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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]

• 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]

Calving interval (CI) measures the number of days between two consecutive calves of the same cow, and previous studies based on phenotype and pedigree data reported low heritability for this trait. However, the genetic architecture of CI in the Nellore breed was not evaluated based on genomic data. Thus, this study aimed to estimate the heritability based on genomic data and carry out a genome-wide association study (GWAS) for CI in the Nellore breed, using 12,599 pedigree records, 5078 CI records, and 3818 animals genotyped with 50k SNPchip panel. Both quality control and GWAS were performed in BLUPF90 family packages, which use the single-step genomic best linear unbiased predictor (ssGBLUP) method. The average CI was 427.6 days, with a standard deviation of 106.9 and a total range of 270–730 days. The heritability estimate was 0.04 ± 0.04. The p-values of GWAS analysis resulted in a genomic inflation factor (lambda) of 1.08. The only significant SNP (rs136725686) at the genome-wide level (p-value = 1.53E-06) was located on BTA13. Other 19 SNPs were significant at the chromosome-wide level, distributed on BTA1, 2, 3, 6, 10, 13, 14, 17, 18, 22, and 26. Functional annotation analysis found thirty-six protein-coding genes, including genes related to cell cycle (RAD21 , BCAR3), oocyte function (LHX8 , CLPX , UTP23), immune system (TXK , TEC , NFATC2), endocrine function (LRRFIP2 , GPR158), estrous cycle (SLC38A7), and female fertility (CCK , LYZL4 , TRAK1 , FOXP1 , STAC). Therefore, CI is a complex trait with small heritability in Nellore cattle, and various biological processes may be involved with the genetic architecture of CI in Nellore cattle. • This is the first GWAS analysis for the calving interval in a Zebu cattle breed. • GWAS analysis found 20 SNPs associated with calving interval. • 36 protein-coding genes were found near the SNPs associated with calving interval. • Various significant SNPs are in regions where 70 QTLs were previously reported. • Various significant SNPs are in signature selection reported for cattle. [ABSTRACT FROM AUTHOR]

Type III polyketide synthases (type III PKSs) are single homodimeric enzymes that produce diverse products such as phloroglucinol, pyrones, resorcinols and chalcones which are biotechnologically important molecules. In an attempt to identify new type III PKS from extreme environments, the deep-sea sediment metagenome from Bay of Bengal was screened for type III PKS genes. BLASTX analyses of Nanopore sequence derived metagenome with the in-house created PKS database revealed a full length type III PKS from a 5 kb fragment. The annotated full length type III PKS, S9PKS showed 25–30 % sequence identity towards previously characterized enzymes. To functionally characterize the gene, it was synthesized, cloned into pET28a and pColdI vectors under T7 and csp promoters, respectively, and expressed in Escherichia coli Rosetta(DE3) pLysS. The optimized PKS (OptiPKS) was expressed as inclusion bodies under both promoters. The inclusion bodies were successfully solubilised using low concentration of urea, refolded and purified using Ni-NTA Agarose resin. The purified OptiPKS was tested for functionality using fatty acyl-CoA substrates at various temperatures. High performance liquid chromatography (HPLC) analyses revealed that OptiPKS produced tri and tetraketide pyrones using C 4 to C 10 acyl-CoA starter substrates. Further characterization and mutation of the enzyme would reveal its functional significance. Thus, the study could be a lead for the annotation and functional characterization of putative type III PKS from environmental metagenome data. [Display omitted] [ABSTRACT FROM AUTHOR]

The therapeutic response to lithium in patients with bipolar disorder is highly variable and has a polygenic basis. Genome-wide association studies investigating lithium response have identified several relevant loci, though the precise mechanisms driving these associations are poorly understood. We aimed to prioritise the most likely effector gene and determine the mechanisms underlying an intergenic lithium response locus on chromosome 21 identified by the International Consortium on Lithium Genetics (ConLi+Gen). We conducted in-silico functional analyses by integrating and synthesising information from several publicly available functional genetic datasets and databases including the Genotype-Tissue Expression (GTEx) project and HaploReg. The findings from this study highlighted TMPRSS15 as the most likely effector gene at the ConLi+Gen lithium response locus. TMPRSS15 encodes enterokinase, a gastrointestinal enzyme responsible for converting trypsinogen into trypsin and thus aiding digestion. Convergent findings from gene-based lookups in human and mouse databases as well as co-expression network analyses of small intestinal RNA-seq data (GTEx) implicated TMPRSS15 in the regulation of intestinal nutrient absorption, including ions like sodium and potassium, which may extend to lithium. Although the findings from this study indicated that TMPRSS15 was the most likely effector gene at the ConLi+Gen lithium response locus, the evidence was circumstantial. Thus, the conclusions from this study need to be validated in appropriately designed wet-lab studies. The findings from this study are consistent with a model whereby TMPRSS15 impacts the efficacy of lithium treatment in patients with bipolar disorder by modulating intestinal lithium absorption. • TMPRSS15 is a novel regulator of lithium response in patients with bipolar disorder. • It is the most likely effector gene at a known lithium response locus. • The gene encodes enterokinase (ENTK), a key modulator of intestinal absorption. • ENTK likely impacts lithium response through the modulation of lithium absorption. [ABSTRACT FROM AUTHOR]

Environmental pollution has gained negative attention in recent years. The pesticides and heavy metals are top list of environmental toxicants directly endangering the survival and development of Apis cerana cerana. Cyclin-dependent kinases (CDKs) are heteromeric serine/threonine kinases that participate in cell cycle regulation and have a vital role in pesticide and heavy metal stress in Apis cerana cerana. In this experiment, we filtered out CDK8 gene from Apis cerana cerana (AccCDK8) and investigated its functions of pesticide and heavy metals resistance. Sequence analysis indicated that AccCDK8 is highly homologous to multiple CDK8s and contains a highly conserved CDK active site sequence. Phylogenetic analysis showed that AmCDK8 and AccCDK8 were closely related evolutionarily in Apis mellifera. Transcriptome analysis revealed that AccCDK8 expression was differentially affected after exposure to pesticide and heavy metal stresses. This indicates that AccCDK8 has a significant role in the resistance of Apis cerana cerana to pesticide and heavy metal stresses. It has implications for studying the function of CDK in other insects in response to stress. [Display omitted] • Pesticides and heavy metals affect the survival of Apis cerana cerana. • CDK8 takes part in the oxidative stress response of Apis cerana cerana. • CDK8 is involved in the growth and reproduction of Apis cerana cerana. • AccCDK8 plays an important role in pesticide and heavy metals stresses. • We highlight the effects of some pesticides on the health of Apis cerana cerana. [ABSTRACT FROM AUTHOR]

• A total of 3439 DEGs were co-regulated by Cd treatment in cultivar 'F' and 'Z'. • Root cell wall polysaccharide provided protection against Cd and increased the Cd tolerance of kenaf. • Genes involved in antioxidant mechanism and Cd chelation, compartmentalization and efflux of root play key roles in kenaf Cd tolerance. • Cd uptake and transport could be mediated by HcZIP2 in kenaf. Kenaf is considered to have great potential for remediation of heavy metals in ecosystems. However, studies on molecular mechanisms of root Cd accumulation and tolerance are still inadequate. In this study, two differently tolerant kenaf cultivars were selected as materials and the physiological and transcriptomic effects were evaluated under Cd stress. This study showed that 200 µmol/L CdCl 2 treatment triggered the reactive oxygen species (ROS) explosion and membrane lipid peroxidation. Compared with the Cd-sensitive cultivar 'Z', the Cd-tolerant cultivar 'F' was able to resist oxidative stress in cells by producing higher antioxidant enzyme activities and increasing the contents of ascorbic acid (AsA) and glutathione (GSH). The root cell wall of 'F' exhibited higher polysaccharide contents under Cd treatment, providing more Cd-binding sites. There were 3,439 differentially expressed genes (DEGs) that were co-regulated by Cd treatment in two cultivars. Phenylpropanoid biosynthesis and plant hormone signal transduction pathways were significantly enriched by functional annotation analysis. DEGs associated with pectin, cellulose, and hemi-cellulose metabolism were involved in Cd chelation of root cell wall; V-ATPases, ABCC3 and Narmp3 could participated in vacuolar compartmentalization of Cd; PDR1 was responsible for Cd efflux; the organic acid transporters contributed to the absorption of Cd in soil. These genes might have played key roles in kenaf Cd tolerance and Cd accumulation. Moreover, HcZIP2 was identified to be involved in Cd uptake and transport in kenaf. Our findings provide a deeper understanding of the molecular pathways underlying Cd accumulation and detoxification mechanisms in kenaf. [Display omitted] [ABSTRACT FROM AUTHOR]

NEDD4L is a HECT-type E3 ligase that catalyzes the addition of ubiquitin to intracellular substrates such as the cardiac voltage-gated sodium channel, NaV1.5. The intramolecular interactions of NEDD4L regulate its enzymatic activity which is essential for proteostasis. For NaV1.5, this process is critical as alterations in Na+ current is involved in cardiac diseases including arrhythmias and heart failure. In this study, we perform extensive biochemical and functional analyses that implicate the C2 domain and the first WW-linker (1,2-linker) in the autoregulatory mechanism of NEDD4L. Through in vitro and electrophysiological experiments, the NEDD4L 1,2-linker was determined to be important in substrate ubiquitination of NaV1.5. We establish the preferred sites of ubiquitination of NEDD4L to be in the second WW-linker (2,3-linker). Interestingly, NEDD4L ubiquitinates the cytoplasmic linker between the first and second transmembrane domains of the channel (DI-DII) of NaV1.5. Moreover, we design a genetically encoded modulator of NaV1.5 that achieves Na+ current reduction using the NEDD4L HECT domain as cargo of a NaV1.5-binding nanobody. These investigations elucidate the mechanisms regulating the NEDD4 family and furnish a new molecular framework for understanding NaV1.5 ubiquitination. [ABSTRACT FROM AUTHOR]

Seawater is one of the most abundant sources of hydrogen on Earth, so its decomposition for producing hydrogen has a significant advantage. However, because of the presence of high concentration of chloride ion (Cl−) in seawater, it has corrosive effect on the catalyst. Therefore, the exploration and construction of highly robust anticorrosive OER electrocatalyst were studied. Furthermore, this work describes Co 9 S 8 @Ni 3 S 2 /NF as a catalyst, which provides a current density of 100 mA cm−2 with a required overpotential of only 154 mV, with emphasis on their remarkable OER selectivity. The experimental analysis demonstrate that the promotion of Co 9 S 8 @Ni 3 S 2 /NF catalyst activity can be attributed to the construction of heterogeneous interface, the rapid transfer of charge and the exposure of more reaction centers. Density functional theory analysis demonstrates that the Co 9 S 8 material presents greater water adsorption energy, indicating that water preferentially adsorbs on its surface. The introduction of the Ni 3 S 2 electrode greatly promotes the synergistic effect of the Co 9 S 8 @Ni 3 S 2 /NF electrode. It is the synergistic catalysis of these two electrodes that enhances the catalytic activity and selectivity of the materials. The work furnishes a novel idea for the exploration of efficient, environmentally friendly and highly selective electrodes for seawater splitting. This work describes Co 9 S 8 @Ni 3 S 2 /NF as a catalyst, which provides a current density of 100 mA cm−2 with a required overpotential of only 154 mV, with emphasis on their remarkable OER selectivity for seawater splitting. [Display omitted] • Co 9 S 8 @Ni 3 S 2 electrodes was synthesized for the first time through hydrothermal processes. • The overpotential of Co 9 S 8 @Ni 3 S 2 electrode is only 154 m V at 100 mA cm−2 for OER. • Density functional theory analysis demonstrates that the Co 9 S 8 material presents greater water adsorption energy. [ABSTRACT FROM AUTHOR]

[Display omitted] Monoclonal antibodies-based medicines are widely used in the treatment of different diseases. These medicines are very sensitive to exposure to different environmental conditions and their handling in hospitals may affect their safety and efficacy. This is the case for pembrolizumab (Keytruda®, 25 mg/mL), for which there is not yet much information on its risk behaviour associated with routine handling or unintentional mishandling. Here we performed a wider physicochemical and functional analysis of pembrolizumab medicine including controlled degradation studies: heat, freeze/thaw, agitation, accelerated light exposure and high hypertonic solution. After that, the samples were analysed by a set of analytical techniques to evaluated critical quality attributes: Far-UV CD, IT-FS, DLS, RP/UHPLC(UV)-MS, SE/UHPLC(UV), RP/UHPLC(UV)-MS/MS and ELISA. The results provide an in-depth understanding of the biochemical and biophysical properties of pembrolizumab, showing that the medicine is affected by accelerated light exposure and temperature of 60 °C, demonstrated by the detection of non-natural dimers and HMWS. Light exposure also revealed different isoform profile and increase in oxidations. Regarding functionality by means of the interaction antigen–antibody binding, all the stressors promoted a decrease in pembrolizumab capacity to bind to PD-1 receptor, although the biological activity remained still high for all of them, being 60 °C and accelerated light exposure the most affected. [ABSTRACT FROM AUTHOR]

The γ-secretase complexes are intramembrane cleaving proteases involved in the generation of the Aβ peptides in Alzheimer's disease. The complex consists of four subunits, with Presenilin harboring the catalytic site. Here, we study the role of the smallest subunit, PSENEN or Presenilin enhancer 2, encoded by the gene Psenen, in vivo and in vitro. We find a profound Notch deficiency phenotype in Psenen-/- embryos confirming the essential role of PSENEN in the γ-secretase complex. We used Psenen-/- fibroblasts to explore the structure-function of PSENEN by the scanning cysteine accessibility method. Glycine 22 and proline 27, which border the membrane domains 1 and 2 of PSENEN, are involved in complex formation and stabilization of γ-secretase. The hairpin structured hydrophobic membrane domains 1 and 2 are exposed to a water-containing cavity in the complex, while transmembrane domain 3 is not water exposed. We finally demonstrate the essential role of PSENEN for the cleavage activity of the complex. PSENEN is more than a structural component of the γ-secretase complex and might contribute to the catalytic mechanism of the enzyme. [ABSTRACT FROM AUTHOR]

Cystargolides are natural products originally isolated from Kitasatospora cystarginea NRRL B16505 as inhibitors of the proteasome. They are composed of a dipeptide backbone linked to a β-lactone warhead. Recently, we identified the cystargolide biosynthetic gene cluster, but systematic genetic analyses had not been carried out because of the lack of a heterologous expression system. Here, we report the discovery of a homologous cystargolide biosynthetic pathway in Streptomyces durhamensis NRRL-B3309 by genome mining. The gene cluster was cloned via transformation-associated recombination and heterologously expressed in Streptomyces coelicolor M512. We demonstrate that it contains all genes necessary for the production of cystargolide A and B. Single gene deletion experiments reveal that only five of the eight genes from the initially proposed gene cluster are essential for cystargolide synthesis. Additional insights into the cystargolide pathway could be obtained from in vitro assays with CysG and chemical complementation of the respective gene knockout. This could be further supported by the in vitro investigation of the CysG homolog BelI from the belactosin biosynthetic gene cluster. Thereby, we confirm that CysG and BelI catalyze a cryptic SAM-dependent transfer of a methyl group that is critical for the construction of the cystargolide and belactosin β-lactone warheads. [ABSTRACT FROM AUTHOR]

Orphan genes (OGs) are protein-coding genes without a significant sequence similarity in closely related species. Despite their functional importance, very little is known about the underlying molecular mechanisms by which OGs participate in diverse biological processes. Here, we discuss the evolutionary mechanisms of OGs' emergence with relevance to species-specific adaptations. We also provide a mechanistic view of the involvement of OGs in multiple processes, including growth, development, reproduction, and carbon-metabolism-mediated immunity. We highlight the interconnection between OGs and the sucrose nonfermenting 1 (SNF1)-related protein kinases (SnRKs)–target of rapamycin (TOR) signaling axis for phytohormone signaling, nutrient metabolism, and stress responses. Finally, we propose a high-throughput pipeline for OGs' interspecies and intraspecies gene transfer through a transgenic approach for future biotechnological advances. Orphan genes (OGs) are taxonomically restricted, without significant sequence similarities to closely related species; they might have evolved from noncoding sequences via rearrangements or duplication and divergence. OGs from divergent species can interact with conserved regulators – such as sucrose non-fermenting 1 (SNF1)-related protein kinases (SnRKs), nuclear factor Y subunit C4 (NF-YC4) – and display the evolutionarily conserved functions. OGs have been shown to promote growth and development in the carbon metabolism of plants, possibly through the target of rapamycin (TOR)–SnRK1 signaling axis. OGs have been shown to compete with pathogenic effectors for their interaction with central regulators, and thereby participate in a growth–defense trade-off. OGs can retain their function when expressed as transgenes in other species, and can thus be used for biotechnological intervention against various environmental stresses. [ABSTRACT FROM AUTHOR]

To assess taxonomic and functional characteristics of tumor-bearing microbiota and its association with response to neoadjuvant chemoradiation therapy (nCRT) in patients with locally advanced rectal cancer. We performed metagenomic sequencing of biopsy tumoral tissues from 73 patients with locally advanced rectal cancer before nCRT. Patients were classified into poor responders (PR) and good responders (GR) according to response to nCRT. Subsequent investigation of network alteration, key community, microbial biomarkers, and function related to nCRT responses were carried out. The network-driven analysis systematically revealed 2 co-occurring bacteria modules that exhibited opposite relationship with rectal cancer radiosensitivity. In the 2 modules, prominent alteration of global graph properties and community structure was observed between networks of PR and GR group. By quantifying changes in between-group association patterns and abundances, a total of 115 discriminative biomarker species linked to nCRT response were found, and 35 microbial variables were selected to establish the optimal randomForest classifier for nCRT response prediction. It yielded an area under the curve value of 85.5% (95% CI, 73.3%-97.8%) in the training cohort and 88.4% (95% CI, 77.5%-99.4%) in the validation cohort. In a comprehensive consideration, 5 key bacteria showed high relevance with inducing resistance to nCRT, including Streptococcus equinus, Schaalia odontolytica, Clostridium hylemonae, Blautia producta , and Pseudomonas azotoformans. One key hub including several butyrate-formation bacteria involving with driving network alteration from GR to PR indicate that microbiota-derived butyrate may also be involved in reducing the antitumor effects of nCRT, especially Coprococcus. The functional analysis of metagenome linked the nitrate and sulfate-sulfur assimilation, histidine catabolic process, and resistance to cephamycin to the reduced therapeutic response. It also linked to leucine degradation, isoleucine biosynthesis, taurine, and hypotaurine metabolism to the improved response to nCRT. Our data offer novel potential microbial factors and shared metagenome function linked to resistance to nCRT. [ABSTRACT FROM AUTHOR]

• Functional analysis of newly identified RYR1 variants identified in 68 MHS patients or their family members from 8 families, diagnosed by the IVCT was performed. • Our results demonstrate that the 5 newly identified RyR1 variant cause hypersensitivity to RyR1 agonist-mediated calcium release. • According to the EMHG scoring matrix the five genetic variants we investigated can be classified as follows: c.8638G>A (p.E2880K) likely pathogenic, c.11314C>T (p.R3772W) variant of unknown significance, c.11416G>A (p.G3806R), c.14627A>G (p.K4876R) and c.14813T>C (p.I4938T) pathogenic. • Based on the in silico analysis together with our functional tests of the mutations, we propose that the newly characterized RYR1 variants, pathogenic and likely pathogenic, be included in the panel of variants to be used for the molecular diagnosis of MHS. Malignant hyperthermia is a pharmacogenetic disorder triggered by halogenated anesthetic agents in genetically predisposed individuals. Approximately 70 % of these individuals carry mutations in RYR1 , the gene encoding the ryanodine receptor calcium channel of skeletal muscle. In this study, we performed functional analysis of 5 RYR1 variants identified in members from 8 families who had been diagnosed by the IVCT. Of the 68 individuals enrolled in the study, 43 were diagnosed as MHS, 23 as MHN, and 2 individuals were not tested. Here we demonstrate that the 5 RyR1 variants cause hypersensitivity to RyR1 agonist-mediated calcium release. According to the EMHG scoring matrix these five genetic variants can be classified as follows: c.8638G>A (p.E2880K) and c.11314C>T (p.R3772W) likely pathogenic, c.11416G>A (p.G3806R), c.14627A>G (p.K4876R) and c.14813T>C (p.I4938T), pathogenic (RefSeq NM_000540.3). We propose that the newly functionally characterized RYR1 variants, be included in the panel of variants to be used for the molecular diagnosis of MHS. [ABSTRACT FROM AUTHOR]

The purpose of this study was to identify proteins associated with differences in the freezing tolerance of sheep sperm and to analyze their functions. Qualified fresh semen from four breeds of rams, the Australian White, white-head Dorper, Black-head Dorper, and Hu sheep breeds, were selected for cryopreservation. The sperm freezing tolerance was investigated by evaluation of the overall vitality, progressive vitality, and rapidly advance vitality of the sperm. A differential model of sperm freezing tolerance was constructed for sheep breeds showing significant differences. Differentially expressed proteins associated with sperm freezing tolerance were identified using iTRAQ and the protein functions were analyzed. It was found that sperm freezing tolerance was best in Hu sheep and worst in white-head Dorper sheep. These two breeds were used for the construction of a model based on differences in freezing tolerance and the identification of sperm proteins expressed differentially before freezing and after thawing. A total of 128 differentially expressed proteins (88 up-regulated and 40 down-regulated) were identified before freezing and after thawing in Hu sheep sperm (fresh/frozen Hu sheep sperm referred to as HL vs. HF), while 219 differentially expressed proteins (106 up-regulated and 113 down-regulated) were identified in white-head Dorper sheep (fresh/frozen white-head Dorper sheep sperm referred to as WL vs. WF). A comparison of these differentially expressed proteins showed that 57 proteins overlapped between the two breeds while 71 were only expressed in Hu sheep and 162 were only expressed in white-head Dorper sheep. Functional annotation and enrichment analyses of differentially expressed proteins down-regulated in Hu sheep involved in phosphorylation of phosphatidylinositol phosphate kinases, regulation of GTPase activity and glycolysis/gluconeogenesis signaling pathway. Up-regulated proteins of Hu sheep participated in oxidoreductase activity and oxidative phosphorylation process of sperm freezing. Furthermore, down-regulated in white-head Dorper sheep involved in the metabolic regulation of carbohydrate and nuclear sugar metabolism. Up-regulated proteins of white-head Dorper sheep involved in the ferroptosis and oxidative phosphorylation pathways. Collectively, These proteins were found to participate mainly in oxidative phosphorylation as well as phosphorylation and metabolic processes in the mitochondria to affect the freezing tolerance of sheep sperm. • The purpose of this study was to identify proteins associated with differences in freezing tolerance of sheep sperm and analyze their functions. • A differential model of sperm freezing tolerance was constructed for sheep breeds showing significant differences. • It was found that sperm freezing tolerance was best in Hu sheep and worst in white-head Dorper sheep. • Differentially expressed proteins associated with sperm freezing tolerance were identified using iTRAQ and proteins functions were analyzed. [ABSTRACT FROM AUTHOR]

This study aims to define the best method (slow freezing or vitrification) and fragment size (1, 5, or 9 mm³) for prepubertal goat testis cryopreservation, as well as to evaluate testicular morphological integrity after cryopreservation and in vitro culture (IVC). Initially (experiment I), 1, 5, or 9 mm³ testis fragments were cryopreserved by slow freezing using a Mr. Frosty container with 20% Dimethylsulfoxide (DMSO) or vitrified using the Ovarian Tissue Cryosystem (OTC) device, (Equilibration solution – ES: 10% DMSO and 10% ethylene glycol – EG; Vitrification solution - VS: 20% DMSO and 20% EG) and then subjected to morphological analysis, type I and III collagen quantification and gene expression (Oct4, C-kit, Bax, and Bcl-2). Subsequently, (experiment II), fresh or cryopreserved by slow freezing testis fragments were cultured in vitro and submitted to morphological analysis by scanning electron microscopy. The data from the experiment I revealed fewer morphological alterations in 1 and 5 mm³ fragments after vitrification and slow freezing, respectively. The percentage of type I collagen fibers in 5 and 9 mm³ frozen was higher than in fresh or vitrified fragments. For type III collagen, fresh or frozen fragments of 1 and 5 mm3 showed a higher percentage than fragments of 9 mm3. Gene expression for Oct4 and C-kit after slow freezing or vitrification in the 5 mm3 fragments was lower than that observed in the fresh fragments. The Bax:Bcl-2 ratio in the 1 and 9 mm³ fragments was lower than in the 5 mm³ fragments for fresh fragments or after freezing. In experiment II, fragments cultured in vitro, previously frozen or not, showed more morphological alterations than fresh or frozen fragments. We concluded that slow freezing of 5 mm³ fragments was the best protocol for cryopreserving prepubertal goat testis and although the results of IVC are encouraging, it still needs improvement to restore testicular function after cryopreservation. • SF is the appropriate method for cryopreserving prepubertal goat testis. • SF of 5 mm3 fragments its appropriate protocol for cryopreservation of prepubertal goat testis. • Fragments cultured in vitro showed more morphological alterations. [ABSTRACT FROM AUTHOR]

Hereditary antithrombin (AT) deficiency type I causes venous thrombosis due to decreased levels of AT antigen in the blood. We identified one novel and one known abnormal variant in two unrelated Japanese families with venous thrombosis. In this study, we analyzed the mechanism by which these abnormal variants cause type I AT deficiency. Wild-type and variant AT expression vectors were constructed and transiently expressed in human embryonic kidney 293 cells, and AT antigen levels and N -glycosylation of cell lysates and culture medium were evaluated by western blot analysis. Subcellular co-localization of AT was also examined using confocal microscopy, and chase experiments with cycloheximide and MG132 were performed to investigate the degradation pathway of AT variants. Genetic analysis identified a novel variant, c.613delC (p.Leu205Trpfs⁎79), and the known variant c.283T>C (p.Tyr95His). These AT variants exhibited significantly reduced extracellular secretion compared with the wild-type; N -glycosylation of the AT protein was normal. Co-localization analysis suggested that the transport of these abnormal AT proteins to the Golgi apparatus was impaired. The c.613delC variant was degraded early by the proteasome, suggesting that the c.283T>C variant is stored in the endoplasmic reticulum (ER). The AT variants identified here synthesize abnormal AT proteins that exhibit suppressed secretion and impaired transport from the ER to the Golgi apparatus. These results provide clues that could help elucidate the mechanism of type I AT deficiency and facilitate therapy development. • We identified novel and previously reported variants in the SERPINC1 gene. • The two variants, p.L205Wfs⁎79 and p.Y95H, may cause type I antithrombin deficiency. • These abnormal proteins may be inefficiently transported to the Golgi apparatus. • The glycosylation pattern of the p.Y95H variant was similar to that of the wild type. • The p.L205Wfs variant is degraded early in the proteasome. [ABSTRACT FROM AUTHOR]

Several studies in the field of fMRI have reported the synchrony between the brain regions using instantaneous phase (IP) representation (derived from analytic representation of BOLD time series). We hypothesized that instantaneous amplitude (IA) representation from different brain regions might give additional information to the functional brain networks. To validate this, we explored this representation of resting state BOLD fMRI signal for deriving resting state networks (RSNs) and compared it with the IP representation based RSNs. Resting state fMRI data of 100 healthy adults (age=20–35 years, 54 females) from the population of 500 Subjects of HCP dataset were studied. Data was acquired using a 3T scanner in four runs (15-min each) with the phase encoding directions: Left to Right (LR), Right to Left (RL). These four runs were acquired in two sessions, and subjects were asked to keep their eyes open with a fixation on a white cross. The IA and IP representations were derived from a narrow-band filtered BOLD time series using Hilbert transforms and a seed-based approach is used to compute the RSNs in the brain. The experimental results demonstrate that within the frequency range 0.01–0.1 Hz, IA representation based RSNs have the highest similarity score between the two sessions for the motor network. Whereas for fronto-parietal network, IP based activation maps have the highest similarity score for all the frequency bands. For higher frequency band (0.198–0.25 Hz) consistency of the obtained RSNs across two sessions reduced for both IA and IP representations. Fusion of IA and IP representations based RSNs in comparison to those of IP based representation, leads to 3–10% improvement in the similarity scores between the default mode network obtained for the two sessions. In addition, the same comparison demonstrates 15–20% improvement for the motor network in the frequency bands: 0.01–0.04 Hz, 0.04–0.07 Hz, slow5 (0.01–0.027 Hz) and slow-4 (0.027–0.073 Hz). It is also observed that the similarity score between two sessions using instantaneous frequency (IF) (derivative of unwrapped IP) representation in exploring functional connectivity (FC) networks is comparable with those obtained using IP representation. Our findings suggest that IA-representation based measures can estimate RSNs with the reproducibility between the sessions comparable to that of the IP representation-based methods. This study demonstrates that IA and IP representations contain the complementary information of BOLD signal, and their fusion improves the results of FC. • Instantaneous amplitude (IA), Instantaneous frequency (IF), and Instantaneous phase (IP) of brain regions can be explored using a narrowband-filtered BOLD signal. • In this study, we hypothesized that incorporating IA, IF, and IP representations could enhance BOLD fMRI signal-based RSNs analysis. • The experimental results demonstrate that the fusion of the IA and IP functional connectivity maps improves the consistency of the obtained RSNs. [ABSTRACT FROM AUTHOR]

The overwhelming majority of Palaeolithic and Mesolithic sites recorded on the North European Plains are composed exclusively of lithic assemblages. Numerous macro- and microscopic surface trace studies have been conducted with the aim of the identification of micro-wear traces visible on flint tools and the classification of these traces. The main trace categories are related to the main groups of materials processed on the site, like wood, hide, bone, antler or plants. However, it is problematic to take the next step forward and interpret what exactly the flint tool may have been used for. This difficulty can be partially overcome by research of peatbog sites located next to biogenic deposits filling river valleys and lake basins that preserve artefacts made of organic materials. One such site is Dąbki, in northern Poland, on the southern Baltic coastal zone. The paleogeographic context of the site appears to be an island within an ancient lake. Over twenty years of archeological research has led to the recovery of tens of thousands of animal bones, including a rich collection of bone and antler tools. This fortunate circumstance allows us to conduct a microwear study from a reverse perspective: instead of starting with a flint tool and finishing with some general conclusions about what materials were processed, we begun with the analysis of bone and antler tools, describing first the primary activities, techniques and morphology of tools necessary to make a final product. Only later we moved to use-wear analysis describing the traces of bone and antler working observable on flint tools. Together with morphological features distinguished in the course of technological analysis of antler and bone tools it was the foundation for initial selection of flint and stone materials later detailly analyzed microscopically. Basing on this approach, we distinguished specific sets of flint tools used for manufacturing certain categories of bone and antler tools. [ABSTRACT FROM AUTHOR]

Cumulus granulosa cells (CGCs), an important type of ovarian somatic cells, carries out various functions related to oogenesis, follicular development, and steroidogenesis. Studying the biological mechanisms involved in the development and function of CGCs makes a great contribution to understanding the reproductive regulation in female animals. Stanniocalcin-1 (STC1) is an important Ca2+-regulated glycoprotein hormone that exhibits high expression levels in ovaries. In this study, we cloned the coding sequence of the yak STC1 , predicted the structure of STC1 protein, detected the expression and localization of STC1 in yak ovaries, and analyzed the functions of STC1 in yak CGCs. The CDS (coding sequence) region of yak STC1 gene was found to be 744 bp and encoded 247 amino acids. Homology comparison revealed that STC1 protein was highly conserved among mammals. The STC1 mRNA displayed dynamic expression profiles in different stages of yak ovaries, and the highest expression was found in the follicular phase. Regarding localization, STC1 protein was widely distributed in various kinds of yak ovarian cells, including oocytes, mural granulosa cells, CGCs, and thecal cells. Repressing the expression of STC1 resulted in defective proliferation and survival of yak CGCs. In addition, knockdown the expression of STC1 repressed the secretion of progesterone and promoted the secretion of estrogen. Overexpression of STC1 partially rescued the proliferation of CGCs and resulted in opposite effects on the secretion of progesterone and estrogen. Several apoptosis and steroidogenesis-related genes, including BAX , BCL2 , HSD3B1 , HSD17B1, CYP11A1 and CYP17A1 showed altered expressions after repressing or increasing the expression of STC1 in yak CGCs. To the best of our knowledge, this study is the first to focus on the role of STC1 in yak CGCs, and the outcomes offer fresh insights into the mechanism governing yak reproduction. • Cloning the coding sequence of the yak STC1 gene and predicting the structure of STC1 protein. • Identifying the expression and localization of STC1 protein in yak ovaries. • STC1 is essential for the survival and steroidogenesis in yak cumulus granulosa cells. [ABSTRACT FROM AUTHOR]

In recent years, functional analysis of brain networks based on graph theory properties has attracted considerable attention. This approach has usually been exploited for structural and functional brain analysis, while its potential in motor decoding tasks has remained unexplored. This study aimed to investigate the feasibility of using graph-based features in hand direction decoding in movement execution and preparation intervals. Hence, EEG signals were recorded from nine healthy subjects while performing a four-target center-out reaching task. The functional brain network was calculated based on the magnitude-squared coherence (MSC) at six frequency bands. Then, the features based on eight graph theory metrics were extracted from brain networks. The classification was performed with a support vector machine classifier. The results revealed that in four-class direction discrimination, the mean accuracy of the graph-based method surpassed 63% and 53% on movement and pre-movement data, respectively. Additionally, a feature fusion approach that combines the graph theory features with power features was proposed. The fusion method raised the classification accuracy to 70.8% and 61.2% for movement and pre-movement intervals, respectively. This work has verified the feasibility of using graph theory properties and their superiority over band power features in a hand movement decoding task. • Investigating the feasibility of using graph theory analysis in movement decoding. • Both movement and pre-movement intervals were investigated. • Graph theory metrics attain superior results compare to band power features. • The fusion approach of graph metrics with power features led to best results. [ABSTRACT FROM AUTHOR]

Neuroscientific evidence suggests that the pathological symptoms associated with autism spectrum disorders (ASD) are not confined to a single brain region but involve networks of the brain on a larger spatial scale. Analyzing diagrams of edge-edge interactions could provide important perspectives on the organization and function of complex systems. Resting-state fMRI data from 238 ASD patients and 311 healthy controls (HCs) were included in the current study. We used the thalamus as the mediating node to calculate the edge functional connectivity (eFC) of the brain network and compared the ASD subjects and HCs. Compared with the HCs, the ASD subjects exhibited abnormalities in the central node thalamus and four brain regions (amygdala, nucleus accumbens, pallidum and hippocampus), as well as in the eFC formed by the inferior frontal gyrus (IFG) (or middle temporal gyrus (MTG)). In addition, ASD subjects showed variable characteristics of the eFC between nodes in different networks. The changes in these brain regions may be due to the disturbance in the reward system, which leads to coherence in the instantaneous comovement of the functional connections formed by these brain regions in ASD. This notion also reveals a functional network feature between the cortical and subcortical regions in ASD. • Reward system has been shown to be disrupted in autism spectrum disorders (ASD) compared to normal individuals. • However, reward systems are extremely complex and encompass multiple brain regions (especially the thalamus). • Exploring this issue is important to unravel the network characteristics of ASD. • Our study found that the present results provide targets for potential interventions using brain stimulating tools and behavioural training. [ABSTRACT FROM AUTHOR]

Bone retouchers were part of the human toolkit since the Lower Palaeolithic. These tools are essential to the understanding of lithic technology and raw materials exploitation in cultural complexes associated with both Homo neanderthalensis and Homo sapiens. They are also considered to be among the oldest bone tools ever made. On account of their great morphological variability and the lack of any standardised shaping, bone retouchers are often classified as expedient tools rather than as a true bone industry. The present work proposes a new approach to the use-wear study of bone retouchers through the application of 3D imaging microscopy. The results show several advantages in the identification and description of retouch-induced use-wear. The comparison with current methodologies suggests the need to rethink approaches to this bone industry. Through a more in-depth technological and functional study procedure, bone retouchers can potentially play a crucial role in understanding the subsistence strategies of hominin groups throughout the Lower, Middle and Upper Palaeolithic. [ABSTRACT FROM AUTHOR]

The results of traceological (technological and use-wear) studies of osseous artefacts discovered in the Mesolithic burial no 57 and Neolithic burial no 164 from the cemetery in Zvejnieki, Latvia are discussed. This research identified significant differentiation in the techniques used to make animal tooth pendants deposited in the Mesolithic grave and, by contrast, identified relative uniformity in the methods used to make those from the Neolithic grave. In addition, use-wear traces were observed on many of the Mesolithic pendants and were absent from almost all Neolithic ones, indicating the Neolithic examples were probably made for funerary purposes. This research also identified that the bone points from both graves were made in a similar manner and had been used. The technological and functional similarities and differences between the artefacts from the Mesolithic and Neolithic burials are discussed in the context of their probable origin and on observations made on other collections of similar chronology in the region. [ABSTRACT FROM AUTHOR]

In the previous exoskeleton research, the development method of the exoskeleton-function-expectation prediction in the initial design stage is lacking, which is not conducive to reviewing the system-parameter influences on exoskeleton performances, nor to exploring the exoskeleton optimization direction. In this paper, a human-exoskeleton oscillation model is designed by integrating the main functions of one load-supporting exoskeleton in the gravity direction into the double-mass coupled oscillator model. The model simplifies the human-exoskeleton coupling motion into the human-exoskeleton oscillation motion in the gravity direction, and in the oscillation process qualitatively calculates the multiple functional expectations of the exoskeleton, such as the load-supporting capability, the human-exoskeleton interaction force, the oscillation response of the backpack and the power-assistance ability. By comparing the test results of the model with previous research, the model performance was analyzed. And further, the reasons for the unsatisfying load-supporting efficiency of previous exoskeletons were explained and the influences of system parameters for the system expectations were evaluated, which helps to provide a theoretical basis for improving the exoskeleton load-supporting efficiency and human-body comfort. In addition, the combination of the exoskeleton supporting static load and the suspension system buffering dynamic load is a new direction, and the model of the paper is also beneficial to evaluate the interference degree of the exoskeleton to the suspension system. [ABSTRACT FROM AUTHOR]

Bacteria and fungi catabolize plant-derived aromatic compounds by funneling into one of seven dihydroxylated aromatic intermediates, which then undergo ring fission and conversion to TCA cycle intermediates. Two of these intermediates, protocatechuic acid and catechol, converge on β-ketoadipate which is further cleaved to succinyl-CoA and acetyl-CoA. These β-ketoadipate pathways have been well characterized in bacteria. The corresponding knowledge of these pathways in fungi is incomplete. Characterization of these pathways in fungi would expand our knowledge and improve the valorization of ligninderived compounds. Here, we used homology to characterize bacterial or fungal genes to predict the genes involved in the β- ketoadipate pathway for protocatechuate utilization in the filamentous fungus Aspergillus niger.Wefurther used the following approaches to refine the assignment of the pathway genes: whole transcriptome sequencing to reveal genes upregulated in the presence of protocatechuic acid; deletion of candidate genes to observe their ability to grow on protocatechuic acid; determination by mass spectrometry of metabolites accumulated by deletion mutants; and enzyme assays of the recombinant proteins encoded by candidate genes. Based on the aggregate experimental evidence, we assigned the genes for the five pathway enzymes as follows: NRRL3_01405 (prcA) encodes protocatechuate 3,4-dioxygenase; NRRL3_02586 (cmcA) encodes 3-carboxy-cis,cis-muconate cyclase; NRRL3_01409 (chdA) encodes 3-carboxymuconolactone hydrolase/decarboxylase; NRRL3_01886 (kstA) encodes β-ketoadipate:succinyl-CoA transferase; and NRRL3_01526 (kctA) encodes β-ketoadipyl- CoA thiolase. Strain carrying ΔNRRL3_00837 could not grow on protocatechuic acid, suggesting that it is essential for protocatechuate catabolism. Its function is unknown as recombinant NRRL3_00837 did not affect the in vitro conversion of protocatechuic acid to β-ketoadipate. [ABSTRACT FROM AUTHOR]

[Display omitted] • New EEG channel selection method integrating (non) linear functional connectivity (FC). • A generic measure of similarity using kernel matrix from nonlinear manifold learning. • FC changes in Alzheimer's between the occipital and regions along the frontoparietal. • FC changes along the frontoparietal and rest of the EEG are important in Alzheimer's. Dynamical, causal, and cross-frequency coupling analysis using the electroencephalogram (EEG) has gained significant attention for diagnosing and characterizing neurological disorders. Selecting important EEG channels is crucial for reducing computational complexity in implementing these methods and improving classification accuracy. In neuroscience, measures of (dis) similarity between EEG channels are often used as functional connectivity (FC) features, and important channels are selected via feature selection. Developing a generic measure of (dis) similarity is important for FC analysis and channel selection. In this study, learning of (dis) similarity information within the EEG is achieved using kernel-based nonlinear manifold learning. The focus is on FC changes and, thereby, EEG channel selection. Isomap and Gaussian Process Latent Variable Model (Isomap-GPLVM) are employed for this purpose. The resulting kernel (dis) similarity matrix is used as a novel measure of linear and nonlinear FC between EEG channels. The analysis of EEG from healthy controls (HC) and patients with mild to moderate Alzheimer's disease (AD) are presented as a case study. Classification results are compared with other commonly used FC measures. Our analysis shows significant differences in FC between bipolar channels of the occipital region and other regions (i.e. parietal, centro-parietal, and fronto-central) between AD and HC groups. Furthermore, our results indicate that FC changes between channels along the fronto-parietal region and the rest of the EEG are important in diagnosing AD. Our results and its relation to functional networks are consistent with those obtained from previous studies using fMRI, resting-state fMRI and EEG. [ABSTRACT FROM AUTHOR]

• Increased generalised theta with posterior pre-alpha relative power are reproducible findings in Parkinson's Disease. • Functional Data Analysis is a potential tool to overcome potential limitations of epochs averaging in rs-EEG spectral analysis. • Functional Data Analysis constitutes a reliable method to analyse epoch-to-epoch variability of the rs-EEG. This study aims 1) To analyse differences in resting-state electroencephalogram (rs-EEG) spectral features of Parkinson's Disease (PD) and healthy subjects (non-PD) using Functional Data Analysis (FDA) and 2) To explore, in four independent cohorts, the external validity and reproducibility of the findings using both epoch-to-epoch FDA and averaged-epochs approach. We included 169 subjects (85 non-PD; 84 PD) from four centres. Rs-EEG signals were preprocessed with a combination of automated pipelines. Sensor-level relative power spectral density (PSD), dominant frequency (DF), and DF variability (DFV) features were extracted. Differences in each feature were compared between PD and non-PD on averaged epochs and using FDA to model the epoch-to-epoch change of each feature. For averaged epochs, significantly higher theta relative PSD in PD was found across all datasets. Also, higher pre-alpha relative PSD was observed in three of four datasets in PD patients. For FDA, similar findings were achieved in theta, but all datasets showed consistently significant posterior pre-alpha differences across multiple epochs. Increased generalised theta, with posterior pre-alpha relative PSD, was the most reproducible finding in PD. Rs-EEG theta and pre-alpha findings are generalisable in PD. FDA constitutes a reliable and powerful tool to analyse epoch-to-epoch the rs-EEG. [ABSTRACT FROM AUTHOR]

[Display omitted] • Increased low-frequency cross-frequency couplings observed in Alzheimer's cases. • Importance of wide range of cross-frequency interactions is reduced in Alzheimer's cases. • Information integration in Alzheimer's relies on δ - δ , δ - θ and γ - β couplings. • Information segregation in Alzheimer's relies more on the interactions with γ band. • Bispectrum predicts Alzheimer's with higher accuracy (83.39%) than spectrum baseline (79.71%). Alzheimer's disease (AD) is a neurodegenerative disorder known to affect functional connectivity (FC) across many brain regions. Linear FC measures have been applied to study the differences in AD by splitting neurophysiological signals, such as electroencephalography (EEG) recordings, into discrete frequency bands and analysing them in isolation from each other. We address this limitation by quantifying cross-frequency FC in addition to the traditional within-band approach. Cross-bispectrum, a higher-order spectral analysis approach, is used to measure the nonlinear FC and is compared with the cross-spectrum, which only measures the linear FC within bands. This work reports the reconstruction of a cross-frequency FC network where each frequency band is treated as a layer in a multilayer network with both inter- and intra-layer edges. Cross-bispectrum detects cross-frequency differences, mainly increased FC in AD cases in δ - θ coupling. Overall, increased strength of low-frequency coupling and decreased level of high-frequency coupling is observed in AD cases in comparison to healthy controls (HC). We demonstrate that a graph-theoretic analysis of cross-frequency brain networks is crucial to obtain a more detailed insight into their structure and function. Vulnerability analysis reveals that the integration and segregation properties of networks are enabled by different frequency couplings in AD networks compared to HCs. Finally, we use the reconstructed networks for classification. The extra cross-frequency coupling information can improve the classification performance significantly, suggesting an important role of cross-frequency FC. The results highlight the importance of studying nonlinearity and including cross-frequency FC in characterising AD. [ABSTRACT FROM AUTHOR]

Our study introduces a novel approach for examining the functional relationship between the pragmatic marker "you know" and its co-occurring gestures. It draws on 401 instances of "you know" identified in the Nottingham Multimodal Corpus. Based on the speech patterns in the data, a framework of six functions of "you know" was established (i.e., 'editing', 'introducing', 'inviting inferences', 'elaborating', 'marking reported speech', 'approximating'). 74 gestures that primarily co-occur with "you know" were selected for analysis based on a functional framework mainly adopted from Kendon (2004) : pragmatic, referential, beat and deictic gestures. The main results show that three of the functions (i.e., 'editing', 'introducing' and 'elaborating') account for 81% of the whole dataset, and share a similar function of emphasizing the intention of presenting further information. In addition, they tend to co-occur with the pragmatic gestures that embody a similar pragmatic function. The results illustrate the functional coordination between pragmatic markers and gestures, and demonstrate the value of using a multimodal corpus pragmatic approach for exploring the patterns of speech and gesture, and for developing a more nuanced profile of pragmatic markers that, in the history of pragmatics, have largely been described on the sole basis of their speech instantiation. • Our research explores gesture patterns that co-occur with pragmatic markers. • A functional speech-gesture framework of "you know" is established based on speech patterns. • The spoken instantiation of "you know" mainly marks forthcoming information. • The most frequently co-occurring gestures with the spoken instantiation of 'you know' also signal information provision. [ABSTRACT FROM AUTHOR]

Despite efforts to improve targeting accuracy of the dorsolateral prefrontal cortex (DLPFC) as a repetitive transcranial magnetic stimulation (rTMS) target for Major Depressive Disorder (MDD), the heterogeneity in clinical response remains unexplained. We sought to compare the patterns of functional connectivity from the DLPFC treatment site in patients with MDD who were TMS responders to those who were TMS non-responders. Baseline anatomical T1 magnetic resonance imaging (MRI), resting-state functional MRI, and diffusion weighted imaging scans were obtained from 37 participants before they underwent a course of rTMS to left Brodmann area 46. A novel machine learning method was utilized to identify brain regions associated with each item of the Beck's Depression Inventory II (BDI-II), and for 26 participants who underwent rTMS treatment over the left Brodmann area 46, identify regions differentiating rTMS responders and non-responders. Nine parcels of the Human Connectome Project Multimodal Parcellation Atlas matched to at least three items of the Beck's Depression Inventory II (BDI-II) as predictors of response to rTMS, with many in the temporal, parietal and cingulate cortices. Additionally, pre-treatment mapping for 17 items of the BDI-II demonstrated significant variability in symptom to parcel mapping. When parcels associated with symptom presence and symptom resolution were compared, 15 parcels were uniquely associated with resolution (potential targets), and 12 parcels were associated with both symptom presence and resolution (blockers or biomarkers). Machine learning approaches show promise for the development of pathoanatomical diagnosis and treatment algorithms for MDD. Prospective studies are required to facilitate clinical translation. • Novel machine learning was used on MRI scans of individuals with depression. • It was found that Human Connectome Project parcels were found as predictors of response to TMS. • 12 parcels were found to be related to both symptom presence and resolution following TMS. • These could provide insight into new potential symptom-specific targets for TMS. [ABSTRACT FROM AUTHOR]

• We formulated a new class of piecewise impulsive dynamic systems on arbitrary time domain by using the time scales theory. • Study the existence of solutions via fixed point theorems. Also establish the stability results of the considered problem. • Provide some necessary and sufficient conditions for the controllability of the piecewise linear system. • Develop a new class of control function and establish sufficient conditions for the controllability of nonlinear systems. • Some numerical simulations for different time domains are given to verify the proposed theoretical results. The main objective of this article is to establish the existence of solutions, stability, and controllability results for piecewise nonlinear impulsive dynamic systems on an arbitrary time domain. Using the Banach fixed point theorem, we prove the existence of a unique solution while by applying Schauder's fixed point theorem, we prove the existence of at least one solution. Further, we establish the controllability results by converting the controllability problem into a fixed point problem of an operator equation in some suitable function space. Mainly, we used the fixed point theorems, Gramian type matrices, functional analysis, and time scales theory to establish these results. Since the problem is formulated by using the theory of time scales, therefore, the obtained results are true for the continuous-time domain, discrete-time domain, as well as any combination of these two, which shows that the obtained results are non-trivial and generalize the existing ones. In the last, we have given a simulated example for two different time domains to verify the obtained analytical results. [ABSTRACT FROM AUTHOR]

The aims of this study were (1) to identify genomic regions associated with a N efficiency index (NEI) and its composition traits and (2) to analyze the functional annotation of identified genomic regions. The NEI included N intake (NINT1), milk true protein N (MTPN1), milk urea N yield (MUNY1) in primiparous cattle, and N intake (NINT2+), milk true protein N (MTPN2+), and milk urea N yield (MUNY2+) in multiparous cattle (2 to 5 parities). The edited data included 1,043,171 records on 342,847 cows distributed in 1,931 herds. The pedigree consisted of 505,125 animals (17,797 males). Data of 565,049 SNPs were available for 6,998 animals included in the pedigree (5,251 females and 1,747 males). The SNP effects were estimated using a single-step genomic BLUP approach. The proportion of the total additive genetic variance explained by windows of 50 consecutive SNPs (with an average size of about 240 kb) was calculated. The top 3 genomic regions explaining the largest rate of the total additive genetic variance of the NEI and its composition traits were selected for candidate gene identification and quantitative trait loci (QTL) annotation. The selected genomic regions explained from 0.17% (MTPN2+) to 0.58% (NEI) of the total additive genetic variance. The largest explanatory genomic regions of NEI, NINT1, NINT2+, MTPN1, MTPN2+, MUNY1, and MUNY2+ were Bos taurus autosome 14 (1.52–2.09 Mb), 26 (9.24–9.66 Mb), 16 (75.41–75.51 Mb), 6 (8.73–88.92 Mb), 6 (8.73–88.92 Mb), 11 (103.26–103.41 Mb), 11 (103.26–103.41 Mb). Based on the literature, gene ontology, Kyoto Encyclopedia of Genes and Genomes, and protein-protein interaction, 16 key candidate genes were identified for NEI and its composition traits, which are mainly expressed in the milk cell, mammary, and liver tissues. The number of enriched QTL related to NEI, NINT1, NINT2+, MTPN1, and MTPN2+ were 41, 6, 4, 11, 36, 32, and 32, respectively, and most of them were related to the milk, health, and production classes. In conclusion, this study identified genomic regions associated with NEI and its composition traits, and identified key candidate genes describing the genetic mechanisms of N use efficiency-related traits. Furthermore, the NEI reflects not only its composition traits but also the interactions among them. [ABSTRACT FROM AUTHOR]

Polynucleotide kinase 30-phosphatase (PNKP), an essential DNA end-processing enzyme in mammals with 30-phosphatase and 50-kinase activities, plays a pivotal role in multiple DNA repair pathways. Its functional deficiency has been etiologically linked to various neurological disorders. Recent reports have shown that mutation at a conserved glutamine (Gln) in PNKP leads to late-onset ataxia with oculomotor apraxia type 4 (AOA4) in humans and embryonic lethality in pigs. However, the molecular mechanism underlying such phenotypes remains elusive. Here, we report that the enzymatic activities of the mutant versus WT PNKP are comparable; however, cells expressing mutant PNKP and peripheral blood mononuclear cells (PBMCs) of AOA4 patients showed a significant amount of DNA double-strand break accumulation and consequent activation of the DNA damage response. Further investigation revealed that the nuclear localization of mutant PNKP is severely abrogated, and the mutant proteins remain primarily in the cytoplasm. Western blot analysis of AOA4 patientderived PBMCs also revealed the presence of mutated PNKP predominantly in the cytoplasm. To understand the molecular determinants, we identified that mutation at a conserved Gln residue impedes the interaction of PNKP with importin alpha but not with importin beta, two highly conserved proteins that mediate the import of proteins from the cytoplasm into the nucleus. Collectively, our data suggest that the absence of PNKP in the nucleus leads to constant activation of the DNA damage response due to persistent accumulation of doublestrand breaks in the mutant cells, triggering death of vulnerable brain cells--a potential cause of neurodegeneration in AOA4 patients. [ABSTRACT FROM AUTHOR]

The protoplast system is robust and versatile for plant genetic engineering works. There are various ways to deliver nucleic acid materials into the protoplasts, but polyethylene glycol (PEG)-mediated method offers minimal damage compared to others. Therefore, an established PEG-mediated transformation protocol with optimised parameters is needed to improve the system's reproducibility and reliability. This study utilised oil palm mesophyll protoplasts as transformation cells and the red fluorescent protein (DsRED) as a visual reporter. Based on the transformation efficiency scored after 72 h, a method with the following parameters: 5 min incubation in 35% PEG, 10 min incubation with 50 µg DNA, and 90 s heat-shock treatment at 42 °C was found to be the best for oil palm protoplast PEG-mediated transfection. A significant improvement in transformation efficiency at about 56% was achieved using this method compared to the previous study (5%). This newly developed protocol was then used to evaluate the efficiency in terms of the relative strength of 7 promoters, including two plant constitutive promoters, three oil palm constitutive promoters, and two oil palm tissue-specific promoters in regulating the expression of the transgene in oil palm. Based on the results from three individual replicates, CaMV35S showed to be the most efficient amongst the tested promoters in driving the transgene expression in oil palm mesophyll protoplasts, followed by oil palm translationally control tumour protein (TCTP) and maize-ubiquitin (Ubi1) promoters. [Display omitted] • An efficient PEG-mediated transformation of oil palm mesophyll protoplasts. • High transformation efficiency compared to the previous protocol. • A reliable and reproducible oil palm protoplast-based transient gene expression assay. • The CaMV35S promoter was efficient for transgene expression in oil palm protoplasts. [ABSTRACT FROM AUTHOR]

Tempe is a fermented food prepared by fermenting soybeans with Rhizopus species. However, there have recently been concerns about the stable supply of raw soybeans due to global warming and other factors. Moringa is a plant whose cultivation area is expected to expand in the future, and its seeds contain abundant proteins and lipids, and thus could be used as an alternative to soybeans. To develop a novel functional Moringa food, we fermented dehulled Moringa seeds with Rhizopus oligosporus and Rhizopus stolonifer using the solid fermentation method of tempe and investigated changes in the functional components, such as free amino acids and polyphenols, of the respective obtained Moringa tempe Rm and Rs. After 45 h of fermentation, the total content of free amino acids, mainly including gamma-aminobutyric acid and l -glutamic acid, in Moringa tempe Rm was about three times higher, while that in Moringa tempe Rs was almost the same, compared to that in unfermented Moringa seeds. Moreover, after 70 h of fermentation, both Moringa tempe Rm and Rs had approximately four times higher polyphenol content and significantly higher antioxidant activity than did unfermented Moringa seeds. Further, the content of each residual chitin-binding protein of defatted Moringa tempe Rm and Rs was almost the same as that of unfermented Moringa seeds. Taken together, Moringa tempe was rich in free amino acids and polyphenols, exhibited better antioxidant activity, and retained the levels of its chitin-binding proteins, suggesting that Moringa seeds could be used as an alternative to soybean for tempe preparation. [ABSTRACT FROM AUTHOR]

Soybean (Glycine max), a significant oilseed and protein source for humans and livestock feed, needs short day photoperiod for floral induction. Further, soybean has a paleopolyploid genome with multiple copies of flowering genes adding to the complexity of genetic regulation of flowering, and seed set, especially in investigating the role of the noncoding genome. microRNAs, a class of noncoding RNA, play a regulatory role in plant development. miR156 and miR172 are major components of the essential regulatory hub controlling juvenile and vegetative developments and initiation of reproductive phase change leading to flowering. These microRNAs have been originally isolated and studied from model plant, Arabidopsis. However, a study on soybean microRNAs is lacking. We investigated the temporal expression patterns of gma-miR156a and gma-miR172a and found inversely related - gma-miR156a expression was higher in the vegetative stage, and gma-miR172a expression was elevated under inductive flowering conditions. The functions of gma-miR156a and gma-miR172a were evaluated via heterologous expressions in transgenic tobacco plants (Nicotiana tabacum L.). The analysis of overexpression transgenic lines highlighted that gma-miR156a plays a role in juvenile development via repression of the SPL transcription factor family. In contrast, gma-miR172a plays a pivotal role in the reproductive development phase by down-regulating its target genes, AP2. In addition , ectopic expression of gma-miR156a and gma-miR172a affected plant morphology and physiology during plant growth. Collectively, our results suggest that gma-miR156a and gma-miR172a regulate multiple morpho-physiological traits that could be used to enhance crop yield under changing climate conditions. • Ectopic expression of gma-miR156a and gma-miR172a have effects on plant morphology and physiology during plant growth. • Higher expression of gma-miR156 in the vegetative stage. • Elevated expression of gma-miR172 under flowering inductive conditions. • Ectopic expression of gma-miR156a in tobacco plants induced prolonged vegetative phase with juvenile traits in leaves. • gma-miR156a and gma-miR172a are involved in flowering initiation and flower morphological traits. Soybean microRNA module, gma-miR156a and gma-miR172a, modulate floral transition and regulate multiple morpho-physiological traits that could be used to enhance crop yield under changing climate conditions. [ABSTRACT FROM AUTHOR]

Cold and drought stresses are serious problems of strawberry cultivation in temperate and subtropical regions. In the molecular regulation system of cold and drought stresses, ICE transcription factors (TFs) are crucial. In this research, the FvICE1 was isolated from Fragaria vesca 'Hawaii 4' , a bioinformatics analysis was conducted, overexpression vector and CRISPR/cas9 vector were constructed. The results showed that FvICE1 was a member of the bHLH TF family, with a length of 1608 bp, encoding 535 amino acids, and its molecular formula was C 2504 H 3987 N 745 O 811 S 22. By observing the fusion protein 35S-FvICE1-GFP, it was found that FvICE1 was a nuclear protein. The qRT-PCR results demonstrated that FvICE1 was significantly upregulated in different tissues of Fragaria vesca after cold, drought, salt and heat treatments. The wild type (WT) strawberry was selected as the control group, FvICE1 -overexpression strawberries showed high tolerance to cold and drought treatments at the phenotypic and physiological levels. On the contrary, fvice1 mutant strawberries obtained by CRISPR/cas9 editing technology had lower tolerance to cold and drought treatments. Moreover, the expression of FvCBF1 , FvCBF2 , FvCBF3 , FvCOR413 , FvRD22 and FvKIN1 was positively regulated in the FvICE1 -overexpression strawberries and inhibited in fvice1 mutant strawberries. Overall, the current results suggested that FvICE1 functioned as a positively regulator of cold and drought resistances. • Using overexpression and CRISPR/Cas9 technologies to study the function of FvICE1. • FvICE1 was induced by cold, drought, salt and heat stresses. • FvICE1 -overexpression strawberries improved cold and drought stresses tolerance. • FvICE1 mutant strawberries had lower tolerance to cold and drought stresses. [ABSTRACT FROM AUTHOR]

We consider error estimates and post-processing technique of the lowest order Raviart–Thomas mixed finite element method for parabolic problems. A super-convergence of the original unknown and flux is established, which is based on negative norm error estimates. At given time step, we introduce an auxiliary elliptic problem and propose a recovery strategy to obtain one-order higher finite element solutions. Corresponding results are well-known for Lagrange finite element methods for parabolic equations. By using discrete functional analysis tools developed for Discontinuous Galerkin finite element methods, we extend the analyses to the lowest order Raviart–Thomas mixed method and prove second order accuracy of the recovered numerical solutions rigorously. The proposed post-processing technique is suitable on general meshes for both two and three dimensional problems. Numerical results are provided to verify our theoretical analysis and demonstrate the efficiency of the proposed recovery methods. [ABSTRACT FROM AUTHOR]

(E)-β-farnesene (EBF) is a typical and ecologically important infochemical in tri-trophic level interactions among plant-aphid-natural enemies. However, the molecular mechanisms by which parasitoids recognize and utilize EBF are unclear. In this study, we functionally characterized 8 AgifOBPs in Aphidifus gifuensis , one dominant endo -parasitoid of wheat aphid as well as peach aphid in China. Among which, AgifOBP6 was the only OBP upregulated by various doses of EBF, and it showed a strong binding affinity to EBF in vitro. The lack of homology between AgifOBP6 and EBF-binding proteins from aphids or from other aphid natural enemies supported that this was a convergent evolution among insects from different orders driven by EBF. Molecular docking of AgifOBP6 with EBF revealed key interacting residues and hydrophobic forces as the main forces. AgifOBP6 is widely expressed among various antennal sensilla. Furthermore, two bioassays indicated that trace EBF may promote the biological control efficiency of A. gifuensis, especially on winged aphids. In summary, this study reveals an OBP (AgifOBP6) that may play a leading role in aphid alarm pheromone detection by parasitoids and offers a new perspective on aphid biological control by using EBF. These results will improve our understanding of tri-trophic level interactions among plant-aphid-natural enemies. • Nanogram level of E-β-farnesene (EBF) significantly increased the parasitism rate of Aphidifus gifuensis especially to winged aphids. • OBP expression showed strong plasticity to EBF, while only AgifOBP6 consistently upregulated to EBF at all doses in A. gifuensis. • AgifOBP6 is expressed commonly in the wasp sensilla, namely placodea, coeloconica, and trichaidea of antennae. • AgifOBP6 displayed a strong binding affinity with EBF and EBF analog mainly due to the hydrophobic interactions. • EBF binding proteins for aphid and its natural enemy, wasp, had evolved independently along convergent involution. [ABSTRACT FROM AUTHOR]

In contrast to bacterial, yeast and animal systems, topoisomerases (topo) from plants have not been well studied. In this report, we generated four truncated topoisomerase II (Topo II) cDNA fragments encoding different functional domains of Nicotiana tabacum topo II (NtTopoII). Each of these recombinant polypeptides was expressed alone or in combination in temperature-sensitive topoisomerase II yeast mutants. Recombinant NtTopoII with truncated polypeptides fails to target the yeast nuclei and does not rescue the temperature-sensitive phenotype. In contrast complementation was achieved with the full-length NtTopoII, which localized to the yeast nucleus. These observations suggested the presence of a potent nuclear localization signal (NLS) in the extreme C-terminal 314 amino acid residues of NtTopoII that functioned effectively in the heterologous yeast system. Biochemical characterization of purified recombinant full-length and the partial NtTopoII polypeptides revealed that the ATP-binding and hydrolysis region of NtTopoIIwas located at 413 amino acid N-terminal region and this ATPase domain is functional both when it is expressed as a separate polypeptide or as part of the holoenzyme. The present findings also revealed that all NtTopoII truncated polypeptides were detrimental for in vitro supercoiled DNA relaxation and/or DNA nicking and ligation activity. Further, we discuss the possible disruption of coordinated macromolecular interface movements and the dimer interactions in truncated NtTopoII that are required for functional topoisomerase activity. • TopoII evolved by the fusion of ancestral genes encoding different subunits, fully supported by the sequence homology. • In eukaryotes, TopoII enzyme require nuclear targeting sequence to functionally complement TopoII-defective phenotype. • N-terminal ATPase domain retains ATPase active whether it is a part of the holoenzyme or expressed as a separate polypeptide. • The C-terminal (314 AA) of NtTopoII variable region is essential for nuclear localization and also functional in yeast. • Reconstitution of truncated TopoII polypeptides fails to assemble for structurally stable enzyme for transient DNA cleavage. [ABSTRACT FROM AUTHOR]

The green bug Apolygus lucorum is a notorious pest that feeds on multiple crops, including fruit trees, vegetables, and cotton. The odorant-binding proteins (OBPs) are considered to perform crucial roles in regulating A. lucorum behaviors such as mating and feeding. In this study, we first identified OBPs in the A. lucorum genome. Then, we calculated the expression levels of these OBP genes in different tissues and stages. Thereafter, we conducted ligand-binding assay to test the interactions between nine selected AlucOBPs and multiple chemical compounds. The result showed that there were 31 OBP genes encoding 39 transcripts in the A. lucorum genome, and several OBP clusters were found. Comprehensive expression profiling revealed the tissue-specific expression of some OBP genes. The results of fluorescence competitive binding assays showed that these nine AlucOBPs could specifically bind to plant volatiles, nonvolatile compounds, and synthetic analogs thereof. Additionally, AlucOBP19 was suggested to function in gustatory sensing to avoid deleterious plant secondary metabolites, as AlucOBP19 showed high expression in the mouthparts and legs and could interact with quercetin. Our findings highlight the potential biotechnological application of plant volatiles and their synthetic analogs as ecological attractants and provide new gene targets for control of A. lucorum. [ABSTRACT FROM AUTHOR]

Transfer RNAs undergo diverse posttranscriptional modifications to regulate a myriad of cellular events including translation, stress response, and viral replication. These posttranscriptional modifications are synthesized by site-specific modification enzymes. Recent RNA-seq techniques have revealed multiple features of tRNA such as tRNA abundance, tRNA modification, and tRNA structure. Here, we adapt a tRNA-sequencing technique and design a new functional analysis where we perform mutational profiling of tRNA modifications to gain mechanistic insights into how tRNA modification enzymes recognize substrate tRNA. Profiling of Geobacillus stearothermophilus tRNAs and protein orthology analysis predict the existence of natural modifications in 44 tRNA molecular species of G. stearothermophilus. We selected the 1-methyladenosine modification at position 22 (m¹A22) and tRNA (m¹A22) methyltransferase (TrmK) for further analysis. Relative quantification of m1A22 levels in 59 tRNA transcripts by mutational profiling reveals that TrmK selectively methylates a subset of tRNAs. Using 240 variants of tRNALeu transcripts, we demonstrate the conserved nucleosides including U8, A14, G15, G18, G19, U55, Purine57, and A58 are important for the methyl transfer reaction of TrmK. Additional biochemical experiments reveal that TrmK strictly recognizes U8, A14, G18, and U55 in tRNA. Furthermore, these findings from tRNALeu variants were crossvalidated using variants of three different tRNA species. Finally, a model of the TrmK--tRNA complex structure was constructed based on our findings and previous biochemical and structural studies by others. Collectively, our study expands functional analyses of tRNA modification enzyme in a high-throughput manner where our assay rapidly identifies substrates from a large pool of tRNAs. [ABSTRACT FROM AUTHOR]

Fatty acyl-CoA reductases (FARs) catalyze the synthesis of fatty alcohols from corresponding fatty acid precursors in organisms. However, the function of FARs in insect fecundity and embryogenesis remains largely unclear. Here, a total of 22 putative FAR proteins were identified in the brown planthopper Nilaparvata lugens , a hemipteran insect pest of rice, and most of them were highly expressed in embryonic stages. Among them, NlFAR10 was specifically and highly expressed in the later embryogenesis, but was promiscuously expressed in tissues of adults. The heterologously expressed NlFAR10 was able to produce the intermediate fatty acid alcohols from the corresponding acyl-CoA precursors. When NlFAR10 was silenced through RNAi in vivo, the embryogenesis was obviously inhibited, resulting in low hatching rates. Moreover, the metabolome analyses indicated that loss of NlFAR10 affected lipid metabolism and purine metabolism during embryogenesis. To the best of our knowledge, this is the first report of a FAR member affecting insect embryogenesis, thus providing a new target for future pest management. [ABSTRACT FROM AUTHOR]

Silicon (Si) has crucial effects on plant development and stress resistance. Silicon transporters regulate Si absorption, transport, and distribution in plants. In this study, we identified and characterized the Si transporter gene family of moso bamboo (Phyllostachys edulis) and cloned seven putative Si transporter genes. Moso bamboo Si transporters contain conserved functional domains that mediate the accumulation of considerable amounts of Si. The analysis of gene duplication patterns and divergence times suggested that the expansion of the moso bamboo Si transporter family was mainly due to segmental duplications. The expression of moso bamboo Si transporter genes, which varied among organs, was significantly modulated by Si treatments. The subcellular localization analysis showed that Si transporters are plasma membrane proteins. The Si content increased in transgenic Arabidopsis overexpressing PeLsi1-1 or PeLsi1-2 , which affected vegetative and reproductive growth. Our single-particle tracking analysis revealed the four diffusion modes of PeLsi1-1 on the plasma membrane. Moreover, the particle velocity, dwell time, and motion range of PeLsi1-1 decreased in response to Si treatments. The results of this study will further clarify the molecular mechanisms underlying Si absorption and accumulation in bamboo plants. • Moso bamboo has the molecular basis of high silicon accumulation. • The excessive accumulation of silicon affected the growth of transgenic Arabidopsis. • The distribution and dynamic changes of PeLsi1-1 were affected by silicon. • A hypothetical model for silicon transport in moso bamboo seedlings was established. [ABSTRACT FROM AUTHOR]

Uridine diphosphate (UDP) glycosyltransferases (UGTs) involved in many metabolic processes and are essential for plant growth and development. Although UGTs proteins have been studied in many plants, the biological functions of UGT genes in cotton leaf senescence are still unknown. In the present study, we performed a genome-wide survey and identified 157 GrUGT , 152 GaUGT and 261 GHUGT genes in Gossypium raimondii , G. arboreum , and G. hirsutum , respectively, that were classified into 15 groups. Analysis of protein motif and gene structure demonstrated that structural and functional conservation occurred within same groups but diverged among the different groups. Gene duplication analysis indicated the different duplication ways happened between tetraploid G. hirsutum and the two diploid species. Whole genome or segmental duplications played a main role in the expansion of the GHUGT family in cotton, and experienced purifying selection during the long evolutionary process in cotton. Cis -acting regulatory elements analysis indicated that they were associated with complex hormone regulatory networks and the stress response. Additionally, to identify GHUGT candidate genes responsive to leaf senescence, we analyzed the expression patterns of GHUGT genes using our transcriptome data from two cultivars of upland cotton with contrasting tolerance to leaf senescence. Subsequently, gene expression profiling based on real-time quantitative PCR showed that selected GHUGT candidate genes might be involved in ABA and JA regulation. Through further functional verification, silencing GHUGT116 gene via VIGS (Virus-induced gene silencing) delayed dark-induced leaf senescence. Overall, the results provide useful and valuable information for understanding the evolution of cotton UGTs genes and the function in leaf senescence. [ABSTRACT FROM AUTHOR]

Background: A major bottleneck to the introduction of noninvasive presymptomatic diagnostic tests for the pharmacogenetic disorder malignant hyperthermia is the lack of functional data for associated variants.Methods: We screened 50 genes having a potential role in skeletal muscle calcium homeostasis using the HaloPlex™ (Agilent Technologies, Santa Clara, CA, USA) target enrichment system and next-generation sequencing. Twenty-one patients with a history of a clinical malignant hyperthermia reaction together with a positive in vitro contracture test were included. Eight variants in RYR1 were subsequently introduced into the cDNA for the human ryanodine receptor gene and tested in cultured human embryonic kidney (HEK293) cells for their effect on calcium release from intracellular stores in response to the ryanodine receptor-1 agonist 4-chloro-m-cresol using fura-2 as calcium indicator. Each variant was subjected to in silico curation using the European Malignant Hyperthermia Group scoring matrix and ClinGen RYR1 variant curation expert panel guidelines.Results: Potentially causative RYR1 variants were identified in 15 patients. Of these, two families carried two RYR1 variants, five variants had been previously reported as 'pathogenic', two variants had been previously reported as 'likely benign', and eight were of 'uncertain significance'. Of these eight variants, four showed hypersensitivity to 4-chloro-m-cresol. Three variants were reclassified as either 'pathogenic' or 'likely pathogenic'. Two were classified as 'benign', whilst three remained of 'uncertain significance'.Conclusions: Three (p.Tyr1711Cys, p.Val2280Ile, and p.Arg4737Gln) additional variants can be added to the list of RYR1 disease-associated variants managed by the European Malignant Hyperthermia Group. These can therefore be used diagnostically in the future. Three variants (p.Glu2348Gly, p.Asn2634Lys, and p.Arg3629Trp) that remained classified as of uncertain significance require further family studies or a different functional test to determine clinical relevance in malignant hyperthermia. [ABSTRACT FROM AUTHOR]