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Environmental DNA and environmental RNA: Current and prospective applications for biological monitoring.

Sci Total Environ 2021 Apr 5;782:146891. Epub 2021 Apr 5.

Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada; Faculty of Science and Technology and Athabasca River Basin Research Institute, Athabasca University, Athabasca, Alberta, Canada.

Traditional environmental biomonitoring approaches have limitations in terms of species detectability and their capacity to account for spatial and temporal variation. Furthermore, as invasive techniques they can be harmful to individual organisms, populations and habitats. The application of non-invasive sampling methods that extract, isolate and identify nucleic acid sequences (i. Read More

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Research progress and application opportunities of nanoparticle-protein corona complexes.

Biomed Pharmacother 2021 Apr 10;139:111541. Epub 2021 Apr 10.

Department of immunology, School of Basic Medical Sciences and School of Pharmacy, Nanchang University, Nanchang 330006, China.

Nanoparticles (NPs) can be used to design for nanomedicines with different chemical surface properties owing to their size advantages and the capacity of specific delivery to targeted sites in organisms. The discovery of the presence of protein corona (PC) has changed our classical view of NPs, stimulating researchers to investigate the in vivo fate of NPs as they enter biological systems. Both NPs and PC have their specificity but complement each other, so they should be considered as a whole. Read More

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MAPLE: A Microbiome Analysis Pipeline Enabling Optimal Peptide Search and Comparative Taxonomic and Functional Analysis.

J Proteome Res 2021 Apr 13. Epub 2021 Apr 13.

Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, Maryland 21201, United States.

Metaproteomics by mass spectrometry (MS) is a powerful approach to profile a large number of proteins expressed by all organisms in a highly complex biological or ecological sample, which is able to provide a direct and quantitative assessment of the functional makeup of a microbiota. The human gastrointestinal microbiota has been found playing important roles in human physiology and health, and metaproteomics has been shown to shed light on multiple novel associations between microbiota and diseases. MS-powered proteomics generally relies on genome data to define search space. Read More

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Expression, Purification, and Solution-State NMR Analysis of the Two Human Single-Stranded DNA-Binding Proteins hSSB1 (NABP2/OBFC2B) and hSSB2 (NAPB1/OBFC2A).

Methods Mol Biol 2021 ;2281:229-240

School of Science, Western Sydney University, Penrith, NSW, Australia.

Single-stranded DNA-binding proteins (SSBs) are essential to all living organisms as protectors and guardians of the genome. Apart from the well-characterized RPA, humans have also evolved two further SSBs, termed hSSB1 and hSSB2. Over the last few years, we have used NMR spectroscopy to determine the molecular and structural details of both hSSBs and their interactions with DNA and RNA. Read More

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January 2021

The Essential, Ubiquitous Single-Stranded DNA-Binding Proteins.

Methods Mol Biol 2021 ;2281:1-21

Department of Chemistry, Auburn University at Montgomery, Montgomery, AL, USA.

Maintenance of genomes is fundamental for all living organisms. The diverse processes related to genome maintenance entail the management of various intermediate structures, which may be deleterious if unresolved. The most frequent intermediate structures that result from the melting of the DNA duplex are single-stranded (ss) DNA stretches. Read More

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January 2021

Nanopore long-read RNA-seq and absolute quantification delineate transcription dynamics in early embryo development of an insect pest.

Sci Rep 2021 Apr 12;11(1):7878. Epub 2021 Apr 12.

McGill Genome Centre, Department of Human Genetics, McGill University, Montréal, Québec, Canada.

The olive fruit fly, Bactrocera oleae, is the most important pest for the olive fruit but lacks adequate transcriptomic characterization that could aid in molecular control approaches. We apply nanopore long-read RNA-seq with internal RNA standards allowing absolute transcript quantification to analyze transcription dynamics during early embryo development for the first time in this organism. Sequencing on the MinION platform generated over 31 million reads. Read More

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Characterization and transcriptomic analysis of a novel yellow-green leaf wucai (Brassica campestris L.) germplasm.

BMC Genomics 2021 Apr 12;22(1):258. Epub 2021 Apr 12.

College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei, 230036, Anhui, China.

Background: Leaf color mutants are the ideal materials to explore the pathways of chlorophyll (Chl) metabolism, chloroplast development, and photosynthesis system. In this study, a spontaneous yellow-green leaf wucai (Brassica campestris L.) mutant "WY16-13" was identified, which exhibited yellow-green leaf color during its entire growth period. Read More

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Norcyanine-Carbamates Are Versatile Near-Infrared Fluorogenic Probes.

J Am Chem Soc 2021 Apr 12. Epub 2021 Apr 12.

Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States.

Fluorogenic probes in the near-infrared (NIR) region have the potential to provide stimuli-dependent information in living organisms. Here, we describe a new class of fluorogenic probes based on the heptamethine cyanine scaffold, the most broadly used NIR chromophore. These compounds result from modification of heptamethine norcyanines with stimuli-responsive carbamate linkers. Read More

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Occurrence and bioaccumulation of sulfonamide antibiotics in different fish species from Hangbu-Fengle River, Southeast China.

Environ Sci Pollut Res Int 2021 Apr 12. Epub 2021 Apr 12.

School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, Anhui, China.

As a class of synthetic sulfur drugs, sulfonamides (SAs) have been used to treat diseases and promote organism growth. Different concentrations of SAs have been detected in the water environment, which has threatened the ecological environment. In this study, the contamination of 9 SAs in water, sediments, and 8 fish species from the Hangbu-Fengle River, China, were analyzed using UPLC-MS/MS. Read More

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Pinealectomy and gonadectomy modulate amplitude, but not photoperiodic modulation of Clock gene expression in the Syrian hamster suprachiasmatic nuclei.

Eur J Neurosci 2021 Apr 11. Epub 2021 Apr 11.

Institute of Cellular and Integrative Neurosciences, CNRS and University of Strasbourg, Strasbourg, France.

The duration of daytime light phase (photoperiod) controls reproduction in seasonal mammals. Syrian hamsters are sexually active when exposed to long photoperiod, while gonadal atrophy is observed after exposure to short photoperiod. The photorefractory period, or photorefractoriness, is a particular state of spontaneous recrudescence of sexual activity that occurs after a long-term exposure to short photoperiod. Read More

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Validation Study for PathogenDx EnviroX-Rv assay for the Detection of SARS-CoV-2 from Stainless Steel Environmental Surface Swabs Performance Tested MethodSM 122003.

J AOAC Int 2021 Apr 11. Epub 2021 Apr 11.

PathogenDx, Inc, 9375 E. Shea Blvd. Ste. 100, Scottsdale, AZ, 85260.

Background: The PathogenDx EnviroX-Rv uses endpoint PCR + DNA microarray technology to detect SARS-CoV-2, the causative agent of COVID-19, from stainless steel environmental sample swabs.

Objective: : To validate the PathogenDx EnviroX-Rv assay as part of the Emergency Response Validation Performance Tested Method  SM program.

Methods: : The PathogenDx EnviroX-Rv assay was evaluated for specificity using in silico analysis of ≥ 41 000 SARS-CoV-2 sequences and over 50 exclusivity organisms (both near neighbors and background organisms). Read More

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Microalgal photosynthesis induces alkalization of aquatic environment as a result of H uptake independently from CO concentration - New perspectives for environmental applications.

J Environ Manage 2021 Apr 8;289:112546. Epub 2021 Apr 8.

Department of Biology, University of Crete, Voutes University Campus, GR-70013, Heraklion, Crete, Greece. Electronic address:

The photosynthetic process in microalgae and the extracellular proton environment interact with each other. The photosynthetic process in microalgae induces a pH increase in the aquatic environment as a result of cellular protons uptake rather than as an effect of CO consumption. The photosynthetic water photolysis and the reduction/oxidation cycle of the plastoquinone pool provide lumen with protons. Read More

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Development of omics biomarkers for estrogen exposure using mRNA, miRNA and piRNAs.

Aquat Toxicol 2021 Mar 12;235:105807. Epub 2021 Mar 12.

US Environmental Protection Agency, Office of Research and Development, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, United States. Electronic address:

The number of chemicals requiring risk evaluation exceeds our capacity to provide the underlying data using traditional methodology. This has led to an increased focus on the development of novel approach methodologies. This work aimed to expand the panel of gene expression-based biomarkers to include responses to estrogens, to identify training strategies that maximize the range of applicable concentrations, and to evaluate the potential for two classes of small non-coding RNAs (sncRNAs), microRNA (miRNA) and piwi-interacting RNA (piRNA), as biomarkers. Read More

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Challenges of Automation and Scale: Bioinformatics and the Evaluation of Proteins to Support Genetically Modified Product Safety Assessments.

J Invertebr Pathol 2021 Apr 7:107587. Epub 2021 Apr 7.

Bayer Crop Science, 700 Chesterfield Pkwy West, Chesterfield, MO 63017.

Bioinformatic analyses of protein sequences play an important role in the discovery and subsequent safety assessment of insect control proteins in Genetically Modified (GM) crops. Due to the rapid adoption of high-throughput sequencing methods over the last decade, the number of protein sequences in GenBank and other public databases has increased dramatically. Many of these protein sequences are the product of whole genome sequencing efforts, coupled with automated protein sequence prediction and annotation pipelines. Read More

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Remodeling of Arctic char (Salvelinus alpinus) lipidome under a stimulated scenario of Arctic warming.

Glob Chang Biol 2021 Apr 10. Epub 2021 Apr 10.

Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada.

Arctic warming associated with global climate change poses a significant threat to populations of wildlife in the Arctic. Since lipids play a vital role in adaptation of organisms to variations in temperature, high-resolution mass spectrometry based lipidomics can provide insights into adaptive responses of organisms to a warmer environment in the Arctic and help to illustrate potential novel roles of lipids in the process of thermal adaption. In this study, we studied an ecologically and economically important species-Arctic char (Salvelinus alpinus), with a detailed multi-tissue analysis of the lipidome in response to chronic shifts in temperature by use of a validated lipidomics workflow. Read More

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Commentary: Osland et al. (2021): Tropicalization of temperate ecosystems in North America: The northward range expansion of tropical organisms in response to warming winter temperatures.

Glob Chang Biol 2021 Apr 10. Epub 2021 Apr 10.

Biological Sciences, Nicholls State University, Thibodaux, LA, USA.

Tropicalization is, "the transformation of temperate ecosystems by poleward-moving tropical organisms in response to warming temperatures" (Osland et al. 2021). In their newly published Research Review article in Global Change Biology, Osland and colleagues provide important context, diverse examples, and discuss critical knowledge gaps on tropicalization for the lower latitudes of North America where species assemblages are changing via range expansions or invasions. Read More

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Experimental field evidence shows milkweed contaminated with a common neonicotinoid decreases larval survival of monarch butterflies.

J Anim Ecol 2021 Apr 10. Epub 2021 Apr 10.

Department of Integrative Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1.

1. Neonicotinoid insecticides are the most widely used class of insecticides in the world and can have both lethal and sub-lethal effects on non-target organisms in agricultural areas. Monarch butterflies (Danaus plexippus) have experienced dramatic declines in recent decades and, given that a large proportion of milkweed on the landscape grows in agricultural areas, there is concern about the negative effects of neonicotinoids on this non-target insect. Read More

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Educational use of animals in Europe indicates a reluctance to implement alternatives.

ALTEX 2021 Apr 7. Epub 2021 Apr 7.

The Norwegian Animal Protection Alliance (Dyrevernalliansen), Oslo, Norway.

Animals have been considered an indispensable tool to teach about the functioning of living organisms, to obtain skills necessary for practicing human and veterinary medicine, as well as for acquiring skills for caring for and conducting experiments on animals in laboratories. However, the efficacy of this practice has been questioned in the last decades and societal views have evolved to put a much larger emphasis on animal welfare and ethics that needs to be reflected in our teaching and training practices. Currently, many alternatives to harmful animal use are available, and it is not clear why thousands of animals continue to be used every year for educational and training purposes. Read More

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Chronotropic effects and mechanisms of long-chain omega-3 polyunsaturated fatty acids on heartbeat: the latest insights.

Authors:
Weiguo Zhang

Nutr Rev 2021 Apr 9. Epub 2021 Apr 9.

W. Zhang is with the Las Colinas Institutes, Irving, Texas, USA.

The roles of the resting heart rate (RHR) have been actively investigated and increasingly recognized in recent decades, because of the growing evidence that fast RHR is associated with and predicts the risk of developing cardiovascular and metabolic disorders, as well as all-cause mortality. Long-chain omega-3 polyunsaturated fatty acids (PUFAs) (eg, eicosapentaenoic acid and docosahexaenoic acid) have been shown to have chronotropic effects on heartbeat in both healthy people and patients with various disease conditions. The aims of this review are (1) to briefly summarize the importance of elevated RHR in disease pathogenesis and mortality; (2) to provide an update on the negative chronotropic effect of omega-3 PUFAs on the heart; (3) to highlight how omega-3 PUFAs regulate heart rate through the autonomic nervous system - a central control mechanism; and (4) to highlight how omega-3 PUFAs modulate the trans-membrane ionic channels in cardiomyocytes - a fundamental mechanism of cardiac automaticity. Read More

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Single-cell RNA sequencing reveals the mesangial identity and species diversity of glomerular cell transcriptomes.

Nat Commun 2021 04 9;12(1):2141. Epub 2021 Apr 9.

Karolinska Institute/AstraZeneca Integrated Cardio Metabolic Center (ICMC), Huddinge, Sweden.

Molecular characterization of the individual cell types in human kidney as well as model organisms are critical in defining organ function and understanding translational aspects of biomedical research. Previous studies have uncovered gene expression profiles of several kidney glomerular cell types, however, important cells, including mesangial (MCs) and glomerular parietal epithelial cells (PECs), are missing or incompletely described, and a systematic comparison between mouse and human kidney is lacking. To this end, we use Smart-seq2 to profile 4332 individual glomerulus-associated cells isolated from human living donor renal biopsies and mouse kidney. Read More

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Kinetic analysis reveals that independent nucleation events determine the progression of polyglutamine aggregation in .

Proc Natl Acad Sci U S A 2021 Mar;118(11)

Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL 60208-3500;

Protein aggregation is associated with a wide range of degenerative human diseases with devastating consequences, as exemplified by Alzheimer's, Parkinson's, and Huntington's diseases. In vitro kinetic studies have provided a mechanistic understanding of the aggregation process at the molecular level. However, it has so far remained largely unclear to what extent the biophysical principles of amyloid formation learned in vitro translate to the complex environment of living organisms. Read More

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Revealing lineage-related signals in single-cell gene expression using random matrix theory.

Proc Natl Acad Sci U S A 2021 Mar;118(11)

School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138.

Gene expression profiles of a cellular population, generated by single-cell RNA sequencing, contains rich information about biological state, including cell type, cell cycle phase, gene regulatory patterns, and location within the tissue of origin. A major challenge is to disentangle information about these different biological states from each other, including distinguishing from cell lineage, since the correlation of cellular expression patterns is necessarily contaminated by ancestry. Here, we use a recent advance in random matrix theory, discovered in the context of protein phylogeny, to identify differentiation or ancestry-related processes in single-cell data. Read More

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The unicellular red alga Cyanidioschyzon merolae - the simplest model of a photosynthetic eukaryote.

Plant Cell Physiol 2021 Apr 9. Epub 2021 Apr 9.

Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan.

Several species of unicellular eukaryotic algae exhibit relatively simple genomic and cellular architecture. Laboratory cultures of these algae grow faster than plants and often provide homogeneous cellular populations exposed to an almost equal environment. These characteristics are ideal for conducting experiments at the cellular and subcellular levels. Read More

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Mass Spectrometry-based Metabolomics in Translational Research.

Adv Exp Med Biol 2021 ;1310:509-531

Department of Convergence Medicine, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea.

Metabolomics is the systematic study of metabolite profiles of complex biological systems, and involves the systematic identification and quantification of metabolites. Metabolism is integrated with all biochemical reactions in biological systems; thus metabolite profiles provide collective information on biochemical processes induced by genetic or environmental perturbations. Transcriptomes or proteomes may not be functionally active and not always reflect phenotypic variations. Read More

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The Interconnected Health Initiative: A Smithsonian Framework to Extend One Health Research and Education.

Front Vet Sci 2021 23;8:629410. Epub 2021 Mar 23.

Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, United States.

To better tackle diseases and sustain healthy ecosystems, One Health programs must efficiently bridge health in humans, domestic/livestock species, wild animals and plants, agriculture/aquaculture, and the environment. The Smithsonian Institution proposes to address this by considering 'health' in a broad sense - the absence of undue pathogens and unnecessary stress for any organisms as well as access to good living conditions in functional environments. Considering the interconnectedness of all life forms, the Smithsonian plans to create a framework that will integrate cultural, social, and educational components into health research on humans, animals, plants, or ecosystems. Read More

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A review of biochemical diversity and metabolic modeling of EBPR process under specific environmental conditions and carbon source availability.

J Environ Manage 2021 Apr 7;288:112362. Epub 2021 Apr 7.

Civil engineering, York university, 4700 Keele St, Toronto, M3J 1P3, ON, Canada. Electronic address:

Enhanced biological phosphorus removal (EBPR) is one of the most promising technologies as an economical and environmentally sustainable technique for removal of phosphorus from wastewater (WW). However, with high capacity of EBPR, insufficient P-removal is a major yet common issue of many full-scale wastewater treatment plants (WWTP), due to misinterpreted environmental and microbial disturbance. By developing a rather extensive understanding on biochemical pathways and metabolic models governing the anaerobic and aerobic/anoxic processes; the optimal operational conditions, environmental changes and microbial population interaction are efficiently predicted. Read More

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