432 Matching Annotations
  1. Last 7 days
    1. Transmitting the same power using a higher voltage and lower current loses less of power over the length of the cable. This is more efficient and why the main power grid is hundreds of volts and not 5V.

      A good clarification here on stackexchange - https://electronics.stackexchange.com/a/25571

    1. obtained transcriptional measurements from mid-exponential-phase cultures

      Could be repeated for stationary phase expression?

    1. mobilizable plasmids, possess their own transfer origin and encode a relaxase but need the help of a conjugative plasmid for their transfer from a donor to a recipient

      Why do mobilizable plasmids encode the mob gene? Can't it be provided in trans by the mobilizing helper strain?

    2. Plasmid pBBR1 thus appears to be a new member of this group, even though it resides in gram-negative bacteria and does not replicate via a rolling-circle mechanism
    1. bind the transposon DNA at the flanking inverted repeat sequences, excise the transposon, and paste it into a random TA dinucleotide on a target DNA
  2. Jan 2020
    1. To prepare V. natriegens cells for −80 °C storage, an overnight culture of V. natriegens was washed in fresh medium before storage in glycerol
    1. we successfully demonstrated challenging clonings such as Gibson Assembly with 5 and Aquacloning with 3 fragments as well as 8 part golden-gate reactions.
    1. stationary-phase cultures grown in rich medium could be refrigerated for more than 1 month without substantial loss of viability

      Barick lab discourages storage at 4C, instead recommending room temperature storage for 2-3 days due to concerns of ROS production. This recommendation was for both plates and liquid cultures


    2. transformation efficiencies were sufficient for routine construction of plasmids from multiple fragments

      How many fragments?

    3. Four inducible promoters were found to function in V. natriegens

      Lac, Pbad (arabinose), lambda promoter

    4. Plasmids with the RK2 replicon could also replicate but were successfully delivered only via conjugation

      Interesting, I wonder why electroporation doesn't work. Does it have something to do with methylation state or other restriction based mechanisms that allow DNA coming in through legitimate means rather than forced means!?

    1. Vmax has a low-level natural resistance to kanamycin but is more susceptible to other antibiotics. When selecting on Kan plates, Vmax with KanR will simply grow faster than Vmax without KanR. Larger colonies=KanR. Other antibiotics select against Vmax but must have a dosage change compared to E. coli.
    1. A spacer could compensate for any steric hindrance effect on recruiting the transcriptional machinery at the promoter of the next module in the assembly line; such an effect could be induced by the supercoiling that results when the transcription of the previous module is taking place. However, there is no direct evidence that this may cause a problem, and therefore the argument in favor of using a spacer remains speculative.
    1. As his ideas have permeated the rest of the field, Sanders’s own candidacy appears less radical—or at least less exceptional.

      This is a significant achievement in itself.- Politics is an organized, institutionalized form of conversation and the Bernie 2016 campaign has started the most important conversations in the USA!

    1. . If you are agreeable, you care about your family, your community, society, your country, more than you care about yourself. And if you are disagreeable, then you are a little bit more egotistical.

      This is an interesting categorization. I would assume most people would have some fluidity where people oscillate between these modes according to their life experiences with triggers from the world around them.

    1. do: deregulate, and fast

      deregulation in what aspects? - not all of them are good, certain regulation is necessary and is better for the economy in the long term.This is easier said than done

    2. Gujarat often produced growth faster than the national average, fewer regulations, better infrastructure and less corruption
    1. We are taught that we should be defined by the things other people find impressive, not by the things that bring us joy

      Good point

    1. Get good at knowing what your friends and fans like to see and interact with

      This is just stupid advice. I intend to have an audience in order to read what I write, not the other way around - like Ayn Rand's quote.

    2. he rarely posts status updates and I post pretty frequently and often get good conversations going in the comments.

      Shouldn't rare posts be given higher precedence like twitter does, because rare commodities are more valuable? People who take more time and effort to post valuable content for discussion are bound to post more rarely compared to daily personal updates of what I eat, do etc.

      Twitter notifies me - look at this post, this person has posted something after a long time.

    1. Calling out Uncle Bot’s past vote for Trump threatens his ego and encourages him to double down on his support for the president. Self-esteem is a fundamental human need. If you want people to change their opinion, bolster their ego and help them save face
    2. Fully explore the other person’s perspective before sharing your own to ensure you understand where they are coming from. As with all questions, follow-up inquiries should be nonjudgmental, open-ended and curious.
    1. The concentration of GFP in the sample had been measured using a nanodrop and was ~120μM

      How was the protein quantified? I assume UV absorption or Bradford assay was used.

    1. The fundamental issue surrounding bacterial culture growth measurements is that an absorbance spectrophotometer is being asked to determine light scattering caused by particulates in suspension. In this case, transmittance is not related to absorbance in the classical sense. Under normal true absorbance conditions, spectrophotometers can be comparable to one another because the sample actually absorbs electromagnetic energy. In the case of a reduction of transmittance caused by light scattering, readings are very dependent on the optics of a specific spectrophotometer as well as the cell type in suspension
    2. generally accepted extinction coefficients for nucleic acids are: • Double-stranded DNA: 50 • Single-stranded DNA: 33 • RNA: 40
    1. After all, the rise in antibiotic resistance doesn’t mean that we shouldn’t have invented antibiotics at all.

      It does mean though, that we should try to forsee unintended consequences and not dismiss skeptics without judging the merit of their skepticism with sound scientific discussions. It is famed that Alexander Fleming who discovered the first antibiotic - penicillin, mentioned the observation of resistant bacteria and advised caution in antibiotic usage. This caution went unheeded in the subsequent golden era of antibiotics where all alternatives like phage therapy were shelved from research and development. This is the real lesson we should learn

    2. If a corporation wants to use a gene drive to “cancel out” the herbicide resistance that some weeds have now developed, would that really benefit the planet — or just the corporation that can now sell more of the herbicide that caused the problem in the first place?

      If evolution has any lesson from the development of resistance to the herbicide, it is that some way or other, maybe slower than herbicide resistance, surely the weeds will find a way to subvert any gene drive

    3. With its ability to create powerful changes invisibly, genetic engineering can feel eerie to even the most rational of us

      When things as fundamental as genomes are being modified and amplified through generations, the unforseen consequences have likelihood of being essentially anything. The most rational might be skeptical because of this. Positive feedback system with added noise blows up to infinity or zero; it's an unstable system mathematically

    4. Do we really want the process of scientific research and technology to become democratic — one in which fundamental decisions about public health, like vaccines and vector-control measures, are put up for a vote?

      This is a great debate topic

    5. the lay public’s view is, once you say the person is a scientist, they must know everything.”

      hahaha! so true

    6. and hand control to Big Ag

      How the fuck did big agrobusinesses get so big? Don't these GMO skeptics want to talk about that? About monopolies and anti-trust laws in general? and regulatory capture in other fields as well? Aren't these related issues whereby preventing either of these would have averted the big ag crisis we see today?

      We need discussions around these connected points and not in isolation

    7. s a general idea that these groups aren’t scientific, so their arguments are less valid

      Then the public including the activists and regulatory agents should urgently be 'educated' properly about the technology before moving on to influence their lives irreversibly.

      I believe they are also invited at some of the conferences for such high watch technologies too.

    8. activist groups are more likely to tap into unconscious values and emotions — like using the term “Frankenfoods” to describe G.M.O.s
    9. a misleading focus on “high-profile savior applications” like anti-malarial and conservation efforts

      How is this misleading? Are there any applications that need to be talked about?

    10. compared gene drives to the atomic bomb and accused researchers of using malaria as a Trojan horse to cover up the development of agricultural gene drives for corporate profit
    11. Local and national governments would work with regulatory organizations like the United Nations and the World Health Organization,

      I wish the local and national governments were trustworthy and not corrupted so easily like Monsanto can get them to be

    12. Their financial interest in the intellectual property and their regulatory interest in making sure these products were able to come to market got conflated with the science, so nobody was willing to trust the kind of research they were doing. The end result was that all G.M.O. research got tainted.”

      This speaks volumes of keeping regulatory bodies highly circumspect of lobbyists from the regulated organizations especially when they are near monopolistic.

    13. the technology was controlled primarily by the global agricultural giant Monsanto
    14. struck most people as vaguely creepy
    15. a weapon — say by sabotaging the pollinators that support agriculture, or by altering the genes of innocuous wild insects so they could transmit disease
    16. Could a gene drive stop one virus only to open the way for another, more virulent one? Could it jump from one species to a related one? What would be the environmental effects, if any, of altering the genes of entire species? How about eliminating a species entirely?
    17. Besides combating malaria, gene drives could be used to alter, or even eliminate, other disease-causing insects, from the sand flies that transmit leishmaniasis to ticks that carry Lyme disease in the United States.
    1. power of the people is not only limited to the right of vote, but it extends further and provides us the right to participate in a democratic system by observing, suggesting and discussing, contemplating, questioning, negotiating and dissenting its system or function in various circumstances
    1. CES (combinatorial enhancer solution). 5X CES = 2.7 M betaine, 6.7 mM DTT, 6.7% DMSO, and 55 ug/ml BSA
    2. capable of checking multiple annealing temperatures at a time

      How does this compare with touch up or touch down? Aren't those protocols covering a larger range of temperatures? What are the use cases that differentiate between these two methods

    3. increasing the magnesium concentration, which improves amplification

      Also reduces fidelity?

    4. but the 5’ end is more important

      Do you mean 3'? This is where the extension happens and the GC clamp is recommended

    1. We must stop building new nuclear power plants, and find a real solution to our existing nuclear waste problem.

      We urgently need a debate to discuss and rethink this idea against nuclear energy. I strongly opine that nuclear power generation will be necessary at-least in the short term during the transition into clean energy, hopefully eventually leading to purely sustainable energy and minimizing nuclear energy.

      This article expresses the same point and points out to the German experience of not being able to contain carbon emmissions despite going green energy sans nuclear - https://theweek.com/articles/862988/what-bernie-sanders-elizabeth-warren-wrong-about-nuclear-power

    1. More broadly, we hope that others, especially the hundreds of new startups in synthetic biology, consider sharing pre-competitive ideas, methods, tools, etc. We think the community will be stronger as a result.

      This is a great initiative. Hat's off to this company - Octant-bio for encouraging open sourcing of their hard work and optimization.

    2. we usually need 400-1200 colonies, it’s still easier and faster to do this manually than by colony picker. Also, colony pickers typically cost >$100K and don’t seem appropriate for our scale. 
    3. manually analyzing the data was about as painful as waiting for the results

      I recall someone in Bader lab at JHU had a Perl script to automate alignment of sanger sequencing data; (would be nice to get it onto Github)

    4. OCTOPUS, a light-weight, cost-effective, and robust method for full-plasmid sequence verification using next-generation sequencing
    1. Biosensing intracellular concentrations of metabolites can provide an efficient high-throughput screen of hyperproducing strains.


    2. Chemical inducers such as carbon sources, metabolites, and antibiotics, environmental signals such as light, pH, oxygen, or temperature, and autoregulatory quorum-sensing molecules can all be sensed by TFs

      Common inducer molecule types

    1. It boils down to priors: do we have reasons to expect large variance in opaqueness? Do we have reason to expect low variance in opaqueness?

      Great point! A lot of debate boils down to competing apriori assumptions by the different parties.

    2. A final word: when we do not understand something, it does not look like there is anything to be understood at all - it just looks like random noise. Just because it looks like noise does not mean there is no hidden structure.

      Excellent statement! Could this be the guiding principle of the current big data boom in biology?

    3. because the receptor both activates and deactivates the internal signal, its concentration cancels out in the equilibrium expression


    1. we were far in advance of Westerners in science and technology at that time.  Today we are far behind them, so what happened?  Why did we not have an Industrial Revolution?  Why did we lag behind?  This is known as Needham’s question or Needham’s Grand Question

      Needham's question

    2. In India, on the other hand, there is tremendous diversity, because whichever group of immigrants came into India brought in their own culture, their religion, their language etc.

      Are there facts supporting the argument that the diversity of India is reflected in the diversity of the incoming immigrants or the source populations? Or is it that the people who settled evolved different cultures and languages on their own?

    1. Nevertheless, fierce Carter administration pressure mounted for him to abdicate.

      This statement is very misleading. It totally misses out the high intensity 1979 Islamic revolution against the Shah, his secret police and favouratist policies, ie) strong factors from with-in Iran that was the actual cause of the 'abdication'

    1. If we reunite, we can pool in our resources and overcome these problems in 15-20 years

      We can say there is a 'possibility' to do it better if we unite, there is no guaranty.

    2. they do not want another China

      China is not an ideal that we want to embrace in this regard, either socio-culturally or economically it is simply not feasible to emulate China given that we are at the brink of industrialization driven global warming and climate change with disastrous consequences

    3. communalism is an artificially-created phenomenon, and can easily be suppressed by a strong secular government.

      That is a very strong assumption and can go either ways.

      Once sown, commununalism can never be sterelized from the population, it will linger on as radical extremist movements continuing to draw support and sympathies. This might be a tiny fraction of the population that can be dismissed as irrelevant or it can amplify and destabilize any 'artificially' created united government as well.

    1. Interactions between Mycobacterium tuberculosis (Mtb) and human (players) are often included in the Mtb’s strategies to invade host responses, to replicate and persist within the host,

      Does the M.Tb have knowledge of the host responses or is it merely adapting bet hedging strategies (a mix of multiple strategies across population) and whatever survived is what we see.

      This will have major implications in treating the problem in a game theoretic fashion

    1. Borate, which is present in LB and SB, causes reversible crosslinks with DNA, reducing the separation of larger DNA fragments unless low % gels are made of high-strength agarose
    1. use of the strong UAAU signal in highly expressed genes and for the occurrence of the weaker UGAC signal at several recording sites.

      three types of recoding events: stop-codon readthrough, –1 ribosome frameshifting and translational bypassing

      (Rodnina, Marina V., et al. "Translational recoding: canonical translation mechanisms reinterpreted." Nucleic acids research (2019).)

    1. suggestive of protein extension, especially at UGA codons, which rely exclusively on the reduced function RF2 variant of the K-12 strain for termination
    1. Since capitalists make money from every hour of workers’ labor, they will get increasingly rich over time, while workers won’t because they’re too busy making money for capitalists

      This is not entirely obvious, it depends on the competing interests of the owners of the means of production vs the workers. The current economic and social organization that disincentivises labour unions and any forms of collective organization on the worker side reduces their bargaining power and hastens this statement. But there can be alternative ways of structuring companies and the macroeconomics to balance both the forces.

      Am I missing something here?

    2. the rich pocket, rather than reinvest, their tax cuts

      Or they reinvest a smaller than expected fraction of it?

      It would be great to see some data on this as the intuition can go both ways. One argument says -

      • Rich do not pocket their wealth, they spend it on overpriced luxury items and long term invesents (really?), whereas working class people spend it in short term purchases for livelihood which does not have as much of a ripple effect on the economy.
  3. Dec 2019
    1. should reject the influence of both liberal capitalism and communism, ideas that inspired the revolutionary slogan "Neither East, nor West – Islamic Republic!"

      In a post cold-war world, viewed in increasing binaries of left and right winds be it social liberal - conservative or socialist-capitalist tendancies, it seems incomprehensible as to how one can reject both USA's and Soviet's socio-economic models. I'm curious to know how they organize their economy in this case.

      One part why the western world hates the Islamic revolution might be their lack of understanding about this exact phrase, other than the fact that Iran became a theocracy.

    1. Religious conflict in any form is often far more impervious to pragmatic solutions, and can prove more dangerous than national conflicts.

      This is debatable. National identity and religion are often both entwined in complex historical factors quite like Judaism and the land of Judea. Whereas national identity is more moldable and dynamic when combined with democratic developments like the Arab spring, religious identity would change slower and might be more important to guard for the conservatives (I'm not sure on this, but it's a gut feeling)

      In such a case, conflicts are easier to understand when cast in terms of religious or sub-religious basis but I definitely think a purely religious conflict (an ideal construct) is more likely to find a pragmatic solution, although I doubt if any thing of that sort exists!

    1. A single transformant may have a mutation at a low level that will eventually sweep through the population

      How does transforming a pure plasmid (miniprep) produce a mixed population?

      • Is a single colony on the transformation plate not really clonal due to evolution occurring in growth from the single founder cell?
      • And also the outgrowth steo prior to plating is introducing additional variation that differentiates different colonies
      • Hence adding these two statements together, picking 3 colonies from a plate streaked from a glycerol stock (derived from a clonal population) has lower variability than 3 colonies picked from a fresh transformation?

      Does this make any suggestion of using one or the other method for generating independent biological replicates?

    2. promoter mutations remove the metabolic load at both the transcriptional and translational levels

      Is there any other sequence dependent feature that might explain why promoters are more predisposed to mutation than RBS?

    3. in the normal MG1655 strain that does not overproduce LacI

      Should have knocked out the LacI for a more robust constitutive activity?

    4. a few simple design principles: high expression of genetic circuits comes with the cost of low evolutionary stability, avoid repeated sequences, and the use of inducible promoters increases stability. Inclusion of an antibiotic resistance gene within the circuit does not ensure evolutionary stability.
    1. Engineering as a practice has not, however, been successful in such endeavors as controlling the weather or avoiding natural disasters, due largely to the scale, complexity and uncertainty inherent to those problems. So we must ask: is the conventional paradigm of engineering appropriate for biology?

      Great point!

    1. CRISPRi-ME prevents evolutionary failure of a burdensome plasmid in E. coli.

      It reduces the rate of evolutionary failure but does not prevent

    1. SDS in loading buffer may contribute to band smearing in precast GelRed® gels. If this occurs, we recommend using the post-staining protocol
    1. Lithium Acetate Borate (LAB) buffer is an agarose gel electrophoresis media for DNA gels

      Lithium and Borate are both teratogenic.. Is it worth the risk?

    1. 50 μg/ml RNase (ThermoFisher #EN053) freshly added. 2 ml of lysis buffer

      Fresh RNAse is really critical. Otherwise this will result in 10 fold more RNA contaminant than DNA; which implies the nanodrop reading and gel visualized DNA will be 10 - 100 fold different. (from personal experience of 1 prep only)

    1. deep-well plates, require a faster shaking speed for proper aeration

      Deepwell plates (24 well plates with 3ml cultures as well as 96 well with 1 ml) require 800 rpm shakers

      • by Bennett Biodesign lab @ Rice University
    1. we recommend calibrating OD using serial dilution of silica microspheres, which readily produces highly precise calibration (95.5% of teams having residuals less than 1.2-fold), is easily assessed for quality control, and as a side effect also assesses the effective linear range of an instrument.
    1. Bacteria are less likely to develop resistance against a pro-drug as it becomes active only after getting inside the bacteria. The active components formed from the pro-drug are potent and short-lived, thus not giving the bacteria sufficient time to develop resistance.

      Would like to see some evidence for this!

    1. which ends up being much less efficient

      Has this been quantified properly? I see a lot of new methods relying on in-vivo homologous recombination now-a-days - ex: FastCloning: a highly simplified, purification-free, sequence- and ligation-independent PCR cloning method

    1. “death phase,” where at least 99% of the cells in the culture lose viability

      So the 'death' in death phase is only loss of viability?

      I thought the cells lyse and are eaten up by neighbours; while reducing the OD (due to cell lysis)

    1. this system enables longer duration production, and could be readily applied to burdensome or toxic products not readily produced in bacteria
    2. Application of synthetic biology is limited by the capacity of cells to faithfully execute burdensome engineered functions in the face of Darwinian evolution
    1. To add a data mask so you can refer to variables in a data frame as if they are variables in an environment.

      Similar to a with() function?

    1. plasmid-based circuits suffer from multiple limitations: high intercellular variation in gene expression, genetic instability from random partitioning of plasmids during cell division, and plasmid loss in environments for which antibiotic use could disrupt native microbial communities or is economically infeasible
  4. Nov 2019
    1. , science proceeds by the falsification and refinement of hypotheses. Thus, for most papers, the only way is down.

      That one nails it!

    2. despite Blatt’s carefully worded insinuations, PubPeer does not allow “hearsay”, “allegations” or invite “innuendo” (and we aim to act on all reports of such comments)

      Blatt does mention that the pubpeer site moderators are anonyomous in contrast to the journal editors. This somehow reduces their credibility on effective moderation of abusive or trolling comments. This sounds like a recursive argument: A central authority brings credibility but also corruptibility. I can see parallels in the debate about Bitcoin cryptocurrency vs federally backed currency and about the trustworthiness vs corruptibility of a central authority as compared to a distributed crowd authority.

    3. authors, journals and institutions are all unquestionably exposed to conflicts of interest when it comes to correcting problems

      A retraction once published does not reflect well on all of these parties and is clearly a conflict of interest even though they may claim that it is in their benefit. Somehow a pre-publication review is being given more importance than a post-publication review because of this reason.

    1. in much of biology, readers have to trust the authors to describe their experiments accurately, and there are many more opportunities for mistakes and dishonesty

      Good point

    1. alleging their negative appraisals of his work had resulted in a university rescinding a job offer

      Oh, and what does he have to say about the 20 retractions he as so far then?

      I is like a real wrongdoer criticising the police for investing in the first place.

    1. Commenting on a scientific paper, in particular when the comments are not positive, is risky business for academics

      Could someone elaborate on this? Why exactly does negative commenting cause a researcher to be discriminated against?

    1. That means gram-negative bacteria cannot change the BamA protein without losing their ability to infect.

      It 'suggests' that would have been better. There might also be other resistance pathways that might retain infectivity. This will depend on the environment used for the resistance evolution experiment

    1. (a+b+c)^2 - a:b is identical to a + b + c + b:c + a:c

      This example is not clear. I do not understand what a:b means

    1. Ina Schuppe Koistinen, Abhishek Krishnagopal, Sangeetha Kadur, Pooja Gupta etc gave me the inspiration to do what I wanted to do. Along the way I got exposed to more art and science creators like Gemma Anderson, Monica Zoppe, Drew Barry, Ina S. Koistinen, Christian Sardet, Sandra Black Culliton, Amanda Phingbodhipakkiya

      science communication - art + science

    1. we present an overview of our current understanding of these rules for the genetic manipulation of prokaryotic microbes and the available genetic tools to expand our ability to genetically engineer nonmodel systems
    1. s used fluorescein-labelled oligonucleotides as our probe for DNA delivery

      DNA delivery assessment

    2. required removal of salts results in osmotic stress - particularly challenging for a notoriously temperamental marine bacterium like Prochlorococcus

      Electroporation buffers cause osmotic stress and need osmoprotectants like glycerol

    3. the 6-month multi-step procedure is vulnerable to user variability

      The doubling time is 3.3 days!

      • Genetic Manipulation of Prochlorococcus Strain MIT9313: Green Fluorescent Protein Expression from an RSF1010 Plasmid and Tn5 Transposition
    4. This cell is the simplest photosynthetic “machine” designed by nature – an attractive foundation for manipulation
    5. small size (hence high surface/volume ratio), which enhances its ability to compete for limiting nutrients
    6. Such projects are not suitable for graduate students or post-docs because of the high risk involved, nor are they easily funded

      that is wisdom!

    7. genetic transformation protocols requires tedious trial and error, and methods developed for one strain are often unsuccessful in close relatives
    8. To avoid the pursuit of unproductive paths, we report here what has not worked in our hands, as well as our progress developing a method to screen the most efficient electroporation parameters for optimal DNA delivery into Prochlorococcus cells

      negative results

    1. HGT typically adds new catabolic routes to microbial metabolic networks. This increases the chance of new metabolic interactions between bacteria
    1. 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
    1. 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
    2. 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

    1. 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?

    1. 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.
    2. 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
    1. 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.
    1. 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?

    2. 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.
    3. 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

    4. 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
    1. single copy phylogenetic marker gene

      How is this marker gene strictly single copy? How do you know?

    2. 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?

    3. unequal efficiencies of PCR-primers in different species

      This should presumably also affect your 40 housekeeping marker genes.

  5. facultypatchbook.pressbooks.com facultypatchbook.pressbooks.com
    1. 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

    1. 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?

    2. Susceptibility to antibiotics and human-targeted drugs correlates across bacterial species

      This is interesting

    1. EDTA-extractable fraction

      Why EDTA extraction? How does this compare with a water extraction?

    1. o perform multiple replacements in each element

      This should be clarified better

      • Does it mean multiple replacements of a single pattern or replacements of different patterns with their corresponding replacement
      • The second one is what this is supposed to mean right?
    1. transient events

      Need better examples of transient events


    1. 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?

  6. Oct 2019
    1. 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.
    1. A biofilm was prepared

      Biofilms are never prepared, they are grown!

    2. 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

    1. 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

    2. 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?

    1. 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?

    2. 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?

    1. it then moves in a directed path through the pore space, a process we call hopping

      How is this different from the 'run'