PHEIGES: all-cell-free phage synthesis and selection from engineered genomes

Bacteriophages constitute an invaluable biological reservoir for biotechnology and medicine. The ability to exploit such vast resources is hampered by the lack of methods to rapidly engineer, assemble, package genomes, and select phages. Cell-free transcription-translation (TXTL) offers experimental settings to address such a limitation. Here, we describe PHage Engineering by In vitro Gene Expression and Selection (PHEIGES) using T7 phage genome and Escherichia coli TXTL. Phage genomes are assembled in vitro from PCR-amplified fragments and directly expressed in batch TXTL reactions to produce up to 1011 PFU/ml engineered phages within one day. We further demonstrate a significant genotype-phenotype linkage of phage assembly in bulk TXTL. This enables rapid selection of phages with altered rough lipopolysaccharides specificity from phage genomes incorporating tail fiber mutant libraries. We establish the scalability of PHEIGES by one pot assembly of such mutants with fluorescent gene integration and 10% length-reduced genome.

Analysis of DNA Barcodes Using DNA Subway

DNA Subway makes bioinformatic analysis of DNA barcodes classroom friendly, eliminating the need for software installations or command line tools. Subway bundles research-grade bioinformatics software into workflows with an easy-to-use interface. This chapter covers DNA Subway's DNA barcoding analysis workflow (Blue Line) starting with one or more Sanger sequence reads. During analysis, users can view trace files and sequence quality, pair and align forward and reverse reads, create and trim consensus sequences, perform BLAST searches, select reference data, align multiple sequences, and compute phylogenetic trees. High-quality sequences with the required metadata can also be submitted as barcode sequences to NCBI GenBank.

Simple, Robust Invertebrate DNA Barcoding: Chelex-Based DNA Extraction and Optimized COI Amplification

Chelex-based DNA extractions are well suited for student DNA barcoding research because they are simple, safe, and inexpensive and can be performed without specialized laboratory equipment, allowing them to be performed in classrooms or at home. Extracted DNA is stable in Chelex solution for at least a week at ambient temperature, allowing collection of DNA samples from remote students. These extractions provide quality DNA for many taxa and are optimal for barcoding invertebrates, especially in combination with novel cytochrome c oxidase I (COI) primer cocktails and PCR cycling conditions.

A Rapid, Equipment-Free DNA Isolation Method for DNA Barcoding

This rapid, equipment-free DNA isolation procedure using chromatography paper is a simple method that can be performed in less than 30 min and requires no wet lab experience. With minimal expense, it offers an affordable alternative for anyone wanting to explore biodiversity. It also provides an excellent option for use in classrooms or other activities that are time limited. The method works best for plants or lichens, producing stable DNA on Whatman® chromatography paper at room temperature, which can be eluted as needed.

Cost-Effective DNA Extraction for DNA Barcoding Diverse Biological Samples

DNA barcoding employs standard molecular techniques (e.g., DNA extraction, PCR, and Sanger sequencing) to taxonomically identify biological samples. While DNA barcoding is a useful experimental workflow for in-class active learning exercises, extracting DNA from diverse sample types in a time and cost-effective manner can be challenging in a classroom setting. Here, we provide two time and cost-effective methods that have been used by novice students to successfully extract DNA from a variety of animal, fungal, algal, and plant tissues for DNA barcoding.

Cell-Free Synthesis and Quantitation of Bacteriophages

Cell-free transcription-translation (TXTL) enables achieving an ever-growing number of applications, ranging from the rapid characterization of DNA parts to the production of biologics. As TXTL systems gain in versatility and efficacy, larger DNAs can be expressed in vitro extending the scope of cell-free biomanufacturing to new territories. The demonstration that complex entities such as infectious bacteriophages can be synthesized from their genomes in TXTL reactions opens new opportunities, especially for biomedical applications. Over the last century, phages have been instrumental in the discovery of many ground-breaking biotechnologies including CRISPR. The primary function of phages is to infect bacteria. In that capacity, phages are considered an alternative approach to tackling current societal problems such as the rise of antibiotic-resistant microbes. TXTL provides alternative means to produce phages and with several advantages over in vivo synthesis methods. In this chapter, we describe the basic procedures to purify phage genomes, cell-free synthesize phages, and quantitate them using an all-E. coli TXTL system.

Assessing microbial diversity in soil samples along the Potomac River: implications for environmental health

IMPORTANCE

This study integrates microbial analysis into an undergraduate chemistry class, offering students a hands-on approach to environmental research. We examined the soil along the urbanized Potomac River, discovering a mix of common marine microbes and others that are indicators of urban waste and pollution. Our findings provide valuable insights into the environmental impacts of urbanization on soil health and reveal the effectiveness of using modern genetic tools to teach students about real-world issues. This innovative educational approach not only deepens students' understanding of chemistry and ecology but also prepares them to be thoughtful, informed participants in addressing contemporary environmental challenges while shedding light on the state of the soil microbiome near and around the DC metro area.

The Functional Biogeography of eDNA Metacommunities in the Post-Fire Landscape of the Angeles National Forest

Wildfires have continued to increase in frequency and severity in Southern California due in part to climate change. To gain a further understanding of microbial soil communities’ response to fire and functions that may enhance post-wildfire resilience, soil fungal and bacterial microbiomes were studied from different wildfire areas in the Gold Creek Preserve within the Angeles National Forest using 16S, FITS, 18S, 12S, PITS, and COI amplicon sequencing. Sequencing datasets from December 2020 and June 2021 samplings were analyzed using QIIME2, ranacapa, stats, vcd, EZBioCloud, and mixomics. Significant differences were found among bacterial and fungal taxa associated with different fire areas in the Gold Creek Preserve. There was evidence of seasonal shifts in the alpha diversity of the bacterial communities. In the sparse partial least squares analysis, there were strong associations (r > 0.8) between longitude, elevation, and a defined cluster of Amplicon Sequence Variants (ASVs). The Chi-square test revealed differences in fungi−bacteria (F:B) proportions between different trails (p = 2 × 10−16). sPLS results focused on a cluster of Green Trail samples with high elevation and longitude. Analysis revealed the cluster included the post-fire pioneer fungi Pyronema and Tremella. Chlorellales algae and possibly pathogenic Fusarium sequences were elevated. Bacterivorous Corallococcus, which secretes antimicrobials, and bacterivorous flagellate Spumella were associated with the cluster. There was functional redundancy in clusters that were differently composed but shared similar ecological functions. These results implied a set of traits for post-fire resiliency. These included photo-autotrophy, mineralization of pyrolyzed organic matter and aromatic/oily compounds, potential pathogenicity and parasitism, antimicrobials, and N-metabolism.

Quantum optimization of maximum independent set using Rydberg atom arrays

Realizing quantum speedup for practically relevant, computationally hard problems is a central challenge in quantum information science. Using Rydberg atom arrays with up to 289 qubits in two spatial dimensions, we experimentally investigate quantum algorithms for solving the Maximum Independent Set problem. We use a hardware-efficient encoding associated with Rydberg blockade, realize closed-loop optimization to test several variational algorithms, and subsequently apply them to systematically explore a class of graphs with programmable connectivity. We find the problem hardness is controlled by the solution degeneracy and number of local minima, and experimentally benchmark the quantum algorithm's performance against classical simulated annealing. On the hardest graphs, we observe a superlinear quantum speedup in finding exact solutions in the deep circuit regime and analyze its origins.

DNA barcoding Brooklyn (New York): A first assessment of biodiversity in Marine Park by citizen scientists

DNA barcoding is both an important research and science education tool. The technique allows for quick and accurate species identification using only minimal amounts of tissue samples taken from any organism at any developmental phase. DNA barcoding has many practical applications including furthering the study of taxonomy and monitoring biodiversity. In addition to these uses, DNA barcoding is a powerful tool to empower, engage, and educate students in the scientific method while conducting productive and creative research. The study presented here provides the first assessment of Marine Park (Brooklyn, New York, USA) biodiversity using DNA barcoding. New York City citizen scientists (high school students and their teachers) were trained to identify species using DNA barcoding during a two-week long institute. By performing NCBI GenBank BLAST searches, students taxonomically identified 187 samples (1 fungus, 70 animals and 116 plants) and also published 12 novel DNA barcodes on GenBank. Students also identified 7 ant species and demonstrated the potential of DNA barcoding for identification of this especially diverse group when coupled with traditional taxonomy using morphology. Here we outline how DNA barcoding allows citizen scientists to make preliminary taxonomic identifications and contribute to modern biodiversity research.

A survey of new temperature-sensitive, embryonic-lethal mutations in C. elegans: 24 alleles of thirteen genes

To study essential maternal gene requirements in the early C. elegans embryo, we have screened for temperature-sensitive, embryonic lethal mutations in an effort to bypass essential zygotic requirements for such genes during larval and adult germline development. With conditional alleles, multiple essential requirements can be examined by shifting at different times from the permissive temperature of 15°C to the restrictive temperature of 26°C. Here we describe 24 conditional mutations that affect 13 different loci and report the identity of the gene mutations responsible for the conditional lethality in 22 of the mutants. All but four are mis-sense mutations, with two mutations affecting splice sites, another creating an in-frame deletion, and one creating a premature stop codon. Almost all of the mis-sense mutations affect residues conserved in orthologs, and thus may be useful for engineering conditional mutations in other organisms. We find that 62% of the mutants display additional phenotypes when shifted to the restrictive temperature as L1 larvae, in addition to causing embryonic lethality after L4 upshifts. Remarkably, we also found that 13 out of the 24 mutations appear to be fast-acting, making them particularly useful for careful dissection of multiple essential requirements. Our findings highlight the value of C. elegans for identifying useful temperature-sensitive mutations in essential genes, and provide new insights into the requirements for some of the affected loci.

Light regulation of the synthesis of the large subunit of ribulose-1,5-bisphosphate carboxylase in peas: Evidence for translational control

The specific activity of ribulose-1,5-bisphosphate carboxylase (EC 4.1.1.39) increases 30- to 50-fold when dark-grown pea seedlings are shifted into the light. The large subunit (LS) of this multimeric protein is known to be synthesized in the chloroplast, but plastids from dark-grown cells contain relatively low levels of LS. However, despite the low level of LS synthesis in the plastids of dark-grown plants, these organelles contain significant levels of LS mRNA. Hybridization studies showed that the amount of LS mRNA increased about 3-fold, relative to total plant RNA, when dark-grown plants were illuminated. This increase in LS mRNA can be accounted for by a similar increase in chloroplast genome copy number. It was found that the amount of translatable LS mRNA per mug of plastid RNA is similar when isolated from either dark-grown plants or dark-grown plants subjected to light. These results suggest that although light can increase the level of LS mRNA by increasing the copy number of this gene, the primary regulation of LS synthesis by light in pea chloroplasts is at the level of translation.

The forkhead transcription factor UNC-130 is required for the graded spatial expression of the UNC-129 TGF-beta guidance factor in C. elegans

Secreted proteins required for cellular movements along the circumference of the body wall in Caenorhabditis elegans include UNC-6/netrin and the novel TGF-beta UNC-129. Expression of these proteins is graded along the dorsoventral (D/V) axis, providing polarity information to guide migrations. Here we show that the graded expression of UNC-129 in dorsal but not ventral body muscles depends on unc-130, which encodes a Forkhead transcription factor. The phenotype of unc-130 mutants closely mimics the reported effects of ectopically expressing unc-129 in both dorsal and ventral body muscles (). This fits our present finding that unc-130 cell autonomously represses unc-129 expression in the ventral body muscles. Thus the cell-specific effects of unc-130 on ventral, but not dorsal, body muscle expression of unc-129 accounts for the D/V polarity information required for UNC-129-mediated guidance. Genetic interactions between unc-130 and other guidance genes show that several molecular pathways function in parallel to guide the ventral to dorsal migration of distal tip cells (DTCs) and axonal growth cones in C. elegans. Genetic interactions confirm that UNC-129 does not require the only known type II TGF-beta receptor in C. elegans (DAF-4) for its guidance functions. Also, unc-130 is partially required for male tail morphogenesis and for embryogenesis.

Are preferences for equity over efficiency in health care allocation "all or nothing"?

BACKGROUND

In a previous study we showed that within a budget constraint, most people would rather offer a less effective screening test to 100% of a Medicaid population, thereby saving 1,000 lives, than a more effective test to 50% of the population, thereby saving 1,100 lives. We present here a study exploring whether this preference for equity over efficiency persists when neither test can be offered to the entire population.

METHODS

Members of Physicians' Online and prospective jurors at the Philadelphia County Courthouse randomly received 1 of 3 questionnaires (Q1, Q2, or Q3) describing a limited budget to screen Medicaid enrollees for colon cancer. In all questionnaires, test 1 was said to save 1,000 lives, and test 2, a more effective and more expensive test, was said to save 1,100. In Q1, test 1 was offered to 100% and test 2 to 50% of the population. In Q2, the 2 tests could be offered to 50% and 25%, respectively; in Q3, to 90% and 40%, respectively. Respondents indicated which test they recommended and provided justification.

RESULTS

The majority of physicians (59%) and the general public (56%) receiving Q1 favored the less effective screening test However, of those receiving Q2, only 26% of physicians and 27% of the general public recommended the less effective screening test. And of those receiving Q3, only 38% of physicians and 28% of the general public recommended the less effective test. Justifications for these recommendations were based largely on concerns for equality of treatment among those who chose the less effective test and concerns for saving the most lives among those who preferred the more effective test.

CONCLUSIONS

Although most respondents show a preference for equity over efficiency when equity means that 100% of a population can receive a service, many fewer respondents maintain this preference when equity is no longer absolute. This result suggests that the preference for equity is sometimes "all or none."

The influence of nutritional status on the feeding behaviour of the field slug, Deroceras reticulatum (Müller)

The field slug, Deroceras reticulatum, a common pest of agricultural and horticultural crops, is a generalist herbivore with distinct preferences for particular food items. However, these preferences are not fixed, but are influenced by the recent dietary history of the slugs. In particular, slugs tend to select novel food items ('neophilia'). We investigated the basis of such influences, using artificial diets in which protein and carbohydrate composition could be controlled and non-nutritional ('secondary') chemicals added as flavours. The slugs showed no general inclination for neophilia based on taste alone. There was a possible learned association between protein content and taste, but this was weakly expressed. However, the slugs selected food items, when given a choice, containing nutrients that were deficient in earlier diets, even though all the food items contained the same familiar secondary taste chemicals. Injections of missing nutrients into the haemocoel of slugs inhibited such changes in food preference, indicating that slugs' feeding preferences are influenced directly by their internal nutritional status. We suggest that neophilia in D. reticulatum is a physiological response to a nutritional imbalance arising from a suboptimal diet. Copyright 2000 The Association for the Study of Animal Behaviour.

Evaluation of ozone injury on foliage of black cherry (Prunus serotina) and tall milkweed (Asclepias exaltata) in Great Smoky Mountains National Park

The incidence and severity of visible foliar ozone injury on black cherry (Prunus serotina) seedlings and saplings and tall milkweed (Asclepias exaltata) plants in Great Smoky Mountains National Park (GRSM) were determined by surveys along selected trails conducted during late summer 1992. The incidence (% injured plants) of ozone injury on black cherry was 47% and the percent injured leaves/injured plant and average leaf area injured were 43 and 6%, respectively. Maximum severity (avg. leaf area of the most severely injured leaf) was 12%. Black cherry seedlings and saplings exhibiting ozone injury were taller than non-injured plants. When insect feeding was present, it occurred 96% of the time on plants with ozone injury. Significantly more injury (p=0.007) on black cherry (% injured leaves/injured black cherry) occurred in the NW section of GRSM compared with the other Park sections. Regression analyses showed no relationships in ozone injury with respect to aspect, slope or elevation. Tall milkweed was evaluated twice during August for ozone injury. The incidence (% injured plants) of ozone injury was 74 and 79% for the first and second survey, respectively. The percentage of injured leaves per plant from the first to second survey was 63 to 79%, respectively. Tall milkweeds showing ozone injury were taller than the non-injured plants. The percentage of insect-damaged plants was 50% among plants without ozone injury and 60% among ozone-injured plants. Non-injured tall milkweed had fewer flowers and/or pods than the injured plants. Mean leaf area injured increased over time, and mean maximum leaf area injured increased from 8 to 11% during the same period. Regression analyses showed no differences in ozone injury regarding aspect, slope or elevation. Our findings indicate that ozone injury is widespread throughout the Park on sensitive vegetation.

Innovations in non-isotopic DNA sequencing: using an electrotransfer unit to blot sequencing gels and an automated membrane processor for detecting DNA sequences

As alternatives to radiolabeled DNA sequencing, chemiluminescent and chromogenic sequencing methods can be comparable in both sensitivity and resolution. Chemiluminescent/chromogenic detection procedures are safer because they completely eliminate the handling and use of radioisotopes. One method involves standard dideoxy DNA sequencing reactions that are initiated with biotinylated primers, separated by gel electrophoresis, transferred onto nylon membrane and detected utilizing chemiluminescent 1,2-dioxetane substrates for alkaline-phosphatase. Alkaline phosphatase is linked to the biotinylated sequencing products by a streptavidin/alkaline phosphatase conjugate (SAAP). In this paper we describe an optimized procedure for transferring sequencing gels. The procedure is based on a semidry method developed at Hoefer Laboratories using the GeneSweep Sequencing Gel Transfer Unit. Transfer is rapid, uniform and reliable from gel to gel. We also describe automation of the development process using a fully programmable Gel/Membrane Processor that automates delivery, incubation and disposal of reagents. All crucial points for electrotransfer of sequencing gels and the detection of biotinylated DNA sequencing reaction products are discussed.

K-ras mutations in benzotrichloride-induced lung tumors of A/J mice

Benzotrichloride (BTC) is used extensively as a chemical intermediate in the synthesis of benzoyl chloride and benzoyl peroxide. Epidemiological data suggest that BTC is a human lung carcinogen. BTC is also a carcinogen in the A/J mouse lung tumor bioassay. Activated K-ras protooncogenes were detected in BTC-induced lung tumors from A/J mice. The polymerase chain reaction was used to amplify specific DNA segments likely to contain activating mutations, and the amplified DNAs were sequenced to identify the mutation. The activating mutation present in the K-ras gene from all BTC-induced lung tumors (24/24) was a GC-->AT transition in codon 12. Thus, BTC may exert its carcinogenic action by activation of the K-ras protooncogene through a genotoxic mechanism.

Safe and cost-effective cleaning of pressure-monitoring transducers

The CDC category I recommendation for high-level disinfection of pressure-monitoring transducers between uses imposes substantial costs. This practice has not been shown to be useful when disposable transducer domes are used. A prospective, randomized, double-blind study assessed the consequences of wiping transducers with alcohol between uses rather than sterilizing with ethylene oxide. We studied 5,197 transducer courses with disposable domes involving 2,202 patients in intensive care units during 15 months. There was no significant difference between the two treatment regimens in the risk of positive cultures of fluids from monitored lines, of cultures of cannula tips or of a positive blood culture. We conclude that under normal conditions, ie, in the absence of a cluster of transducer-related bacteremias, wiping transducers with alcohol between uses is sufficient when disposable domes are used.

Membrane translocation and insertion of NH2-terminally anchored gamma-glutamyl transpeptidase require a signal recognition particle

The two subunits of the renal brush border enzyme, gamma-glutamyl transpeptidase (EC 2.3.2.2), are derived from a single-chain propeptide. The membrane-spanning domain consists of a hydrophobic sequence near its NH2-terminus and the protein is oriented with its NH2-terminus on the cytoplasmic side. The enzyme is synthesized without a cleavable signal sequence. Translocation and insertion of this enzyme have been shown to be dependent on the signal recognition particle and presumably require the same translocation machinery that other secretory and membrane proteins use for these processes.

A multivariate analysis of risk factors for hepatitis B virus infection among hospital employees screened for vaccination

Previous studies of risk factors for hepatitis B virus infection among hospital employees have been based on surveys in single institutions or have been analyzed with univariate techniques. From November 1980 through August 1981, the authors performed a multi-institutional seroepidemiologic survey of hospital employees screened for entrance into a hepatitis B vaccine trial who represented groups at high risk for hepatitis B infection. Using a logistic regression model for the analysis of risk factors, the investigators determined the relative odds and 95% confidence intervals for risk of hepatitis B infection to be as follows: race (nonwhite/white: 3.4; 2.4-4.8) (p less than 0.001); history of acute viral hepatitis of an unspecified type (3.6; 2.2-5.9) (p less than 0.001); and employment at hospitals 1 through 5 as compared with hospital 6 (1.8; 1.1-2.9) (p = 0.015). In addition, certain job categories and the duration of employment within some of these categories were associated with increasing risk for hepatitis B infection over time. Laboratory workers (1.4; 1.2-1.7), surgical staff (1.2; 1.1-1.4), and medical staff (1.3; 1.1-1.5) had significant (p less than 0.05) increased risk of prior infection with longer duration of employment. Such time-job interaction was not demonstrable for nursing staff, anesthesiology staff, dental personnel, pathology staff, or ancillary personnel. The logistic regression model also shows that the highest gradient of risk for laboratory workers, surgeons, and medical staff occurs during the first five years of employment. An effective preventive strategy, such as the use of hepatitis B vaccine, should be targeted for these groups at the time of initial employment.

In vitro translation and processing of rat kidney gamma-glutamyl transpeptidase

Rat kidney gamma-glutamyl transpeptidase is composed of two nonidentical glycosylated subunits. The enzyme is localized on the lumenal surface of the brush-border membranes of proximal tubule epithelial cells; it is attached to the membranes via an NH2-terminal segment of the larger of the two subunits. Tissue-labeling experiments followed by immunoprecipitation with antibodies directed against the enzyme and its two subunits demonstrate that a glycosylated single chain precursor (Mr = 78,000), containing the elements of both the subunits, is initially synthesized. Pulse-chase studies in the presence of pactamycin, and inhibitor of protein synthesis initiation, indicate that the larger of the two subunits is located at the NH2 terminus of the Mr = 78,000 precursor. The initial events in the biosynthesis and processing of gamma-glutamyl transpeptidase were investigated by in vitro translation of rat kidney mRNA. Such translation results in the synthesis of a Mr = 63,000 unglycosylated polypeptide which has been shown immunologically to contain the domains for both subunits. The Mr = 63,000 species is processed to a Mr = 78,000 core-glycosylated polypeptide when translation of mRNA is carried out in the presence of dog pancreas microsomes. This processing does not appear to be associated with cleavage of an NH2-terminal leader sequence. The Mr = 78,000 polypeptide is integrated into the microsomal membranes with an orientation that is analogous to that found on the brush-border membranes. Glycosylation and membrane integration of transpeptidase are cotranslational events. Upon longer incubation, the Mr = 78,000 species sequestered within the microsomal vesicles is cleaved to species corresponding in size to the two subunits of the kidney enzyme.

Biosynthesis of rat renal gamma-glutamyl transpeptidase. Evidence for a common precursor of the two subunits

Rat kidney gamma-glutamyl transpeptidase is an amphipathic heterodimer, anchored to the lumenal surface of brush-border membranes via the NH2-terminal portion of its heavy subunit. The Mr values of the two subunits of detergent-solubilized enzyme are approximately 51,000 (heavy) and 22,000 (light), respectively. Biosynthesis of transpeptidase was studied in renal slices incubated with L-[35S]methionine. Transpeptidase-related proteins were isolated by immunoprecipitation with anti-transpeptidase antibodies. The major species seen after relatively short pulse times is a 78,000-dalton protein. Immunological characterization, kinetic, and pulse-chase studies indicate that the Mr = 78,000 species is the precursor of the two subunits of the enzyme. Like the dimeric enzyme, the Mr = 78,000 species contains both the core and the peripheral sugar, fucose, on its oligosaccharide moieties. Since, only the labeled dimeric enzyme appears in the brush-border membranes, conversion of the Mr = 78,000 species to the two subunits presumably occurs after its arrival at the Golgi but before its transport to the brush-border surface.