Short Region Research Articles

Sexually reproducing organisms make haploid gametes—oocytes and spermatocytes—that combine during fertilization to make an embryo. While both gametes contain similar DNA content, oocytes contain the bulk of the cytoplasm including maternally supplied mRNAs and proteins required prior to zygotic gene activation. RNA-binding proteins are key regulators of these maternal transcripts. In Caenorhabditis elegans, the tandem zinc finger proteins OMA-1 and OMA-2 are required for fertilization. Here, we show that OMA-1 RNA-binding activity requires a short basic region immediately upstream of the canonical tandem zinc finger domain. Mutation of this region in animals produces a phenotype distinct from a genetic null. Oocytes can be fertilized, but fail to form an intact chitin eggshell, frequently fragment in utero, and arrest prior to morphogenesis. Our results identify a critical region outside of the canonical RNA-binding domain required for both RNA-binding activity as well as revealing a new role for OMA-1 during the oocyte-to-embryo transition.

The origins of CpG islands (CGIs) are not known. They are relatively short GC-rich regions of DNA with a higher-than-expected occurrence of CpG dinucleotides compared to most of the genome. They constitute less than 1% of the human genome but harbor approximately 40% of all transcription start sites (TSSs). CGIs are usually modulated by histone modifications in somatic cells or, in a minority of cases, permanently silenced by CpG methylation. Those that do not have TSSs are called "orphan CGIs". Here, we show that CGIs containing TSSs almost never contain any of three major classes of transposable elements (TEs) and orphan CGIs rarely do. We hypothesize that CGIs persist across evolutionary time due to counterselection against TE insertion in the germ line. The 99% of the vertebrate genome, which is not CG rich, contains 60% of TSSs and putative enhancers. We postulate that conversion of an ancestral CpG-rich genome into the current CpG-depleted version present in vertebrates may also have allowed reversible DNA methylation to function in complex and dynamic gene control circuits. Therefore, we propose an evolutionary model in which vertebrate TEs are indirectly responsible for the existence of CGIs, and the formation of regulatory elements such as TSSs and enhancers that can potentially utilize dynamic DNA methylation for gene control.

This paper deals with the surface heterogeneity in the near-surface region of the high strength low alloyed steel MC 1100. The remarkable surface thermal softening takes place due to decarburization during hot rolling, which in turn avoids very fine short twins within the grain interior during the accelerated cooling. The depth and extent of this twin-free region strongly vary along the sheet width, whereas this effect only fringes along the sheet length. The high sensitivity of the Barkhausen noise technique against the variable depth extent of short twins free region originates from the interaction among the domain walls in motion and lattice imperfection in which very fine short twins play a strong role due to their high pinning strength. The study demonstrates that the influence of residual stresses can be neglected. On the other hand, evolution between the tensile stress and Barkhausen noise is strongly altered as a function of microstructure heterogeneity. For this reason, employing the Barkhausen noise technique to monitor the stress state of components made of MC 1100 in real operation can be a quite complex task.

Transfer RNA Recognition Mechanism of Thermoplasma acidophilum Trm56, a SPOUT tRNA Methyltransferase that Possesses an Unusually Long C-terminal Region.

The compressible equivalent boundary layer model developed by Li et al. [“Inflow turbulence generation for compressible turbulent boundary layers,” Phys. Fluids 36, 025132 (2024)], which generates inflow turbulence for direct numerical simulations, has been extended to provide inflow for large-eddy simulations. Due to the inherent uncertainty of the subgrid-scale model, only the momentum balance in the streamwise direction and the energy balance are intended to be approximately recovered in this extended model compared with the original one, which primarily governs the equivalence to boundary layer flows. The performance of this extended method has been validated through two distinct test cases: a flat plate and a cone with a half-angle of 7°. The results indicate that this extended method can maintain a relatively short recovery region in large-eddy simulations, meeting the criteria of skin friction and heat transfer, Reynolds stresses, and density fluctuations at the wall, and is applicable to complex geometries with minimal additional effort.

BackgroundMitochondrial DNA sequences are used for inter- and intra-specific comparison analysis in ecological studies. Instead of using short regions as marker sequences, analyzing longer regions, such as whole mitochondrial DNA sequences, can improve the accuracy of such studies by increasing the likelihood of detecting species or specific sequences. However, current methods for sequencing whole mitochondrial DNA require primer design for each target species or long fragments of genomic DNA as a PCR template. We developed a method and accompanying tool for PCR-based long-read sequencing of whole mitochondrial DNA, named MitoCOMON, which is applicable to wide-target taxonomic clades and partially digested template DNA.ResultsPCR amplification of whole mitochondrial DNA as four fragments facilitates the successful assembly of the whole mitochondrial DNA sequence, even when a sample is a mixture of multiple species or partially degraded. The tool that we developed consists of two modules that can design a primer set for species in a target taxonomic clade and assemble the whole mitochondrial DNA sequence from amplicons which were amplified using the designed primer set. Primer sets were designed for mammal and bird species, which showed a high success rate for whole mitochondrial DNA sequencing with high sequence accuracy. Multiple whole mitochondrial DNA sequences were also assembled from samples mixed with the genomic DNA of several species without forming chimeric sequences. In addition to the accuracy, some assembled sequences also retained a long duplication at the D-loop region, suggesting that the method addresses large rearrangements. Compared with a method that amplifies the whole mitochondrial DNA as a single amplicon, our method was effective for partially degraded samples.ConclusionsOur method and accompanying tool, named MitoCOMON, enables an easier acquisition of whole mitochondrial DNA sequences from samples with some DNA degradation without designing species-specific primers. This approach can enhance the accessibility of mitochondrial genomic data and is expected to improve the resolution of ecological analyses, including accurate species identification and individual-level discrimination.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12864-025-12010-0.

BackgroundThe microorganisms in breast tissue and its surrounding environment play a critical role in the development and progression of breast cancer (BC). This study aims to characterize BC-associated microbiota via 16S ribosomal RNA (rRNA) sequencing to explore potential pathogenic mechanisms and support early diagnosis and personalized treatment.MethodsTumor and normal adjacent tissue (NAT) samples from 31 BC patients were analyzed by 16S rRNA sequencing targeting five variable regions. Microbial composition was analyzed via the Short MUltiple Regions Framework (SMURF) pipeline. Alpha and beta diversity analyses were conducted to compare the microbial communities between the BC and NAT groups, and among different BC subgroups stratified by the molecular subtype, clinical stage, histological grade, and proliferation index (Ki-67). Differential microbial taxa were identified using the Wilcoxon signed-rank test and linear discriminant analysis effect size (LEfSe). Functional pathways were predicted using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.ResultsNo significant differences in alpha or beta diversity were observed between the BC and NAT groups (P>0.05). The LEfSe revealed that Flavobacteriales, Comamonas, and Delftia were enriched in BC. The KEGG pathway predictions showed that the ascorbate and aldarate metabolism, lysosome, and other glycan degradation pathways were upregulated in BC. Brevundimonas was the dominant genus in the high Ki-67 (H-Ki-67) group, in which, the glycolysis/gluconeogenesis, bacterial toxins, and isoflavonoid biosynthesis pathways were also shown to be upregulated (P<0.05).ConclusionsOverall, microbial diversity was similar between the BC and NAT groups; however, distinct microbial profiles were identified in the BC tissue group and among the clinicopathological subgroups. Brevundimonas was the predominant genus in the H-Ki-67 group. This study provides novel insights and potential targets that may extend our understanding of BC-related microbial mechanisms and advance microbiota-based therapies.

Comparative genomic studies of Marek’s disease virus (MDV) have suggested that attenuated and virulent strains share >98% sequence identity. However, these estimates fail to account for variation in regions of the MDV genome harboring tandem repeats. To resolve these loci and enable assessments of intrapopulation diversity, we used a PacBio Sequel II platform to sequence MDV strains CVI988/Rispens (attenuated), HPRS-B14 (virulent), Md5 (very virulent) and 675A (very virulent plus). This approach enabled us to identify patterns of variation in tandem repeat regions that may contribute to the known phenotypic differences between these strains, including the proline-rich regions of the meq oncogene (Meq-PRR) and MDV049/UL36 (UL36-PRR), the multiple telomeric repeats (mTMR) region of the a-like sequence, the promoter region of the latency-associated transcript (LAT), and the MDV006.5/MDV075.2 transcripts. We also found CVI988/Rispens variants showing a 4.3-kb deletion in the Unique Short (US) region, resulting in the loss of SORF1, SORF2, US1, US10, SORF3, and US2. Despite the conventional wisdom that MDV harbors little genomic diversity even when compared to other herpesviruses, we found MDV tandem repeat regions to be highly variable both within individual samples and across strains. In addition to providing a foundation for future studies seeking to explore a potential link between MDV tandem repeats and phenotypic traits like virulence and attenuation, these findings provide detailed support for the premise that DNA viruses can harbor high levels of within-sample diversity in tandem repeat regions.

Wastewater-based surveillance (WBS) has modernized in recent years and emerged as an important tool for the monitoring of viral pathogens, including monkeypox virus (MPXV). Here we describe a novel targeted amplicon sequencing method developed for clade and subclade characterization of MPXV from municipal wastewater. This new method addresses the limitations of PCR-based methods and the challenges of sequencing a pathogen displaying low viral load in municipal wastewater samples. A tiled amplicon scheme composed of 11 primer pairs targeting a 4.2kb portion of the inverted terminal repeat (ITR) region of the MPXV genome was designed and tested. In silico analysis demonstrated high accuracy for clade and subclade calls using the full target region, with specific amplicons also exhibiting strong performance individually. An MPXV consensus sequence representing the entire target region was successfully sequenced from a wastewater sample and differentiated from positive controls by a distinct deletion within a short homopolymeric region. Notably, clade-informing data was also achieved from partial sequences recovered from lower abundance samples. This study presents a new sequencing method targeting MPXV with enhanced genomic resolution compared to existing PCR-based approaches, providing critical genomic-level information informing MPXV surveillance and public health interventions.

Oxalis triangularis, a perennial Oxalidaceae ornamental with biological functions, had its full cpDNA sequenced: a 152,115 bp circular genome with two 25,436 bp inverted repeat regions, an 83,309 bp large single-copy region and a 16,934 bp short single-copy region. The overall GC content was 36.48%. A total of 109 genes were annotated, including 76 protein-coding genes, 29 tRNA genes and 4 rRNA genes, all starting with AUG. Furthermore, 70 simple sequence repeats were also found. Phylogenetic analysis groups it with 10 Oxalis species, closely related to O. latifolia, O. drummondii, and O. corymbosa, providing resources for its molecular identification and evolutionary studies.

Photonic integrated circuits (PICs) are gaining significant attention in the visible and short near-infrared spectral regions for diverse applications such as spectroscopy, optical atomic clocks, quantum optics, and optical communications. Among various material platforms, silicon nitride (SiN) is particularly noteworthy due to its wide bandgap, low propagation losses, broad transparency, and well-established fabrication processes. Furthermore, thin-film lithium niobate (LN) has emerged as a promising platform for high-speed, power-efficient modulation in these spectral regimes, complementing the capabilities of SiN. Consequently, the integration of SiN and LN is well-suited for optical communication transmitters. However, on-chip receivers for such systems remain unexplored. We present the first demonstration of an optical coherent communication system at a short near-infrared window, utilizing a SiN-based integrated 90° optical hybrid. Our demonstration operates over a 13.9-THz bandwidth with 10-Gbaud binary phase-shift-keyed signals, which is comparable to or even more than the bandwidth of the conventional fiber-optic systems. Furthermore, we demonstrate a 2.2-m free-space optical transmission using the SiN chip as an application of visible and short near-infrared coherent communication. This demonstration highlights the potential of fully integrated high-performance coherent transceivers for new wavelength windows.

Epileptic seizures and EEG findings in 3p deletion syndrome involving SLC6A1.

ABSTRACT Cryptodontia is a diverse and widespread group of Permian dicynodonts, although its exact membership has been a subject of uncertainty in recent phylogenetic analyses. Cryptodont fossils were first reported from the Lopingian Usili Formation (Ruhuhu Basin, Tanzania) in 1932, with the current composition of the Usili cryptodont assemblage emerging from taxonomic revisions in the mid-2000s. Here we describe a new cryptodont, Mdomowabata trilobops, gen. et sp. nov., from the Usili Formation. Diagnostic characters of M. trilobops include: transversely expanded caniniform process of the maxilla that has a bluntly rounded ventral tip; paired nasal bosses; hatchet-shaped exposure of the postfrontal on the dorsal surface of the skull; parietals that are widely exposed dorsally; intertemporal portion of the postorbital that is oriented vertically with a concave lateral surface; triangular exposure of the postparietal on the skull roof; low, close-set anterior median palatal ridges; large palatine pad with a rugose posterior section and a smoother anterior section that is flush with the premaxillary secondary palate; transversely broad and anteroposteriorly short symphyseal region of the mandible; and prominent, round muscle scar anterior to the external mandibular fenestra. The plow-shaped snout and evidence of increased facial sensitivity suggest that Mdomowabata used its snout to interact with the substrate. A phylogenetic analysis recovers M. trilobops within a monophyletic Cryptodontia, on the stem leading to a clade comprising Oudenodontidae and Rhachiocephalidae. However, persistent problems in recovering stable relationships suggest that a critical reassessment of the character data underlying current dicynodont phylogenies is needed.

PurposeWearable filters that reduce light in the short wavelength region of the visible spectrum, or “blue-blocking glasses,” are increasingly available and offer an individualized, low-cost tool for enhancing sleep and circadian health. However, their effectiveness depends on filtering properties, application, timing, and implementation. If these factors are disregarded, blue-blocking glasses may be ineffective or lead to counterproductive outcomes.MethodsWe introduce a new metric, melanopic daylight filtering density (mDFD), to quantify a filter's capacity to decrease melanopic input, providing an alternative to ad-hoc measures. We applied mDFD to 26 commercially available glasses, estimating their potential to reduce circadian and related physiological effects of light across common applications in the context of consensus-based metrics and recommendations. We also reviewed intervention studies that used blue-blocking glasses.ResultsProducts varied considerably in mDFD, with only those rated at mDFD ≥1 providing sufficient reductions in melanopic input to justify the “blue-blocking” label and associated claims. At least one relevant sleep or circadian-related outcome improved with blue-blocking interventions in the studies reviewed. In addition to filtering strength, appropriate timing and usage are critical to effectiveness.ConclusionsThe efficacy of blue-blocking glasses depends on both spectral filtering and proper usage. The mDFD metric offers a consistent, evidence-based approach for evaluating, selecting, and designing products that reduce photic input for non-visual physiological effects of light.Translational RelevanceStandardized characterization of blue-blocking glasses using mDFD facilitates reliable product comparisons, evidence-based selection, and rational design of lenses that are optimized for circadian health across a range of applications.

High-quality nuclear, chloroplast, and preliminary mitochondrial genomes have been assembled and annotated for the B genome diploid (BB: 2n = 2x = 18) figleaf goosefoot (Chenopodium ficifolium). The primary objective was to advance a simplified model system for genetic characterization and improvement of allotetraploid (AABB: 2n = 4x = 36) quinoa (Chenopodium quinoa), a nutritionally valuable, halophytic orphan crop. In addition to its diploidy and favorably small genome size, the C. ficifolium model provides a shorter generational period and smaller overall plant size as compared to C. quinoa, while displaying relevant agronomic trait variations amenable to gene-trait association studies. The C. ficifolium "Portsmouth" nuclear genome was sequenced using PacBio HiFi long-read technology and assembled using Hifiasm. After manual adjustments, the final ChenoFicP_1.0 assembly consisted of 9 pseudochromosomes spanning 730 Mbp, while 22,617 genes were identified and annotated. BUSCO analyses indicated a nuclear genome completeness of 97.5% and a proteome and transcriptome completeness of 98.4%. The chloroplast genome assembly detected 2 equally represented structural haplotypes differing in the orientation of the short single copy region relative to the long single copy region. Phylogenetic and parentage analyses pointed to an unspecified AA diploid species and away from C. ficifolium as the likely maternal chloroplast and mitochondrial genome donor(s) during the initial tetraploidization event in the C. quinoa lineage. Using the new ChenoFicP_1.0 reference genome, a genome-wide association study was performed on a previously studied C. ficifolium F2 population to further define region(s) implicated in the control of 3 key agronomic traits: days to flowering, plant height, and branch number. This analysis localized control of all 3 traits to a 7-Mb interval on pseudochromosome Cf4. This region contains ∼770 genes, including the FTL1 locus, thus confirming and extending our prior, single-marker analysis showing association of these 3 traits with an FTL1 amplicon length polymorphism. The use of these data to further develop C. ficifolium as a model species for genetics and breeding of quinoa serves to expand knowledge and germplasm resources for quinoa improvement.

Abstract This research comprehensively studies the hydrodynamic characteristics of a semiplaning ship hull, R/V Athena, across different cruising speeds using OpenFOAM numerical simulations. Results were validated against experimental data for 11 Froude numbers ranging from 0.14 to 1.0. Key findings reveal (1) the hull resistance exhibits a near-linear relationship with Froude number, (2) the sinkage follows a distinct V-shaped curve with a short saddle region where simulations tend to under-predict values, and (3) the trim demonstrates an oblique “S” shape pattern. Free surface elevation analysis showed that their intensity increased while the number of side waves decreased with increasing Froude numbers. Additionally, tail waves moved further from the stern and exhibited greater intensity and wavelength at higher Froude numbers. Local pressure distributions and spray patterns were also analyzed, revealing complex flow physics around the hull. This study validates computational methods for simulating planing hulls at higher speeds and provides valuable insights into the transitional hydrodynamics between displacement and planing regimes.

The Schlafen (SLFN) genes are induced by interferons, underscoring their roles in the immune response and viral replication inhibition. SLFN14, a member of SLFN family, is associated with multiple human diseases; however, neither its functions nor its disease mechanisms are fully understood. Herein, human SLFN14 biochemically is characterized, demonstrating that it specifically cleaves RNAs containing short duplex regions, such as hairpin RNAs and tRNAs, but does not have ATPase or helicase activity. Cryogenic electron microscopy structures of SLFN14 apoenzyme (2.84 Å) and SLFN14‐hairpin RNA complex (2.88 Å) are determined, revealing that SLFN14 assembles into a ring‐like dimer and dimerization is mainly mediated by hydrophobic contacts. Two N‐terminal RNase domains of SLFN14 are organized head‐to‐tail, forming an RNA‐binding groove that can accommodate a 12‐bp hairpin RNA. The hairpin RNA is recognized mainly through phosphate backbone interactions. Further, SLFN14 is shown to inhibits HIV‐1 pseudovirus replication. The anti‐HIV‐1 activity of SLFN14 is via codon‐usage‐dependent translational inhibition and impairment of the programmed ‐1 ribosomal frameshifting, with an efficiency comparable to that of Shiftless. Using tRNA PCR arrays, SLFN14 and SLFN11 are found to decrease both nuclear‐encoded and mitochondrial tRNAs in cells. Together, these results provide novel insights into the function of SLFN14 and its role in HIV‐1 restriction.

A full-length 16S survey using Nanopore sequencing to uncover the bacterial microbiome in Ixodes ricinus ticks from a single UK woodland, collected across three springs (2019-2021).

Diet plays a pivotal role in human health and disease. Yet, nutrition studies have long relied on self-report methods for collecting dietary intake data despite known limitations. Although new technologies for dietary intake assessment and biomarker identification are in development, the integration of genomics has been limited. DNA metabarcoding, a method that identifies many taxa at once using a short region of DNA, has recently been adapted for use in stool samples from free-living humans. This process, called FoodSeq, provides an objective way to determine the foods people eat. FoodSeq has numerous advantages over self-report methods, is a necessary complement to other methodological innovations in dietary intake assessment, and holds considerable promise for application on an epidemiologic scale, enabling more robust analysis of global dietary patterns.

Amyloid aggregates are pathological hallmarks of many human diseases, but how soluble proteins nucleate to form amyloids is poorly understood. Here, we use combinatorial mutagenesis, a kinetic selection assay, and machine learning to massively perturb the energetics of the nucleation reaction of amyloid-β (Aβ42), the protein that aggregates in Alzheimer’s disease. In total, we measure the nucleation rates of >140,000 variants of Aβ42 to accurately quantify the changes in free energy of activation of the reaction for all possible amino acid substitutions in a protein and, in addition, to quantify >600 energetic interactions between mutations. Strong energetic couplings suggest that the Aβ42 nucleation reaction transition state is structured in a short C-terminal region, providing a structural model for the reaction that may initiate Alzheimer’s disease. Using this approach it should be possible to reveal the energetic structures of additional amyloid transition states and, in combination with additional selection assays, protein transition states more generally.