- Nov 2019
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www.nature.com www.nature.com
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key attributes needed to produce a worthy PhD thesis are a readiness to accept failure; resilience; persistence; the ability to troubleshoot; dedication; independence; and a willingness to commit to very hard work — together with curiosity and a passion for research
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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key challenge is to quantify the functional roles of bacterial taxa in nature to understand how the properties of ecosystems change over time or under different environmental conditions
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Hemicellulase activity was elevated in pairwise mixtures of communities that placed interacting phylotypes together (interactions, n = 9 mixtures) but not in communities that did not place interacting phylotypes together (no interactions, n = 56 mixtures)
Very interesting way to validate correlative phenotypes in communities
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oiss.rice.edu oiss.rice.edu
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For F-1 and J-1 students, on-campus work is limited to part-time (20 hours or less per week) during the fall and spring semesters when school is in session
Does RA count for 20 h?
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www.biorxiv.org www.biorxiv.org
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tools described here can be used to mimic complex expression patterns, such as the ones found for pneumococcal virulence factors, paving the way for in vivo investigations of the importance of gene expression control on the pathogenicity of S. pneumoniae.
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It is challenging to study how pneumococci control virulence factor expression, because cues of natural environments and the presence of an immune system are difficult to simulate in vitro
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library.bryant.edu library.bryant.edu
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When you present information visually (using slides, a poster, video, handout, etc.), you must provide a full written citation.
citing sources
- When you present information visually (using slides, a poster, video, handout, etc.), you must provide a full written citation.
- A parenthetical citation should directly accompany images, videos, quotes, or anything that is directly referenced in your presentation.
- works cited or references list should appear at the end of your presentation for all sources.
- When you present information orally, you must provide an abbreviated citation that should include the name of the creator, title, and publication date.
- When you present information visually (using slides, a poster, video, handout, etc.), you must provide a full written citation.
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www.nature.com www.nature.com
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these two highly active enzymes were functionalized with an affinity binding motif through the genetic fusion of a carbohydrate binding module (CBM) from Cellulomonas fimi with specificity to cellulose (CBM2a)
Why should the enzyme be functionalized to bind cellulose, should the carbohydrate binding be on the phage capsid?
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optical nanostructures, surface enhanced Raman spectroscopy, flow cytometry, etc.) have shown promise as sensitive detection methods, they typically process only small, relatively clean samples. The true bottleneck to rapid detection methods remains the separation of a target analyte from a large complex matrix.
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EPA Method 1603 is an approved drinking water assay that quantifies generic E. coli
This drinking water assay contains a membrane (0.45 µm) filtration step to remove bacteria from the water sample prior to enrichment on selective and differential media. The bacteria CFUs are quantified directly on the filter following a lengthy enrichment
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most probable number (MPN) method. The MPN is determined by serial diluting the water sample in triplicate or pentaplicate followed by incubation in selective growth media
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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single copy phylogenetic marker gene
How is this marker gene strictly single copy? How do you know?
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known to introduce biases in composition estimates due to, for instance, variations in 16S rRNA gene copy numbers per genome
Are the other marker genes known to be single copy?
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unequal efficiencies of PCR-primers in different species
This should presumably also affect your 40 housekeeping marker genes.
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facultypatchbook.pressbooks.com facultypatchbook.pressbooks.com
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Students who are less exposed to what we propose here may resist at first, simply because it is unfamiliar, but it is our experience that, overall, students will embrace and appreciate these modifications to the way assessments are conducted.
The initial student resistance is a very good point
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opening new paths for side effect control
This is a tall claim. Is the microbiome's contribution to side effects well studied? Is it a significant contribution compared to off target human pathways and pleiotropic effects?
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Susceptibility to antibiotics and human-targeted drugs correlates across bacterial species
This is interesting
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pubs-acs-org.ezproxy.rice.edu pubs-acs-org.ezproxy.rice.edu
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EDTA-extractable fraction
Why EDTA extraction? How does this compare with a water extraction?
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www.pnas.org www.pnas.org
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we define the physiological and environmental parameters that mediate the transition from cooperation to competition
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Local file Local file
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transient events
Need better examples of transient events
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www.nature.com www.nature.com
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Illustration by Sébastien Thibault
Cool illustration! It does speak a 1000 words indeed
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www.nature.com www.nature.com
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SDS affects the oligomerization state of Aβ42 oligomers, thus providing flawed information on their order and distribution.
The fact that SDS affects protein structures and oligomerization seems to be well known.
I thought people did a variant called 'native PAGE' where SDS is not added and the protein is treated in non-denaturing conditions. Did you compare your method to this?
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www.nature.com www.nature.com
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except for those that catalyze irreversible reactions in the TCA, such as citrate synthase
Why is this irreversible
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www.sciencedirect.com www.sciencedirect.com
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molecular explanations of whether such shifts represent cause or effect of the disease itself are limited
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- Oct 2019
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www-sciencedirect-com.ezproxy.rice.edu www-sciencedirect-com.ezproxy.rice.edu
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Graphical abstract
This is a decent graphical abstract compared to other engineering or wastewater papers
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www.aeesp.org www.aeesp.org
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includes creation of innovative solutions for bio energy, resource recovery, and emerging public health concerns by leveraging synthetic or molecular biology tools, novel biological systems (genetic circuits, enzymes, genetically engineered microbes), fundamental biological and chemical concepts, artificial intelligence, and big data science, as well as collaborations in Computer Science, Public Health, Plant Biology, or related fields.
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www.sciencedirect.com www.sciencedirect.com
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A biofilm was prepared
Biofilms are never prepared, they are grown!
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biofilm
Wrong use of words. You should call it a layer of immobilized bacteria. Biofilm is when cells deliberately stick to a surface and secrete a matrix
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www.sciencedirect.com www.sciencedirect.com
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values measured by using luminous E. coli had tendency of about 30–40% lower than that of BOD5, it could be observed an apparent correlation between the two values
I don't think this is robust correlation. It will depend on the organic composition of the BOD
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bioluminescence was observed during the incubation time between 90 and 150 min in the presence of a sole carbon source such as glucose, acetate, l-glutamate and BOD standard solution (GGA solution)
So this is a limited BOD sensor for only the subset of organic compounds that E. coli can metabolize?
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en.wikipedia.org en.wikipedia.org
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is dosed with seed microorganisms and stored for 5 days in the dark room at 20 °C to prevent DO production via photosynthesis
Does the BOD measurement and interpretation depend on the organism the sample is seeded with?
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The generally lower values in the U.S. derive from the much greater water use per capita than in other parts of the world
Wow, that is amazing to know. Wonder how this cultural shift started historically?
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www.nature.com www.nature.com
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not suitable for process control in wastewater treatment and the real-time monitoring of water environments, such as rivers, streams, ponds, and ground water
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onlinelibrary.wiley.com onlinelibrary.wiley.com
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is independent of the general recombination pathway
What is this general recombination pathway?
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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it then moves in a directed path through the pore space, a process we call hopping
How is this different from the 'run'
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www.frontiersin.org www.frontiersin.org
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Phase variation is often mediated by the presence of highly mutagenic simple tandem DNA repeats, and genes containing such sequences can be easily identified
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chaibisket.com chaibisket.com
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ఎప్పటికైనా Knowledge Centric Value Based Education రావాలని కోరుకుందాం
I like the problem statement, but what is this knowledge centric value based education? Is this a good solution?
It is essential to realize that there is no magic bullet that can solve such a complex problem that is so central to our life, livelihood and the urban upper middle class (shall I call brahminical!?) way of life. There must be many solutions working together towards the same idea. But first we should be clear on the problem and acknowledge it!
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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observations are consistent with a previous report showing that AHLs preferentially partition to the biofilm, reaching concentrations 600-fold in excess of the signal concentration in the surrounding bulk liquid medium
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www-sciencedirect-com.ezproxy.rice.edu www-sciencedirect-com.ezproxy.rice.edu
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the best way to correct for the analyte signal suppression or enhancement is to co-elute a stable isotope labelled (SIL) analogue of the analyte
It is not straight forward to get isotope labelled standards for every compound
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www.biorxiv.org www.biorxiv.org
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We also show how our toolbox can be used to deploy the FBP in planta to build auto-luminescent reporters for the study of gene-expression and hormone fluxes
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aiche.onlinelibrary.wiley.com aiche.onlinelibrary.wiley.com
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We tested a broad range of Enterobacteriaceae conjugative plasmids for their sensitivity to the growth stage of the donors and identified three distinct regulation types.
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indicate that even low concentrations of just a single type of antibiotic leads to resistance to multiple classes of antibiotics.
I doubt this claim, do you mean they are correlated?
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www.sciencedirect.com www.sciencedirect.com
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Overall, the low contamination level of antibiotics and high absolute abundance of ARGs indicated that ARGs previously introduced to an environment can self-amplify and persist in the environment
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suggesting that STPs have become an important source of contamination for their receiving rivers
Read these references: Saying antibiotic resistance is proliferating in wastewater treatment plants
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Additionally, the concentrations of antibiotics and the abundance of ARGs might increase after the sewage treatment process.
Wow, that is a strong and counter-intuitive claim. Is this rigorously determined?
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theconversation.com theconversation.com
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Perhaps we ultimately need to be prepared to accept less standardised and slightly more expensive food in order to accommodate less intense and more diverse agriculture. You might never be quite sure what to expect when you peeled a banana, but the result could be a more robust and sustainable food system without a major crisis every few decades.
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www.nature.com www.nature.com
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With this approach, neurons that show E-SARE–driven expression in response to stimuli are permanently labeled by the fluorescent protein during the time window specified by the drug
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Expression of a drug-inducible Cre recombinase downstream of E-SARE enabled imaging of neuronal populations that respond to monocular visual stimulation and tracking of their long-distance thalamocortical projections in living mice
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www-sciencedirect-com.ezproxy.rice.edu www-sciencedirect-com.ezproxy.rice.edu
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The feedback loop permits sustained induction of recombinant proteins without massive quantities of inducer.
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journals.plos.org journals.plos.org
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We have demonstrated that small RNAs can tightly repress their target genes when their synthesis rate is smaller than some threshold, but have little or no effect when the synthesis rate is much larger than that threshold
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a threshold-linear response with a tunable threshold, a robust noise resistance characteristic, and a built-in capability for hierarchical cross-talk.
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www.sciencedirect.com www.sciencedirect.com
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In particular, small RNAs are shown to establish a threshold for the expression of their target, providing safety mechanism against random fluctuations and transient signals. The threshold level is set by the transcription rate of the small RNA and can thus be modulated dynamically to reflect changing environmental conditions.
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www.annualreviews.org www.annualreviews.org
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in the absence of tamoxifen, it exhibits some activity
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A technique common in rodents is the use of Cre recombinase lines that are inducible at specific developmental time points (Figure 3b). The most common form of inducible Cre is CreERT2, which contains a modified estrogen receptor binding domain that prevents Cre from entering the nucleus in the absence of a ligand
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strong promoters capable of driving expression of microbial opsins or fluorescent proteins in specific populations can exhibit leaky expression elsewhere. This low-level leak may be virtually undetectable as light responsiveness or fluorescence but can be a serious issue when expressing Cre recombinase.
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onlinelibrary.wiley.com onlinelibrary.wiley.com
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Our analysis demonstrates that its structure is shaped more by stochasticity than selection.
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www.biorxiv.org www.biorxiv.org
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To investigate how ciprofloxacin 35resistance is affected by the presence of metals,
Ciprofloxacin's activity (MIC, IC50 etc.) could also depend on Zn presence, was this investigaged before going into selection and evolution?
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www.nature.com www.nature.com
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creating improved technologies for large-scale recordings of neural activity in the live brain is a crucial goal in neuroscience
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www.frontiersin.org www.frontiersin.org
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new toolkits for chronic labeling of active ensembles will provide a much awaited experimental basis to interrogate various aspects of neuronal circuits underlying long-term plastic changes of the brain, such as during nervous system development, during establishment of long-lasting remote memory over months, or in association with age-related neuronal changes over several years.
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new direction of functional labeling involves conversion of transient expression from activity-dependent promoters into a permanent labeling based on tamoxifen-dependent recombinases
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onlinelibrary.wiley.com onlinelibrary.wiley.com
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presence of the donor strain on the surface of the mutant selection plates, prevents the use of these plates for replica plating
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aem.asm.org aem.asm.org
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In soil, bacteria tend to live in a state of dormancy due to prevailing oligotrophic conditions, which would not be particularly favorable for the development of competence
It can also be argued that the transformed DNA is a good resource of phosphates, nitrogen etc., so might be favoured in oligotrophic conditions?
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sackler.tufts.edu sackler.tufts.eduTitle1
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bacteria generally express genes only when and where needed, and thus do not readily reveal their pathogenic armament outside of infected tissues
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This gene fusion approach will allow us to assay the induction of gene expression in as few as one cell
Recombinase memory as a reporter for expression in 1 cell
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www.nature.com www.nature.com
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causes of microbial ‘uncultivability’ are numerous
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aac.asm.org aac.asm.org
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The stability of susceptibility patterns allowed the antibiograms to be used as aids in the preliminary differentiation of these organisms.
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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regulate gene expression, typically by occluding or exposing regulatory features, such as ribosome binding sites (RBSs) in the case of translation or intrinsic terminator hairpins in the case of transcription
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www.thehindu.com www.thehindu.com
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improvement of soil health should be a priority agenda in India’s agricultural policy. We need steps to check wind and water erosion of soils. We need innovative technologies to minimise physical degradation of soils due to waterlogging, flooding and crusting. We need to improve the fertility of saline, acidic, alkaline and toxic soils by reclaiming them
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Indian soils are poor in organic matter content. About 59% of soils are low in available nitrogen; about 49% are low in available phosphorus; and about 48% are low or medium in available potassium. Indian soils are also varyingly deficient in micronutrients, such as zinc, iron, manganese, copper, molybdenum and boron
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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In culture conditions that enhance cell-to-cell contact, conjugation rates approach 100% with the cis-acting plasmid
high efficiency
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www.sciencedirect.com www.sciencedirect.com
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wastewater treatment plants are hotspots for the release of antibiotics, and transmission of diverse antibiotic resistance bacteria (ARB) as well as ARGs into various environments
That's a strong claim, not backed by strong evidence
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Recent findings have indicated that most ARGs could not be efficiently removed by traditional anaerobic digestion treatment
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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Detection of AHL by LC-FTMS was much more sensitive than by TLC bioassay, because TLC bioassay was implied to be affected by the presence of quorum quenching molecules in activated sludge.
does not make sense
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iwaponline-com.ezproxy.rice.edu iwaponline-com.ezproxy.rice.edu
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Biofilms grown under higher shear were more rigid and had a greater yield shear stress than those grown under lower shear.
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pubs-acs-org.ezproxy.rice.edu pubs-acs-org.ezproxy.rice.edu
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Because growth conditions (i.e., fluid dynamics and nutrient composition) can also have a profound effect on when QS is important,(71-75) there is a need to study biofilm formation and QS of BNR bacteria under various potential operating conditions.
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Many QS-controlled genes relate to biofilm formation and function and may be important for some water and wastewater treatment biofilms
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science-sciencemag-org.ezproxy.rice.edu science-sciencemag-org.ezproxy.rice.edu
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it become possible to engineer these microbial structures to allow bacteria to form a stable granular sludge instead of flocculent sludge
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www.annualreviews.org www.annualreviews.org
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The actual availability of NH4+ and NO3− is difficult to measure in soil. When rates of microbial N transformations and/or plant uptake are rapid, then NH4+ or NO3− levels can be undetectable in soil
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www.embopress.org www.embopress.org
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it can be useful for reducing leaky expression of toxic proteins
antisense transcription
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aem.asm.org aem.asm.org
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We report the construction of a family of vectors that contain a reengineered lacIq-lac promoter-operator complex in which cloned genes are strongly repressed in the absence of inducer.
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www.nature.com www.nature.com
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difficult to observe in situ at the microscale, hence mechanisms and time scales relevant for bacterial spatial organization remain largely qualitative.
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www.nature.com www.nature.com
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simulate the activated sludge process of a municipal waste water treatment plant and so better understand the fate of nanoplastics in urban environments
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www.nature.com www.nature.com
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it has become a seemingly essential part of our life. It helps us to preserve food, keep warm, communicate with the world and much more
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www.nature.com www.nature.com
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Frequency of QS among genome- sequenced bacteria
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aem.asm.org aem.asm.org
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RP4 has been shown to exhibit a very broad host range and has been demonstrated to efficiently transfer in activated sludge (22, 40), chicken manure (24), and the rhizospheres of various plants (38, 39).
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For in situ studies of AHL-dependent signaling in complex habitats, biosensors utilizing fluorescent proteins (GFP and RFP) as reporter genes have been developed
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biosensors were employed to demonstrate AHL-mediated communication in swarm colonies of Serratia liquefaciens
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they are induced in a way that correlates well with the AHL species produced by the strain
This is a baseless statement, made from only 1 strain p. aerofaciens, which makes C6-AHL
- Two strains P. Putida and E. coli do not produce AHLs (you mention this)
How does it correlate well then with 1 data point?
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After 8 days of incubation, we detected cells that were only green fluorescent, indicating that the sensor plasmid had been transferred to indigenous AHL-producing organisms
It could also just mean that there are some AHL producers in the viscinity, just like the explanation given for yellow donor cells.
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QS systems have been experimentally analyzed in more than 50 different bacterial species and shown to control expression of a wide spectrum of functions, including bioluminescence, virulence, symbiosis, different forms of motility, biofilm formation, production of antibiotics and toxins, and conjugation (49).
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academic.oup.com academic.oup.com
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Over 20 orthogonal serine integrases have been characterized to date (6,11), and many now have identified RDFs.
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www.pnas.org www.pnas.org
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it is unclear to what extent these results are relevant in natural habitats, as the standard assays neglect the different surface chemistries, interactions with other species, and physical constraints of natural environments.
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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Images were prepared for publication using CorelDraw (Corel Corporation) and PowerPoint (Microsoft) software.
Great that you cite the software
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PpuI, which directs the biosynthesis of the two AHLs 3-oxo-C10 and 3-oxo-C12 as major products; PpuR, the AHL receptor; and RsaL a repressor of ppul
P. putida IsoF, isolated from tomato rhizosphere - quorum sensing
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with pegs of polystyrene microtiter lid (catalog no. 445497; Nunc TSP system) immersed for bacterial biofilm formation
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aac.asm.org aac.asm.org
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Planktonic stationary-phase cells were used in dose-response killing experiments, for a better comparison to biofilms
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www.sciencedirect.com www.sciencedirect.com
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it may be possible to tag specific organisms and use these as monitor systems to estimate local chemical composition directly in the biofilms
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- Sep 2019
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www.pnas.org www.pnas.org
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placed at a 45° angle, nylon-mesh side up. Roots grew downward, collided with the bottom slide of the microcosm, and traveled along it. This method allowed observation of the root system by epifluorescence microscopy
well explained!
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The rhizosphere is the volume of soil directly under the influence of plant roots; it is bounded by the root surface on one side and extends millimeters into the soil. It is populated with a high density of bacteria, fungi, protists, and nematodes supported by relatively labile organic compounds, such as sugars, amino acids, organic acids, and polysaccharides. These compounds are actively and passively lost from living and dying root tissues (12, 13). This rhizodeposition allows 5–100 times more organisms per unit volume to be supported in the rhizosphere than in nearby bulk soil, where the microbial community is thought to be carbon limited
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This biosensor will help identify organic substrates that potentially support microbial growth and activity before and during nodulation
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Such biosensors can reveal intriguing aspects of the environment and the physiology of the free-living soil S. meliloti before and during the establishment of nodulation, and they provide a nondestructive, spatially explicit method for examining rhizosphere soil chemical composition
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gage.mcb.uconn.edu gage.mcb.uconn.edu
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Chemically, the differencebetween the DI water and the 0.25×M9 EPS solution aresome simple salts and just 14.5μg/ml glucose equivalent ofEPS
Should have compared with M9 + equivalent glucose (un-polymerized) as a better control for osmolarity reasons
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rupress-org.ezproxy.rice.edu rupress-org.ezproxy.rice.edu
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if n is very small (for example n = 3), rather than showing error bars and statistics, it is better to simply plot the individual data points.
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For n to be greater than 1, the experiment would have to be performed using separate stock cultures, or separate cell clones of the same type
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besjournals.onlinelibrary.wiley.com besjournals.onlinelibrary.wiley.com
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quantifying biogeochemical fluxes resulting from these reactions remains a challenge
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These tools provide insights into processes such as N uptake at the scale of individual root tips, allowing observation of plant–microbe interactions on scales at which they actually occur, instead of being masked by a whole‐core average
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aem.asm.org aem.asm.org
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detection of methyl halides at femtomolar levels and quantification at concentrations above 10 pM
This is approximately 6 molecules per cell - seems too low. (assuming cell volume is 1 um^3 - for e coli) - https://bionumbers.hms.harvard.edu/bionumber.aspx?id=100004&ver=20&trm=100004&org=
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www.inkscapeforum.com www.inkscapeforum.com
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The following might be a pretty cumbersome workaround for tiled clones with spacing e.g. in millimeters instead of %.
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www.chronicle.com www.chronicle.com
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A narrative weaves together otherwise isolated bits of information into a meaningful whole, linking them in important ways but also chunking the information so that it takes up less space in working memory and connects to existing threads in long-term memory
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students quite often reported choosing their major based on taking introductory courses with particularly dynamic professors.
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your enthusiasm as an instructor is indeed contagious and helps predict variables like student motivation in the course.
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make the entire course relevant to students’ daily lives. All of the labs center around chemicals and materials that students interact with regularly. For instance, they evaluate bottled water versus tap water, test both for pH, conductivity, and taste, and then debate why so many people choose bottled over tap
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You can also make class activities relevant to contemporary social movements, to future careers in your major, or to some transcendent purpose
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Jennifer Gonzalez, editor of the teaching blog Cult of Pedagogy, summed up the concept quite nicely in the title of a blog post: “To Learn, Students Need to DO Something.”
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www.chronicle.com www.chronicle.com
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essential goal for me in every course has always been to make students feel comfortable participating in class, and to encourage as many of them as possible to speak up. Peer instruction, aided by electronic polling, gave me an opportunity to invite quiet students to engage more actively in class, both through the polls and through the subsequent discussions
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teachanywhere.byu.edu teachanywhere.byu.edu
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When new knowledge is integrated with and connected to existing knowledge, that new knowledge is easier to understand and to remember. A professor’s job is to build scaffolding from existing knowledge on which to hang incoming new knowledge. Using a concept map is one way to build that scaffolding.
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www.sciencedirect.com www.sciencedirect.com
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exogenous addition of AHLs to sludge resulted in long-lasting impacts on phenol degradation
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medium.com medium.com
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text files? Gloriously simple, ready made for your favorite text editor and perfect for version control.
Latex files can do version control vs word files
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stackoverflow.com stackoverflow.com
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R markdown has the possibility of executing R code inline (and rendering the result to html) or rendering graphs inline. That saves time and makes the documentation maintainable as you don't need to manually prepare the output of that function or manually prepare and save a graph since it's rendered on the fly.
R markdown makes documentation of code easy
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www.sciencedirect.com www.sciencedirect.com
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more convenient and effective methods is required for qualitative and quantitative analysis of AHLs
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enzymatic quenching mechanism of AHL signals is also present in enzyme-producing bacteria, such as Anabaena sp. PCC7120, Ralstonia sp. XJ12B, P. aeruginosa PAO1, Agrobacterium tumefaciens C58, Bacillus sp. strain 240B1, Rhodococcus erythropolis strain W2
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Membrane biofouling remains to be one of the most serious operational problems for MBR applications, which results in permeate flux and water quality decline, trans-membrane pressure (TMP) and operating costs increase, frequent membrane cleaning and replacement necessary
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activated sludge flocs are complicated aggregates containing inorganic and organic particles as well as a high-density microbial consortium embedded in a matrix of extracellular polymeric substances
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www.nature.com www.nature.com
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Coordinated behaviours include bioluminescence3,4, virulence factor production5,6, secondary metabolite production7, competence for DNA uptake8,9 and biofilm formation10,11.
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We focus on how quorums are detected and how quorum sensing controls group behaviours in complex and dynamically changing environments such as multi-species bacterial communities, in the presence of flow, in 3D non-uniform biofilms and in hosts during infection.
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www.sciencedirect.com www.sciencedirect.com
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Laboratory strains of Escherichia coli do not show significant ability to attach to solid surfaces and to form biofilms
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www-sciencedirect-com.ezproxy.rice.edu www-sciencedirect-com.ezproxy.rice.edu
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stabilization of microbial community
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AHL was found to play important roles in wastewater treatment processes, in particular, formation of aerobic sludge granules
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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bacterial QQ does not completely prevent biofouling; it simply postpones its occurrence
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it has been assumed that the effectiveness of Pseudomonas sp. 1A1 in mitigating membrane biofouling could be expected to be more significant, given that the QQ enzyme that it produces (acylase) is extracellular
The acylase might not be functional or stable in the extracellular wastewater environment
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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Design of the LOCKR system.
It would be amazing if you could fit the rate constants from experimental data
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pubs-rsc-org.ezproxy.rice.edu pubs-rsc-org.ezproxy.rice.edu
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different fouling patterns were observed for replicate MBRs seeded with the same inoculum and maintained under identical operating conditions, with similar levels of biomass, soluble microbial products, and extracellular polymeric substances
The reactors were not maintained under the same conditions - 1 had backpulsing and the other was subjected to relaxation
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www.sciencedirect.com www.sciencedirect.com
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achieved only a 10% increase of permeate flux when backpulsing was used in the filtration of a biological wastewater containing a high mixed liquor suspended solids
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pubs-acs-org.ezproxy.rice.edu pubs-acs-org.ezproxy.rice.edu
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Figure 5
Why did the QQ-MBR go down on day 20?
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Figure 2. TMP profiles during the operation of two one-stage MBRs in two phases.
Fouling seems to happen exponentially once it starts => following a first order reaction. What is the mechanism behind this?
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C8-HSL was chosen as a representative AHL molecule because it is one of the dominant AHL molecules in MBRs for wastewater treatment
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a critical issue in MBR that awaits a technological advancement to solve is membrane biofouling, which leads to high energy consumption and thus high operating costs
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pubs.acs.org pubs.acs.org
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TMP-Jump
Why does TMP jump so rapidly?
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www.biorxiv.org www.biorxiv.org
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Plasmids (IncP/N/W)with 373short and rigid pili only transfer efficiently on solid surfaces, unlike those with longand flexible 374pili (IncF/H/T/J),capable of transferring equally well in liquidand on solid surfaces[35,36]
Plasmid group vs pili length
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manoshidatta.github.io manoshidatta.github.io
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identify mechanistic drivers of microbial activity, infer meaningful interaction networks, and rationally engineer microbial communities.
Mechanistic insights in microbial ecology
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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Next, a microfluidic device is used to co-encapsulate these clusters with gel beads, each containing uniquely barcoded forward 16S rRNA amplification primers
Isn't the spatial information lost while encapsulation? Is the barcode capturing the spatial information in some way? It is not clear
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current microbiome profiling approaches such as metagenomic sequencing require homogenization of input material, which means that underlying spatial information is lost
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www-sciencedirect-com.ezproxy.rice.edu www-sciencedirect-com.ezproxy.rice.edu
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recording past events, to study localization of single-cell transcriptional events within the gut
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www.nature.com www.nature.com
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These carboxylated AHLs facilitated the transition from a short cell to filamentous growth, with an altered carbon metabolic flux that favoured the conversion of acetate to methane and a reduced yield in cellular biomass
Carboxylated AHL signalling favours methanogenesis in Methanosaeta herundinacea 6Ac
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URL
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jb.asm.org jb.asm.org
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Deletion of genes thatproduceN-acyl-L-homoserine lactone signals resulted in an increase in denitrification activity, which wasrepressed by exogenous signal molecules.
AHL is lowering denitrification in Psuedomonas aeruginosa
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biologydirect.biomedcentral.com biologydirect.biomedcentral.com
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The prokaryotic CRISPR-Cas system of defense against mobile elements seems to function via a bona fide Lamarckian mechanism
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www.nature.com www.nature.com
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scientists are uncovering and debating an increasing array of other evolutionary processes at work in bacteria, some of which are suspiciously Lamarckian in character4–6
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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Instead, most particle-attached bacteria may be secondary consumers that recycle waste products from primary degraders.
What factors determine their relative abundance then?
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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co-occur out of cooperative relations or a similar niche preference
similar niche evokes competition rather than cooperation, this is contradictory
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www.pnas.org www.pnas.org
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beneficial commensal
mutualist?
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antibodies against siderophores in the intestine, which hindered proliferation of the gut pathogen Salmonella
What about normal gut microbiota? I presume they need iron too
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mbio-asm-org.ezproxy.rice.edu mbio-asm-org.ezproxy.rice.edu
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At the micrometer-centimeter scale, electrochemical and optical probes have been productively used to profile gradients in pH, redox, and oxygen; however, these probes and their associated equipment are intrusive to the ecosystem and often expensive, limiting their application to only a few point measurements or limited time series, and their fragile nature makes them best suited for laboratory use
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blogs.ei.columbia.edu blogs.ei.columbia.edu
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CustoMem in the UK uses synthetic biology to create a granular material that attracts and sticks to micropollutants such as pesticides, pharmaceuticals, and certain chemicals in wastewater
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Now synthesized microbial biosensors are able to target specific toxins such as arsenic, cadmium, mercury, nitrogen, ammonium, nitrate, phosphorus and heavy metals, and respond in a variety of ways. They can be engineered to generate an electrochemical, thermal, acoustic or bioluminescent signal when encountering the designated pollutant.
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remediating arsenic contamination of groundwater by stimulating natural bacteria to produce substances that arsenic sticks to
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MicroBio Engineering Inc., a research and engineering consulting firm specializing in developing improved algal strains and cultivation processes for wastewater reclamation, animal feeds, higher value products and, yes, biofuels.
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blogs.ei.columbia.edu blogs.ei.columbia.edu
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In Japan, scientists are developing synthetically altered soy plants and yeast that produce glycyrrhizen, a compound in licorice root that is 150 to 300 times sweeter than sugar
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www.sciencedirect.com www.sciencedirect.com
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The modified freeze-squeeze method was more efficient in cleaning up small DNA fragments from agarose gels compared to commercial kits.
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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move away from identifying correlative relationships between characteristics of the microbiome and system-level processes, and towards identifying more causative and mechanistic relationships
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- Aug 2019
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www.sciencedirect.com www.sciencedirect.com
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endogenous AHL-based QS and QQ are existing and coexisting in biological wastewater treatments; the leading role for AHL-based QS or QQ phenomenon in biological wastewater treatments can be determined by bacterial AHL concentration.
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www.frontiersin.org www.frontiersin.org
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, QQ has been successfully employed to reduce the pathogenicity of common plant pathogens (Zhang et al., 2007)
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Rattanarat et al.73 created a three-dimensional μPAD (Fig. 1A) that combined colorimetric and electrochemical detection on separate layers for quantifying Ni, Cu, Fe, Pb, Cr(VI), and Cd
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pubs.rsc.org pubs.rsc.org
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Immobilization efficiency was improved by manipulating the bacterial genetics (overproducing curli protein),
e coli immobilization
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diagnosis of antibiotic interference in the major biosynthetic pathways of bacteria: the biosynthesis of DNA by the yorB promoter, of RNA by the yvgS promoter, of proteins by the yheI promoter, of the cell wall by the ypuA promoter, and of fatty acids by the fabHB promoter.
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www.sciencedirect.com www.sciencedirect.com
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chief advantage of this approach is that the entire sensor, including all signal-processing and communication functions, can be produced as a single-chip, low-power, rugged, inexpensive device
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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Heat following
How are the pellet and supernatant same CT here?
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www.nature.com www.nature.com
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crude DNA extraction methods, such as boiling, are not recommended to obtain the lower detection limit for a microorganism
You are effectively boiling as well when you subject to thermal cycling. It is very confusing when you do two rounds of PCR cycling
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www.sciencedirect.com www.sciencedirect.com
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outstanding possibilities for studying phenomena such as competition, niche partitioning and predation in the microbial world, under more environmentally realistic conditions than can be achieved in pure culture studies.
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the maintenance of the pluripotent state of animal stem cells requires hypoxic conditions, whereas higher oxygen tension promotes cell differentiation
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onlinelibrary.wiley.com onlinelibrary.wiley.com
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broad‐scale functional parameters increased as biodiversity decreased, e.g. thymidine incorporation, growth on added nutrients, and the decomposition rate of plant residues. Other more specific parameters decreased as biodiversity decreased, e.g. nitrification, denitrification and methane oxidation.
functional parameters of a community
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jlmc.medium.com jlmc.medium.com
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But because they ignore so much of the data, they don’t work well with small sets of data
don't use median with small data sets
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extremes help to tell you what’s possible, and could suggest a very different distribution in your data from what you expect
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journals.plos.org journals.plos.org
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we observed that codon usage biases are better correlates of growth rates than any other trait, including rRNA copy number
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www.sciencedirect.com www.sciencedirect.com
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capable of transferring resistance to non-resistant strains
Has this been demonstrated?
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The level of ARBs is extremely high in most of the river systems (up to 98% of the total detected bacteria)
That seems totally unfeasible; What was the methodology? How can you estimate such when most of the species are unculturable?
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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relationships between characteristics of microbiomes and the system-level processes that they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field
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www.nature.com www.nature.com
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Here, we show how three phenomena—Simpson’s paradox, context-dependence, and nonlinear averaging—can lead to erroneous conclusions about population parameters and species interactions when samples contain heterogeneous mixtures of populations or communities.
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These issues can be overcome by measuring and accounting for spatial heterogeneity at very small scales
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www3.nd.edu www3.nd.edu
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we emphasize how processes and interactions at one spatial or temporal scale contribute to emergent processes and properties at larger or longer scales. Most often the emergent processes we investigate are aquatic ecosystem services, including carbon burial, greenhouse gas emissions, nutrient removal, and recreational fisheries
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onlinelibrary.wiley.com onlinelibrary.wiley.com
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some of the key questions of microbial community assembly, maintenance and function could be answered by intensively studying one (or a few) synthetic model community
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bmcevolbiol.biomedcentral.com bmcevolbiol.biomedcentral.com
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Time-resolved analysis of individual cells revealed that past exposure to low levels of antibiotics increases tolerance to future exposure for the sessile but not for the motile cell
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news.rice.edu news.rice.edu
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Now we can ask, ‘Have I seen iron at some threshold?’ ‘Have I seen some nitrate?’ And have every microbe write it down. As one thinks about long-term incubation, this is a really powerful tool, because even six months later we can pull out the DNA and see what happened.”
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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Growth history influences starvation-induced expression of uspA, grpE, and rpoS and subsequent cryotolerance in Escherichia coli O157:H7
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in E. coli a form of ‘memory’ of past phosphate limitation leads to a faster response to successive periods of phosphate limitation, and that this faster response may be survival enhancing
phosphate starvation memory
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academic-oup-com.ezproxy.rice.edu academic-oup-com.ezproxy.rice.edu
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This article discusses, and challenges, some of the often implicit assumptions made in community studies. It suggests greater focus on ecological questions, more critical analysis of accepted concepts and consideration of the fundamental mechanisms controlling microbial processes and interactions in situ
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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quantitative physiological characteristics such as maximum specific growth rate; saturation constant; optimum, minimum or maximum pH or temperature for growth; susceptibility to predation; and the speed of recovery after starvation.
Quantitative physiological characteristics of microbes
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www.sciencedirect.com www.sciencedirect.com
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qPCR
no template control has absolutely no amplification!
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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In minimal media, cell growth and division slow considerably, while protein overproduction from plasmids can continue
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www-sciencedirect-com.ezproxy.rice.edu www-sciencedirect-com.ezproxy.rice.edu
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While these techniques offer good repression, they exhibit leakiness that precludes the gene of interest from being completely turned off
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biotium.com biotium.com
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Or
Contradicts previous calculation - should be 1.5 ul/ 1 ml Master mix
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1.8 uL diluted ROX per 20 uL
9 ul/ 1 ml master mix
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Researchers could use the method to study poorly-understood aspects of the sulfur cycle or bacterial methane production
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onlinelibrary.wiley.com onlinelibrary.wiley.com
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they upregulate biofilm formation and maturation (Sturbelle et al. 2015)
The reference cited has nothing to do with biofilms
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www-nature-com.ezproxy.rice.edu www-nature-com.ezproxy.rice.edu
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We overexpressed corresponding RT–Cas1 and Cas2 proteins from a plasmid that also contained their predicted CRISPR array
Crispr array on a plasmid
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www-sciencedirect-com.ezproxy.rice.edu www-sciencedirect-com.ezproxy.rice.edu
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these technologies all require destruction of samples and prevent us from analyzing dynamic changes in molecular profiles, phenotypes, and behaviors of individual cells in a complex system
current omics and single cell technologies => High resolution x destructive single time-point measurements
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