Accurate Inference of the Polyploid Continuum Using Forward-Time Simulations.

Multiple rounds of whole-genome duplication (WGD) followed by diploidization have occurred throughout the evolutionary history of angiosperms. Much work has been done to model the genomic consequences and evolutionary significance of WGD. While researchers have historically modeled polyploids as either allopolyploids or autopolyploids, the variety of natural polyploids span a continuum of differentiation across multiple parameters, such as the extent of polysomic versus disomic inheritance, and the degree of genetic differentiation between the ancestral lineages.

A high-quality genome of the convergent lady beetle, Hippodamia convergens.

Here, we describe a high-quality genome assembly and annotation of the convergent lady beetle, Hippodamia convergens (Coleoptera: Coccinellidae). The highest quality unmasked genome comprises 619 megabases (Mb) of chromosomal DNA, organized into 899 contigs, with a contig N50 score of 89 Mbps. The genome was assessed to be 96% complete (BUSCO).

Phenotypic differentiation despite gene flow: Beak morphology, bite performance, and population genetics of Loggerhead Shrikes ().

Previous studies of Loggerhead Shrikes (Laniidae: ) in North America have indicated considerable intraspecific genetic and phenotypic differentiation, but the congruence between genetic and phenotypic differentiation remains obscure. We examined phenotypic differences in beak shape and bite force among geographic groupings across a 950 km range, from the lower Imperial Valley to the upper Central Valley of California, USA. We integrated these analyses with a population genetic analysis of six microsatellite markers to test for correspondence between phenotypic and genetic differences among geographic groups.

Characterizing the microbial metagenome of calcareous stromatolite formations in the San Felipe Creek in the Anza Borrego Desert.

We describe the metagenome composition, community functional annotation, and prokaryote diversity in calcareous stromatolites from a dry stream bed of the San Felipe Creek in the Anza Borrego Desert. Analyses show a community capable of nitrogen fixation, assimilatory nitrate reduction, biofilm formation, quorum sensing, and potential thick-walled akinete formation for desiccation resistance.

Go west: Population genomics reveals unexpected population fluctuations and little gene flow in Western hemisphere populations of the predatory lady beetle, .

-the convergent lady beetle, has been used extensively in augmentative biological control of aphids, thrips, and whiteflies across its native range in North America, and was introduced into South America in the 1950s. Overwintering .  populations from its native western range in the United States are commercially collected and released across its current range in the eastern USA, with little knowledge of the effectiveness of its augmentative biological control.

Assessing genome-wide adaptations associated with range expansion in the pink rice borer, Sesamia inferens.

Understanding the genetic basis of adaptive evolution following habitat expansion can have important implications for pest management. The pink rice borer (PRB), Sesamia inferens (Walker), is a destructive pest of rice that was historically restricted to regions south of 34° N latitude in China. However, with changes in global climate and farming practices, the distribution of this moth has progressively expanded, encompassing most regions in North China.

Genomics and conservation: Guidance from training to analyses and applications.

Environmental change is intensifying the biodiversity crisis and threatening species across the tree of life. Conservation genomics can help inform conservation actions and slow biodiversity loss. However, more training, appropriate use of novel genomic methods and communication with managers are needed.

Pro-survival Phenotype of HIF-1α: Neuroprotection Through Inflammatory Mechanisms.

Hypoxia-inducible factor 1 (HIF-1) is a major player in the oxygen sensor system as well as a transcription factor. HIF-1 is also associated in the pathogenesis of many brain diseases including Alzheimer's disease (AD), epilepsy and stroke. HIF-1 regulates the expression of many genes such as those involved in glycolysis, erythropoiesis, angiogenesis and proliferation in hypoxic condition.

Awareness and Practices Regarding Leptospirosis in Andaman and Nicobar Islands, Union Territory of India.

Background Leptospirosis is a worldwide prevalent zoonotic infection and re-emerging disease caused by the bacterium of genus transmitted by infected animals in the environment. Andaman and Nicobar Islands has one of the highest incidence rates of leptospirosis in India with a seroprevalence of 52.7%.

Global patterns of genomic and phenotypic variation in the invasive harlequin ladybird.

Background: The harlequin ladybird Harmonia axyridis (Coleoptera: Coccinellidae), native to Asia, has been introduced to other major continents where it has caused serious negative impacts on local biodiversity. Though notable advances to understand its invasion success have been made during the past decade, especially with then newer molecular tools, the conclusions reached remain to be confirmed with more advanced genomic analyses and especially using more samples from larger geographical regions across the native range. Furthermore, although H.

The detection and prediction of surgical site infections using multi-modal sensors and machine learning: Results in an animal model.

Introduction: Surgical Site Infection (SSI) is a common healthcare-associated infection that imposes a considerable clinical and economic burden on healthcare systems. Advances in wearable sensors and digital technologies have unlocked the potential for the early detection and diagnosis of SSI, which can help reduce this healthcare burden and lower SSI-associated mortality rates.

Methods: In this study, we evaluated the ability of a multi-modal bio-signal system to predict current and developing superficial incisional infection in a porcine model infected with Methicillin Susceptible Staphylococcus Aureus (MSSA) using a bagged, stacked, and balanced ensemble logistic regression machine learning model.

Teaching computational genomics and bioinformatics on a high performance computing cluster-a primer.

The burgeoning field of genomics as applied to personalized medicine, epidemiology, conservation, agriculture, forensics, drug development, and other fields comes with large computational and bioinformatics costs, which are often inaccessible to student trainees in classroom settings at universities. However, with increased availability of resources such as NSF XSEDE, Google Cloud, Amazon AWS, and other high-performance computing (HPC) clouds and clusters for educational purposes, a growing community of academicians are working on teaching the utility of HPC resources in genomics and big data analyses. Here, I describe the successful implementation of a semester-long (16 week) upper division undergraduate/graduate level course in Computational Genomics and Bioinformatics taught at San Diego State University in Spring 2022.

Chronic Ketosis Modulates HIF1α-Mediated Inflammatory Response in Rat Brain.

Hypoxia inducible factor alpha (HIF1α) is associated with neuroprotection conferred by diet-induced ketosis but the underlying mechanism remains unclear. In this study we use a ketogenic diet in rodents to induce a metabolic state of chronic ketosis, as measured by elevated blood ketone bodies. Chronic ketosis correlates with neuroprotection in both aged and following focal cerebral ischaemia and reperfusion (via middle cerebral artery occlusion, MCAO) in mouse and rat models.

Chronic intake of high dietary sucrose induces sexually dimorphic metabolic adaptations in mouse liver and adipose tissue.

Almost all effective treatments for non-alcoholic fatty liver disease (NAFLD) involve reduction of adiposity, which suggests the metabolic axis between liver and adipose tissue is essential to NAFLD development. Since excessive dietary sugar intake may be an initiating factor for NAFLD, we have characterized the metabolic effects of liquid sucrose intake at concentrations relevant to typical human consumption in mice. We report that sucrose intake induces sexually dimorphic effects in liver, adipose tissue, and the microbiome; differences concordant with steatosis severity.

Genome of a novel Sediminibacterium discovered in association with two species of freshwater cyanobacteria from streams in Southern California.

Here, we report the discovery of a novel Sediminibacterium sequenced from laboratory cultures of freshwater stream cyanobacteria from sites in Southern California, grown in BG11 medium. Our genome-wide analyses reveal a highly contiguous and complete genome (97% BUSCO) that is placed within sediminibacterial clades in phylogenomic analyses. Functional annotation indicates the presence of genes that could be involved in mutualistic/commensal relationship with associated cyanobacterial hosts.

Genome of the parasitoid wasp Dinocampus coccinellae reveals extensive duplications, accelerated evolution, and independent origins of thelytokous parthenogeny and solitary behavior.

Dinocampus coccinellae (Hymenoptera: Braconidae) is a generalist parasitoid wasp that parasitizes >50 species of predatory lady beetles (Coleoptera: Coccinellidae), with thelytokous parthenogeny as its primary mode of reproduction. Here, we present the first high-quality genome of D. coccinellae using a combination of short- and long-read sequencing technologies, followed by assembly and scaffolding of chromosomal segments using Chicago + HiC technologies.

Chronic Ketosis Modulates HIF1α-Mediated Inflammatory Response in Rat Brain.

Hypoxia inducible factor alpha (HIF1α) is associated with neuroprotection conferred by diet-induced ketosis, but the underlying mechanism remains unclear. In this study, we use a ketogenic diet in rodents to induce a metabolic state of chronic ketosis, as measured by elevated blood ketone bodies. Chronic ketosis correlates with neuroprotection in both aged and following focal cerebral ischemia and reperfusion (via middle cerebral artery occlusion, MCAO) in mouse and rat models.

The Pop-Gen Pipeline Platform: A Software Platform for Population Genomic Analyses.

The Pop-Gen Pipeline Platform (PPP) is a software platform for population genomic analyses. The PPP was designed as a collection of scripts that facilitate common population genomic workflows in a consistent and standardized Python environment. Functions were developed to encompass entire workflows, including input preparation, file format conversion, various population genomic analyses, and output generation.

Correlation of factors affecting correction of meniscal extrusion and outcome after medial meniscus root repair.

Introduction: Meniscus extrusion in medial meniscus posterior root tears (MMPRT) is a consistent MRI finding and correction of extrusion is a primary objective of the meniscal root repair. The purpose of the study is to evaluate feasibility of correction of extrusion and correlation of various factors affecting the postoperative extrusion correction and outcomes in all degenerative medial meniscus posterior roots (MMPRTs).

Methods: A retrospective study of patients who presented with degenerative MMPRTs following trivial incident (Jun 2014 and Aug 2018) and included isolated Laprade type 2 root tear with extrusion in MRI.

Who are we now? A demographic assessment of three evolution societies.

Scientific societies have the potential to catalyze support for communities that have been historically excluded from science. Many of these societies have formed committees to propose and administer initiatives to promote the career and well-being of their members, with a special emphasis on racial and ethnic minorities. Yet, these societies are rarely armed with data to inform their proposals.

Gastroesophageal Reflux Disease and Foregut Dysmotility in Children with Intestinal Failure.

Gastrointestinal dysmotility is a common problem in a subgroup of children with intestinal failure (IF), including short bowel syndrome (SBS) and pediatric intestinal pseudo-obstruction (PIPO). It contributes significantly to the increased morbidity and decreased quality of life in this patient population. Impaired gastrointestinal (GI) motility in IF arises from either loss of GI function due to the primary disorder (e.

Insights from Population Genomics to Enhance and Sustain Biological Control of Insect Pests.

Biological control-the use of organisms (e.g., nematodes, arthropods, bacteria, fungi, viruses) for the suppression of insect pest species-is a well-established, ecologically sound and economically profitable tactic for crop protection.

Addressing comprehensive primary healthcare in Gujarat through mHealth intervention: Early implementation experience with TeCHO+ programme.

Background: The Health and Family Welfare Department of Gujarat implemented a mHealth Programme called TeCHO+ (Technology for Community Health Operations) in 2018. TeCHO+ is aimed at making progress across all dimensions of the comprehensive primary healthcare services.

Objective: The objective of this study is to record the document rollout and early implementation experience of TeCHO+ programme in Gujarat.

The use of the Ganga Hospital Score to predict the treatment and outcome of open fractures of the tibia.

Aims: Open fractures of the tibia are a heterogeneous group of injuries that can present a number of challenges to the treating surgeon. Consequently, few surgeons can reliably advise patients and relatives about the expected outcomes. The aim of this study was to determine whether these outcomes are predictable by using the Ganga Hospital Score (GHS).