921 Matching Annotations
  1. Last 7 days
    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?

  2. 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

  3. 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.


  4. 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?

  5. Jan 2021
  6. 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

  7. 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?

    1. it was liable to impact the final results of the vaccine trial since, as more participants in the placebo arm would become infected, “the result of those getting the vaccine would obviously look better”.

      Wouldn't patients from both arms be impacted the same way by risky practices induced by the document?

    2. By giving the confidence to participants that they are safe after taking the shots, the participants may become complacent. The people in the placebo group, in reality, have got zero level of protection, hence increasing their chances of getting the infection,” he said.

      editor of the Indian Journal of Medical Ethics Amar Jesani

    1. The discoverers of this Ψ technique


      Karikó, Katalin, et al. "Suppression of RNA recognition by Toll-like receptors: the impact of nucleoside modification and the evolutionary origin of RNA." Immunity 23.2 (2005): 165-175.

    1. it remains unclear exactly why resources are exchanged among trees in the first place

      Maybe focusing on the 'why' rather than the 'how' of a novel scientific study or paradigm prevents acceptance in the scientific community and slow down scientific progress?

    1. We recommend the following changes to the default settings when designing ddPCR assays:

      Primer3 : designing primers and probes for ddPCR

      In the General Settings window, change “Concentration of divalent cations” to 3.8, “Concentration of dNTPs” to 0.8, and “Mispriming/Repeat Library” to the correct organism ■In the Advanced Settings window, change both the “Table of thermodynamic parameters” and “Salt correction formula” to SantaLucia 1998 ■In the Internal Oligo window, we recommend setting 15 for the minimum number of bases for the oligo. We recommend 64°C as the minimum Tm for the probe, 65°C as the optimal Tm for the probe, and 70°C as the maximum Tm for the probe. These parameters can be relaxed to allow for smaller/larger oligos, which may be necessary for high GC or low GC targets. Oligo size should be no smaller than 13 and no larger than 30 nucleotides

      Note: After you have made the desired changes in Primer3Plus, select Save Settings under General Settings and save these parameters in a file. To apply these settings in the future, upload them by selecting Browse in the General Settings tab, find this file, and click Activate Settings.

    2. Strive for a Tm between 50 and 65°C. One way to calculate Tm values is by using the nearest-neighbor method. Use the Tm calculator at http://www.basic.northwestern.edu/biotools/oligocalc.html, with values of 50 mM for salt concentration and 300 nM for oligonucleotide concentration
    1. flow cytometry data were analyzed in R using the flowCore Bioconductor package (
    2. flow cytometry using the red fluorescent nucleic acid dye SYTO17 as a counterstain to improve detection of cells with a low GFP signal
    1. has developed novel bioinformatics software called OliVar, which allows researchers and assay developers to automate and design assays that target regions of the virus genome that have the lowest frequency of mutation
    1. mRNA-1273 vaccine candidate, manufactured by Moderna, encodes the S-2P antigen, consisting of the SARS-CoV-2 glycoprotein with a transmembrane anchor and an intact S1–S2 cleavage site. S-2P is stabilized in its prefusion conformation by two consecutive proline substitutions at amino acid positions 986 and 987, at the top of the central helix in the S2 subunit
    1. Lithium Acetate Borate (LAB) buffer is an agarose gel electrophoresis media for DNA gels

      Lithium and Borate are both teratogenic (reproductive toxicity).. Is it worth the risk?

    1. Cell densities achieved with TB were over 3 times greater than those seen with the most commonly used broth, LB, and DNA yields were 2.5 fold higher

      high cell density => blocks spin columns?

      Have you observed that?

    2. SOC is added to E. coli cells to aid recovery after exposure to high salt concentrations and heat shock in many chemical-based DNA transformation protocols

      Elbing and Brent, 2002, Green and Sambrook, 2012

    3. In this study, we have quantitated yields of low copy and single copy number plasmid DNAs after growth of cells in four widely used broths (SB, SOC, TB, and 2xYT) and compared results to those obtained with LB, the most common E. coli cell growth medium

      TB (terrific broth) consistently generated the greatest amount of plasmid DNA, in agreement with its ability to produce higher cell titers. The superiority of TB was primarily due to its high levels of yeast extract (24 g/L) and was independent of glycerol, a unique component of this broth. Interestingly, simply preparing LB with similarly high levels of yeast extract (LB24 broth) resulted in plasmid yields that were equivalent to those of TB.

    1. Performcalibrations
    2. ROI/Uniformity plate

      A regions of interest (ROI) calibration maps the positions of the wells on the sample block of the Applied Biosystems 7500/7500 Fast Real-Time PCR System. The 7500 software uses the ROI calibration data to associate increases in fluorescence during a run with specific wells of the plate. The instrument uses a set of optic filters to distinguish the fluorescence emissions gathered during runs. You must generate a calibration image for each individual filter to account for minor differences in the optical path.

      ABI 7500 manual:

    3. Custom dyes must excite between 455–672 nm and emit between 505–723 nm.
    1. occupy the fill scale with a slightly darker version of the palette used for color.

      Using colorspace package.

      geom_boxplot(aes(color = season, fill = after_scale(desaturate(lighten(color, .6), .6))), size = 1)

    1. All the existing color palettes are available in Paletteer. Just specify the package and palette names to use!

      Ggplot, color palettes

    1. We report the preclinical development of BNT162b2, a lipid-nanoparticle (LNP) formulated N1-methyl-pseudouridine (m1Ψ) nucleoside-modified mRNA (modRNA) vaccine candidate that encodes P2 S with a native furin cleavage site resulting in the S1 and S2 cleavage fragments
    2. To generate the template for RNA synthesis, a DNA fragment encoding the SARS-CoV-2 P2 279 S protein (based on GenBank: MN908947), including the amino acid exchanges K986P and 280 V987P, was cloned into a starting plasmid vector with backbone sequence elements for 281 improved RNA stability and translational efficiency19,34


    1. The pBHR1 plasmid is a derivative of the small (2.6-kb), mobilizable broad-host-range plasmid pBBR1, which was isolated from the gram-negative bacterium Bordetella bronchiseptica


    1. Antibiotics, according to strain sensitivity, were used at the following concentrations: tetracycline 2 μg/ml for Rm1021, BM7, BM299 and BM300, 4 μg/ml for LMG18864, 10 μg/ml for other Sinorhizobium strains and for E. coli; streptomycin 600 μg/ml and kanamycin 200 μg/ml were used for Rm1021; kanamycin for E. coli S17.1 was used at 40 μg/ml; gentamicin was used at 20 μg/ml for all strains
    2. All Sinorhizobium strains were grown in TY medium (Beringer, 1974) at 30 °C

      TY contained, per litre, 5 g Difco Bacto- Tryptone, 3 g Difco Bacto-yeast extract and 1-3 g CaC1,.6H20.


    1. The slopes and efficiency for the SARS-CoV-2 standard curves were not consistent over time, confirming the need to include a standard curve each run rather than using a single curve for multiple plates.

      Is the standard curve performed with matrix or in pure water?

    1. Look at filmmaker Anubhav Sinha’s last three films. He went for Muslim minority story (Mulk) then he went to do a Dalit-related, anti-caste-related story in Article 15, and now he has gone for domestic violence (Thappad). He has touched religion, caste and gender.
    1. Combining acetate with borate retains the deficiencies of both

      This is counter to the argument that the combination works well - https://bitesizebio.com/25078/faster-even-cooler-dna-gels

      • The article recommends a pH of 6.5, which was the best pH found for sodium borate buffers in this paper
    1. The voltage is kept low, ∼10 V/cm, where cm refers to the length of the gel

      This is wrong - the cm refers to the inter-electrode distance. It is a misonomer that people confuse it with the length of the gel

    1. Between them, the three buffers cover all of the molecular biologist’s DNA gel needs
  8. gmo-crl.jrc.ec.europa.eu gmo-crl.jrc.ec.europa.eu
    1. Since most of the power produced in the electrophoretic process is dissipated as heat the following detrimental effects can result: • an increased rate of diffusion of sample and buffer ions leading to broadening of the separated samples • the formation of convection currents, which leads to mixing of separated samples; • thermal instability of samples that are rather sensitive to heat (e.g. denaturation of DNA) • a decrease of buffer viscosity hence a reduction in the resistance of the medium
    1. Using a lower concentration running buffer (0.25x TAE) and higher voltage (300 V), agarose gels can be run 33% faster.
    1. found that the P R promoter from rhizobial phage 16-3 was active in M. extorquens and engineered the promoter to be inducible by either p-isopropyl benzoate (cumate) or anhydrotetracycline. These hybrid promoters, P R/cmtO and P R/tetO, were found to have high levels of expression in M. extorquens with a regulatory range of 10-fold and 30-fold, respectively
    1. Currently, the majority of quorum sensing systems used in synthetic biology rely on self-produced small molecules that result in spatially and temporally self-organized systems, which can not be easily externally regulated

      Why can't the LasI or LuxI proteins be inducible?

    1. All replication in R6K relies on the two essential components of a minimal replicon, the γ ori, and its cognate Rep, π protein, encoded by the pir gene
    1. appropriately selecting sets of functionally redundant species and adding their abundances can help identify environmental drivers of microbiome composition

      The set of functionally redundant species will be specific to the environmental parameter in question and members could possibly be present in multiple functional groups corresponding to different parameters also.

      For example: When looking at nitrate level, species A,B,C are the same functional group, for sulphate species B, D, E are same group, for early colonizers A, D, F etc.

    2. in most conceivable cases, we study a particular microbiome in order to understand, predict, and potentially control its functioning, with no particular regard for species content.

      this is profound

  9. www.jstage.jst.go.jp www.jstage.jst.go.jp
    1. Since currentanalytical technologies for genes and metabolites provideonly a “snapshot” information at the time of measurement,temporal shift s in plan t an d microbial physiologies hav e bee na majo r obstacl e to detaile d analyses. Therefore, a stabl e syn‐thetic system may facilitate clearer investigations of plant-microbe interactions, leading to unique insights in this field

      snapshot vs dynamic information

    1. Vibrio natriegens strain containing a major extracellular nuclease knockout and insertion of an IPTG-inducible T7 RNA polymerase cassette for expression of genes under a T7 promoter.

      dns nuclease- (Gibson et al)

    2. For best results, use only LB-Miller agar plates. Do not use LB-Lennox or LB-Luriaplates (Vmax™ growth will be suboptimal).
  10. Nov 2020
    1. Here we present a detailed, genome-wide transcriptomics and proteomics dataset of E. coli grown under 34 different conditions. Additionally, we provide measurements of doubling times and in-vivo metabolic fluxes through the central carbon metabolism

      34 different conditions:

      We manipulate concentrations of sodium and magnesium in the growth media, and we consider four different carbon sources glucose, gluconate, lactate, and glycerol. Moreover, samples are taken both in exponential and stationary phase, and we include two extensive time-courses, with multiple samples taken between 3 hours and 2 weeks