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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]

Abstract White striping (WS) is a myopathy of growing concern to the turkey industry. It is rising in prevalence and has negative consequences for consumer acceptance and the functional properties of turkey meat. The objective of this study was to conduct a genome-wide association study (GWAS) and functional analysis on WS severity. Phenotypic data consisted of white striping scored on turkey breast fillets (N = 8422) by trained observers on a 0–3 scale (none to severe). Of the phenotyped birds, 4667 genotypic records were available using a proprietary 65 K single nucleotide polymorphism (SNP) chip. The SNP effects were estimated using a linear mixed model with a 30-SNP sliding window approach used to express the percentage genetic variance explained. Positional candidate genes were those located within 50 kb of the top 1% of SNP windows explaining the most genetic variance. Of the 95 positional candidate genes, seven were further classified as functional candidate genes because of their association with both a significant gene ontology and molecular function term. The results of the GWAS emphasize the polygenic nature of the trait with no specific genomic region contributing a large portion to the overall genetic variance. Significant pathways relating to growth, muscle development, collagen formation, circulatory system development, cell response to stimulus, and cytokine production were identified. These results help to support published biological associations between WS and hypoxia and oxidative stress and provide information that may be useful for future-omics studies in understanding the biological associations with WS development in turkeys.

Abstract Background Soil salinity is one of the primary environmental stresses faced in rice production. When plants are exposed to salt stress, a series of cellular balances will be disrupted. Dufulin is an immune-induced antiviral agent used in plants. The DUF gene family influences plant response to abiotic stress, and the functional role of OsDUF6(ABA98726.1) in rice response to salt stress is being investigated here. Results Based on the transcriptome analysis of Dufulin treatment in inducing salt tolerance in rice, we selected the OsDUF6 protein located on the cell membrane and studied its molecular function by overexpressing OsDUF6. Salt-induced decreases in root, stem, and leaf length and increased leaf yellowing rate and Na+ concentration in the wild-type plant were mitigated in the overexpressed lines. OsDUF6 overexpression increased the enzymatic antioxidant activities of superoxide dismutase, peroxidase, catalase, and phenylalanine ammonia-lyase. OsDUF6 also played a positive role in Na+ transport as reflected by the increased growth of a salt-sensitive yeast mutant complemented with OsDUF6 in the presence of salt stress. In addition, Reverse transcription quantitative PCR analysis confirmed that the overexpression of OsDUF6 significantly changed the expression level of other genes related to growth and stress tolerance. Conclusions Combined with previously published data, our results supported the observation that OsDUF6 is an important functional factor in Dufulin-induced promotion of salt stress tolerance in rice.

Abstract Background Dates contain various minerals that are essential for good health. The major RNA interference (RNAi) gene families play a vital role in plant growth and development by controlling the expression of protein-coding genes against different biotic and abiotic stresses. However, these gene families for date palm are not yet studied. Therefore, this study has explored major RNAi genes and their characteristics in date palm. Results We have identified 4 PdDCLs, 7 PdAGOs, and 3 PdRDRs as RNAi proteins from the date palm genome by using AtRNAi genes as query sequences in BLASTp search. Domain analysis of predicted RNAi genes has revealed the Helicase_C, Dicer_dimer, PAZ, RNase III, and Piwi domains that are associated with the gene silencing mechanisms. Most PdRNAi proteins have been found in the nucleus and cytosol associated with the gene silencing actions. The gene ontology (GO) enrichment analysis has revealed some important GO terms including RNA interference, dsRNA fragmentation, and ribonuclease_III activity that are related to the protein-coding gene silencing mechanisms. Gene regulatory network (GRN) analysis has identified PAZ and SNF2 as the transcriptional regulators of PdRNAi genes. Top-ranked 10 microRNAs including Pda-miR156b, Pda-miR396a, Pda-miR166a, Pda-miR167d, and Pda-miR529a have been identified as the key post-transcriptional regulators of PdRNAi genes that are associated with different biotic/abiotic stresses. The cis-acting regulatory element analysis of PdRNAi genes has detected some vital cis-acting elements including ABRE, MBS, MYB, MYC, Box-4, G-box, I-box, and STRE that are linked with different abiotic stresses. Conclusion The results of this study might be valuable resources for the improvement of different characteristics in date palm by further studies in wet-lab.

Abstract Background By analyzing the proteins which are the workhorses of biological systems, metaproteomics allows us to list the taxa present in any microbiota, monitor their relative biomass, and characterize the functioning of complex biological systems. Results Here, we present a new strategy for rapidly determining the microbial community structure of a given sample and designing a customized protein sequence database to optimally exploit extensive tandem mass spectrometry data. This approach leverages the capabilities of the first generation of Quadrupole Orbitrap mass spectrometer incorporating an asymmetric track lossless (Astral) analyzer, offering rapid MS/MS scan speed and sensitivity. We took advantage of data-dependent acquisition and data-independent acquisition strategies using a peptide extract from a human fecal sample spiked with precise amounts of peptides from two reference bacteria. Conclusions Our approach, which combines both acquisition methods, proves to be time-efficient while processing extensive generic databases and massive datasets, achieving a coverage of more than 122,000 unique peptides and 38,000 protein groups within a 30-min DIA run. This marks a significant departure from current state-of-the-art metaproteomics methodologies, resulting in broader coverage of the metabolic pathways governing the biological system. In combination, our strategy and the Astral mass analyzer represent a quantum leap in the functional analysis of microbiomes. Video Abstract

My main goal here is to develop a functional analysis of cheating and corruption in sports, and to differentiate cheating within the broader category of corruption. Whereas officials can act corruptly, they cannot cheat. In contrast, sports participants, since they occupy two roles, can do both. I argue that although acts of cheating are acts of corruption, not all corrupt acts by competitors are acts of cheating. I also respond to some skeptical challenges and criticisms of the concept of 'cheating' by providing some opposing arguments and a provisional definition. I argue that cheating in sports occurs in the context of a complex institutional practice. It transpires due to some failing in the efforts and/or limitations of sports officials to prohibit it. In central cases it consists in both the functional and ethical violation of the constitutional norms of a sport in the service of obtaining unearned victory for the cheater. [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]

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]

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]

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]

• 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]

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]

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]

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]

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]

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: Class III peroxidases (PODs) perform crucial functions in various developmental processes and responses to biotic and abiotic stresses. However, their roles in wheat seed dormancy (SD) and germination remain elusive. Results: Here, we identified a wheat class III POD gene, named TaPer12-3A, based on transcriptome data and expression analysis. TaPer12-3A showed decreasing and increasing expression trends with SD acquisition and release, respectively. It was highly expressed in wheat seeds and localized in the endoplasmic reticulum and cytoplasm. Germination tests were performed using the transgenic Arabidopsis and rice lines as well as wheat mutant mutagenized with ethyl methane sulfonate (EMS) in Jing 411 (J411) background. These results indicated that TaPer12-3A negatively regulated SD and positively mediated germination. Further studies showed that TaPer12-3A maintained H2O2 homeostasis by scavenging excess H2O2 and participated in the biosynthesis and catabolism pathways of gibberellic acid and abscisic acid to regulate SD and germination. Conclusion: These findings not only provide new insights for future functional analysis of TaPer12-3A in regulating wheat SD and germination but also provide a target gene for breeding wheat varieties with high pre-harvest sprouting resistance by gene editing technology. [ABSTRACT FROM AUTHOR]

White striping (WS) is a myopathy of growing concern to the turkey industry. It is rising in prevalence and has negative consequences for consumer acceptance and the functional properties of turkey meat. The objective of this study was to conduct a genome-wide association study (GWAS) and functional analysis on WS severity. Phenotypic data consisted of white striping scored on turkey breast fillets (N = 8422) by trained observers on a 0–3 scale (none to severe). Of the phenotyped birds, 4667 genotypic records were available using a proprietary 65 K single nucleotide polymorphism (SNP) chip. The SNP effects were estimated using a linear mixed model with a 30-SNP sliding window approach used to express the percentage genetic variance explained. Positional candidate genes were those located within 50 kb of the top 1% of SNP windows explaining the most genetic variance. Of the 95 positional candidate genes, seven were further classified as functional candidate genes because of their association with both a significant gene ontology and molecular function term. The results of the GWAS emphasize the polygenic nature of the trait with no specific genomic region contributing a large portion to the overall genetic variance. Significant pathways relating to growth, muscle development, collagen formation, circulatory system development, cell response to stimulus, and cytokine production were identified. These results help to support published biological associations between WS and hypoxia and oxidative stress and provide information that may be useful for future-omics studies in understanding the biological associations with WS development in turkeys. [ABSTRACT FROM AUTHOR]

Oxytocin is a neuropeptide associated with both psychological and somatic processes like parturition and social bonding. Although oxytocin homologs have been identified in many species, the evolutionary timeline of the entire oxytocin signaling gene pathway has yet to be described. Using protein sequence similarity searches, microsynteny, and phylostratigraphy, we assigned the genes supporting the oxytocin pathway to different phylostrata based on when we found they likely arose in evolution. We show that the majority (64%) of genes in the pathway are 'modern'. Most of the modern genes evolved around the emergence of vertebrates or jawed vertebrates (540 - 530 million years ago, 'mya'), including OXTR, OXT and CD38. Of those, 45% were under positive selection at some point during vertebrate evolution. We also found that 18% of the genes in the oxytocin pathway are 'ancient', meaning their emergence dates back to cellular organisms and opisthokonta (3500–1100 mya). The remaining genes (18%) that evolved after ancient and before modern genes were classified as 'medium-aged'. Functional analyses revealed that, in humans, medium-aged oxytocin pathway genes are highly expressed in contractile organs, while modern genes in the oxytocin pathway are primarily expressed in the brain and muscle tissue. A study on the evolution of the oxytocin system illustrates the varied role of this neuropeptide in physiology and behavior [ABSTRACT FROM AUTHOR]

Breast cancer (BC) is the most common cancer among women with high morbidity and mortality. Therefore, new research is still needed for biomarker detection. GSE101124 and GSE182471 datasets were obtained from the Gene Expression Omnibus (GEO) database to evaluate differentially expressed circular RNAs (circRNAs). The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) databases were used to identify the significantly dysregulated microRNAs (miRNAs) and genes considering the Prediction Analysis of Microarray classification (PAM50). The circRNA-miRNA-mRNA relationship was investigated using the Cancer-Specific CircRNA, miRDB, miRTarBase, and miRWalk databases. The circRNA–miRNA–mRNA regulatory network was annotated using Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. The protein-protein interaction network was constructed by the STRING database and visualized by the Cytoscape tool. Then, raw miRNA data and genes were filtered using some selection criteria according to a specific expression level in PAM50 subgroups. A bottleneck method was utilized to obtain highly interacted hub genes using cytoHubba Cytoscape plugin. The Disease-Free Survival and Overall Survival analysis were performed for these hub genes, which are detected within the miRNA and circRNA axis in our study. We identified three circRNAs, three miRNAs, and eighteen candidate target genes that may play an important role in BC. In addition, it has been determined that these molecules can be useful in the classification of BC, especially in determining the basal-like breast cancer (BLBC) subtype. We conclude that hsa_circ_0000515/miR-486-5p/SDC1 axis may be an important biomarker candidate in distinguishing patients in the BLBC subgroup of BC. [ABSTRACT FROM AUTHOR]

Dragon fruit peel, often discarded, is a valuable source of commercial pectin. This study investigates different extraction methods, including cold-water (CW), hot-water (HW), ultrasound (US), and novel enzyme extraction (xylanase: EZX), to extract pectins from dragon fruit peel and compare their characteristics. The pectin yield ranged from 10.93% to 20.22%, with significant variations in physicochemical properties across methods (p < 0.05). FTIR analysis revealed that extraction methods did not alter the primary structural configuration of the pectins. However, molecular weights (Mws) varied significantly, from 0.84 to 1.21 × 103 kDa, and the degree of esterification varied from 46.82% to 51.79% (p < 0.05). Monosaccharide analysis identified both homogalacturonan (HG) and rhamnogalacturonan-I (RG-I) pectic configurations in all pectins, predominantly comprising galacturonic acid (77.21–83.12 %mol) and rhamnose (8.11–9.51 %mol), alongside minor side-chain sugars. These properties significantly influenced pectin functionalities. In the aqueous state, a higher Mw impacted viscosity and emulsification performance, while a lower Mw enhanced antioxidant activities and promoted the prebiotic function of pectin (Lactis brevies growth). This study highlights the impact of extraction methods on dragon fruit peel pectin functionalities and their structure–function relationship, providing valuable insights into predicting dragon fruit peel's potential as a food-grade ingredient in various products. [ABSTRACT FROM AUTHOR]

Objective: Endothelial specific molecule-1 (ESM1) is implicated as an oncogene in multiple human cancers. However, the function of ESM1 in papillary thyroid cancer (PTC) is not well understood. The current study aimed to investigate the effect of ESM1 on the growth, migration, and invasion of PTC to provide a novel perspective for PTC treatment. Methods: The expression levels of ESM1 in PTC tissues form 53 tumor tissue samples and 59 matching adjacent normal tissue samples were detected by immunohistochemical analysis. Knockdown of ESM1 expression in TPC-1 and SW579 cell lines was established to investigate its role in PTC. Moreover, cell proliferation, apoptosis, wound healing, and transwell assays were conducted in vitro to assess cell proliferation, migration and invasion. Results: The findings revealed that ESM1 expression was significantly higher in PTC tissues than that found in paraneoplastic tissues (P<0.0001). Knockdown of ESM1 expression inhibited the proliferation, migration, and invasion of TPC-1 and SW579 cells in vitro. Compared with the control group, the mRNA and protein levels of ESM1 in PTC cells were significantly reduced following knockdown of its expression (P<0.01). In addition, ESM1-knockdown cells indicated decreased proliferation and decreased migratory and invasive activities (P<0.01, P<0.01, P<0.001, respectively). Conclusions: ESM1 was identified as a major gene in the occurrence and progression of PTC, which could increase the proliferation, migration, and invasion of PTC cells. It may be a promising diagnostic and therapeutic target gene. [ABSTRACT FROM AUTHOR]

Functional analysis methods allow clinicians to determine the variable(s) that maintain destructive behavior. Previous reviews of functional analysis outcomes have included large samples of published and unpublished data sets (i.e., clinical samples). The purpose of this review was to conduct a large retrospective consecutive controlled case series of clinical functional analyses. We sought to identify the prevalence of differentiation, procedural modifications for undifferentiated and differentiated cases, and identified function(s) of destructive behavior. In addition, we extended the existing literature by determining whether functional analysis differentiation and function varied when single or multiple behavior topographies were consequated in the functional analysis. We discuss our findings considering previously published functional analysis reviews, provide avenues for future research, and offer suggestions for clinical practice. [ABSTRACT FROM AUTHOR]

This study examines interpoint distance-based tests for random elements from probability distributions in infinite-dimensional space. Some asymptotic properties such as the limiting distributions and the asymptotic power of the Biswas–Ghosh type test (Biswas and Ghosh in J Multivar Anal 123: 160–171, 2014) are presented using the theory of U-statistic. In addition, the p-value approximation based on the jackknife variance estimators and the Welch–Satterthwaite equation is proposed. Simulation studies are conducted to evaluate the performance of the proposed test statistics in functional data analysis. The proposed tests are shown to have better power than the existing method for functional data in some situations. [ABSTRACT FROM AUTHOR]

Background: Teriparatide, a recombinant parathyroid hormone, is pivotal in osteoporosis treatment, particularly in post-surgical recovery for hip fractures. This study investigates its efficacy in functional recovery post-hip fracture surgery in elderly patients, a demographic particularly susceptible to osteoporotic fractures. Methods: In this retrospective cohort study, 150 elderly patients with proximal femoral fractures undergoing open reduction and internal fixation were enrolled. They were categorized into two groups: receiving 20 µg of daily teriparatide injections for 18 months and receiving standard antiresorptive medications during a 24-month follow-up. Detailed records of patient demographics, Fracture Risk Assessment Tool scores, and comorbidities were kept. Key outcomes, including bone mineral density (BMD) and functional scores (Barthel Index and Visual Analog Scale for hip pain), were evaluated at 3 and 24 months post-surgery. Results: Out of the original cohort, 126 patients (20 men and 106 women with an average age of 85.5 ± 9.3 years) completed the study. The teriparatide group exhibited significant enhancements in both functional scores and BMD when compared to the control group. Notably, functional improvements were less pronounced in male patients compared to female patients. Additionally, the incidence of new fractures was markedly lower in the teriparatide group. Conclusion: Administering teriparatide daily for 18 months post-surgery for proximal femoral fractures significantly benefits very elderly patients by improving functionality and bone density, with observed differences in recovery between genders. These results reinforce the efficacy of teriparatide as a potent option for treating osteoporosis-related fractures in the elderly and highlight the importance of considering gender-specific treatment and rehabilitation strategies. [ABSTRACT FROM AUTHOR]

Cryptococcus neoformans has been designated as critical fungal pathogens by the World Health Organization, mainly due to limited treatment options and the prevalence of antifungal resistance. Consequently, the utilization of novel antifungal agents is crucial for the effective treatment of C. neoformans infections. This study exposed that the minimum inhibitory concentration (MIC) of isobavachalcone (IBC) against C. neoformans H99 was 8 µg/mL, and IBC dispersed 48-h mature biofilms by affecting cell viability at 16 µg/mL. The antifungal efficacy of IBC was further validated through microscopic observations using specific dyes and in vitro assays, which confirmed the disruption of cell wall/membrane integrity. RNA-Seq analysis was employed to decipher the effect of IBC on the C. neoformans H99 transcriptomic profiles. Real-time quantitative reverse transcription PCR (RT-qPCR) analysis was performed to validate the transcriptomic data and identify the differentially expressed genes. The results showed that IBC exhibited various mechanisms to impede the growth, biofilm formation, and virulence of C. neoformans H99 by modulating multiple dysregulated pathways related to cell wall/membrane, drug resistance, apoptosis, and mitochondrial homeostasis. The transcriptomic findings were corroborated by the antioxidant analyses, antifungal drug sensitivity, molecular docking, capsule, and melanin assays. In vivo antifungal activity analysis demonstrated that IBC extended the lifespan of C. neoformans-infected Caenorhabditis elegans. Overall, the current study unveiled that IBC targeted multiple pathways simultaneously to inhibit growth significantly, biofilm formation, and virulence, as well as to disperse mature biofilms of C. neoformans H99 and induce cell death. [ABSTRACT FROM AUTHOR]

Scientifically validating the value of rural heritage and exploring construction wisdom has emerged as a significant challenge in the study of rural settlements worldwide. Rural heritage shows significant differences according to the natural environment, history, culture, and socio-economic factors. However, the assessment of the authenticity and effectiveness of heritage values have yet to be quantified due to the difficulty in obtaining evidence directly from samples. By constructing a multi-dimensional model of villages for quantitative analysis, we proposed a multifaceted spatial visibility analysis method based on individual and combined defense structures to empirically study the remains of eight towers in Moluo village, western China. This study demonstrated that towers serve as regional defense structures and are essential for constructing a comprehensive and effective visual defensive system (VDS) in Moluo village, a typical military defense village. The effectiveness and coverage of the towers vary depending on their location, height, type, and other factors. They form a complementary and synergistic relationship, playing a dual mechanism of public and private, local and overall defense. In summary, this method enables the feasible quantification and analysis of the functional value of rural heritage through landscape visual analysis. It provides a new perspective for studying the authenticity of heritage functions. [ABSTRACT FROM AUTHOR]

Background: Ruminal microbial communities enriched on lignocellulosic biomass have shown considerable promise for the discovery of microorganisms and enzymes involved in digesting cell wall compounds, a key bottleneck in the development of second-generation biofuels and bioproducts, enabling a circular bioeconomy. Cardoon (Cynara cardunculus) is a promising inedible energy crop for current and future cellulosic biorefineries and the emerging bioenergy and bioproducts industries. The rumen microbiome can be considered an anaerobic "bioreactor", where the resident microbiota carry out the depolymerization and hydrolysis of plant cell wall polysaccharides (PCWPs) through the catalytic action of fibrolytic enzymes. In this context, the rumen microbiota represents a potential source of microbes and fibrolytic enzymes suitable for biofuel production from feedstocks. In this study, metatranscriptomic and 16S rRNA sequencing were used to profile the microbiome and to investigate the genetic features within the microbial community adherent to the fiber fractions of the rumen content and to the residue of cardoon biomass incubated in the rumen of cannulated cows. Results: The metatranscriptome of the cardoon and rumen fibre-adherent microbial communities were dissected in their functional and taxonomic components. From a functional point of view, transcripts involved in the methanogenesis from CO2 and H2, and from methanol were over-represented in the cardoon-adherent microbial community and were affiliated with the Methanobrevibacter and Methanosphaera of the Euryarchaeota phylum. Transcripts encoding glycoside hydrolases (GHs), carbohydrate-binding modules (CBMs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), and glycoside transferases (GTs) accounted for 1.5% (6,957) of the total RNA coding transcripts and were taxonomically affiliated to major rumen fibrolytic microbes, such as Oscillospiraceae, Fibrobacteraceae, Neocallimastigaceae, Prevotellaceae, Lachnospiraceae, and Treponemataceae. The comparison of the expression profile between cardoon and rumen fiber-adherent microbial communities highlighted that specific fibrolytic enzymes were potentially responsible for the breakdown of cardoon PCWPs, which was driven by specific taxa, mainly Ruminococcus, Treponema, and Neocallimastigaceae. Conclusions: Analysis of 16S rRNA and metatranscriptomic sequencing data revealed that the cow rumen microbiome harbors a repertoire of new enzymes capable of degrading PCWPs. Our results demonstrate the feasibility of using metatranscriptomics of enriched microbial RNA as a potential approach for accelerating the discovery of novel cellulolytic enzymes that could be harnessed for biotechnology. This research contributes a relevant perspective towards degrading cellulosic biomass and providing an economical route to the production of advanced biofuels and high-value bioproducts. [ABSTRACT FROM AUTHOR]

Bats are efficient reservoirs of a number of viruses with zoonotic potential, and are involved directly in the transmission cycle of many zoonoses. In the present study, which is part of a larger project that is documenting the viromes of the bat species found in the Mid-North states of Maranhão and Piauí, we analyzed 16 pooled samples obtained from four species of bat of the genus Artibeus—Artibeus obscurus, Artibeus cinereus, Artibeus lituratus and Artibeus planirostris. We describe and identify a Hepatovirus, denominated Hepatovirus H isolate sotense, which was found in a pool of internal organs (liver and lungs) extracted from a specimen of A. planirostris, a frugivorous bat, collected in the Cerrado biome of Maranhão state. This material was analyzed using new generation sequencing, which produced a contig of 7390 nucleotides and presented a degree of identity with a number of existing Hepatovirus sequences available for bats (amino acid identity of 61.5% with Bat hepatovirus C of Miniopterus cf. manavi, 66.6% with Bat hepatovirus G of Coleura afra, 67.4% with Hepatovirus G2 of Rhinolophus landeri, and 75.3% with Hepatovirus H2 of Rhinolophus landeri). The analysis of the functional domains of this contig confirmed a pattern consistent with the characteristics of the genus Hepatovirus (Picornaviridae). In the phylogenetic tree with several other Hepatovirus species, this genome also grouped in a monophyletic clade with Hepatovirus H (HepV-H1; HepV-H2, and HepV-H3) albeit on an external branch, which suggests that it may be a distinct genotype within this species. This is the first isolate of Hepatovirus H identified in bats from South America, and represents an important discovery, given that most studies of viruses associated with bats in the state of Maranhão have focused on the family Rhabdoviridae. [ABSTRACT FROM AUTHOR]

Background: Dendrobium huoshanense, a traditional medicinal and food plant, has a rich history of use. Recently, its genome was decoded, offering valuable insights into gene function. However, there is no comprehensive gene functional analysis platform for D. huoshanense. Result: To address this, we created a platform for gene function analysis and comparison in D. huoshanense (DhuFAP). Using 69 RNA-seq samples, we constructed a gene co-expression network and annotated D. huoshanense genes by aligning sequences with public protein databases. Our platform contained tools like Blast, gene set enrichment analysis, heatmap analysis, sequence extraction, and JBrowse. Analysis revealed co-expression of transcription factors (C2H2, GRAS, NAC) with genes encoding key enzymes in alkaloid biosynthesis. We also showcased the reliability and applicability of our platform using Chalcone synthases (CHS). Conclusion: DhuFAP (www.gzybioinformatics.cn/DhuFAP) and its suite of tools represent an accessible and invaluable resource for researchers, enabling the exploration of functional information pertaining to D. huoshanense genes. This platform stands poised to facilitate significant biological discoveries in this domain. [ABSTRACT FROM AUTHOR]

【Objective】MYB305 as a member of the MYB R2R3 subfamily, plays an important role in plant nectary development, nectar protein expression, starch accumulation and hydrolysis, and flavonoid synthesis. Therefore, it is of great significance to study the expression profile and function of MYB305 for the molecular mechanism study of Liriodendron tulipifera floral nectary.【Method】Having floral nectary of nectariferous plant L. tulipifera as materials, the anthocyanidin content in five stages of floral nectary was detected by spectrophotometry, LtMYB305 gene was cloned via RACE（rapid-amplification of cDNA ends）technology, and relative expressions among different tissues were analyzed by RT-qPCR assay. Then, subcellular localization of LtMYB305 protein was verified using tobacco leaves as materials, and the function of LtMYB305 gene was studied by genetic transformation approaches of wild type Arabidopsis thaliana（col）.【Result】The anthocyanidin in the nectaries of L. tulipifera was accumulated from the late expanding stage, increased sharply at the early flowering stage, and reached the highest of 27.14 μg/g at the withering stage, which was consistent with the process of nectar secretion and coloring. The full-length of LtMYB305 was 931 bp encoding 198 amino acids and its protein was hydrophilic and non-transmembrane. LtMYB305 was expressed highly only in the nectary of L. tulipifera at anthesis stage, and hardly in other tissues. LtMYB305 protein was localized in the nucleus. After the overexpression of LtMYB305, the nectary groove of the lateral nectary disappeared and deepened, the expressions of AtMYB30, AtPIN, AtSWEET9 genes related to flower nectary were up-regulated, and the expressions of AtCRC, AtBOP1/2, AtMYB21, AtSWEET3/4/7 genes were down-regulated.【Conclusion】 The LtMYB305 has typical characteristics of transcription factor and is involved to the nectary development in L. tulipifera. [ABSTRACT FROM AUTHOR]

Microplastics are widespread pollutants, but few studies have linked field prevalence in organisms to laboratory uptakes. Aquatic filter feeders may be particularly susceptible to microplastic uptake, with the potential for trophic transfer to higher levels, including humans. Here, we surveyed microplastics from a model freshwater shrimp, common caraidina (Caridina nilotica) inhabiting the Crocodile River in South Africa to better understand microplastic uptake rates per individual. We then use functional response analysis (feeding rate as a function of resource density) to quantify uptake rates by shrimps in the laboratory. We found that microplastics were widespread in C. nilotica, with no significant differences in microplastic abundances among sampled sites under varying land uses, with an average abundance of 6.2 particles per individual. The vast majority of microplastics found was fibres (86.1%). Shrimp microplastic accumulation patterns were slightly higher in the laboratory than the field, where shrimp exhibited a hyperbolic Type II functional response model under varying exposure concentrations. Maximum feeding rates of 20 particles were found over a 6 h feeding period, and uptake evidenced at even the lowest laboratory concentrations (~10 particles per mL). These results highlight that microplastic uptake is widespread in field populations and partly density dependent, with field concentrations corroborating uptake rates recorded in the laboratory. Further research is required to elucidate trophic transfer from these taxa and to understand potential physiological impacts. [ABSTRACT FROM AUTHOR]

This paper is dedicated to the memory of the esteemed Serbian mathematician Slaviša B. Prešić (1933–2008). The primary aim of this survey paper is to compile articles on Prešić-type mappings published since 1965. Additionally, it introduces a novel class of symmetric contractions known as Prešić–Menger and Prešić–Ćirić–Menger contractions, thereby enriching the literature on Prešić-type mappings. The paper endeavors to furnish young researchers with a comprehensive resource in functional and nonlinear analysis. The relevance of Prešić's method, which generalizes Banach's theorem from 1922, remains significant in metric fixed point theory, as evidenced by recent publications. The overview article addresses the growing importance of Prešić's approach, coupled with new ideas, reflecting the ongoing advancements in the field. Additionally, the paper establishes the existence and uniqueness of fixed points in Menger spaces, contributing to the filling of gaps in the existing literature on Prešić's works while providing valuable insights into this specialized domain. [ABSTRACT FROM AUTHOR]

This paper deals with a singular two dimensional initial boundary value problem for a Caputo time fractional parabolic equation supplemented by Neumann and non-local boundary conditions. The well posedness of the posed problem is demonstrated in a fractional weighted Sobolev space. The used method based on some functional analysis tools has been successfully showed its efficiency in proving the existence, uniqueness and continuous dependence of the solution upon the given data of the considered problem. More precisely, for proving the uniqueness of the solution of the posed problem, we established an energy inequality for the solution from which we deduce the uniqueness. For the existence, we proved that the range of the operator generated by the considered problem is dense. [ABSTRACT FROM AUTHOR]

Osteoarthritis (OA) is a degenerative joint disease, causing impaired mobility. There are currently no effective therapies other than palliative treatment. Mesenchymal stromal cells (MSCs) and their secreted extracellular vesicles (MSC-EVs) have shown promise in attenuating OA progression, promoting chondral regeneration, and modulating joint inflammation. However, the precise molecular mechanism of action driving their beneficial effects has not been fully elucidated. In this study, we analyzed MSC-EV-treated human OA chondrocytes (OACs) to assess viability, proliferation, migration, cytokine and catabolic protein expression, and microRNA and mRNA profiles. We observed that MSC-EV-treated OACs displayed increased metabolic activity, proliferation, and migration compared to the controls. They produced decreased proinflammatory (Il-8 and IFN-γ) and increased anti-inflammatory (IL-13) cytokines, and lower levels of MMP13 protein coupled with reduced expression of MMP13 mRNA, as well as negative microRNA regulators of chondrogenesis (miR-145-5p and miR-21-5p). In 3D models, MSC-EV-treated OACs exhibited enhanced chondrogenesis-promoting features (elevated sGAG, ACAN, and aggrecan). MSC-EV treatment also reversed the pathological impact of IL-1β on chondrogenic gene expression and extracellular matrix component (ECM) production. Finally, MSC-EV-treated OACs demonstrated the enhanced expression of genes associated with cartilage function, collagen biosynthesis, and ECM organization and exhibited a signature of 24 differentially expressed microRNAs, associated with chondrogenesis-associated pathways and ECM interactions. In conclusion, our data provide new insights on the potential mechanism of action of MSC-EVs as a treatment option for early-stage OA, including transcriptomic analysis of MSC-EV-treated OA, which may pave the way for more targeted novel therapeutics. [ABSTRACT FROM AUTHOR]

Meso-diaminopimelate dehydrogenase (meso-DAPDH) from Corynebacterium glutamicum ATCC13032 (CgDAPDH) is a type I meso-DAPDH that shows obvious preference toward meso-diaminopimelate (meso-DAP) and exhibits almost no amination activity toward 2-keto acids. There are seven distinct conserved insertions and deletions (indels) between type I and type II meso-DAPDH. The current functional analysis of indels is not comprehensive in meso-DAPDH. Continuing from our previous work on these indels, we first examined the functions of the other indels shown as insertion residues in type I CgDAPDH. Alanine mutations in M216, T240, K289, and Q290 lost at least 40% of their activity, highlighting the importance of these four sites in CgDAPDH. Molecular dynamic analysis indicated that the four non-active sites altered the dynamic network of interactions within the protein. Subsequently, these four sites together with the previously identified indel-related residues R180, L176, and H193 were targeted by site-saturation mutagenesis to improve the amination ability of CgDAPDH toward pyruvic acid. The most significant improvement was observed with the mutant CgL176R, which showed a six-fold increase toward pyruvic acid in kcat/Km compared to wild-type CgDAPDH. Overall, our study provides new hotspots and ideas for the subsequent protein engineering of CgDAPDH, which may also be applied to other meso-DAPDHs. [ABSTRACT FROM AUTHOR]

This document is a special issue of the journal Axioms titled "Topology and Functional Analysis" in honor of María Jesús Chasco's 65th birthday. It includes papers on topological groups, topological semi-groups, and topological vector spaces, highlighting the interaction between topology and functional analysis. The papers cover various topics such as factorization of groups into thin subsets, extensions of characters defined on subgroups, distinguished subgroups of compact Abelian groups, preservation of min-subgroup structure under aggregation functions, bounded sets in topological spaces subject to the action of a monoid, and the distinguished property in tensor products and weak* dual spaces. María Jesús Chasco is recognized for her contributions to mathematics, particularly in the field of duality in topological groups. [Extracted from the article]

Simple Summary: Mating behavior plays a crucial role in the survival and reproduction of insect populations. The fruitless (fru) gene, recognized for regulating male mating behaviors in Drosophila melanogaster, acts as a central "tuner", shaping courtship behavior through sex-specific expression patterns within the courtship neural circuit. While fru homologs and sex-specific isoforms have been identified in other holometabolan insects, controlling mating behavior, hemimetabolous insects show the generation of non-sex-specific mRNAs by the fru gene, suggesting potential functional differences. This study focuses on fru homologs (Nlfru) in the Hemiptera species Nilaparvata lugens, utilizing RNAi-mediated knockdown to explore Nlfru functions in male mating behavior and tissue development. Our research contributes to understanding the regulation of mating behavior in N. lugens and sheds light on the evolution of the fru gene across insect species. The fruitless (fru) gene functions as a crucial "tuner" in male insect courtship behavior through distinct expression patterns. In Nilaparvata lugens, our previous research showed doublesex (dsx) influencing male courtship songs, causing mating failures with virgin females. However, the impact of fru on N. lugens mating remains unexplored. In this study, the fru homolog (Nlfru) in N. lugens yielded four spliceosomes: Nlfru-374-a/b, Nlfru-377, and Nlfru-433, encoding proteins of 374aa, 377aa, and 433aa, respectively. Notably, only Nlfru-374b exhibited male bias, while the others were non-sex-specific. All NlFRU proteins featured the BTB conserved domain, with NlFRU-374 and NlFRU-377 possessing the ZnF domain with different sequences. RNAi-mediated Nlfru or its isoforms' knockdown in nymph stages blocked wing-flapping behavior in mating males, while embryonic knockdown via maternal RNAi resulted in over 80% of males losing wing-flapping ability, and female receptivity was reduced. Nlfru expression was Nldsx-regulated, and yet courtship signals and mating success were unaffected. Remarkably, RNAi-mediated Nlfru knockdown up-regulated the expression of flightin in macropterous males, which regulated muscle stiffness and delayed force response, suggesting Nlfru's involvement in muscle development regulation. Collectively, our results indicate that Nlfru functions in N. lugens exhibit a combination of conservation and species specificity, contributing insights into fru evolution, particularly in Hemiptera species. [ABSTRACT FROM AUTHOR]

Human and viral microRNAs (miRNAs) are involved in the regulation of gene transcription, and the establishment of their profiles in acute (AHI) and chronic (CHI) HIV infections may shed light on the pathogenetic events related to different phases of HIV disease. Next-generation sequencing (NGS) of miRNA libraries was performed, and the reads were used to analyze miRNA differential expression in the plasma with AHI and CHI. Functional analysis was then undertaken to investigate the biological processes characterizing the two phases of HIV infection. Except for hsa-miR-122-5p, which was found in 3.39% AHI vs. 0.18% CHI, the most represented human miRNAs were similarly represented in AHI and CHI. However, when considering the overall detected miRNAs in AHI and CHI, 15 displayed differential expression (FDR p < 0.05). Functional analysis identified 163 target mRNAs involved in promoting angiogenesis activation in AHI versus CHI through the action of hsa-miR10b-5p, hsa-miR1290, hsa-miR1-3p, and hsa-miR296-5p. The viral miRNAs detected, all belonging to herpesviruses, accounted for only 0.014% of total reads. The present data suggest that AHI patients exhibit strong innate immune activation through the upregulation of hsa-miR-122-5p and early activation of angiogenesis. More specific investigations are needed to study the role of viral miRNAs in HIV pathogenesis. [ABSTRACT FROM AUTHOR]

Bacterial–algal interactions strongly influence marine ecosystems. Bacterial communities in cultured dinoflagellates of the family Symbiodiniaceae have been characterized by metagenomics. However, little is known about whole‐genome analysis of marine bacteria associated with these dinoflagellates. We performed in silico analysis of four bacterial genomes from cultures of four dinoflagellates of the genera Symbiodinium, Breviolum, Cladocopium and Durusdinium. Comparative analysis showed that the former three contain the alphaproteobacterial family Parvibaculaceae and that the Durusdinium culture includes the family Sphingomonadaceae. There were no large genomic reductions in the alphaproteobacteria with genome sizes of 2.9–3.9 Mb, implying they are not obligate intracellular bacteria. Genomic annotations of three Parvibaculaceae detected the gene for diacetylchitobiose deacetylase (Dac), which may be involved in the degradation of dinoflagellate cell surfaces. They also had metabolic genes for dissimilatory nitrate reduction to ammonium (DNRA) in the nitrogen (N) cycle and cobalamin (vitamin B12) biosynthetic genes in the salvage pathway. Those three characters were not found in the Sphingomonadaceae genome. Predicted biosynthetic gene clusters for secondary metabolites indicated that the Parvibaculaceae likely produce the same secondary metabolites. Our study suggests that the Parvibaculaceae is a major resident of Symbiodiniaceae cultures with antibiotics. [ABSTRACT FROM AUTHOR]

Introduction: Asthma is a common chronic inflammatory respiratory disease worldwide. The long non-coding RNA (lncRNA) BCYRN1 has been shown to function in the inhibition of smooth muscle cell differentiation and vascular development, but its function and potential molecular mechanisms of lncRNA BCYRN1 in bronchial smooth muscle cells (BSMCs) in asthma remain unknown. Methods: Quantitative real-time polymerase chain reaction (RT-qPCR) was performed to detect the expression level of lncRNA BCYRN1 in blood and sputum of asthma patients. The effects of lncRNA BCYRN1 on the proliferation and migration of BSMCs were explored by cell counting kit-8, Transwell, colony formation, and flow cytometry analysis. Differentially expressed genes between lncRNA BCYRN1 overexpression and knockdown cells were identified using RNA-seq and verified using RT-qPCR. Results: LncRNA BCYRN1 was upregulated in asthma patients. Overexpression of lncRNA BCYRN1 significantly promoted the proliferation and migration of BSMCs, inhibited cell apoptosis and affected cell cycle arrest, promoting DNA replication. These effects were reversed after lncRNA BCYRN1 inhibition. RNA-seq identified 434 common differentially expressed genes in the lncRNA BCYRN1 overexpression and knockdown groups and verified their expression levels by RT-qPCR. Gene ontology, Kyoto Encyclopedia of Genes and Genomes and Gene set enrichment analysis indicated that these genes were mainly involved in external stimulus, cell cycle, growth factor activity, cytokine interactions, and inflammatory response. Conclusion: The identification of the highly expressed lncRNA BCYRN1 in patients with asthma, combined with functional experiments and transcriptional data, suggests that lncRNA BCYRN1 can mediate the development of asthma and can be used as a promising diagnostic and prognostic biomarker for asthma. Plain Language Summary: Asthma is a common chronic inflammatory respiratory disease worldwide. The lncRNA BCYRN1 has been shown to function in the inhibition of smooth muscle cell differentiation and vascular development, but its function and potential molecular mechanisms of lncRNA BCYRN1 in bronchial smooth muscle cells (BSMCs) in asthma remain unknown. In this study, the expression of lncRNA BCYRN1 was found to be upregulated in the blood and sputum of patients with asthma. Cell counting kit-8, colony formation and flow cytometric analysis revealed that overexpression of lncRNA BCYRN1 significantly promoted the proliferation and migration of BSMCs, inhibited cell apoptosis and affected cell cycle arrest, promoting DNA replication. These effects were reversed after lncRNA BCYRN1 inhibition. RNA-seq identified 434 common differentially expressed genes in the lncRNA BCYRN1 overexpression and knockdown groups, and verified their expression levels by RT-qPCR. Gene ontology, Kyoto Encyclopedia of Genes and Genomes and Gene set enrichment analysis indicated that these genes were mainly involved in external stimulus, cell cycle, growth factor activity, cytokine interactions, and inflammatory response. The identification of the highly expressed lncRNA BCYRN1 in patients with asthma, combined with functional experiments and transcriptional data, suggests that lncRNA BCYRN1 can mediate the development of asthma and can be used as a promising diagnostic and prognostic biomarker for asthma. [ABSTRACT FROM AUTHOR]

Apicomplexan parasites are aetiological agents of numerous diseases in humans and livestock. Functional genomics studies in these parasites enable the identification of biological mechanisms and protein functions that can be targeted for therapeutic intervention. Recent improvements in forward genetics and whole‐genome screens utilising CRISPR/Cas technology have revolutionised the functional analysis of genes during Apicomplexan infection of host cells. Here, we highlight key discoveries from CRISPR/Cas9 screens in Apicomplexa or their infected host cells and discuss remaining challenges to maximise this technology that may help answer fundamental questions about parasite–host interactions. [ABSTRACT FROM AUTHOR]