Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams

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Allele-specific expression (ASE) is pivotal in understanding the genetic underpinnings of phenotypic variation within species, differences in disease susceptibility, and responses to environmental factors. We processed 11 different tissue types collected f ...

Dwindling fossil resources and their associated environmental concerns have increased interest in biobased products. In particular, many approaches to convert lignocellulosic biomass into small-molecule building blocks are being explored via thermal, chemi ...

Motivation Many machine learning (ML) models developed to classify phenotype from gene expression data provide interpretations for their decisions, with the aim of understanding biological processes. For many models, including neural networks, interpretati ...

High-throughput transcriptomics is of increasing fundamental biological and clinical interest. The generation of molecular data from large collections of samples, such as biobanks and drug libraries, is boosting the development of new biomarkers and treatm ...

Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preampli ...

Understanding the ecological impacts of viruses on natural and engineered ecosystems relies on the accurate identification of viral sequences from community sequencing data. To maximize viral recovery from metagenomes, researchers frequently combine viral ...

Global change exposes ecosystems to changes in the frequency, magnitude, and concomitancy of disturbances, which impact the composition and functioning of these systems. Here, we experimentally evaluate the effects of salinity disturbances and eutrophicati ...

The pathway of dense river inflows into lakes, which affects the lake water quality, is not accurately predicted by existing models. The pathway of a dense riverine inflow in a lake with a submerged canyon is analyzed based on measurements during a 4-month ...

Glacier-fed streams are the cold, ultra-oligotrophic, and unstable streams that are fed by glacial meltwater. Despite these extreme conditions, they harbour a diverse and abundant microbial diversity that develops into biofilms, covering the boulders and s ...

Tidal freshwater marshes are threatened by seawater intrusion globally due to freshwater discharge reduction and sea-level rise. However, terrestrial nitrate (NO3−) transport responding to seawater intrusion remains poorly understood in tidal marshes. Afte ...

The self-assembly of molecular components into organized nanomaterials is a fundamental process observed in nature, crucial for various biological functions. Gaining a deepened understanding of the underlying self-assembly principles provides valuable insi ...

Author summaryIn recent years, the application of deep learning represented a breakthrough in the mass spectrometry (MS) field by improving the assignment of the correct sequence of amino acids from observable MS spectra without prior knowledge, also known ...

Automating experimental procedures has resulted in an unprecedented increase in the volume of generated data, which, in turn, has caused an accumulation of unprocessed data. As a result, the need to develop tools to analyze data systematically has been ris ...

Stream periphytons are candidate ecosystem engineers in proglacial margins. Here, we quantify the extent to which they are engineers for the case of hillslope-fed tributaries in the terrace zones of proglacial margin alluvial plains. Candidate ecosystem en ...

Sediment transport in geophysical boundary layer flows has relevance to a broad spectrum of sciences ranging from the physical and chemical, to the biological, ecological and geological. Advances in sediment transport modelling and prediction strongly suff ...

PremiseA novel protocol for rapid plant DNA extraction using microneedles is proposed, which supports botanic surveys, taxonomy, and systematics. This protocol can be conducted in the field with limited laboratory skills and equipment. The protocol is vali ...

The sequence-dependent statistical mechanics of double-stranded nucleic acid, or dsNA, is believed to be essential in its biological functions. In turn, the equilibrium statistical mechanics behaviour of dsNA depends strongly both on sequence-dependent per ...

Increased periods of bottom water anoxia in deep temperate lakes due to decreasing frequency and depth of water column mixing in a warming climate may result in the reductive dissolution of iron minerals and increased flux of nutrients from the sediment in ...

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

Improper use of chemical fertilizers has led to land degradation. Organic crops, which are farmed using organic fertilizers to reduce the negative environmental effects, are considered an alternative solution to develop the ecosystem health and improve the ...

Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams

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Genome-wide allele-specific expression in multi-tissue samples from healthy male baboons reveals the transcriptional complexity of mammals

Aldehyde-Stabilization Strategies for Building Biobased Consumer Products around Intact lignocellulosic Structures

A comparative analysis of gene expression profiling by statistical and machine learning approaches

Multi-well plate lid for single-step pooling of 96 samples for high-throughput barcode-based sequencing

Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics

Benchmarking informatics approaches for virus discovery: caution is needed when combining in silico identification methods

The cost of adaptability: resource availability constrains functional stability under pulsed disturbances

Field Observations Reveal How Plunging Mixing and Sediment Resuspension Affect the Pathway of a Dense River Inflow Into a Deep Stratified Lake

The microbial genomics of glacier-fed streams: adaptations to an extreme ecosystem

Seawater Intrusion Inhibits Nitrate Removal in Tidal Marsh Aquifers

Exploring the self-assembly of supramolecular crystals with DNA tiles

Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics

Modeling, analysis, and design of complex biological networks

Ecosystem engineering by periphyton in Alpine proglacial streams

Ultrasonic sediment flux profiling with ACVP Technology: application to sediment-laden Boundary Layer flows

A field-capable rapid plant DNA extraction protocol using microneedle patches for botanical surveying and monitoring

cgNA plus web : A Visual Interface to the cgNA plus Sequence-dependent Statistical Mechanics Model of Double-stranded Nucleic Acids

Iron Reduction in Profundal Sediments of Ultraoligotrophic Lake Tahoe under Oxygen-Limited Conditions

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

Economic and commercial analysis of reusing dam reservoir sediments