Biology Dark Matter

Transcripts are potential therapeutic targets, yet bacterial transcripts remain biological dark matter with uncharacterized biodiversity. We developed and applied an algorithm to predict transcripts for Escherichia coli K12 and E2348/69 strains (Bacteria:gamma-Proteobacteria) with newly generated ONT direct RNA sequencing data while predicting transcripts for Listeria monocytogenes strains Scott A and RO15 (Bacteria:Firmicute), Pseudomonas aeruginosa strains SG17M and NN2 strains (Bacteria:gamma-Proteobacteria), and Haloferax volcanii (Archaea:Halobacteria) using publicly available data...

Recent studies have increasingly focused on the occurrence of plastic leachate and its impacts on aquatic ecosystems. Nonetheless, the environmental fate of this leachate in the presence of abundant natural organic matter (NOM)-a typical scenario in environments contaminated with plastics-remains underexplored. This study investigates the photo-induced leaching behaviors of dissolved organic matter (DOM) from terrestrial-sourced particles (forest soil and leaf litter) and microplastics (MPs), specifically polystyrene (PS) and polyvinyl chloride (PVC), over a two-week period...

Bacteriophages infecting Mycobacterium smegmatis mc2 155 are numerous and, hence, are classified into clusters based on nucleotide sequence similarity. Analyzing phages belonging to clusters/subclusters can help gain deeper insights into their biological features and potential therapeutic applications. In this study, for genomic characterization of B1 subcluster mycobacteriophages, a framework of online tools was developed, which enabled functional annotation of about 55% of the previously deemed hypothetical proteins in B1 phages...

Cell type-specific expression of genes plays a pivotal role in the development and evolution of multicellular organisms over millions of years. The majority of regulatory control resides within the non-coding regions of the genome, referred to as 'dark matter', which contains cis -regulatory modules. These cis -regulatory modules function collectively and can impact gene expression even when located far from the target gene, exhibiting context-specific behaviour. Consequently, the cis -regulatory code governing gene expression patterns is intricate, in contrast to the universally understood genetic code...

This perspective begins with a speculative consideration of the properties of the earliest proteins to appear during evolution. What did these primitive proteins look like, and how were they of benefit to early forms of life? I proceed to hypothesize that primitive proteins have been preserved through evolution and now serve diverse functions important to the dynamics of cell morphology and biological regulation. The primitive nature of these modern proteins is easy to spot. They are composed of a limited subset of the 20 amino acids used by traditionally evolved proteins and thus are of low sequence complexity...

Up to 80% of the human genome produces "dark matter" RNAs, most of which are noncapped RNAs (napRNAs) that frequently act as noncoding RNAs (ncRNAs) to modulate gene expression. Here, by developing a method, NAP-seq, to globally profile the full-length sequences of napRNAs with various terminal modifications at single-nucleotide resolution, we reveal diverse classes of structured ncRNAs. We discover stably expressed linear intron RNAs (sliRNAs), a class of snoRNA-intron RNAs (snotrons), a class of RNAs embedded in miRNA spacers (misRNAs) and thousands of previously uncharacterized structured napRNAs in humans and mice...

Microbes represent the most common organisms on Earth; however, less than 2% of microbial species in the environment can undergo cultivation for study under laboratory conditions, and the rest of the enigmatic, microbial world remains mysterious, constituting a kind of "microbial dark matter" (MDM). In the last two decades, remarkable progress has been made in culture-dependent and culture-independent techniques. More recently, studies of MDM have relied on culture-independent techniques to recover genetic material through either unicellular genomics or shotgun metagenomics to construct single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs), respectively, which provide information about evolution and metabolism...

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Ultralight dark photons and axions are well-motivated hypothetical dark matter candidates. Both dark photon dark matter and axion dark matter can resonantly convert into electromagnetic waves in the solar corona when their mass is equal to the solar plasma frequency. The resultant electromagnetic waves appear as monochromatic signals within the radio-frequency range with an energy equal to the dark matter mass, which can be detected via radio telescopes for solar observations. Here we show our search for converted monochromatic signals in the observational data collected by the high-sensitivity Low Frequency Array (LOFAR) telescope and establish an upper limit on the kinetic mixing coupling between dark photon dark matter and photon, which can reach values as low as 10-13 within the frequency range of 30 - 80 MHz...

The paper discusses the perspectives of further implementation of the autocatalytic properties of a soluble biopolymer (SBP) derived from municipal biowastes for the realisation of a biorefinery producing value-added bio-products for consumer use. The reaction of an SBP and water is reported to cause the depolymerisation and oxidation of the pristine SBP organic matter with the formation of carboxyl-functionalised polymers having lower molecular weight and CO2 . These findings demonstrate the oxidation of the SBP via water, which could only occur through the production of O and OH radicals catalysed by the SBP...

Charge and spin are two intrinsic attributes of carriers governing almost all of the physical processes and operation principles in materials. Here, we demonstrate the manipulation of electronic and spin states in designed Co-quantum dot/WS2 (Co-QDs/WS2 ) heterostructures by employing a metal-dielectric composite substrate and via scanning tunneling microscope. By repeatedly scanning under a unipolar bias, switching the bias polarity, or applying a pulse through nonmagnetic or magnetic tips, the Co-QDs morphologies exhibit a regular and reproducible transformation between bright and dark dots...

Approximately half of the human genome includes repetitive sequences, and these DNA sequences (as well as their transcribed repetitive RNA and translated amino-acid repeat sequences) are known as the repeatome. Within this repeatome there are a couple of million tandem repeats, dispersed throughout the genome. These tandem repeats have been estimated to constitute ∼8% of the entire human genome. These tandem repeats can be located throughout exons, introns and intergenic regions, thus potentially affecting the structure and function of tandemly repetitive DNA, RNA and protein sequences...

Increased production of renewable energy sources is becoming increasingly needed. Amidst other strategies, one promising technology that could help achieve this goal is biological hydrogen production. This technology uses micro-organisms to convert organic matter into hydrogen gas, a clean and versatile fuel that can be used in a wide range of applications. While biohydrogen production is in its early stages, several challenges must be addressed for biological hydrogen production to become a viable commercial solution...

Microplastics (MPs), an emerging class of pollutants, significantly impact the photoconversion dynamics of tetracycline (TC). But the effect of prevalent dissolved organic matter (DOM) on TC photodegradation in the presence of MPs remains a gap in current research. In this study, the photoconversion behavior and mechanism of TC under simulated sunlight conditions were systematically investigated, both in the presence of DOM and in combination with polystyrene (PS) MPs. The results demonstrated that both DOM and MPs enhanced the photodegradation of TC when compared to its direct degradation...

BACKGROUND: Fraction of functional sequence in the human genome remains a key unresolved question in Biology and the subject of vigorous debate. While a plethora of studies have connected a significant fraction of human DNA to various biochemical processes, the classical definition of function requires evidence of effects on cellular or organismal fitness that such studies do not provide. Although multiple high-throughput reverse genetics screens have been developed to address this issue, they are limited to annotated genomic elements and suffer from non-specific effects, arguing for a strong need to develop additional functional genomics approaches...

Nutrient deficiency is the primary obstacle in tailing ecological restoration besides high heavy metal content. Biological soil crusts (BSCs) are known for their C and N fixation capabilities and play a crucial role in soil P cycle. BSCs are widespread in tailings and provide a potential ecological restoration approach. In 2022, we carried out an on-site restoration on a PbZn tailing pond in Yunnan Province, China. BSCs were propagated by natural moss crust fragment inoculation. The induced moss crusts (IMCs) were monitored at 0, 45, 90, and 135 days and compared with natural moss crusts (NMCs)...

Small peptides represent a subset of dark matter in plant proteomes. Through differential expression patterns and modes of action, small peptides act as important regulators of plant growth and development. Over the past 20 years, many small peptides have been identified due to technical advances in genome sequencing, bioinformatics, and chemical biology. In this article, we summarize the classification of plant small peptides and experimental strategies used to identify them as well as their potential use in agronomic breeding...

Soil harbors a vast expanse of unidentified microbes, termed as microbial dark matter, presenting an untapped reservo)ir of microbial biodiversity and genetic resources, but has yet to be fully explored. In this study, we conduct a large-scale excavation of soil microbial dark matter by reconstructing 40,039 metagenome-assembled genome bins (the SMAG catalogue) from 3304 soil metagenomes. We identify 16,530 of 21,077 species-level genome bins (SGBs) as unknown SGBs (uSGBs), which expand archaeal and bacterial diversity across the tree of life...

Light-matter interaction in the ultrastrong coupling regime is attracting considerable attention owing to its applications to coherent control of material properties by a vacuum fluctuation field. However, electrical access to such an ultrastrongly coupled system is very challenging. In this work, we have fabricated a gate-defined quantum point contact (QPC) near the gap of a terahertz (THz) split-ring resonator (SRR) fabricated on a GaAs two-dimensional (2D) electron system. By illuminating the system with external THz radiation, the QPC shows a photocurrent spectrum which exhibits significant anticrossing that arises from coupling between the cyclotron resonance of the 2D electrons and the SRR...

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...