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

ఎప్పటికైనా Knowledge Centric Value Based Education రావాలని కోరుకుందాం

observations are consistent with a previous report showing that AHLs preferentially partition to the biofilm, reaching concentrations 600-fold in excess of the signal concentration in the surrounding bulk liquid medium

the best way to correct for the analyte signal suppression or enhancement is to co-elute a stable isotope labelled (SIL) analogue of the analyte

We also show how our toolbox can be used to deploy the FBP in planta to build auto-luminescent reporters for the study of gene-expression and hormone fluxes

We tested a broad range of Enterobacteriaceae conjugative plasmids for their sensitivity to the growth stage of the donors and identified three distinct regulation types.

indicate that even low concentrations of just a single type of antibiotic leads to resistance to multiple classes of antibiotics.

Overall, the low contamination level of antibiotics and high absolute abundance of ARGs indicated that ARGs previously introduced to an environment can self-amplify and persist in the environment

suggesting that STPs have become an important source of contamination for their receiving rivers

Additionally, the concentrations of antibiotics and the abundance of ARGs might increase after the sewage treatment process.

Perhaps we ultimately need to be prepared to accept less standardised and slightly more expensive food in order to accommodate less intense and more diverse agriculture. You might never be quite sure what to expect when you peeled a banana, but the result could be a more robust and sustainable food system without a major crisis every few decades.

With this approach, neurons that show E-SARE–driven expression in response to stimuli are permanently labeled by the fluorescent protein during the time window specified by the drug

Expression of a drug-inducible Cre recombinase downstream of E-SARE enabled imaging of neuronal populations that respond to monocular visual stimulation and tracking of their long-distance thalamocortical projections in living mice

The feedback loop permits sustained induction of recombinant proteins without massive quantities of inducer.

We have demonstrated that small RNAs can tightly repress their target genes when their synthesis rate is smaller than some threshold, but have little or no effect when the synthesis rate is much larger than that threshold

a threshold-linear response with a tunable threshold, a robust noise resistance characteristic, and a built-in capability for hierarchical cross-talk.

In particular, small RNAs are shown to establish a threshold for the expression of their target, providing safety mechanism against random fluctuations and transient signals. The threshold level is set by the transcription rate of the small RNA and can thus be modulated dynamically to reflect changing environmental conditions.

in the absence of tamoxifen, it exhibits some activity

A technique common in rodents is the use of Cre recombinase lines that are inducible at specific developmental time points (Figure 3b). The most common form of inducible Cre is CreERT2, which contains a modified estrogen receptor binding domain that prevents Cre from entering the nucleus in the absence of a ligand

strong promoters capable of driving expression of microbial opsins or fluorescent proteins in specific populations can exhibit leaky expression elsewhere. This low-level leak may be virtually undetectable as light responsiveness or fluorescence but can be a serious issue when expressing Cre recombinase.

Our analysis demonstrates that its structure is shaped more by stochasticity than selection.

To investigate how ciprofloxacin 35resistance is affected by the presence of metals,

creating improved technologies for large-scale recordings of neural activity in the live brain is a crucial goal in neuroscience

new toolkits for chronic labeling of active ensembles will provide a much awaited experimental basis to interrogate various aspects of neuronal circuits underlying long-term plastic changes of the brain, such as during nervous system development, during establishment of long-lasting remote memory over months, or in association with age-related neuronal changes over several years.

new direction of functional labeling involves conversion of transient expression from activity-dependent promoters into a permanent labeling based on tamoxifen-dependent recombinases

presence of the donor strain on the surface of the mutant selection plates, prevents the use of these plates for replica plating

In soil, bacteria tend to live in a state of dormancy due to prevailing oligotrophic conditions, which would not be particularly favorable for the development of competence

bacteria generally express genes only when and where needed, and thus do not readily reveal their pathogenic armament outside of infected tissues

This gene fusion approach will allow us to assay the induction of gene expression in as few as one cell

causes of microbial ‘uncultivability’ are numerous

The stability of susceptibility patterns allowed the antibiograms to be used as aids in the preliminary differentiation of these organisms.

regulate gene expression, typically by occluding or exposing regulatory features, such as ribosome binding sites (RBSs) in the case of translation or intrinsic terminator hairpins in the case of transcription

improvement of soil health should be a priority agenda in India’s agricultural policy. We need steps to check wind and water erosion of soils. We need innovative technologies to minimise physical degradation of soils due to waterlogging, flooding and crusting. We need to improve the fertility of saline, acidic, alkaline and toxic soils by reclaiming them

Indian soils are poor in organic matter content. About 59% of soils are low in available nitrogen; about 49% are low in available phosphorus; and about 48% are low or medium in available potassium. Indian soils are also varyingly deficient in micronutrients, such as zinc, iron, manganese, copper, molybdenum and boron

In culture conditions that enhance cell-to-cell contact, conjugation rates approach 100% with the cis-acting plasmid

wastewater treatment plants are hotspots for the release of antibiotics, and transmission of diverse antibiotic resistance bacteria (ARB) as well as ARGs into various environments

Recent findings have indicated that most ARGs could not be efficiently removed by traditional anaerobic digestion treatment

Detection of AHL by LC-FTMS was much more sensitive than by TLC bioassay, because TLC bioassay was implied to be affected by the presence of quorum quenching molecules in activated sludge.

Biofilms grown under higher shear were more rigid and had a greater yield shear stress than those grown under lower shear.

Because growth conditions (i.e., fluid dynamics and nutrient composition) can also have a profound effect on when QS is important,(71-75) there is a need to study biofilm formation and QS of BNR bacteria under various potential operating conditions.

Many QS-controlled genes relate to biofilm formation and function and may be important for some water and wastewater treatment biofilms

it become possible to engineer these microbial structures to allow bacteria to form a stable granular sludge instead of flocculent sludge

The actual availability of NH4+ and NO3− is difficult to measure in soil. When rates of microbial N transformations and/or plant uptake are rapid, then NH4+ or NO3− levels can be undetectable in soil

it can be useful for reducing leaky expression of toxic proteins

We report the construction of a family of vectors that contain a reengineered lacIq-lac promoter-operator complex in which cloned genes are strongly repressed in the absence of inducer.

difficult to observe in situ at the microscale, hence mechanisms and time scales relevant for bacterial spatial organization remain largely qualitative.

simulate the activated sludge process of a municipal waste water treatment plant and so better understand the fate of nanoplastics in urban environments

it has become a seemingly essential part of our life. It helps us to preserve food, keep warm, communicate with the world and much more

Frequency of QS among genome- sequenced bacteria

RP4 has been shown to exhibit a very broad host range and has been demonstrated to efficiently transfer in activated sludge (22, 40), chicken manure (24), and the rhizospheres of various plants (38, 39).

For in situ studies of AHL-dependent signaling in complex habitats, biosensors utilizing fluorescent proteins (GFP and RFP) as reporter genes have been developed

biosensors were employed to demonstrate AHL-mediated communication in swarm colonies of Serratia liquefaciens

they are induced in a way that correlates well with the AHL species produced by the strain

After 8 days of incubation, we detected cells that were only green fluorescent, indicating that the sensor plasmid had been transferred to indigenous AHL-producing organisms

QS systems have been experimentally analyzed in more than 50 different bacterial species and shown to control expression of a wide spectrum of functions, including bioluminescence, virulence, symbiosis, different forms of motility, biofilm formation, production of antibiotics and toxins, and conjugation (49).

Over 20 orthogonal serine integrases have been characterized to date (6,11), and many now have identified RDFs.

it is unclear to what extent these results are relevant in natural habitats, as the standard assays neglect the different surface chemistries, interactions with other species, and physical constraints of natural environments.

Images were prepared for publication using CorelDraw (Corel Corporation) and PowerPoint (Microsoft) software.

PpuI, which directs the biosynthesis of the two AHLs 3-oxo-C10 and 3-oxo-C12 as major products; PpuR, the AHL receptor; and RsaL a repressor of ppul

with pegs of polystyrene microtiter lid (catalog no. 445497; Nunc TSP system) immersed for bacterial biofilm formation

Planktonic stationary-phase cells were used in dose-response killing experiments, for a better comparison to biofilms

it may be possible to tag specific organisms and use these as monitor systems to estimate local chemical composition directly in the biofilms

placed at a 45° angle, nylon-mesh side up. Roots grew downward, collided with the bottom slide of the microcosm, and traveled along it. This method allowed observation of the root system by epifluorescence microscopy

The rhizosphere is the volume of soil directly under the influence of plant roots; it is bounded by the root surface on one side and extends millimeters into the soil. It is populated with a high density of bacteria, fungi, protists, and nematodes supported by relatively labile organic compounds, such as sugars, amino acids, organic acids, and polysaccharides. These compounds are actively and passively lost from living and dying root tissues (12, 13). This rhizodeposition allows 5–100 times more organisms per unit volume to be supported in the rhizosphere than in nearby bulk soil, where the microbial community is thought to be carbon limited

This biosensor will help identify organic substrates that potentially support microbial growth and activity before and during nodulation

Such biosensors can reveal intriguing aspects of the environment and the physiology of the free-living soil S. meliloti before and during the establishment of nodulation, and they provide a nondestructive, spatially explicit method for examining rhizosphere soil chemical composition

Chemically, the differencebetween the DI water and the 0.25×M9 EPS solution aresome simple salts and just 14.5μg/ml glucose equivalent ofEPS

if n is very small (for example n = 3), rather than showing error bars and statistics, it is better to simply plot the individual data points.

For n to be greater than 1, the experiment would have to be performed using separate stock cultures, or separate cell clones of the same type

quantifying biogeochemical fluxes resulting from these reactions remains a challenge

These tools provide insights into processes such as N uptake at the scale of individual root tips, allowing observation of plant–microbe interactions on scales at which they actually occur, instead of being masked by a whole‐core average

detection of methyl halides at femtomolar levels and quantification at concentrations above 10 pM

The following might be a pretty cumbersome workaround for tiled clones with spacing e.g. in millimeters instead of %.

A narrative weaves together otherwise isolated bits of information into a meaningful whole, linking them in important ways but also chunking the information so that it takes up less space in working memory and connects to existing threads in long-term memory

students quite often reported choosing their major based on taking introductory courses with particularly dynamic professors.