R. Daniel

Nanoparticles co-delivering siRNA and mRNA for simultaneous restoration and silencing of gene/protein expression in vitro and invivo

This study develops nanoparticles that co-deliver siRNA and mRNA to simultaneously silence and restore gene/protein expression in vitro and in vivo.

Isolation and characterization of Sporomusa carbonis sp. nov., a carboxydotrophic hydrogenogen in the genus of Sporomusa isolated from a charcoal burning pile

This study isolates and characterizes a new bacterial species, Sporomusa carbonis, from a charcoal burning pile, describing its genomic and metabolic features.

Knock-down of genes essential for homoacetogenic growth using sugar inducible promoters in the thermophile Thermoanaerobacter kivui

This paper develops sugar-inducible promoters in Thermoanaerobacter kivui to enable controlled gene knock-down and study metabolic pathways.

Aldehydic load as an objective imaging biomarker of mild traumatic brain injury

This study develops a CEST-MRI contrast agent to detect aldehydes in mTBI, showing increased aldehyde levels and neuroinflammation in mice with ALDH2 deficiency.

Control of three-carbon amino acid homeostasis by promiscuous importers and exporters in Bacillus subtilis: Role of the sleeping beauty family of amino acid exporters

This study identifies import and export systems for three-carbon amino acids in B. subtilis, revealing the role of the 'sleeping beauty' family of amino acid exporters in maintaining homeostasis under toxic conditions.

Novel insights into phage biology of the pathogen Clostridioides difficile based on the active virome

This study identifies active phages in C. difficile strains under natural stress conditions and discovers novel phage-mediated DNA transfer mechanisms.

A patchwork pathway of apparently recent origin enables degradation of the synthetic buffer compound TRIS in bacteria

The paper discovers a recently evolved bacterial pathway for degrading TRIS, a synthetic buffer, through horizontal gene transfer and shows its global distribution.

The previously uncharacterized RnpM (YlxR) protein modulates the activity of ribonuclease P in Bacillus subtilis

The paper identifies RnpM (YlxR) as a novel modulator of RNase P activity in B. subtilis, reducing its ability to process pre-tRNAs.

Direct and culture-independent detection of low-abundant Clostridioides difficile in environmental DNA via PCR

This paper develops a PCR method to detect low-abundant Clostridioides difficile in environmental samples, revealing biases in strain isolation due to antibiotic-based enrichment.

Pan-genome analysis of six complete Paracoccus type strain genomes from hybrid next generation sequencing

This study analyzes six complete Paracoccus genomes to understand genomic adaptation and diversity across ecological niches.

Landscape heterogeneity and soil biota are central to multi-taxa diversity for landscape restoration

The paper tests if increasing landscape heterogeneity through tree islands enhances multi-taxa diversity in monoculture-dominated landscapes and finds that it does by fostering unique species.

Identification of a SARS-CoV-2 host metalloproteinase-dependent entry pathway differentially used by SARS-CoV-2 and variants of concern Alpha, Delta, and Omicron

This study identifies a MMP2/9-dependent entry pathway for SARS-CoV-2 and variants, showing differential usage and reduced activity in Omicron.

Transcriptional Landscape of Ectomycorrhizal Fungi and Their Host Provide Insight into N Uptake from Forest Soil

The paper examines the transcriptional responses of ectomycorrhizal fungi and their host beech tree to nitrogen fluctuations, showing fungal resistance and host dynamic metabolism.

Forest tree species composition and abiotic site conditions drive soil fungal communities and functional groups

The paper investigates how tree species composition and abiotic site conditions influence soil fungal communities and their functional groups in temperate forests.

Exploiting synergistic interactions of Medicago sativa L. and Paraburkholderia tropica for enhanced biodegradation of diesel fuel hydrocarbons

This study examines the synergistic interactions between Medicago sativa and Paraburkholderia tropica to enhance diesel fuel hydrocarbon degradation in contaminated soils.

Metagenomic insight into the plant growth-promoting potential of a diesel-degrading bacterial consortium for enhanced rhizoremediation application

The paper identifies a bacterial consortium capable of promoting plant growth and degrading diesel fuel hydrocarbons, showing potential for rhizoremediation applications.

Diversity and metagenome analysis of a hydrocarbon-degrading bacterial consortium from asphalt lakes located in Wietze, Germany

This study isolates and analyzes a hydrocarbon-degrading bacterial consortium from a petroleum-contaminated site, identifying Acidocella as a key genus for diesel fuel degradation.

Metagenomic screening for lipolytic genes reveals an ecology-clustered distribution pattern

The paper screens metagenomes for lipolytic genes using function-driven and sequence-based methods, revealing ecological factors influence their distribution.

Nitrogen availability drives gene length of dominant prokaryotes and diversity of genes acquiring Nitrogen-species in oceanic systems

The paper shows that nitrogen availability affects gene length and diversity of nitrogen-acquiring genes in oceanic prokaryotes.

Extracellular endosulfatase Sulf-2 harbours a chondroitin/dermatan sulfate chain that modulates its enzyme activity

This study identifies a chondroitin/dermatan sulfate chain in Sulf-2 that modulates its enzyme activity, revealing a new paradigm for Sulfs' function.

Impact of nitrogen and phosphorus addition on resident soil and root mycobiomes in beech forests

This study examines how nitrogen and phosphorus fertilization affects soil and root mycobiomes in beech forests, finding shifts in fungal community composition and functional potential.

CAZymes in Maribacter dokdonensis 62-1 from the Patagonian shelf: Genomics and physiology compared to related flavobacteria and a co-occurring Alteromonas strain

This study characterizes CAZymes in Maribacter dokdonensis 62-1, showing its ability to utilize alginate and other polysaccharides, and compares its genomic features with related strains and an Alteromonas strain.

Essentiality of c-di-AMP in Bacillus subtilis: Bypassing mutations converge in potassium and glutamate homeostasis

This paper identifies suppressor mutations in Bacillus subtilis that allow growth of a c-di-AMP-free strain under toxic conditions, revealing the role of potassium and glutamate homeostasis in c-di-AMP essentiality.

Quasi-essentiality of RNase Y in Bacillus subtilis is caused by its critical role in the control of mRNA homeostasis

This study shows that RNase Y is quasi-essential in Bacillus subtilis due to its role in mRNA homeostasis, as suppressor mutations in RNA polymerase subunits alleviate its deletion effects.

Resistance to serine in Bacillus subtilis: Identification of the serine transporter YbeC and of a metabolic network that links serine and threonine metabolism

This study identifies YbeC as the major serine transporter in Bacillus subtilis and reveals a metabolic link between serine and threonine that causes serine toxicity.

Mitochondria tether to Focal Adhesions during cell migration and regulate their size.

The paper shows mitochondria tether to focal adhesions during cell migration and regulate their size by controlling ATP production.

Characterization of three Yarrowia lipolytica strains in respect to different cultivation temperatures and metabolite secretion

The paper characterizes three Yarrowia lipolytica strains under different temperatures and media, finding temperature-dependent sugar alcohol production and no clear genotype-phenotype links.

Alanine Metabolism in Bacillus subtilis

This study characterizes alanine metabolism in Bacillus subtilis, identifying key genes and pathways involved in D-alanine uptake and biosynthesis.

The cell cycle regulator GpsB functions as cytosolic adaptor for multiple cell wall enzymes

This study identifies GpsB as a cytosolic adaptor that coordinates cell wall synthesis with the bacterial cell cycle by interacting with multiple enzymes and proteins.