss of metabolites), as shown in Table 1. Only four of the co-cultured streptomycetes were not activated by anySee Answer
Q10:Advanced Cell Biology Topic: Genome Editing Aim: To demonstrate an ability to explain scientific research to a non-specialist audience. This is a key skill for all scientists and helps clarify our thinking about what is most important about a particular piece of work. Most funding applications for research require a lay summary, and this is considered an essential part of public engagement and scientific accountability. Similarly, many jobs in science involve communication of complex data to non-specialist audiences such as the general public, shareholders, or politicians. For a wider context, see also: https://www.nature.com/articles/d41586-020-00580-w The Task: Write a lay summary of not more than 250 words explaining the research described in the technical abstract below from a controversial scientific paper about genome editing in human embryos. Use the example from class to guide you in structuring the summary. You will be introduced to the scientific concepts described in the abstract in the Genome Editing lectures on the ACB course.See Answer
Q11: Imagine you started the Tree Building Challenge with columbines starting on Peak 2 (HINT - you can actually do this by resetting the simulation until they start there!). Which of the following steps could be involved in making the tree below (the same one from the workbook)? Select all that apply- they might not be in order, but that's okay. Just pick the ones that you would actually have to do to build the correct tree.THERE MAY BE MORE THAN ONE WAY TO BUILD THIS TREE!!That's okay. Just choose from the steps that would work to make this happen. \Gamma \quad \text { peak } 2->\text { peak } 1 \text { peak 2 -> peak } 3 \square \quad \text { peak 1 -> peak 4 } \text { peak 3 ->peak } 4 peak 3-> peak 1 peak 1-> peak 2See Answer
Q12: Consider the tree below that was obtained by doing the Growing Tree exercise. Which traits do you expect to differ between the flowers on Peak 4 and those of the common ancestor of all populations? Select all that apply. stripes spur length petal tips spur colour anthers blade colour stigmas petal colourSee Answer
Q13: Given your experience with playing around building trees,evaluate the statement below: The structure of the phylogenetic trees tell us something about the order in which the peaks were colonized.See Answer
Q14: In the columbine populations, how to new traits arise? by moving seeds to different mountains by mating flowers with one anotherC' by mutationSee Answer
Q15: In the columbine tree, what do branch lengths represent? the branch lengths arbitrary (they do not represent anything)are the branch lengths correspond to the number of mutations that have occurred the branch lengths correspond to time the branch lengths correspond to the number of seeds that established a new populationSee Answer
Q16: As time passes, when and where do new traits arise in the columbine populations? randomlyon different peaks, but at regular intervals through time randomly through time, but always when a population appears on apreviously uninhabited peak at the same time as they establish a population on a new peak randomly through time and randomly on different peaksSee Answer
Q17: The tree below is the one that you are looking at (or should be!) for this exercise. Your classmate says that if you rotate around the node that joins Peaks 1 and 4, the flowers on Peak1 will have blue spurs. What would you say about this? "If you do this, then both Peak 1 and Peak 4 columbines will have blue spurs" "Rotating nodes does not change the evolution of the traits on the tree" If I rotated around the node that joins Peaks 1, 3 and 4 There is no way this can changeSee Answer
Q18: Your classmate says that when they ran their simulation,anthers were the first trait to mutate (from white to yellow).When you tell your classmate that in your tree the anthers did not mutate after 800 years, they indicate that they think you did something wrong. What would you tell your classmate?Choose the answer that best fits this situation. "You are right. All of the mutations should show up within 800 years." "Hmmm. I guess I did do something wrong. My tree should be the same as yours." "Every simulation is different, and the mutations arise at random. It is completely possible that another colour might not mutate at all."See Answer
Q19: Consider the tree of columbines below. Given what you see here, which peak had columbines on it first? Peak 1 Peak 2 Peak 3 Peak 4See Answer
Q20: Imagine that you wanted to build a tree where columbines onPeak 2 were most closely related to only columbines on Peak3. What would you do when building your tree to accomplish this? Make sure your simulation starts on Peak 3 and then immediately move columbines to Peak 2 Move columbines between the two peaks at the last step Make sure your simulation starts on Peak 2 and then immediately move columbines to Peak 3 Move columbines between the two peaks at the first stepSee Answer

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