DNA Sequence Research Articles

Rare Pleurotus species with veiled basidiomata from the Neotropics: neotypification of Pleurotus magnificus and epityfication of Pleurotus rickii

Knowledge of Pleurotus in Brazil dates back to the 19th century, when European mycologists studied and described numerous Neotropical taxa. Some of these long-described species remain poorly known, mostly due to the lack of recent records, detailed morphological descriptions, and molecular data. During field surveys in Southeast and Southern Brazil, specimens of two rare Pleurotus species with veiled basidiomata, i.e. P. magnificus and P. rickii, were collected. These species are recorded for the first time in the state of Santa Catarina, Brazil, and P. magnificus for the first time in the states of Minas Gerais, Paraná and São Paulo. Updated and detailed morphological descriptions are provided. DNA sequences of the ITS and nLSU molecular markers were obtained for both species, and phylogenetic analyses were conducted to explore their relationships within Pleurotus. A neotype is designated for P. magnificus, and a lectotype and epitype are designated for P. rickii.

Cost‐Effective DNA Storage System with DNA Movable Type

AbstractIn the face of exponential data growth, DNA‐based storage offers a promising solution for preserving big data. However, most existing DNA storage methods, akin to traditional block printing, require costly chemical synthesis for each individual data file, adopting a sequential, one‐time‐use synthesis approach. To overcome these limitations, a novel, cost‐effective “DNA‐movable‐type storage” system, inspired by movable type printing, is introduced. This system utilizes prefabricated DNA movable types‐short, double‐stranded DNA oligonucleotides encoding specific payload, address, and checksum data. These DNA‐MTs are enzymatically ligated/assembled into cohesive sequences, termed “DNA movable type blocks,” streamlining the assembly process with the automated BISHENG‐1 DNA‐MT inkjet printer. Using BISHENG‐1, 43.7 KB of data files are successfully printed, assembled, stored, and accurately retrieved in diverse formats (text, image, audio, and video) in vitro and in vivo, using only 350 DNA‐MTs. Notably, each DNA‐MT, synthesized once (2 OD), can be used up to 10000 times, reducing costs to $122/MB—outperforming existing DNA storage methods. This innovation circumvents the need to synthesize entire DNA sequences encoding files from scratch, offering significant cost and efficiency advantages. Furthermore, it has considerable untapped potential to advance a robust DNA storage system, better meeting the extensive data storage demands of the big‐data era.

Ichthyobodo necator infection as a first record in cultured Dicentrarchus labrax: morphomolecular characterization and infestation patterns in correlation to water quality parameters

Abstract Ichthyobodo necator is a damaging and economically important protozoan parasite; however, its clinical patterns and incidence, correlated to environmental factors, are still poorly understood. This study provides the first report of Ichthyobodo necator infestation among Dicentrarchus labrax. We recorded significant mortalities in the cultured D. labrax of average size (5.92 g weight, and 11.55 cm length) in El-Max Station, National Institute of Oceanography and Fisheries, NIOF, Egypt, during the period extending from early summer to early fall (June to October) 2023. Behavioral and gross lesions of the infested fish were recorded; besides, dead and moribund fish were collected. Wet smears of the skin and gill of the affected fish were examined by compound light microscopy. Moreover, water samples from the affected ponds were collected and examined for their physicochemical parameters. The bodonid biflagellated Ichthyobodo necator (Henneguy) C. Pinto, 1928 was isolated from the skin and gills and identified based on specific morphological characteristics. DNA sequencing of PCR products and phylogenetic analysis confirmed identification, with clustering of the current isolates with I. necator isolates from different fish species. The multivariate analysis revealed a positive correlation between the prevalence and infestation intensity of Ichthyobodo, increased temperature levels, decreased dissolved oxygen DO, and also correlated with higher ammonia, and pH values. Additionally, the elevated concentrations of iron, calcium, magnesium, zinc, and copper in pond water were positively correlated with infestation and mortalities. These water parameter levels promote respiratory distress, accelerated prevalence, and infestation intensities of I. necator, particularly during the infestation peak in August and September. This study bridges the knowledge gap regarding I. necator parasite infestations and their correlation with water quality parameters.

Abstract B001: Intra- and inter-tumoral heterogeneity of melanoma across different metastatic sites

Abstract Melanoma, a highly metastatic skin cancer, exhibits variations in prognosis and response to therapy based on the site of metastasis. Despite the success of immunotherapy and targeted therapies in melanoma, over half of metastatic melanoma patients will experience disease progression due to therapy resistance. The heterogeneity and plasticity of melanoma cells contribute to metastatic dissemination and therapy resistance. Our aim is to determine whether distinct clones and/or their transcriptional cell states can predict the formation of tumors in various organs and assess how these clones change over time. To identify melanoma clones across different metastatic sites, NOD scid gamma (NSG) mice and C57BL/6 mice were injected subcutaneously, intravenously or intracranially with the same pool of cells of barcoded luciferase expressing YUMMER1.7 murine melanoma cells. Transduction conditions ensured that one DNA barcode integrated into cell genomes at one barcode per cell, serving as a lineage tag. Bioluminescence imaging was performed once a week to monitor tumor growth of mice injected intravenously and intracranially. Subcutaneous tumors were measured by calliper. Mice were euthanized at different time points; day 8, 15, 22, 29 post-implantation and at ethical endpoints. Tumors were harvested and DNA sequencing was performed to identify barcodes expressed by the tumor cells. All mice developed tumors, with 100% penetrance in NSG mice. However, in C57BL/6 mice, 10% of mice intravenously injected and 27% of subcutaneously implanted mice showed complete lesion regression, suggesting that the immune system may be responsible for tumor regression. Analysis of barcodes allowed us to assess the heterogeneity of melanoma tumors at different metastatic sites and their evolution over time. Lineage tracing and clonal heterogeneity will be evaluated using the state of art technology, SPLINTR (Single-cell Profiling and LINeage Tracing), enabling us to match a cells evolution with changes in transcriptional states. Barcode analysis performed before implanting the cells and, at different timepoints in subcutaneous and lung tumors showed that dominant subclones at the baseline were also dominant in subcutaneous and lung tumors in immunocompromised mice. In contrast, dominant subclones in immunocompetent mice was those present in lower proportion at baseline. Additionally, greater variability of subclones was observed especially in lung and brain tumors, across immunocompetent mice, likely as a mechanism of resistance, enabling these tumors to overcome immunoediting. Understanding the variability of clonality between different metastatic sites and over time will improve our comprehension of the role of different subclones in organ- specific metastasis and their transcriptional cell states. Citation Format: Veronica L. Aedo Lopez, Reem Saleh, Benjamin Blyth, Xin Du, Dane Vassiliadis, Katie Fennell, Davide Moi, Roberta Mazzieri, Riccardo Dolcetti, Karen E. Sheppard, Grant A. McArthur. Intra- and inter-tumoral heterogeneity of melanoma across different metastatic sites [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr B001.

Widely acclaimed but poorly named: Phylogeny and systematics of the African daisy genus Dimorphotheca (Asteraceae, Calenduleae)

AbstractPhylogenetic relationships in the South African daisy genus Dimorphotheca have long been uncertain, with the taxonomy of the genus relying on a few morphological traits, most prominently capitulum sexual system (e.g., cypsela type) and ray colour, which may not be evolutionarily conserved. Here we present the first well‐sampled molecular phylogeny of Dimorphotheca, based on nuclear ribosomal (ITS, ETS) and plastid trnL‐trnF region DNA sequences from multiple accessions per species. Although the relationships suggested by these markers are broadly congruent, we do find some instances of incongruence which we resolve using a combined decomposition and deletion approach. Using our best estimate of phylogenetic relationships, we reconstruct the evolution of capitulum fertility and ray colour to assess the evolutionary conservatism of these traits and their taxonomic utility. We find support for the monophyly of Dimorphotheca, excluding the recently segregated Osteospermum polypterum, and our data thus support the modern, enlarged circumscription of the genus incorporating the former genus Castalis and Osteospermum sect. Acanthotheca and O. sect. Blaxium. Major subclades within Dimorphotheca are largely cohesive in terms of geographic distribution and morphological traits such as growth form and cypsela structure. While many species are resolved as monophyletic, the polyphyly of a few species suggests a need for taxonomic re‐evaluation. On the basis of both morphological and molecular data, we describe one new species, and elevate one variety to species level. A full taxonomic key to the enlarged genus is presented for the first time. Ancestral reconstructions show that capitulum sexual system and ray lamina colour are not evolutionarily conserved and that neither can therefore be used to delimit major lineages within Dimorphotheca. While our findings resolve some taxonomic problems, they also highlight the need for further species‐level taxonomic work on Dimorphotheca.

The Impact of Biotechnology in Shaping the Modern Agriculture

Advances in biotechnology have created new opportunities for food diversity in terms of both quantity and quality, as well as for collecting food in proportion to the world's expanding population and ensuring food security. With the advancement of molecular biology, DNA sequencing, and recombinant DNA in the middle of the 20th century, modern-day advancement of molecular breeding gave rise to genetic engineering and recombinent DNA techniques that are today frequently connected to biotechnology. This expansion has been facilitated by a variety of fields, including genetics, molecular biology, and biotechnology. The use of genetic engineering in agriculture has grown due to its ability to precisely create and insert a gene from any living organism. Molecular markers are also utilized to identify disease and pest resistance in order to increase agricultural output using traditional techniques. Genetic engineering plays a crucial role in agriculture, representing the scientific and technical advancement of traditional methods for crop enhancement. Recombinant DNA technology, RNA interference, and CRISPR genomic editing are some of the instruments and methods used in genetic engineering. The emergence of biotechnological innovations aimed at improving the nutritional composition of individual foods has led to the growing problem of a malnourished world population, where a growing number of people rely on large regions of the world for food used as the only source of protein, carbohydrates, fats and several essential minerals and vitamins, in addition to being a source of energy.

Incidence, clinical manifestations and characterization of Enterovirus in the last decade (2014-2023) in Asturias (Spain). Effect of the SARS-CoV-2 pandemic.

Enteroviruses (EVs) are a large group of genotypes that cause a variety of pathologies, some of them very serious. This study analyzed the last 10 years (2014-2023) of EVs diagnosis and classification. In 166,674 samples collected, EVs were found in 9,535 (5.7%) by rt-RT-PCR, and 332 (3.5%) were classified by Sanger methods. Symptoms were analyzed in 7623 cases. EVs were found in 5718/63,829 (8.9%) before, 1384/42,373 (3.3%) during and 2433/60,472 (4%) after the Covid pandemic (p < 0.0001), and in 7249/69,700 (10.4%) children under 6 years and in 2286/96,974 (2.35%) in oldest (p < 0.0001). The positive rate of EVs was high but decreased during the Covid period. In the youngest children EVs-A (associated with exantematohous disorders as well as respiratory manifestations and febrile syndromes) was most common, while EVs-B (frequent in neurological symptoms) was most common in children aged 6-15 years and EVs-D (associated to respiratory manifestations) in adults.

Faecal sample storage without ethanol for up to 24h followed by freezing performs better than storage with ethanol for shotgun metagenomic microbiome analysis in patients with inflammatory and non-inflammatory intestinal diseases and healthy controls.

The influence of different faecal collection methods on metagenomic analyses remains under discussion, and there is no general agreement on which collection method is preferable for gut microbiome research. We compared faecal samples collected in tubes without preservatives with those containing 10mL of 96% ethanol for gut microbiome research when the timeframe from defecation to freezing at -80°C was up to 24h. We aimed to compare the collection methods on faeces from participants with inflammatory and non-inflammatory gastrointestinal disorders and healthy controls to investigate the most suitable method when considering data yield, human fraction of sequencing reads, and ease of use. We also examined the faecal sample homogeneity. Faeces collected in tubes without preservatives resulted in more sequencing reads compared to faeces collected in tubes with 96% ethanol and were also easier to handle. The human fraction of total reads in faeces collected in ethanol from participants with inflammatory bowel disease was higher than all other samples. DNA extraction and sequencing from two different locations in the same faecal sample gave similar results and showed sample homogeneity.

Orchid phylogenetics and evolution: history, current status and prospects.

Orchidaceae are one of the two largest families of angiosperms; they exhibit a host of changes -- morphological, ecological and molecular -- that make them excellent candidates for evolutionary study. Such studies are most effectively performed in a phylogenetic context, which provides direction to character change. Understanding of orchid relationships began in the pre-evolutionary classification systems of the 1800's that were based solely on morphology, and now is largely based on genomic analysis. The resulting patterns have been used to update family classification and to test many evolutionary hypotheses in the family. Recent analyses with dense sampling and large numbers of nuclear loci have yielded well-supported trees that have confirmed many longstanding hypotheses and overturned others. They are being used to understand evolutionary change and diversification in the family. These include dating the origination of the family, analysis of change in ecological habit (from terrestrial to epiphytic and back again in some cases), revealing significant plastid genome change in leafless holomycotrophs, studying biogeographic patterns in various parts of the world, and interpreting patterns of fungal associations with orchids. Understanding of orchid relationships has progressed significantly in recent decades, especially since DNA sequence data have been available. These data have contributed to an increasingly refined classification of orchids and the pattern has facilitated many studies on character evolution and diversification in the family. Whole genome studies of the family are just beginning and promise to reveal fine-level details underlying structure and function in these plants, and, when set in a phylogenetic context, provide a much richer understanding of how the family has been so successful in diversification.

Joseph G. Gall (1928-2024): Cell biologist, naturalist, and mentor extraordinaire.

Joseph Grafton Gall (1928-2024), a founder of modern cell biology, made foundational discoveries on eukaryotic chromosomes and RNA biogenesis. His major contributions include the development of in situ hybridization (later called FISH), demonstration of one DNA double helix/chromosome, isolation of the first eukaryote gene, localization of satellite DNA to centromeric heterochromatin, determination of the first telomeric DNA sequence, and elucidating the structure and functions of Cajal bodies. He was an expert microscopist, a scholar of science history, and an avid naturalist. These attributes, together with his ready embrace of new technologies, contributed to his remarkable success. He was also an early and strong supporter of women in science. His contributions to science and mentoring were recognized by numerous awards including the American Society for Cell Biology's E.B. Wilson Medal, the Society for Developmental Biology's Lifetime Achievement Award, the Albert Lasker Special Achievement Award in Medical Research, and the AAAS Mentor Award for Lifetime Achievement.

The Genomic SSR Millets Database (GSMDB): enhancing genetic resources for sustainable agriculture.

The global population surge demands increased food production and nutrient-rich options to combat rising food insecurity. Climate-resilient crops are vital, with millets emerging as superfoods due to nutritional richness and stress tolerance. Given limited genomic information, a comprehensive genetic resource is crucial to advance millet research. Whole-genome sequencing provides an unprecedented opportunity, and molecular genetic methodologies, particularly simple sequence repeats (SSRs), play a pivotal role in DNA fingerprinting, constructing linkage maps, and conducting population genetic studies. SSRs are composed of repetitive DNA sequences where one to six nucleotides are repeated in tandem and distributed throughout the genome. Different millet species exhibit genomic variations attributed to the presence of SSRs. While SSRs have been identified in a few millet species, the existing information only covers some of the sequenced genomes. Moreover, there is an absence of complete gene annotation and visualization features for SSRs. Addressing this disparity and leveraging the de-novo millet genome assembly available from the NCBI, we have developed the Genomic SSR Millets Database (GSMDB; https://bioinfo.icgeb.res.in/gsmdb/). This open-access repository provides a web-based tool offering search functionalities and comprehensive details on 6.747645 million SSRs mined from the genomic sequences of seven millet species. The database, featuring unrestricted public access and JBrowse visualization, is a pioneering resource for the research community dedicated to advancing millet cultivars and related species. GSMDB holds immense potential to support myriad studies, including genetic diversity assessments, genetic mapping, marker-assisted selection, and comparative population investigations aiming to facilitate the millet breeding programs geared toward ensuring global food security. Database URL: https://bioinfo.icgeb.res.in/gsmdb/.

Morphological and molecular data demonstrate the existence of Betula fruticosa and B. middendorffii and the absence of B. ovalifolia in northeastern China

Abstract Shrub birches are important components of massive wetlands in Northeast China, although much of these habitats have been lost over the past two decades. However, the taxonomy of shrub birches has been ambiguous owing to their morphological variation. In this study, we incorporated morphological and molecular data to address the taxonomic challenges associated with shrub birches. We characterized the morphological variation in the leaves, seeds, and bracts of 11 shrub birch populations in Northeast China and a population of Betula ovalifolia in northern Japan. We genotyped birch individuals from Northeast China at 15 microsatellite loci as well as a subset of individuals, using restriction site-associated DNA sequencing (RAD-seq). The populations in Northeast China consisted of B. fruticosa and B. middendorffii. These two species and B. ovalifolia differ in the width of their seed wings and the angle between the side lobes of their bracts, despite substantial intraspecific variation. Our genetic data revealed two distinct clusters, corresponding to B. fruticosa and B. middendorffii. Ploidy level assessment via RAD-seq revealed that B. fruticosa is diploid and B. middendorffii is tetraploid. Phylogenetic analysis revealed that B. fruticosa formed a sister clade to diploid B. humilis, and B. middendorffii formed a clade with diploid B. nana. Our results indicate the existence of B. fruticosa and B. middendorffii and the probable absence of B. ovalifolia in the northern Daxing’an Range, as all the tetraploid individuals sampled there represented B. middendorffii. In addition, our results suggest that B. humilis and B. nana may have served as diploid parents of the tetraploid species B. ovalifolia and B. middendorffii, respectively.

Unraveling the DNA methylation landscape in dog blood across breeds.

DNA methylation is a covalent bond modification that is observed mainly at cytosine bases in the context of CG pairs. DNA methylation patterns reflect the status of individual tissues, such as cell composition, age, and the local environment, in mammals. Genetic factors also impact DNA methylation, and the genetic diversity among various dog breeds provides a valuable platform for exploring this topic. Compared to those in the human genome, studies on the profiling of methylation in the dog genome have been less comprehensive. Our study provides extensive profiling of DNA methylation in the whole blood of three dog breeds using whole-genome bisulfite sequencing. The difference in DNA methylation between breeds was moderate after removing CpGs overlapping with potential genetic variation. However, variance in methylation between individuals was common and often occurred in promoters and CpG islands (CGIs). Moreover, we adopted contextual awareness methodology to characterize DNA primary sequences using natural language processing (NLP). This method could be used to effectively separate unmethylated CGIs from highly methylated CGIs in the sequences that are identified by the conventional criteria. This study presents a comprehensive DNA methylation landscape in the dog blood. Our observations reveal the similar methylation patterns across dog breeds, while CGI regions showed high variations in DNA methylation level between individuals. Our study also highlights the potential of NLP approach for analyzing low-complexity DNA sequences, such as CGIs.

PSATdb 2.0: a database of organellar common, polymorphic, and unique microsatellites.

Microsatellites, or simple sequence repeats (SSRs), are repetitive DNA sequences typically composed of 1-6 nucleotides. These repetitive sequences are found in almost all genomes, including chloroplasts and mitochondria, and are widely distributed throughout the genomes. Microsatellites are highly polymorphic, and their length may differ from species to species. Consequently, microsatellites are widely used as molecular markers and play pivotal roles in various biological research. However, comprehensive information about the length variation of microsatellites in various organellar genome sequences is not available. Therefore, to provide mined information and explore the variability in the length of microsatellites across species, we developed a comprehensive resource named pSATdb 2.0 (polymorphic microSATellites database; https://bioinfo.icgeb.res.in/psatdb/ ). This upgraded version of its predecessor pSATdb provides comprehensive information on the frequency and distribution of 348,894 microsatellites identified in organellar genome sequences. These sequences originate from 15,681 organisms spanning 3252 genera within Metazoa and Viridiplantae. Remarkably, pSATdb 2.0 is the only database that offers information on common and polymorphic microsatellites detected between organisms, along with unique microsatellites specific to each genus. Furthermore, this database features unrestricted access and includes pioneer functionalities such as Advanced Search, BLAST, and JBrowse, which facilitate user-specific microsatellite search and its visualization within the database. The pSATdb holds immense potential for the research community to support diverse studies, including genetic diversity, genetic mapping, marker-assisted selection, and comparative population investigations.

A genome-wide association study in Swedish colorectal cancer patients with gastric- and prostate cancer in relatives.

A complex inheritance has been suggested in families with colorectal-, gastric- and prostate cancer. Therefore, we conducted a genome-wide association study (GWAS) in colorectal cancer patients, who's relatives had prostate-, and/or gastric cancer. The GWAS analysis consisted of 685 cases of colorectal cancer and 4780 healthy controls from Sweden. A sliding window haplotype analysis was conducted using a logistic regression model.Thereafter, we performed sequencing to find candidate variants, finally to be tested in a nested case-control study. Candidate loci/genes on ten chromosomal regions were suggested with odds ratios between1.71-3.62 and p-values < 5 × 10-8 in the analysis. The regions suggested were 1q32.2, 3q29, 4q35.1, 4p15.31, 4q26, 8p23.1, 13q33.3, 13q13.3, 16q23.3 and 22q11.21. All regions, except one on 1q32.2, had protein coding genes, many already shown to be involved in cancer, such as ZDHHC19, SYNPO2, PCYT1A, MYO16, TXNRD2, COMT, and CDH13. Sequencing of DNA from 122 colorectal cancer patients with gastric- and/or prostate cancer in their families was performed to search for candidate variants in the haplotype regions. The identified candidate variants were tested in a nested case-control study of similar colorectal cancer cases and controls. There was some support for an increased risk of colorectal-, gastric-, and/or prostate cancer in all the six loci tested. This study demonstrated a proof of principle strategy to identify risk variants found by GWAS, and identified ten candidate loci that could be associated with colorectal, gastric- and prostate cancer.

Open-ended molecular recording of sequential cellular events into DNA.

Genetically encoded DNA recorders noninvasively convert transient biological events into durable mutations in a cell's genome, allowing for the later reconstruction of cellular experiences by DNA sequencing. We present a DNA recorder, peCHYRON, that achieves high-information, durable, and temporally resolved multiplexed recording of multiple cellular signals in mammalian cells. In each step of recording, prime editor, a Cas9-reverse transcriptase fusion protein, inserts a variable triplet DNA sequence alongside a constant propagator sequence that deactivates the previous and activates the next step of insertion. Insertions accumulate sequentially in a unidirectional order, editing can continue indefinitely, and high information is achieved by coexpressing a variety of prime editing guide RNAs (pegRNAs), each harboring unique triplet DNA sequences. We demonstrate that the constitutive expression of pegRNA collections generates insertion patterns for the straightforward reconstruction of cell lineage relationships and that the inducible expression of specific pegRNAs results in the accurate recording of exposures to biological stimuli.

Virus susceptibility of a new cell line derived from the muscle of koi (Cyprinus carpio koi).

In this study, a continuous cell line (KM cells) derived from koi (Cyprinus carpio koi) muscle was established and characterized. The KM cells were subcultured for more than 70 passages and showed high viability after long-term cryopreservation. The KM cell line was optimally cultured in medium 199 containing 10% foetal bovine serum at 25°C. A chromosome analysis indicated that the cell line remained diploid, with a mean chromosome count of 100. DNA sequencing and comparative analysis of the 16S rRNA and cytochrome oxidase I gene sequences showed that the KM cell line originated from koi. In transfection experiments using the plasmid pEGFP, KM cells demonstrated a high level of transfection efficiency, suggesting their potential for use in foreign gene expression studies. Inoculation with spring viraemia of carp virus (SVCV) resulted in a substantial cytopathic effect, and the level of production of SVCV in KM cells was higher than that in the epithelioma papulosum cyprinid (EPC) cell line that is normally used to produce the virus. However, no cytopathic effect was observed when these cells were inoculated with koi herpesvirus, carp oedema virus, or grass carp reovirus. These observations suggest that the newly established KM cell line will be a valuable tool for investigating the pathogenesis of infection with spring viraemia of carp virus.

Cohesin distribution alone predicts chromatin organization in yeast via conserved-current loop extrusion.

Inhomogeneous patterns of chromatin-chromatin contacts within 10-100-kb-sized regions of the genome are a generic feature of chromatin spatial organization. These features, termed topologically associating domains (TADs), have led to the loop extrusion factor (LEF) model. Currently, our ability to model TADs relies on the observation that in vertebrates TAD boundaries are correlated with DNA sequences that bind CTCF, which therefore is inferred to block loop extrusion. However, although TADs feature prominently in their Hi-C maps, non-vertebrate eukaryotes either do not express CTCF or show few TAD boundaries that correlate with CTCF sites. In all of these organisms, the counterparts of CTCF remain unknown, frustrating comparisons between Hi-C data and simulations. To extend the LEF model across the tree of life, here, we propose the conserved-current loop extrusion (CCLE) model that interprets loop-extruding cohesin as a nearly conserved probability current. From cohesin ChIP-seq data alone, we derive a position-dependent loop extrusion rate, allowing for a modified paradigm for loop extrusion, that goes beyond solely localized barriers to also include loop extrusion rates that vary continuously. We show that CCLE accurately predicts the TAD-scale Hi-C maps of interphase Schizosaccharomyces pombe, as well as those of meiotic and mitotic Saccharomyces cerevisiae, demonstrating its utility in organisms lacking CTCF. The success of CCLE in yeasts suggests that loop extrusion by cohesin is indeed the primary mechanism underlying TADs in these systems. CCLE allows us to obtain loop extrusion parameters such as the LEF density and processivity, which compare well to independent estimates.

The secondary metabolism collaboratory: a database and web discussion portal for secondary metabolite biosynthetic gene clusters.

Secondary metabolites are small molecules produced by all corners of life, often with specialized bioactive functions with clinical and environmental relevance. Secondary metabolite biosynthetic gene clusters (BGCs) can often be identified within DNA sequences by various sequence similarity tools, but determining the exact functions of genes in the pathway and predicting their chemical products can often only be done by careful, manual comparative analysis. To facilitate this, we report the first release of the secondary metabolism collaboratory (SMC), which aims to provide a comprehensive, tool-agnostic repository of BGC sequence data drawn from all publicly available and user-submitted bacterial and archaeal genome and contig sources. On the website, users are provided a searchable catalog of putative BGCs identified from each source, along with visualizations of gene and domain annotations derived from multiple sequence analysis tools. SMC's data is also available through publicly-accessible application programming interface (API) endpoints to facilitate programmatic access. Users are encouraged to share their findings (and search for others') through comment posts on BGC and source pages. At the time of writing, SMC is the largest repository of BGC information, holding 13.1M BGC regions from 1.3M source sequences and growing, and can be found at https://smc.jgi.doe.gov.

PVACview: an interactive visualization tool for efficient neoantigen prioritization and selection.

Neoantigen-targeting therapies including personalized vaccines have shown promise in the treatment of cancers, particularly when used in combination with checkpoint blockade therapy. At least 100 clinical trials involving these therapies have been initiated globally. Accurate identification and prioritization of neoantigens is crucial for designing these trials, predicting treatment response, and understanding mechanisms of resistance. With the advent of massively parallel DNA and RNA sequencing technologies, it is now possible to computationally predict neoantigens based on patient-specific variant information. However, numerous factors must be considered when prioritizing neoantigens for use in personalized therapies. Complexities such as alternative transcript annotations, various binding, presentation and immunogenicity prediction algorithms, and variable peptide lengths/registers all potentially impact the neoantigen selection process. There has been a rapid development of computational tools that attempt to account for these complexities. While these tools generate numerous algorithmic predictions for neoantigen characterization, results from these pipelines are difficult to navigate and require extensive knowledge of the underlying tools for accurate interpretation. This often leads to over-simplification of pipeline outputs to make them tractable, for example, limiting prediction to a single RNA isoform or only summarizing the top ranked of many possible peptide candidates. In addition to variant detection, gene expression, and predicted peptide binding affinities, recent studies have also demonstrated the importance of mutation location, allele-specific anchor locations, and variation of T-cell response to long versus short peptides. Due to the intricate nature and number of salient neoantigen features, presenting all relevant information to facilitate candidate selection for downstream applications is a difficult challenge that current tools fail to address. We have created pVACview, the first interactive tool designed to aid in the prioritization and selection of neoantigen candidates for personalized neoantigen therapies including cancer vaccines. pVACview has a user-friendly and intuitive interface where users can upload, explore, select, and export their neoantigen candidates. The tool allows users to visualize candidates at multiple levels of detail including variant, transcript, peptide, and algorithm prediction information. pVACview will allow researchers to analyze and prioritize neoantigen candidates with greater efficiency and accuracy in basic and translational settings. The application is available as part of the pVACtools software at pvactools.org and as an online server at pvacview.org.