Environmental DNA sequencing dataset from Lake Erie algal blooms using Oxford Nanopore MinION.

Here we describe a publicly available environmental DNA (eDNA) sequence dataset, consisting of samples collected from a National Oceanic and Atmospheric Administration (NOAA) Great Lakes Environmental Research Laboratory (GLERL) on Lake Erie. We sequenced samples drawn from before, during, and after a 2019 harmful algal bloom (HAB) using 3rd generation sequencing with the Oxford Nanopore MinION device. We classified the eDNA reads taxonomically, and estimated the abundances of all taxa in each sample.

Characteristics, Origins, and Biosignature Preservation Potential of Carbonate-Bearing Rocks Within and Outside of Jezero Crater.

Carbonate minerals have been detected in Jezero crater, an ancient lake basin that is the landing site of the Mars 2020 Perseverance rover, and within the regional olivine-bearing (ROB) unit in the Nili Fossae region surrounding this crater. It has been suggested that some carbonates in the margin fractured unit, a rock unit within Jezero crater, formed in a fluviolacustrine environment, which would be conducive to preservation of biosignatures from paleolake-inhabiting lifeforms. Here, we show that carbonate-bearing rocks within and outside of Jezero crater have the same range of visible-to-near-infrared carbonate absorption strengths, carbonate absorption band positions, thermal inertias, and morphologies.

Characterization and comparison of innate and adaptive immune responses at vaccine sites in melanoma vaccine clinical trials.

The strength and durability of systemic anti-tumor immune responses induced by cancer vaccines depends on adjuvants to support an immunogenic vaccine site microenvironment (VSME). Adjuvants include water-in-oil emulsions with incomplete Freund's adjuvant (IFA) and combinations of toll-like receptor (TLR) agonists, including a preparation containing TLR4 and TLR9 agonists with QS-21 (AS15). IFA-containing vaccines can promote immune cell accumulation at the VSME, whereas effects of AS15 are largely unexplored.

The influence of metal ions on native silk rheology.

Whilst flow is the basis for silk fibre formation, subtle changes in a silk feedstocks' chemical environment may serve to increase both energetic efficiency and control hierarchical structure development during spinning. Despite the role of pH being largely understood, the influence of metal ions is not, only being inferred by correlative work and observations. Through a combination of rheology and microscopy, we provide a causative study of how the most abundant metal ions in the silk feedstock, Ca and K, affect its flow properties and structure.

Sexually Dimorphic Crosstalk at the Maternal-Fetal Interface.

Context: Crosstalk through receptor ligand interactions at the maternal-fetal interface is impacted by fetal sex. This affects placentation in the first trimester and differences in outcomes. Sexually dimorphic signaling at early stages of placentation are not defined.

Mars Extant Life: What's Next? Conference Report.

On November 5-8, 2019, the "Mars Extant Life: What's Next?" conference was convened in Carlsbad, New Mexico. The conference gathered a community of actively publishing experts in disciplines related to habitability and astrobiology. Primary conclusions are as follows: A significant subset of conference attendees concluded that there is a realistic possibility that Mars hosts indigenous microbial life.

Incomplete Freund's adjuvant reduces arginase and enhances Th1 dominance, TLR signaling and CD40 ligand expression in the vaccine site microenvironment.

Background: Immunogenicity of cancer vaccines is impacted by adjuvants and schedule, but systematic assessments of their effects have not been performed. Montanide ISA-51, an incomplete Freund's adjuvant (IFA), is used in many vaccine trials, but concerns have been raised about negative effects in murine studies. We found in humans that IFA enhances systemic immune responses and that repeat vaccination at one site (same site vaccination (SSV)) creates tertiary lymphoid structures (TLS) in the vaccine site microenvironment (VSME).

A deletion in Eml1 leads to bilateral subcortical heterotopia in the tish rat.

Children with malformations of cortical development (MCD) are at risk for epilepsy, developmental delays, behavioral disorders, and intellectual disabilities. For a subset of these children, antiseizure medications or epilepsy surgery may result in seizure freedom. However, there are limited options for treating or curing the other conditions, and epilepsy surgery is not an option in all cases of pharmacoresistant epilepsy.

Inflammation Triggers Liver X Receptor-Dependent Lipogenesis.

Immune cell function can be modulated by changes in lipid metabolism. Our studies indicate that cholesterol and fatty acid synthesis increases in macrophages between 12 and 18 h after the activation of Toll-like receptors with proinflammatory stimuli and that the upregulation of lipogenesis may contribute to the resolution of inflammation. The inflammation-dependent increase in lipogenesis requires the induction of the liver X receptors, members of the nuclear receptor superfamily of transcription factors, by type I interferons in response to inflammatory signals.

Cannabinoid receptor 1 knockout alleviates hepatic steatosis by downregulating perilipin 2.

The endocannabinoid (EC) system has been implicated in the pathogenesis of several metabolic diseases, including nonalcoholic fatty liver disease (NAFLD). With the current study we aimed to verify the modulatory effect of endocannabinoid receptor 1 (CB1)-signaling on perilipin 2 (PLIN2)-mediated lipophagy. Here, we demonstrate that a global knockout of the cannabinoid receptor 1 gene (CB1) reduced the expression of the lipid droplet binding protein PLIN2 in the livers of CB1 and hepatitis B surface protein (HBs)-transgenic mice, which spontaneously develop hepatic steatosis.

Gene Essentiality and Metabolism in Bordetella pertussis.

is the causative agent of whooping cough, a serious respiratory illness affecting children and adults, associated with prolonged cough and potential mortality. Whooping cough has reemerged in recent years, emphasizing a need for increased knowledge of basic mechanisms of growth and pathogenicity. While previous studies have provided insight into gene essentiality of this organism, very little is known about gene essentiality, a critical gap in knowledge, since has no previously identified environmental reservoir and is isolated from human respiratory tract samples.

Comparative Transcriptomic Analysis Identifies a Range of Immunologically Related Functional Elaborations of Lymph Node Associated Lymphatic and Blood Endothelial Cells.

Lymphatic and blood vessels are formed by specialized lymphatic endothelial cells (LEC) and blood endothelial cells (BEC), respectively. These endothelial populations not only form peripheral tissue vessels, but also critical supporting structures in secondary lymphoid organs, particularly the lymph node (LN). Lymph node LEC (LN-LEC) also have been shown to have important immunological functions that are not observed in LEC from tissue lymphatics.

In situ 10-cell RNA sequencing in tissue and tumor biopsy samples.

Single-cell transcriptomic methods classify new and existing cell types very effectively, but alternative approaches are needed to quantify the individual regulatory states of cells in their native tissue context. We combined the tissue preservation and single-cell resolution of laser capture with an improved preamplification procedure enabling RNA sequencing of 10 microdissected cells. This in situ 10-cell RNA sequencing (10cRNA-seq) can exploit fluorescent reporters of cell type in genetically engineered mice and is compatible with freshly cryoembedded clinical biopsies from patients.

Differential gene expression during placentation in pregnancies conceived with different fertility treatments compared with spontaneous pregnancies.

Objective: To identify differences in the transcriptomic profiles during placentation from pregnancies conceived spontaneously vs. those with infertility using non-in vitro fertilization (IVF) fertility treatment (NIFT) or IVF.

Design: Cohort study.

Extensional flow behaviour and spinnability of native silk.

Silk fibres are assembled via flow. While changes in the physiological environment of the gland as well as the shear rheology of silk are largely understood, the effect of extensional flow fields on native silk proteins is almost completely unknown. Here we demonstrate that filament stretching on a conventional tensile tester is a suitable technique to assess silk's extensional flow properties and its ability to form fibres under extensional conditions characteristic of natural spinning.

Sex differences in the late first trimester human placenta transcriptome.

Background: Development of the placenta during the late first trimester is critical to ensure normal growth and development of the fetus. Developmental differences in this window such as sex-specific variation are implicated in later placental disease states, yet gene expression at this time is poorly understood.

Methods: RNA-sequencing was performed to characterize the transcriptome of 39 first trimester human placentas using chorionic villi following genetic testing (17 females, 22 males).

Correction: Prevalence and extent of heteroresistance by next generation sequencing of multidrug-resistant tuberculosis.

[This corrects the article DOI: 10.1371/journal.pone.

Prevalence and extent of heteroresistance by next generation sequencing of multidrug-resistant tuberculosis.

Amplicon-based Next Generation Sequencing (NGS) is an emerging method for Mycobacterium tuberculosis drug susceptibility testing (DST) but has not been well described. We examined 158 clinical multidrug-resistant M. tuberculosis isolates via NGS of 11 resistance-associated gene regions covering 3519 nucleotides.

Targetable T-type Calcium Channels Drive Glioblastoma.

Glioblastoma (GBM) stem-like cells (GSC) promote tumor initiation, progression, and therapeutic resistance. Here, we show how GSCs can be targeted by the FDA-approved drug mibefradil, which inhibits the T-type calcium channel Cav3.2.

Progress and Trends in Artificial Silk Spinning: A Systematic Review.

More than 400 million years of natural selection acting throughout the arthropoda has resulted in highly specialized and energetically efficient processes to produce protein-based fibers with properties that are a source of inspiration for all. As a result, for over 80 years researchers have been inspired by natural silk production in their attempts to spin artificial silks. While significant progress has been made, with fibers now regularly outperforming silkworm silks, surpassing the properties of superior silks, such as spider dragline, is still an area of considerable effort.

Investigation of Genetic Variants Associated with Alzheimer Disease in Parkinson Disease Cognition.

Background: Meta-analysis of genome-wide association studies have implicated multiple single nucleotide polymorphisms (SNPs) and associated genes with Alzheimer disease. The role of these SNPs in cognitive impairment in Parkinson disease (PD) remains incompletely evaluated.

Objective: The objective of this study was to test alleles associated with risk of Alzheimer disease for association with cognitive impairment in Parkinson disease (PD).

Systems Analysis of Adaptive Responses to MAP Kinase Pathway Blockade in BRAF Mutant Melanoma.

Fifty percent of cutaneous melanomas are driven by activated BRAFV600E, but tumors treated with RAF inhibitors, even when they respond dramatically, rapidly adapt and develop resistance. Thus, there is a pressing need to identify the major mechanisms of intrinsic and adaptive resistance and develop drug combinations that target these resistance mechanisms. In a combinatorial drug screen on a panel of 12 treatment-naïve BRAFV600E mutant melanoma cell lines of varying levels of resistance to mitogen-activated protein kinase (MAPK) pathway inhibition, we identified the combination of PLX4720, a targeted inhibitor of mutated BRaf, and lapatinib, an inhibitor of the ErbB family of receptor tyrosine kinases, as synergistically cytotoxic in the subset of cell lines that displayed the most resistance to PLX4720.

Characterization of the nasopharyngeal microbiota in health and during rhinovirus challenge.

Background: The bacterial communities of the nasopharynx play an important role in upper respiratory tract infections (URTIs). Our study represents the first survey of the nasopharynx during a known, controlled viral challenge. We aimed to gain a better understanding of the composition and dynamics of the nasopharyngeal microbiome during viral infection.

Species matter: the role of competition in the assembly of congeneric bacteria.

Interspecific competition is an important driver of community assembly in plants and animals, but phylogenetic evidence for interspecific competition in bacterial communities has been elusive. This could indicate that other processes such as habitat filtering or neutral processes are more important in bacterial community assembly. Alternatively, this could be a consequence of the lack of a consistent and meaningful species definition in bacteria.