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  1. Last 7 days
    1. If that is too limited, you need to use a nested or split workflow

      One issue is group_map removes the name of the group from the list output

      When information of grouping variables are important, I prefer using tidyr::nest %>% purrr::map instead of groupmap. The document also recommends to use nest or split when functionalities of group* are too limited (?group_map). https://github.com/tidyverse/dplyr/issues/4531

    1. o perform multiple replacements in each element

      This should be clarified better. It means swapping multiple different patterns with their corresponding replacements within each element

      This can be taken to mean

      • multiple replacements of a single pattern
  2. Aug 2020
    1. ultimate conclusion of the thesis reads “the unknown virus lead to severe pneumonia could be: The SARS-like-CoV from the Chinese rufous horseshoe bat.

      Does the fact that the Crux of the thesis was not published in a peer reviewed paper suggest that the evidence was more strong enough for the conclusion or there were other reasons not to publish?

    1. However, we recommend that other qPCR targets, including the RdRp or envelope (E) genes are used for the routine detection of 2019-nCoV

      What's the reason for this recommendation? Is it because the S gene could mutate further complicating detection efforts?

    1. The relationship between this diversity and the invasion of antibiotic resistance was investigated using a dilution-to-extinction approach coupled with high-capacity quantitative PCR

      It seems likely that both diversity and invasion of antibiotic resistance is regulated by initial microbial density/abundance.

      Support for the initial abundance and pervasiveness of antibiotic resistance is offered by this paper:Alexander, PNAS 2020 (Stochastic bacterial population dynamics restrict the establishment of antibiotic resistance from single cells)

      It is not clear from the fig5 but seems like the paper only tested for microbial abundance at the measurement timepoint as a confounding variable, and not initial abundance.

    2. showing the relationships of ARG abundance with OTU richness, diversity andevenness.

      Is this combining all conditions and all days?

    3. Bars represent averages of four replicates

      Standard deviations were not reported?

    4. Little is known, however, about the barriers that microbial diversity provides against microbial invasion

      Not true. There are a lot of studies on colonization resistance in gut bacteria

    1. we measured the relative abundance of dead cells in cultures of the resistant strain grown at sub-MICR concentrations of streptomycin

      Have you measured the same for sensitive cells as well?

  3. Jul 2020
    1. LoD = LoB + 1.645(SD low concentration sample)

      LoD is the lowest analyte concentration likely to be reliably distinguished from the LoB and at which detection is feasible. LoD is determined by utilising both the measured LoB and test replicates of a sample known to contain a low concentration of analyte.

      LoB is the highest apparent analyte concentration expected to be found when replicates of a blank sample containing no analyte are tested.

      LoB = meanblank + 1.645(SDblank)

    1. Formula for Calculating Concentration
    2. There is a simple mathematical relationship between the fraction of droplets that are unoccupied (black bar) and the concentration of target molecules.
    3. the concentration is calculated based on the fraction of droplets that is empty (that is, the fraction that does not contain any target DNA).
    4. Some droplets are lost in transfer steps and others are eliminated by the stringent metrics applied by QuantaSoft Software as the droplets pass through the Droplet Reader, resulting ultimately in data from 12,000–16,000 droplets being used in subsequent concentration calculations
    1. Mathematical Analysis of Copy Number Variation in a DNA Sample Using Digital PCR on a Nanofluidic Device.
    2. An estimate of par-titioning error can be found based on the analysis of Dube et al.,39 which models the partitioning as a binomial process.
    3. Digital assays have two sources of error: subsampling error and partitioning error
    4. Partitioning the sample into small containers results in a statistical distribu-tion of targets
    5. because it measures indi-vidual molecules rather than an ensemble concentration
    6. purifying the target of interest from interfering compounds.
    7. Subsampling error sets the lower detection limit at low concentrations and is independent of the instrument, while partitioning error domi-nates at high concentrations and may depend on the sampling and partitioning instrument
    1. The average number of droplets read for each ddPCR was 13,825 with a standard deviation of 1,892 droplets
    2. NTCs showed a low-level background signal of approximately three positive droplets per NTC assay, which could possibly be attributed to low-level template contamination during the preparation of the reaction mixture
    3. simple calibration procedure generated an instrument-specific color compensation matrix that was subsequently stored on the droplet reader and automatically applied to data to eliminate cross talk between FAM and VIC labeled probes.
    1. Poisson distribution can be used in place of other standard curves to determine template concentration, which means that data can be reliably obtained from the same samples across multiple instruments and laboratories.
    1. minimizing the need for local variables

      This makes it harder to debug

  4. Jun 2020
    1. We recommend the following changes to the default settings when designing ddPCR assays:

      Primer3 : designing primers and probes for ddPCR

    1. the lowest copy number sample points impacted faster and sronger, then you just need to stabilize by adding a neutral nucleic acid background in your standard curve. I usually use water containig 10ng/microl yeast tRNA to perform serial dilutions. This will first create a reaction background similar to your RTQPCR reaction, but also stabilize your DNA copies; I can freeze and thaw (min 20C) more than 50 times the same standard curve sample without any loss in Cts, from 10E6 to 10E2 copies. When I tested the same standard curve but diluted in water only, then the 10E2 started to be slightly affected after one freeze and thaw and then crashed further; then higher copy numbers samples were also affected after 2 to 3 freeze and thaw.
  5. www.gene-quantification.de www.gene-quantification.de
    1. t is important that the threshold is set at a fixed level for all samples that are to be compared
    1. If you use an inter-plate calibrator for each different GOI and reference gene, then you would have the rationale to use a different threshold for each target and ref. gene on each different plate.

      Best way to rule out possible variability between different qPCR experiments is to use a day to day control. Ideally a cell line cDNA that could also be used as a positive control for other target genes. You simply include this sample in each plate and set the treshold line so that you get identical CT values after each run. Korcan Ayata University of Basel

    1. In most programming languages, you can only access the values of a function’s arguments. In R, you can also access the code used to compute them. This makes it possible to evaluate code in non-standard ways: to use what is known as non-standard evaluation
    1. a single TaqMan Fast Virus 1-Step Master Mix protocol has been developed to assay both types of nucleic acid, so you can perform RNA and DNA virus queries next to each other on the same plate using the same handling steps

      All 1 step RT-qPCR can detect DNA right? What's special about this?

    1. The present study identifies the best assay for norovirus GI and GII to amplify norovirus genomes efficiently.

      Why don't you summarize about the best study in the abstract?!

    1. A known copy (104/reaction) of Oncorhynchus keta (O. keta) was added in the DNAse and RNAse free water and the Cq value obtained acted as a reference point. If the Cq value of a wastewater sample increases compared to the reference Cq value, the sample is considered to have PCR inhibitors.

      Was this RNA or DNA that was spiked in?

      • O. Keta is a salmon fish
      • The reference cited here (Haugland et al., 2005) uses a DNA standard of O.keta 16s rRNA gene
  6. May 2020
    1. adjusted for the time lag, the virus RNA concentrations were highly correlated with the COVID-19 epidemiological curve (R2=0.99) and local hospital admissions (R2=0.99)

      The correlations are made with smoothed data - which is misleading

    1. The Rn value, or normalized reporter value, is the fluorescent signal from SYBR Green normalized to (divided by) the signal of the passive reference dye for a given reaction. The delta Rn value is the Rn value of an experimental reaction minus the Rn value of the baseline signal generated by the instrument. This parameter reliably calculates the magnitude of the specific signal generated from a given set of PCR conditions
    1. observed discrepancies among RT-qPCR N1, N2 and N3 assays for several water samples in agreement to a previous report (Medema et al., 2020)

      Which is the most sensitive?

    1. But if we do not lift the lockdown with immediate effect, we shall be confronted with mass ruin and a breakdown of all our structures — social, economic and emotional.

      Do we have measures in place to prevent the burst of infections expected to happen post lockdowns?

      Or does it come down to choosing between the lesser of two evils?

    1. Rosario et al. recovered between 63 and 77% of spiked PMMoV in treated wastewater using centrifugal ultrafiltration

      From seawater

    1. Although unnecessary for simple singleplex amplifications, spectral calibration is critical for multiplexed assays so that overlapping fluorescent signals can be resolved from one another.
    1. to concentrate the viruses, the 1‐l aliquot was acidified with 1 mol l−1 acetic acid to pH ~3·0 and then viruses were filtered onto a 47‐mm, 0·45‐μm HA negatively charged nitrocellulose filter
    1. PMMoV concentrations vary over space and time, 106 to 1010 gene copies per liter of domestic wastewater are consistently detected
    2. By far, the most abundant RNA virus identified in the feces of healthy individuals was PMMoV [6], which has also been readily identified in untreated wastewater from numerous locations
    1. may be due to bacterial extracellular enzyme activity and protozoan or metazoan predation

      Protozoa grazing on viruses - as a nutrient source?

      Evidence- Grazing by marine nanoflagellates on viruses and virus-sized particles: ingestion and digestion (Marine ecology press, 1993

    2. Samples were spiked to achieve final virus concentrations of 5 × 104 PFU mL–1 for MHV, and 6—8 × 105 PFU mL–1 for ϕ6, MS2, and T3—these were low enough to be feasible concentrations present in wastewater (<106 PFU mL–1)

      Why is this different for the different viruses and how these concentrations were determined?

    3. The spiked samples were stirred and then incubated at 4 °C; this temperature is at the low-end of mean municipal wastewater temperatures in the U.S.

      Adsorption is lower at low temperatures - So the value here is the least adsorption possible?

    4. Likewise, methods to concentrate and recover nonenveloped enteric viruses from wastewater and other environmental matrices may not be suitable for enveloped viruses.

      This makes sense if the goal of the extraction is to get intact viral particles.

      Does it make as much of a difference if only viral nucleic acids are detected?

      • Other than partition into solid phase that might reduce enveloped virus in both detections
    5. a SARS coronavirus outbreak in an apartment complex in Hong Kong was attributed to the transport of viruses in wastewater to the air ducts

      transport of aerosolized virus from flushing the toilet

    6. and some enveloped viruses were measured in wastewater biosolid residuals

      only the genetic material of some enveloped viruses was detected in the paper cited here (10)

    1. Powdery mildew is a common disease which affects a wide variety of vegetable crops including eggplant, peppers and tomatoes, all in the nightshade family
    1. All assays 36testedwere found to be highlyspecific for SARS-CoV-2, with no cross-reactivity with other respiratory 37viruses observed in our analysesregardless of the primer/probe set or kit used.

      This is a misleading statement considering the narrow range of other respiratory viruses tested. Corman et al's primers were designed to be broad enough to detect multiple bat CoVs and SARS-CoV1 in the sarbecovirus lineage

      This collection includes samples positive for: rhinovirus (3 samples within the set), influenza B (2), influenza A (2), parainfluenza virus 1 (1), parainfluenza virus 3 (2), parainfluenza virus 4 (1), adenovirus (2), metapneumovirus (1), bocavirus (2), respiratory syncytial virus (2), and coronavirus (25). The coronaviruses included in the sample set are non-SARS-CoV-2 samples

    2. Of the 217sevendifferent primer/probe sets and one testing kit that we evaluated, all were found to be highly 218specific withno false positive results observed when assays were run on samples positive for a number 219of other respiratory viruses.

      E gene, annotated as sarbeco gene in the Corman et al was designed to detect the sarbeco family of viruses which includes SARS-CoV1 (since they did not have SARS-CoV2 samples to test with)

    3. we evaluatedassays using sevendifferent primer/probe setsand one assay kit

      We found that the most sensitive assays were those that used the E-gene primer/probe set described by Corman et al. [Eurosurveillance 25, 2020] (https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000045) and the N2 set developed by the CDC

    1. ice nucleation activity of A. tumefaciens(pAHL-Ice) remained stable for up to 20 h when cells were incubated in the presence of oxo-C6-HSL

      What sets the 20 h limit?

    1. Our results demonstrated that the predicted T90 (time for 90% inactivation) of Phi6 under the 12 evaluated conditions varied from 24 min to 117 days depending on temperature, biological activity, and aqueous media composition.

      Persistence measured by counting invective viral plaque forming units

    1. The period from the beginning of antibiotic treatment (50 to 60 years ago) to the emergence of bacteria expressing effective resistance mechanisms is too short to explain the development of resistance factors from other proteins by spontaneous mutation

      Interesting thought - applicable for complex mechanisms of resistance involving a totally new function or involving multiple proteins

      cooperative action of several proteins (e.g., vancomycin resistance) the de novo generation of such a resistance mechanism in the pathogen is very unlikely

      Other simpler mutations - efflux pumps gaining affinity to the antibiotic, mutation of the target protein (rpsL ribosomal mutations) are more likely to occur on short timescales

    1. plasmid fitness benefits in multiple phylotypes

      Is there experimental evidence suggesting fitness benefits here?

      This statement should rather be lack of fitness burden maybe?

    2. To persist, plasmids lacking stringent post-segregational killing systems thus depend on one or both of two mechanisms: fitness cost amelioration and horizontal transfer

      Plasmids lacking stringent segregation regulation but having no fitness cost would persist in quite low fraction of the population?

    1. The harsh environmental conditions found on leaf surface require high metabolic performances of the bacteria in order to survive.

      Why is it harsh?

    1. Remove secreted beta-lactamase from the starter cultures. This can be done by pelleting and re-suspending the starter culture in fresh, antibiotic-free medium before innoculating the main culture.
    1. These and other breakthroughs promoted a feeling of optimism that, with the tools of quantum mechanics, the secrets of life could finally be laid bare.

      What is the connection between the microscope, X-ray mutagenesis, ultracentrifugation and quantum mechanics? It should be made more clear

    1. Scientist's Guide to Poster Presentations, by Peter J. Gosling; Preparing Scientific Illustrations: A Guide to Better Posters, Presentations, and Publications, by Mary Helen Briscoe; Displaying Your Findings: A Practical Guide for Presenting Figures, Posters, and Presentations, by Adelheid A. M. Nicol, et.al.
    1. Fourth, a minimal insert region (amino acids 310 to 518) was found to be sufficient to convert the SL-CoV S from non-ACE2 binding to human ACE2 binding, indicating that the SL-CoV S is largely compatible with SARS-CoV S protein both in structure and in function

      193 amino acids in a 510 amino acid protein is by no means minimal. It constitutes 40% of the protein

      • Also there seems to be a typo here. The paragraph below says 318 - 510 is the receptor binding domain
    1. a minimal insert region (amino acids 310 to 518)

      193 amino acids in a 510 amino acid protein is by no means minimal. It constitutes 40% of the protein

    2. It only takes a few changes ("exchange of a relatively small sequence segment") between two coronaviruses to result in a third coronavirus that can infect other animals ("host-switching")

      This cannot be said based on the above paper since one of the recombining fragments was the human infecting SARS-CoV itself.

      It should instead read as "it only takes a few changes to a coronavirus to result in a novel variant that can infect other animals"

    3. The odds of this happening are pretty good!

      There is no mention of the odds of such an even happening in the paper so this conclusion is misleading and not based on evidence

    4. it is equally possible that the virus originated somewhere else entirely

      If this is equally possible then why is the seafood market origin "unlikely" in the rest of this article?

    5. While Mr. Fu here seems to believe the virus originated from the market, we know from the Lancet study that it is unlikely

      It should not be struck down as unlikely, just because there is another possibility that is equally likely (stated 2 paragraphs above)

    6. Because 34% of cases did not have exposure to the market yet were exposed to the virus, it is highly unlikely the market is the origin point of SARS-CoV-2

      This claim is poorly made and not backed up by alternative explanations. It is quite plausible that the 66% who were exposed in the market transmitted to others through asymptomatic contacts who could not be epidemiologically traced

    7. meaning that the first patient at the market was not responsible for spreading the virus to other cases

      hasty generalization

    1. Research on enveloped virus presence and fate in water is hindered by the lack of proven detection methods. Detecting and quantifying viruses in environmental samples requires first concentrating the viruses in the sample into a smaller volume to improve detection limits
    1. virus-loaded filters were rinsed with an acidic solution to eliminate remaining cations before elution with NaOH or other alkaline buffers

      Elution with alkaline buffer only works when using negatively charged membranes. ion exchange chromatography?

    1. The 1MDS-method and the HA-method did not provide as high recovery yields of the virions as the Mg-method.

      The reason for this could be the beef extract used to elute the virions from both these membranes. The other two successful methods (Mg and Al) used H2SO4 for elution.

    1. low-pathogenic viruses often acquire multiple basic amino acids at the HA cleavage site, which is recognized by ubiquitous cellular proteases such as furin and PC6

      Why the emphasis on basic amino acids, are they more prone to protease activity?

  7. Apr 2020
    1. . When E. coli metabolizes Collilert-18’s nutrient-indicator, MUG, the sample also fluoresces. It is reported that the method is able to detect a single viable coliform or E. coli per sample
    1. The daily flow rate of wastewater was calculated as a point estimate using the product of the at-home population in the catchmentofapproximately 600,000 persons(capita), andthe observed average per capita wastewater rate of 250 L/person/day

      Isn't the daily flow rate of wastewater directly measurable in the treatment plant?

    1. a defined quantity of a nonhuman control virus (seal herpes virus [SHV], kindly provided by H. G. M. Niesters, University of Rotterdam, The Netherlands) was spiked into each sample prior to DNA and RNA extraction. Since constant DNA quantities of the control virus are coextracted even when RNA isolation kits are used (H. G. M. Niesters, personal communication; our own unpublished observations), the virus can also serve as a control in RNA virus detection assays.
    1. We investigated the biodistribution of SARS-CoV-2 among different tissues of inpatients with coronavirus disease 2019 (COVID-19)

      It would have been good to include 2-3 negative control samples in the data

    2. Four SARS-CoV-2 positive fecal specimens with high copy numbers were cultured
    1. scientists have found limited instances of infectious virus in fecal matter

      Did people test in spit or nasal secretions which would also be inside wastewater?

    2. wastewater monitoring in Israel, for example, picked up a polio outbreak before any clinical cases appeared at all, according to a 2018 study.
    1. However, using metabolites as reporters requires more precise control than what is necessary for most metabolic engineering applications, since small amounts of enzyme can produce visible amounts of pigment and overproduction of certain metabolites can be toxic to the cell.

      Is this amplification the result of the multi-step pathway? Is beta-galactosidase + x-gal not a good single step substitute for generating blue colouration?

    2. In this paper, we designed a system that could fully repress lycopene production in the absence of an inducer and produce visible lycopene within two hours of induction. We engineered Lac, Ara, and T7 systems to be up to 10 times more repressible, but these improved systems could still not fully repress lycopene. Translational modifications proved much more effective in controlling lycopene. By decreasing the strength of the ribosomal binding sites on the crtEBI genes, we enabled full repression of lycopene
    1. the paper-based device has the potential to be used as a small, portable device to detect SARS-CoV-2 in wastewater on site

      Zhugen Yang's Sensors lab seems to be making these devices for CoV2 - https://www.cranfield.ac.uk/press/news-2020/wastewater-test-could-provide-early-warning-of-covid-19

    1. Although infective SARS-CoV-2 has not yet been confirmed in stool samples, the SARS-CoV-2 RNA shedding pattern suggests viruses are replicating in the GI tract

      Four SARS-CoV-2 positive fecal specimens with high copy numbers were cultured

      Source: Wang, Wenling, et al. "Detection of SARS-CoV-2 in different types of clinical specimens." Jama (2020).

    2. Viruses have a direct connection to wastewater and drinking water purification when they are excreted in feces or urine

      How does this compare with spit and nasal secretions which also connect to the wastewater? Is this a bigger source of viral particles in the case of a respiratory virus?

    1. colonization by this strain does not require pre-administration of antibiotics

      This has only been demonstrated in the immune compromised IL-/- and 129X1/SvJ strains right?

    2. Detection of tetrathionate in the presence of fluctuating and low-level inflammation that remained below histological detection further demonstrates the ability of PAS638 to detect a subclinical inflammatory environment.

      This is a poorly backed statement. How did you assume that it is detecting tetrationate?

      If you don't understand why there is inflammation in this mouse model and you have not not been able to locate inflammation by histology, you should have measured the tetrathionate by other methods as in fig 2C.

      Otherwise this statement sounds like a circular logic to support the use of this new tool while trying to verify its function.

    3. this concentration is on the order of the in vitro EC50 of our sensor

      Which might not be desirable if the goal is to detect with high sensitivity right?

    4. ability to turn off memory under repeated streaking

      Why is memory turning off?

    5. E. coli strain NGF-1

      Isolated from BALB/c mice. Colonizes gut atleast 6 months even post modification

      Source: Escherichia coli NGF-1, a Genetically Tractable, Efficiently Colonizing Murine Gut Isolate, 2018

    1. A few points to summarize and comment on part one

      1. Community relationships vs arms-length transactions

      The benefits of reliance on community relationships with lesser emphasis on finances are clear when there is a close knit group. When applied to large communities with disparate groups, it translates to the creation of castes/subcategories, disparate advantages to the socially powerful creating a powerful feedback loop to sustain power, nepotism and other evils. There are successful examples showing the benefits of banking on the community such as Grameen bank's microfinance business model by Mohammad Yunus

      1. Direct payments by insurance creating a disconnect between the patient and the cost
  8. watermark.silverchair.com watermark.silverchair.com
    1. According to a 2013 report by the American Academy of Microbiology (AAM), How Microbes Can Help Feed the World,
    1. More than a dozen research groups worldwide have started analysing wastewater for the new coronavirus as a way to estimate the total number of infections in a community

      This article lacks references :(

      1. Netherlands - Presence of SARS-Coronavirus-2 in sewage - medRxiv
    2. de Roda Husman’s group detected traces of SARS-CoV-2 in wastewater at Schiphol Airport in Tilburg only four days after the Netherlands confirmed its first case of COVID-19 using clinical testing

      Source: Lancet30087-X/fulltext) correspondence, April 1, 2020 - SARS-CoV-2 in wastewater: potential health risk, but also data source

    1. ultrafiltration method resulted in mean recoveries (±SD) of 25.1% (±3.6%) and 18.2% (±9.5%) for the enveloped MHV and ϕ6, respectively

      The efficiency here is measured by the functional viral particles (using plaque assays).

      • It is not relevant if the internal standard is solely for PCR based viral measurements
    1. The SARS outbreak was fueled by bioaerosol generation during the collection and transport of sewage that allowed for distant disease transmission (Roy and Milton, 2004; Yu et al., 2014)

      movement of SARS-contaminated sewage through the floor drains generated high concentrations of aerosolized virus that remained virulent and of sufficient dose to cause infection after airborne travel a considerable distance from the original source

    2. wastewater treatment disease transmission studies from that time did not usually consider respiratory pathogens.

      During the 1980s, there were few pathogens that were both known to initiate infection in the lungs and frequently occur in wastewater (U.S. Environmental Protection Agency, 1980). It was viewed as an anomaly if an enteric pathogen was “uniquely infectious by the aerosol route”, with the noted exception of the respiratory bacterium Mycobacterium tuberculosis



    1. To collect, process, and act on information, cells must be able to accurately record signals.

      This premise needs more substantiation. Why do we need to study memory devices

    1. the number of ionized water molecules is so low (1.0 X 10-7 mol in 1000 mL water)

      Ss this value derived, measured or is it a covention?

    1. dA-tailing to add an “A” base to the 3′ end of the fragment
    2. Sequencing begins at the single-stranded 5′ end of the Y adapter, followed by the “template” strand
    1. In an attempt to mitigate the problem of DNA from inactive cells influencing microbial analysis, molecular techniques have been developed to remove or bind the extracellular DNA prior to cell lysis

      Are inactive cells considered to be dead and lysed such that they release their DNA extracellularly?

      • Is there a possibility of intact but inactive cells?
    1. It is unlikely that colistin pressure in the environment and animals, especially in water environment, may be the only cause of the existence of such an ubiquitous presence of these enzymes that could be mobilized within bacteria.

      Is it possible that the gene exists in the population by being neutral - imposing no burden and causing no benefit?

    2. Our innovative approach, i.e. massive genome analysis, appears to be a powerful tool and a new concept that opens a new field of big data analysis and research

      Is this massive genome search a new concept? I feel that it is too simple to have not been done before. Also innovative does not sound like the right adjective for this work

    1. in bacterial communities where prior evolution led to greater persistence of conjugative plasmids encoding resistance to different antibiotics, we expect the likelihood of hosts acquiring multiple distinct plasmids to be higher, thereby priming the emergence of MDR.

      The plasmid persistence enhancing mutations discussed here are either specific to the plasmid system (conjugation, post segregation killing) or the specific antibiotic resistance mechanism (cost alleviating mutations in the genome).

      Does this mean that evolving for persistence of 1 plasmid does not necessarily enhance the persistence of a different plasmid

    1. Conclusion

      The contribution of the microbial characterization to this conclusion seems very meager. Was it really worth performing?

      Considering that the two main takeaways from this study have already been established in literature cited in this paper, what exactly is this paper adding to the body of scientific knowledge and understanding?

      1. Higher denitfication rates in I. pseudacorus could be explained by higher root exudate release
      2. Higher nitrification rates in P. australis can be explained by higher oxygen release from roots
      3. The microbial diversity between both the plants is different but there is no explanation as to how it is linked to the nitrification-denitrification rates
    1. The assays detected IgG antibody to HIV-1

      What is the antigenic epitope of these antibodies that were detected?

    1. pharmacological studies indicate that essential oil of garlic is an exceptional source of organosulfur compounds, possessing strong antioxidant, antibacterial, antifungal, anticancer, and antimicrobial properties


    2. As mentioned above, the high organosulfur compounds in garlic essential oil are expected to have strong interactions with the amino acids of the ACE2 protein

      Why are organosulfur compounds expected to interact strongly with ACE2?

      I did not find any previous reference to this as mentioned in here

    3. The fact is that the study of HIV-1 resistance to reverse transcriptase inhibitors was reported by Tarasova et al

      how does this fit into this paragraph? I did not understand the context

    1. One option is to treat it as a nominal variable with five (or seven, or however many) items

      Why is it not a ranked variable instead?

    1. if you depend heavily on Google Doc for writing, or read primarily on a synced mobile device, then unfortunately it will be difficult to use.

      Zotero has google docs support now and it works decently as far as I have seen. I haven't tested it in large documents with many citations but I have heard there might be difficulties

    1. Would the ingestion of probiotic cultures, which may act as donors or recipients, therefore increase the antibiotic resistance gene pool in the enteric ecosystem?

      How would the resistance gene pool increase if ingested cultures act as recipients?

      • Most of the ingested microbes do not colonize the enteric ecosystem right?
    1. Variability in the components of complex samples such as blood can affect the readouts

      Especially difficult to account for, when the components of the matrix vary between tests. Does blood components vary from person to person enough to complicate measurements?

    2. a parallelized calibration scheme that uses the patient sample to generate custom reference curves

      This great idea for on site calibration is what is converting a qualitative colour output into a quantitative output!

    1. DOC causes a significant decrease in the signal when evaluating flavonoids having three (naringenin) and four (luteolin) hydroxyl groups, but not with a flavonoid having five hydroxyl groups (quercetin)


    2. various flavonoids have distinct chemical properties and functional groups, these mechanisms have the potential to differentially affect flavonoid movement through the soil matrix

      Why were flavinoids chosen? There are other below ground communication molecules as well that can be chosen like strigolactones

      the interaction between plant roots and mycorrhizal fungi depends on diverse secondary metabolites, including strigolactones and terpene lactone carotenoid derivatives. source: Ref 6

    3. few studies have considered the influence of abiotic environmental parameters on the efficiency of signal transmission through soils.

      Maybe because they are likely to be non-specific?

    4. signaling repression occurs between dissolved OC and flavonoids

      What is the mechanism?

    1. In the biosensor, the promoter regions of lasI, rhlI, pqsA, and ambB (QS genes) controlled the fluorescent reporter genes of Turbo YFP, mTag BFP2, mNEON Green, and E2-Orange
    1. however, their presence in cosmopolitan thermophilic phototrophic mats remains largely unknown

      That is not a satisfactory reason for studying them

    1. intelligent

      Claiming a certain thing as 'intelligent' is in itself not falsifiable.

    2. All cities are designed, in that they are the product of human minds

      This is a pedantic argument. The author means that there is no central top-down design in many cities. Those cities come up by actions of small agents, which is design by human agents but decentralized.

    3. The falsification of intelligent design is Darwinism. The falsification of Darwinism is intelligent design.

      This is a fallacy. Falsification of darwinism is by no means supporting intelligent design. This two are not mutually exclusive.

    1. Soil moisture content, if determined by rainfall, will vary temporally at scales from minutes to months, and changes in community composition will only occur for those organisms that react at the same time scales.

      Important idea of time-lag of cause and effect relationships

    2. Most are descriptive, do not address scientific aims or questions and are not designed to increase understanding or test hypotheses.

      Wow, that is a bold statement!

    1. In this review, the most common traditional techniques, such as cyclic voltammetry, chronoamperometry, chronopotentiometry, impedance spectroscopy, and various field-effect transistor based methods are presented along with selected promising novel approaches, such as nanowire or magnetic nanoparticle-based biosensing

      Good comprehensive review

    1. Promoter, terminator, and operator sites should be indicated as described by Bachmann and Low

      For operon abcDEF, in which abcD is the first gene transcribed, the naming would be abcDo (operator), abcDp (promoter), abcDe(leader), abcDa (attenuator), andabcDi (initiator) Linkage map of E.coli K12 - Edition 6

    1. a significant proportion of cases

      Should mention the actual number and the proportion

    1. Do the studies, make the vaccines, but allow doctors to have what they feel is working now.

      Bad suggestion. Doctors gut feeling is no substitute for clinical trials

    1. Better monitoring of coronaviruses in biofilms might be necessary to prevent outbreaks.

      What do bacterial biofilms have to do with human coronaviruses? Is it expected to stick by hydrophobic interactions?

    1. While, whathappened in Gujarat was vile and reprehensible, how does it make sense to help othercountries declare sanctions on India? Who does it hurt most?

      If certain actions cause severe punishments, is that a valid argument to hide the truth? Who does it hurt is not the right question, but who benefits from this testimony?

      Your claim is that international forces benefit, to Indian state's loss.

      Maybe in an ideal world, this works as a deterrent in the future. But it is true that the personal standing or fame of the person might have been the motive. It is a debatable decision but certainly not objectively wrong

    2. Then what do we say about those who might plot against the obscenity that blights theirland, as Stauffenberg did, who fight to free India of it? Are they patriots? If so, what ifthey welcomed a force from abroad that toppled this hypothetical regime, as many Iraqisdid? Are they still patriots?
    1. ions. The stationary continuance of the functioning of certain social institutions is easily regarded as desirable when those institutions are "explained" in terms of the-possibly vital-functions they are performing in the existing s
    1. parents are being asked to somehow work and entertain housebound children

      How big of a problem is taking care of really young children vs entertaining children > 10 y age?

    1. then it takes on any given value between f(a) and f(b) at some point within the interval

      What is the definition of 'any' given value. Is it any value in the co-domain or the range?

      I'm wondering in the context of a function that is defined on rational numbers -> real numbers. Where certain values of real numbers are not possible because the domain is restricted.

      Specific example of \(x^2 - 2\), not taking 0 because domain is restricted to rational numbers discussed here

    1. Using the median, the case fatality rate for India drops to 0.4 deaths per 100 patients, nearly ten times.

      It is unclear what the median is for. Is it statewide data within india or data for different countries?

  9. Mar 2020
    1. Cool ideas as extensions to this paper Can this be done in vivo - in the sand filter? - Zach Has anyone analysed cells with plasmid vs cell expressing the genes? - Zach Analyzing a mobilizable vs a conjugative plasmid simultaneously (or even independently) in the same community

      - The two plasmids should be identical except for the removal of self mobilizing features (that will be present on a helper plasmid or integrated into the donor)

      Does permissivity change if in a biofilm - assuming sand filters are housing biofilms?

      What are the goals of spreading a catabolic gene inside a native community?

      1. Long term residence in the community
      2. Target to organisms capable of high expression or function
      3. Residence in high abundance and highly active community members

      To maximize all these goals, we can develop a blanket strategy that combines best aspects of all Create a combinatorial library of all plasmid origins, all host organisms, transposons with your payload in it This will enable the widest possible dissemination of the desired function in the community at the expense of understanding

    1. Instead of letting the faucet run while you’re shaving so you can clean off the razor, fill up your sink with some water

      It us better to have a small container filled with water than filling up a whole sink

    1. we must abide by the voluntary quarantine rules verbatim

      Why is this quarantine voluntary? What purpose does this achieve compared to a legally enforced quarantine?

    2. Turkey’s government says it is not disclosing the location of cases to prevent the risk of increasing transmission rates by encouraging people to move from areas with high rates to places where there are no or few cases.

      I'm amused as to how many possible reasons governments come up with to not disclose data.

      I do not understand how likely people are to move between areas, do people have more than 1 housing options?

      There is an obvious conflict of interest in a government hiding information that is bound to invite questions or make their performance look poor in contrast to other countries etc.

    1. demonstrate that adapting a strain to the intended growth condition increases fitness and in turn improves the stability of the engineered function over hundreds of generations

      Does this imply that an organism taken from a native environment, modified with a plasmid and re-introduced is likely to be stable?

    2. selected after transformation and used to inoculate liquid cultures

      Would the variability be the same if the colonies were picked from a streaked plate (from glycerol stock) instead of a transformation plate?

      I would expect the glycerol stock method to have more variability, but it would be good to test

    3. While encoding the function did not measurably affect host fitness

      Could the fitness difference be finite but undetectable? In which case we can think of a multi-day competition experiment to enhance the fitness differences.

    1. There is no discussion about the presence or titres of SARS-CoV-2 in wastewater and the sensitivity of detection of the assays.

      • Considering that it is a respiratory pathogen, which rarely enters the enteric system and feaces, how much of the viral load do we expect to find in the wastewater?
      • What is the detection limit of the paper based assays in the presence of other matter from wastewater?

      Given the lack of this critical points, the article does very little to answer the question raised in the title except educate us about paper based diagnostics

      Can a Paper-Based Device Trace COVID-19 Sources with Wastewater-Based Epidemiology?

    1. but the nature of that relationship remains unstated)

      This is where icons come in handy

    2. Sentences can express many more relationships

      The assumption is that the readers have enough time to read everything

    1. the start-up (achieving 70% TN removal) was shortened from 21 days to 5 days when Anammox sludge concentration increased from 0.02 g VSS L−1 to 0.2 g VSS L−1 with 2 g VSS L−1 AS as inoculum
  10. link.springer.com link.springer.com