Structural variation in the pangenome of wild and domesticated barley.

Pangenomes are collections of annotated genome sequences of multiple individuals of a species. The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants. Here we report a pangenome of barley comprising long-read sequence assemblies of 76 wild and domesticated genomes and short-read sequence data of 1,315 genotypes.

Pangenome and pantranscriptome as the new reference for gene family characterisation - a case study of basic helix-loop-helix (bHLH) genes in barley.

Genome-wide identification and comparative gene family analyses have been commonly performed to investigate species-specific evolution linked to various traits and molecular pathways. However, most previous studies were limited to gene screening in a single reference genome, failing to account for the gene presence/absence variations (gPAVs) in a species. Here, we propose an innovative pangenome-based approach of gene family analyses based on orthologous gene groups (OGGs).

Discrepancies in Mass Shootings and Access to Trauma Care Across the United States, 2014-2018.

Introduction: The United States has one of the highest rates of gun violence and mass shootings. Timely medical attention in such events is critical. The objective of this study was to assess geographic disparities in mass shootings and access to trauma centers.

Venovenous Extracorporeal Membrane Oxygenation Usage Following Bullet Embolism to the Pulmonary Artery.

Pulmonary artery embolus is a rare complication following gunshot wounds that creates a unique and serious challenge for trauma surgeons. While the majority of bullets that embolize through the vascular system end in the peripheral circulation, approximately one-third enter the central venous circulation. We present the case of a bullet embolus to the left pulmonary artery following gunshot wounds to the right chest and the abdomen, with the abdominal ballistic traversing the liver before entering the vena cava and embolizing.

Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication.

Background: Gene duplication is a prevalent phenomenon and a major driving force underlying genome evolution. The process leading to the fixation of gene duplicates following duplication is critical to understand how genome evolves but remains fragmentally understood. Most previous studies on gene retention are based on gene duplicate analyses in single reference genome.

Wheat Panache: A pangenome graph database representing presence-absence variation across sixteen bread wheat genomes.

Bread wheat (Triticum aestivum L.) is one of humanity's most important staple crops, characterized by a large and complex genome with a high level of gene presence-absence variation (PAV) between cultivars, hampering genomic approaches for crop improvement. With the growing global population and the increasing impact of climate change on crop yield, there is an urgent need to apply genomic approaches to accelerate wheat breeding.

How Did the COVID-19 Pandemic Affect Trauma Volume at an Urban Level I Trauma Center?

Introduction: The COVID-19 pandemic changed the face of health care worldwide. While the impacts from this catastrophe are still being measured, it is important to understand how this pandemic impacted existing health care systems. As such, the objective of this study was to quantify its effects on trauma volume at an urban Level 1 trauma center in one of the earliest and most significantly affected US cities.

Does Time to Pelvic Fixation Influence Outcomes in Trauma Patients?

Background: Pelvic fractures cause significant morbidity in the trauma population. Many factors influence time to fracture fixation. No previous study has determined the optimal time window for pelvic fixation.

Compression of the Right Atrium and Inferior Vena Cava from an Extrahepatic Biloma Following Liver Trauma.

A 26-year-old male presented to a Level 1 trauma center following a motorcycle crash. Workup of his injuries demonstrated a grade 5 liver laceration with active extravasation, grade 5 kidney laceration, right apical pneumothorax, and a sternal fracture. The patient underwent hepatic artery embolization with interventional radiology (IR) followed by an exploratory laparotomy, liver packing, and small bowel resection with primary anastomosis.

Gastroduodenal Artery Pseudoaneurysm Causing Obstructive Jaundice.

Visceral artery aneurysms and pseudoaneurysms are uncommon phenomena with a high mortality rate in cases of rupture. These rare vascular pathologies are usually asymptomatic and are therefore generally discovered incidentally on computed tomography or magnetic resonance imaging examination. Current therapeutic options have trended toward a minimally invasive approach because of evolving endovascular treatment options, with open operations typically reserved for cases of intraabdominal hemorrhage.

Lessons Learned From an Early Hotspot During the COVID-19 Pandemic.

The Covid-19 pandemic has provided challenges for surgical residency programs demanding fluid decision making focused on providing care for our patients, maintaining an educational environment, and protecting the well-being of our residents. This brief report summarizes the impact of the impact on our residency programs clinical care and education. We have identified opportunities to improve our program using videoconferencing, managing recruitment, and maintaining a satisfactory caseload to ensure the highest possible quality of surgical education.

BarleyVarDB: a database of barley genomic variation.

Barley (Hordeum vulgare L.) is one of the first domesticated grain crops and represents the fourth most important cereal source for human and animal consumption. BarleyVarDB is a database of barley genomic variation.

Genomic Analysis of Circulating Tumor DNA Using a Melanoma-Specific UltraSEEK Oncogene Panel.

The analysis of circulating tumor DNA provides a minimally invasive molecular interrogation that has the potential to guide treatment selection and disease monitoring. Here, the authors evaluated a custom UltraSEEK melanoma panel for the MassARRAY system, probing for 61 mutations over 13 genes. The analytical sensitivity and clinical accuracy of the UltraSEEK melanoma panel was compared with droplet digital PCR.

The pseudogenes of barley.

Pseudogenes have a reputation of being 'evolutionary relics' or 'junk DNA'. While they are well characterized in mammals, studies in more complex plant genomes have so far been hampered by the absence of reference genome sequences. Barley is one of the economically most important cereals and has a genome size of 5.

Plant Proteogenomics: Improvements to the Grapevine Genome Annotation.

Grapevine is an important perennial fruit to the wine industry, and has implications for the health industry with some causative agents proven to reduce heart disease. Since the sequencing and assembly of grapevine cultivar Pinot Noir, several studies have contributed to its genome annotation. This new study further contributes toward genome annotation efforts by conducting a proteogenomics analysis using the latest genome annotation from CRIBI, legacy proteomics dataset from cultivar Cabernet Sauvignon and a large RNA-seq dataset.

Gene-enriched draft genome of the cattle tick Rhipicephalus microplus: assembly by the hybrid Pacific Biosciences/Illumina approach enabled analysis of the highly repetitive genome.

The genome of the cattle tick Rhipicephalus microplus, an ectoparasite with global distribution, is estimated to be 7.1Gbp in length and consists of approximately 70% repetitive DNA. We report the draft assembly of a tick genome that utilized a hybrid sequencing and assembly approach to capture the repetitive fractions of the genome.

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv.

A chromosome conformation capture ordered sequence of the barley genome.

Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.

High-throughput parallel proteogenomics: a bacterial case study.

In recent years, a new paradigm for genome annotation has emerged, termed "proteogenomics," that leverages peptide MS to annotate a genome. This is achieved by mapping peptides to a six-frame translation of a genome, including available splice databases, which may suggest refinements to gene models. Using this approach, it is possible to refine gene regions such as exon boundaries, novel genes, gene boundaries, frame shifts, reverse strands, translated UTRs, and novel splice junctions.

Applying polygenic risk scores to postpartum depression.

The etiology of major depressive disorder (MDD) is likely to be heterogeneous, but postpartum depression (PPD) is hypothesized to represent a more homogenous subset of MDD. We use genome-wide SNP data to explore this hypothesis. We assembled a total cohort of 1,420 self-report cases of PPD and 9,473 controls with genome-wide genotypes from Australia, The Netherlands, Sweden and the UK.

Common variants in the CYP2C19 gene are associated with susceptibility to endometriosis.

Objective: To follow-up previous studies highlighting a possible role for cytochrome P450, family 2, subfamily C, 19 (CYP2C19) in susceptibility to endometriosis by searching for additional variants in the CYP2C19 gene that may be associated with the disease.

Design: Case-control study.

Setting: Academic research.

Molecular analysis of common polymorphisms within the human Tyrosinase locus and genetic association with pigmentation traits.

We have compared the melanogenic activities of cultured melanocytes carrying two common TYR alleles as homozygous 192S-402R wild-type, heterozygous and homozygous variant. This includes assays of TYR protein, DOPAoxidase activity, glycosylation and temperature sensitivity of protein and DOPAoxidase levels. Homozygous wild-type strains on average had higher levels of TYR protein and enzyme activity than other genotypes.

Association analysis of the SLC22A11 (organic anion transporter 4) and SLC22A12 (urate transporter 1) urate transporter locus with gout in New Zealand case-control sample sets reveals multiple ancestral-specific effects.

Introduction: There is inconsistent association between urate transporters SLC22A11 (organic anion transporter 4 (OAT4)) and SLC22A12 (urate transporter 1 (URAT1)) and risk of gout. New Zealand (NZ) Māori and Pacific Island people have higher serum urate and more severe gout than European people. The aim of this study was to test genetic variation across the SLC22A11/SLC22A12 locus for association with risk of gout in NZ sample sets.