974 Matching Annotations
  1. Last 7 days
    1. this mechanism may broadly contribute to the importance of IncQ plasmids as agents of bacterial gene transfer in nature

      what special features of IncQ make this mechanism viable? - the replication mechanism?

    1. that uses highly accessible and inexpensive materials.

      How easily are these materials available?

      1. Gold nanoparticles
      2. ACE2 protein
      3. The electrical detection unit
    2. gold nanoparticles (AuNPs)

      are gold nanoparticles highly accessible in developing countries?

  2. Jul 2021
    1. pBGC was introduced into the wild-type isolate collection by electroporation, and all pOXA-48-carrying and pOXA-48-free clones were competed against their pBGC-carrying parental strain

      Is the burden of carrying pBGC included somehow in the analysis?

      Were pBGC carrying isolates competed with the parent isolates without any plasmid to do this?

    2. The presence of the entire pOXA-48_K8 plasmid was confirmed by sequencing the complete genomes of the 50 transconjugant clones, which also revealed the genetic relatedness of the isolates

      was this done after the growth to determine fitness effects? could the plasmid be lost midway through that experiment?

    3. replicate plasmid fitness effects in natural bacterial hosts, which remain largely unexplored

      fitness effects would also be greatly dependent on the environment and measuring fitness as max growth rate, max OD in well shaken single species liquid cultures also might not replicate plasmid fitness effects in the natural gut ecosystem.

      Given this, what is the specific advantage in using natural isolates?

    4. select clones which were naive to pOXA-48_K8, but ecologically compatible with it

      How can residence in a patient from a certain ward be termed as "ecological compatibility"

    1. all downstream manipulations with V. natriegens ATCC14048 Δdns cells were performed with antibiotic selection (kanamycin (200 μg/mL), chloramphenicol (2 μg/mL), carbenicillin (100 μg/mL))
    1. To facilitate indel identification, we developed an online tool called Poly Peak Parser (available at http://yost.genetics.utah.edu/software.php) that is able to separate chromatogram data containing ambiguous base calls into wild-type and mutant allele sequences
    1. TURBO™ DNase is a genetically engineered form of bovineDNase I with greater catalytic efficiency than conventionalDNase I at higher salt concentrations and lower DNAconcentrations.

      salt here => monovalent salts (Na+ etc.)

    1. Encapsulation also helped cells survive acidic environments (pH 4)

      How? isnt the media in equilibrium with the core?

  3. Jun 2021
    1. Escherichia coli was not reliably distinguished from Shigella and other Escherichia species sharing the high 16S rRNA gene sequence similarity to each other

      Is this due to sequencing error rate of nanopore or the 16s are really that identical?

    1. Goals of this paper

      1. What are the barriers of HGT across organisms of increasing phylogenetic distance?
      2. What determines the host range of conjugative elements (ICE, MGE, plasmids etc.)


      1. What does two plasmids being "related" mean to you guys? What does the sequence similarity or proteome similarity tell?

      Evidence for functional relevance of PTU

      1. PTUs have some correspondence with Inc groups and Mob types (both being more functionally informative) `
    2. ANIL20 refers to the total length of the shortest plasmid in the comparison.

      What does this mean if the shortest plasmid is really short - < 5 kb like the engineered plasmids and the larger plasmid is a real 50 kb plasmid? What does similarity of such a small region to such a large plasmid mean?

    3. This causes that otherwise unrelated plasmids show certain fragments of their genomes with high ANI values

      If they share the same MGE sequences, what else do you mean by otherwise unrelated? What does two plasmids being related mean to you guys?

    4. this trend dissipated when we looked within the Enterobacteriaceae family (Fig. 1e, f), indicating that the plasmid-encoded genome is widely shared among different genera in this family

      This could be an artifact due to proteobacteria being by far, the most studied family among bacteria?

    5. it is unclear whether, at the distal end of this phylogeny, there is anything similar to a “molecular species”: a group of genetically coherent genomes that evolve together.

      Considering that the concept of microbial species with functional similarity based on genetic similarity is itself debated. For example: There could be two strains, differing by a single nucleotide of some important gene, loosing a function with a huge consequence.. The same could be true for plasmids too if there are mutations in a particular origin of replication etc.

    6. determining the host range of a certain plasmid requires ways to establish which plasmids can be considered equivalent

      Or to determine the functional elements that determine host range and establish equivalence only within those sequences

    1. To separate cells from electronic background noise and abiotic particles, it is recommended to include nucleic acid stains

      Is a stain expected to be more homogenous signal compared to a fluorescent protein expression population of cells?

    1. Bacterial cells are typically one thousandth the volume of mammalian cells, which places them near the edge of instrument detection. At this size it can be challenging to differentiate viable cells from debris of similar size
    1. Because of the technical complexity of manufacturing coronavirus vaccines, waiving intellectual-property rights, by itself, would have little effect

      Is this only relevant to the newer mRNA technology?

    1. However, even in unexposed barley seedlings 16% of the cells were induced after 24 h, suggesting the presence of other aromatic compounds were inducing xis-int expression from the regulatable tbuT promoter.

      or leaky expression of the Xis-int?

    1. two isogenic mutants of the bacterium Pseudomonas stutzeri.

      If they each have a deletion in individual genes, how can they be called isogenic?

      Their growth rates might also be different

    2. . Thus, we conclude that genetic variants of the consumer are unlikely to cause the emergence of the two patterns of spatial self-organization.

      The conclusion should be that this assay cannot test for the genetic variant theory unless variants can be isolataed prima-facie and the experiment reproduced with variant (of one or both strains) vs the original mixed population

    3. If the “consumer first” pattern were caused by genetic variants, then the number of “consumer first” patterns that emerge per range expansion should depend on the initial cell densities of the producer or consumer.

      The pattern is caused by the interaction of the two strains, so altering their ratio will also change the pattern even if it is not caused by genetic variants. How do you control for that?

    1. From this result, we considered that las promoter (BBa_J64010) was not regulated by lasR and 3O-C12-HSL.

      Could the RBS be too weak that expression is not seen?

    1. As the speed of unperturbed electrophoretic polynucleotide passage precludes the resolution of individual nucleotides, a DNA- or RNA-binding motor enzyme is added to the system to gain a processive and slowed down passage (millisecond scale per nucleotide) of the polynucleotide through the nanopore
    2. single-stranded polynucleotide is electrophoretically threaded through a protein or solid-state nanopore.
    1. . For example, if a miscalling occurs at the end of a hairpin in a top strand read, the bottom strand read would correctly basecall this sequence before the hairpin is encountered

      strand bias example

    2. prepared for nanopore sequencing. This procedure involves end preparation, adapter ligation and incubation with the motor protein

      What is this motor protein, helicase? It is not mentioned in the nanopore ligation sequencing kit explanation. Does it come attached to the adapters?

    1. The Hardware may be used solely with the Consumables.

      this is very limiting and seems to go overboard to normal patent protection

    1. sequencing adapters, supplied in the kit, are ligated onto the prepared ends.

      What is the function of these adapters

  4. May 2021
    1. The basal level of T7-dependent tran-scription in this strain can be reduced by constitutive produc-tion of T7 lyzozyme, a natural inhibitor of T7 RNAP, usingplasmids pLysS and pLysE



    1. simultaneously regulating transcription and translation, we show how basal expression of an inducible system can be reduced, with little impact on the maximum expression rate. Using this approach, we create several stringent expression systems displaying >1000-fold change in their output after induction

      From fig 4a: basal expression did not really reduce in 2 out of 3 stringent expression systems designed and seems to be already low in the native Ptac (black line). This is a misleading claim in the abstract which could have been worded better. file

      I do see that table 1 reflects basal expression as a percentage of the maximum expression, so maybe this is what is being referred to in the abstract?

    2. Both L2 and the gene of interest (GOI) are separately transcribed by PL1 promoters and the product of L2 activates translation of the GOI transcript.

      Repeating the same promoter Pl1 twice could cause evolutionary instability due to recombination. How to avoid that?

    1. mf-Lon does not recognize or degrade ec-ssrA, providing a protease and cognate degradation tag with orthogonal functionality in E. coli

      I wonder if this insulation will be applicable to other gram negatives? (or other gram positives too?)

    1. the very idea that you could "know" what certain mutations would do — i.e., that you'd know what you'd create and what effect it would have on humans

      This is a disingenuous argument. there are many things whose effects on humans can be fairly hypothesised without such experimentation.

      It seems that there is precedent and scientific merit to the expectation that a furin cleavage site between the S1 and S2 subunits of the spike proteins can enhance the fusion and hence infectivity of the holder of the spike protein.

    2. None of the staff at the Wuhan Institute were infected with SARS-CoV-2; they were PCR/antibody negative

      Isn't this rather suspicious that nobody from this institute happened to be infected as a part of the general transmission in the city?

    3. it should be the default hypothesis.


    1. explain the puzzling fact that SARS2 has not changed since it first appeared in humans

      how substantial of a change are you considering? There have been many mutations in the spike protein which have gotten fixed in distinct sub-populations of variants in various regions/countries..

    1. pMgrB; PLfurOpMgrB; PLfurO

      Does using the same promoter for the Cr and the Ta cause recombination?

    1. conjugative plasmids have broad-host ranges23, are resistant to restriction-modification systems24, are easy to engineer with large coding capacities25, and do not require a cellular receptor26 that would provide a facile mechanism for bacterial resistance.
    1. Using the phoA gene and phoA fusions to monitor expression in these vectors, we show that the ratio of induction/repression can be 1,200-fold, compared with 50-fold for PTAC-based vectors

      with glucose?

    1. AraC is already a preferred system within the field for experiments requiring low levels of leak.

      With glucose added?

    1. While the talks continue, Iran is keeping up the pressure by adding to its stockpile of highly enriched uranium and the equipment to make it, all in violation of the deal.

      That is an unfair statement, considering that context that the deal is no longer operational.

    1. cells are resuspended in ∼1.5 mL transformation storage buffer

      100 fold concentration from culture volume (150 ml) to final aliquots (1.5 ml) is a lot for chemical competent cells. For E. coli this is generally 10-20 fold only. I have only seen electrocompetent cells being that concentrated.

      This needs to be tried out and verified

    1. It is reported that functional metagenomic selections identify genes with less than 65% amino acid identity to known resistance genes

      How do you verify that these are actually causing resistance and not some native transporters etc. that pre-evolve resistance mechanisms?

    1. simpler ribozymes ('hammerhead' and 'hairpin') are RNAs that catalyse site spe-cific scission of single stranded target RNAs bearing a consensus cleavage site.
    1. to study which conditions are necessary to generate interaction patterns like symbiosis or competition, and how higher order community structure can emerge from these

      By generation, you mean through evolution?

    1. These functions may arise from genomic scale differential expression and genetic polymorphism at the protein level, established throughout the microbiome/plant co-evolution and could explain its superiority over the maize resident plant-borne microbiome.

      Could the differential gene expression have something to do with being passaged on artificial culture media and other in vitro manipulations such as cryo-preservation?

      Repeating the same experiment but this time sampling the native maize microbiome into culture based collections and inoculating sterelized maize with this might explain a part of this?

    2. more than one-third of the total stalk bacterial endophytes grew specifically in one of the three culture media used, regardless of the type of media

      Is this a one off thing due to random variation or reproducible?

    3. A total of 17 wells containing highly abundant bacteria from the sugarcane core microbiome was selected to construct a synthetic community.

      Also curious to see the results on growth promotion of Maize, if all the wells are included (both high and low abundance bacteria)

    4. tested for growth viability

      on plates/solid medium

    1. see Figure S2 for transformation efficiencies using a chemical transformation protocol

      max of 2e5 CFU/ug plasmid

    2. ssrA degradation tags depend on a short sequence on the N terminus of the protein for quick degradation by the ClpX system in E. coli

      Shouldn't it be C terminus?

    1. found that conjugation frequency curves strongly resemble bacterial growth curves, with a lag phase occurring after initial mixing of donor and recipient cells, followed by a period of increasing conjugation (e.g., an exponential phase) that typically ends in a plateau (e.g., a stationary phase)

      Does it depend on what growth phase the initial donor and recipients were taken from before mixing?

  5. Apr 2021
    1. The FDA clearance and a marked up media highlighting the popularity of the drug prior to the publication of its research could also be the reason why human cognitive biases could have added to the ‘placebo effect’ in a small number of patients

      This is a very interesting positive feedback loop. It is almost hypothesizing that the official approval or positive press of any intervention would increase the magnitude of the placebo effect. I wonder how this could be tested in a rigorous manner ... some kind of delayed arms in a trial?

    1. At the same time, many quorum-sensing systems are known to regulate traits that strongly depend on the local cell composition, like conjugative transfer6,7,8, which suggests that cells may profit from limiting their communication range to nearby cells.

      Conjugative transfer is one of the phenotypes of quorum sensing, there are many others which could be activated simultaneously. The argument says that conjugative transfer depends on the local cell composition, but why does that translate to cells profiting from limiting the communication range?

    2. This enables cells to accurately detect micron scale changes in the community composition

      This seems like an unsubstantiated phenotype being attributed to short range quorum sensing

    1. GelRed, SYBR-Gold, and SYBR-Green must be applied after the run (staining bath) and can't be used with the precast method.

      This exception should also be applicable for TAE gels right? But many labs in Rice U use prestained gelgreen gels for TAE -- so why would LAB not work?

      What about gelgreen?


    1. the concentration is calculated based on the fraction of droplets that is empty (that is, the fraction that does not contain any target DNA).
    2. Formula for Calculating Concentration
    3. unexpected extra cluster of positive droplets with fluorescence intensity less than the cluster containing the target of interest can be caused by a sequence variant in the target of interest
    1. The solution is multilateral action in international institutions and international endeavors outside the WTO.

      I hate to say that this solution is very vague and needs to be elaborated

    2. undermining private IP rights would eliminate the incentives that inspire innovation, thus preventing the discovery and development of knowledge for new goods and services that the world needs

      Much of the discovery of knowledge is publicly funded research which has little to do with intellectual property rights and is not justified to be included in this statement.

    3. The primary justification for granting and protecting IP rights is that they are incentives for innovation, which is the main source for long‐​term economic growth and enhancements in the quality of human life

      Innovation for it's own sake when the products of such innovation are not reaching their intended consumers in order to alleviate the actual problem they were designed to solve seems rather pointless. Intellectual property rights were designed to encourage innovation, with the goal that such innovation would eventually be beneficial to society. Here there should always be a nuanced balance between the theoretical benefits of innovation and the actual benefits it is leading to on the ground. Hence any discussion of innovation should include the access and utility of such innovations to all stakeholders.

    4. practical reality of a world in which many medicines would simply not exist if it were not for the existence of IP rights and the protections they are afforded.

      There are always alternate incentives such as fixed cash awards, and subsidy transfers with fixed ceiling which could serve as incentive for innovation in such pandemic situations. It is not all or none

    5. have warned that allowing their COVID-19 vaccines to be copied without their permission through recourse to compulsory licensing “would undermine innovation and raise the risk of unsafe viruses

      Innovation is one thing but the safety of vaccines is for regulatory bodies to determine. Pharmaceutical companies have absolutely no say in this matter hence this is a straw man fallacy argument

    6. There is no evidence that intellectual property rights are a genuine barrier for accessibility of COVID‐​19‐​related medicines and technologies

      There are serious vaccine shortages in the developing countries, one key reason for which is that the developed countries have earmarked a lions share of the initial vaccine doses and due to limited manufacturing of the vaccine to satisfy the whole world's needs. Increased vaccine availability by enabling generic local manufacturers would enable much faster vaccination in all countries and providing essential doses for modest vaccination in the poorer countries

    1. Earthworms don’t do well in these hot temperatures compared to red wigglers which have a higher tolerance for temperature differences (they can survive at temperatures between 32 and 95°F / 0 - 35°C).

      Earthworms can survive 0-35C

    1. The similarity between pBBR1 and some plasmids of gram-positive bacteria has led us to precisely examine its mobilization function

      These similarities are all located in the RSA and the amino-terminal half of the pBBR1 Mob protein. Source: from the same paper below

    1. For many scientists, a new discovery is followed by a plan to make money, to form a company and get a patent.

      I doub't this assertion is valid.

    1. bacteria10

      Only intracellular pathogen bacteria infecting mammalian cells has been reported in 10. Would be interesting to see if this works for a culture of E. coli

    1. this expression contains two infix calls:

      Infix is where the function is not prefixed like usual f(.,.) so a <- b or a + b are infix calls

    1. , a hot-start PCR enzyme that prevents non-specific amplification from mispriming or primer-dimer formation during reaction mixture preparation

      So it doesn't prevent primer dimers forming during the reaction then? That is misleading marketing

    1. dsDNA substrate is best for insertions or deletions greater than approximately 20 nucleotides, while ssDNA substrate is best for point mutations or changes of only a few base pairs. 
    1. In contrast, SLiCE is an in vitro recombination method facilitated by bacterial cell extracts.

      What is the advantage of in vitro recombination by bacterial extracts as opposed to in vivo method?

      • Is the limitation the transformation efficiency of individual fragments?
    1. perhaps immunity will fade faster, for instance. But holding to the current dosing schedules means a slower vaccination program and more deaths.

      But going ahead to gamble with what could be an not sufficiently effective or temporary single dose without a line of sight for second dose could mean that once they discover and suggest people to take second doses, many people might lose trust and not show up for the second dose. This will be an irreversible effect on public trust on the vaccine

    1. when assembling Escherichia coli K12 MG1655. This genome can only be assembled into a single contig when the read length exceeds the size of the longest repeat in the genome, a multi-copy rDNA operon

      Demonstrates that if the read length exceeds the longest repeat, then automated assembly becomes straightforward

  6. Mar 2021
    1. AS-PCR was developed over 30 years ago (Petruska et al., 1988; Wu et al., 1989) and is commonly used for molecular genotyping in laboratory diagnostics
    1. When you have the data-variable in a function argument (i.e. an env-variable that holds a promise2), you need to embrace the argument by surrounding it in doubled braces, like filter(df, {{ var }})
    1. will show in real-time what downstream processes have been completed for each sample.

      This is impossible unless we upload data after each step. That would be too much work to expect from people who are busy in the wetlab

    1. filtered onto a track-etched membrane (pore size: 0.2 µm, Whatman CycloporeTM, UK). Filters were placed on agar-solidified (15 g/l) SW or MC medium
    1. Phanta Max Super-Fidelity DNA Polymerase is a new generation superior enzyme based on Pfu DNA Polymerase for robust PCR with extreme fidelity. High amplification efficiency and template adaptability makes Phanta Max suitable for almost all PCR reactions. The unique extension factor, specificity-promoting factors and plateau-inhibiting factor in Phanta Max greatly improve its long-fragment amplification ability, specificity and yield
    1. The enzyme offers fast amplification and strong strand displacement capabilities, making it ideal for nucleic acid amplification methods such as whole genome amplification, multiple displacement amplification and isothermal amplification.

      IsoFast™ Bst Polymerase

    1. patent protections and the profits they derive are a requirement for the innovation that yields lifesaving medicines.

      This is true. But if there are many lives that are not being saved, then what's the use of this innovation other than being a paper tiger?

    1. the kinetics of hybridization remain poorly understood, and no models or algorithms have been reported that accurately predict hybridization rate constants from sequence and reaction conditions (temperature and salinity). This knowledge deficiency has adversely impacted the research community by requiring either trial-and-error optimization of DNA primer and probe sequences for new genetic regions of interest, or brute-force use of thousands of DNA probes for target enrichment

      Why does kinetics impact the design of primer and probe sequences? Isn't it determined completely by thermodynamics?

    1. use of plasmid DNA enabled lower depth sequencing, and assemblies sufficient for full antimicrobial resistance gene annotation were obtained with as few as 2,000 to 5,000 reads, which could be acquired in 20 min of sequencing
    1. Make sure the 3′ end of the primer contains a C or G residue, because T and A residues bind more easily to DNA in a non-specific way

      This sounds wrong. G/C bind stronger hence provide for a better anchor for polymerase to start.

      G/C has more propensity for non specific binding though

    1. methylated motifs. These motifs often differ among species and strains24,25, making it possible to use combinations of methylated motifs (endogenous epigenetic barcode) for metagenomic binning.

      This is interesting. If methyl transferases are carried on mobile genetic elements, horizontally transferred to closely related organisms, shouldn't they share methylation signatures?

      Which would make the motifs not differ among species and strains?

    2. A survey of 230 diverse bacterial and archaeal genomes found evidence of DNA methylation in 93% of genomes, with a diverse array of methylated motifs (834 distinct motifs; average of three motifs per organism)
    3. Our method takes advantage of these endogenous epigenetic barcodes to resolve individual reads and assembled contigs into species- and strain-level bins

      Do individual strains or closely related species vary so much in their methylation signatures?

    1. This work facilitates the reporting of promoters in absolute units, the variability in their activity across a population, and their quantitative toll on cellular resources

      Looks like this has been done in the past. Ido Golding's work already measures low numbers of copy number, mRNA counts simultaneously in phage infected E coli using microscopy + clever statistics

      • Wang, Mengyu, et al. "Measuring transcription at a single gene copy reveals hidden drivers of bacterial individuality." Nature microbiology 4.12 (2019): 2118-2127.nature
    1. getting severely ill when infected with TB if they inherited two copies of a rare variant of the immune gene TKY2, called P1104A.

      The article could have benefited from a short mechanistic explanation of the mechanism behind this

    1. The TURBO DNA-free™ Kit contains reagents for the efficient, complete digestion of DNA along with the removal of the enzyme and divalent cations post-digestion.
    1. Pointing to the country's priority list, announced way ahead of the vaccine rollout earlier this month, he said, "In the first seven to eight months, we are focused on the 30 crore people, about which we have talked quite often and we know who those people are, who are the needier".

      Is this an appeal for their votes?

    1. viXra will be open to anybody for both reading and submitting articles. We will not prevent anybody from submitting and will only reject articles in extreme cases of abuse, e.g. where the work may be vulgar, libellous, plagiaristic or dangerously misleading.

      What if ArXiv claimed they were also rejecting articles only in extreme cases. But since they don't have the staff to vet all the submissions they receive, they came up with the endorsement system.

      I don't see this new platform as solving any problem - this model will break when the scale of submissions increases

    1. Our preferred gender pronoun for generic references is the female: “she”, “her”, etc.


  7. Feb 2021
    1. Plate-reader measurements of bacterial growth in the presence of various antibiotic concentrations were used for MIC values. For the strains used in conjugative experiments (both within and across genera) as well as the post-conjugation transconjugants,

      Can the presence of the sweetness affect the MIC on any way? Can this be controlled for?

    1. He picked himself for the match so as to fulfill the BCCI criterion (which requires state administrators to have at least one first-class match experience) for becoming a selector at the state level. After the match, he appointed himself as the chairman of selectors of HPCA Ranji trophy cricket team

      Wow! smells like conflict of interest, ain't it?

    1. curcumin doesn’t have any of the basic qualifications of a good pharmaceutical. Studies have shown that rats absorb less than 1% of the curcumin they eat.

      This is a great argument if curcumin is being talked about as a pharmaceutical in the typical sense.

      But when consumed as a regular part of Indian cuisine, turmeric is generally added into hot oil along with other whole spices - this could possibly alter the bio availability of curcumin (as it could for fat soluble vitamins?)

    1. Urban Governance in India -- Episode 31 of The Seen and the Unseen (w Shruti Rajagopalan)

      Disconnect between power and accountability. Decentralization in politics

    1. A ribosome typically covers 10 codon positions and hence ℓ = 10 with the A-site of the ribosome located at the sixth codon position in this segment

      6th position from the downstream (3') side?

  8. Jan 2021
  9. www-pnas-org.ezproxy.rice.edu www-pnas-org.ezproxy.rice.edu
    1. Aminimumof%20basepairsinacompletelyhomologoussegmentisrequiredforsignificantrecombination.Thereisanexponentialincreaseinthefre-quencyofrecombinationwhenthelengthofhomologousDNAisincreasedfrom20basepairsto74basepairsandanapparentlylinearincreasewithlongerDNAsegments.Mis-matcheswithinahomologoussegmentcandramaticallyde-creasethefrequencyofrecombination.

      A minimum of 20 base pairs in a completely homologous segment is required for significant recombination. There is an exponential increase in the frequency of recombination when the length of homology increases from 20 to 74 bp and an apparently linear increase with longer DNA segments. Mismatches within a homologous segment can dramatically decrease the frequency of recombination.

    1. However, to our knowledge, there is no study that compares microbial communities in different CW designs with different wetland plant species treating pesticides.

      I would want to see a more persuasive reason for why the different designs need to be studied rather than just that no study has done it so far

    1. newly acquired spacers derived from pTrig were 34 times more prevalent in response to the signal than without, increasing from 0.038(±0.004)% to 1.28(±0.03)% among all arrays in the cell populations

      Dynamic range of 34 is much smaller than 400. It is interesting to understand what causes this.

    2. cellular data recorders offer the capacity to measure biologically relevant signals15,16,17,18,19 in places that are otherwise difficult to access, such as inside the body20,21, and over time22
    3. Recently, redox-responsive biomolecules such as phenazines have been used in several electrochemical strategies to interrogate a range of biological activities30,31 and to control gene expression in living cells32,33, where the redox status of the biomolecules could be measured or manipulated by application of electronic potentials
    1. Dr Samiran Panda, a scientist at the Indian Council of Medical Research (ICMR), told The Wire Science earlier this week that the “mode” is effectively a single-arm clinical trial that wouldn’t have have a placebo and whose results wouldn’t be published in peer-reviewed journals – but with everything else being the same.
    1. Key points from explainer video - Soil biodiversity conservation Youtube

      1. Need to be able to see the soil biodiversity (microscopic) - visuals
        • to get people excited
      2. Need data to figure out where this needs conservation
      • Above ground biodiversity is not correlated with below ground (!)
      • Need to harmonize protocols to collect this across the world
      • Along with biodiversity, we should measure function - how the biodiversity affects ecosystem functions
    1. Here, we present the development and application of the BioMe plate, a redesigned microplate device in which pairs of wells are separated by porous membranes
    1. This variant presents 14 non-synonymous mutations, 6 synonymous mutations and 3 deletions. The multiple mutations present in the viral RNA encoding for the spike protein (S) are of most concern, such as the deletion Δ69-70, deletion Δ144, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H
    1. RSF1010 is maintained at a copy-number of about 10-12 per chromosome in E coli, P. aeruginosa and S. enterica sv.Typhimurium (Frey and Bagdasarian, 1989)
    1. ResCap capture library is a homemade core reference database (which will be available upon request) that comprises both well-known and hypothetical genes encoding resistance to antimicrobials

      Why is it not deposited along with this open-access paper? Isn't full data disclosure a part of the journal ethics?

    2. SeqCapEZ (NimbleGene) technology, which includes probes for 8667 canonical resistance genes (7963 antibiotic resistance genes and 704 genes conferring resistance to metals or biocides), and 2517 relaxase genes (plasmid markers) and 78,600 genes homologous to the previous identified targets (47,806 for antibiotics and 30,794 for biocides or metals)

      I wonder how the resistome is defined - does this also include single nucleotide variants that confer resistance? I assume it might be hard to capture such single nucleotide variants with probes

      For example of such variants Ramanathan, Babu, et al. "Next generation sequencing reveals the antibiotic resistant variants in the genome of Pseudomonas aeruginosa." PloS one 12.8 (2017): e0182524.

    1. the bacteria of the recipient strain was unable to grow on the plate containing ampicillin (> 100 mg/L) and gentamicin (> 50 mg/L) by drug sensitivity test

      Chlorine could affect the activity of the antibiotic ampicillin - was this tested for in the drug sensitivity test with various antibiotics?

    2. Non-lethal dose chlorine (0.5 mg/L) increased the conjugation transfer frequency,which confirmed that the mRNA expression levels of type IV secretion system (T4SS) proteins vir4D, vir5B and vir10B were significantly enhanced

      Does the fold change of increase in conjugation mirror the fold change of increase in mRNA expression of any of these genes?

      fig 4b -> conjugative transfer frequency increases by ~ 10 fold at 0.5 mg/l chlorine fig 4h -> genes increase only by 1.5 fold

      • on a side note, it is wonderful that the authors looked for a causal expression for increase in the conjugation. It is incredibly rare in these kinds of studies
    1. something that the alternative online media has been unable to do is where mainstream media platforms are still unrivalled – being a one-stop repository for different sets of news consumers. MSM digital platforms, despite many flaws, thrive as catch-all baskets for round-the-clock information seekers, ranging from politics to cricket, from fashion to music and important news (which doesn’t only mean the unusual massacres) from a hamlet in Arwal district in Bihar to that from a Delhi suburb.

      This will be impossible for a small digital media startup to achieve.

      I rather see the independent digital news as a gateway to important, contentious, controversial or rather plain and non flashy news. News of the kind ignored by mainstream media due to their perverse incentive structures.

      I don't think the coverage on cricket for example or entertainment from newslaundry would be any drastically different from mainstream media. In that sense it would be wiser not to compete and squander resources on such kind of reporting just to be a one stop shop.

    1. we developed a vastly improved INTEGRATE system that uses streamlined expression vectors to direct highly accurate insertions at ~100% efficiency effectively in a single orientation, independent of the cargo size, without requiring selection markers

      Efficiency sounds too exciting to not try!

    1. This work provides CasTn as a new method for host-independent, programmable, targeted DNA insertions to expand the genomic engineering toolbox.
    1. Indeed, the cell-lysate approach was found to be associated with superior sensitivity in some cases5.
    2. using a commercially available reagent (Bio-Rad SPR) that generates RT-qPCR-ready cell lysates with minimal manipulations. Similar reagents are now available from a number of sources (Ambion Cells-to-CT, Invitrogen CellsDirect, Roche RealTime Ready Cell Lysis, etc.)
    1. we demonstrate improved PCR-enhancing cocktails containing nonionic detergent, l-carnitine, d-(+)-trehalose, and heparin. These cocktails, in combination with two inhibitor-resistant Taq mutants, OmniTaq and Omni Klentaq, enabled efficient amplification of exogenous, endogenous, and high-GC content DNA targets directly from crude samples containing human plasma, serum, and whole blood without DNA purification.
    1. We found that a lysis solution containing both the non-ionic detergent (IGEPAL CA-630, chemically equivalent to Nonidet P-40 or NP-40) and bovine serum albumin (BSA) gave the best RT-qPCR yield. This direct lysis to reverse transcription protocol outperformed a column-based extraction method using a commercial kit.
    1. However, by the time scientific studies make it to the real world, shortcomings and limitations are removed to present palatable (and often wrong) conclusions to a general audience.
    2. There are many commercial interests invested in persuading us to eat things that may be edible, but shouldn’t really be considered food

      :) very funny

    1. While no serious climate scientist doubts the fact that human activities are causing climate change, this can’t be proved through experimentation on another Earth.

      In both cases, the answers should be clear when looking at the evidence and the mechanisms at play without an ideological bias

  10. Dec 2020
    1. Biosciences Robert Sabin 713-348-4324 Charles Stewart

      library contact person

    1. Transfer of plasmid RP4 during bacterial conjugation requires the plasmid-encoded TraJ protein, which binds to a 19-base pair invert sequence repetition within the transfer origin

      can it not be encoded in the host or a helper plasmid? Donor E. coli MFDpir already has it

    1. Fluorescence values for sfGFP (excitation, 485 nm; emission, 528 nm) and mCherry (excitation, 580 nm; emission, 610 nm)

      peak emission of sfGFP is 510 nm, why was 528 used here? fpbase

    2. . Some SsGCs exhibited universal activation across all hosts in both reporters (constructs A–C

      What do the sequence IDs (1-12) in this image correspond to the oligo ID?

  11. science.thewire.in science.thewire.in