Standards recommendations for the Earth BioGenome Project.

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals.

Coral composition and bottom-wave metrics improve understanding of the patchiness of cyclone damage on reefs.

Coral reefs are likely to be exposed to more intense cyclones under climate change. Cyclone impacts are spatially highly variable given complex hydrodynamics, and coral-specific sensitivity to wave impacts. Predicting reef vulnerability to cyclones is critical to management but requires high resolution environmental data that are difficult to obtain over broad spatial scales.

Vaccination of Gilthead Seabream After Continuous Xenoestrogen Oral Exposure Enhances the Gut Endobolome and Immune Status GPER1.

In fish culture settings, the exogenous input of steroids is a matter of concern. Recently, we unveiled that in the gilthead seabream (), the G protein-coupled estrogen receptor agonist G-1 (G1) and the endocrine disruptor 17α-ethinylestradiol (EE) are potent modulators in polyreactive antibody production. However, the integral role of the microbiota upon immunity and antibody processing in response to the effect of EE remains largely unexplored.

The activation of D2-like receptors by intranasal dopamine facilitates the extinction of contextual fear and prevents conditioned fear-induced antinociception.

Fear extinction (FExt) is used to treat patients with posttraumatic stress disorder (PTSD). However, fear related to traumatic events can be persistent and return even after successful extinction. The neurochemical control of extinction seems to be performed by several neurotransmitters, including dopamine (DA), through D1 and D2 receptors.

Towards integrated modeling of the long-term impacts of oil spills.

Although great progress has been made to advance the scientific understanding of oil spills, tools for integrated assessment modeling of the long-term impacts on ecosystems, socioeconomics and human health are lacking. The objective of this study was to develop a conceptual framework that could be used to answer stakeholder questions about oil spill impacts and to identify knowledge gaps and future integration priorities. The framework was initially separated into four knowledge domains (ocean environment, biological ecosystems, socioeconomics, and human health) whose interactions were explored by gathering stakeholder questions through public engagement, assimilating expert input about existing models, and consolidating information through a system dynamics approach.

The Saggy Ink Cap Medicinal Mushroom, Coprinus comatus (Agaricomycetes), Protein Attenuates Acute Alcoholic Liver Injury in Association with Changes in the Gut Microbiota of Mice.

This study aims to investigate the hepatoprotective effects of Coprinus comatus protein (CCP) in a mouse model of acute alcoholic liver injury by regulating gut microbiota dysbiosis. Mice were divided into four groups, including the control group (CG), alcohol group (AG), biphenyldicarboxylate group (BG), and protein group (PG). The results showed that alcohol can increase the liver organ index, which could be adjusted by CCP.

Gene body DNA methylation in seagrasses: inter- and intraspecific differences and interaction with transcriptome plasticity under heat stress.

The role of DNA methylation and its interaction with gene expression and transcriptome plasticity is poorly understood, and current insight comes mainly from studies in very few model plant species. Here, we study gene body DNA methylation (gbM) and gene expression patterns in ecotypes from contrasting thermal environments of two marine plants with contrasting life history strategies in order to explore the potential role epigenetic mechanisms could play in gene plasticity and responsiveness to heat stress. In silico transcriptome analysis of CpG ratios suggested that the bulk of Posidonia oceanica and Cymodocea nodosa genes possess high levels of intragenic methylation.

Genomic evidence for the Chinese mountain cat as a wildcat conspecific () and its introgression to domestic cats.

The Qinghai-Tibet Plateau endemic Chinese mountain cat has a controversial taxonomic status, whether it is a true species or a wildcat () subspecies and whether it has contributed to cat () domestication in East Asia. Here, we sampled lineages across China and sequenced 51 nuclear genomes, 55 mitogenomes, and multilocus regions from 270 modern or museum specimens. Genome-wide analyses classified the Chinese mountain cat as a wildcat conspecific , which was not involved in cat domestication of China, thus supporting a single domestication origin arising from the African wildcat ().

Draft de novo Genome Assembly of the Elusive Jaguarundi, Puma yagouaroundi.

The Puma lineage within the family Felidae consists of 3 species that last shared a common ancestor around 4.9 million years ago. Whole-genome sequences of 2 species from the lineage were previously reported: the cheetah (Acinonyx jubatus) and the mountain lion (Puma concolor).

Phenotypic plasticity under rapid global changes: The intrinsic force for future seagrasses survival.

Coastal oceans are particularly affected by rapid and extreme environmental changes with dramatic consequences for the entire ecosystem. Seagrasses are key ecosystem engineering or foundation species supporting diverse and productive ecosystems along the coastline that are particularly susceptible to fast environmental changes. In this context, the analysis of phenotypic plasticity could reveal important insights into seagrasses persistence, as it represents an individual property that allows species' phenotypes to accommodate and react to fast environmental changes and stress.

Acute intranasal dopamine application counteracts the reversal learning deficit of spontaneously hypertensive rats in an attentional set-shifting task.

Rationale: Studies on the attention-deficit/hyperactivity disorder (ADHD) have concluded that the disorder might be caused by a deficit in the inhibitory control of executive functions because of dopamine hypofunction. Recently, the intranasal route has emerged as an effective alternative means for sending dopamine directly to the brain. However, whether the treatment can ameliorate the deficits of inhibitory control in ADHD remains unknown.

Enhancing the Nutritional Value of Red Meat through Genetic and Feeding Strategies.

Consumption of red meat contributes to the intake of many essential nutrients in the human diet including protein, essential fatty acids, and several vitamins and trace minerals, with high iron content, particularly in meats with high myoglobin content. Demand for red meat continues to increase worldwide, particularly in developing countries where food nutrient density is a concern. Dietary and genetic manipulation of livestock can influence the nutritional value of meat products, providing opportunities to enhance the nutritional value of meat.

A Tentative Study of the Effects of Heat-Inactivation of the Probiotic Strain Ppd11 on Senegalese Sole () Intestinal Microbiota and Immune Response.

Concerns about safety, applicability and functionality associated with live probiotic cells have led to consideration of the use of non-viable microorganisms, known as paraprobiotics. The present study evaluated the effects of dietary administration of heat-inactivated cells of the probiotic strain Ppd11 on the intestinal microbiota and immune gene transcription in . Results obtained were evaluated and compared to those described after feeding with viable Pdp11 cells.

African and Asian leopards are highly differentiated at the genomic level.

Leopards are the only big cats still widely distributed across the continents of Africa and Asia. They occur in a wide range of habitats and are often found in close proximity to humans. But despite their ubiquity, leopard phylogeography and population history have not yet been studied with genomic tools.

Ginseng polysaccharides: A potential neuroprotective agent.

The treatments of nervous system diseases (NSDs) have long been difficult issues for researchers because of their complexity of pathogenesis. With the advent of aging society, searching for effective treatments of NSDs has become a hot topic. Ginseng polysaccharides (GP), as the main biologically active substance in ginseng, has various biological properties in immune-regulation, anti-oxidant, anti-inflammation and etc.

LMP2-DC Vaccine Elicits Specific EBV-LMP2 Response to Effectively Improve Immunotherapy in Patients with Nasopharyngeal Cancer.

Objective: To evaluate the safety and effectiveness of a vaccine based on latent membrane protein 2 (LMP2) modified dendritic cells (DCs) that boosts specific responses of cytotoxic T lymphocytes (CTLs) to LMP2 before and after intradermal injection in patients with nasopharyngeal carcinoma (NPC).

Methods: DCs were derived from peripheral blood monocytes of patients with NPC. We prepared LMP2-DCs infected by recombinant adenovirus vector expressing LMP2 (rAd-LMP2).

Genome-wide association study identifies new loci associated with risk of HBV infection and disease progression.

Background: Recent studies have identified susceptibility genes of HBV clearance, chronic hepatitis B, liver cirrhosis, hepatocellular carcinoma, and showed the host genetic factors play an important role in these HBV-related outcomes.

Methods: Collected samples from different outcomes of HBV infection and performed genotyping by Affymetrix 500 k SNP Array. GCTA tool, PLINK, and Bonferroni method were applied for analysis of genotyping and disease progression.

Integrating Transcriptomics and Metabolomics to Characterize Metabolic Regulation to Elevated CO in Chlamydomonas Reinhardtii.

With atmospheric CO increasing, a large amount of CO is absorbed by oceans and lakes, which changes the carbonate system and affects the survival of aquatic plants, especially microalgae. The main aim of our study was to explore the responses of Chlamydomonas reinhardtii (Chlorophyceae) to elevated CO by combined transcriptome and metabolome analysis under three different scenarios: control (CK, 400 ppm), short-term elevated CO (ST, 1000 ppm), and long-term elevated CO (LT, 1000 ppm). The transcriptomic data showed moderate changes between ST and CK.