One of the most useful features of Quarto reveal.js slides is absolute position, which allows you to specifically place elements on a slide.

using the FastStart High Fidelity PCR System

515F GTGCCAGCMGCCGCGGTAA Universal Turner et al. 1999

PCR primers F-968-GC (59-CGC CCG GGG CGC GCC CCG GGCGGG GCG GGG GCA CGG GGG GAA CGC GAA GAA CCT TAC-39)

968f968–984AACGCGAAGAACCTTACNübel et al., 1996

In code, use comments to explain the “why” not the “what” or “how”.

Fluorescence Activated Cell Sorting (FACS).  From sorting cells for single cell genomics to identifying the host range of a plasmid; from detecting metabolically active cells in an environmental sample to studying colitogenic-driving intestinal bacteria, FACS can be used in a multitude of applications to study microbial communities (Rinke et al. 2014, Klumper et al. 2015, Kalyuzhnaya et al. 2008, Hatzenpichler et al. 2016, Palm et al. 2014).

zygotically inducible

we report on a new approach to quantify the fraction of a bacterial community that is able to receive and maintain an exogenous conjugal plasmid termed community permissiveness

This pool best represents the cells that had the potential to receive the plasmid, compared with the initial wastewater community before mating, i.e. before the few rounds of division that occur on the filter during incubation

Conjugation events were visualized by stereomicroscopy and quantified by automated image analysis

Filters were incubated for 48 h at 25 °C, before 72 h storage at 4 °C for GFP maturation.

a shows the sorting of the initial soil bacterial recipient community

(d) shows the enrichment of transconjugants after the first fast enrichment sorting step to over 80% transconjugal cells

To be right, it must be possible to be wrong

This model allows for the lessons to remain free from brand integrations and sponsor messages, without introducing paywalls.

I wash and dry my pan immediately after each use, but it’s what happens next that matters: I heat it gently over a low flame and add a bit of ghee. Then, I grab my dedicated “cast iron cloth” and rub the oil into the bottom and sides of the pan. I wait until the pan feels warm, but the ghee isn’t shimmering and snapping. Then I simply turn off the heat and let the pan cool naturally. This small step keeps it glossy and well-seasoned.

To save a copy of the slide with your drawings, your best option is to print your presentation from the browser.

When creating line art, please use the following guidelines:

White space must be cropped from the image, and excess space between panel labels and the image must be eliminated.

The blastn parameters used for VecScreen are significantly more stringent than the default blastn parameters

what economists call rents: that is, value extracted through the ownership of a limited resource

Any abuse of market power is likely to show up first on the supply side

The marketplace is designed and controlled by its owners, and that design shapes “who gets what and why” (to use the marvelous phrase from Alvin E. Roth, who received a Nobel prize in economics for his foundational work in the field of market design.

control the market through the algorithms and design features that decide which products users will see and be able to choose from. And these choices are not always in consumers’ best interests.

Likewise, Google does not just compete with other search engines like Bing and DuckDuckGo, but with everyone who produces content on the world wide web. Apple’s iPhone and Google’s Android don’t just compete with each other as smartphone platforms, but also with the app vendors who rely on smartphones to sell their products.

To do so, we prepared 96-well plates with two-fold dilutions of each antibiotic, ranging from 400–6.25 µg/ml, in 100 µl of medium per well

However, Google Docs has several limitations (like not automatically doing sequentially number headings - a plugin to do this available but is buggy) so I would like to do the final polishing in Word

Note: option -u was replaced by -b in Mash v1.1.

Download the pre-sketched RefSeq archive (reads not provided here; 10x-100x coverage of a single genome with anysequencing technology should work):refseq.genomes.k21.s1000.msh

P. lundensis is a Gram-negative, polar flagellated bacterium belonging to the Pseudomonas fragi clade of the Pseudomonas fluorescens species complex

sample size must be between 3 and 5,000 in order to use the shapiro.test() function.

RNA guides and corresponding target RNA, ranging from 25 to 373 nt, present signals

You can also create human-readable block identifiers by adding a blank space followed by the identifier, for example ^quote-of-the-day, at the end of a block:

30 - 60 sec/kb

When subjects are instructed togenerate a random sequence of hypotheticaltosses of a fair coin

mapping these reads back onto high-quality OTUs/ASVs if matching at ≥ 97% sequence identity

In contrast, it is the removal of rare taxa that would appear to remove valid data.

mRNAs triphosphorylated at their 5′ ends.

However, few examples of such multi-level regulation have been implemented to date20,21. This has resulted in an unclear picture of how best stringent multi-level control can be achieved and the trade-offs that exist between performance, regulatory complexity, and cellular burden when designing these systems.

The LasR sensing module includes the gene encoding LasR (BBa_C0078)

Others argue for a more ecumenical approach, encouraging researchers to try multiple methods on the same data set.

or replicates, no statistics should be shown, because they give only an indication of the fidelity with which the replicates were created: they might indicate how good the pipetting was, but they have no bearing on the hypothesis being tested6.

errors would reflect the accuracy of pipetting, not the reproduciblity of the differences between the experimental cells and the control cells

chose the introduction because this section of a paper is fairly easy for ChatGPT to write if it has access to background literature

rigid pili, such as Inc N, P and W, conjugate at rates 2–4 orders of magnitude higher on solid surfaces

flexible pili (e.g. Inc F, H and I), transfer equally well in liquid as in solid surfaces

synthetic arrays of regulatory RNA could be created that achieved our design goals

these commonly used artifacts are small code snippets that are entirely functional in nature and, therefore, when used in isolation, don't enjoy copyright protection at all.

The donor and recipient populations grow according to the following standard exponential growth equations

The primary color palette uses three colors. Grey and white should be employed liberally ashigh-contrast elements. Red should be used sparingly to label and decorate symbols and information.We use this pink/red because it is more gender-neutral than the typically masucline color palettes ofother space/geospatial-focused groups and it is distinct from the green/earth tones of conservationgroups. It’s also effective for drawing attention to specific elements

apparent permissiveness (AP). It is defined as the ratio of the relative abundance of an ASV in the transconjugant pool to the corresponding recipient pool

triggering homologous recombination and creating genetic instability10,11,12,13

We applied machine learning to explain how specific interactions controlled the promoters’ transcription rates.

Wilcoxon rank sum tests were used to test for significant differences between two groups

Each template molecule in a sample is tagged with a UMI sequence consisting of 10–20 random bases, which can subsequently be used to sort and analyze reads based on their original template molecule

Three distinct rRNA sequences exist in the operon, encoding for the two subunits of the ribosome; the 5S and 23S sequences code for the large subunit, while the 16S sequence encodes for the small subunit.

demonstrate that targeting of 16S variable regions with short-read sequencing platforms cannot achieve the taxonomic resolution afforded by sequencing the entire (~1500 bp) gene

New methods are needed that can manage and help organize this scale of data. To address this, we consider the general problem of computing an approximate distance between two sequences

we inferred the parameters of a linear function fit to the log transformed gDNA concentration versus detection time (Fig. 2d–g). The inferred slope of the linear function is determined by the cell doubling time (~0.5 h) and intercept is determined by the background mutation frequency

gDNA concentration versus the detection time for the (d) EC sensor, (e) ST sensor, (f) SA sensor and (g) CD sensor

A threshold of GFP fluorescence 400 arbitrary units (a.u.) was used to determine the detection time for each gDNA concentration.

expressed from the IPTG-inducible promoter Phyperspank

cell-based DNA detection is relatively simple and cost-effective. In comparison, other DNA detection methods such as next-generation sequencing and quantitative polymerase chain reaction require specialized instruments

Next-generation engineered bacteria hold tremendous promise

supplemented with 0.3 mM diaminopimelic acid (DAP)

p + theme(legend.position="top")

ubstantial contributions to conception anddesign, or acquisition of data, or analysis andinterpretation of data;

Your questions should be reasonably scoped. If you can imagine an entire book that answers your question, you’re asking too much.

A method was developed for oriented immobilization of bacteriophage T4 through introduction of specific binding ligands into the phage head using a phage display technique

Several review papers on PFAS occurrence, distribution, and exposure have been published in the last decades.

UMAP embedding of Record-seq data

metabolites and RNA are short-lived, omics-based measurements of transient stimuli only yield a snapshot of highly dynamic processes.

Lactococcal strains were routinely grown in M17 medium (49) supplemented with 1% glucose (GM17 medium) or, when needed, in chemically defined SA medium (26) at 30°C without shaking

Acinetobacter baylyi ADP1 (30) and ADP1-ISx (11) were grown at 30°C in LB-Miller (10 g NaCl, 10 g tryptone and 5 g yeast extract per liter) or ABMS minimal medium (40)

We have sought to investigate the combined impacts of complex substrates and presence of electron acceptors.

a biologically driven cryptic cycle was determined by identifying metabolically active sulfate reducing and sulfur oxidizing lineages co-locating within the sediments, effectively masking sulfide production through re-oxidation back to sulfate.

Why Make Memories?

Corynebacteriumglutamicum

Making universal media for bacterial strains

typically between 1010 and 1011 microbial cells per wet-weight gram of faeces7,8,9.

This figure is commonly mentioned in the microbiome literature, but its source has been difficult to ascertain

increased activity has brought with it a degree of hype and misinformation, which can undermine progress and public confidence in the research

Compare and Merge revisions √ Learn about comparing and merging documents

Proteinase K to the reaction to a final concentration of 50–100μg/ml. Incubate at 37–56°C for at least 1 hour. R

Differences in growth rate, e.g. induced by sub-lethal antibiotic concentrations or temperature, can also significantly bias conjugation rate estimates.

The default (50nM) works well with the standard protocol used at the Whitehead/MIT Center for Genome Research

a rerun of those identical amplicons (from the same reaction tubes) on a different date yielded “normal” results

A normal blood sodium level is between 135 and 145 milliequivalents per liter (mEq/L).

adjust the sample richness of each ecosystem by adding to it an estimate of the number of unobserved species

Adjusting for sample size when comparing different groups of observations without discarding data is widely prevalent in the sciences, and discarding data to adjust for unequal sample sizes is the exception

there is substantial negative bias in the estimates

since estimates for alpha diversity metrics are heavily biased when taxa are unobserved, comparing alpha diversity using either raw or rarefied data should not be undertaken

We currently do not account for measurement error in microbial diversity studies.

unique property of microbiome experiments and alpha diversity analysis is that samples do not faithfully represent the entire microbial community under study

The samples are not of particular interest, except that they reflect the environment from which they were sampled

Based on these results and well-established statistical theory, we advocate that investigators avoid rarefying altogether. We have provided microbiome-specific extensions to these tools in the R package, phyloseq.

Well-established statistical theory is available that simultaneously accounts for library size differences and biological variability using an appropriate mixture model

since the most commonly  used models are underdispersed relative to the data, standard errors are almost always zero. The result is that ecologists see incredibly small p values, but replicating results is rare.

We care about producing high-quality software and making our papers reproducible.

the key aspect of a protocol’s ability to accurately reflect the original sample composition can only be assessed with the help of standardized controls like mock communities

sRNAs that repress transcription have been engineered to create orthogonal and composable regulators that can be used to construct RNA-only transcriptional networks

techniques, such as transposition with Mu 11, Tn5 12 and Tn7 13, have been used to add fluorescent gene markers to plasmids

Alongside this, we used pKJK5::gfp, a plasmid lacking these additional payload genes

none of the organisms identified are known to produce particularly small cells that could pass 0.2 µm filters

Nanopore sequencing is used to rapidly and inexpensively assess part composition and create a composition-to-barcode index

For the terminus, we used primers that amplified part of the dcp gene: 5′-TTGAGCTGCGCCTCATCAAG-3′ and 5′-TCAACGTGCGAGCGATGAAT-3′

Capra Biosciences harnesses the superpowers of a biofilm-forming organism Marinobacter atlanticus to make fat-soluble products like retinol which is used in anti-aging face creams, and high-end industrial lubricants for electric car engines

Some startups, like MicroByre, have been working to domesticate those reluctant, recalcitrant, and rebellious microbes by adapting them for use in the lab and creating genetic tools to manipulate them

Filter and trim

binding of the Mob protein to the 52-bp sequence could thus allow the formation of a protein-DNA complex with a double function: relaxosome formation andmob gene regulation.

Student's t-Test

3.3.1 Citation Styles

focus on the content

approaches, which typically encapsulate bacteria in hydrogels, have produced deployable optical sensors for explosives14, heavy metals15 and chemical inducers16,17

current state-of-the-art whole-cell biosensors for field applications34,35, such as hydrogel-based20,36 and liquid-in-a-cartridge devices37

Translocation to a cell’s surface utilizes a signal peptide (for inner membrane translocation) and AIDAc as an outer membrane autotransporter pore

AHL communication modules with functional devices built from the biological components of the las18, tra18, rpa18, rhl19, cin19 and esa20 quorum-sensing systems

Receiver plasmids contained the synthetic PlasR promoter fused to a strong RBS (BBa_B0034) and GFP gene (BBa_E0040) from the IGEM registry. These plasmids additionally contained a pMB1 origin from pET28a and either a chloramphenicol (CmR) or a kanamycin (KanR) selectable marker.

folA gene from the evolved and naive populations was amplified by PCR

Evolution in regulatory regions rapidly compensates the cost of nonoptimal codon usage

masked by mechanisms affecting the abundance and function of the protein products of the transferred genes downstream to transcription and translation steps, and, therefore, being unrelated to codon bias

very high antibiotic concentrations used in this study (up to 30-fold the minimal inhibitory concentration [MIC]) potentially minimized the effect of sequence composition on fitness

Computational studies that analyzed HGT events among bacterial genomes revealed that HGT frequency positively and strongly correlates with the similarity of tRNA pools between donors and acceptors

5′-end mRNA, the fitness contribution of mRNA folding stability dominates over that of codon optimality.

We constructed an Escherichia coli donor strain that can deliver a genetic payload into target recipients by broad-host-range bacterial conjugation

The mixes were spotted on PBS + 1.5% agar plates and incubated at 37 °C

In contrast, it is the removal of rare taxa that would appear to remove valid data

programming environmental microbes have been applied to a wide range of organisms. Some examples of newly-programmable microbes include

Because biosensors detect at the temporal scales of microbial behaviors, they hold the potential to monitor fast chemical transformations in the environment that are hard to observe, often described as cryptic

and AHL controls in this process remain poorly understood.

There has been an ongoing debate on whether rarefaction is a statistically defensible procedure.

instead of being used to endlessly study one environment after another, in situ techniques should be coupled with efforts to model HGT in attached communities by facilitating comparisons between predicted and experimental observations, and assist in establishing predictive frameworks.

Only fluorescence genes have been used for the in situ detection of HGT in natural environments, as no substrate has to be added to detect the product of the expressed reporter gene.

The fluorescent marker gene approach is of specific importance in this thesis.Compared to the other reporter gene approaches it allows for quasi-immediate detection of plasmid transfer, even in individual cells, without theneed of substrate addition or taking the strains out of their natural environ-ment.

Christensen et al. (5) which used a specific positive induction of gfp in the recipient rather than a down regulation in the donor as in the system used here.

The mobilizing, conjugal plasmid can, now, after retromobilization, co-occurring with RSF1010 in the transconjugant, be subsequently isolated within its original environmental host.

mobilizable plasmids might less frequently reach dead ends once acquired, since they can utilize the conjugal connections build through adapted resident plasmids in their new host

To date, serine integrases have not been used extensively in plant systems

Prokaryotic genes are often subjected to frequent horizontal gene transfer [12–16], and one therefore might expect that this could also affect their gene connectivity.

our newly developed biosensor our studies demonstrate the detection of DPO in rodent and human samples.

Bacteria evolve rapidly not only by mutation and rapid multiplication, but also by transfer of DNA, which can result in strains with beneficial mutations from more than one parent.

conditions amenable to optical outputs for fluorescent reporters, they cannot be applied in native communities growing within non-transparent environmental materials

Seedlings were transferred to 10-cm square petri dishes containing Fahraeus agar (Somasegaran and Hoben, 1994) covered with sterile filter paper

While flowFrame objects store the underlying data matrix inthe exprs slot as an R object, cytoframe objects store the matrix (as well as the data from theother slots) in a C data structure that is accessed through an external pointer. This allows for greateroptimization of data operations including I/O, parsing, transformation, and gating.

Collaborative publications, in which the student is one of several authors/creators, are permitted. In every case, the Preface must clearly describe the student's contribution to the research and creation—including, where applicable, the student's role in publications with several authors, or in material created by several authors.