Biology Dark Matter

Since antiquity, numerous advantages of olive oil and its by-products have been recognized in various domains, including cooking, skincare, and healthcare. Extra virgin olive oil is a crucial component of the Mediterranean diet; several of its compounds exert antioxidant, anti-proliferative, anti-angiogenic and pro-apoptotic effects against a variety of cancers, and also affect cellular metabolism, targeting cancer cells through their metabolic derangements. Numerous olive tree parts, including leaves, can contribute metabolites useful to human health...

Artificial light at night (ALAN) affects many areas of the world and is increasing globally. To date, there has been limited and inconsistent evidence regarding the consequences of ALAN for plant communities, as well as for the fitness of their constituent species. ALAN could be beneficial for plants as they need light as energy source, but they also need darkness for regeneration and growth. We created model communities composed of 16 plant species sown, exposed to a gradient of ALAN ranging from 'moonlight only' to conditions like situations typically found directly underneath a streetlamp...

For a long time, cyclical changes in the body were assumed to be caused by the cyclicity of the environment (day-night, seasons). The concept of daily and seasonal changes was first documented in the 18th century by astronomer D'Ortous de Mairan, who demonstrated that plant leaf motions varied depending on the time of day, and by Linné's description of his floral clock in 1751. In 1832, De Candolle was the first to experimentally establish the endogeneity of rhythms in plants, underlining the notion of what we now term free-running rhythms...

Owing to the ineffectiveness of traditional culture techniques for the vast majority of microbial species, culture-independent analyses utilizing next-generation sequencing and bioinformatics have become essential for gaining insight into microbial ecology and function. This mini-review focuses on two essential methods for obtaining genetic information from uncultured prokaryotes, metagenomics and single-cell genomics. We analyzed the registration status of uncultured prokaryotic genome data from major public databases and assessed the advantages and limitations of both the methods...

Rich electron-matter interactions fundamentally enable electron probe studies of materials such as scanning transmission electron microscopy (STEM). Inelastic interactions often result in structural modifications of the material, ultimately limiting the quality of electron probe measurements. However, atomistic mechanisms of inelastic-scattering-driven transformations are difficult to characterize. Here, we report direct visualization of radiolysis-driven restructuring of rutile TiO2 under electron beam irradiation...

Ultralight axion-like particles are well-motivated relics that might compose the cosmological dark matter and source anomalous time-dependent magnetic fields. We report on terrestrial bounds from the Noble And Alkali Spin Detectors for Ultralight Coherent darK matter (NASDUCK) collaboration on the coupling of axion-like particles to neutrons and protons. The detector uses nuclei of noble-gas and alkali-metal atoms and operates in the Spin-Exchange Relaxation-Free (SERF) regime, achieving high sensitivity to axion-like dark matter fields...

Enormous viral populations have been identified in activated sludge systems, but their ecological and biochemical roles in landfill leachate treatment plants remain poorly understood. To address this knowledge gap, we conducted an in-depth analysis using 36 metagenomic datasets that we collected and sequenced during a half-year time-series sampling campaign at six sites in a full-scale landfill leachate treatment plant (LLTP), elucidating viral distribution, virus‒host dynamics, virus-encoded auxiliary metabolic genes (AMGs), and viral contributions to the spread of virulence and antibiotic resistance genes...

We are now entering a new era in protein sequence and structure annotation, with hundreds of millions of predicted protein structures made available through the AlphaFold database1 . These models cover nearly all proteins that are known, including those challenging to annotate for function or putative biological role using standard homology-based approaches. In this study, we examine the extent to which the AlphaFold database has structurally illuminated this 'dark matter' of the natural protein universe at high predicted accuracy...

Patescibacteria, also known as the candidate phyla radiation (CPR), are a diverse group of bacteria that constitute a disproportionately large fraction of microbial dark matter. Its few cultivated members, belonging mostly to Saccharibacteria, grow as epibionts on host Actinobacteria. Due to a lack of suitable tools, the genetic basis of this lifestyle and other unique features of Patescibacteira remain unexplored. Here, we show that Saccharibacteria exhibit natural competence, and we exploit this property for their genetic manipulation...

Archaea constitute a substantial fraction of marine microbial biomass and play critical roles in the biogeochemistry of oceans. However, studies on their distribution and ecology in the Arctic Ocean are relatively scarce. Here, we studied the distributions of archaea and archaeal ammonia monooxygenase (amoA) gene in the western Arctic Ocean, using the amplicon sequencing approach from the sea surface to deep waters up to 3040 m depth. A total of five archaeal phyla, Nitrososphaerota, "Euryarchaeota", "Halobacteriota," "Nanoarchaeota", and Candidatus Thermoplasmatota, were detected...

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The diverse rumen virome can modulate the rumen microbiome, but it remains largely unexplored. Here, we mine 975 published rumen metagenomes for viral sequences, create a global rumen virome database (RVD), and analyze the rumen virome for diversity, virus-host linkages, and potential roles in affecting rumen functions. Containing 397,180 species-level viral operational taxonomic units (vOTUs), RVD substantially increases the detection rate of rumen viruses from metagenomes compared with IMG/VR V3. Most of the classified vOTUs belong to Caudovirales, differing from those found in the human gut...

The present study aimed to evaluate and compare feeding responses of the non-native and native bivalves, the dark false mussel Mytilopsis leucophaeata and the scorched mussel Brachidontes darwinianus , respectively, by offering different concentrations of seston from the coastal lagoon where these species coexist after dark false mussel introduction (Rodrigo de Freitas Lagoon, Rio de Janeiro-Brazil). For this purpose, independent laboratory experiments were carried out under five concentrations of seston to test the differences in clearance and ingestion rates of bivalves as a function of increasing concentrations of suspended particulate matter (SPM) on seston...

We introduce an ultrafast all-optical approach for efficient chiral recognition that relies on the interference between two low-order nonlinear processes that are ubiquitous in nonlinear optics: sum-frequency generation and third-harmonic generation. In contrast to traditional sum-frequency generation, our approach encodes the medium's handedness in the intensity of the emitted harmonic signal, rather than in its phase, and it enables full control over the enantiosensitive response. We show how, by sculpting the sub-optical-cycle oscillations of the driving laser field, we can force one molecular enantiomer to emit bright light while its mirror twin remains dark, thus reaching the ultimate efficiency limit of chiral sensitivity via low-order nonlinear light-matter interactions...

BACKGROUND: Conversion or editing of adenosine (A) into inosine (I) catalyzed by specialized cellular enzymes represents one of the most common post-transcriptional RNA modifications with emerging connection to disease. A-to-I conversions can happen at specific sites and lead to increase in proteome diversity and changes in RNA stability, splicing, and regulation. Such sites can be detected as adenine-to-guanine sequence changes by next-generation RNA sequencing which resulted in millions reported sites from multiple genome-wide surveys...

Transcriptomics, or more specifically mRNA sequencing, is a powerful tool to study gene expression at the single-cell level (scRNA-seq) which enables new insights into a plethora of biological processes. While methods for single-cell RNA-seq in eukaryotes are well established, application to prokaryotes is still challenging. Reasons for that are rigid and diverse cell wall structures hampering lysis, the lack of polyadenylated transcripts impeding mRNA enrichment, and minute amounts of RNA requiring amplification steps before sequencing...

The improvement of our knowledge of the virosphere, which includes unknown viruses, is a key area in virology. Metagenomics tools, which perform taxonomic assignation from high throughput sequencing datasets, are generally evaluated with datasets derived from biological samples or in silico spiked samples containing known viral sequences present in public databases, resulting in the inability to evaluate the capacity of these tools to detect novel or distant viruses. Simulating realistic evolutionary directions is therefore key to benchmark and improve these tools...

Terahertz spectroscopy is a powerful tool for investigating the properties and states of biological matter. Here, a systematic investigation of the interaction of THz wave with "bright mode" resonators and "dark mode" resonators has been conducted, and a simple general principle of obtaining multiple resonant bands has been developed. By manipulating the number and positions of bright mode and dark mode resonant elements in metamaterials, we realized multi-resonant bands terahertz metamaterial structures with three electromagnetic-induced transparency in four-frequency bands...

Burial mounds represent a challenge for microbiologists. Could ancient buried soils preserve microbiomes as they do archaeological artifacts? To investigate this question, we studied the soil microbiome under a burial mound dating from 2500 years ago in Western Kazakhstan. Two soil profile cuts were established: one under the burial mound and another adjacent to the mound surface steppe soil. Both soils represented the same dark chestnut soil type and had the same horizontal stratification (A, B, C horizons) with slight alterations...

The Vrolik ethnographical collection consisted of roughly 300 skulls, mummified heads, skeletons, pelvises, wet-preserved preparations, and plaster models, collected by Gerard Vrolik (1775-1859) and his son Willem (1801-1863). Most prominent in this collection were the skulls, of which 177 remain in the collection of present-day Museum Vrolik. These skulls-a troubling heritage of colonialism and scientific racism-are the central subjects of this paper, which considers the changing meanings and values of these skulls for racial science over approximately 160 years, between ± 1800 and 1960...