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

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

Improvement compared to what?

high fat high sugar diet

low fat high plant polysaccharide diet

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

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

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

Citations?

Why are organosulfur compounds expected to interact strongly with ACE2?

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

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

Why is it not a ranked variable instead?

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

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?

exploratory culture from environments

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?

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

Mechanism?

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

Maybe because they are likely to be non-specific?

What is the mechanism?

That is not a satisfactory reason for studying them

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

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.

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

Important idea of time-lag of cause and effect relationships

Wow, that is a bold statement!

Good comprehensive review

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

Should mention the actual number and the proportion

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

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

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

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

Source: https://www.rediff.com/news/2003/may/03dilip.htm

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

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

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

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

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

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

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.

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

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

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.

CRISPR on a plasmid

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?

This is where icons come in handy

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

sentence is incomplete

Who reports differences in terms of fold logs? It is very confusing what this means

What is functional group?

What is the explanation for this decline, cell death?

Should point out the exact differences between the artificial environment and the North sea

Do the multispecies experiments run parallel to the pairwise experiments?

Is it possible that presence of other species affect the growth rates and R* values of the two species in the pairwise study by unknown interactions (symbiosis?) with other species in the mixed community? .

They don't seem the same. The nanochloropsis differs by ~10 fold it looks like from figure 4

Implies that species composition upon nutrient fluctuation is not predictable

• Does this theory also imply that there is no steady state in time?

should definitely include the sample size of this study here.

There were 191 patients in total

Interesting to know that the virus has a tropism that extends beyond the lung epithelial cells into kidney epithelial cells

This report hints at this point multiple times without elaborating how the measures were draconian. This is unfair to the subject and takes away from neutrality of reporting

How did an infected household get groceries?

Does the mobilized plasmid need to have a Mob relaxase along with the OriT?

in Staphylococcus aureus

24$ per day (on 20 March 2020)

Is there any reason to assume all conjugative plasmids are not mobilizers?

Aren't all conjugative plasmids capable of mobilizing? According to the paper -

IncP, IncN, and IncW are conjugative plasmids that transfer and can be maintained in a diverse array of bacterial hosts

Is a minimal origin for IncP-1beta plasmids known?

Why would anybody represent such a high number as a %? increases by 14 fold is a much better way to represent this

Is it known that antibodies against a virus are able to protect against infection from a different family of virus?

Is the glucose secretion low or zero? Does it secrete galactose?

Wow! It is the height of foolishness from the establishment democrats if they can still not understand that their moderate-centrist policies are unable to connect with the bulk of the populace, increasingly disillusioned with status quo.

Unfortunately Bernie wasn't able to do much to broaden the party base as he was tasked to do since 2016. But there was no doubt of his intentions to unite the party when he endorsed Hillary after losing the primary as he said he would this time too. It is just plain undemocratic for the establishment to continue this attitude and blaming any outsiders bringing in new ideas, trying to connect with people (think Ralph Nader) when it is increasingly clear that they are no longer representing priorities important to the electorate.

Similar to peer review process in science? (probably applicable more so to post-publication review)

Why not invest in an android app as well? I would assume it would lead to more widespread use on personal devices

Essentially might not be easily and universally agreed upon

Each and every word of this can be debated upon.

What comes under basic infrastructure?

• I presume everyone thinks about high investment hard infrastructure like roads, rail networks, fibre optic and electric lines, airports etc.

• Are public schools and colleges included?

• Are medicare and social safety nets counted as basic infrastructure?
• Is defining criteria of intellectual property and granting patents counted?
• What about public transportation?
• Funding early scientific research?

Or do we expect all of these to be funded through charity?

3635 x g (calculated with rotor radius of 184 mm)

Does this include transit through airports on the EU of aliens originating travel from nom-EU locations?

From the paper -

we identified a PAM site in the closest proximity (within the 70 bp coverage of the MAGE oligo) and we introduced a secondary silent mutation that disrupts the nearby PAM sequence while coding for the same amino acid

Why should the community come into picture? Individual cell metabolism can also explain reduced growth yield right?

Does the proteobacterial specificity arise from the RP4 or from the donor being Psuedomonas?

Indicates that expression will occur after conjugation. This term comes from developmental biology field for genes expressed in the zygote - https://en.wikipedia.org/wiki/Maternal_to_zygotic_transition

That is quite low

Good references for bio-monitoring in situ

• Purely analytical methods, not biosensors

Other points from the same paper

• capable of monitoring the chemical properties of fermentation broths such as biomass, glucose, and protein concentration.
• infrared spectroscopy can have problems with sensitivity, for low abundance products such as protein products or substrates such as glycerol or glucose.
• fermentation broths are extremely complex and hence there might be interference?

1st order decay

double terminators

Did you test the double terminator strength against your library?

Is there any discussion on how these AHLs are affecting gram positive vs gram negative bacteria?

• AHLs are linked more often to gram negative bacteria in both production and response, so do they find these connections as well?

What is the definition of a 'cognizable' offense? Are the police allowed to interpret the definition of this term and refuse to file an FIR as we hear in the news on multiple occasions?

I found a definition and some useful information here - https://www.humanrightsinitiative.org/publications/police/fir.pdf

What is the connection of these countries to China?

• Travel?
• Trade?

Or is it just a case of random chance?

This is a very interesting fact. Anyone know different sources for this fact?

Only is a strong word, we do not know alternate scenarios

Cheapest way might not be the best or long lasting way

There are lot of shortcomings of large dams - most importantly mass migration of people

Maybe the specific olutions you are talking about are being opposed for a reason. This statement is wrong.

A problem does not have unique solution and opposing bad solutions is as important as finding good solutions or adapting the bad ones to be better

These have a whole slew of problems - especially on overpopulated areas. Look at Narmada river in India

This is a contentious link between weapons of mass restrictions and peace. Is there wide agreement about this?

Is this a significant pathway in a possible cycle in the environment? The photochemical reduction seems quite slow compared to the oxidation, there may be a much faster biotic reduction in the actual envirnoment right. Comments?

Is this really a cycle? The timescales seem very different

Fe(2) -> Fe(3) complete in 8 days and growth almost stalls after 14 days. Maybe 8-14 days growth requires the Fe(3) -> Fe(2) step and that's why its a cycle?

Timescales of this reduction are very slow compared to bacterial oxidation

Can Fe(3) also be determined easily? Would have been good supplementary information to prove that Fe(2) is being converted to Fe(3)

Why do you need light for the bacteria to oxidize Fe(2)?

• Isn't there simultaneous photochemical reduction of Fe(3) happening in this experiment?

Why is this higher than the previous experiment?

• Previous one was 0.1 mM, this is 2 mM of Fe ions

Does it make sense to fit enzyme kinetics curves to these reactions rather than join the data points?

• Might be complicated since there are multiple steps involved - Substrate import into cells, Enzymatic degratation

Also dotted lines are distracting

• Why didn't you measure Fe(3) concentrations?

This will miss any Fe compound induced gene activation a which might give higher rates to the redox reactions.

• Gene transcription and translation is not as efficient in stationary phase for most growth associated genes

This should have been reported for 54 h like the Fe(3) reduction experiment in Fig.2

?

This could also be explained by epigenetic inheritance. Basically something hereditary - either genetic or epigenetic

But unfortunately Democratic party is dead centre, and does not represent the people as much as it could

Bernie Sanders is championing the causes of the working class and had has always been consistent in his track record. It is justified to fear the ill effects of general perception of 'socialism' but it is high time the americans stop vilifying 'isms' and looking at policies for what they are, the details.

This column does a very bad job at recognizing working class issues, the same issues that got the republicans into power and Bernie Sanders had the exact mandate to really connect the democratic party with the masses, which I unfortunately think has not been successfully done

Yes, keeping investment banking and consumer banking separate is a good idea. Glass Stegall act is a good regulation to do so.

I heard economists argue on both sides of the spectrum but the main question is why is this article so motivated to paint the Sanders campaign as bad?

But a few highly skilled among them have the possibility of emigrating to Germany?

I am curious as to why German workers are more productive? Can the other EU nations implement any policies to improve their human resources likewise?

Well articulated!

That reference to computer games is awesome but the problem comes down the the fact that winners of the corporate game are influencing the rules - the corporate tax law, regulations etc.

Now this is also another problem with how the rulemakers are chosen or how the rules are made. So maybe the solution is to rectify the few rules that influence many other rules being made!

"It is like riding a white tiger" - Byrraju Ramalingaraju. Former chairman of Satyam, convicted of corporate account fudging (a similar game of artificially upholding the value of an entity - except, in this case it was illegal) Source: outlook India

Maybe the game is not exciting anymore if everyone always 'had' to play that move

Citation?

Does the host range of transfer go wider than the population where GFP is observed?

This is my idea of distinctive overlapping categories of host range as venn diagrams.

Does the leaky expression not hinder the detecting and quantification of transconjugants in epifluorescence microscopy?

This makes the objects no longer editable

Viruses are in size range of 100-500 nm. This is very close to the diffraction limit of light. How is the assumption that anything smaller than bacteria is a virus like particle justified and quantitatively accurate in this regard?

What is the % similarity? How can an abstract be so vague?

Isn't this circular logic? The testing empirical data is the same as the data used to build the model

Why is this?

That is a teleological statement.

Aren't most comics based on cultural references like hollywood that are not universal across different cultures and languages. What is a good way to relate to wider general audience?

This seems like the new thing here compared to Ref 22

It is unclear if the plates contain V2 salts or not

Why not 10% glycerol?

:) funny!

Is this true? I don't know if there is a precise and widely accepted definition of socialism but I would think that socialism is about community ownership of means of production. (I see a complex definition of socialism and capitalism here - https://plato.stanford.edu/entries/socialism/)

Community can mean the elected government, but in a local sense, it could also be adapted to mean the community that owns, operates, works-in and is frequently served by a given industry. I can think of a simple example of a coffee shop or restaurant in a small town.

Is it worthwhile to envision a society where people's motives are pre-anticipated or controllable?

I think social systems should be robust enough to account for stable functioning of society, independent of the motives and only depending on actions.

Only actions can be observed, and hence only actions can be regulated in any form of organized society and highly so in capitalism.

Workers controlling the means of production sounds like co-operative industries. This paradigm is not antithetical to 'capitalism' in the sense that there is still private ownership of the means of production. I disagree with the statement that democratic socialists do not support capitalism.

A good debate on this topic here - https://politics.stackexchange.com/questions/323/are-worker-cooperatives-socialist-capitalist-or-their-own-category

A ranked order in the plot would have been more insighful

Do you mean the same organism able to simultaneously perform or switch between the two functions of synthesis and degradation? Or does this mean sharing within the community?

How does the efficiency compare with Gibson assembly and other in vitro methods? Specifically

• # of colonies
• Fraction of successful assemblies among the colonies

Which resources?

Good guide here - https://llimllib.github.io/bloomfilter-tutorial/

How does the BIGSI method address this concern?

• Do the k-mers span between reads or
• Do you make k smaller if there is partial match at the edges of reads?

Unlike natural language where vocabulory does not change as new content is added

The search database - would be a better term

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

Could be repeated for stationary phase expression?

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