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  1. Last 7 days
    1. 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
    2. 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
    1. The feedback loop permits sustained induction of recombinant proteins without massive quantities of inducer.
    1. 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
    2. a threshold-linear response with a tunable threshold, a robust noise resistance characteristic, and a built-in capability for hierarchical cross-talk.
    1. 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.
    1. in the absence of tamoxifen, it exhibits some activity
    2. 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
    3. 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.
    1. To investigate how ciprofloxacin 35resistance is affected by the presence of metals,

      Ciprofloxacin's activity (MIC, IC50 etc.) could also depend on Zn presence, was this investigaged before going into selection and evolution?

    1. creating improved technologies for large-scale recordings of neural activity in the live brain is a crucial goal in neuroscience
    1. 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.
    2. new direction of functional labeling involves conversion of transient expression from activity-dependent promoters into a permanent labeling based on tamoxifen-dependent recombinases
  2. Oct 2019
    1. 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

      It can also be argued that the transformed DNA is a good resource of phosphates, nitrogen etc., so might be favoured in oligotrophic conditions?

  3. sackler.tufts.edu sackler.tufts.edu
    1. bacteria generally express genes only when and where needed, and thus do not readily reveal their pathogenic armament outside of infected tissues
    1. This gene fusion approach will allow us to assay the induction of gene expression in as few as one cell

      Recombinase memory as a reporter for expression in 1 cell

    1. 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
    1. 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
    2. 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
    1. In culture conditions that enhance cell-to-cell contact, conjugation rates approach 100% with the cis-acting plasmid

      high efficiency

    1. 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

      That's a strong claim, not backed by strong evidence

    2. Recent findings have indicated that most ARGs could not be efficiently removed by traditional anaerobic digestion treatment
    1. 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.

      does not make sense

    1. 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.
    2. Many QS-controlled genes relate to biofilm formation and function and may be important for some water and wastewater treatment biofilms
    3. Many QS-controlled genes relate to biofilm formation and function and may be important for some water and wastewater treatment biofilms
    1. it become possible to engineer these microbial structures to allow bacteria to form a stable granular sludge instead of flocculent sludge
    1. 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
    1. 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.
    1. difficult to observe in situ at the microscale, hence mechanisms and time scales relevant for bacterial spatial organization remain largely qualitative.
    1. 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
    1. 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).
    2. For in situ studies of AHL-dependent signaling in complex habitats, biosensors utilizing fluorescent proteins (GFP and RFP) as reporter genes have been developed
    3. biosensors were employed to demonstrate AHL-mediated communication in swarm colonies of Serratia liquefaciens
    4. they are induced in a way that correlates well with the AHL species produced by the strain

      This is a baseless statement, made from only 1 strain p. aerofaciens, which makes C6-AHL

      • Two strains P. Putida and E. coli do not produce AHLs (you mention this)

      How does it correlate well then with 1 data point?

    5. 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

      It could also just mean that there are some AHL producers in the viscinity, just like the explanation given for yellow donor cells.

    6. 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).
    1. 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.
    1. Images were prepared for publication using CorelDraw (Corel Corporation) and PowerPoint (Microsoft) software.

      Great that you cite the software

    2. 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

      P. putida IsoF, isolated from tomato rhizosphere - quorum sensing

    1. with pegs of polystyrene microtiter lid (catalog no. 445497; Nunc TSP system) immersed for bacterial biofilm formation
    1. Planktonic stationary-phase cells were used in dose-response killing experiments, for a better comparison to biofilms
    1. it may be possible to tag specific organisms and use these as monitor systems to estimate local chemical composition directly in the biofilms
  4. Sep 2019
    1. 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

      well explained!

    2. 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
    3. This biosensor will help identify organic substrates that potentially support microbial growth and activity before and during nodulation
    4. 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
    1. Chemically, the differencebetween the DI water and the 0.25×M9 EPS solution aresome simple salts and just 14.5μg/ml glucose equivalent ofEPS

      Should have compared with M9 + equivalent glucose (un-polymerized) as a better control for osmolarity reasons

    1. 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.
    2. 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
    1. quantifying biogeochemical fluxes resulting from these reactions remains a challenge
    2. 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
    1. detection of methyl halides at femtomolar levels and quantification at concentrations above 10 pM

      This is approximately 6 molecules per cell - seems too low. (assuming cell volume is 1 um^3 - for e coli) - https://bionumbers.hms.harvard.edu/bionumber.aspx?id=100004&ver=20&trm=100004&org=

    1. The following might be a pretty cumbersome workaround for tiled clones with spacing e.g. in millimeters instead of %.
    1. 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
    2. students quite often reported choosing their major based on taking introductory courses with particularly dynamic professors.
    3. your enthusiasm as an instructor is indeed contagious and helps predict variables like student motivation in the course.
    4. make the entire course relevant to students’ daily lives. All of the labs center around chemicals and materials that students interact with regularly. For instance, they evaluate bottled water versus tap water, test both for pH, conductivity, and taste, and then debate why so many people choose bottled over tap
    5. You can also make class activities relevant to contemporary social movements, to future careers in your major, or to some transcendent purpose
    6. Jennifer Gonzalez, editor of the teaching blog Cult of Pedagogy, summed up the concept quite nicely in the title of a blog post: “To Learn, Students Need to DO Something.”
    1. essential goal for me in every course has always been to make students feel comfortable participating in class, and to encourage as many of them as possible to speak up. Peer instruction, aided by electronic polling, gave me an opportunity to invite quiet students to engage more actively in class, both through the polls and through the subsequent discussions
    1. When new knowledge is integrated with and connected to existing knowledge, that new knowledge is easier to understand and to remember. A professor’s job is to build scaffolding from existing knowledge on which to hang incoming new knowledge. Using a concept map is one way to build that scaffolding.
    1. text files? Gloriously simple, ready made for your favorite text editor and perfect for version control.

      Latex files can do version control vs word files

    1. R markdown has the possibility of executing R code inline (and rendering the result to html) or rendering graphs inline. That saves time and makes the documentation maintainable as you don't need to manually prepare the output of that function or manually prepare and save a graph since it's rendered on the fly.

      R markdown makes documentation of code easy

    1. more convenient and effective methods is required for qualitative and quantitative analysis of AHLs
    2. enzymatic quenching mechanism of AHL signals is also present in enzyme-producing bacteria, such as Anabaena sp. PCC7120, Ralstonia sp. XJ12B, P. aeruginosa PAO1, Agrobacterium tumefaciens C58, Bacillus sp. strain 240B1, Rhodococcus erythropolis strain W2
    3. Membrane biofouling remains to be one of the most serious operational problems for MBR applications, which results in permeate flux and water quality decline, trans-membrane pressure (TMP) and operating costs increase, frequent membrane cleaning and replacement necessary
    4. activated sludge flocs are complicated aggregates containing inorganic and organic particles as well as a high-density microbial consortium embedded in a matrix of extracellular polymeric substances
    1. Coordinated behaviours include bioluminescence3,4, virulence factor production5,6, secondary metabolite production7, competence for DNA uptake8,9 and biofilm formation10,11.
    2. We focus on how quorums are detected and how quorum sensing controls group behaviours in complex and dynamically changing environments such as multi-species bacterial communities, in the presence of flow, in 3D non-uniform biofilms and in hosts during infection.
    1. bacterial QQ does not completely prevent biofouling; it simply postpones its occurrence
    2. it has been assumed that the effectiveness of Pseudomonas sp. 1A1 in mitigating membrane biofouling could be expected to be more significant, given that the QQ enzyme that it produces (acylase) is extracellular

      The acylase might not be functional or stable in the extracellular wastewater environment

    1. Design of the LOCKR system.

      It would be amazing if you could fit the rate constants from experimental data

    1. different fouling patterns were observed for replicate MBRs seeded with the same inoculum and maintained under identical operating conditions, with similar levels of biomass, soluble microbial products, and extracellular polymeric substances

      The reactors were not maintained under the same conditions - 1 had backpulsing and the other was subjected to relaxation

    1. achieved only a 10% increase of permeate flux when backpulsing was used in the filtration of a biological wastewater containing a high mixed liquor suspended solids
    1. Figure 5

      Why did the QQ-MBR go down on day 20?

    2. Figure 2. TMP profiles during the operation of two one-stage MBRs in two phases.

      Fouling seems to happen exponentially once it starts => following a first order reaction. What is the mechanism behind this?

    3. C8-HSL was chosen as a representative AHL molecule because it is one of the dominant AHL molecules in MBRs for wastewater treatment
    4. a critical issue in MBR that awaits a technological advancement to solve is membrane biofouling, which leads to high energy consumption and thus high operating costs
    1. Plasmids (IncP/N/W)with 373short and rigid pili only transfer efficiently on solid surfaces, unlike those with longand flexible 374pili (IncF/H/T/J),capable of transferring equally well in liquidand on solid surfaces[35,36]

      Plasmid group vs pili length

    1. identify mechanistic drivers of microbial activity, infer meaningful interaction networks, and rationally engineer microbial communities.

      Mechanistic insights in microbial ecology

    1. Next, a microfluidic device is used to co-encapsulate these clusters with gel beads, each containing uniquely barcoded forward 16S rRNA amplification primers

      Isn't the spatial information lost while encapsulation? Is the barcode capturing the spatial information in some way? It is not clear

    2. current microbiome profiling approaches such as metagenomic sequencing require homogenization of input material, which means that underlying spatial information is lost
    1. These carboxylated AHLs facilitated the transition from a short cell to filamentous growth, with an altered carbon metabolic flux that favoured the conversion of acetate to methane and a reduced yield in cellular biomass

      Carboxylated AHL signalling favours methanogenesis in Methanosaeta herundinacea 6Ac

    1. Deletion of genes thatproduceN-acyl-L-homoserine lactone signals resulted in an increase in denitrification activity, which wasrepressed by exogenous signal molecules.

      AHL is lowering denitrification in Psuedomonas aeruginosa

    1. scientists are uncovering and debating an increasing array of other evolutionary processes at work in bacteria, some of which are suspiciously Lamarckian in character4–6
    1. Instead, most particle-attached bacteria may be secondary consumers that recycle waste products from primary degraders.

      What factors determine their relative abundance then?

    1. co-occur out of cooperative relations or a similar niche preference

      similar niche evokes competition rather than cooperation, this is contradictory

    1. beneficial commensal

      mutualist?

    2. antibodies against siderophores in the intestine, which hindered proliferation of the gut pathogen Salmonella

      What about normal gut microbiota? I presume they need iron too

    1. At the micrometer-centimeter scale, electrochemical and optical probes have been productively used to profile gradients in pH, redox, and oxygen; however, these probes and their associated equipment are intrusive to the ecosystem and often expensive, limiting their application to only a few point measurements or limited time series, and their fragile nature makes them best suited for laboratory use
    1. CustoMem in the UK uses synthetic biology to create a granular material that attracts and sticks to micropollutants such as pesticides, pharmaceuticals, and certain chemicals in wastewater
    2. Now synthesized microbial biosensors are able to target specific toxins such as arsenic, cadmium, mercury, nitrogen, ammonium, nitrate, phosphorus and heavy metals, and respond in a variety of ways. They can be engineered to generate an electrochemical, thermal, acoustic or bioluminescent signal when encountering the designated pollutant.
    3. remediating arsenic contamination of groundwater by stimulating natural bacteria to produce substances that arsenic sticks to
    1. MicroBio Engineering Inc., a research and engineering consulting firm specializing in developing improved algal strains and cultivation processes for wastewater reclamation, animal feeds, higher value products and, yes, biofuels.
    1. In Japan, scientists are developing synthetically altered soy plants and yeast that produce glycyrrhizen, a compound in licorice root that is 150 to 300 times sweeter than sugar
    1. move away from identifying correlative relationships between characteristics of the microbiome and system-level processes, and towards identifying more causative and mechanistic relationships
  5. Aug 2019
    1. endogenous AHL-based QS and QQ are existing and coexisting in biological wastewater treatments; the leading role for AHL-based QS or QQ phenomenon in biological wastewater treatments can be determined by bacterial AHL concentration.
    1. Rattanarat et al.73 created a three-dimensional μPAD (Fig. 1A) that combined colorimetric and electrochemical detection on separate layers for quantifying Ni, Cu, Fe, Pb, Cr(VI), and Cd
    1. Immobilization efficiency was improved by manipulating the bacterial genetics (overproducing curli protein),

      e coli immobilization

    1. diagnosis of antibiotic interference in the major biosynthetic pathways of bacteria: the biosynthesis of DNA by the yorB promoter, of RNA by the yvgS promoter, of proteins by the yheI promoter, of the cell wall by the ypuA promoter, and of fatty acids by the fabHB promoter.
    1. chief advantage of this approach is that the entire sensor, including all signal-processing and communication functions, can be produced as a single-chip, low-power, rugged, inexpensive device
    1. crude DNA extraction methods, such as boiling, are not recommended to obtain the lower detection limit for a microorganism

      You are effectively boiling as well when you subject to thermal cycling. It is very confusing when you do two rounds of PCR cycling

    1. outstanding possibilities for studying phenomena such as competition, niche partitioning and predation in the microbial world, under more environmentally realistic conditions than can be achieved in pure culture studies.
    1. the maintenance of the pluripotent state of animal stem cells requires hypoxic conditions, whereas higher oxygen tension promotes cell differentiation
    1. broad‐scale functional parameters increased as biodiversity decreased, e.g. thymidine incorporation, growth on added nutrients, and the decomposition rate of plant residues. Other more specific parameters decreased as biodiversity decreased, e.g. nitrification, denitrification and methane oxidation.

      functional parameters of a community

    1. But because they ignore so much of the data, they don’t work well with small sets of data

      don't use median with small data sets

    2. extremes help to tell you what’s possible, and could suggest a very different distribution in your data from what you expect
    1. we observed that codon usage biases are better correlates of growth rates than any other trait, including rRNA copy number
    1. capable of transferring resistance to non-resistant strains

      Has this been demonstrated?

    2. The level of ARBs is extremely high in most of the river systems (up to 98% of the total detected bacteria)

      That seems totally unfeasible; What was the methodology? How can you estimate such when most of the species are unculturable?

    1. relationships between characteristics of microbiomes and the system-level processes that they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field
    1. Here, we show how three phenomena—Simpson’s paradox, context-dependence, and nonlinear averaging—can lead to erroneous conclusions about population parameters and species interactions when samples contain heterogeneous mixtures of populations or communities.
    2. These issues can be overcome by measuring and accounting for spatial heterogeneity at very small scales
    1. we emphasize how processes and interactions at one spatial or temporal scale contribute to emergent processes and properties at larger or longer scales. Most often the emergent processes we investigate are aquatic ecosystem services, including carbon burial, greenhouse gas emissions, nutrient removal, and recreational fisheries
    1. some of the key questions of microbial community assembly, maintenance and function could be answered by intensively studying one (or a few) synthetic model community
    1. Time-resolved analysis of individual cells revealed that past exposure to low levels of antibiotics increases tolerance to future exposure for the sessile but not for the motile cell
    1. Now we can ask, ‘Have I seen iron at some threshold?’ ‘Have I seen some nitrate?’ And have every microbe write it down. As one thinks about long-term incubation, this is a really powerful tool, because even six months later we can pull out the DNA and see what happened.”
    1. Growth history influences starvation-induced expression of uspA, grpE, and rpoS and subsequent cryotolerance in Escherichia coli O157:H7
    2. in E. coli a form of ‘memory’ of past phosphate limitation leads to a faster response to successive periods of phosphate limitation, and that this faster response may be survival enhancing

      phosphate starvation memory

    1. This article discusses, and challenges, some of the often implicit assumptions made in community studies. It suggests greater focus on ecological questions, more critical analysis of accepted concepts and consideration of the fundamental mechanisms controlling microbial processes and interactions in situ
    1. quantitative physiological characteristics such as maximum specific growth rate; saturation constant; optimum, minimum or maximum pH or temperature for growth; susceptibility to predation; and the speed of recovery after starvation.

      Quantitative physiological characteristics of microbes

    1. In minimal media, cell growth and division slow considerably, while protein overproduction from plasmids can continue
    1. Or

      Contradicts previous calculation - should be 1.5 ul/ 1 ml Master mix

    2. 3 uL diluted ROX per 20 uL reaction

      1.5ul/1ml master mix

    3. 1.8 uL diluted ROX per 20 uL

      9 ul/ 1 ml master mix

    1. they upregulate biofilm formation and maturation (Sturbelle et al. 2015)

      The reference cited has nothing to do with biofilms