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Since the development of generalized gradient approximations in the 1990s, approximations based on density functional theory have dominated electronic structure theory calculations. Modern approximations can yield energy differences that are precise enough to be predictive in many instances, as validated by large- and small-scale benchmarking efforts. However, assessing the quality of densities has been the subject of far less attention, in part because reliable error measures are difficult to define. To this end, this work introduces the mean-field error, which directly assesses the quality of densities from approximations. The mean-field error is contextualized within existing frameworks of density functional error analysis and understanding and shown to be part of the density-driven error. It is demonstrated in several illustrative examples. Its potential use in future benchmarking protocols is discussed, and some conclusions are drawn. [ABSTRACT FROM AUTHOR]

There is an ever increasing use of local density dependent potentials in the mesoscale modeling of complex fluids. Questions remain, though, about the dependence of the thermodynamic and structural properties of such systems on the cutoff distance used to calculate these local densities. These questions are particularly acute when it comes to the stability and structure of the vapor/liquid interface. In this article, we consider local density dependent potentials derived from an underlying van der Waals equation of state. We use simulation and density functional theory to examine how the bulk thermodynamic and interfacial properties vary with the cutoff distance, rc, used to calculate the local densities. We show quantitatively how the simulation results for bulk thermodynamic properties and vapor–liquid equilibrium approach the van der Waals limit as rc increases and demonstrate a scaling law for the radial distribution function in the large rc limit. We show that the vapor–liquid interface is stable with a well-defined surface tension and that the interfacial density profile is oscillatory, except for temperatures close to critical. Finally, we show that in the large rc limit, the interfacial tension is proportional to rc and, therefore, unlike the bulk thermodynamic properties, does not approach a constant value as rc increases. We believe that these results give new insights into the properties of local density dependent potentials, in particular their unusual interfacial behavior, which is relevant for modeling complex fluids in soft matter. [ABSTRACT FROM AUTHOR]

The mechanism of gate threshold voltage (VT) shifts observed in high κ/metal gate stacks is investigated by a density functional theory. This finds that VT depends on the band alignments and the chemical trends between the component oxide layers, such as HfO2, SrO, La2O3, Al2O3, and SiO2. Based on the electron counting rule, we have built three insulating SiO2/SrO, SiO2/La2O3, and SiO2/Al2O3 interfaces, all of which feature a clean bandgap. Two methods have been adopted to derive the band alignments between these four oxides, which are consistent with each other. The results show staggered, "staircase" band alignments and enable La2O3 and Al2O3 layers to shift the metal electrode Fermi level in opposite directions and to approach the Si conduction band and valence band edge positions, respectively. This analysis updates previous empirical models of this effect based on metal oxide ion densities or electronegativity scales and confirms that the oxide layer scheme is suitable for controlling the effective metal work functions in metal–oxide–semiconductor field-effect transistors. [ABSTRACT FROM AUTHOR]

Many different strains of Streptococcus thermophilus are commonly used as starter cultures, and search for new safe strains with desired industrial and probiotic properties is an important issue. In this article, genomes of two new S. thermophilus strains—Str16t and Str159—were sequenced, and the main genome characteristics were determined. In silico analysis of the sequenced genomes revealed the absence of transmissible antibiotic resistance genes, virulence genes associated with pathogenicity, and integrated plasmids; gene clusters encoding class I and class II bacteriocins were found. In vitro tests showed phosphatase, peptidase, β-galactosidase, and esterase activity of both strains. Both strains were capable of fermenting glucose, lactose, sucrose, and ribose; in addition, Str16t fermented mannose. In conclusion, it was demonstrated that both Str16t and Str159 are promising strains for application as starter and probiotic cultures. [ABSTRACT FROM AUTHOR]

Summary: Branch angle (BA) is a critical morphological trait that significantly influences planting density, light interception and ultimately yield in plants. Despite its importance, the regulatory mechanism governing BA in rapeseed remains poorly understood. In this study, we generated 109 transcriptome data sets for 37 rapeseed accessions with divergent BA phenotypes. Relative to adaxial branch segments, abaxial segments accumulated higher levels of auxin and exhibited lower expression of six TCP1 homologues and one GA20ox3. A co‐expression network analysis identified two modules highly correlated with BA. The modules contained homologues to known BA control genes, such as FUL, YUCCA6, TCP1 and SGR3. Notably, a homoeologous exchange (HE), occurring at the telomeres of A09, was prevalent in large BA accessions, while an A02‐C02 HE was common in small BA accessions. In their corresponding regions, these HEs explained the formation of hub gene hotspots in the two modules. QTL‐seq analysis confirmed that the presence of a large A07‐C06 HE (~8.1 Mb) was also associated with a small BA phenotype, and BnaA07.WRKY40.b within it was predicted as candidate gene. Overexpressing BnaA07.WRKY40.b in rapeseed increased BA by up to 20°, while RNAi‐ and CRISPR‐mediated mutants (BnaA07.WRKY40.b and BnaC06.WRKY40.b) exhibited decreased BA by up to 11.4°. BnaA07.WRKY40.b was exclusively localized to the nucleus and exhibited strong expression correlations with many genes related to gravitropism and plant architecture. Taken together, our study highlights the influence of HEs on rapeseed plant architecture and confirms the role of WRKY40 homologues as novel regulators of BA. [ABSTRACT FROM AUTHOR]

Inspired by recent developments in the theory of Banach and operator algebras of locally compact groups, we construct several new classes of bifunctors (A,B)\mapsto A\otimes _{\alpha } B, where A\otimes _\alpha B is a cross norm completion of A\odot B for each pair of C*-algebras A and B. For the first class of bifunctors considered (A,B)\mapsto A{\otimes _p} B (1\leq p\leq \infty), A{\otimes _p} B is a Banach algebra cross-norm completion of A\odot B constructed in a fashion similar to p-pseudofunctions \text {PF}^*_p(G) of a locally compact group. Taking a cue from the recently introduced symmetrized p-pseudofunctions due to Liao and Yu and later by the second and the third named authors, we also consider {\otimes _{p,q}} for Hölder conjugate p,q\in [1,\infty ] – a Banach *-algebra analogue of the tensor product {\otimes _{p,q}}. By taking enveloping C*-algebras of A{\otimes _{p,q}} B, we arrive at a third bifunctor (A,B)\mapsto A{\otimes _{\mathrm C^*_{p,q}}} B where the resulting algebra A{\otimes _{\mathrm C^*_{p,q}}} B is a C*-algebra. For G_1 and G_2 belonging to a large class of discrete groups, we show that the tensor products \mathrm C^*_{\mathrm r}(G_1){\otimes _{\mathrm C^*_{p,q}}}\mathrm C^*_{\mathrm r}(G_2) coincide with a Brown-Guentner type C*-completion of \mathrm \ell ^1(G_1\times G_2) and conclude that if 2\leq p'

This study intends to introduce kernel mean embedding of probability measures over infinite‐dimensional separable Hilbert spaces induced by functional response statistical models. The embedded function represents the concentration of probability measures in small open neighborhoods, which identifies a pseudo‐likelihood and fosters a rich framework for statistical inference. Utilizing Maximum Mean Discrepancy, we devise new tests in functional response models. The performance of new derived tests is evaluated against competitors in three major problems in functional data analysis including Function‐on‐Scalar regression, functional one‐way ANOVA, and equality of covariance operators. [ABSTRACT FROM AUTHOR]

Reward motivation in individuals with high levels of negative schizotypal traits (NS) has been found to be lower than that in their counterparts. But it is unclear that whether their reward motivation adaptively changes with external effort-reward ratio, and what resting-state functional connectivity (rsFC) is associated with this change. Thirty-five individuals with high levels of NS and 44 individuals with low levels of NS were recruited. A 3T resting-state functional brain scan and a novel reward motivation adaptation behavioural task were administrated in all participants. The behavioural task was manipulated with three conditions (effort > reward condition vs. effort < reward condition vs. effort = reward condition). Under each condition were rated 'wanting' and 'liking' for rewards. The seed-based voxel-wise rsFC analysis was conducted to explore the rsFCs associated with the 'wanting' and 'liking' ratings in individuals with high levels of NS. 'Wanting' and 'liking' ratings of individuals with high levels of NS significantly declined in the effort > reward condition but did not rebound as high as their counterparts in the effort < reward condition. The rsFCs in NS group associated with these ratings were altered. The altered rsFCs in NS group involved regions in the prefrontal lobe, dopaminergic brain regions (ventral tegmental area, substantia nigra), hippocampus, thalamus and cerebellum. Individuals with high levels of NS manifested their reward motivation adaptation impairment as a failure of adjustment adaptively during effort-reward imbalance condition and altered rsFCs in prefrontal, dopaminergic and other brain regions. [ABSTRACT FROM AUTHOR]

This article is concerned with the practical stability performance of nonlinear impulsive stochastic functional differential systems driven by G-Brownian motion (G-ISFDSs). Comparing with traditional Lyapunov stability theory, practical stability can portray qualitative behaviour and quantitative properties of suggested systems. By employing G-Itô formula, Lyapunov–Razumikhin approach and stochastic analysis theory, some novel conditions for pth moment practical exponential stability and quasi-sure global practical uniform exponential stability of G-ISFDSs are established. The obtained results show that impulses may influence dynamic behaviour of the addressed system. Two numerical examples are given to verify the validity of our developed results. [ABSTRACT FROM AUTHOR]

Clock genes are essential for the daily functions of vertebrates and invertebrates and participate in a wide variety of biological functions including biochemical, physiological, and behavioral processes. Circadian clock disorders are detrimental to both humans and fish, and therefore research on the regulation of genes involved in the circadian clock has attracted increasing attention. Period 2 (per2) is an important gene whose expression is closely related to melatonin secretion, in addition to being affected by the photoperiod length. To gain more insights into the potential biological function of per2, we have cloned and expressed per2 in Amur minnow (Phoxinus lagowskii). We also analyzed melatonin content and AANAT2 gene expression under different short or long-term photoperiod conditions. In the present study, the secretion of melatonin in P. lagowskii was highest in the dark phase under short-term experiments. In the pituitary, the expression of the per2 gene was highest during the dark phase in both the 16L: 8D and 8L: 16D groups. The expression of the per2 gene in the brain was also highest during the dark phase in the 12L: 12D group. Though the expression of the per2 gene was not the highest in the dark phase for the other groups, there were no significant differences compared to the highest value. In addition, in the brain and pituitary, AANAT2 expression was highest during the light phase, except in the 8L: 16D group. Our findings suggested that Amper2 may participate in the feedback regulation of melatonin by regulating the expression of AANAT2. Fluorescence in situ hybridization analyses confirmed that per2 mRNA was expressed during the dark phase, especially in 16L: 8D group. Immunohistochemistry analyses confirmed that PER2 protein was expressed higher in 8L: 16D group. The dual luciferase experiment first validated the promotion of Wnt/β-Catenin expression by the per2 gene. Our results provide novel insights into the expression and location of per2, which contributes to a better understanding of the role of clock genes in the circadian rhythm and seasonal responses of high-latitude fish and might provide useful information of practical interest for high-latitude aquaculture. [ABSTRACT FROM AUTHOR]

A global analysis of the functional characteristics of meta-assemblages of estuary-associated fishes was undertaken at the marine ecoregion level. Marine ecoregions were grouped into broad biogeographic regions (bioregions) and functional attributes of the fish assemblages compared based on a numerical fish estuary association score, as well as estuarine use functional groups. Relationships between selected environmental characteristics and fish functional attributes were also examined. A significant relationship between ecoregion environmental variables and estuarine fish functional assemblages was recorded, with the key environmental factors identified being related to habitat (estuarine area and macrophyte vegetation), connectivity (mean annual runoff), and physico-chemical (sea surface temperature and sea surface salinity) variables. [ABSTRACT FROM AUTHOR]

We examined the initial stages of orthographic learning in real time as literate adults learned spellings for spoken pseudowords during fMRI scanning. Participants were required to learn and store orthographic word forms because the pseudoword spellings were not uniquely predictable from sound to letter mappings. With eight learning trials per word form, we observed changes in the brain's response as learning was taking place. Accuracy was evaluated during learning, immediately after scanning, and 1 week later. We found evidence of two distinct learning systems—hippocampal and neocortical—operating during orthographic learning, consistent with the predictions of dual systems theories of learning/memory such as the complementary learning systems framework [McClelland, J. L., McNaughton, B. L., & O'Reilly, R. C. Why there are complementary learning systems in the hippocampus and neocortex: Insights from the successes and failures of connectionist models of learning and memory. Psychological Review, 102, 419–457, 1995]. The bilateral hippocampus and the visual word form area (VWFA) showed significant BOLD response changes over learning, with the former exhibiting a rising pattern and the latter exhibiting a falling pattern. Moreover, greater BOLD signal increase in the hippocampus was associated with better postscan recall. In addition, we identified two distinct bilateral brain networks that mirrored the rising and falling patterns of the hippocampus and VWFA. Functional connectivity analysis revealed that regions within each network were internally synchronized. These novel findings highlight, for the first time, the relevance of multiple learning systems in orthographic learning and provide a paradigm that can be used to address critical gaps in our understanding of the neural bases of orthographic learning in general and orthographic word-form learning specifically. [ABSTRACT FROM AUTHOR]

Parkinson's disease is a progressive neurodegenerative disorder with multifactorial causes, among which genetic risk factors play a part. The RAB GTPases are regulators and substrates of LRRK2, and variants in the LRRK2 gene are important risk factors for Parkinson's disease. We aimed to explore genetic variability in RAB GTPases within cases of familial Parkinson's disease. We did whole-exome sequencing in probands from families in Canada and Tunisia with Parkinson's disease without a genetic cause, who were recruited from the Centre for Applied Neurogenetics (Vancouver, BC, Canada), an international consortium that includes people with Parkinson's disease from 36 sites in 24 countries. 61 RAB GTPases were genetically screened, and candidate variants were genotyped in relatives of the probands to assess disease segregation by linkage analysis. Genotyping was also done to assess variant frequencies in individuals with idiopathic Parkinson's disease and controls, matched for age and sex, who were also from the Centre for Applied Neurogenetics but unrelated to the probands or each other. All participants were aged 18 years or older. The sequencing and genotyping findings were validated by case–control association analyses using bioinformatic data obtained from publicly available clinicogenomic databases (AMP-PD, GP2, and 100 000 Genomes Project) and a private German clinical diagnostic database (University of Tübingen). Clinical and pathological findings were summarised and haplotypes were determined. In-vitro studies were done to investigate protein interactions and enzyme activities. Between June 1, 2010, and May 31, 2017, 130 probands from Canada and Tunisia (47 [36%] female and 83 [64%] male; mean age 72·7 years [SD 11·7; range 38–96]; 109 White European ancestry, 18 north African, two east Asian, and one Hispanic] underwent whole-exome sequencing. 15 variants in RAB GTPase genes were identified, of which the RAB32 variant c.213C>G (Ser71Arg) cosegregated with autosomal dominant Parkinson's disease in three families (nine affected individuals; non-parametric linkage Z score=1·95; p=0·03). 2604 unrelated individuals with Parkinson's disease and 344 matched controls were additionally genotyped, and five more people originating from five countries (Canada, Italy, Poland, Turkey, and Tunisia) were identified with the RAB32 variant. From the database searches, in which 6043 individuals with Parkinson's disease and 62 549 controls were included, another eight individuals were identified with the RAB32 variant from four countries (Canada, Germany, UK, and USA). Overall, the association of RAB32 c.213C>G (Ser71Arg) with Parkinson's disease was significant (odds ratio [OR] 13·17, 95% CI 2·15–87·23; p=0·0055; I 2=99·96%). In the people who had the variant, Parkinson's disease presented at age 54·6 years (SD 12·75, range 31–81, n=16), and two-thirds had a family history of parkinsonism. RAB32 Ser71Arg heterozygotes shared a common haplotype, although penetrance was incomplete. Findings in one individual at autopsy showed sparse neurofibrillary tangle pathology in the midbrain and thalamus, without Lewy body pathology. In functional studies, RAB32 Arg71 activated LRRK2 kinase to a level greater than RAB32 Ser71. RAB32 Ser71Arg is a novel genetic risk factor for Parkinson's disease, with reduced penetrance. The variant was found in individuals with Parkinson's disease from multiple ethnic groups, with the same haplotype. In-vitro assays show that RAB32 Arg71 activates LRRK2 kinase, which indicates that genetically distinct causes of familial parkinsonism share the same mechanism. The discovery of RAB32 Ser71Arg also suggests several genetically inherited causes of Parkinson's disease originated to control intracellular immunity. This shared aetiology should be considered in future translational research, while the global epidemiology of RAB32 Ser71Arg needs to be assessed to inform genetic counselling. National Institutes of Health, the Canada Excellence Research Chairs program, Aligning Science Across Parkinson's, the Michael J Fox Foundation for Parkinson's Research, and the UK Medical Research Council. [ABSTRACT FROM AUTHOR]

This paper develops a new nonparametric estimator of the scalar-on function modal regression that is used to analyse the co-variability between a functional regressor and a scalar output variable. The new estimator inherits the smoothness of the kernel method and the robustness of the quantile regression. We assume that the functional observations are structured as a strong mixing functional time series data and we establish the almost complete consistency (with rate) of the constructed estimator. A discussion highlighting the impact of this new estimator in nonparametric functional data analysis is also given. The usefulness of this new estimator is shown using an artificial data example. [ABSTRACT FROM AUTHOR]

Crispr/CAS9‐enabled homologous recombination to insert a tag in frame with an endogenous gene can circumvent difficulties such as context‐dependent promoter activity that complicate analysis of gene expression and protein accumulation patterns. However, there have been few reports examining whether such gene targeting/gene tagging (GT) can alter expression of the target gene. The enzyme encoded by Δ1‐pyrroline‐5‐carboxylate synthetase 1 (P5CS1) is key for stress‐induced proline synthesis and drought resistance, yet its expression pattern and protein localisation have been difficult to assay. We used GT to insert YFP in frame with the 5′ or 3′ ends of the endogenous P5CS1 and At14a‐Like 1 (AFL1) coding regions. Insertion at the 3′ end of either gene generated homozygous lines with expression of the gene‐YFP fusion indistinguishable from the wild type allele. However, for P5CS1 this occurred only after selfing and advancement to the T5 generation allowed initial homozygous lethality of the insertion to be overcome. Once this was done, the GT‐generated P5CS1‐YFP plants revealed new information about P5CS1 localisation and tissue‐specific expression. In contrast, insertion of YFP at the 5′ end of either gene blocked expression. The results demonstrate that GT can be useful for functional analyses of genes that are problematic to properly express by other means but also show that, in some cases, GT can disrupt expression of the target gene. Summary statement: Gene tagging (GT) of Arabidopsis thaliana P5CS1 and AFL1 shows the potential of GT for functional analysis of stress‐related genes, but also provides examples of how GT can dramatically disrupt expression of the target gene. [ABSTRACT FROM AUTHOR]

This study investigates the impact of casein hydrolysates on the poultry ceca inoculated with Campylobacter focusing on microbial molecular preferences for different protein sources in the presence of Campylobacter jejuni. Three casein sources (intact casein (IN), casein enzyme hydrolysate (EH), and casein acid hydrolysate (AH)) were introduced to cecal contents in combination with inoculated C. jejuni in an in vitro model system incubated for 48 h at 42°C under microaerophilic conditions. Samples were collected at 0, 24, and 48 h. Genomic DNA was extracted and amplified using custom dual-indexed primers, followed by sequencing on an Illumina MiSeq platform. The obtained sequencing data were then analyzed via QIIME2-2021.11. Metabolite extracts were analyzed with ultra-high-performance liquid orbitrap chromatography-mass spectrometry (UHPLC-MS). Statistical analysis of metabolites was conducted using MetaboAnalyst 5.0, while functional analysis was performed using Mummichog 2.0 with a significance threshold set at P < 0.00001. DNA sequencing and metabolomic analyses revealed that C. jejuni was most abundant in the EH group. Microbial diversity and richness improved in casein supplemented groups, with core microbial differences observed, compared to non-supplemented groups. Vitamin B-associated metabolites significantly increased in the supplemented groups, displaying distinct patterns in vitamin B6 and B9 metabolism between EH and AH groups (P < 0.05). Faecalibacterium and Phascolarctobacterium were associated with AH and EH groups, respectively. These findings suggest microbial interactions in the presence of C. jejuni and casein supplementation are influenced by microbial community preferences for casein hydrolysates impacting B vitamin production and shaping competitive dynamics within the cecal microbial community. These findings underscore the potential of nutritional interventions to modulate the poultry GIT microbiota for improved health outcomes. [ABSTRACT FROM AUTHOR]

Background: Information on the microbiome's human pathways and active members that can affect SARS-CoV-2 susceptibility and pathogenesis in the salivary proteome is very scarce. Here, we studied a unique collection of samples harvested from April to June 2020 from unvaccinated patients. Methods: We compared 10 infected and hospitalized patients with severe (n = 5) and moderate (n = 5) coronavirus disease (COVID-19) with 10 uninfected individuals, including non-COVID-19 but susceptible individuals (n = 5) and non-COVID-19 and nonsusceptible healthcare workers with repeated high-risk exposures (n = 5). Results: By performing high-throughput proteomic profiling in saliva samples, we detected 226 unique differentially expressed (DE) human proteins between groups (q-value ≤ 0.05) out of 3376 unambiguously identified proteins (false discovery rate ≤ 1%). Major differences were observed between the non-COVID-19 and nonsusceptible groups. Bioinformatics analysis of DE proteins revealed human proteomic signatures related to inflammatory responses, central cellular processes, and antiviral activity associated with the saliva of SARS-CoV-2-infected patients (p-value ≤ 0.0004). Discriminatory biomarker signatures from human saliva include cystatins, protective molecules present in the oral cavity, calprotectins, involved in cell cycle progression, and histones, related to nucleosome functions. The expression levels of two human proteins related to protein transport in the cytoplasm, DYNC1 (p-value, 0.0021) and MAPRE1 (p-value, 0.047), correlated with angiotensin-converting enzyme 2 (ACE2) plasma activity. Finally, the proteomes of microorganisms present in the saliva samples showed 4 main microbial functional features related to ribosome functioning that were overrepresented in the infected group. Conclusion: Our study explores potential candidates involved in pathways implicated in SARS-CoV-2 susceptibility, although further studies in larger cohorts will be necessary. [ABSTRACT FROM AUTHOR]

Background: Mangrove sediment microbes are increasingly attracting scientific attention due to their demonstrated capacity for diverse bioremediation activities, encompassing a wide range of environmental contaminants. Materials and methods: The microbial communities of five Avicennia marina mangrove sediment samples collected from Al Rayyis White Head, Red Sea (KSA), were characterized using Illumina amplicon sequencing of the 16S rRNA genes. Results: Our study investigated the microbial composition and potential for organohalide bioremediation in five mangrove sediments from the Red Sea. While Proteobacteria dominated four microbiomes, Bacteroidetes dominated the fifth. Given the environmental concerns surrounding organohalides, their bioremediation is crucial. Encouragingly, we identified phylogenetically diverse organohalide-respiring bacteria (OHRB) across all samples, including Dehalogenimonas, Dehalococcoides, Anaeromyxobacter, Desulfuromonas, Geobacter, Desulfomonile, Desulfovibrio, Shewanella and Desulfitobacterium. These bacteria are known for their ability to dechlorinate organohalides through reductive dehalogenation. PICRUSt analysis further supported this potential, predicting the presence of functional biomarkers for organohalide respiration (OHR), including reductive dehalogenases targeting tetrachloroethene (PCE) and 3-chloro-4-hydroxyphenylacetate in most sediments. Enrichment cultures studies confirmed this prediction, demonstrating PCE dechlorination by the resident microbial community. PICRUSt also revealed a dominance of anaerobic metabolic processes, suggesting the microbiome's adaptation to the oxygen-limited environment of the sediments. Conclusion: This study provided insights into the bacterial community composition of five mangrove sediments from the Red Sea. Notably, diverse OHRB were detected across all samples, which possess the metabolic potential for organohalide bioremediation through reductive dehalogenation pathways. Furthermore, PICRUSt analysis predicted the presence of functional biomarkers for OHR in most sediments, suggesting potential intrinsic OHR activity by the enclosed microbial community. [ABSTRACT FROM AUTHOR]

Background: The homodomain-leucine zipper (HD-Zip) is a conserved transcription factor family unique to plants that regulate multiple developmental processes including lignificaion. Stone cell content is a key determinant negatively affecting pear fruit quality, which causes a grainy texture of fruit flesh, because of the lignified cell walls. Results: In this study, a comprehensive bioinformatics analysis of HD-Zip genes in Chinese white pear (Pyrus bretschneideri) (PbHBs) was performed. Genome-wide identification of the PbHB gene family revealed 67 genes encoding PbHB proteins, which could be divided into four subgroups (I, II, III, and IV). For some members, similar intron/exon structural patterns support close evolutionary relationships within the same subgroup. The functions of each subgroup of the PbHB family were predicted through comparative analysis with the HB genes in Arabidopsis and other plants. Cis-element analysis indicated that PbHB genes might be involved in plant hormone signalling and external environmental responses, such as light, stress, and temperature. Furthermore, RNA-sequencing data and quantitative real-time PCR (RT-qPCR) verification revealed the regulatory roles of PbHB genes in pear stone cell formation. Further, co-expression network analysis revealed that the eight PbHB genes could be classified into different clusters of co-expression with lignin-related genes. Besides, the biological function of PbHB24 in promoting stone cell formation has been demonstrated by overexpression in fruitlets. Conclusions: This study provided the comprehensive analysis of PbHBs and highlighted the importance of PbHB24 during stone cell development in pear fruits. [ABSTRACT FROM AUTHOR]

Patterns of single nucleotide polymorphisms (SNPs) in eukaryotic DNA are traditionally attributed to selective pressure, drift, identity descent, or related factors—without accounting for ways in which bias during de novo SNP formation, itself, might contribute. A functional and phenotypic analysis based on evolutionary resilience of DNA points to decreased numbers of non-synonymous SNPs in human and other genomes, with a predominant component of SNP depletion in the human gene pool caused by robust preferences during de novo SNP formation (rather than selective constraint). Ramifications of these findings are broad, belie a number of concepts regarding human evolution, and point to a novel interpretation of evolving DNA across diverse species. [ABSTRACT FROM AUTHOR]

Background: Alpha synuclein (α-synuclein) is coded by SNCA gene and found in a helical form with phospholipids or in an unfolded arrangement in the cytosol and belongs to the synuclein family other than beta synuclein and gamma synuclein. It is a short protein made of 140 amino acids with three domains: an N-terminal lipid binding helix, a non-amyloid-ß component (NAC), and an acidic tail at the C-terminus. α-Synuclein is present in aggregated and fibrillar form in Lewy bodies and its association has been related to multiple system atrophy (MSA), Parkinson's disease (PD), and Dementia with Lewy bodies (DLB). Our objective is to investigate and prioritise the possible nsSNPs in the α-synuclein protein that have been potentially connected to human neurodegenerative diseases. Results: We used the series of computational tools to predict the mutation's harmful effect on three-dimensional structure of α-synuclein based on consensus approach. Our findings pointed to a significant computational blueprint for discovering nsSNPs connected to neurodegenerative illnesses from a large SNP data set while also minimising the expenses of experimentally showing harmful nsSNPs. Conclusions: The prioritised G25S (rs1433622151), V66E (rs1261243630), and V77D (rs745815563) mutations can be employed in additional experimental studies to assess the α-synuclein protein mutation in relation to neurodegenerative illnesses and develop a therapeutics against them. [ABSTRACT FROM AUTHOR]

Amaranth species are C4 plants that are rich in betalains, and they are tolerant to salinity stress. A small family of plant-specific TCP transcription factors are involved in the response to salt stress. However, it has not been investigated whether amaranth TCP1 is involved in salt stress. We elucidated that the growth and physiology of amaranth were affected by salt concentrations of 50–200 mmol·L−1 NaCl. The data showed that shoot and root growth was inhibited at 200 mmol·L−1, while it was promoted at 50 mmol·L−1. Meanwhile, the plants also showed physiological responses, which indicated salt-induced injuries and adaptation to the salt stress. Moreover, AtrTCP1 promoted Arabidopsis seed germination. The germination rate of wild-type (WT) and 35S::AtrTCP1-GUS Arabidopsis seeds reached around 92% by the seventh day and 94.5% by the second day under normal conditions, respectively. With 150 mmol·L−1 NaCl treatment, the germination rate of the WT and 35S::AtrTCP1-GUS plant seeds was 27.0% by the seventh day and 93.0% by the fourth day, respectively. Under salt stress, the transformed 35S::AtrTCP1 plants bloomed when they grew 21.8 leaves after 16.2 days of treatment, which was earlier than the WT plants. The transformed Arabidopsis plants flowered early to resist salt stress. These results reveal amaranth's growth and physiological responses to salt stress, and provide valuable information on the AtrTCP1 gene. [ABSTRACT FROM AUTHOR]

The pil gene cluster for Type IV pilus (Tfp) biosynthesis is commonly present and highly conserved in Streptococcus sanguinis. Nevertheless, Tfp-mediated twitching motility is less common among strains, and the factors determining twitching activity are not fully understood. Here, we analyzed the functions of three major pilin proteins (PilA1, PilA2, and PilA3) in the assembly and activity of Tfp in motile S. sanguinis CGMH010. Using various recombinant pilA deletion strains, we found that Tfp composed of different PilA proteins varied morphologically and functionally. Among the three PilA proteins, PilA1 was most critical in the assembly of twitching-active Tfp, and recombinant strains expressing motility generated more structured biofilms under constant shearing forces compared to the non-motile recombinant strains. Although PilA1 and PilA3 shared 94% identity, PilA3 could not compensate for the loss of PilA1, suggesting that the nature of PilA proteins plays an essential role in twitching activity. The single deletion of individual pilA genes had little effect on the invasion of host endothelia by S. sanguinis CGMH010. In contrast, the deletion of all three pilA genes or pilT, encoding the retraction ATPase, abolished Tfp-mediated invasion. Tfp- and PilT-dependent invasion were also detected in the non-motile S. sanguinis SK36, and thus, the retraction of Tfp, but not active twitching, was found to be essential for invasion. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) are a group of endogenous small non-coding RNAs in plants. They play critical functions in various biological processes during plant growth and development. Salvia miltiorrhiza is a well-known traditional Chinese medicinal plant with significant medicinal, economic, and academic values. In order to elucidate the role of miRNAs in S. miltiorrhiza, six small RNA libraries from mature roots, young roots, stems, mature leaves, young leaves and flowers of S. miltiorrhiza and one degradome library from mixed tissues were constructed. A total of 184 miRNA precursors, generating 137 known and 49 novel miRNAs, were genome-widely identified. The identified miRNAs were predicted to play diversified regulatory roles in plants through regulating 891 genes. qRT-PCR and 5′ RLM-RACE assays validated the negative regulatory role of smi-miR159a in SmMYB62, SmMYB78, and SmMYB80. To elucidate the function of smi-miR159a in bioactive compound biosynthesis, smi-miR159a transgenic hairy roots were generated and analyzed. The results showed that overexpression of smi-miR159a caused a significant decrease in rosmarinic acid and salvianolic acid B contents. qRT-PCR analysis showed that the targets of smi-miR159a, including SmMYB62, SmMYB78, and SmMYB80, were significantly down-regulated, accompanied by the down-regulation of SmPAL1, SmC4H1, Sm4CL1, SmTAT1, SmTAT3, SmHPPR1, SmRAS, and SmCYP98A14 genes involved in phenolic acid biosynthesis. It suggests that smi-miR159a is a significant negative regulator of phenolic acid biosynthesis in S. miltiorrhiza. [ABSTRACT FROM AUTHOR]

Low-complexity domains (LCDs) in proteins are typically enriched in one or two predominant amino acids. As a result, LCDs often exhibit unusual structural/biophysical tendencies and can occupy functional niches. However, for each organism, protein sequences must be compatible with intracellular biomolecules and physicochemical environment, both of which vary from organism to organism. This raises the possibility that LCDs may occupy sequence spaces in select organisms that are otherwise prohibited in most organisms. Here, we report a comprehensive survey and functional analysis of LCDs in all known reference proteomes (>21k organisms), with added focus on rare and unusual types of LCDs. LCDs were classified according to both the primary amino acid and secondary amino acid in each LCD sequence, facilitating detailed comparisons of LCD class frequencies across organisms. Examination of LCD classes at different depths (i.e., domain of life, organism, protein, and per-residue levels) reveals unique facets of LCD frequencies and functions. To our surprise, all 400 LCD classes occur in nature, although some are exceptionally rare. A number of rare classes can be defined for each domain of life, with many LCD classes appearing to be eukaryote-specific. Certain LCD classes were consistently associated with identical functions across many organisms, particularly in eukaryotes. Our analysis methods enable simultaneous, direct comparison of all LCD classes between individual organisms, resulting in a proteome-scale view of differences in LCD frequencies and functions. Together, these results highlight the remarkable diversity and functional specificity of LCDs across all known life forms. Author summary: Many protein sequences contain "low-complexity domains" (LCDs), which are regions in the sequence mostly comprised of only one or two different types of amino acids. Since there are 20 main types of amino acids found in natural proteins, many "flavors" of LCDs are possible, with each flavor having unique structural and functional properties. However, the functions and prevalence of each type of LCD across organisms has not been explored extensively. In this study, we divided LCDs into 400 categories based on the one or two amino acids that were most common in each LCD sequence. Then, using a representative set of all known organisms, we examined how prevalent each type of LCD was and which functions were most often linked to each type of LCD. We uncovered LCD functions common to many organisms as well as LCD functions restricted to certain organisms or LCD types. Some organisms had unusually high levels of specific types of LCDs, suggesting that adaptations in these organisms or special conditions in their environment have aided in the tolerance–or even usage–of those LCD types. Our results give both broad and in-depth views of LCDs, their functions, and their frequencies in nature. [ABSTRACT FROM AUTHOR]

Background: Culex pipiens pallens is a well-known mosquito vector for several diseases. Deltamethrin, a commonly used pyrethroid insecticide, has been frequently applied to manage adult Cx. pipiens pallens. However, mosquitoes can develop resistance to these insecticides as a result of insecticide misuse and, therefore, it is crucial to identify novel methods to control insecticide resistance. The relationship between commensal bacteria and vector resistance has been recently recognized. Bacteriophages (= phages) are effective tools by which to control insect commensal bacteria, but there have as yet been no studies using phages on adult mosquitoes. In this study, we isolated an Aeromonas phage vB AhM-LH that specifically targets resistance-associated symbiotic bacteria in mosquitoes. We investigated the impact of Aeromonas phage vB AhM-LH in an abundance of Aeromonas hydrophila in the gut of Cx. pipiens pallens and its effect on the status of deltamethrin resistance. Methods: Phages were isolated on double-layer agar plates and their biological properties analyzed. Phage morphology was observed by transmission electron microscopy (TEM) after negative staining. The phage was then introduced into the mosquito intestines via oral feeding. The inhibitory effect of Aeromonas phage vB AhM-LH on Aeromonas hydrophila in mosquito intestines was assessed through quantitative real-time PCR analysis. Deltamethrin resistance of mosquitoes was assessed using WHO bottle bioassays. Results: An Aeromonas phage vB AhM-LH was isolated from sewage and identified as belonging to the Myoviridae family in the order Caudovirales using TEM. Based on biological characteristics analysis and in vitro antibacterial experiments, Aeromonas phage vB AhM-LH was observed to exhibit excellent stability and effective bactericidal activity. Sequencing revealed that the Aeromonas phage vB AhM-LH genome comprises 43,663 bp (51.6% CG content) with 81 predicted open reading frames. No integrase-related gene was detected in the vB AH-LH genome, which marked it as a potential biological antibacterial. Finally, we found that Aeromonas phage vB AhM-LH could significantly reduce deltamethrin resistance in Cx. pipiens pallens, in both the laboratory and field settings, by decreasing the abundance of Aeromonas hydrophila in their midgut. Conclusions: Our findings demonstrate that Aeromonas phage vB AhM-LH could effectively modulate commensal bacteria Aeromonas hydrophila in adult mosquitoes, thus representing a promising strategy to mitigate mosquito vector resistance. [ABSTRACT FROM AUTHOR]

Within the islets of Langerhans, beta cells orchestrate synchronized insulin secretion, a pivotal aspect of metabolic homeostasis. Despite the inherent heterogeneity and multimodal activity of individual cells, intercellular coupling acts as a homogenizing force, enabling coordinated responses through the propagation of intercellular waves. Disruptions in this coordination are implicated in irregular insulin secretion, a hallmark of diabetes. Recently, innovative approaches, such as integrating multicellular calcium imaging with network analysis, have emerged for a quantitative assessment of the cellular activity in islets. However, different groups use distinct experimental preparations, microscopic techniques, apply different methods to process the measured signals and use various methods to derive functional connectivity patterns. This makes comparisons between findings and their integration into a bigger picture difficult and has led to disputes in functional connectivity interpretations. To address these issues, we present here a systematic analysis of how different approaches influence the network representation of islet activity. Our findings show that the choice of methods used to construct networks is not crucial, although care is needed when combining data from different islets. Conversely, the conclusions drawn from network analysis can be heavily affected by the pre-processing of the time series, the type of the oscillatory component in the signals, and by the experimental preparation. Our tutorial-like investigation aims to resolve interpretational issues, reconcile conflicting views, advance functional implications, and encourage researchers to adopt connectivity analysis. As we conclude, we outline challenges for future research, emphasizing the broader applicability of our conclusions to other tissues exhibiting complex multicellular dynamics. Author summary: Islets of Langerhans, multicellular microorgans in the pancreas, are pivotal for whole-body energy homeostasis. Hundreds of beta cells within these networks synchronize to produce insulin, a crucial hormone for metabolic control. Coordinated activity disruptions in these multicellular networks contribute to irregular insulin secretion, a hallmark of diabetes. Recognizing the significance of collective activity, network science approaches have been increasingly applied in islet research. However, variations in experimental setups, imaging techniques, signal processing, and connectivity analysis methods across different research groups pose challenges for integrating findings into a comprehensive picture. Therefore, we present here a systematic analysis of various approaches impacting results in islet activity network representation. We find that methods for constructing functional connectivity maps aren't critical, but caution is necessary when aggregating data from different islets. Network analysis conclusions are notably influenced by factors such as time series pre-processing, the oscillatory component of signals, and experimental preparation. Despite these challenges, this paper advocates for the adoption of connectivity analysis in future islet research, emphasizing that the insights gained extend beyond pancreatic islets to provide valuable contributions for understanding connectivity in other multicellular systems. [ABSTRACT FROM AUTHOR]

Understanding the influence of cis‐regulatory elements on gene regulation poses numerous challenges given complexities stemming from variations in transcription factor (TF) binding, chromatin accessibility, structural constraints, and cell‐type differences. This review discusses the role of gene regulatory networks in enhancing understanding of transcriptional regulation and covers construction methods ranging from expression‐based approaches to supervised machine learning. Additionally, key experimental methods, including MPRAs and CRISPR‐Cas9‐based screening, which have significantly contributed to understanding TF binding preferences and cis‐regulatory element functions, are explored. Lastly, the potential of machine learning and artificial intelligence to unravel cis‐regulatory logic is analyzed. These computational advances have far‐reaching implications for precision medicine, therapeutic target discovery, and the study of genetic variations in health and disease. [ABSTRACT FROM AUTHOR]

The GO DNA repair system protects against GC → TA mutations by finding and removing oxidized guanine. The system is mechanistically well understood but its origins are unknown. We searched metagenomes and abundantly found the genes encoding GO DNA repair at the Lost City Hydrothermal Field (LCHF). We recombinantly expressed the final enzyme in the system to show MutY homologs function to suppress mutations. Microbes at the LCHF thrive without sunlight, fueled by the products of geochemical transformations of seafloor rocks, under conditions believed to resemble a young Earth. High levels of the reductant H2 and low levels of O2 in this environment raise the question, why are resident microbes equipped to repair damage caused by oxidative stress? MutY genes could be assigned to metagenome-assembled genomes (MAGs), and thereby associate GO DNA repair with metabolic pathways that generate reactive oxygen, nitrogen and sulfur species. Our results indicate that cell-based life was under evolutionary pressure to cope with oxidized guanine well before O2 levels rose following the great oxidation event. [ABSTRACT FROM AUTHOR]

Background: Standard ChIP-seq and RNA-seq processing pipelines typically disregard sequencing reads whose origin is ambiguous ("multimappers"). This usual practice has potentially important consequences for the functional interpretation of the data: genomic elements belonging to clusters composed of highly similar members are left unexplored. Results: In particular, disregarding multimappers leads to the underrepresentation in epigenetic studies of recently active transposable elements, such as AluYa5, L1HS and SVAs. Furthermore, this common strategy also has implications for transcriptomic analysis: members of repetitive gene families, such the ones including major histocompatibility complex (MHC) class I and II genes, are under-quantified. Conclusion: Revealing inherent biases that permeate routine tasks such as functional enrichment analysis, our results underscore the urgency of broadly adopting multimapper-aware bioinformatic pipelines –currently restricted to specific contexts or communities– to ensure the reliability of genomic and transcriptomic studies. [ABSTRACT FROM AUTHOR]

Background: Recent studies have revealed the correlation between serum vitamin D (VD) level and polycystic ovary syndrome (PCOS), but the causality and specific mechanisms remain uncertain. Objective: We aimed to investigate the cause-effect relationship between serum VD and PCOS, and the role of testosterone in the related pathological mechanisms. Methods: We assessed the causality between serum VD and PCOS by using genome-wide association studies (GWAS) data in a bidirectional two-sample Mendelian randomization (TS-MR) analysis. Subsequently, a MR mediation analysis was conducted to examine the mediating action of testosterone in the causality between serum VD and PCOS. Ultimately, we integrated GWAS data with cis-expression quantitative loci (cis-eQTLs) data for gene annotation, and used the potentially related genes for functional enrichment analysis to assess the involvement of testosterone and the potential mechanisms. Results: TS-MR analysis showed that individuals with lower level of serum VD were more likely to develop PCOS (OR = 0.750, 95% CI: 0.587–0.959, P = 0.022). MR mediation analysis uncovered indirect causal effect of serum VD level on the risk of PCOS via testosterone (OR = 0.983, 95% CI: 0.968–0.998, P = 0.025). Functional enrichment analysis showed that several pathways may be involved in the VD-testosterone-PCOS axis, such as steroid hormone biosynthesis and autophagy process. Conclusion: Our findings suggest that genetically predicted lower serum VD level may cause a higher risk of developing PCOS, which may be mediated by increased testosterone production. [ABSTRACT FROM AUTHOR]

In this article, we present a meticulous computational study to foresee the effect of an oxygen-rich macrocycle on the reactivity for C–H activation. For this study, a widely studied nonheme Fe(IV)O molecule with a TMC (1,4,8,11-tetramethyl 1,4,8,11-tetraazacyclotetradecane) macrocycle that is equatorially attached to four nitrogen atoms (designated as N4) and acetonitrile as an axial ligand has been taken into account. For the goal of hetero-substitution, step-by-step replacement of the N4 framework with O atoms, i.e., N4, N3O1, N2O2, N1O3, and O4 systems, has been considered, and dihydroanthracene (DHA) has been used as the substrate. In order to neutralise the system and prevent the self-interaction error in DFT, triflate counterions have also been included in the calculations. The study of the energetics of these C–H bond activation reactions and the potential energy surfaces mapped therefore reveal that the initial hydrogen abstraction, which is the rate-determining step, follows the two-state reactivity (TSR) pattern, which means that the originally excited quintet state falls lower in the transition state and the product. The reaction follows the hydrogen atom transfer (HAT) mechanism, as indicated by the spin density studies. The results revealed a fascinating reactivity order, in which the reactivity increases with the enrichment of the oxygen atom in the equatorial position, namely the order follows N4 < N3O1 < N2O2 < N1O3 < O4. The impacts of oxygen substitution on quantum mechanical tunneling and the H/D kinetic isotope effect have also been investigated. When analysing the causes of this reactivity pattern, a number of variables have been identified, including the reactant-like transition structure, spin density distribution, distortion energy, and energies of the electron acceptor orbital, i.e., the energy of the LUMO (σ*z2), which validate the obtained outcome. Our results also show very good agreement with earlier combined experimental and theoretical studies considering TMC and TMCO-type complexes. The DFT predictions reported here will undoubtedly encourage experimental research in this biomimetic field, as they provide an alternative with higher reactivity in which heteroatoms can be substituted for the traditional nitrogen atom. [ABSTRACT FROM AUTHOR]

• A total number of 24 AAP and 14 CAT proteins in maize were identified. • Among all, 22 AAPs and 12 CATs were basic proteins localized in plasma membrane. • ZmAAPs and CATs showed significant structural variation. • Promoters of analyzed genes consist phytohormone and stress-related cis-elements. • Genes distributed in different chromosomes showed significant upregulation in drought. In maize, the amino acid permease (AAP) and the cationic amino acid transporters (CAT) play a significant role in amino nitrogen (N) uptake, transport, utilization, and homeostasis. Hence, genome-wide analysis of maize AAP and CAT resulted in 24 AAP (1-24) and 14 CAT (1-14) proteins in maize having significant variation in molecular weights. Most proteins are basic and localized in the plasma membrane. AAPs and CATs showed up to 7 and 14 introns respectively. All proteins showed multiple motifs, alpha-helices, transmembrane helices (except ZmAAP23), and coiled in nature. The ZmAAP and ZmCAT promoters consisted of phytohormone, plant growth and development, and stress-related cis -elements. All genes are distributed in different chromosomes. All the above properties are consistent with the same in Arabidopsis, which represent their functional similarities. Significantly higher transcription of some AAPs and CATs in vegetative and/or reproductive tissues reveal their great potential to source-sink transport and reuptake of leaked amino N from the rhizosphere. Interestingly, some members of the above-mentioned families are also upregulated during drought stress revealing their great role in drought tolerance or acclimatization during the stress. For increasing drought tolerance, these transporters might interact with the genes regulating the turgor pressure of the guard cells for increasing stomatal closure and reducing transpiration in leaves through controlling cellular osmotic homeostasis. [ABSTRACT FROM AUTHOR]

Copy number variation is a common contributor to phenotypic diversity, yet its involvement in ecological adaptation is not easily discerned. Instances of parallelly evolving populations of the same species in a similar environment marked by strong selective pressures present opportunities to study the role of copy number variants (CNVs) in adaptation. By identifying CNVs that repeatedly occur in multiple populations of the derived ecotype and are not (or are rarely) present in the populations of the ancestral ecotype, the association of such CNVs with adaptation to the novel environment can be inferred. We used this paradigm to identify CNVs associated with recurrent adaptation of the Mexican tetra (Astyanax mexicanus) to cave environment. Using a read‐depth approach, we detected CNVs from previously re‐sequenced genomes of 44 individuals belonging to two ancestral surfaces and three derived cave populations. We identified 102 genes and 292 genomic regions that repeatedly diverge in copy number between the two ecotypes and occupy 0.8% of the reference genome. Functional analysis revealed their association with processes previously recognized to be relevant for adaptation, such as vision, immunity, oxygen consumption, metabolism, and neural function and we propose that these variants have been selected for in the cave or surface waters. The majority of the ecotype‐divergent CNVs are multiallelic and display copy number increases in cavefish compared to surface fish. Our findings suggest that multiallelic CNVs – including gene duplications – and divergence in copy number provide a fast route to produce novel phenotypes associated with adaptation to subterranean life. [ABSTRACT FROM AUTHOR]

The occasion for this survey article was the 70th birthday of Jan Stochel, professor at Jagiellonian University, former head of the Chair of Functional Analysis and a prominent member of the Kraków school of operator theory. In the course of his mathematical career, he has dealt, among other things, with various aspects of functional analysis, single and multivariable operator theory, the theory of moments, the theory of orthogonal polynomials, the theory of reproducing kernel Hilbert spaces, and mathematical aspects of quantum mechanics. [ABSTRACT FROM AUTHOR]

Background: Children with Down syndrome often engage in contextually inappropriate social behavior, which researchers suggest may function to escape from difficult activities to preferred social interactions. Caregivers may reinforce the behavior, perceiving it only as evidence of the child's social strength, when, in fact, the pattern may also prevent or slow the development of critical skills. Unlike overt forms of challenging behavior, contextually inappropriate social behavior had never been subjected to experimental analysis. Aims: The purpose of the current study was to identify and demonstrate functional control of contextually inappropriate social behavior to caregiver-informed contingencies. Method and Procedures: We interviewed caregivers and subjected contextually inappropriate social behavior to functional analyses for nine young children with Down syndrome. Outcomes and Results: We found sensitivity to the caregiver-informed contingencies for all nine participants with strong functional control and large effect sizes for most. Conclusions and Implications: Caregivers may not perceive contextually inappropriate social behavior as problematic, yet patterns of contextually inappropriate and other problem behaviors suggest decreased engagement and poor task persistence. Assessments that lead to intervention decisions may be more informative when they include questions about social topographies of behavior not typically considered as problematic. Once caregivers are aware of the pattern, they may be better prepared to intervene. [ABSTRACT FROM AUTHOR]

Background: WOX genes are a class of plant-specific transcription factors. The WUSCHEL-related homeobox (WOX) family is a member of the homeobox transcription factor superfamily. Previous studies have shown that WOX members play important roles in plant growth and development. However, studies of the WOX gene family in blueberry plants have not been reported. Results: In order to understand the biological function of the WOX gene family in blueberries, bioinformatics were used methods to identify WOX gene family members in the blueberry genome, and analyzed the basic physical and chemical properties, gene structure, gene motifs, promoter cis-acting elements, chromosome location, evolutionary relationships, expression pattern of these family members and predicted their functions. Finally, 12 genes containing the WOX domain were identified and found to be distributed on eight chromosomes. Phylogenetic tree analysis showed that the blueberry WOX gene family had three major branches: ancient branch, middle branch, and WUS branch. Blueberry WOX gene family protein sequences differ in amino acid number, molecular weight, isoelectric point and hydrophobicity. Predictive analysis of promoter cis-acting elements showed that the promoters of the VdWOX genes contained abundant light response, hormone, and stress response elements. The VdWOX genes were induced to express in both stems and leaves in response to salt and drought stress. Conclusions: Our results provided comprehensive characteristics of the WOX gene family and important clues for further exploration of its role in the growth, development and resistance to various stress in blueberry plants. [ABSTRACT FROM AUTHOR]

Methods for functional analysis of proteins specifically localizing to lipid monolayers such as rubber particles and lipid droplets are limited. We have succeeded in establishing a system in which artificially prepared lipid monolayer particles are added to a cell-free translation system to confirm the properties of proteins that specifically bind to lipid monolayers in a translation-coupled manner. [ABSTRACT FROM AUTHOR]

Functional genes encode various biological functions required for the life activities of organisms. By analyzing the functional genes of edible and medicinal fungi, varieties of edible and medicinal fungi can be improved to enhance their agronomic traits, growth rates, and ability to withstand adversity, thereby increasing yield and quality and promoting industrial development. With the rapid development of functional gene research technology and the publication of many whole-genome sequences of edible and medicinal fungi, genes related to important biological traits have been mined, located, and functionally analyzed. This paper summarizes the advantages and disadvantages of different functional gene research techniques and application examples for edible and medicinal fungi; systematically reviews the research progress of functional genes of edible and medicinal fungi in biological processes such as mating type, mycelium and fruit growth and development, substrate utilization and nutrient transport, environmental response, and the synthesis and regulation of important active substances; and proposes future research directions for functional gene research for edible and medicinal fungi. The overall aim of this study was to provide a valuable reference for further promoting the molecular breeding of edible and medicinal fungi with high yield and quality and to promote the wide application of edible and medicinal fungi products in food, medicine, and industry. [ABSTRACT FROM AUTHOR]

Hemifacial microsomia (HFM) is a rare congenital genetic syndrome primarily affecting the first and second pharyngeal arches, leading to defects in the mandible, external ear, and middle ear. The pathogenic genes remain largely unidentified. Whole-exome sequencing (WES) was conducted on 12 HFM probands and their unaffected biological parents. Predictive structural analysis of the target gene was conducted using PSIPRED (v3.3) and SWISS-MODEL, while STRING facilitated protein-to-protein interaction predictions. CRISPR/Cas9 was applied for gene knockout in zebrafish. In situ hybridization (ISH) was employed to examine the spatiotemporal expression of the target gene and neural crest cell (NCC) markers. Immunofluorescence with PH3 and TUNEL assays were used to assess cell proliferation and apoptosis. RNA sequencing was performed on mutant and control embryos, with rescue experiments involving target mRNA injections and specific gene knockouts. CDC27 was identified as a novel candidate gene for HFM, with four nonsynonymous de novo variants detected in three unrelated probands. Structural predictions indicated significant alterations in the secondary and tertiary structures of CDC27. cdc27 knockout in zebrafish resulted in craniofacial malformation, spine deformity, and cardiac edema, mirroring typical HFM phenotypes. Abnormalities in somatic cell apoptosis, reduced NCC proliferation in pharyngeal arches, and chondrocyte differentiation issues were observed in cdc27−/− mutants. cdc27 mRNA injections and cdkn1a or tp53 knockout significantly rescued pharyngeal arch cartilage dysplasia, while sox9a mRNA administration partially restored the defective phenotypes. Our findings suggest a functional link between CDC27 and HFM, primarily through the inhibition of CNCC proliferation and disruption of pharyngeal chondrocyte differentiation. [ABSTRACT FROM AUTHOR]

The process of domestication, despite its short duration as it compared with the time scale of the natural evolutionary process, has caused rapid and substantial changes in the phenotype of domestic animal species. Nonetheless, the genetic mechanisms underlying these changes remain poorly understood. The present study deals with an analysis of the transcriptomes from four brain regions of gray rats (Rattus norvegicus), serving as an experimental model object of domestication. We compared gene expression profiles in the hypothalamus, hippocampus, periaqueductal gray matter, and the midbrain tegmental region between tame domesticated and aggressive gray rats and revealed subdivisions of differentially expressed genes by principal components analysis that explain the main part of differentially gene expression variance. Functional analysis (in the DAVID (Database for Annotation, Visualization and Integrated Discovery) Bioinformatics Resources database) of the differentially expressed genes allowed us to identify and describe the key biological processes that can participate in the formation of the different behavioral patterns seen in the two groups of gray rats. Using the STRING- DB (search tool for recurring instances of neighboring genes) web service, we built a gene association network. The genes engaged in broad network interactions have been identified. Our study offers data on the genes whose expression levels change in response to artificial selection for behavior during animal domestication. [ABSTRACT FROM AUTHOR]

Congenital hyperinsulinism (CHI; OMIM: 256450) is characterized by persistent insulin secretion despite severe hypoglycemia. The most common causes are variants in the ATP‐binding cassette subfamily C member 8(ABCC8) and potassium inwardly‐rectifying channel subfamily J member 11(KCNJ11) genes. These encode ATP‐sensitive potassium (KATP) channel subunit sulfonylurea receptor 1 (SUR1) and inwardly rectifying potassium channel (Kir6.2) proteins. A 7‐day‐old male infant presented with frequent hypoglycemic episodes and was clinically diagnosed with CHI, underwent trio‐whole‐exome sequencing, revealing compound heterozygous ABCC8 variants (c.307C>T, p.His103Tyr; and c.3313_3315del, p.Ile1105del) were identified. In human embryonic kidney 293 (HEK293) and rat insulinoma cells (INS‐1) transfected with wild‐type and variant plasmids, KATP channels formed by p.His103Tyr were delivered to the plasma membrane, whereas p.Ile1105del or double variants (p.His103Tyr coupled with p.Ile1105del) failed to be transported to the plasma membrane. Compared to wild‐type channels, the channels formed by the variants (p.His103Tyr; p.Ile1105del) had elevated basal [Ca2+]i, but did not respond to stimulation by glucose. Our results provide evidence that the two ABCC8 variants may be related to CHI owing to defective trafficking and dysfunction of KATP channels. [ABSTRACT FROM AUTHOR]

Laminaripentaose (L5)‐producing β‐1,3‐glucanases can preferentially cleave the triple‐helix curdlan into β‐1,3‐glucooligosaccharides, especially L5. In this study, a newly identified member of the glycoside hydrolase family 64, β‐1,3‐glucanase from Streptomyces pratensis (SpGlu64A), was functionally and structurally characterized. SpGlu64A shared highest identity (30%) with a β‐1,3‐glucanase from Streptomyces matensis. The purified SpGlu64A showed maximal activity at pH 7.5 and 50 °C, and exhibited strict substrate specificity toward curdlan (83.1 U·mg−1). It efficiently hydrolyzed curdlan to produce L5 as the end product. The overall structure of SpGlu64A consisted of a barrel domain and a mixed (α/β) domain, which formed an unusually wide groove with a crescent‐like structure. In the two complex structures (SpGlu64A–L3 and SpGlu64A–L4), two oligosaccharide chains were captured and the triple‐helical structure was relatively compatible with the wide groove, which suggested the possibility of binding to the triple‐helical β‐1,3‐glucan. A catalytic framework (β6–β9–β10) and the steric hindrance formed by the side chains of residues Y161, N163, and H393 in the catalytic groove were predicted to complete the exotype‐like cleavage manner. On the basis of the structure, a fusion protein with the CBM56 domain (SpGlu64A–CBM) and a mutant (Y161F; by site‐directed mutation) were obtained, with 1.2‐ and 1.7‐fold increases in specific activity, respectively. Moreover, the combined expression of SpGlu64A–CBM and ‐Y161F improved the enzyme activity by 2.63‐fold. The study will not only be helpful in understanding the reaction mechanism of β‐1,3‐glucanases but will also provide a basis for further enzyme engineering. [ABSTRACT FROM AUTHOR]

Understanding factors that influence the efficacy of functional communication training has both practical and conceptual benefits. The current study extended research in this area by exploring data from 95 consecutive applications of functional communication training with extinction across two independent clinics. We selected candidate predictor variables based on conceptual analysis, conducted preliminary exploratory analyses, and then selectively applied quantitative methods that are used in precision medicine to examine their accuracy and predictive utility. Treatment outcomes were better when challenging behavior was maintained by a single function than they were when it was maintained by multiple functions; however, these differences were most apparent among cases with an escape function. We also analyzed within‐session responding to explore the potential influence of unprogrammed establishing operations on decrements in treatment efficacy. Our within‐session measure only distinguished responders from nonresponders when escape was one of the multiple functions. Additional research is needed to validate these findings with an independent sample and to address a number of clinical conceptual issues. [ABSTRACT FROM AUTHOR]

Caspase-8, a member of the caspase family, is an initiating caspase and plays a crucial role in apoptosis. In this study, the full-length cDNA of caspase8-like (CASP8-like) was isolated from Crassostrea hongkongensis (C. hongkongensis) by RACE-PCR. ChCASP8-like contained a 1599-bp open reading frame (ORF) encoding 533 amino acids with two conserved death effector domains (DEDs) and a cysteine aspartase cysteine structural domain (CASc). Amino acid sequence comparison showed that ChCASP8-like shared the highest identity (85.4%) with CASP8-like of C. angulata. The tissue expression profile showed that ChCASP8-like was constitutively expressed in gills, hepatopancreas, mantle, adductor muscle, hemocytes and gonads, and was significantly upregulated in hemocytes, hepatopancreas and gills under hyper-salinity stress. The apoptosis-related genes, including ATR, CHK1, BCL-XL, CASP8-like, CASP9 and CASP3, were significantly activated by hyper-salinity stress, but were remarkably inhibited by ChCASP8-like silencing. The caspase 8 activity was increased by 1.7-fold after hyper-salinity stress, and was inhibited by 9.4% by ChCASP8-like silencing. Moreover, ChCASP8-like silencing clearly alleviated the apoptosis resulting from hyper-salinity stress. These results collectively demonstrated that ChCASP8-like played a crucial role in inducing apoptosis against hyper-salinity stress. [ABSTRACT FROM AUTHOR]

Genetic variation facilitates the evolution, environmental adaptability, and biodiversity of organisms. Danish Large White (LW) pigs have more desirable phenotypes compared with local Chinese pigs, which have difficulty adapting to the modern swine industry. However, the genome-wide mutational differences between these pig breeds are yet to be evaluated. Therefore, this study aimed to evaluate genomic variation and identify breed-specific SNPs in Danish LW pigs. Here, 43 LW, 15 Diqing Tibetan (DQZ), and 15 Diannan small-ear (DN) pigs whose genomes were re-sequenced with 5× depth were selected. This was followed by a conjoined analysis of our previous resequencing data of 24 Anqing six-end white (AQ) and six Asian wild (SS) pigs. In total, 39,158,378 SNPs and 13,143,989 insertion–deletions were obtained in all breeds. The variation number of LW pigs was the lowest, with 287,194 breed-specific and 1289 non-synonymous SNPs compared with Chinese breeds. Functional analysis of the breed-specific non-synonymous SNPs indicated that these mutations were mainly associated with the reproductive performance, feed intake, and feed conversion ratio of LW pigs. These findings provide a theoretical basis for genetic improvements in the Chinese swine industry. [ABSTRACT FROM AUTHOR]

To investigate the role of candidate genes for salt–alkali tolerance in cucumber (Cucumis sativus L.), this study screened CsTAU1 in the glutathione pathway from previous transcriptome data for cloning and functional analysis. Clone cucumber CsTAU1 contains one 675 bp open reading frame, containing one GST-N-Tau domain and one GST-C-Tau domain, and is expressed in cytoplasm. After successfully constructing overexpression vectors of CsTAU1 (+) and CsTAU1 (−), they were transferred into cucumber varieties 'D1909' (high salt alkali resistance) and 'D1604' (low salt alkali resistance) for salt–alkali resistance identification. It was found that under salt–alkali stress, CsTAU1 (+)-overexpressing plants showed strong resistance to salt–alkali stress, while CsTAU1 (−)-overexpressing plants showed the opposite situation. qRT-PCR analysis was performed on other glutathione pathway-related genes in CsTAU1-overexpressing plants. The expression patterns of LOC101219529 and LOC105434443 were the same as CsTAU1, and the introduction of CsTAU1 (+) increased the chlorophyll, α-Naphthylamine oxidation, glutathione S-transferase (GST), and catalase (CAT) content of cucumber. The research results provide a theoretical basis for cultivating salt–alkali-tolerant cucumber varieties. [ABSTRACT FROM AUTHOR]

The ionic toxicity induced by salinization has adverse effects on the growth and development of crops. However, researches on ionic toxicity and salt tolerance in plants have focused primarily on cations such as sodium ions (Na+), with very limited studies on chloride ions (Cl−). Here, we cloned the homologous genes of Arabidopsis thaliana AtCLCc, GhCLCc-1A/D, from upland cotton (Gossypium hirsutum), which were significantly induced by NaCl or KCl treatments. Subcellular localization showed that GhCLCc-1A/D were both localized to the tonoplast. Complementation of Arabidopsis atclcc mutant with GhCLCc-1 rescued its salt-sensitive phenotype. In addition, the silencing of the GhCLCc-1 gene led to an increased accumulation of Cl− in the roots, stems, and leaves of cotton seedlings under salt treatments, resulting in compromised salt tolerance. And ectopic expression of the GhCLCc-1 gene in Arabidopsis reduced the accumulation of Cl− in transgenic lines under salt treatments, thereby enhancing salt tolerance. These findings elucidate that GhCLCc-1 positively regulates salt tolerance by modulating Cl− accumulation and could be a potential target gene for improving salt tolerance in plants. [ABSTRACT FROM AUTHOR]

This study utilized 16S rRNA high-throughput sequencing technology to analyze the community structure and function of endophytic bacteria within the roots of three plant species in the vanadium–titanium–magnetite (VTM) mining area. The findings indicated that mining activities of VTM led to a notable decrease in both the biodiversity and abundance of endophytic bacteria within the root systems of Eleusine indica and Carex (p < 0.05). Significant reductions were observed in the populations of Nocardioides, concurrently with substantial increments in the populations of Pseudomonas (p < 0.05), indicating that Pseudomonas has a strong adaptability to this environmental stress. In addition, β diversity analysis revealed divergence in the endophytic bacterial communities within the roots of E. indica and Carex from the VTM mining area, which had diverged to adapt to the environmental stress caused by mining activity. Functional enrichment analysis revealed that VTM mining led to an increase in polymyxin resistance, nicotinate degradation I, and glucose degradation (oxidative) (p < 0.05). Interestingly, we found that VTM mining did not notably alter the endophytic bacterial communities or functions in the root systems of Dodonaea viscosa, indicating that this plant can adapt well to environmental stress. This study represents the primary investigation into the influence of VTM mining activities on endophytic bacterial communities and the functions of nearby plant roots, providing further insight into the impact of VTM mining activities on the ecological environment. [ABSTRACT FROM AUTHOR]