socialists do not support capitalism, meaning they want workers to control the means of production

The main priorities of different ELN features

whether shared systems of signalling synthesis and degradation

a single-tube, single-step PCR, performed in <2 hours from setup to transformation

Rice alumni with accounts on the Alumni Portal are automatically allowed to access a few of the university's licensed electronic resources through the EZproxy server

Bloom filter

if applied to raw sequence data they would only find matches completely contained within a single read.

our use case, where each new microbial dataset brings new variation

input data

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

obtained transcriptional measurements from mid-exponential-phase cultures

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

Plasmid pBBR1 thus appears to be a new member of this group, even though it resides in gram-negative bacteria and does not replicate via a rolling-circle mechanism

bind the transposon DNA at the flanking inverted repeat sequences, excise the transposon, and paste it into a random TA dinucleotide on a target DNA

J23119 is the "consensus" promoter sequence and the strongest member of the family

2-25 ug/mL

100x concentration of the initial culture.

J23100 2547

stationary-phase cultures grown in rich medium could be refrigerated for more than 1 month without substantial loss of viability

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

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

A spacer could compensate for any steric hindrance effect on recruiting the transcriptional machinery at the promoter of the next module in the assembly line; such an effect could be induced by the supercoiling that results when the transcription of the previous module is taking place. However, there is no direct evidence that this may cause a problem, and therefore the argument in favor of using a spacer remains speculative.

As his ideas have permeated the rest of the field, Sanders’s own candidacy appears less radical—or at least less exceptional.

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

do: deregulate, and fast

Gujarat often produced growth faster than the national average, fewer regulations, better infrastructure and less corruption

We are taught that we should be defined by the things other people find impressive, not by the things that bring us joy

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

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

Calling out Uncle Bot’s past vote for Trump threatens his ego and encourages him to double down on his support for the president. Self-esteem is a fundamental human need. If you want people to change their opinion, bolster their ego and help them save face

Fully explore the other person’s perspective before sharing your own to ensure you understand where they are coming from. As with all questions, follow-up inquiries should be nonjudgmental, open-ended and curious.

The concentration of GFP in the sample had been measured using a nanodrop and was ~120μM

The fundamental issue surrounding bacterial culture growth measurements is that an absorbance spectrophotometer is being asked to determine light scattering caused by particulates in suspension. In this case, transmittance is not related to absorbance in the classical sense. Under normal true absorbance conditions, spectrophotometers can be comparable to one another because the sample actually absorbs electromagnetic energy. In the case of a reduction of transmittance caused by light scattering, readings are very dependent on the optics of a specific spectrophotometer as well as the cell type in suspension

generally accepted extinction coefficients for nucleic acids are: • Double-stranded DNA: 50 • Single-stranded DNA: 33 • RNA: 40

mCherry2 might have decreased cytotoxicity in E. coli.

After all, the rise in antibiotic resistance doesn’t mean that we shouldn’t have invented antibiotics at all.

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

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

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

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

and hand control to Big Ag

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

activist groups are more likely to tap into unconscious values and emotions — like using the term “Frankenfoods” to describe G.M.O.s

a misleading focus on “high-profile savior applications” like anti-malarial and conservation efforts

compared gene drives to the atomic bomb and accused researchers of using malaria as a Trojan horse to cover up the development of agricultural gene drives for corporate profit

Local and national governments would work with regulatory organizations like the United Nations and the World Health Organization,

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

the technology was controlled primarily by the global agricultural giant Monsanto

struck most people as vaguely creepy

a weapon — say by sabotaging the pollinators that support agriculture, or by altering the genes of innocuous wild insects so they could transmit disease

Could a gene drive stop one virus only to open the way for another, more virulent one? Could it jump from one species to a related one? What would be the environmental effects, if any, of altering the genes of entire species? How about eliminating a species entirely?

Besides combating malaria, gene drives could be used to alter, or even eliminate, other disease-causing insects, from the sand flies that transmit leishmaniasis to ticks that carry Lyme disease in the United States.

power of the people is not only limited to the right of vote, but it extends further and provides us the right to participate in a democratic system by observing, suggesting and discussing, contemplating, questioning, negotiating and dissenting its system or function in various circumstances

CES (combinatorial enhancer solution). 5X CES = 2.7 M betaine, 6.7 mM DTT, 6.7% DMSO, and 55 ug/ml BSA

capable of checking multiple annealing temperatures at a time

increasing the magnesium concentration, which improves amplification

but the 5’ end is more important

relative granulocity/internal complexity (Side Scatter - SSC)

relative size (Forward Scatter - FSC)

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

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

we usually need 400-1200 colonies, it’s still easier and faster to do this manually than by colony picker. Also, colony pickers typically cost >$100K and don’t seem appropriate for our scale. 

manually analyzing the data was about as painful as waiting for the results

OCTOPUS, a light-weight, cost-effective, and robust method for full-plasmid sequence verification using next-generation sequencing

Biosensing intracellular concentrations of metabolites can provide an efficient high-throughput screen of hyperproducing strains.

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

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

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

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

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

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

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

Today, over 40% of the world’s people speak a mother tongue descended from the language of those nomads of the steppe.

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

they do not want another China

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

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

Borate, which is present in LB and SB, causes reversible crosslinks with DNA, reducing the separation of larger DNA fragments unless low % gels are made of high-strength agarose

use of the strong UAAU signal in highly expressed genes and for the occurrence of the weaker UGAC signal at several recording sites.

suggestive of protein extension, especially at UGA codons, which rely exclusively on the reduced function RF2 variant of the K-12 strain for termination

Since capitalists make money from every hour of workers’ labor, they will get increasingly rich over time, while workers won’t because they’re too busy making money for capitalists

the rich pocket, rather than reinvest, their tax cuts

should reject the influence of both liberal capitalism and communism, ideas that inspired the revolutionary slogan "Neither East, nor West – Islamic Republic!"

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

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

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

in the normal MG1655 strain that does not overproduce LacI

a few simple design principles: high expression of genetic circuits comes with the cost of low evolutionary stability, avoid repeated sequences, and the use of inducible promoters increases stability. Inclusion of an antibiotic resistance gene within the circuit does not ensure evolutionary stability.

Engineering as a practice has not, however, been successful in such endeavors as controlling the weather or avoiding natural disasters, due largely to the scale, complexity and uncertainty inherent to those problems. So we must ask: is the conventional paradigm of engineering appropriate for biology?

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

SDS in loading buffer may contribute to band smearing in precast GelRed® gels. If this occurs, we recommend using the post-staining protocol

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

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

Composition of H15 growth medium

valorization of waste chemicals accumulating in industry is one of the pillars of the circular economy and the 4th Industrial Revolution

we recommend calibrating OD using serial dilution of silica microspheres, which readily produces highly precise calibration (95.5% of teams having residuals less than 1.2-fold), is easily assessed for quality control, and as a side effect also assesses the effective linear range of an instrument.

Bacteria are less likely to develop resistance against a pro-drug as it becomes active only after getting inside the bacteria. The active components formed from the pro-drug are potent and short-lived, thus not giving the bacteria sufficient time to develop resistance.

which ends up being much less efficient

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

E. coli in 2xYT broth which takes faster (8 h) to grow compared to LB

this system enables longer duration production, and could be readily applied to burdensome or toxic products not readily produced in bacteria

Application of synthetic biology is limited by the capacity of cells to faithfully execute burdensome engineered functions in the face of Darwinian evolution

sequential lineage tracing studies aimed at unraveling the relationships between cellular precursors and mature cell types

To add a data mask so you can refer to variables in a data frame as if they are variables in an environment.

plasmid-based circuits suffer from multiple limitations: high intercellular variation in gene expression, genetic instability from random partitioning of plasmids during cell division, and plasmid loss in environments for which antibiotic use could disrupt native microbial communities or is economically infeasible

, science proceeds by the falsification and refinement of hypotheses. Thus, for most papers, the only way is down.

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

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

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

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

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

auxotrophic for specific amino acids

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

Reference values for the Z-position

5 nM fluorescein in 0.01 M NaOH was measured in black 96-well microplates

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

enquo() uses some dark magic to look at the argument, see what the user typed, and return that value as a quosure

landscape vs. portrait.

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

we present an overview of our current understanding of these rules for the genetic manipulation of prokaryotic microbes and the available genetic tools to expand our ability to genetically engineer nonmodel systems

s used fluorescein-labelled oligonucleotides as our probe for DNA delivery

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

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

This cell is the simplest photosynthetic “machine” designed by nature – an attractive foundation for manipulation

small size (hence high surface/volume ratio), which enhances its ability to compete for limiting nutrients

Such projects are not suitable for graduate students or post-docs because of the high risk involved, nor are they easily funded

genetic transformation protocols requires tedious trial and error, and methods developed for one strain are often unsuccessful in close relatives

To avoid the pursuit of unproductive paths, we report here what has not worked in our hands, as well as our progress developing a method to screen the most efficient electroporation parameters for optimal DNA delivery into Prochlorococcus cells

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

key attributes needed to produce a worthy PhD thesis are a readiness to accept failure; resilience; persistence; the ability to troubleshoot; dedication; independence; and a willingness to commit to very hard work — together with curiosity and a passion for research

key challenge is to quantify the functional roles of bacterial taxa in nature to understand how the properties of ecosystems change over time or under different environmental conditions

Hemicellulase activity was elevated in pairwise mixtures of communities that placed interacting phylotypes together (interactions, n = 9 mixtures) but not in communities that did not place interacting phylotypes together (no interactions, n = 56 mixtures)

For F-1 and J-1 students, on-campus work is limited to part-time (20 hours or less per week) during the fall and spring semesters when school is in session

tools described here can be used to mimic complex expression patterns, such as the ones found for pneumococcal virulence factors, paving the way for in vivo investigations of the importance of gene expression control on the pathogenicity of S. pneumoniae.

It is challenging to study how pneumococci control virulence factor expression, because cues of natural environments and the presence of an immune system are difficult to simulate in vitro

When you present information visually (using slides, a poster, video, handout, etc.), you must provide a full written citation.

these two highly active enzymes were functionalized with an affinity binding motif through the genetic fusion of a carbohydrate binding module (CBM) from Cellulomonas fimi with specificity to cellulose (CBM2a)

optical nanostructures, surface enhanced Raman spectroscopy, flow cytometry, etc.) have shown promise as sensitive detection methods, they typically process only small, relatively clean samples. The true bottleneck to rapid detection methods remains the separation of a target analyte from a large complex matrix.

EPA Method 1603 is an approved drinking water assay that quantifies generic E. coli

most probable number (MPN) method. The MPN is determined by serial diluting the water sample in triplicate or pentaplicate followed by incubation in selective growth media

single copy phylogenetic marker gene

known to introduce biases in composition estimates due to, for instance, variations in 16S rRNA gene copy numbers per genome

unequal efficiencies of PCR-primers in different species

Students who are less exposed to what we propose here may resist at first, simply because it is unfamiliar, but it is our experience that, overall, students will embrace and appreciate these modifications to the way assessments are conducted.

opening new paths for side effect control

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

EDTA-extractable fraction

we define the physiological and environmental parameters that mediate the transition from cooperation to competition

transient events

Illustration by Sébastien Thibault

SDS affects the oligomerization state of Aβ42 oligomers, thus providing flawed information on their order and distribution.

except for those that catalyze irreversible reactions in the TCA, such as citrate synthase

molecular explanations of whether such shifts represent cause or effect of the disease itself are limited

Graphical abstract

includes creation of innovative solutions for bio energy, resource recovery, and emerging public health concerns by leveraging synthetic or molecular biology tools, novel biological systems (genetic circuits, enzymes, genetically engineered microbes), fundamental biological and chemical concepts, artificial intelligence, and big data science, as well as collaborations in Computer Science, Public Health, Plant Biology, or related fields.

A biofilm was prepared

biofilm

values measured by using luminous E. coli had tendency of about 30–40% lower than that of BOD5, it could be observed an apparent correlation between the two values

bioluminescence was observed during the incubation time between 90 and 150 min in the presence of a sole carbon source such as glucose, acetate, l-glutamate and BOD standard solution (GGA solution)

is dosed with seed microorganisms and stored for 5 days in the dark room at 20 °C to prevent DO production via photosynthesis

The generally lower values in the U.S. derive from the much greater water use per capita than in other parts of the world

not suitable for process control in wastewater treatment and the real-time monitoring of water environments, such as rivers, streams, ponds, and ground water

is independent of the general recombination pathway

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

Phase variation is often mediated by the presence of highly mutagenic simple tandem DNA repeats, and genes containing such sequences can be easily identified

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