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With the help of the one-dimensional random Potts-like model, we study the origins of fine structures observed on differential melting profiles of double-stranded DNA. We theoretically assess the effects of sequence arrangement on DNA melting curves through the comparison of results for random, correlated, and block sequences. Our results re-confirm the smearing out of the fine structure with the increase in chain length for all types of sequence arrangements and suggest that the fine structure is a finite-size effect. We have found that the fine structures on melting curves of chains comprised of blocks with correlations in sequence are more persistent, probably because of increased sequence disorder the blocks introduce. Many natural DNAs show a well-expressed fine structure of melting profiles. Our results for block sequences may suggest the existence of such sequence motifs in natural DNA sequences. [ABSTRACT FROM AUTHOR]

Probiotics have emerged as agents that improve a wide range of conditions and provide essential ingredients for potential health benefits. Probiotics exhibit a diverse array of effects by engaging in [...]

G-quadruplexes are four-stranded DNA structures that have been found in the cell and are thought to act as elements of control in genomic events. The measurements of the thermodynamic stability, ΔG, of G-quadruplexes shed light on the molecular forces involved in the stabilization of these structures. In thermodynamic studies, the differential heat capacity, ΔCP, of the folded and unfolded states of a G-quadruplex is a fundamental property that describes the temperature dependences of the differential enthalpy, ΔH, entropy, ΔS, and free energy, ΔG. Despite its recognized importance, the ΔCP of G-quadruplex unfolding has not been measured directly. Here, we use differential scanning calorimetry to evaluate changes in heat capacity, ΔCP, accompanying the unfolding transitions of G-quadruplexes formed by modified DNA sequences from the promoter regions of the c-MYC, VEGF, and Bcl-2 oncogenes. The average value of ΔCP is 0.49 ± 0.12 kcal mol−1 K−1. Our analysis revealed that disregarding ΔCP leads to significant errors in extrapolated values of the differential enthalpy, ΔH, and entropy, ΔS, of the folded and unfolded DNA conformations. Although the compensation between ΔH and ΔS weakens the effect of ΔCP on the differential free energy, ΔG, neglecting ΔCP may still result in relative errors in ΔG extrapolated to room temperature as great as 140%. We emphasize the importance of proper consideration of the effect of ΔCP in conformational studies of guanine-rich DNA molecules. [ABSTRACT FROM AUTHOR]

In 2023 in Aichi Prefecture, shiso plant growth in a deep flow technique (DFT) hydroponic system was delayed from mid-March to late April with roots showing evidence of rotting. An oomycete species was isolated from the roots and identified as Phytopythium helicoides based on morphological characteristics and DNA sequence homology. Identical symptoms appeared on shiso plants after inoculating seedlings with zoospores from the strain, and the same oomycete species was reisolated from the diseased plants. This study is the first report in the world of root rot caused by P. helicoides in shiso in a DFT hydroponic system. [ABSTRACT FROM AUTHOR]

Potato production in Mexico is affected by Rhizoctonia solani, causing severe yield losses. The most important criterion for distinguishing R. solani isolates is differentiation by anastomosis groups (AGs). However, the limitations of traditional AG differentiation have prompted the use of DNA sequence analysis as a valuable tool for distinguishing AGs. This study aimed to determine the diversity of anastomosis groups and the aggressiveness of R. solani isolates collected from commercial potato fields in northern Sinaloa, Mexico. A total of 118 R. solani isolates were obtained from symptomatic sprouts and tubers collected from 32 commercial fields distributed in the municipalities of Ahome, Guasave and El Fuerte in northern Sinaloa, Mexico. Fifty-two representative isolates were selected for anastomosis group determination and pathogenicity tests. Phylogenetic analysis with rpb2 gene sequences clearly distinguished 30 isolates belonging to AG-3 PT and 22 isolates to AG-4 HGI. The aggressiveness of these R. solani isolates was evaluated using mini-tubers of potato cv. Fianna, and colonized rice grains were used as inoculum source. The disease severity caused by R. solani on potato plants was evaluated 40 days after emergence. Aggressiveness was estimated as the percentage of necrotic area on underground stems. The results revealed that all R. solani isolates were pathogenic and differences were observed in aggressiveness among the isolates. Of the total of 52 isolates evaluated, 7% were highly aggressive; 61% had intermediate aggressiveness; and 32% exhibited low aggressiveness. These findings regarding the diversity of anastomosis groups and the aggressiveness of R. solani isolates in northern Sinaloa are fundamental for subsequent epidemiology and fungicide resistance studies. [ABSTRACT FROM AUTHOR]

Jumping spiders (Salticidae) are a diverse group of non‐web‐building predators and the most species‐rich spider family. The Salticidae Tribe Nannenini consists of a small group of Oriental jumping spiders that are very poorly known. The use of explicit phylogenetic analyses to establish its affinities has so far remained limited. The Nannenini genus Epidelaxia has a peculiar morphology, making its systematic position uncertain. In this study, we present a comprehensive dataset combining molecular and morphological data for Nannenini, including exemplars from all genera. This dataset comprises DNA sequences of approximately 2400 bp, including nuclear genes (18S, 28S and H3) and the mitochondrial gene CO1, sequenced for 40 taxa (20 ingroups and 20 outgroups), along with 61 morphological characters. Notably, both DNA sequences and morphological traits were analysed separately and concurrently for the first time. The Nannenini clade is recovered with high support. Further, Epidelaxia is monophyletic and sister to Tubalaxia gen. n. This is the first hypothesis on the internal phylogenetic structure of Epidelaxia and its placement within the Tribe Nannenini. A new genus Tubalaxia gen. n. and the following new species are described: E. bharathi sp. n., E. somasundaram sp. n., T. castanea sp. n., T. aurea sp. n. The following new combination is proposed: Tubalaxia minuta (Prószyński, 1992) comb. n. Epidelaxia albostellata, E. albocruciata and E. obscura are redescribed. It is worth noting that the newly described species face endangerment due to their limited distribution and small population sizes. [ABSTRACT FROM AUTHOR]

Among gastrointestinal nematodes, Haemonchus contortus (Rudolphi) Cobb (order Strongylidae; family Trichostrongylidae) is one of pathogenic and economic importance in domestic and wild ruminants, including the European bison, Bison bonasus Linnaeus (order Cetartiodactyla; family Bovidae); a species on the International Union for Conservation of Nature's Red List of Threatened Species. Carabus granulatus Linnaeus (order Coleoptera; family Carabidae) is one of the most prevalent species of ground beetle, inhabiting a wide range of terrestrial ecosystems in Poland. Twenty‐six ground beetles of this species inhabiting the Białowieża Primeval Forest in eastern Poland were screened for the presence of DNA of pathogenic gastrointestinal nematodes of ruminants. Extracted DNA was sequenced and compared to reference sequences. In six insects, the presence of H. contortus DNA was detected. The obtained nucleotide sequences were homologous to each other and to the majority of the published DNA sequences of H. contortus isolates. The sequences were also identical to a sequence of H. contortus isolated from European bison in Poland. The study provides the first molecular evidence of the presence of H. contortus DNA in C. granulatus. The finding suggests that ground beetles may play a role in the transmission dynamics of this parasite. [ABSTRACT FROM AUTHOR]

The molecular characterization of soft tissue and bone tumors is a rapidly evolving field that has changed the perspective of how these tumors are diagnosed today. Morphology and clinico-radiological context still represent the cornerstone of diagnostic considerations but are increasingly complemented by molecular data that aid in objectifying and confirming the classification. The spectrum of analyses comprises mutation or gene fusion specific immunohistochemical antibodies, fluorescence in situ hybridization, DNA and RNA sequencing as well as CpG methylation profiling. This article provides an overview of which tools are presently available to characterize bone and soft tissue neoplasms molecularly, what limitations should be considered, and what conclusions can be drawn from the individual findings. [ABSTRACT FROM AUTHOR]

The primary objective of this research is to isolate and distinguish indigenous fungal strains capable of breaking down hydrocarbons from soils contaminated with oil. This study encompasses various geographical sites within the oilfields of the Kurdistan Region of Iraq (KRI). The extracted DNA from the hypha was used for polymerase chain reaction (PCR) amplification using a universal primer (ITS1/ITS2). PCR product sequencing analyses were compared with the other related sequences in GenBank (NCBI) for molecular evolutionary analyses. Results showed that, out of 68 screened fungal strains, only two genera (i.e., Aspergillus spp. and Penicillium sp.) were identified as the most potent hydrocarbon degrading fungi. This was consistent with the highest hydrocarbon degradation percentage values (91.76% and 81.87%) calculated for Aspergillus spp. and Penicillium sp., respectively, after two months of bioremediation. DNA sequence analysis confirmed the validity of the species as A. fumigatus-KU321562.1, A. flavus-MH270609.1, A. niger-K452260.1, and P. chrysogenum-MK696383.1. In conclusion, molecular techniques employed in fungal taxonomy provide a high degree of accuracy and enable identification that doesn't depend on cultivation, relying on stable genetic markers. These markers furnish reliable and uniform data, granting researchers the ability to fine-tune the level of detail, thus proving indispensable for comprehending fungal diversity and a wide array of practical uses. [ABSTRACT FROM AUTHOR]

Invasive species pose serious threats to global biodiversity, prompting studies to identify factors underlying invasion and establishment success. However, it's difficult to discern these factors due to the absence of survey data since the initial invasion, because introduced species often remain unnoticed until their population becomes large enough. Here, we investigated the establishment process of the alien zooplankton, Daphnia pulicaria, in the past 30 years using sedimentary archives at Lake Biwa. We performed genetic analysis on mitochondrial DNA sequences of the control region and ND5 gene of ephippia in sediments, as well as present females from water samples. Furthermore, we investigated the relationships between the abundance of D. pulicaria and its major predator fish, Ayu, based on the catch data, as well as its competitor, Daphnia galeata whose abundance was inferred from claw remains. Our analyses showed the studied mitochondrial sequences were identical between all samples. The abundance of D. pulicaria was not correlated with that of a competitor but was negatively with that of a predator. These findings suggest the successful establishment of D. pulicaria was primarily influenced by reduced predation pressure, with a limited impact from competitive interactions and potential hindrance for adaptation caused by loss of genetic variation. [ABSTRACT FROM AUTHOR]

The study aims to enhance students' system thinking skills through phylogenetic analysis based on DNA sequencing results. The study is carried out through three steps: (i) pretest: evaluate students' knowledge, (ii) treatment: analysis of affinity relationships through phylogenetics using DNA sequence data, and (iii) postest: measurement of improvement in systems thinking skills after implementation. Evaluations are conducted using written tests as well as worksheets and supported by surveys, questionnaires, and interviews for qualitative analysis. The experiment began with the isolation of citrus DNA, determination of concentration and purity, amplification, reading of sequencing results, and phylogenetics. The results of the teaching analysis show that there is a significant improvement in students' mastery of conceptual and system thinking skills, and there is a high correlation between the pretest and posttest. The problem analysis of interviews and questionnaires is also done to see the enthusiasm for activities as well as the effectiveness of the worksheets used. The study comes with new information on determining the relationship between local citrus in Bengkulu and improving the students' system thinking skills. [ABSTRACT FROM AUTHOR]

Single-molecule techniques are ideally poised to characterize complex dynamics but are typically limited to investigating a small number of different samples. However, a large sequence or chemical space often needs to be explored to derive a comprehensive understanding of complex biological processes. Here we describe multiplexed single-molecule characterization at the library scale (MUSCLE), a method that combines single-molecule fluorescence microscopy with next-generation sequencing to enable highly multiplexed observations of complex dynamics. We comprehensively profiled the sequence dependence of DNA hairpin properties and Cas9-induced target DNA unwinding-rewinding dynamics. The ability to explore a large sequence space for Cas9 allowed us to identify a number of target sequences with unexpected behaviors. We envision that MUSCLE will enable the mechanistic exploration of many fundamental biological processes. [ABSTRACT FROM AUTHOR]

In the age of information explosion, the exponential growth of digital data far exceeds the capacity of current mainstream storage media. DNA is emerging as a promising alternative due to its higher storage density, longer retention time, and lower power consumption. To date, commercially mature DNA synthesis and sequencing technologies allow for writing and reading of information on DNA with customization and convenience at the research level. However, under the disconnected and nonspecialized mode, DNA data storage encounters practical challenges, including susceptibility to errors, long storage latency, resource-intensive requirements, and elevated information security risks. Herein, we introduce a platform named DNA-DISK that seamlessly streamlined DNA synthesis, storage, and sequencing on digital microfluidics coupled with a tabletop device for automated end-to-end information storage. The single-nucleotide enzymatic DNA synthesis with biocapping strategy is utilized, offering an ecofriendly and cost-effective approach for data writing. A DNA encapsulation using thermo-responsive agarose is developed for on-chip solidification, not only eliminating data clutter but also preventing DNA degradation. Pyrosequencing is employed for in situ and accurate data reading. As a proof of concept, DNA-DISK successfully stored and retrieved a musical sheet file (228 bits) with lower write-to-read latency (4.4 min of latency per bit) as well as superior automation compared to other platforms, demonstrating its potential to evolve into a DNA Hard Disk Drive in the future. [ABSTRACT FROM AUTHOR]

Utilizing valuable genes and alleles from crop wild relatives (CWRs) and transferring them to elite varieties requires a thorough understanding of species cross compatibility and reproductive systems. In this review, we examine interspecific crossing among peanut CWRs, chromosome pairing during meiosis, and pollen viability of Filial 1 hybrids. We analyze each parameter in relation to phylogenetic distances and current taxonomic and genomic classification, aiming to develop a cross‐compatibility scheme for the crop's secondary gene pool. Analysis of passport information and species names from research groups worldwide over the past 60 years revealed diverse frequencies of genome combinations (17) and species (26) used in hybridization assays. However, only eight species accounted for nearly 50% of successful hybridizations. In intragenomic hybrids, bivalent frequency ranged from 9.1 to 10, with pollen viability typically between 30% and 60%. Intergenomic hybrids exhibited bivalent frequency between 4.8 and 8.5, with pollen viability below 10%. Outliers were observed in the various parameters and hybrids were analyzed. Phylogenetic distance presented an inverse relationship with all variables; the correlation was low with crossing success while moderate with bivalent frequency and pollen viability. These findings suggest that differences in DNA sequences are not the sole determinants of interspecific cross‐compatibility, indicating the presence of pre‐ or postzygotic hybridization barriers. This organized information is crucial for establishing a framework to facilitate the rational selection of parents with desired traits and appropriate genome combinations, ultimately aiding in the development of new amphidiploids compatible with peanut varieties. [ABSTRACT FROM AUTHOR]

The use of environmental DNA (eDNA) is becoming prevalent as a novel method of ecological monitoring. Although eDNA can provide critical information on the distribution and biomass of particular taxa, the DNA sequences of an organism remain unaltered throughout its existence, which complicates the accurate identification of crucial events, including spawning. Therefore, we examined DNA methylation as a novel source of information from eDNA, considering that the methylation patterns in eggs and sperm released during spawning differ from those of somatic tissues. Despite its potential applications, little is known about eDNA methylation, including its stability and methods for detection and quantification. Therefore, we conducted tank experiments and performed methylation analysis targeting 18S rDNA through bisulphite amplicon sequencing. In the target region, eDNA methylation was not affected by degradation and was equivalent to the methylation rate of genomic DNA from somatic tissues. Unmethylated DNA, abundant in the ovaries, was detected in the eDNA released during fish spawning. These results indicate that eDNA methylation is a stable signal reflecting targeted gene methylation and further demonstrate that germ cell‐specific methylation patterns can be used as markers for detecting fish spawning. [ABSTRACT FROM AUTHOR]

ABSTRACT The woody bamboos (Bambusoideae) exhibit distinctive biological traits within Poaceae, such as highly lignified culms, rapid shoot growth, monocarpic mass flowering and nutlike or fleshy caryopses. Much of the remarkable morphological diversity across the subfamily exists within a single hexaploid clade, the paleotropical woody bamboos (PWB), making it ideal to investigate the factors underlying morphological evolution in woody bamboos. However, the origin and biogeographical history of PWB remain elusive, as does the effect of environmental factors on the evolution of their morphological characters. We generated a robust and time‐calibrated phylogeny of PWB using single nucleotide polymorphisms retrieved from optimized double digest restriction site associated DNA sequencing, and explored the evolutionary trends of habit, inflorescence, and caryopsis type in relation to environmental factors including climate, soil, and topography. We inferred that the PWB started to diversify across the Oligocene–Miocene boundary and formed four major clades, that is, Melocanninae, Racemobambosinae s.l. (comprising Dinochloinae, Greslanlinae, Racemobambosinae s.str. and Temburongiinae), Hickeliinae and Bambusinae s.l. (comprising Bambusinae s.str. plus Holttumochloinae). The ancestor of PWB was reconstructed as having erect habit, indeterminate inflorescence and basic caryopsis. The characters including climbing/scrambling habit, determinate inflorescence, and nucoid/bacoid caryopsis have since undergone multiple changes and reversals during the diversification of PWB. The evolution of all three traits was correlated with, and hence likely influenced by, aspects of climate, topography, and soil, with climate factors most strongly correlated with morphological traits, and soil factors least so. However, topography had more influence than climate or soil on the evolution of erect habit, whereas both factors had greater effect on the evolution of bacoid caryopsis than did soil. Our results provide novel insights into morphological diversity and adaptive evolution in bamboos for future ecological and evolutionary research. [ABSTRACT FROM AUTHOR]

Entamoeba nuttalli is genetically the closest to Entamoeba histolytica, the causative agent of human amebiasis. E. nuttalli is found in Macaca species, exhibiting no symptoms while potentially virulent. Using comparative genomics of Entamoeba species, we identified a gene encoding an E. nuttalli‐specific protein containing 42 repeats of an octapeptide (PTORS). In the present study, we analyzed the genes in E. nuttalli strains derived from various geographic locations and host species. Sequence analysis of genomic DNA from four strains indicated 43, 44, and 48 repeat types in addition to 42 repeats and remarkable genetic diversity in the repeat region, although all nucleotide substitutions were synonymous. In contrast, the sequences of the N‐terminal side region and C‐terminus were identical among the strains. Monoclonal antibodies prepared against recombinant PTORS were reactive to the repeat regions but not to the N‐terminal side regions. Polyclonal antibodies did not react with the N‐terminal region, demonstrating that the repeat region had higher antigenicity. Analysis using synthetic peptides revealed that the two repeats of the octapeptide functioned as epitopes. Immunofluorescence microscopy using monoclonal antibodies demonstrated the surface localization of PTORS. These results suggest that the repeat region of PTORS plays an important role in host–parasite interactions. [ABSTRACT FROM AUTHOR]

We are witnessing a steep increase in model development initiatives in genomics that employ high-end machine learning methodologies. Of particular interest are models that predict certain genomic characteristics based solely on DNA sequence. These models, however, treat the DNA as a mere collection of four, A, T, G and C, letters, dismissing the past advancements in science that can enable the use of more intricate information from nucleic acid sequences. Here, we provide a comprehensive database of quantum mechanical (QM) and geometric features for all the permutations of 7-meric DNA in their representative B, A and Z conformations. The database is generated by employing the applicable high-cost and time-consuming QM methodologies. This can thus make it seamless to associate a wealth of novel molecular features to any DNA sequence, by scanning it with a matching k-meric window and pulling the pre-computed values from our database for further use in modelling. We demonstrate the usefulness of our deposited features through their exclusive use in developing a model for A->C mutation rates. [ABSTRACT FROM AUTHOR]

Several members of the genus Peziza sensu stricto occur at the edge of melting snow. These nivicolous species have been widely reported in the Northern Hemisphere and are also known from Australia and New Zealand. We have used 16 specimens from North America and Australia to study morphology and to perform DNA sequencing. In sequence analyses, we have used ITS1 and ITS2 (internal transcribed spacers), 28S, RPB2 (RNA polymerase II gene), and two genes new to these studies, GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and HSP90 (heat shock protein 90). Although not all regions are available for all samples, we have recognized the following species: Peziza heimii, P. nivalis, and P. nivis. Phylogenetic analyses were done using ITS alone; combined ITS1-5.8S-ITS2, 28S, and RPB2; ITS, and 28S, RPB2, GAPDH, and HSP90. Even with this augmented set of genes and despite their widespread occurrence in North America, Europe, Australia, and New Zealand, we have not definitively distinguished species within this group. To assess these results, pairwise homoplasy index (PHI) analysis was employed. This showed evidence of recombination among the samples of P. nivalis and further supports the view of P. nivalis as a monophyletic cosmopolitan species. As part of this study, we also examined the variation in ITS copies in P. echinospora, for which a genome is available. [ABSTRACT FROM AUTHOR]

A commentary is provided on the seven formally published proposals to modify the provisions of Chapter F of the International Code of Nomenclature for algae, fungi, and plants (ICNafp) that will be dealt with by the Fungal Nomenclature Session (FNS) of the 12th International Mycological Congress (IMC12) in August 2024. The proposals deal with: fungi whose morph-names have the same epithet; the listing of synonyms under entries for protected names in the Code Appendices; the processes of protection and rejection; the use of DNA sequences as nomenclatural types; the use of genomes as nomenclatural types; and the designation of fungi known only from DNA sequences. Information is also provided on the composition and role of the Fungal Nomenclature Bureau, the operation of the FNS and the pre-Congress Guiding vote. [ABSTRACT FROM AUTHOR]

Historical periods of rapid climate change and associated direct and indirect impacts such as glaciation and restructuring of drainage systems are important in shaping biodiversity, lineage divergence, and contemporary genetic variation amongst many aquatic taxa. Through an understanding of the impacts of these ancient changes in land‐ and waterscapes on current diversity, practitioners can account for a species' unique evolutionary history when developing conservation strategies. We investigated intraspecific genetic diversity of the critically endangered freshwater mussel, Lampsilis rafinesqueana, endemic to the interior region of the U.S.A. Our study (1) characterises genetic variation within and amongst populations to infer biogeographic history and (2) applies genetic information to potential conservation strategies. We applied restriction‐site associated DNA sequencing and mitochondrial DNA sequencing to investigate genetic diversity within and amongst populations of L. rafinesqueana from across the species' distribution. We then considered this information in the context of historical riverscape processes and applicability to conservation. Variation within rivers was similar, but we found different genetic populations associated with two major ecoregions, the Central Interior Highlands and Osage Plains. The plains population displayed an Ne value approximately 10‐fold lower than the highlands population. Historical demographic modelling suggests the two populations diverged approximately 1.2 million years ago and then both populations underwent a substantial decrease in population size around 19,700 years ago. These two major events are each correlated with known periods of historic rapid climate change. We identified two distinct populations of a federally endangered mussel, L. rafinesqueana. Contemporary genetic diversity of this species was strongly influenced by direct and indirect impacts of rapid historic shifts in climate. The highlands population has undergone a recent expansion, typical of post‐Pleistocene climate change, while also having a much larger Ne value than the plains population. Our results suggest low levels of gene flow amongst the two distinct populations across generations. We recommend that conservation managers for this species take into account relative difference in diversity between populations when developing management strategies. In many species, assisted gene flow amongst genetically unique populations should only be considered in extreme circumstances; however, in L. rafinesqueana, low levels of assisted migration amongst populations may be a valuable tactic to maintain natural levels of genetic variation. Our study shows that biogeographical frameworks can be useful for developing conservation strategies that serve to retain important genomic variation that represents the evolutionary potential of target freshwater species. [ABSTRACT FROM AUTHOR]

Next-generation sequencing (NGS) has revolutionized genomic research by enabling high-throughput, cost-effective genome and transcriptome sequencing accelerating personalized medicine for complex diseases, including cancer. Whole genome/transcriptome sequencing (WGS/WTS) provides comprehensive insights, while targeted sequencing is more cost-effective and sensitive. In comparison to short-read sequencing, which still dominates the field due to high speed and cost-effectiveness, long-read sequencing can overcome alignment limitations and better discriminate similar sequences from alternative transcripts or repetitive regions. Hybrid sequencing combines the best strengths of different technologies for a more comprehensive view of genomic/transcriptomic variations. Understanding each technology's strengths and limitations is critical for translating cutting-edge technologies into clinical applications. In this study, we sequenced DNA and RNA libraries of reference samples using various targeted DNA and RNA panels and the whole transcriptome on both short-read and long-read platforms. This study design enables a comprehensive analysis of sequencing technologies, targeting protocols, and library preparation methods. Our expanded profiling landscape establishes a reference point for assessing current sequencing technologies, facilitating informed decision-making in genomic research and precision medicine. [ABSTRACT FROM AUTHOR]

Tandem repeat (TR) proteins are abundant in nature and show diverse biochemical and mechanical properties. However, these proteins can be difficult to synthesize in a precise way because of their repetitive nature. Using a supramolecular polymerization scheme known as hybridization chain reaction, we show how to generate the DNA sequences encoding such TR proteins. The polymerization mechanism allows for identical "monomers" to selectively create TR proteins of different molecular weight. We demonstrate this strategy with examples from elastin‐like polypeptides (ELPs) and mussel foot proteins (mfps). Moreover, the scheme can be adapted to create protein libraries through the use of multiple DNA hairpin "monomers." [ABSTRACT FROM AUTHOR]

Aims: Compared to primary breast sarcoma (BSs), radiotherapy-induced sarcoma (RIS) is a less frequent type of secondary breast sarcoma. Undifferentiated pleomorphic sarcoma (UPS) is an even rarer occurrence within the RIS category. This study aimed to present the clinicopathologic and molecular features of breast radiotherapy-induced UPS. Methods: A retrospective study was conducted at the Third Affiliated Hospital of Soochow University to analyze three patients with radiation-induced undifferentiated pleomorphic sarcoma (UPS) following breast cancer, spanning from 2006 to 2023. The clinical and pathological variables were extracted from the medical records, while immunohistochemistry was employed to analyze the immunophenotypes of these tumors. Genomic characteristics were assessed through DNA and RNA sequencing techniques. Another 15 cases from the literature were also reviewed to better characterize the tumor. Results: The affected areas encompass the chest wall and breasts, with an incubation period ranging from 6 to 17 years. The tumor cells exhibit pleomorphism and demonstrate a high degree of pathological mitosis. Notably, two cases displayed an accelerated disease progression, characterized by recurrent tumors and metastases occurring within short intervals of 48 and 7 months respectively subsequent to the initial diagnosis. The two prevailing identified genes were TP53 (2/3, 66.7%) and RB1 (1/3, 33.3%). Through analysis of somatic copy number variation (CNV), it was discovered that two oncogenes, MCL1 (1/3, 33.3%) and MYC (1/3, 33.3%), had experienced gains in CNV. The Tumor Mutational Burden (TMB) values for case 1, case 2, and case 3 were 5.9 mut/Mb, 1.0 mut/Mb, and 3.0 mut/Mb, respectively. Moreover, the analysis of RNA-NGS (next-generation sequencing) revealed the presence of a novel gene fusion, named COL3A1-GULP1, in case 2. Conclusions: Based on our thorough analysis of research findings and previous reports, it is evident that radiotherapy-induced UPS exhibits a highly diverse and frequently severe clinical and biological behavior. Identifying tumor formation using genome sequencing can help understand its biological behavior and determine personalized treatments. [ABSTRACT FROM AUTHOR]

Seven proposals or sets of proposals to modify the provisions of Chapter F of the International Code of Nomenclature for algae, fungi, and plants (ICNafp) have been received. These proposals are formally presented together here. The topics addressed relate to: fungi whose morph-names have the same epithet; the listing of synonyms under entries for protected names in the Code Appendices; the processes of protection and rejection; the use of DNA sequences as nomenclatural types; the use of genomes as nomenclatural types; and the designation of fungi known only from DNA sequences. In addition, a suggestion is included to update the mention of the World Directory of Culture Collections in Article 40.7 Note 4. A Synopsis of the formal proposals will be provided in early July 2024, and the mycological community will be invited to provide a guiding vote on the proposals with a closing date of 2 August 2024. Final decisions on the proposals will be made following debate at the Fungal Nomenclature Session of IMC12 in August 2024. [ABSTRACT FROM AUTHOR]

Schoenus vacillans is a sedge described from New Zealand in 1878 by Thomas Kirk. However, for over one hundred years, S. vacillans has been considered a synonym of the morphologically-variable S. apogon, which occurs in New Zealand, Australia, Taiwan, New Guinea and possibly Japan. Here we investigate the taxonomic status of S. vacillans by examining chloroplast and nuclear DNA sequences alongside morphology. Our analyses showed that S. vacillans and S. apogon are genetically distinct and are not sister taxa. Furthermore, S. vacillans is easily distinguished morphologically from S. apogon by its diffuse, many noded but few flowered inflorescences. Our results indicated that S. vacillans should be reinstated at species rank. Furthermore, it appears to be endemic to New Zealand and not conspecific with the Australian S. laxiflorus Steud., another putative segregate of S. apogon. Herbarium records indicate a distribution of S. vacillans from the central North Island northwards but there are few recent records and known populations are small. We suggest a threat ranking of Nationally Critical, with a Data Poor qualifier. Schoenus vacillans appears to prefer shady, damp sites on the sides of gullies and banks, particularly on slips. [ABSTRACT FROM AUTHOR]

X-linked dystonia-parkinsonism (XDP) is a severe neurodegenerative disorder resulting from an inherited intronic SINE-Alu-VNTR (SVA) retrotransposon in the TAF1 gene that causes dysregulation of TAF1 transcription. The specific mechanism underlying this dysregulation remains unclear, but it is hypothesized to involve the formation of G-quadruplexes (G4) structures within the XDP-SVA that impede transcription. In this study, we show that ZNF91, a critical repressor of SVA retrotransposons, specifically binds to G4-forming DNA sequences. Further, we found that genetic deletion of ZNF91 exacerbates the molecular phenotype associated with the XDP-SVA insertion in patient cells, while no difference was observed when ZNF91 was deleted from isogenic control cells. Additionally, we observed a significant age-related reduction in ZNF91 expression in whole blood and brain, indicating a progressive loss of repression of the XDP-SVA in XDP. These findings indicate that ZNF91 plays a crucial role in controlling the molecular phenotype associated with XDP. Since ZNF91 binds to G4-forming DNA sequences in SVAs, this suggests that interactions between ZNF91 and G4-forming sequences in the XDP-SVA minimize the severity of the molecular phenotype. Our results showing that ZNF91 expression levels significantly decrease with age provide a potential explanation for the age-related progressive neurodegenerative character of XDP. Collectively, our study provides important insights into the protective role of ZNF91 in XDP pathogenesis and suggests that restoring ZNF91 expression, destabilization of G4s, or targeted repression of the XDP-SVA could be future therapeutic strategies to prevent or treat XDP. [ABSTRACT FROM AUTHOR]

Background: Decoding human genomic sequences requires comprehensive analysis of DNA sequence functionality. Through computational and experimental approaches, researchers have studied the genotype-phenotype relationship and generate important datasets that help unravel complicated genetic blueprints. Thus, the recently developed artificial intelligence methods can be used to interpret the functions of those DNA sequences. Methods: This study explores the use of deep learning, particularly pre-trained genomic models like DNA_bert_6 and human_gpt2-v1, in interpreting and representing human genome sequences. Initially, we meticulously constructed multiple datasets linking genotypes and phenotypes to fine-tune those models for precise DNA sequence classification. Additionally, we evaluate the influence of sequence length on classification results and analyze the impact of feature extraction in the hidden layers of our model using the HERV dataset. To enhance our understanding of phenotype-specific patterns recognized by the model, we perform enrichment, pathogenicity and conservation analyzes of specific motifs in the human endogenous retrovirus (HERV) sequence with high average local representation weight (ALRW) scores. Results: We have constructed multiple genotype-phenotype datasets displaying commendable classification performance in comparison with random genomic sequences, particularly in the HERV dataset, which achieved binary and multi-classification accuracies and F1 values exceeding 0.935 and 0.888, respectively. Notably, the fine-tuning of the HERV dataset not only improved our ability to identify and distinguish diverse information types within DNA sequences but also successfully identified specific motifs associated with neurological disorders and cancers in regions with high ALRW scores. Subsequent analysis of these motifs shed light on the adaptive responses of species to environmental pressures and their co-evolution with pathogens. Conclusions: These findings highlight the potential of pre-trained genomic models in learning DNA sequence representations, particularly when utilizing the HERV dataset, and provide valuable insights for future research endeavors. This study represents an innovative strategy that combines pre-trained genomic model representations with classical methods for analyzing the functionality of genome sequences, thereby promoting cross-fertilization between genomics and artificial intelligence. [ABSTRACT FROM AUTHOR]

Cancer continues to present a substantial global health challenge, with its incidence and mortality rates persistently reflecting its significant impact. The emergence of precision oncology has provided a breakthrough in targeting oncogenic drivers previously deemed "undruggable" by conventional therapeutics and by limiting off-target cytotoxicity. Two groundbreaking technologies that have revolutionized the field of precision oncology are primarily CRISPR-Cas9 gene editing and more recently PROTAC (PROteolysis TArgeting Chimeras) targeted protein degradation technology. CRISPR-Cas9, in particular, has gained widespread recognition and acclaim due to its remarkable ability to modify DNA sequences precisely. Rather than editing the genetic code, PROTACs harness the ubiquitin proteasome degradation machinery to degrade proteins of interest selectively. Even though CRISPRCas9 and PROTAC technologies operate on different principles, they share a common goal of advancing precision oncology whereby both approaches have demonstrated remarkable potential in preclinical and promising data in clinical trials. CRISPR-Cas9 has demonstrated its clinical potential in this field due to its ability to modify genes directly and indirectly in a precise, efficient, reversible, adaptable, and tissue-specific manner, and its potential as a diagnostic tool. On the other hand, the ability to administer in low doses orally, broad targeting, tissue specificity, and controllability have reinforced the clinical potential of PROTAC. Thus, in the field of precision oncology, gene editing using CRISPR technology has revolutionized targeted interventions, while the emergence of PROTACs has further expanded the therapeutic landscape by enabling selective protein degradation. Rather than viewing them as mutually exclusive or competing methods in the field of precision oncology, their use is context-dependent (i.e., based on the molecular mechanisms of the disease) and they potentially could be used synergistically complementing the strengths of CRISPR and vice versa. Herein, we review the current status of CRISPR and PROTAC designs and their implications in the field of precision oncology in terms of clinical potential, clinical trial data, limitations, and compare their implications in precision clinical oncology. [ABSTRACT FROM AUTHOR]

Population-scale genome modification can alter the composition or fate of wild populations. Synthetic gene drives provide one set of tools, but their use is complicated by scientific, regulatory, and social issues associated with transgene persistence and flow. Here we propose an alternative approach. An Allele Sail consists of a genome editor (the Wind) that introduces DNA sequence edits, and is inherited in a Mendelian fashion. Meanwhile, the edits (the Sail) experience an arithmetic, Super-Mendelian increase in frequency. We model this system and identify contexts in which a single, low frequency release of an editor brings edits to a very high frequency. We also identify conditions in which manipulation of sex determination can bring about population suppression. In regulatory frameworks that distinguish between transgenics (GMO) and their edited non-transgenic progeny (non-GMO) Allele Sails may prove useful since the spread and persistence of the GM component can be limited. Population-scale genome modification can alter the composition or fate of wild populations. Here the authors introduce Allele Sails as a method for spreading genetic changes throughout a population. [ABSTRACT FROM AUTHOR]

Background: The clinical differentiation between essential tremor plus (ETP) and dystonic tremor (DT) is challenging. This study aimed at the genetic diagnosis of ETP and DT. Methods: Whole exome sequencing was performed on 50 probands (ETP = 25; DT = 25) and analysed to identify variants in known genes linked with dystonia and essential tremor plus phenotypes. Results: We identified pathogenic/likely pathogenic variants [THAP1 (n = 1) and ANO3 (n = 1)] in two patients with DT. In addition, one DT patient had a variant of uncertain significance in FUS and four patients had benign variants [CIZ1 (n = 1), COL6A3 (n = 1), GCH1 (n = 1), TENM4 (n = 1)]. One patient with ETP was detected to have a variant of uncertain significance in TENM4 and five patients with ETP had benign variants [COL6A3 (n = 2), VPS16 (n = 1), TAF1 (n = 1), KMT2B (n = 1)]. Conclusion: Genetic studies may be in an important biomarker in differentiating patients with ET plus from DT which is challenging in a clinical setting. [ABSTRACT FROM AUTHOR]

Background: DNA sequencing is a critical tool in modern biology. Over the last two decades, it has been revolutionized by the advent of massively parallel sequencing, leading to significant advances in the genome and transcriptome sequencing of various organisms. Nevertheless, challenges with accuracy, lack of competitive options and prohibitive costs associated with high throughput parallel short-read sequencing persist. Results: Here, we conduct a comparative analysis using matched DNA and RNA short-reads assays between Element Biosciences' AVITI and Illumina's NextSeq 550 chemistries. Similar comparisons were evaluated for synthetic long-read sequencing for RNA and targeted single-cell transcripts between the AVITI and Illumina's NovaSeq 6000. For both DNA and RNA short-read applications, the study found that the AVITI produced significantly higher per sequence quality scores. For PCR-free DNA libraries, we observed an average 89.7% lower experimentally determined error rate when using the AVITI chemistry, compared to the NextSeq 550. For short-read RNA quantification, AVITI platform had an average of 32.5% lower error rate than that for NextSeq 550. With regards to synthetic long-read mRNA and targeted synthetic long read single cell mRNA sequencing, both platforms' respective chemistries performed comparably in quantification of genes and isoforms. The AVITI displayed a marginally lower error rate for long reads, with fewer chemistry-specific errors and a higher mutation detection rate. Conclusion: These results point to the potential of the AVITI platform as a competitive candidate in high-throughput short read sequencing analyses when juxtaposed with the Illumina NextSeq 550. [ABSTRACT FROM AUTHOR]

Introduction Aim Methods and Results Conclusion Congenital factor V (FV) deficiency is a rare clotting disorder affecting ∼1 in 1,000,000, with bleeding severity that ranges broadly for poorly understood reasons.To help understand the molecular basis of the observed phenotype in FV deficient patients, the genetics and biochemistry causing a patient's FV deficiency were evaluated.A 71‐year‐old female, who had serious life‐long bleeding upon provocation and profound menorrhagia that lead to hysterectomy, was found to have 3% of normal plasma FV antigen with normal electrophoretic mobility. Platelet FV was similarly low, although the banding pattern was less fragmented than normal. Plasma clotting activity was <1% of normal. Familial inheritance and DNA sequence analysis from peripheral blood leukocytes were consistent with novel compound heterozygosity with missense mutations in exon XVII, Leu1821 to Ser (L1821S) and exon XXV, Gly2192 to Cys (G2192C). The respective single‐mutation variants were expressed and purified. Explaining why the antigen level and activity were inequivalent, thrombin activation of recombinant (r) FV/L1821S was impaired, and rFV/G2192C was unable to bind to a procoagulant phospholipid membrane.These findings are consistent with the observed phenotype, highlighting the importance of understanding FV biochemical function to rationalize clinical bleeding severity when the circulating antigen level is discordant. [ABSTRACT FROM AUTHOR]

Gregarine apicomplexans are ubiquitous endosymbionts of invertebrate hosts. Despite their ecological and evolutionary importance, inferences about the phylogenetic relationships of major gregarine groups, such as the Lecudinidae and Urosporidae, have been hindered by vague taxonomic definitions and limited molecular and morphological data. In this study, we investigated five gregarine species collected from four families of polychaete hosts (Nereididae, Oenonidae, Hesionidae, and Phyllodocidae) using light microscopy (LM) and scanning electron microscopy (SEM). We also generated small subunit ribosomal DNA sequences from these species and conducted molecular phylogenetic analyses to elucidate the evolutionary relationships within the Lecudinoidea. Our results include new molecular and morphological data for two previously described species (Lecudina cf. platynereidis and Lecudina cf. arabellae), the discovery of a new species of Lecudina (L. oxydromus n. sp.), and the discovery of two novel species, namely Amplectina cordis n. gen. et. n. sp. and Sphinctocystis inclina n. sp. These two species exhibited unique shapes and movements, resembling those of urosporids but with a phylogenetic affinity to lecudinids, blurring the border between lecudinids and urosporids. Our study emphasizes the need for further investigations into this highly diverse group, which has achieved great success across multiple animal phyla with diverse shapes and movements. [ABSTRACT FROM AUTHOR]

Objective: In past work in budding yeast, we identified a nucleosomal region required for proper interactions between the histone chaperone complex yFACT and transcribed genes. Specific histone mutations within this region cause a shift in yFACT occupancy towards the 3' end of genes, a defect that we have attributed to impaired yFACT dissociation from DNA following transcription. In this work we wished to assess the contributions of DNA sequences at the 3' end of genes in promoting yFACT dissociation upon transcription termination. Results: We generated fourteen different alleles of the constitutively expressed yeast gene PMA1, each lacking a distinct DNA fragment across its 3' end, and assessed their effects on occupancy of the yFACT component Spt16. Whereas most of these alleles conferred no defects on Spt16 occupancy, one did cause a modest increase in Spt16 binding at the gene's 3' end. Interestingly, the same allele also caused minor retention of RNA Polymerase II (Pol II) and altered nucleosome occupancy across the same region of the gene. These results suggest that specific DNA sequences at the 3' ends of genes can play roles in promoting efficient yFACT and Pol II dissociation from genes and can also contribute to proper chromatin architecture. [ABSTRACT FROM AUTHOR]

Tumor‐specific microRNA (miRNA) imaging strategies are critical for investigating mechanisms associated with cancer progression; however, nonspecific signal leakage and false‐positive signaling limit their selectivity and efficiency. In this paper, an endogenously activated and self‐reinforced DNA lipid nanodevice (LND) for spatial‐specific and high‐contrast imaging of miRNAs in living cells and animals is presented. The LND is functionalized on cholesterol‐based lipid micelles (CLMs) containing smart response and self‐fueling DNA components that display redox‐activatable and autocatalytic miRNA probing activities, respectively. The LNDs are initially silenced and selectively activated using glutathione, an endogenous microenvironmental factor overexpressed in tumor cells, to prevent nonspecific signal leakage. Subsequently, an autocatalytic DNA circuit is used for tumor‐specific and high‐contrast miRNA imaging. It is demonstrated that robust CLM nanoparticles can be easily assembled from a cholesterol‐conjugated G‐rich DNA sequence by stirring in a buffered solution, enabling the LND to enter cells naturally. In addition, in vitro and in vivo data illustrate that the enhanced biostability of DNA components on the surface of LNDs can be realized for minimizing false‐positive signals, making the system ideal for miRNA imaging in living mice. This smart LND technique has great potential for precise biomedical imaging and clinical diagnosis. [ABSTRACT FROM AUTHOR]

AbstractIn genomic research, identifying the exon regions in eukaryotes is the most cumbersome task. This article introduces a new promising model-independent method based on short-time discrete Fourier transform (ST-DFT) and fine-tuned variational mode decomposition (FTVMD) for identifying exon regions. The proposed method uses the N/3 periodicity property of the eukaryotic genes to detect the exon regions using the ST-DFT. However, background noise is present in the spectrum of ST-DFT since the sliding rectangular window produces spectral leakage. To overcome this, FTVMD is proposed in this work. VMD is more resilient to noise and sampling errors than other decomposition techniques because it utilizes the generalization of the Wiener filter into several adaptive bands. The performance of VMD is affected due to the improper selection of the penalty factor (α), and the number of modes (K). Therefore, in fine-tuned VMD, the parameters of VMD (K and α) are optimized by maximum kurtosis value. The main objective of this article is to enhance the accuracy in the identification of exon regions in a DNA sequence. At last, a comparative study demonstrates that the proposed technique is superior to its counterparts. [ABSTRACT FROM AUTHOR]

The Fusarium graminearum species complex (FGSC) is a worldwide phytopathogenic fungus of small grain cereals. Genetics and bioinformatics tools have been providing an efficient strategy for identifying FGSC. However, the potential reliability of tef1−α sequencing in FGSC members has not been well investigated. In this study, the tef1−α sequencing data of 246 FGSC members, one F. culmorum, and one F. solani isolate were subjected to distance-, character-, and PCA-based phylogenetic analysis. Linux terminals and the R programming language were used in phylogenetic analysis. The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) and maximum likelihood methods produced relatively more homogenous F. graminearum sensu stricto (Fgss) and F. asiaticum isolates. Fgss and F. asiaticum isolates co-clustered in two separate sub-divisions in the ML and UPGMA methods, with significant differences in the Chi2 test (p < 0.05). PCA profiling revealed a low level of variation in FGSC members, with 99–99.5% percentages in axis 1. An increased number of taxa and isolates would be tested for tef1−α in future studies. To our knowledge, this is also the first study to combine phylogenetic methods with PCA tests for comprehensive characterization of FGSC members. [ABSTRACT FROM AUTHOR]

Epidemics have significant impacts on primate populations. In 2016, yellow fever spread rapidly to the most densely populated states of Brazil, resulting in the death of hundreds of humans and thousands of nonhuman primates. The Yellow Fever Surveillance Program (Programa de Vigilância da Febre Amarela) implemented by the Brazilian government was designed to prevent and control yellow fever outbreaks. In 2020, the regional reference laboratory at the Oswaldo Cruz Institute in Rio de Janeiro state in Brazil, responsible for yellow fever diagnosis, gave us access to 24 DNA samples from capuchin monkeys, which had tested negative for yellow fever virus. The samples were all from sites in Brazil where Sapajus nigritus is the only species of capuchin monkey present. We attempted to sequence two mitochondrial molecular markers commonly used for Cebidae, but five samples did not amplify. In this study, we performed additional DNA amplification and the Basic Local Alignment Search Tool (BLAST) to confirm the species identity of the 19 samples, which amplified and identify the taxon of the five samples that had failed to amplify. Among the 19 samples correctly identified as Sapajus, one was not Sapajus nigritus but another Sapajus species. Of the five samples that previously failed to amplify, three were similar to Callicebus nigrifrons, one was similar to Alouatta guariba clamitans, and one failed to amplify successfully for any marker. These findings show an error rate of 5/24 (21%) in the original taxonomic identification. Misidentification occurred at the genus level as well as the species level. Our findings highlight the importance of precise taxonomic classification in obtaining reliable data on the consequences of the yellow fever epidemic for primates. [ABSTRACT FROM AUTHOR]

Nematodes belonging to the genus Oesophagostomum frequently infect wild chimpanzees (Pan troglodytes) across widely separated field sites. Nodular lesions (granulomas) containing Oesophagostomum are commonly seen in the abdomen of infected chimpanzees post‐mortem. At Taï National Park, Côte d'Ivoire, previous studies have identified larvae of a variety of Oesophagostomum spp. in wild chimpanzee stool, based on sequencing of larval DNA, and nodular lesions associated with Oesophagostomum, identified morphologically to the genus level but not sequenced. Here we present three recent cases of parasitic granulomas found post‐mortem in chimpanzees at Taï. We complement descriptions of gross pathology, histopathology and parasitology with PCR and sequencing of DNA isolated from the parasitic nodules and from adult worms found inside the nodules. In all three cases, we identify Oesophagostomum stephanostomum as the causative agent. The sequences from this study were identical to the only other published sequences from nodules in nonhuman primates—those from the wild chimpanzees of Gombe, Tanzania. Research highlights: Chimpanzees in Taï National Park (Côte d'Ivoire) commonly have a small number of abdominal parasitic nodules, observed post‐mortem.A variety of Oesophagostum spp. has been found in the stool of Taï chimps.The nodules are caused by Oesophagostomum stephanostomum, and the ITS‐2 sequence is identical to the only other sequence obtained from chimp nodules (in Gombe, Tanzania). [ABSTRACT FROM AUTHOR]

Persimmon is classified as either pollination-constant non-astringent (PCNA) or non-PCNA on the basis of the loss of astringency in fruit. PCNA trait of persimmon has attracted much research attention owing to its economical merit, as there is no cost in removing astringency. To efficiently develop new PCNA cultivars in crossbreeding, marker-assisted selection plays a crucial role. Here, we describe a cleaved amplified polymorphic sequence (CAPS) marker that can be used to select PCNA persimmon. A sequence-characterized amplified region (SCAR) marker used to screen for PCNA offspring is unsuitable for populations recently derived from two non-PCNA parents ('Yoshidagosho' and 'Toyoichi'), resulting in the selection of non-PCNA offspring as PCNA. To detect specific polymorphisms for these non-PCNA offspring, we analyzed fragment sizes of SCAR marker products by capillary DNA sequencing. A slightly lower-molecular-weight fragment at 353 bp was specifically detected in non-PCNA offspring but not in PCNA offspring. We treated the SCAR marker products with the StuI restriction enzyme and demonstrated that the smaller 353-bp fragment corresponded to allele a353-1, one of four previously identified sequence polymorphisms at the 353-bp peak, and a353-1 is linked to non-PCNA trait. Comprehensive analysis of 130 germplasms by the CAPS marker, detecting the truncated fragment after StuI treatment, indicated the presence of a353-1 in 38 non-PCNA cultivars. Our findings suggest the potential use of the CAPS marker for selecting PCNA offspring derived from these 38 non-PCNA cultivars. [ABSTRACT FROM AUTHOR]

Solid state nanochannels provide significant practical advantages in many fields due to their interesting properties, such as controllable shape and size, robustness, ion selectivity. But their complex preparation processes severely limit their application. In this study, a simple cost‐effective method to fabricate single nanochannel by embedding a single polyethylene oxide (PEO) nanofiber is presented. Firstly, PEO nanofibers are prepared by electrospinning, and then a single PEO nanofiber are precisely transferred to the target sample using a micromanipulation platform. Then, PDMS is used for embedding, and finally, the PEO nanofiber is dissolved to obtain a single nanochannel. Unlike other methods of preparing nanochannels by embedding nanofibers, this method can prepare single nanochannel. The diameter of nanochannel can be as fine as 100 nm, and the length can reach several micrometers. The power generation between two potassium chloride solutions with various combinations of concentrations was investigated using the nanochannel. This low‐cost flexible nanochannel can also be used in various applications, including DNA sequencing and biomimetic ion channel. [ABSTRACT FROM AUTHOR]

Next-generation sequencing (NGS) has emerged as a promising tool for diagnosing fungal infections. It enables the identification of a wide range of fungal species and provides more accurate and rapid results than traditional diagnostic methods. NGS-based approaches involve the sequencing of DNA or RNA from clinical samples, which can be used to detect and identify fungal pathogens in complex clinical samples. The development of targeted gene panels and whole-genome sequencing has allowed for identifying genetic markers associated with antifungal drug resistance, enabling clinicians to tailor patient treatment options. NGS can also provide insights into the pathogenesis of fungal infections and aid in discovering novel drug targets. Although NGS has some limitations, such as cost and data analysis, it can potentially revolutionize the future diagnosis and treatment of fungal infections. [ABSTRACT FROM AUTHOR]

Modern diagnostic techniques based on DNA sequence similarity are currently the gold standard for the detection of existing and emerging pathogens. Whilst individual assays are inexpensive to use, assay development is costly and carries risks of not being sensitive or specific enough to capture an increasingly diverse range of targets. Sequencing can provide the entire nucleic acid content of a sample and may be used to identify all pathogens present in the sample when the depth of coverage is sufficient. Targeted enrichment techniques have been used to increase sequence coverage and improve the sensitivity of detection within virus samples, specifically, to capture sequences for a range of different viruses or increase the number of reads from low-titre virus infections. Vertebrate viruses have been well characterised using in-solution hybridisation capture to target diverse virus families. The use of probes for genotyping and strain identification has been limited in plants, and uncertainty around sensitivity is an impediment to the development of a large-scale virus panel to use within regulatory settings and diagnostic pipelines. This review aims to compare significant studies that have used targeted enrichment of viruses to identify approaches to probe design and potential for use in plant virus detection and characterisation. [ABSTRACT FROM AUTHOR]

Series Maximi is a group within Desmodesmus (Chlorophyta) which contains the three species D. maximus, D. perforatus and D. tropicus. Besides their large cell sizes, the most striking morphological trait unique to the members of this genus is the presence of large perforations between the coenobial cells. The perforations are either present (D. perforatus and D. tropicus) or the space between the cells is completely sealed (D. maximus). We report here a fourth species of the series based on two strains (AICB 1155 and AICB 1572) from freshwater environments of the Danube Delta, Romania. The ultrastructure of the cell walls revealed a partial closure of the space between the cells which creates slightly visible perforations in light microscopy. Analyses of DNA sequences and secondary structure of the ITS2 fragment by coalescent (PTP, GMYC), distance (ASAP), and evolutionary modelbased methods (ML, BI) indicated a fourth candidate species which included both the AICB strains investigated and other strains with similar morphological traits from reference literature. Despite its poor representation in public databases, analysis of the SSU rDNA gene for the series Maximi strengthened the ITS2 results. Therefore, based on its larger cell sizes relative to the other members of the series, cell morphology, the presence of partial perforations and other peculiarities of the cell wall ultrastructure, the independent phylogenetic position, CBCs analysis, and a different 'DNA signature' within the ITS2 fragment we suggest that this clade should be described as a new taxon of the series Maximi, Desmodesmus pseudoperforatus sp. nov. Morphological differences and DNA-based lines of evidence indicate new species. Microperforations of the space between the coenobial cells. Strains have the largest cell sizes in the series Maximi. [ABSTRACT FROM AUTHOR]

Background: The insulin-like growth factor (IGF-I) and growth hormone (GH) genes have been identified as major regulators of milk yield and composition, and reproductive performance in cattle. Genetic variations/polymorphism in these genes have been found to influence milk production, yield and quality. This investigation aimed to explore the association between IGF-I and GH polymorphisms and milk yield and composition, and reproductive performance in a herd consisting of 1000 Holstein–Friesian (HF) dairy cattle from El-Alamia farm. The experimental animals were 76 ± 7.25 months in age, with an average live weight of 750 ± 50.49 kg, and raised under the same conditions of feeding and weather. The studied animals were divided into three categories; high producers (n = 280), medium producers (n = 318) and low producers (n = 402). Results: The digestion of 249 bp for IGF-I-SnaBI using the Restriction-fragment-length-polymorphism (RFLP) technique yielded two alleles; T (0.59) and C (0.41) and three genotypes; TT (0.52), TC (0.39) and CC (0.09) and this agrees with the results of DNA/gene sequencing technique. The sequencing analysis of the IGF-I gene revealed polymorphism in position 472 (C > T). Nucleotide sequencing of the amplified fragment of the IGF-I gene of different genotypes was done and submitted to the NCBI GenBank with Accession no. MH156812.1 and MH156811.1. While the digestion of 432 bp for GH-AluI using the RFLP technique yielded two alleles; A (0.81) and G (0.19) and two genotypes; AA (0.77) and AG (0.23) and this agrees with the results of DNA/gene sequencing technique. The sequencing analysis of the GH gene revealed polymorphism in the position 1758 C > G and in turn led to changes in amino acid sequence as Alanine for (A) compared to Glycine for (G). Nucleotide sequencing of the amplified fragment of the GH gene was done and submitted to the NCBI GenBank with Accession no. MH156810.1. The results of this study demonstrate the effects of variants of the GH-IGF-I somatotrophic axis on milk production and composition traits in commercial HF cattle. The greatest values of milk yield and reproductive performance were observed on IGF-I-SnaBI-TC and GH-AluI-AG genotypes. While the greatest % fat and % protein values were observed on IGF-I-SnaBI-CC and GH-AluI-AA genotyped individuals. Conclusion: The genetic variation of the studied genes can be utilized in selecting animals with superior milk yield, composition and reproductive performance in Holstein–Friesian Dairy Cattle under subtropical conditions. [ABSTRACT FROM AUTHOR]

At least 1–2% of DNA sequences annotated as Blastocystis in GenBank represent organisms other than Blastocystis or sequence artefacts. As well as being biologically incorrect, such practice can lead to overestimates of genetic diversity, underestimated host specificity, and incorrect classification of samples tested for Blastocystis using DNA-based methods. [ABSTRACT FROM AUTHOR]

Recent advances in DNA sequencing technology have enabled the precise decoding of genomes in non-model organisms, providing a basis for unraveling the patterns and mechanisms of sex chromosome evolution. Studies of different species have yielded conflicting results regarding the traditional theory that sex chromosomes evolve from autosomes via the accumulation of deleterious mutations and degeneration of the Y (or W) chromosome. The concept of the 'sex chromosome cycle,' emerging from this context, posits that at any stage of the cycle (i.e. differentiation, degeneration, or loss), sex chromosome turnover can occur while maintaining stable sex determination. Thus, understanding the mechanisms that drive both the persistence and turnover of sex chromosomes at each stage of the cycle is crucial. In this review, we integrate recent findings on the mechanisms underlying maintenance and turnover, with a special focus on several organisms having unique sex chromosomes. Our review suggests that the diversity of sex chromosomes in the maintenance of stable sex determination is underappreciated and emphasizes the need for more research on the sex chromosome cycle. [ABSTRACT FROM AUTHOR]

Summary Nanopore ion channels are a promising solution for certain molecular structure analyses. Large arrays of nanopore channels and their associated readout circuits are used in many molecular studies such as DNA sequencing. Readout circuits must meet challenging performance criteria such as low noise operation, low power consumption, in‐channel digitization capability, and high linearity. Previously, sigma–delta modulators have been presented to address these criteria; however, their specifications show drifts with temperature. In this paper, an approach is presented to keep modulator performance constant with temperature variations. For this purpose, the sigma–delta modulator's feedforward and feedback branches are modified so that their gain coefficient remains constant over a certain temperature range. With large sensors arrays, solutions employing high bias currents in the feedback paths are not suitable due to power consumption limitations. Here, the design gives the possibility of switching low current levels in the feedback paths without affecting the ENOB. The proposed temperature compensation solution shows good performance when temperature is swept from 27°C to 100°C. Over the mentioned temperature range, the gain and bandwidth of the modulator show a change of less than 0.4%. It is further shown that for a 10 kHz input current signal with an amplitude of 600 pA, the ENOB and power consumption are 12.9 and 4.6 mW, respectively. [ABSTRACT FROM AUTHOR]

SUMMARY: Genome annotation files play a critical role in dictating the quality of downstream analyses by providing essential predictions for gene positions and structures. These files are pivotal in decoding the complex information encoded within DNA sequences. Here, we generated experimental data resolving RNA 5′‐ and 3′‐ends as well as full‐length RNAs for cassava TME12 sticklings in ambient temperature and cold. We used these data to generate genome annotation files using the TranscriptomeReconstructoR (TR) tool. A careful comparison to high‐quality genome annotations suggests that our new TR genome annotations identified additional genes, resolved the transcript boundaries more accurately and identified additional RNA isoforms. We enhanced existing cassava genome annotation files with the information from TR that maintained the different transcript models as RNA isoforms. The resultant merged annotation was subsequently utilized for comprehensive analysis. To examine the effects of genome annotation files on gene expression studies, we compared the detection of differentially expressed genes during cold using the same RNA‐seq data but alternative genome annotation files. We found that our merged genome annotation that included cold‐specific TR gene models identified about twice as many cold‐induced genes. These data indicate that environmentally induced genes may be missing in off‐the‐shelf genome annotation files. In conclusion, TR offers the opportunity to enhance crop genome annotations with implications for the discovery of differentially expressed candidate genes during plant–environment interactions. Significance Statement: Our work has broad implications for transcriptome analyses of plant–environment interactions: differentially expressed genes may be absent in commonly used annotations and would thus be missed. As solution, we suggest merging TR‐based annotations for specific conditions with existing genome annotation files. [ABSTRACT FROM AUTHOR]