[ECOLOG-L] Updates on sampling air microbes
Hi, Ecologers, I asked about sampling air microbes several weeks ago. We have got many useful suggestions, thanks everyone! Several people told me that they actually failed in getting workable samples for sequencing. I think this is a real situation to many people, and highlight the current challenge to this field. Several researchers pointed me to cyclonic air sampler. This is what we end up using in our current testing. I also got several suggestions about pass the air through a solution, but this is not quite portable for us. Of course passive sampling is among the most suggested. We have included this too in our plan for getting genome resources. For our own testing, we used a portable cyclonic air sampler to pass the air onto a filter paper placed on a petri dish. The filter paper was then extracted for DNA using a MO BIO water kit. In general, we did not get enough DNA for shotgun metagenomics, but kind of enough for amplicon sequencing. We are planning on a trial sequencing this month. I’ll keep update. Cheers, Zewei -- 宋泽伟 Zewei Song 华大生命科学研究院 宏基因组研究所 BGI-Shenzhen Institute of Metagenomics 电话 Tel: +86 13632929180 邮件 Email: songze...@genomics.cn 邮件 Email: songze...@outlook.com
[ECOLOG-L] Microbial air sampling method?
Dear Ecologers, Can some one point us to any approach in sampling air-borne microbes? We would like to avoid the passive, petri dish method, and would like to use active collection for the “total” community. It would be helpful if you can point us to any published documents on equipment, choice of membrane, and/or sampling protocols. Thanks! Zewei -- 宋泽伟 Zewei Song 华大生命科学研究院 宏基因组研究所 BGI-Shenzhen Institute of Metagenomics 电话 Tel: +86 13632929180 邮件 Email: songze...@genomics.cn 邮件 Email: songze...@outlook.com
Re: [ECOLOG-L] Plagiarizing methods...
I think it is not a big deal. As what you wrote in Method part is some standard method for PCR, it may be developed by someone and you are just using it as a technique in the paper. I suggest that reading some similar paper first, then discard them and write some of your own word, it should be sightly different. You can also citing some paper at the end. Hope this could help Zewei On Fri, Jun 5, 2009 at 9:28 AM, Cara Lin Bridgman cara@msa.hinet.netwrote: One of my students did a quick survey of 18 papers from 9 journals and found a total of four ways of describing conditions for PCR reactions. I’ve tried to standardize these examples for temperatures and times. Ten papers used this formula: “All PCR reactions included an initial denaturation of 94*C for 30 s, 35 cycles of 94*C for 30 s, 58*C for 45 s, and 72*C for 2 min, followed by a final elongation step at 72*C for 7.” Five papers used this formula: “30 s denaturation at 95*C, 45 s annealing at 58*C and 2 min extension at 72*C, a final extension step of 7 min at 72*C.” Two papers used this formula: “PCR cycling conditions of an initial denaturation step (94*C, 30 s), followed by 35 cycles at 94*C (30 s), 58*C (45 s), 72*C (2 min) and a final extension step of 7 min at 72*C.” One paper used this formula: “The reaction was cycled 35 times with 94*C (30 s), 58*C (45 s) and 72*C (2 min).” The question is this: When writing your own paper, does using (or copying) one of these four ways constitute plagiarism? If it does constitute plagiarism, then are these papers plagiarizing each other? Also, how does one go about describing methods for PCR reactions without commiting plagiarism? My students and I agree that the ways are rather limited--especially since there is not much diversity in these 18 published papers. This is a real dilemma, because these conditions have to be described in each paper that uses PCR--the details in terms of times, temperatures, and cycle number change with every study and every experiment. If it does not constitute plagiarism, then how much of the descriptions for other methods (statistical analysis, definitions for formula, figure legends, table titles, etc.) can be copied before it constitutes plagiarism? (My students and I can see a slippery slope here...) When writing her own PCR methods, my student tried going around this problem by finding a paper that came close to doing the same things she did, citing that paper, and adding a sentence to explain the changes in times or temperatures to describe what she actually did. We do not find this a very satisfactory solution because my student did not use the cited paper when actually deciding how to do her PCR reactions or in any other part of her thesis. In other words, citing that paper gives it undue credit for helping her with her methods. Finding ourselves in an impasse, I told my students I'd ask you here at Ecolog what you think and how you cope with these sorts of dilemmas. Thanks, CL ~~ Cara Lin Bridgman cara@msa.hinet.net P.O. Box 013 Shinjhuang http://megaview.com.tw/~caralinhttp://megaview.com.tw/%7Ecaralin Longjing Township http://www.BugDorm.com Taichung County 43499 TaiwanPhone: 886-4-2632-5484 ~~
[ECOLOG-L] Fungal Diversity in the Wood
Hi, All I'm searching for a simple method to quantify the biodiversity of decomposition fungal in the wood. I plan to see the relationship between wood decomposition and fungal diversity, so I wish to find a simple and fast method that can deal with large quantity of samples. Any suggestion will be helpful. Please email to songze...@gmail.com. Thanks. Cheers. Zewei Dept. of Bioproduct Biosystem Engineering Program of Natural Resources Science Management Biodegradation Lab
[ECOLOG-L] Decrease of carbon concentration in late stage of decomposition?
Hi, Fellows in Ecolog-L I would like to ask for your suggestion on one of our decomposition experiment. We have some wood materials that decomposed for three years. After 2 years, the carbon concentration (mg/g, that is X mg carbon to 1 g of dry material) started to drop below 500mg/g. It reached around 300 mg/g at the end of the 3 years. I'm wonder if there is any reason for the decrease of this carbon concentration. One reason I think possible is that the carbon was respired while O and H were accumulated and form humic like materials. We'll appreciate any input. Thanks. Zewei Song University of Minnesota Dept. of Bioproducts and Biosystems Engineering Lab of Biodegradation
[ECOLOG-L] Introductory reference on neutral theory of biodiversity
Hi, Ecologgers I wonder if there is any good introductory reference on the neutral theory of biodiversity (book or articles). I'm looking for something that can explain it in a non-math way. Thanks. Zewei
[ECOLOG-L] How to get the expectation and variation of a ratio?
Hi, Ecologgers I'm struggling in getting the expected means and standard deviation of a ratio between two independent data. I have data 'A' and 'B' which are population size of two strains of microbe on separate petri dish with a same substrate, the population size of A and B are independent. Now I want to calculate a theoretical ratio of A/B, which may represent the population ratio when A and B are meet at the same petri dish. We want to compare this calculated ratio to the real ratio from experiment. I think the problem is how to calculate the ratio. First what I think is to calculate the ratio of average, which is Average(A) / Average(B), but I fear it should be oversimplifed and also without a standard deviation. Then someone in a statistical forum gave me this: http://en.wikipedia.org/wiki/Taylor_expansions_for_the_moments_of_functions_of_random_variables, which calculate mean and variation by Taylor expansion. But I fell it is way too complex. I wonder if you guys know any similar application in ecology like my situation or any use of the wiki method? Thanks. Zewei
[ECOLOG-L] Open peer review journal for Ecology
Hi, Ecologgers I was wondering if there is any open peer review journal in the field of Ecology? Thanks. -- Zewei University of Minnesota
[ECOLOG-L] Good antibiotics for fungi
Hi, All It seems an easy question, but I'm not sure if I get it right. What is the best choice of antibiotic to exclude fungi on culture medium? I've found people talking about Amphtericin B, but does anyone know how does it work on soil? Thanks. Zewei Song -- Research Fellow University of Minnesota Department of Plant Pathology 612-624-3476
[ECOLOG-L] Amplicon region for bacteria next-gen sequencing
Hi, Ecologers We would like some suggestions on the selection of amplicon region for bacteria. We've been advised by the sequencing facility that shorter amplicons like V4 or V5-V6 had the best results in terms of read numbers and read quality, but not sure if a longer amplicon, such as V4-V6 or V1-V3 will work better in resolving species. Can you share with us on what amplicon region you usual use for bacteria and what do you feel about it? Thanks! Zewei Song -- Post Doc Department of Plant Pathology University of Minnesota 612-624-3476
[ECOLOG-L] Best practice for fungal metagenomics?
Dear Colleagues, I was wondering if you can give me some reference for the current best practice for fungal metagenomics. I’ve noticed some of the nice tools, such as MetaPhlAn and MOCAT, but it seems to me they are more “specialized” for bacteria. I’m not sure either if the reference database for fungi is as good as other microorganisms. I would appreciate if you can give my any information, like tools, or the status of reference database for fungi. Thanks! Zewei -- Zewei Song Postdoctoral Associate University of Minnesota, Twin Cities Department of Plant Pathology Email: songze...@outlook.com Tel: 612-840-0267
[ECOLOG-L] Customized protocol for extracting soil DNA?
Hi, All I was wondering if you have any good protocol in hand for extracting soil DNA? I have been using MO BIO’s PowerSoil for quite a long time, but would like to know if there is any in home recipe that is working. It would be great if you can point me to any of the available protocol, and if better how good they are in removing the PCR inhibitors. Thanks! Zewei -- 宋泽伟 Zewei Song 华大基因研究院 宏基因组研究所 BGI-Shenzhen Institute of Metagenomics 电话 Tel: +86 13632929180 邮件 Email: songze...@genomics.cn 邮件 Email: songze...@outlook.com
[ECOLOG-L] Research Scientist Positions on Environmental Microbiology at BGI-Research
Institute of Metagenomics at BGI-Research has several research scientist positions at the area of environmental microbiology. The candidates will work with Dr. Zewei Song at the lab of Environmental Ecology on various projects from forest ecology to agricultural management at BGI-Research located at the China National GeneBank (CNGB) at Shenzhen, China. Institute of Metagenomics currently have long term collaborations with University of Minnesota, Twin Cities, University of Ljubljana, Chinese Academy of Sciences, and Chinese Academy of Agricultural Sciences. The goal of BGI-Research is to conduct long-term and large-scale studies related with environmental microbial communities, including natural and manmade ecosystems. Ongoing projects have covered a wide range of area from the vertical structure of rainforest canopy, to the influence of plant diversity, to novel method of agricultural management. At the same time, BGI-Research is also focusing on developing novel sequencing techniques, largely based on the BGISEQ platform. Description of duties: The main duty of the candidates is to maintain the progress of research projects. The candidate also has opportunities to take part in developing new sequencing techniques, especially for metagenomics. Potential tasks include, but not limit to: 1. Coordinate with collaborators on the progress of research projects. This include the coordination on study plan, sample transportation, bioinformatics, and stuff exchange. Short term travel to the site of collaborators is possible. 2. Analyze microbiome data with scientific outcomes. This include the analysis of amplicon and metagenomics sequencing data, various bioinformatics on community composition and function, as well as writing manuscripts for high tier peer review journals. 3. Participate in developing novel bioinformatic and sequencing tools for metagenomics. This includes moderate programing, discussing with scientists from other institutes, and some lab work. Required skills: We are looking for candidates with comprehensive research experience at the field of environmental microbiology, molecular ecology, or any area related with the study of microbial communities focusing on non-human objects. 1. Experience on environmental microbiology with sequencing as a main study tool. 2. Prominent publication record. 3. Experienced on analyzing microbial data using various tools in R and/or Python (or other languages). 4. Capability of programing is preferred. 5. Experience of lab work (include basic molecular experiment) is preferred. 6. Good communication skills and fluence in English. Interested candidates may contact Dr. Zewei Song or our HR Ma Yongchao for details, or an arrangement for interview. Candidates near Shenzhen are welcome to take a field trip at CNGB at the time of convenient. Zewei Song songze...@genomics.cn or songze...@outlook.com Ma Yongchao mayongc...@genomics.cn -- 宋泽伟 Zewei Song 华大生命科学研究院 宏基因组研究所 环境生态实验室 BGI-Shenzhen Institute of Metagenomics Lab of Environmental Ecology 电话 Tel: +86 13632929180 邮件 Email: songze...@genomics.cn 邮件 Email: songze...@outlook.com
