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Point mutations can be used as biomarkers to perform diagnosis for diseases. In this study, a nanorobot for low-abundance point mutation enrichment was constructed using DNA origami. The novel design achieved limits of detection of 0.1% and 1% for synthesized DNA samples and clinical gene samples, respectively. Resettability was a key property of this method, which also involved a simpler process, lower cost and shorter detection duration than traditional enrichment methods. This novel DNA nanorobot may enable the detection of tumor markers, potentially facilitating early cancer diagnosis.

Rare earth elements (REE) are used in products requiring high technology and the defense industry and they have recently been on the agenda with their strategic importance. With the restrictions imposed on exports by China, which has a monopoly in terms of production and reserve, other countries producing high technology have started to search for new REE resources. Primary commercial REE minerals are bastnasite, monazite, and xenotime. Countries that do not have these mineral resources have begun to search for new sources and new processes using secondary REE minerals such as eudialyte, loparite, pyrochlore, anklicite and aegirine. Within the scope of this study, after giving general information such as REE minerals, reserves and production status in the world, and their usage areas, information about the concentration methods from primary and secondary mineral resources, case studies, and process flow charts are compiled., Nadir toprak elementleri (NTE), sahip olduğu özellikler sayesinde yüksek teknoloji gerektiren ürünlerde ve savunma sanayiinde kullanılmakta olup, stratejik öneme sahip olmaları ile son zamanlarda gündemdedirler. Üretim ve rezerv konusunda tekel konumda olan Çin’in ihracata getirdiği sınırlamalar ile birlikte yüksek teknoloji üreten ülkeler kaynak arayışına başlamıştır. Ticari olarak birincil NTE mineralleri bastnazit, monazit ve ksenotimdir. Bu minerallere sahip olmayan ülkeler ikincil NTE minerallerinden [Eudialyte (Ödalit), loparit, piroklor, anklisit, aegirine (egrin)] üretimleri araştırmaya ve işlemeye başlamışlardır. Bu çalışma kapsamında NTE mineralleri, dünyadaki rezerv ve üretim durumu, kullanım alanları gibi genel bilgilere değinildikten sonra, birincil ve ikincil mineral kaynaklarından konsantre elde edilmesinde uygulanan yöntemler, yapılan çalışmalar ve proses akım şemaları ile ilgili bilgiler derlenmiştir.

Short open reading frame (sORF)-encoded polypeptides (SEPs) have recently emerged as key regulators of major cellular processes. Computational methods for the annotation of sORFs combined with transcriptomics and ribosome profiling approaches predicted the existence of tens of thousands of SEPs across the kingdom of life. Although, we still lack unambiguous evidence for most of them. The method of choice to validate the expression of SEPs is mass spectrometry (MS)-based peptidomics. Peptides are less abundant than proteins, which tends to hinder their detection. Therefore, optimization and enrichment methods are necessary to validate the existence of SEPs. In this article, we discuss the challenges for the detection of SEPs by MS and recent developments of biochemical approaches applied to the study of these peptides. We detail the advances made in the different key steps of a typical peptidomics workflow and highlight possible alternatives that have not been explored yet.

The problem of intelligent information retrieval and semantic enrichment becomes more and more popular due to the difficulty of searching and analyzing large text datasets. The common approach assumes user manual queries in natural language. Various semantic enrichment methods and intelligent text searching allow obtaining more accurate results leading to broader knowledge and user satisfaction. This research presents state-of-the-art methods of searching with enrichment and building rankings of results for the expert recruitment process in IT industry. The proposed model implements full-text search, semantic enrichment, and machine learning to match experts with job offers. Different data sources on expert competencies were used, including curricula vitae, historical data, and Internet resources. The testing results confirm an improvement in the search quality compared to the existing systems in the recruitment company.

Protein post-translational modifications and protein interactions are the central research areas in mass-spectrometry-based proteomics. Protein post-translational modifications affect protein structures, stabilities, activities, and all cellular processes are achieved by interactions among proteins and protein complexes. With the continuing advancements of mass spectrometry instrumentations of better sensitivity, speed, and performance, selective enrichment of modifications/interactions of interest from complex cellular matrices during the sample preparation has become the overwhelming bottleneck in the proteomics workflow. Therefore, many strategies have been developed to address this issue by targeting specific modifications/interactions based on their physical properties or chemical reactivities, but only a few have been successfully applied for systematic proteome-wide study. In this review, we summarized the highlights of recent developments in the affinity enrichment methods focusing mainly on low stoichiometric protein lipidations. Besides, to identify potential glyoxal modified arginines, a small part was added for profiling reactive arginine sites using an enrichment reagent. A detailed section was provided for the enrichment of protein interactions by affinity purification and chemical cross-linking, to shed light on the potentials of different enrichment strategies, along with the unique challenges in investigating individual protein post-translational modification or protein interaction network.

Environmental DNA (eDNA) metabarcoding from water samples has, in recent years, shown great promise for biodiversity monitoring. However, universal primers targeting the cytochrome oxidase I (COI) marker gene popular in metazoan studies have displayed high levels of nontarget amplification. To date, enrichment methods bypassing amplification have not been able to match the detection levels of conventional metabarcoding. This study evaluated the use of universal metabarcoding primers as capture probes to either isolate target DNA or to remove nontarget DNA, prior to amplification, by using biotinylated versions of universal metazoan and bacterial barcoding primers, namely metazoan COI (mlCOIintF) and bacterial 16S (515F). Additionally, each step of the protocol was assessed by amplifying for both metazoan COI (mlCOIintF/jgHCO2198) and bacterial 16S (515F/806R) to investigate the effect on the metazoan and bacterial communities. Bacterial read abundance increased significantly in response to the captures (COI library), while the quality of the captured DNA was also improved. The metazoan-oriented probe captured bacterial DNA in a range that was also amplifiable with the 16S primers, demonstrating the ability of capture probes to isolate fragments of DNA spanning over a longer distance than perhaps expected, from eDNA. Although the use of the tested COI probe cannot be recommended for metazoan enrichment, based on the experimental results, the concept of capturing these longer fragments could be applied to metazoan metabarcoding. By using a truly conserved site without a high-level taxonomic resolution as a target for capture, it may be possible to isolate DNA fragments large enough to span over a nearby barcoding region (e.g., COI), which can then be processed through a conventional metabarcoding-by-amplification protocol.

PURPOSE: The objective of the present study was to purify sheep spermatogonial stem cells (SSCs) from testicular isolate using combined enrichment methods and to study the effect of growth factors on SSC stemness during culture. METHODS: The testicular cells from prepubertal male sheep were isolated, and SSCs were purified using Ficoll gradients (10 and 12%) followed by differential plating (laminin with BSA). SSCs were cultured with StemPro®-34 SFM, additives, and FBS for 7 days. The various doses (ng/ml) of growth factors, EGF at 10, 15, and 20, GDNF at 40, 70, and 100 and IGF-1 at 50, 100, and 150 were tested for the proliferation and stemness of SSCs in vitro. The stemness in cultured cells was assessed using SSC markers PLZF, ITGA6, and GFRα1. RESULTS: Ficoll density gradient separation significantly (p

The generation of growth curves is a common and established method for determining the properties of bacterial strains. Such properties can be growth rates in enrichment broths or resistance to antibiotics. Enrichment methods are the gold standard for enumerating bacteria and determining growth properties. Newer methods can use agents that are metabolized during bacterial growth, which leads to a shift in fluorescence. This principle is used, for example, to measure viable bacterial cells. In this work, a real-time thermal cycler was used to cultivate bacteria and measure the change in fluorescence during bacterial growth to determine the generation time of different bacterial strains. The ability of the real-time diagram enables a significant simplification and increase in cost efficiency in the generation of bacterial growth curves. It was also possible to monitor the susceptibility of bacteria to antibiotic resistance, which opened another important application of this technique.

Circulating tumor cell (CTC) analysis as a liquid biopsy can be used for early diagnosis of cancer, evaluating cancer progression, and assessing treatment efficacy. The enrichment of CTCs from patient blood is important for CTC analysis due to the extreme rarity of CTCs. This paper updates recent advances in CTC enrichment methods. We first review single-modality methods, including biophysical and biochemical methods. Hybrid-modality methods, combining at least two single-modality methods, are gaining increasing popularity for their improved performance. Then this paper reviews hybrid-modality methods, which are categorized into integrated and sequenced hybrid-modality methods. The state of the art indicates that the CTC capture efficiencies of integrated hybrid-modality methods can reach 85% or higher by taking advantage of the superimposed and enhanced capture effects from multiple single-modality methods. Moreover, a hybrid method integrating biophysical with biochemical methods is characterized by both high processing rate and high specificity.

Protein synthesis and degradation responding to environmental cues is critical for understanding the mechanisms involved. Chemical proteomics introducing bioorthogonal tagging into proteins and isolation by biotin affinity purification is applicable for enrichment of newly synthesized proteins (NSPs). Current enrichment methods based on biotin-streptavidin interaction lack efficiency to release enriched NSPs under mild conditions. Here we designed a novel method for enriching newly synthesized peptides by click chemistry followed by release of enriched peptides via tryptic digestion based on cleavable bioorthogonal tagging (CBOT). CBOT-modified peptides can further enhance identification in mass spectrometry analysis and provide a confirmation by small mass shift. Our method achieved an improvement in specificity (97.1%) and sensitivity for NSPs in cell lysate, corresponding to profiling at a depth of 4335 NSPs from 2 mg of starting materials in a single LC-MS/MS run. In addition, the CBOT strategy can quantify NSPs when coupling a pair of isotope-labeled azidohomoalanine (AHA/hAHA) with decent reproducibility. Furthermore, we applied it to analyze newly synthesized proteomes in the autophagy process after 6 h rapamycin stimulation in cells, 2910 NSPs were quantified, and 337 NSPs among them were significantly up- and down-regulated. We envision CBOT as an effective and alternative approach for bioorthogonal chemical proteomics to study stimuli-sensitive subsets.

Autologous Chimeric Antigen Receptor (CAR) T cell manufacturing involves the modification and expansion of T cells obtained by apheresis collection from a patient. The mechanism of apheresis collection and the specific clinical features seen in these patients combine to generate apheresis products with high variability of content. Manufacturers often attempt to minimize this variability such that processes can be standardize in accordance with Good Manufacturing Practices (GMP). Such standardization improves efficiency and helps to ensure robustness of the overall process. Apheresis product variability can negatively impact T cell manufacturing success. Patient and collection driven variability often leads to non-T cells entering the apheresis product. Many of these cells can directly or indirectly impair T cell activation and expansion, decreasing the manufacturing success rate. Therefore, patient driven variability observed in apheresis products, must be mitigated through downstream processing. T cell enrichment is one step in the manufacturing cycle that can reduce process variability by generating more uniform downstream material. However, current T cell enrichment methods have limitations. Much of this type of variability can be avoided by collecting patients earlier in their disease or treatment course, this is not current, widespread or standard practice. While variability poses challenges to successful CAR T cell manufacturing and mitigation strategies can be successful, more work is needed in this area.

Pancreatic cancer remains one of the deadliest types of cancer with little or no recent evidence of significant improvement in survival. This is, in large part, due to the current unavailability of effective screening or even early detection methods. Circulating tumor cells (CTCs), particularly with the rapidly improving methods for isolation, enrichment, and characterization methods, have emerged as the next best hope to overcome these challenges. This paper reviews the current state-of-the-art of CTC technologies with particular focus on the various isolation and enrichment methods based on liquid biopsy, the current limitations of these technologies and, consequently, the areas of further research and improvements in CTC methods that are needed to translate it to the clinical setting of routine diagnosis, treatment, and management of pancreatic cancer. Key words: Circulating tumor cells; Pancreatic cancer; Translational medicine

Radon-222 (222Rn) is increasingly being used to measure and map groundwater-surface water interactions in natural waters. However, the direct measurement, without prior enrichment of 222Rn, allowing for a lower limit of detection of 0.2 BqL−1 is not sensitive enough to study 222Rn concentrations in the water close to or below 0.2 BqL−1. 222Rn enrichment prior to measurement, to increase the number of measured 222Rn decays, enables for improved measurement sensitivity. Here we show the influence of every parameter of 222Rn measurement and enrichment to enable optimisation of the 222Rn measurement.

Preparation of high-quality boron nitride nanotubes (BNNTs) from commercially available stock is critical for eventual industry adoption and to perform comprehensive experimental studies of BNNTs. Separation of hexagonal boron nitride (h-BN) and BNNTs is a significant challenge, and equally so, quantification of h-BN content in mixed samples is a major challenge due to their nearly identical properties. This work introduces a simple method of quantifying h-BN content in BNNTs based on FTIR analysis. Quantification is achieved by “spiking” a BNNT sample with pure nanoscale h-BN as an internal standard. To demonstrate the efficacy of the quantification technique two BNNT enrichment methods, surfactant wrapping and centrifugation, and a novel sonication-assisted isovolumetric filtration are introduced. FTIR spectra of enriched samples show clear trends throughout the processes. We propose and demonstrate that FTIR peak ratios of the transverse and buckling modes of mixed h-BN/BNNT samples can be used to calibrate and quantify h-BN content in any BNNT sample. Hopefully, this method enables as-received BNNTs to be quantifiably enriched from low purity commercial feedstocks, enabling future development and study of BNNTs and related technology.

There is an ever-increasing amount of engineered nanoparticles (ENPs) released into aquatic environments due to human activities. The sophisticated and accurate detection of ENPs is imperative to assess the threat of ENPs to the environment and human health, as well as to establish the benchmarks for controlling ENP discharge. The present review aims at summarizing and evaluating the current situation of ENP detection in water systems. Attention has been focused on the development of ENP detection processes and technologies. Given their extremely small size, low mass concentration, high activities, and complex coexisting components in the environmental matrixes, the online or in situ analysis of aquatic ENPs is proposed to be achieved via enrichment–separation–detection. Multiple ENP enrichment methods have been adopted, including coagulation, flotation, filtration (membrane processes), and extraction, followed by microfluidic separation and sorting. The enriched ENPs are then qualitatively and/or quantitatively measured under controlled conditions (by microfluidic devices) in terms of size (via nanoparticle tracking analysis, NTA), concentration (via NTA, inductively coupled plasma mass or Raman spectrometry), and species (via electrochemical and fluorogenic methods). In spite of the technical development, most of the research is carried out in a laboratory or on the bench scale. The lack of online and in situ measurement systems, as well as the implementation in different worldwide regions, have led to the unavailability of a single database of aquatic ENPs.

Enrichment of modified peptides from global peptides is inevitable in mass spectrometric analysis protein modifications because of their importance in the study of cellular functions and low abundance in the global proteomic analysis. Recent advances in enrichment methods for modified peptides such as phosphopeptides and intact glycopeptides (IGPs) show that the methods for proteomic analyses of both protein modifications are robust. We have recently observed and reported a large number of IGPs from phosphoproteomic analysis using IMAC-based phosphopeptides enrichment procedure. To determine whether phosphorylated peptides could be specifically isolated from coenriched IGPs in IMAC experiments with different pH, IMAC procedures were performed at different pH conditions, and we found that the enrichment of phosphopeptides at pH 2.0 was the optimal condition for having the highest number of phosphopeptide identifications; however, coenrichment of phosphopeptides and glycopeptides was inevitable in the entire pH range. The hydrophilic enrichments of IGPs performed before or after IMAC enrichment were evaluated subsequently to determine the optimal workflow for simultaneous analyses of phosphopeptides and glycopeptides, and IMAC enrichment followed by hydrophilic enrichment was chosen as the optimized workflow. Applying the workflow to the TMT-labeled peptides from luminal and basal-like type of breast cancer patient-derived xenograft (PDX) models allowed quantitative analyses of phospho- and glycoproteomics with 17582 phosphopeptides and 3468 glycopeptides identified, and 1237 phosphopeptides and 236 glycopeptides showed significant expression differences between luminal and basal-like, respectively. This method allows simultaneous analyses of phosphoprotein and glycoprotein modifications, extending our understanding of roles of glycosylation and phosphorylation in biology and diseases.

Circulating tumor cells (CTCs) are rare cells shed into the bloodstream by invasive tumors and their analysis offers a promising noninvasive tool to predict and monitor therapeutic responses. CTCs can be isolated from patient blood and their characterization at single‐cell level can inform on the genomic landscape of a tumor. All CTC enrichment methods bear a burden of contaminating normal cells, which mandate a further step of purification to enable reliable downstream genetic analysis. Here, we describe the DEPArray™ technology, a microchip‐based digital sorter, which combines precise microfluidic and microelectronic enabling precise, image‐based isolation of single CTCs, which can then be analyzed by Next Generation Sequencing (NGS) methods. © 2018 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.

The objective of the study was to investigate the efficiency of three enrichment methods to separate boar spermatozoa. Twenty-four ejaculates from 12 boars (2 ejaculates/boar) were extended (30 × 106 spermatozoa/mL) in commercial Beltsville Thawing Solution. Each semen sample was processed with glass wool column (GW) and glass beads (GB) filtration and with the single-layer centrifugation (SLC) technique. Semen samples before (control; C) and after treatment were evaluated for sperm CASA motility/kinetics and concentration, viability, morphology and chromatin integrity. Data were analysed with mixed models. The concentration of total and motile spermatozoa was significantly decreased after treatment in groups GW and SLC, but not in group GB. Group GW showed increased values of WOB compared with both groups C and GB. Group GB showed greater values of rapid movement spermatozoa and lower values of slow movement spermatozoa compared with group C. In group SLC, higher values of VSL, LIN and STR were observed compared with group C. In conclusion, all techniques under examination enhanced various CASA variables. Based on our results, the GB method is a promising alternative separation technique for boar sperm and deserves further research regarding swine in vitro fertilization.

Animals in managed care ideally are provided with environmental stimuli for their psychological and physiological well-being. Most commonly, food-based enrichment methods are used to mimic wild conditions, allowing animals to search and forage. Other sensory stimulation devices may be employed to reduce stereotypical behaviors. However, many of these devices fall short in providing choice and control to animals, an important factor in cognitive engagement. In this paper, we present a case study conducted at the San Diego Zoo that explores such design for two elephants. The resultant system, called Soundyssey, is an active auditory enrichment device for elephants that encourages play behaviors through embodied interaction. Our preliminary results indicate that elephants understood the system and interacted with the interface significantly longer than with passive objects. During the interactions, elephants showed more positive behaviors such as focused exploration, reducing the possibility of negative stereotypical behaviors. We suggest that such technologically-enhanced objects and embodied design can enhance standards of managed animal care.

The circRNAs sequencing results vary due to the different enrichment methods and their performance is needed to systematic comparison. This study investigated the effects of different circRNA enrichment methods on sequencing results, including abundance and species of circRNAs, as well as the sensitivity and precision. This experiment was carried out by following four common circRNA enrichment methods: including ribosomal RNA depletion (rRNA–), polyadenylation and poly (A+) RNA depletion followed by RNase R treatment (polyA+RNase R), rRNA–+polyA+RNase R and polyA+RNase R+ rRNA–. The results showed that polyA+RNase R+ rRNA – enrichment method obtained more circRNA number, higher sensitivity and abundance among them; polyA+RNase R method obtained higher precision. The linear RNAs can be thoroughly removed in all enrichment methods except rRNA depletion method. Overall, our results helps researchers to quickly selection a circRNA enrichment of suitable for own study among many enrichment methods, and it provides a benchmark framework for future improvements circRNA enrichment methods.

Ancient Y-Chromosomal DNA is an invaluable tool for dating and discerning the origins of migration routes and demographic processes that occurred thousands of years ago. Driven by the adoption of high-throughput sequencing and capture enrichment methods in paleogenomics, the number of published ancient genomes has nearly quadrupled within the last three years (2018–2020). Whereas ancient mtDNA haplogroup repositories are available, no similar resource exists for ancient Y-Chromosomal haplogroups. Here, we present aYChr-DB—a comprehensive collection of 1797 ancient Eurasian human Y-Chromosome haplogroups ranging from 44 930 BC to 1945 AD. We include descriptors of age, location, genomic coverage and associated archaeological cultures. We also produced a visualization of ancient Y haplogroup distribution over time. The aYChr-DB database is a valuable resource for population genomic and paleogenomic studies.

Introduction Elevated β-amyloid is used to enroll individuals into preclinical Alzheimer's disease trials, but the screening process is inefficient and expensive. Novel enrichment methods are needed to improve efficiency of enrollment. Methods Alzheimer's disease incidence rates and a polygenic hazard score were used to create a gene- and age-defined ADAge. An ADAge cutpoint was chosen to optimally predict β-amyloid positivity among clinically normal Alzheimer's Disease Neuroimaging Initiative participants and applied to an independent Alzheimer's Disease Research Center validation cohort. The impact of ADAge enrichment on screening costs was evaluated in the Anti-Amyloid Treatment in Asymptomatic Alzheimer's Disease trial data. Results In the validation cohort, the ADAge-enriched sample had a higher proportion of individuals with elevated β-amyloid (difference [95% CI] 0.19[0.07 to 0.33]) than the unenriched sample. ADAge enrichment lowered screening costs by $4.41 million (31.00%) in the real-world clinical trial scenario. Discussion ADAge enrichment provides for a more efficient and cost-effective means to enroll clinically normal individuals with elevated β-amyloid in clinical trials.

Background Whole-genome sequencing (WGS) of Treponema pallidum subspecies pallidum (TPA) has been constrained by the lack of in vitro cultivation methods for isolating spirochetes from patient samples. Methods We built upon recently developed enrichment methods to sequence TPA directly from primary syphilis chancre swabs collected in Guangzhou, China. Results By combining parallel, pooled whole-genome amplification with hybrid selection, we generated high-quality genomes from 4 of 8 chancre-swab samples and 2 of 2 rabbit-passaged isolates, all subjected to challenging storage conditions. Conclusions This approach enabled the first WGS of Chinese samples without rabbit passage and provided insights into TPA genetic diversity in China.

Progress in technology and increasing knowledge of molecular biology resulted in a variety of transcriptomic expression profiling platforms. Bioinformatics supports this development with various computational techniques like, for example, pathway enrichment analysis. The presented study shows a comprehensive comparison of different transcriptomic platforms and methods of signalling pathway enrichment analysis. All analyses were performed on carefully chosen datasets with control after the most common confounding factors (disease phenotype, experimental design and sample size). It was shown that the most significant differences are observed between enrichment methods themselves rather than transcriptomic profiling platforms. Out of tested methods, CERNO and its combination with SPIA show the highest robustness to the molecular biology technique while ORA enrichment method shows little affection to tested platforms.

Various methods exist for the enrichment and detection of Listeria spp. and Listeria monocytogenes from environmental samples. Procedures for the compositing of environmental samples are not as well defined. In this study, different enrichment procedures involving buffered Listeria enrichment broth (BLEB), University of Vermont medium (UVM), and Fraser broth (FB) were evaluated to determine the limits of detection (LODs) for L. monocytogenes from culture and from swabs of stainless steel and to assess the efficacy of composite sampling by wet (pooling of primary enrichments) and dry (pooling of swabs) procedures. For detection of cells in pure culture, the computed values for the LOD at 95% probability (LOD95) using a single-step BLEB or two-step UVM-FB enrichment were 0.33 and 0.49 CFU/225 mL enrichment, respectively. No significant differences in detection were observed for procedures using either two-step BLEB-FB or UVM-FB enrichments for swabs of stainless steel when L. monocytogenes was inoculated at 2 to 6 log CFU; the LOD95 values were 3.82 and 3.62 log CFU per 4-in2 area, respectively. Wet compositing of L. monocytogenes from culture with and without romaine lettuce wash resident microbiota was conducted using BLEB-FB and UVM-FB enrichment methods; both allowed detection of the pathogen at ratios of 1:1, 1:2, 1:4, and 1:7 (1 positive sample to x negative samples) with no loss in sensitivity. From swabs of stainless steel, L. monocytogenes was detected similarly for both wet and dry composites of up to eight samples (1:7) with romaine lettuce wash. However, the BLEB-FB method allowed significantly faster detection (after 24 h of FB incubation) in composites of 1:4 and 1:7 samples compared with the UVM-FB method under the conditions tested. The results of this study provide data to evaluate the efficacies of the different enrichment procedures and aid in assessing the use of wet and dry compositing of environmental samples for use as part of a Listeria control plan in food production and processing facilities. HIGHLIGHTS

BackgroundThe global COVID-19 pandemic has led to an urgent need for scalable methods for clinical diagnostics and viral tracking. Next generation sequencing technologies have enabled large-scale genomic surveillance of SARS-CoV-2 as thousands of isolates are being sequenced around the world and deposited in public data repositories. A number of methods using both short- and long-read technologies are currently being applied for SARS-CoV-2 sequencing, including amplicon approaches, metagenomic methods, and sequence capture or enrichment methods. Given the small genome size, the ability to sequence SARS-CoV-2 at scale is limited by the cost and labor associated with making sequencing libraries.ResultsHere we describe a low-cost, streamlined, all amplicon-based method for sequencing SARS-CoV-2, which bypasses costly and time-consuming library preparation steps. We benchmark this tailed amplicon method against both the ARTIC amplicon protocol and sequence capture approaches and show that an optimized tailed amplicon approach achieves comparable amplicon balance, coverage metrics, and variant calls to the ARTIC v3 approach.ConclusionsThe tailed amplicon method we describe represents a cost-effective and highly scalable method for SARS-CoV-2 sequencing.

Microbiological surveillance of the food chain plays a critical role in improving our understanding of the distribution and circulation of food-borne pathogens along the farm to fork continuum toward the development of interventions to reduce the burden of illness. The application of molecular subtyping to bacterial isolates collected through surveillance has led to the identification of strains posing the greatest risk to public health. Past evidence suggests that enrichment methods for Campylobacter jejuni, a leading bacterial foodborne pathogen worldwide, may lead to the differential recovery of subtypes, obscuring our ability to infer the composition of a mixed-strain sample and potentially biasing prevalence estimates in surveillance data. To assess the extent of potential selection bias resulting from enrichment-based isolation methods, we compared enrichment and non-enrichment isolation of mixed subtype cultures of C. jejuni, followed by subtype-specific enumeration using both colony plate-counts and digital droplet PCR. Results differed from the null hypothesis that similar proportions of C. jejuni subtypes are recovered from both methods. Our results also indicated a significant effect of subtype prevalence on isolation frequency post-recovery, with the recovery of more common subtypes being consistently favored. This bias was exacerbated when an enrichment step was included in the isolation procedure. Taken together, our results emphasize the importance of selecting multiple colonies per sample, and where possible, the use of both enrichment and non-enrichment isolation procedures to maximize the likelihood of recovering multiple subtypes present in a sample. Moreover, the effects of subtype-specific recovery bias should be considered in the interpretation of strain prevalence data toward improved risk assessment from microbiological surveillance data.

Цель исследования усовершенствование способа обогащения растений чеснока селеном до уровня суточной нормы потребления путем обработки вегетирующих растений растворами селенитов натрия и калия в сочетании с поверхностно-активными веществами и диметилсульфоксидом. Исследования проведены во ВНИИО филиале ФГБНУ ФНЦО, в условиях открытого грунта в 20162018 годах, на супесчаной почве, содержание гумуса в которой составляло 3,413,44, рНKCl 6,7, степень обеспеченности питательными веществами: фосфором высокая (содержание P2O5 в слое 020 см составляло 22,7824,62 мг (по Чирикову) калием низкая, содержание К2О в слое 20 см 10,3817,88 мг (по Масловой). Для улучшения минерального питания растений осенью под основную обработку в почву вносили калий хлористый в дозе 50 г/м2, в период вегетации проводили подкормки растений: первую, в фазе начала интенсивного роста листьев аммиачной селитрой 30 г/м2, вторую, через две недели после первой сульфатом калия 50 г/м2. Погодные условия в течение периода исследований были благоприятны для выращивания чеснока. Поливы проводили по мере подсыхания верхнего слоя почвы. Исследования проведены на чесноке озимом сорта Гладиатор. Схема опытов предполагала предпосадочное замачивание зубков в течение 30 мин. и последующую двукратную обработку вегетирующих растений 0,1-ным раствором селенита натрия и калия в сочетании с поверхностно активными веществами (1) и диметилсульфоксидом (1): первый раз в фазе начала интенсивного роста листьев и второй через три недели. Установлено, что некорневая обработка растений селенитом натрия была в 2,3 раза, а селенитом калия в 5,8 раза эффективнее, чем корневая. Сделан вывод о том, что луковицы чеснока, полученные, в результате некорневой обработки растений 0,1-ным раствором селенита натрия и калия в сочетании с поверхностно активными веществами и диметилсульфоксидом содержат в 145,3169,8 раза больше селена, чем контроль, что позволяет получить зубки, содержащие селен в концентрации 6,837,98 мг/кг. Суточная норма потребления чеснока составляет примерно 10 г, средняя потребность в селене составляет от 30 до 70 мкг. Учитывая, что содержание селена в обогащенной продукции составит 68,3 79,8 мкг/10 г чеснока предложенный способ обогащения позволяет в полной мере удовлетворить суточную потребность организма человека в этом микроэлементе., The aim of investigation was to improve the method of enrichment of garlic plants with selenium to the level of daily consumption rate by treatment of vegetative plants with solutions of sodium and potassium selenites in combination with surfactants. The investigations were carried out at ARRIVG branch of FSCVG, in open ground in 20162018, on sandy loam soil with humus content of 3.413.44, pHKCl 6.7, content of phosphorus (P2O5) in the layer 020 cm was 22.7824.62 mg (Chirikov) content of potassium (K2O) 10.3817.88 mg (Maslova). To improve mineral nutrition of plants fall under the basic treatment in the soil was added potassium chloride at a dose of 50 g/m2 during the growing season were plant nutrition: first, in the early phase of intensive growth of leaves ammonium nitrate 30 g/m2, the second, two weeks after the first potassium sulphate and 50 g/m2. Weather conditions during the period of growth were favorable for growing garlic. Watering was carried out at the periods where the top layer of soil was dried. Studies were carried out on variety Gladiator of winter garlic. The experimental design included soaking the cloves for 30 minutes before planting, and subsequent double treatment of vegetating plants with 0.1 solution of sodium and potassium selenite in combination with surfactants (1) and dimethyl sulfoxide (1): the first time in the phase of the beginning of intense leaf growth and the second time after 3 weeks. As a result of the investigations it was found that non-root treatment of plants with solutions containing selenium was more effective than root treatment. Non-root top dressing with sodium selenite was in 2.3 times, and potassium selenite in 5.8 times more effective than root. It is concluded that garlic bulbs obtained as a result of non-root treatment of plants with 0.1 solution of sodium and potassium Selenite in combination with surfactants and dimethylsulfoxide contain 145.3169.8 times more selenium than control, which allows to obtain teeth containing selenium in a concentration of 6.837.98 mg/kg. The daily consumption rate of garlic is approximately 10 g, the average need for selenium element is from 30 to 70 micrograms. Because of content of selenium in enriched products consisted of 68.3-79.8 mcg/10 g of garlic, the proposed method of enrichment allows to fully satisfy the daily need of the human body at this microelement., №1 (2020)