ALBERT

Description: Background Flowering plants (angiosperms) are dominant components of global terrestrial ecosystems, but phylogenetic relationships at the familial level and above remain only partially resolved, greatly impeding our full understanding of their evolution and early diversification. The plastome, typically mapped as a circular genome, has been the most important molecular data source for plant phylogeny reconstruction for decades. Results Here, we assembled by far the largest plastid dataset of angiosperms, composed of 80 genes from 4792 plastomes of 4660 species in 2024 genera representing all currently recognized families. Our phylogenetic tree (PPA II) is essentially congruent with those of previous plastid phylogenomic analyses but generally provides greater clade support. In the PPA II tree, 75% of nodes at or above the ordinal level and 78% at or above the familial level were resolved with high bootstrap support (BP ≥ 90). We obtained strong support for many interordinal and interfamilial relationships that were poorly resolved previously within the core eudicots, such as Dilleniales, Saxifragales, and Vitales being resolved as successive sisters to the remaining rosids, and Santalales, Berberidopsidales, and Caryophyllales as successive sisters to the asterids. However, the placement of magnoliids, although resolved as sister to all other Mesangiospermae, is not well supported and disagrees with topologies inferred from nuclear data. Relationships among the five major clades of Mesangiospermae remain intractable despite increased sampling, probably due to an ancient rapid radiation. Conclusions We provide the most comprehensive dataset of plastomes to date and a well-resolved phylogenetic tree, which together provide a strong foundation for future evolutionary studies of flowering plants.

Description: Background Long non-coding RNAs (lncRNAs) are involved in several immune processes, including the immune response to vaccination, but most of them remain uncharacterised in livestock species. The mechanism of action of aluminium adjuvants as vaccine components is neither not fully understood. Results We built a transcriptome from sheep PBMCs RNA-seq data in order to identify unannotated lncRNAs and analysed their expression patterns along protein coding genes. We found 2284 novel lncRNAs and assessed their conservation in terms of sequence and synteny. Differential expression analysis performed between animals inoculated with commercial vaccines or aluminium adjuvant alone and the co-expression analysis revealed lncRNAs related to the immune response to vaccines and adjuvants. A group of co-expressed genes enriched in cytokine signalling and production highlighted the differences between different treatments. A number of differentially expressed lncRNAs were correlated with a divergently located protein-coding gene, such as the OSM cytokine. Other lncRNAs were predicted to act as sponges of miRNAs involved in immune response regulation. Conclusions This work enlarges the lncRNA catalogue in sheep and puts an accent on their involvement in the immune response to repetitive vaccination, providing a basis for further characterisation of the non-coding sheep transcriptome within different immune cells.

Description: Global access to sanitary water is of utmost importance to human health. Presently, textile dye water pollution and cigarette pollution are both plaguing the environment. Herein, waste cigarette filters (CFs) are converted into useful carbon-based adsorbent materials via a facile, microwave-assisted carbonization procedure. The CFs are activated and co-doped with phosphorus and nitrogen simultaneously to enhance their surface characteristics and adsorbent capability by introducing chemisorptive binding sites to the surface. The doped carbonized CF (DCCF) and undoped carbonized CF (CCF) adsorbents are characterized physically to examine their surface area, elemental composition, and surface charge properties. The maximum adsorption capacity of synthesized adsorbents was determined via batch adsorption experiments and Langmuir modelling. Additionally, the influence of different parameters on the adsorption process was studied by varying the adsorption conditions such as adsorbent dosage, initial concentration, contact time, temperature, and pH. The DCCF adsorbent showed a maximum adsorption capacity of 303 mg g− 1. Adsorption of both adsorbents fit best to Langmuir model and pseudo-second order kinetics, indicating chemisorptive mechanism. Both adsorbents showed endothermic adsorption process which is indicated by increasing adsorption capacity with increased temperatures. DCCF exhibited greater adsorption capability than CCF at all temperatures from 25 to 55 °C. The pH of the solution significantly affected the adsorption capacity of CCF while DCCF adsorption is favorable at a wide pH range due to low value of the adsorbent’s point of zero charge. Reusability results showed that both adsorbents can be used over several cycles for removal of dye. Thus, results conclude that the waste DCCF-based adsorbent does not only show a profound potential as a sustainable solution to combat textile dye water pollution but also addresses the valuable use of the CF pollution simultaneously. This approach, which can target two major pollutants, is attractive due to its ease of preparation, negligible cost, and versatility in application.

Description: Background High-flow nasal cannula (HFNC) oxygen is a non-invasive ventilation system that was introduced as an alternative to CPAP (continuous positive airway pressure), with a marked increase in its use in pediatric care settings. This study aimed to evaluate the cost-effectiveness of early use of HFNC compared to oxygen by nasal cannula in an infant with bronchiolitis in the emergency setting. Methods A decision tree model was used to estimate the cost-effectiveness of HFNC compared with oxygen by nasal cannula (control strategy) in an infant with bronchiolitis in the emergency setting. Cost data were obtained from a retrospective study on bronchiolitis from tertiary centers in Rionegro, Colombia, while utilities were collected from the literature. Results The QALYs per patient calculated in the base-case model were 0.9141 (95% CI 0.913–0.915) in the HFNC and 0.9105 (95% CI 0.910–0.911) in control group. The cost per patient was US$368 (95% CI US$ 323–411) in HFNC and US$441 (95% CI US$ 384–498) per patient in the control group. Conclusions HFNC was cost-effective HFNC compared to oxygen by nasal cannula in an infant with bronchiolitis in the emergency setting. The use of this technology in emergency settings will allow a more efficient use of resources, especially in low-resource countries with high prevalence of bronchiolitis .

Description: Background The detection of environmental cues and signals via the sensory system directs behavioral choices in diverse organisms. Insect larvae rely on input from the chemosensory system, mainly olfaction, for locating food sources. In several lepidopteran species, foraging behavior and food preferences change across larval instars; however, the molecular mechanisms underlying such behavioral plasticity during larval development are not fully understood. Here, we hypothesize that expression patterns of odorant receptors (ORs) change during development, as a possible mechanism influencing instar-specific olfactory-guided behavior and food preferences. Results We investigated the expression patterns of ORs in larvae of the cotton leafworm Spodoptera littoralis between the first and fourth instar and revealed that some of the ORs show instar-specific expression. We functionally characterized one OR expressed in the first instar, SlitOR40, as responding to the plant volatile, β-caryophyllene and its isomer α-humulene. In agreement with the proposed hypothesis, we showed that first but not fourth instar larvae responded behaviorally to β-caryophyllene and α-humulene. Moreover, knocking out this odorant receptor via CRISPR-Cas9, we confirmed that instar-specific responses towards its cognate ligands rely on the expression of SlitOR40. Conclusion Our results provide evidence that larvae of S. littoralis change their peripheral olfactory system during development. Furthermore, our data demonstrate an unprecedented instar-specific behavioral plasticity mediated by an OR, and knocking out this OR disrupts larval behavioral plasticity. The ecological relevance of such behavioral plasticity for S. littoralis remains to be elucidated, but our results demonstrate an olfactory mechanism underlying this plasticity in foraging behavior during larval development.

Description: Background The Agrobacterium strain AB2/73 has a unique host range for the induction of crown gall tumors, and contains an exceptionally large, over 500 kbp mega Ti plasmid. We used whole genome sequencing to fully characterize and comparatively analyze the complex genome of strain AB2/73, including its Ti plasmid and virulence factors. Results We obtained a high-quality, full genomic sequence of AB2/73 by a combination of short-read Illumina sequencing and long-read Nanopore sequencing. The AB2/73 genome has a total size of 7,266,754 bp with 59.5% GC for which 7012 genes (6948 protein coding sequences) are predicted. Phylogenetic and comparative genomics analysis revealed that strain AB2/73 does not belong to the genus Agrobacterium, but to a new species in the genus Rhizobium, which is most related to Rhizobium tropici. In addition to the chromosome, the genome consists of 6 plasmids of which the largest two, of more than 1 Mbp, have chromid-like properties. The mega Ti plasmid is 605 kbp in size and contains two, one of which is incomplete, repABC replication units and thus appears to be a cointegrate consisting of about 175 kbp derived from an unknown Ti plasmid linked to 430 kbp from another large plasmid. In pTiAB2/73 we identified a complete set of virulence genes and two T-DNAs. Besides the previously described T-DNA we found a larger, second T-DNA containing a 6b-like onc gene and the acs gene for agrocinopine synthase. Also we identified two clusters of genes responsible for opine catabolism, including an acc-operon for agrocinopine degradation, and genes putatively involved in ridéopine catabolism. The plasmid also harbours tzs, iaaM and iaaH genes for the biosynthesis of the plant growth regulators cytokinin and auxin. Conclusions The comparative genomics analysis of the high quality genome of strain AB2/73 provided insight into the unusual phylogeny and genetic composition of the limited host range Agrobacterium strain AB2/73. The description of its unique genomic composition and of all the virulence determinants in pTiAB2/73 will be an invaluable tool for further studies into the special host range properties of this bacterium.

Description: Background Occlusions of intravenous (IV) tubing can prevent vital and time-critical medication or solutions from being delivered into the bloodstream of patients receiving IV therapy. At low flow rates (≤ 1 ml/h) the alarm delay (time to an alert to the user) can be up to 2 h using conventional pressure threshold algorithms. In order to reduce alarm delays we developed and evaluated the performance of two new real-time occlusion detection algorithms and one co-occlusion detector that determines the correlation in trends in pressure changes for multiple pumps. Methods Bench-tested experimental runs were recorded in triplicate at rates of 1, 2, 4, 8, 16, and 32 ml/h. Each run consisted of 10 min of non-occluded infusion followed by a period of occluded infusion of 10 min or until a conventional occlusion alarm at 400 mmHg occurred. The first algorithm based on binary logistic regression attempts to detect occlusions based on the pump’s administration rate Q(t) and pressure sensor readings P(t). The second algorithm continuously monitored whether the actual variation in the pressure exceeded a threshold of 2 standard deviations (SD) above the baseline pressure. When a pump detected an occlusion using the SD algorithm, a third algorithm correlated the pressures of multiple pumps to detect the presence of a shared occlusion. The algorithms were evaluated using 6 bench-tested baseline single-pump occlusion scenarios, 9 single-pump validation scenarios and 7 multi-pump co-occlusion scenarios (i.e. with flow rates of 1 + 1, 1 + 2, 1 + 4, 1 + 8, 1 + 16, and 1 + 32 ml/h respectively). Alarm delay was the primary performance measure. Results In the baseline single-pump occlusion scenarios, the overall mean ± SD alarm delay of the regression and SD algorithms were 1.8 ± 0.8 min and 0.4 ± 0.2 min, respectively. Compared to the delay of the conventional alarm this corresponds to a mean time reduction of 76% (P = 0.003) and 95% (P = 0.001), respectively. In the validation scenarios the overall mean ± SD alarm delay of the regression and SD algorithms were respectively 1.8 ± 1.6 min and 0.3 ± 0.2 min, corresponding to a mean time reduction of 77% and 95%. In the multi-pump scenarios a correlation 〉 0.8 between multiple pump pressures after initial occlusion detection by the SD algorithm had a mean ± SD alarm delay of 0.4 ± 0.2 min. In 2 out of the 9 validation scenarios an occlusion was not detected by the regression algorithm before a conventional occlusion alarm occurred. Otherwise no occlusions were missed. Conclusions In single pumps, both the regression and SD algorithm considerably reduced alarm delay compared to conventional pressure limit-based detection. The SD algorithm appeared to be more robust than the regression algorithm. For multiple pumps the correlation algorithm reliably detected co-occlusions. The latter may be used to localize the segment of tubing in which the occlusion occurs. Trial registration Not applicable.

Description: Background Plant miRNAs are involved in the response to biotic and abiotic stresses by altering their expression levels, and they play an important role in the regulation of plant resistance to stress. However, the molecular mechanism that regulates the expression levels of miRNAs in plants with biotic and abiotic stress still needs to be explored. Previously, we found that the expression of the miR482 family was changed in tomato infected by Botrytis cinerea. In this study, we investigated and uncovered the mechanism underlying the response of miR482 to B. cinerea infection in tomato. Results First, RT-qPCR was employed to detect the expression patterns of miR482b in tomato infected by B. cinerea, and results showed that miR482b primary transcripts (pri-miR482b) were up-regulated in B. cinerea-infected leaves, but the mature miR482b was down-regulated. Subsequently, we used rapid amplification cDNA end method to amplify the full-length of pri-miR482b. Result showed that the pri-miR482b had two isoforms, with the longer one (consisting 300 bp) having an extra fragment of 53 bp in the 3’-end compared with the shorter one. In vitro Dicer assay indicated that the longer isoform pri-miR482b-x1 had higher efficiency in the post-transcriptional splicing of miRNA than the shorter isoform pri-miR482b-x2. In addition, the transcription level of mature miR482b was much higher in transgenic Arabidopsis overexpressing pri-miR482b-x1 than that in OE pri-miR482b-x2 Arabidopsis. These results confirmed that this extra 53 bp in pri-miR482b-x1 might play a key role in the miR482b biogenesis of post-transcription processing. Conclusions Extra 53 bp in pri-miR482b-x1 enhanced miR482b biogenesis, which elevated the transcription level of miR482b. This study clarified the response of miR482 to B. cinerea infection in tomato, thereby helping us further understand the molecular mechanisms that regulate the expression levels of other miRNAs.

Description: Background Temperature change affects the myriad of concurrent cellular processes in a non-uniform, disruptive manner. While endothermic organisms minimize the challenge of ambient temperature variation by keeping the core body temperature constant, cells of many ectothermic species maintain homeostatic function within a considerable temperature range. The cellular mechanisms enabling temperature acclimation in ectotherms are still poorly understood. At the transcriptional level, the heat shock response has been analyzed extensively. The opposite, the response to sub-optimal temperature, has received lesser attention in particular in animal species. The tissue specificity of transcriptional responses to cool temperature has not been addressed and it is not clear whether a prominent general response occurs. Cis-regulatory elements (CREs), which mediate increased transcription at cool temperature, and responsible transcription factors are largely unknown. Results The ectotherm Drosophila melanogaster with a presumed temperature optimum around 25 °C was used for transcriptomic analyses of effects of temperatures at the lower end of the readily tolerated range (14–29 °C). Comparative analyses with adult flies and cell culture lines indicated a striking degree of cell-type specificity in the transcriptional response to cool. To identify potential cis-regulatory elements (CREs) for transcriptional upregulation at cool temperature, we analyzed temperature effects on DNA accessibility in chromatin of S2R+ cells. Candidate cis-regulatory elements (CREs) were evaluated with a novel reporter assay for accurate assessment of their temperature-dependency. Robust transcriptional upregulation at low temperature could be demonstrated for a fragment from the pastrel gene, which expresses more transcript and protein at reduced temperatures. This CRE is controlled by the JAK/STAT signaling pathway and antagonizing activities of the transcription factors Pointed and Ets97D. Conclusion Beyond a rich data resource for future analyses of transcriptional control within the readily tolerated range of an ectothermic animal, a novel reporter assay permitting quantitative characterization of CRE temperature dependence was developed. Our identification and functional dissection of the pst_E1 enhancer demonstrate the utility of resources and assay. The functional characterization of this CoolUp enhancer provides initial mechanistic insights into transcriptional upregulation induced by a shift to temperatures at the lower end of the readily tolerated range.

Description: Background The Rhizobiales (Proteobacteria) order is an abundant and diverse group of microorganisms, being extensively studied for its lifestyle based on the association with plants, animals, and humans. New studies have demonstrated that the last common ancestor (LCA) of Rhizobiales had a free-living lifestyle, but the phylogenetic and metabolism characterization of basal lineages remains unclear. Here, we used a high-resolution phylogenomic approach to test the monophyly of the Aestuariivirgaceae family, a new taxonomic group of Rhizobiales. Furthermore, a deep metabolic investigation provided an overview of the main functional traits that can be associated with its lifestyle. We hypothesized that the presence of pathways (e.g., Glycolysis/Gluconeogenesis) and the absence of pathogenic genes would be associated with a free-living lifestyle in Aestuariivirgaceae. Results Using high-resolution phylogenomics approaches, our results revealed a clear separation of Aestuariivirgaceae into a distinct clade of other Rhizobiales family, suggesting a basal split early group and corroborate the monophyly of this group. A deep functional annotation indicated a metabolic versatility, which includes putative genes related to sugar degradation and aerobic respiration. Furthermore, many of these traits could reflect a basal metabolism and adaptations of Rhizobiales, as such the presence of Glycolysis/Gluconeogenesis pathway and the absence of pathogenicity genes, suggesting a free-living lifestyle in the Aestuariivirgaceae members. Conclusions Aestuariivirgaceae (Rhizobiales) family is a monophyletic taxon of the Rhizobiales with a free-living lifestyle and a versatile metabolism that allows these microorganisms to survive in the most diverse microbiomes, demonstrating their adaptability to living in systems with different conditions, such as extremely cold environments to tropical rivers.

Description: Background There is a long-term interest in investigating the genetic basis of the horned/polled phenotype in domestic goats. Here, we report a genome-wide association study (GWAS) to detect the genetic loci affecting the polled phenotype in goats. Results We obtained a total of 13,980,209 biallelic SNPs, using the genotyping-by-sequencing data from 45 Jintang Black (JT) goats, which included 32 female and nine male goats, and four individuals with the polled intersex syndrome (PIS). Using a mixed-model based GWAS, we identified two association signals, which were located at 150,334,857–150,817,260 bp (P = 5.15 × 10− 119) and 128,286,704–131,306,537 bp (P = 2.74 × 10− 15) on chromosome 1. The genotype distributions of the 14 most significantly associated SNPs were completely correlated with horn status in goats, based on the whole-genome sequencing (WGS) data from JT and two other Chinese horned breeds. However, variant annotation suggested that none of the detected SNPs within the associated regions were plausible causal mutations. Via additional read-depth analyses and visual inspections of WGS data, we found a 10.1-kb deletion (CHI1:g. 129424781_129434939del) and a 480-kb duplication (CHI1:150,334,286–150,818,098 bp) encompassing two genes KCNJ15 and ERG in the associated regions of polled and PIS-affected goats. Notably, the 10.1-kb deletion also served as the insertion site for the 480-kb duplication, as validated by PCR and Sanger sequencing. Our WGS genotyping showed that all horned goats were homozygous for the reference alleles without either the structural variants (SVs), whereas the PIS-affected goats were homozygous for both the SVs. We also demonstrated that horned, polled, and PIS-affected individuals among 333 goats from JT and three other Chinese horned breeds can be accurately classified via PCR amplification and agarose gel electrophoresis of two fragments in both SVs. Conclusion Our results revealed that two genomic regions on chromosome 1 are major loci affecting the polled phenotypes in goats. We provided a diagnostic PCR to accurately classify horned, polled, and PIS-affected goats, which will enable a reliable genetic test for the early-in-life prediction of horn status in goats.

Description: Background Two series of benzimidazole based thio-oxadiazole and thio-thiadiazole analogues were designed and synthesised as novel antimicrobial drugs through inhibition of phenylalanyl-tRNA synthetase (PheRS), which is a promising antimicrobial target. Compounds were designed to mimic the structural features of phenylalanyl adenylate (Phe-AMP) the PheRS natural substrate. Methods A 3D conformational alignment for the designed compounds and the PheRS natural substrate revealed a high level of conformational similarity, and a molecular docking study indicated the ability of the designed compounds to occupy both Phe-AMP binding pockets. A molecular dynamics (MD) simulation comparative study was performed to understand the binding interactions with PheRS from different bacterial microorganisms. The synthetic pathway of the designed compounds proceeded in five steps starting from benzimidazole. The fourteen synthesised compounds 5a-d, 6a-c, 8a-d and 9a-c were purified, fully characterised and obtained in high yield. Results In vitro antimicrobial evaluation against five bacterial strains showed a moderate activity of compound 8b with MIC value of 32 μg/mL against S. aureus, while all the synthesised compounds showed weak activity against both E. faecalis and P. aeruginosa (MIC 128 μg/mL). Conclusion Compound 8b provides a lead compound for further structural development to obtain high affinity PheRS inhibitors.

Description: Objective Colon cancer (CC) is one of the most common cancers whose progression is regulated by a number of factors, including circular RNAs (circRNAs). Nonetheless, circ_0038718 is a novel circRNA, and its regulatory mechanism in CC remains unclear. Methods Real-time quantitative PCR (qRT-PCR) was performed to detect the expression of circ_0038718, miR-195-5p and Axin2. Western blot was conducted to determine the protein expression of Axin2 and the key proteins on Wnt/β-catenin signaling pathway. Oligo (dT) 18 primers and RNase R were employed to identify the circular features of circ_0038718, and the location of circ_0038718 in cells was detected via nucleocytoplasmic separation. Dual-luciferase reporter assay and RNA binding protein immunoprecipitation experiment were carried out to investigate the molecular mechanism of circ_0038718/miR-195-5p/Axin2. Additionally, MTT assay was conducted to assess cell proliferation; Transwell assay was performed to evaluate cell migration and invasion, respectively. The effect of circ_0038718 on CC tumor growth was tested through tumor formation in nude mice. Results circ_0038718 was highly expressed in CC and could sponge miR-195-5p in cytoplasm. Silencing circ_0038718 suppressed the proliferative, migratory and invasive abilities of CC cells, while the promoting effect of high circ_0038718 expression on CC cells was reversed upon miR-195-5p over-expression. Axin2 was a downstream target of miR-195-5p and could regulate the Wnt/β-catenin signaling pathway. Axin2 expression was modulated by circ_0038718/miR-195-5p. Knockdown of Axin2 could also attenuate the promoting effect of high circ_0038718 expression on CC cell malignant progression, thus inhibiting tumor growth. Conclusion circ_0038718 is able to facilitate CC cell malignant progression via the miR-195-5p/Axin2 axis, which will provide a new idea for finding a novel targeted treatment of CC.

Description: Background Microrchidia proteins (MORCs) are involved in epigenetic gene silencing in a variety of eukaryotic organisms. Deletion of MORCs result in several developmental abnormalities and their dysregulation has been implicated in developmental disease and multiple cancers. Specifically, mammalian MORC3 mutations are associated with immune system defects and human cancers such as bladder, uterine, stomach, lung, and diffuse large B cell lymphomas. While previous studies have shown that MORC3 binds to H3K4me3 in vitro and overlaps with H3K4me3 ChIP-seq peaks in mouse embryonic stem cells, the mechanism by which MORC3 regulates gene expression is unknown. Results In this study, we identified that mutation in Morc3 results in a suppressor of variegation phenotype in a Modifiers of murine metastable epialleles Dominant (MommeD) screen. We also find that MORC3 functions as an epigenetic silencer of transposable elements (TEs) in mouse embryonic stem cells (mESCs). Loss of Morc3 results in upregulation of TEs, specifically those belonging to the LTR class of retrotransposons also referred to as endogenous retroviruses (ERVs). Using ChIP-seq we found that MORC3, in addition to its known localization at H3K4me3 sites, also binds to ERVs, suggesting a direct role in regulating their expression. Previous studies have shown that these ERVs are marked by the repressive histone mark H3K9me3 which plays a key role in their silencing. However, we found that levels of H3K9me3 showed only minor losses in Morc3 mutant mES cells. Instead, we found that loss of Morc3 resulted in increased chromatin accessibility at ERVs as measured by ATAC-seq. Conclusions Our results reveal MORC3 as a novel regulator of ERV silencing in mouse embryonic stem cells. The relatively minor changes of H3K9me3 in the Morc3 mutant suggests that MORC3 acts mainly downstream of, or in a parallel pathway with, the TRIM28/SETDB1 complex that deposits H3K9me3 at these loci. The increased chromatin accessibility of ERVs in the Morc3 mutant suggests that MORC3 may act at the level of chromatin compaction to effect TE silencing.

Description: Background Non-alcoholic fatty liver disease (NAFLD) has been entitled as metabolic-dysfunction associated fatty liver disease (MAFLD). Therefore anthropometric indicators of adiposity may provide a non-invasive predictive and diagnostic tool for this disease. This study intended to validate and compare the MAFLD predictive and diagnostic capability of eight anthropometric indicators. Methods The study involved a population-based retrospective cross-sectional design. The Fangchenggang area male health and examination survey (FAMHES) was used to collect data of eight anthropometric indicators, involving body mass index (BMI), waist-to-height ratio (WHtR), waist-hip ratio (WHR), body adiposity index (BAI), cardiometabolic index (CMI), lipid accumulation product (LAP), visceral adiposity index (VAI), and abdominal volume index (AVI). Receiver operating characteristics (ROC) curves and the respective areas under the curves (AUCs) were utilized to compare the diagnostic capacity of each indicator for MAFLD and to determine the optimal cutoff points. Binary logistic regression analysis was applied to identify the odds ratios (OR) with 95% confidence intervals (95% CI) for all anthropometric indicators and MAFLD. The Spearman rank correlation coefficients of anthropometric indicators, sex hormones, and MAFLD were also calculated. Results All selected anthropometric indicators were significantly associated with MAFLD (P 

Description: Background The absence of dystrophin has gave a massive impact on myotube development in Muscular Dystrophy pathogenesis. One of the conserved signaling pathways involved in skeletal muscle differentiation is the PI3K/Akt/mTOR pathway that plays a vital role in autophagy regulation. To further understand and establish targeted therapy in dystrophin-deficient myoblasts, protein expression profiling has been determined which provides information on perturbed autophagy modulation and activation. Methods In this study, a dystrophin-deficient myoblast cell line established from the skeletal muscle of a dystrophic (mdx) mouse was used as a model. The dfd13 (dystrophin-deficient) and C2C12 (non-dystrophic) myoblasts were cultured in low mitogen conditions for 10 days to induce differentiation. The cells were subjected to total protein extraction prior to Western blotting assay technique. Protein sub-fractionation has been conducted to determine protein localization. The live-cell analysis of autophagy assay was done using a flow cytometer. Results In our culture system, the dfd13 myoblasts did not achieve terminal differentiation. PTEN expression was profoundly increased in dfd13 myoblasts throughout the differentiation day subsequently indicates perturbation of PI3K/Akt/mTOR regulation. In addition, rictor-mTORC2 was also found inactivated in this event. This occurrence has caused FoxO3 misregulation leads to higher activation of autophagy-related genes in dfd13 myoblasts. Autophagosome formation was increased as LC3B-I/II showed accumulation upon differentiation. However, the ratio of LC3B lipidation and autophagic flux were shown decreased which exhibited dystrophic features. Conclusion Perturbation of the PTEN-PI3K/Akt pathway triggers excessive autophagosome formation and subsequently reduced autophagic flux within dystrophin-deficient myoblasts where these findings are of importance to understand Duchenne Muscular Dystrophy (DMD) patients. We believe that some manipulation within its regulatory signaling reported in this study could help restore muscle homeostasis and attenuate disease progression.

Description: Background Abiotic and biotic stresses induce oxidative processes in plant cells that this process starts with the production of ROSs which cause damage to the proteins. Therefore, plants have increased their antioxidant activity to defend against this oxidative stress to be able to handle stress better. In this research, 14 different tea accessions in a randomized complete block design with two replications were evaluated in two normal and drought stress conditions, and their antioxidant activity was measured by DPPH-free radicals’ assay and gene expression analysis. Results The results of gene expression analysis showed that the 100 and 399 accessions and Bazri cultivar had high values for most of the antioxidant enzymes, ascorbate peroxidase, superoxide dismutase, catalase, and peroxidase under drought stress conditions while the 278 and 276 accessions had the lowest amount of antioxidant enzymes in the same situation. Results showed that the IC50 of the BHT combination was 90.12 μg/ ml. Also, The IC50 of accessions ranged from 218 to 261 μg/ml and 201–264 μg/ml at normal and drought stress conditions, respectively. The 100 and 399 accessions showed the lowest IC50 under normal and drought stress conditions, while 278 and 276 accessions had the highest value for IC50. The antioxidant activity of tea accession extracts under normal conditions was ranged from 25 to 69% for accessions 278 and 100, respectively. While, the antioxidant activities of extracts under drought stress condition was 12 to 83% for accessions 276 and 100, respectively. So, according to the results, 100 and 399 accessions exhibited the least IC50 and more antioxidant activity under drought stress conditions and were identified as stress-tolerant accessions. However, 278 and 276 accessions did not show much antioxidant activity and were recognized as sensitive accessions under drought stress conditions. Conclusions These results demonstrate that total phenol content, antioxidant activity, and the oxygen-scavenging system can be used as a descriptor for identifying drought-tolerant accessions.

Description: Background Blowflies are ubiquitous insects, often shiny and metallic, and the larvae of many species provide important ecosystem services (e.g., recycling carrion) and are used in forensics and debridement therapy. Yet, the taxon has repeatedly been recovered to be para- or polyphyletic, and the lack of a well-corroborated phylogeny has prevented a robust classification. Results We here resolve the relationships between the different blowfly subclades by including all recognized subfamilies in a phylogenomic analysis using 2221 single-copy nuclear protein-coding genes of Diptera. Maximum likelihood (ML), maximum parsimony (MP), and coalescent-based phylogeny reconstructions all support the same relationships for the full data set. Based on this backbone phylogeny, blowflies are redefined as the most inclusive monophylum within the superfamily Oestroidea not containing Mesembrinellidae, Mystacinobiidae, Oestridae, Polleniidae, Sarcophagidae, Tachinidae, and Ulurumyiidae. The constituent subfamilies are re-classified as Ameniinae (including the Helicoboscinae, syn. nov.), Bengaliinae, Calliphorinae (including Aphyssurinae, syn. nov., Melanomyinae, syn. nov., and Toxotarsinae, syn. nov.), Chrysomyinae, Luciliinae, Phumosiinae, Rhiniinae stat. rev., and Rhinophorinae stat. rev. Metallic coloration in the adult is shown to be widespread but does not emerge as the most likely ground plan feature. Conclusions Our study provides the first phylogeny of oestroid calyptrates including all blowfly subfamilies. This allows settling a long-lasting controversy in Diptera by redefining blowflies as a well-supported monophylum, and blowfly classification is adjusted accordingly. The archetypical blowfly trait of carrion-feeding maggots most likely evolved twice, and the metallic color may not belong to the blowfly ground plan.

Description: Background Monilinia blight caused by Monilinia vaccinii-corymbosi (Reade) Honey (M.vc) is a major disease of wild blueberry that can result in severe crop losses in the absence of an integrated disease management programme. The fungus causes blight in the emerging floral and vegetative buds, but the degree of susceptibility varies among the different wild blueberry phenotypes, ranging from the highly susceptible V. a. f. nigrum to the moderately susceptible V. angustifolium and the least susceptible V. myrtilloides. Results The present study evaluated the defense responses of these major phenotypes during their primary infection (floral buds) with M.vc. The temporal expression profiles of PR genes (PR3 and PR4) and the flavonoid pathway structural genes (CHS, ANS, ANR, DFR and FLS) were analysed. The PR3 and PR4 gene expression profiles revealed that V. myrtilloides responded to M.vc infection by activating the expression of both PR genes. V. a. f. nigrum, on the other hand, failed to activate these genes, while V. angustifolium, exhibited an intermediate response. Our study with the flavonoid pathway genes indicated variability in activation of the genes during post-infection time points with ANS and ANR in V. myrtilloides, FLS in V. angustifolium and no response observed in V. a. f. nigrum. Conclusions Altogether, this study highlights that the degree of phenotype susceptibility is associated with the timely activation of host defense responsive genes. Data obtained in this study provided a starting point for a better understanding of the wild blueberry- M. vaccinii-corymbosi pathosystem.

Description: Background Common walnut (Juglans regia L.) is one of the top four most consumed nuts in the world due to its health benefits and pleasant taste. Despite its economic importance, the evolutionary history and genetic control of its adaptation and agronomic traits remain largely unexplored. Results We report a comprehensive walnut genomic variation map based on whole-genome resequencing of 815 walnut accessions. Evolutionary analyses suggest that Chinese J. regia diverged from J. sigillata with extensive hybridizations after the split of the two species. In contrast to annual crops, the genetic diversity and heterozygous deleterious mutations of Chinese common walnut trees have continued to increase during the improvement process. Selective sweep analyses identify 902 genes uniquely selected in the improved common walnut compared to its progenitor population. Five major-effect loci are identified to be involved in walnut adaptations to temperature, precipitation, and altitude. Genome-wide association studies reveal 27 genomic loci responsible for 18 important agronomic traits, among which JrFAD2 and JrANR are the potentially major-effect causative genes controlling linoleic acid content and color of the endopleura of the nut, respectively. Conclusions The largest genomic resource for walnuts to date has been generated and explored in this study, unveiling their evolutionary history and cracking the genetic code for agronomic traits and environmental adaptation of this economically crucial crop tree.

Description: Background Paphiopedilum hirsutissimum is a member of Orchidaceae family that is famous for its ornamental value around the globe, it is vulnerable due to over-exploitation and was listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora, which prevents its trade across borders. Variation in flower color that gives rise to different flower patterns is a major trait contributing to its high ornamental value. However, the molecular mechanism underlying color formation in P. hirsutissimum still remains unexplored. In the present study, we exploited natural variation in petal and labellum color of Paphiopedilum plants and used comparative transcriptome analysis as well as pigment measurements to explore the important genes, metabolites and regulatory pathways linked to flower color variation in P. hirsutissimum. Result We observed that reduced anthocyanin and flavonoid contents along with slightly higher carotenoids are responsible for albino flower phenotype. Comparative transcriptome analysis identified 3287 differentially expressed genes (DEGs) among normal and albino labellum, and 3634 DEGs between normal and albino petals. Two genes encoding for flavanone 3-hydroxylase (F3H) and one gene encoding for chalcone synthase (CHS) were strongly downregulated in albino labellum and petals compared to normal flowers. As both F3H and CHS catalyze essentially important steps in anthocyanin biosynthesis pathway, downregulation of these genes is probably leading to albino flower phenotype via down-accumulation of anthocyanins. However, we observed the downregulation of major carotenoid biosynthesis genes including VDE, NCED and ABA2 which was inconsistent with the increased carotenoid accumulation in albino flowers, suggesting that carotenoid accumulation was probably controlled at post-transcriptional or translational level. In addition, we identified several key transcription factors (MYB73, MYB61, bHLH14, bHLH106, MADS-SOC1, AP2/ERF1, ERF26 and ERF87) that may regulate structural genes involved in flower color formation in P. hirsutissimum. Importantly, over-expression of some of these candidate TFs increased anthocyanin accumulation in tobacco leaves which provided important evidence for the role of these TFs in flower color formation probably via regulating key structural genes of the anthocyanin pathway. Conclusion The genes identified here could be potential targets for breeding P. hirsutissimum with different flower color patterns by manipulating the anthocyanin and carotenoid biosynthesis pathways.

Description: Background Evidence on the relationship between the low−/high-density lipoprotein cholesterol ratio (LDL-C/HDL-C) and carotid plaques remains limited. This study aimed to examine the association between LDL-C/HDL-C and carotid plaques in participants with coronary heart disease (CHD) and to further explore the extent to which a healthy lifestyle reduces the risk of LDL-C/HDL-C-related carotid plaques. Methods This large-scale and multi-centre retrospective study included 9426 CHD patients (aged 35–75 years) between January 1, 2014 and September 30, 2020. The LDL-C/HDL-C values were converted to the following tertiles: lowest ( 3). Healthy lifestyle-related factors referred to whether or not the participant was a non-smoker and non-drinker. Participants were divided into an unfavourable group (those who did not adhere to healthy lifestyle factors), intermediate (only one unhealthy factor), and favourable (neither of the two unhealthy factors). Logistic regression was used for statistical analyses. Results Of the 9426 participants, 6989 (74.15%) CHD patients had carotid plaques. After adjustment for confounders, each unit increase in the LDL-C/HDL-C was significantly associated with carotid plaques (OR: 1.61; 95%CI: 1.43–1.84; P  3) was 1.18 times that of the lowest quartile (

Description: We present SquiggleNet, the first deep-learning model that can classify nanopore reads directly from their electrical signals. SquiggleNet operates faster than DNA passes through the pore, allowing real-time classification and read ejection. Using 1 s of sequencing data, the classifier achieves significantly higher accuracy than base calling followed by sequence alignment. Our approach is also faster and requires an order of magnitude less memory than alignment-based approaches. SquiggleNet distinguished human from bacterial DNA with over 90% accuracy, generalized to unseen bacterial species in a human respiratory meta genome sample, and accurately classified sequences containing human long interspersed repeat elements.

Description: Background ANAT is a Cytoscape plugin for the inference of functional protein–protein interaction networks in yeast and human. It is a flexible graphical tool for scientists to explore and elucidate the protein–protein interaction pathways of a process under study. Results Here we present ANAT3.0, which comes with updated PPI network databases of 544,455 (human) and 155,504 (yeast) interactions, and a new machine-learning layer for refined network elucidation. Together they improve network reconstruction to more than twofold increase in the quality of reconstructing known signaling pathways from KEGG. Conclusions ANAT3.0 includes improved network reconstruction algorithms and more comprehensive protein–protein interaction networks than previous versions. ANAT is available for download on the Cytoscape Appstore and at https://www.cs.tau.ac.il/~bnet/ANAT/.

Description: Background SQUAMOSA promoter binding proteins (SBPs) genes encode a family of plant-specific transcription factors involved in various growth and development processes, including flower and fruit development, leaf initiation, phase transition, and embryonic development. The SBP gene family has been identified and characterized in many species, but no systematic analysis of the SBP gene family has been carried out in sugarcane. Results In the present study, a total of 50 sequences for 30 SBP genes were identified by the genome-wide analysis and designated SsSBP1 to SsSBP30 based on their chromosomal distribution. According to the phylogenetic tree, gene structure and motif features, the SsSBP genes were classified into eight groups (I to VIII). By synteny analysis, 27 homologous gene pairs existed in SsSBP genes, and 37 orthologous gene pairs between sugarcane and sorghum were found. Expression analysis in different tissues, including vegetative and reproductive organs, showed differential expression patterns of SsSBP genes, indicating their functional diversity in the various developmental processes. Additionally, 22 SsSBP genes were predicted as the potential targets of miR156. The differential expression pattern of miR156 exhibited a negative correlation of transcription levels between miR156 and the SsSBP gene in different tissues. Conclusions The sugarcane genome possesses 30 SsSBP genes, and they shared similar gene structures and motif features in their subfamily. Based on the transcriptional and qRT-PCR analysis, most SsSBP genes were found to regulate the leaf initial and female reproductive development. The present study comprehensively and systematically analyzed SBP genes in sugarcane and provided a foundation for further studies on the functional characteristics of SsSBP genes during different development processes.

Description: Background Bladder cancer (BLCA) is a common cancer associated with an unfavorable prognosis. Increasing numbers of studies have demonstrated that lipid metabolism affects the progression and treatment of tumors. Therefore, this study aimed to explore the function and prognostic value of lipid metabolism-related genes in patients with bladder cancer. Methods Lipid metabolism-related genes (LRGs) were acquired from the Molecular Signature Database (MSigDB). LRG mRNA expression and patient clinical data were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. Cox regression analysis and least absolute shrinkage and selection operator (LASSO) regression analysis was used to construct a signature for predicting overall survival of patients with BLCA. Kaplan-Meier analysis was performed to assess prognosis. The connectivity Map (CMAP) database was used to identify small molecule drugs for treatment. A nomogram was constructed and assessed by combining the signature and other clinical factors. The CIBERSORT, MCPcounter, QUANTISEQ, XCELL, CIBERSORT-ABS, TIMER and EPIC algorithms were used to analyze the immunological characteristics. Results An 11-LRG signature was successfully constructed and validated to predict the prognosis of BLCA patients. Furthermore, we also found that the 11-gene signature was an independent hazardous factor. Functional analysis suggested that the LRGs were closely related to the PPAR signaling pathway, fatty acid metabolism and AMPK signaling pathway. The prognostic model was closely related to immune cell infiltration. Moreover, the expression of key immune checkpoint genes (PD1, CTLA4, PD-L1, LAG3, and HAVCR2) was higher in patients in the high-risk group than in those in the low-risk group. The prognostic signature based on 11-LRGs exhibited better performance in predicting overall survival than conventional clinical characteristics. Five small molecule drugs could be candidate drug treatments for BLCA patients based on the CMAP dataset. Conclusions In conclusion, the current study identified a reliable signature based on 11-LRGs for predicting the prognosis and response to immunotherapy in patients with BLCA. Five small molecule drugs were identified for the treatments of BLCA patients.

Description: Background Molecular interaction networks summarize complex biological processes as graphs, whose structure is informative of biological function at multiple scales. Simultaneously, omics technologies measure the variation or activity of genes, proteins, or metabolites across individuals or experimental conditions. Integrating the complementary viewpoints of biological networks and omics data is an important task in bioinformatics, but existing methods treat networks as discrete structures, which are intrinsically difficult to integrate with continuous node features or activity measures. Graph neural networks map graph nodes into a low-dimensional vector space representation, and can be trained to preserve both the local graph structure and the similarity between node features. Results We studied the representation of transcriptional, protein–protein and genetic interaction networks in E. coli and mouse using graph neural networks. We found that such representations explain a large proportion of variation in gene expression data, and that using gene expression data as node features improves the reconstruction of the graph from the embedding. We further proposed a new end-to-end Graph Feature Auto-Encoder framework for the prediction of node features utilizing the structure of the gene networks, which is trained on the feature prediction task, and showed that it performs better at predicting unobserved node features than regular MultiLayer Perceptrons. When applied to the problem of imputing missing data in single-cell RNAseq data, the Graph Feature Auto-Encoder utilizing our new graph convolution layer called FeatGraphConv outperformed a state-of-the-art imputation method that does not use protein interaction information, showing the benefit of integrating biological networks and omics data with our proposed approach. Conclusion Our proposed Graph Feature Auto-Encoder framework is a powerful approach for integrating and exploiting the close relation between molecular interaction networks and functional genomics data.

Description: Background Intraoperative incorporation of radiopaque fiducial markers at the tumor resection surface can provide useful assistance in identifying the tumor bed in postoperative imaging for RT planning and radiological follow-up. Besides titanium clips, iodine containing injectable liquid fiducial markers represent an option that has emerged more recently for this purpose. In this study, marking oral soft tissue resection surfaces, applying low dose injections of a novel Conformité Européenne (CE)-marked liquid fiducial marker based on sucrose acetoisobutyrate (SAIB) and iodinated SAIB (x-SAIB) was investigated. Methods Visibility and discriminability of low dose injections of SAIB/x-SAIB (10 µl, 20 µl, 30 µl) were systematically studied at different kV settings used in clinical routine in an ex-vivo porcine mandible model. Transferability of the preclinical results into the clinical setting and applicability of DE-CT were investigated in initial patients. Results Markers created by injection volumes as low as 10 µl were visible in CT imaging at all kV settings applied in clinical routine (70–120 kV). An injection volume of 30 µl allowed differentiation from an injection volume of 10 µl. In a total of 118 injections performed in two head and neck cancer patients, markers were clearly visible in 83% and 86% of injections. DE-CT allowed for differentiation between SAIB/x-SAIB markers and other hyperdense structures. Conclusions Injection of low doses of SAIB/x-SAIB was found to be a feasible approach to mark oral soft tissue resection surfaces, with injection volumes as low as 10 µl found to be visible at all kV settings applied in clinical routine. With the application of SAIB/x-SAIB reported for tumors of different organs already, mostly applying relatively large volumes for IGRT, this study adds information on the applicability of low dose injections to facilitate identification of the tumor bed in postoperative CT and on performance of the marker at different kV settings used in clinical routine.

Description: Haplotype-aware diploid genome assembly is crucial in genomics, precision medicine, and many other disciplines. Long-read sequencing technologies have greatly improved genome assembly. However, current long-read assemblers are either reference based, so introduce biases, or fail to capture the haplotype diversity of diploid genomes. We present phasebook, a de novo approach for reconstructing the haplotypes of diploid genomes from long reads. phasebook outperforms other approaches in terms of haplotype coverage by large margins, in addition to achieving competitive performance in terms of assembly errors and assembly contiguity.

Description: Background PIWI-interacting RNAs (piRNAs) are an abundant single-stranded type of small non-coding RNAs (sncRNAs), which initially were discovered in gonadal cells, with a role as defenders of genomic integrity in the germline, acting against the transposable elements. With a regular size range of 21-35 nt, piRNAs are associated with a PIWI-clade of Argonaute family proteins. The most widely accepted mechanisms of biogenesis for piRNAs involve the transcription of longer precursors of RNAs to be processed, by complexes of proteins, to functional size, preferentially accommodating uridine residues at the 5’ end and 3’ methylation to increase the stability of these molecules. piRNAs have also been detected in somatic cells, with diverse potential functions, indicating their high plasticity and pleiotropic activity. Discovered about two decades ago, piRNAs are a large and versatile type of sncRNA and that remain insufficiently identified and analyzed, through next-generation sequencing (NGS), to evaluate their processing, functions, and biogenesis in different cell types and during development. piRNAs’ distinction from other sncRNAs has led to controversial results and interpretation difficulties when using existing databases because of the heterogeneity of the criteria used in making the distinction. Description We present “piRNA-IPdb”, a database based uniquely on datasets obtaining after the defining characteristic of piRNAs: those small RNAs bound to PIWI proteins. We selected and analyzed sequences from piRBase that exclusively cover the binding to PIWI. We pooled a total of 18,821,815 sequences from RNA-seq after immunoprecipitation that included the binding to any of the mouse PIWI proteins (MILI, MIWI, or MIWI2). Conclusions In summary, we present the characteristics and potential use of piRNA-IPdb database for the analysis of bona fide piRNAs.

Description: Objective Microbial analysis in milk preserved using heat-assisted Pulsed Electric Field (PEF) need to be assessed. In this study we analyze the microbial quality and virulence-associated genes in milk samples preserved using heat-assisted PEF from several producers in Indonesia. Results Milk samples were collected consisting of raw milk, milks taken after the heating, PEF, mixing, cooling, and packaging. Microbiological and Polymerase Chain Reaction (PCR) detection for virulence genes were performed. Heat-assisted PEF treatment gave 2.7–7.47 log reduction for TPC; 1.6–2.56 log reduction for MPN number; 3.13–6.48 log reduction for S. aureus; and for B. cereus there was an increase of 0.76 log and a reduction of 0.46 log. While milk samples from thermal pasteurization gave log reduction numbers of TPC, MPN, and S. aureus respectively 5.28; 2.56; and 4.73, for B. cereus was increasing 2.4 log. Producer C performed the best results with significant reduction compared with others (p 

Description: Objective The purpose of this study was to reevaluate the high-risk breast non-mass-like lesions (NMLs) in mammography (MG) by target ultrasound (US) and Automated breast ultrasonography (ABUS), and to analyze the correlation between different imaging findings and the factors influencing the classification of lesions. Methods A total of 161 patients with 166 breast lesions were recruited in this retrospectively study. All cases were diagnosed as BI-RADS 4 or 5 by MG and as NML on ultrasound. While all NMLs underwent mammography, target US and ABUS before breast surgery or biopsy in the consistent position of breast. The imaging and pathological features of all cases were collected. All lesions were classified according to the lexion of ACR BI-RADS®. Results There were significant differences between benign and malignant breast NML in all the features of target US and ABUS. US, especially ABUS, was superior to MG in determining the malignant breast NML. There was a significant difference in the detection rate of calcification between MG and Target US (P 

Description: Objective Pebrine, caused by the microsporidium Nosema bombycis, is one of the severe diseases in Thai polyvoltine strains of the silkworm Bombyx mori. Studies showing the presence of Lactobacillus species in the silkworm gut, where the Nosema parasites enter, suggests that these bacteria may have a protective effect. The aim of this study was to investigate the effect of supplementation of Lactobacillus casei on the survival ratio of silkworm larvae challenged with N. bombycis. Results A group of silkworm larvae of the commercial Thai polyvoltine hybrid strain DokBua was supplemented with L. casei on the second day of the 2nd, 3rd, 4th, and 5th instar. When a control group of silkworm larvae were challenged with N. bombycis on the second day of the 4th instar, the survival rate was 68%, but it was 91% for larvae supplemented with L. casei. For those larvae that survived the treatments until pupation, we determined the growth characters larval weight, cocooning ratio, and pupation ratio, and the economic characters cocoon weight and cocoon shell weight. When infected with N. Bombycis, growth characters were significantly higher in larvae also receiving L. casei.

Description: Machine learning and artificial intelligence have entered biomedical decision-making for diagnostics, prognostics, or therapy recommendations. However, these methods need to be interpreted with care because of the severe consequences for patients. In contrast to human decision-making, computational models typically make a decision also with low confidence. Machine learning with abstention better reflects human decision-making by introducing a reject option for samples with low confidence. The abstention intervals are typically symmetric intervals around the decision boundary. In the current study, we use asymmetric abstention intervals, which we demonstrate to be better suited for biomedical data that is typically highly imbalanced. We evaluate symmetric and asymmetric abstention on three real-world biomedical datasets and show that both approaches can significantly improve classification performance. However, asymmetric abstention rejects as many or fewer samples compared to symmetric abstention and thus, should be used in imbalanced data.

Description: An amendment to this paper has been published and can be accessed via the original article.

Description: Background Alternative splicing (AS) is an important mechanism of posttranscriptional modification and dynamically regulates multiple physiological processes in plants, including fruit ripening. However, little is known about alternative splicing during fruit development in fleshy fruits. Results We studied the alternative splicing at the immature and ripe stages during fruit development in cucumber, melon, papaya and peach. We found that 14.96–17.48% of multiexon genes exhibited alternative splicing. Intron retention was not always the most frequent event, indicating that the alternative splicing pattern during different developmental process differs. Alternative splicing was significantly more prevalent at the ripe stage than at the immature stage in cucumber and melon, while the opposite trend was shown in papaya and peach, implying that developmental stages adopt different alternative splicing strategies for their specific functions. Some genes involved in fruit ripening underwent stage-specific alternative splicing, indicating that alternative splicing regulates fruits ripening. Conserved alternative splicing events did not appear to be stage-specific. Clustering fruit developmental stages across the four species based on alternative splicing profiles resulted in species-specific clustering, suggesting that diversification of alternative splicing contributes to lineage-specific evolution in fleshy fruits. Conclusions We obtained high quality transcriptomes and alternative splicing events during fruit development across the four species. Dynamics and nonconserved alternative splicing were discovered. The candidate stage-specific AS genes involved in fruit ripening will provide valuable insight into the roles of alternative splicing during the developmental processes of fleshy fruits.

Description: Background 5-Methylcytosine (5mC) is an important epigenetic mark in eukaryotes. Little information about its role exists for invertebrates. To investigate the contribution of 5mC to phenotypic variation in invertebrates, alteration of methylation patterns needs to be produced. Here, we apply new non-nucleoside DNA methyltransferase inhibitors (DNMTi) to introduce aleatory changes into the methylome of mollusk species. Results Flavanone inhibitor Flv1 was efficient in reducing 5mC in the freshwater snails Biomphalaria glabrata and Physa acuta, and to a lesser degree, probably due to lower stability in sea water, in the oyster Crassostrea gigas. Flv1 has no toxic effects and significantly decreased the 5mC level in the treated B. glabrata and in its offspring. Drug treatment triggers significant variation in the shell height in both generations. A reduced representation bisulfite-sequencing method called epiGBS corroborates hypomethylation effect of Flv1 in both B. glabrata generations and identifies seven Differential Methylated Regions (DMR) out of 32 found both in Flv1-exposed snails and its progeny, from which 5 were hypomethylated, demonstrating a multigenerational effect. By targeted bisulfite sequencing, we confirmed hypomethylation in a locus and show that it is associated with reduced gene expression. Conclusions Flv1 is a new and efficient DNMTi that can be used to induce transient and heritable modifications of the epigenetic landscape and phenotypic traits in mollusks, a phylum of the invertebrates in which epigenetics is understudied.

Description: Objective Athletic performances are dynamic movements that are physically challenging and often predict individual success in ecological contexts. They stem from a complex integration of multiple phenotypic traits—e.g., morphological, physiological and behavioural—that dictate animal survival and individual fitness. However, directly quantifying athletic performances can be particularly challenging in cryptic, slow-moving species or not very reactive in attitude. Here we present and describe a rapid, simple, and low-cost method to measure athletic performance in post-metamorphic individuals of the fire salamander Salamandra salamandra. While extremely reactive during the larval stage, adult salamanders are, in fact, cryptic and relatively slow-moving. Results Forcing terrestrial juveniles to swim under standard, albeit ecologically plausible, laboratory conditions, and using an automatic point-mass tracking tool, we were able to measure maximal and average performance indicators of post-metamorphic individuals. This method avoids inter-individual variation in motivation, as it forces individuals to perform at their best. Moreover, with this method, measures of athletic performance will be directly comparable between larval and terrestrial stages, allowing to study the contribution of carryover effects to the wide range of processes implicated in the eco-evo-devo of athletic performance in salamanders.

Description: Background Health systems globally are investing in integrating secure messaging platforms for virtual care in clinical practice. Implementation science is essential for adoption, scale-up, spread and maintenance of complex evidence-based solutions in clinics with evolving priorities. In response, the mobile Health (mHealth) Research Group modified the existing consolidated framework for implementation research (CFIR) to evaluate implementation of virtual health tools in clinical settings. WelTel® is an evidence-based digital health platform widely deployed in various geographical and health contexts. The objective is to identify the facilitators and barriers for implementing WelTel and to assess the application of the mCFIR tool in facilitating focus groups in different geographical and health settings. Methods Both qualitative and descriptive quantitative approaches were employed. Six mCFIR sessions were held in three countries with 51 key stakeholders. The mCFIR tool consists of 5 Domains and 25 constructs and was distributed through Qualtrics Experience Management (XM). “Performance” and “Importance” scores were valued on a scale of 0 to 10 (Mean ± SD). Descriptive analysis was conducted using R computing software. NVivo 12 Pro software was used to analyze mCFIR responses and to generate themes from the participants’ input. Results We observed a parallel trend in the scores of Importance and Performance. Of the five Domains, Domain 4 (End-user Characteristics) and Domain 3 (Inner Settings) scored highest in Importance (8.9 ± 0.5 and 8.6 ± 0.6, respectively) and Performance (7.6 ± 0.7 and 7.2 ± 1.3, respectively) for all sites. Domain 2 (Outer Setting) scored the lowest in both Importance and Performance for all sites (7.6 ± 0.4 and 5.6 ± 1.8). The thematic analysis produced the following themes: for areas of strengths, the themes brought up were timely diagnosis and response, cost-effectiveness, and user-friendliness. As for areas for improvement, the themes discussed were training, phone accessibility, stakeholder engagement, and literacy. Conclusion The mCFIR tool allowed for a comprehensive understanding of the barriers and facilitators to the implementation, reach, and scale-up of digital health tools. Amongst several important findings, we observed the value of bringing the perspectives of both end users (HCPs and patients) to the table across Domains. Trial Registration: NCT02603536 – November 11, 2015: WelTelOAKTREE: Text Messaging to Support Patients With HIV/AIDS in British Columbia (WelTelOAKTREE). NCT01549457 – March 9, 2012: TB mHealth Study—Use of Cell Phones to Improve Compliance in Patients on LTBI Treatment.

Description: Background The phytopatogen Claviceps paspali is the causal agent of Ergot disease in Paspalum spp., which includes highly productive forage grasses such as P. dilatatum. This disease impacts dairy and beef production by affecting seed quality and producing mycotoxins that can affect performance in feeding animals. The molecular basis of pathogenicity of C. paspali remains unknown, which makes it more difficult to find solutions for this problem. Secreted proteins are related to fungi virulence and can manipulate plant immunity acting on different subcellular localizations. Therefore, identifying and characterizing secreted proteins in phytopathogenic fungi will provide a better understanding of how they overcome host defense and cause disease. The aim of this work is to analyze the whole genome sequences of three C. paspali isolates to obtain a comparative genome characterization based on possible secreted proteins and pathogenicity factors present in their genome. In planta RNA-seq analysis at an early stage of the interaction of C. paspali with P. dilatatum stigmas was also conducted in order to determine possible secreted proteins expressed in the infection process. Results C. paspali isolates had compact genomes and secretome which accounted for 4.6–4.9% of the predicted proteomes. More than 50% of the predicted secretome had no homology to known proteins. RNA-Seq revealed that three protein-coding genes predicted as secreted have mayor expression changes during 1 dpi vs 4 dpi. Also, three of the first 10 highly expressed genes in both time points were predicted as effector-like. CAZyme-like proteins were found in the predicted secretome and the most abundant family could be associated to pectine degradation. Based on this, pectine could be a main component affected by the cell wall degrading enzymes of C. paspali. Conclusions Based on predictions from DNA sequence and RNA-seq, unique probable secreted proteins and probable pathogenicity factors were identified in C. paspali isolates. This information opens new avenues in the study of the biology of this fungus and how it modulates the interaction with its host. Knowledge of the diversity of the secretome and putative pathogenicity genes should facilitate future research in disease management of Claviceps spp.

Description: Background The genetic basis of phenotypic traits is highly variable and usually divided into mono-, oligo- and polygenic inheritance classes. Relatively few traits are known to be monogenic or oligogeneic. The majority of traits are considered to have a polygenic background. To what extent there are mixtures between these classes is unknown. The rapid advancement of genomic techniques makes it possible to directly map large amounts of genomic markers (GWAS) and predict unknown phenotypes (GWP). Most of the multi-marker methods for GWAS and GWP falls into one of two regularization frameworks. The first framework is based on $$ell _1$$ ℓ 1 -norm regularization (e.g. the LASSO) and is suitable for mono- and oligogenic traits, whereas the second framework regularize with the $$ell _2$$ ℓ 2 -norm (e.g. ridge regression; RR) and thereby is favourable for polygenic traits. A general framework for mixed inheritance is lacking. Results We have developed a proximal operator algorithm based on the recent LAVA regularization method that jointly performs $$ell _1$$ ℓ 1 - and $$ell _2$$ ℓ 2 -norm regularization. The algorithm is built on the alternating direction method of multipliers and proximal translation mapping (LAVA ADMM). When evaluated on the simulated QTLMAS2010 data, it is shown that the LAVA ADMM together with Bayesian optimization of the regularization parameters provides an efficient approach with lower test prediction mean-squared-error (65.89) than the LASSO (66.11), Ridge regression (83.41) and Elastic net (66.11). For the real pig data the test MSE of the LAVA ADMM is 0.850 compared to the LASSO, RR and EN with 0.875, 0.853 and 0.853, respectively. Conclusions This study presents the LAVA ADMM that is capable of joint modelling of monogenic major genetic effects and polygenic minor genetic effects which can be used for both genome-wide assoiciation and prediction purposes. The statistical evaluations based on both simulated and real pig data set shows that the LAVA ADMM has better prediction properies than the LASSO, RR and EN. Julia code for the LAVA ADMM is available at: https://github.com/patwa67/LAVAADMM.

Description: Background miRNAs regulate circadian patterns by modulating the biological clocks of animals. In our previous study, we found that the clock gene exhibited a cosine expression pattern in the fallopian tube of chicken uterus. Clock-controlled miRNAs are present in mammals and Drosophila; however, whether there are clock-controlled miRNAs in the chicken uterus and, if so, how they regulate egg-laying rhythms is unclear. In this study, we selected 18 layer hens with similar ovipositional rhythmicity (each of three birds were sacrificed for study per 4 h throughout 24 h); their transcriptomes were scanned to identify the circadian miRNAs and to explore regulatory mechanisms within the uterus of chickens. Results We identified six circadian miRNAs that are mainly associated with several biological processes including ion trans-membrane transportation, response to calcium ion, and enrichment of calcium signaling pathways. Verification of the experimental results revealed that miR-449c-5p exhibited a cosine expression pattern in the chicken uterus. Ca2+-transporting ATPase 4 (ATP2B4) in the plasma membrane is the predicted target gene of circadian miR-449c-5p and is highly enriched in the calcium signaling pathway. We speculated that clock-controlled miR-449c-5p regulated Ca2+ transportation during eggshell calcification in the chicken uterus by targeting ATP2B4. ATP2B4 mRNA and protein were rhythmically expressed in the chicken uterus, and dual-luciferase reporter gene assays confirmed that ATP2B4 was directly targeted by miR-449c-5p. The expression of miR-449c-5p showed an opposite trend to that of ATP2B4 within a 24 h cycle in the chicken uterus; it inhibited mRNA and protein expression of ATP2B4 in the uterine tubular gland cells. In addition, overexpression of ATP2B4 significantly decreased intracellular Ca2+ concentration (P 

Description: Background Mammals have wide variations in testicular position, with scrotal testes in some species and ascrotal testes in others. Although cryptorchidism is hazardous to human health, some mammalian taxa are natural cryptorchids. However, the evolution of testicular position and the molecular mechanisms underlying the maintenance of health, including reproductive health, in ascrotal mammals are not clear. Results In the present study, comparative genomics and evolutionary analyses revealed that genes associated with the extracellular matrix and muscle, contributing to the development of the gubernaculum, were involved in the evolution of testicular position in mammals. Moreover, genes related to testicular position were significantly associated with spermatogenesis and sperm fertility. These genes showed rapid evolution and the signature of positive selection, with specific substitutions in ascrotal mammals. Genes associated with testicular position were significantly enriched in functions and pathways related to cancer, DNA repair, DNA replication, and autophagy. Conclusions Our results revealed that alterations in gubernaculum development contributed to the evolution of testicular position in mammals and provided the first support for two hypotheses for variation in testicular position in mammals, the “cooling hypothesis”, which proposes that the scrotum provides a cool environment for acutely heat-sensitive sperm and the “training hypothesis”, which proposes that the scrotum develops the sperm by exposing them to an exterior environment. Further, we identified cancer resistance and DNA repair as potential protective mechanisms in natural cryptorchids. These findings provide general insights into cryptorchidism and have implications for health and infertility both in humans and domestic mammals.

Description: Background Recent development of single cell sequencing technologies has made it possible to identify genes with different expression (DE) levels at the cell type level between different groups of samples. In this article, we propose to borrow information through known biological networks to increase statistical power to identify differentially expressed genes (DEGs). Results We develop MRFscRNAseq, which is based on a Markov random field (MRF) model to appropriately accommodate gene network information as well as dependencies among cell types to identify cell-type specific DEGs. We implement an Expectation-Maximization (EM) algorithm with mean field-like approximation to estimate model parameters and a Gibbs sampler to infer DE status. Simulation study shows that our method has better power to detect cell-type specific DEGs than conventional methods while appropriately controlling type I error rate. The usefulness of our method is demonstrated through its application to study the pathogenesis and biological processes of idiopathic pulmonary fibrosis (IPF) using a single-cell RNA-sequencing (scRNA-seq) data set, which contains 18,150 protein-coding genes across 38 cell types on lung tissues from 32 IPF patients and 28 normal controls. Conclusions The proposed MRF model is implemented in the R package MRFscRNAseq available on GitHub. By utilizing gene-gene and cell-cell networks, our method increases statistical power to detect differentially expressed genes from scRNA-seq data.

Description: Background KDM6A, encoding a histone demethylase, is one of the top ten mutated epigenetic cancer genes. The effect of mutations on its structure and function are however poorly characterized. Methods Database search identified nonsense and missense mutations in the N-terminal TPR motifs and the C-terminal, catalytic JmjC domain, but also in the intrinsically disordered region connecting both these two well-structured domains. KDM6A variants with cancer-derived mutations were generated using site directed mutagenesis and fused to eGFP serving as an all-in-one affinity and fluorescence tag to study demethylase activity by an ELISA-based assay in vitro, apoptosis by FACS, complex assembly by Co-immunoprecipitation and localization by microscopy in urothelial cells and apoptosis by FACS. Results Independent of the mutation and demethylase activity, all KDM6A variants were detectable in the nucleus. Truncated KDM6A variants displayed changes in complex assemblies affecting (1) known interactions with the COMPASS complex component RBBP5 and (2) KDM6A-DNA associated assemblies with the nuclear protein Nucleophosmin. Some KDM6A variants induced a severe cellular phenotype characterized by multiple acute effects on nuclear integrity, namely, release of nuclear DNA into the cytoplasm, increased level of DNA damage indicators RAD51 and p-γH2A.X, and mitosis defects. These damaging effects were correlated with increased cell death. Conclusion These observations reveal novel effects of pathogenic variants pointing at new specific functions of KDM6A variants. The underlying mechanisms and affected pathways have to be investigated in future research to understand how tumor cells cope with and benefit from KDM6A truncations.

Description: Background Recent studies have substantiated the role of the triglyceride glucose (TyG) index in predicting the prognosis of coronary artery disease (CAD) patients, while no relevant studies have revealed the association between the TyG index and coronary collateralization in the event of coronary chronic total occlusion (CTO). The current study intends to explore whether, or to what extent, the TyG index is associated with impaired collateralization in CAD patients with CTO lesions. Methods The study enrolled 1093 CAD patients undergoing cardiac catheterization for at least one CTO lesion. Data were collected from the Beijing Anzhen Hospital record system. The degree of collaterals was determined according to the Rentrop classification system. The correlation between the TyG index and coronary collateralization was assessed. Results Overall, 318 patients were included in a less developed collateralization (Rentrop classification 0-1) group. The TyG index was significantly higher in patients with impaired collateralization (9.3±0.65 vs. 8.8±0.53, P

Description: Breast cancer is one of the main leading causes of women death. In recent years, attention has been focused on the role of lipoproteins, alterations of cholesterol metabolism and oxidative stress in the molecular mechanism of breast cancer. A role for high density lipoproteins (HDL) has been proposed, in fact, in addition to the role of reverse cholesterol transport (RCT), HDL exert antioxidant and anti-inflammatory properties, modulate intracellular cholesterol homeostasis, signal transduction and proliferation. Low levels of HDL-Cholesterol (HDL-C) have been demonstrated in patients affected by breast cancer and it has been suggested that low levels of HDL-C could represent a risk factor of breast cancer. Contrasting results have been observed by other authors. Recent studies have demonstrated alterations of the activity of some enzymes associated to HDL surface such as Paraoxonase (PON1), Lecithin-Cholesterol Acyltransferase (LCAT) and Phospholipase A2 (PLA2). Higher levels of markers of lipid peroxidation in plasma or serum of patients have also been observed and suggest dysfunctional HDL in breast cancer patients. The review summarizes results on levels of markers of oxidative stress of plasma lipids and on alterations of enzymes associated to HDL in patients affected by breast cancer. The effects of normal and dysfunctional HDL on human breast cancer cells and molecular mechanisms potentially involved will be also reviewed.

Description: Background Alternative splicing (AS) produces transcript variants playing potential roles in proteome diversification and gene expression regulation. AS modulation is thus essential to respond to developmental and environmental stimuli. In grapevine, a better understanding of berry development is crucial for implementing breeding and viticultural strategies allowing adaptation to climate changes. Although profound changes in gene transcription have been shown to occur in the course of berry ripening, no detailed study on splicing modifications during this period has been published so far. We report here on the regulation of gene AS in developing berries of two grapevine (Vitis vinifera L.) varieties, Gewurztraminer (Gw) and Riesling (Ri), showing distinctive phenotypic characteristics. Using the software rMATS, the transcriptomes of berries at four developmental steps, from the green stage to mid-ripening, were analysed in pairwise comparisons between stages and varieties. Results A total of 305 differential AS (DAS) events, affecting 258 genes, were identified. Interestingly, 22% of these AS events had not been reported before. Among the 80 genes that underwent the most significant variations during ripening, 22 showed a similar splicing profile in Gw and Ri, which suggests their involvement in berry development. Conversely, 23 genes were subjected to splicing regulation in only one variety. In addition, the ratios of alternative isoforms were different in Gw and Ri for 35 other genes, without any change during ripening. This last result indicates substantial AS differences between the two varieties. Remarkably, 8 AS events were specific to one variety, due to the lack of a splice site in the other variety. Furthermore, the transcription rates of the genes affected by stage-dependent splicing regulation were mostly unchanged, identifying AS modulation as an independent way of shaping the transcriptome. Conclusions The analysis of AS profiles in grapevine varieties with contrasting phenotypes revealed some similarity in the regulation of several genes with developmental functions, suggesting their involvement in berry ripening. Additionally, many splicing differences were discovered between the two varieties, that could be linked to phenotypic specificities and distinct adaptive capacities. Together, these findings open perspectives for a better understanding of berry development and for the selection of grapevine genotypes adapted to climate change.

Description: Background Cucumber (Cucumis sativus L.) is one of the most important economic crops and is susceptible to various abiotic stresses. The valine-glutamine (VQ) motif-containing proteins are plant-specific proteins with a conserved “FxxhVQxhTG” amino acid sequence that regulates plant growth and development. However, little is known about the function of VQ proteins in cucumber. Results In this study, a total of 32 CsVQ proteins from cucumber were confirmed and characterized using comprehensive genome-wide analysis, and they all contain a conserved motif with 10 variations. Phylogenetic tree analysis revealed that these CsVQ proteins were classified into nine groups by comparing the CsVQ proteins with those of Arabidopsis thaliana, melon and rice. CsVQ genes were distributed on seven chromosomes. Most of these genes were predicted to be localized in the nucleus. In addition, cis-elements in response to different stresses and hormones were observed in the promoters of the CsVQ genes. A network of CsVQ proteins interacting with WRKY transcription factors (CsWRKYs) was proposed. Moreover, the transcripts of CsVQ gene were spatio-temporal specific and were induced by abiotic adversities. CsVQ4, CsVQ6, CsVQ16–2, CsVQ19, CsVQ24, CsVQ30, CsVQ32, CsVQ33, and CsVQ34 were expressed in the range of organs and tissues at higher levels and could respond to multiple hormones and different stresses, indicating that these genes were involved in the response to stimuli. Conclusions Together, our results reveal novel VQ resistance gene resources, and provide critical information on CsVQ genes and their encoded proteins, which supplies important genetic basis for VQ resistance breeding of cucumber plants.

Description: The global coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 coronavirus started in March 2020. The conclusions from numerous studies indicate that people with comorbidities, such as arterial hypertension, diabetes, obesity, underlying cardiovascular disease, are particularly vulnerable to the severe course of COVID-19. The available data also suggest that patients with dyslipidemia, the most common risk factor of cardiovascular diseases, are also at greater risk of severe course of COVID-19. On the other hand, it has been shown that COVID-19 infection has an influence on lipid profile leading to dyslipidemia, which might require appropriate treatment. Owing to antiviral, anti-inflammatory, immunomodulatory, and cardioprotective activity, statin therapy has been considered as valuable tool to improve COVID-19 outcomes. Numerous observational studies have shown potential beneficial effects of lipid-lowering treatment on the course of COVID-19 with significant improved prognosis and reduced mortality.

Description: Abstract Background Quinoa (Chenopodium quinoa) is a high-value grain known for its excellent nutritional balance. It is an allotetraploid species (AABB, 2n = 4x = 36) formed by the hybridization between AA and BB genome diploid (2n = 2x = 18) species. This study reports genetic studies in Chenopodium ficifolium as a potential B genome diploid model system to simplify the genetic studies of quinoa including gene identification and marker-assisted breeding. Results Portsmouth, New Hampshire and Quebec City, Quebec accessions of C. ficifolium were used to develop an F2 population segregating for agronomically relevant traits including flowering time, plant height, the number of branches, branch angle, and internode length. Marker-trait associations were identified for the FLOWERING LOCUS T-LIKE 1 (FTL1) marker gene, where the alternate alleles (A1/A2) were segregating among the F2 generation plants in association with flowering time, plant height, and the number of branches. There was a strong correlation of the flowering time trait with both plant height and the number of branches. Thus, a possible multifaceted functional role for FTL1 may be considered. The parental Portsmouth and Quebec City accessions were homozygous for the alternate FTL1 alleles, which were found to be substantially diverged. SNPs were identified in the FTL1 coding sequence that could have some functional significance in relation to the observed trait variation. Conclusion These results draw further attention to the possible functional roles of the FTL1 locus in Chenopodium and justify continued exploration of C. ficifolium as a potential diploid model system for the genetic study of quinoa. We expect our findings to aid in quinoa breeding as well as to any studies related to the Chenopodium genus.

Description: Background Xyloglucan endotransglycosylase/hydrolases (XTH) can disrupt and reconnect the xyloglucan chains, modify the cellulose-xyloglucan complex structure in the cell wall to reconstruct the cell wall. Previous studies have reported that XTH plays a key role in the aluminum (Al) tolerance of tea plants (Camellia sinensis), which is a typical plant that accumulates Al and fluoride (F), but its role in F resistance has not been reported. Results Here, 14 CsXTH genes were identified from C. sinensis and named as CsXTH1–14. The phylogenetic analysis revealed that CsXTH members were divided into 3 subclasses, and conserved motif analysis showed that all these members included catalytic active region. Furthermore, the expressions of all CsXTH genes showed tissue-specific and were regulated by Al3+ and F− treatments. CsXTH1, CsXTH4, CsXTH6–8 and CsXTH11–14 were up-regulated under Al3+ treatments; CsXTH1–10 and CsXTH12–14 responded to different concentrations of F− treatments. The content of xyloglucan oligosaccharide determined by immunofluorescence labeling increased to the highest level at low concentrations of Al3+ or F− treatments (0.4 mM Al3+ or 8 mg/L F−), accompanying by the activity of XET (Xyloglucan endotransglucosylase) peaked. Conclusion In conclusion, CsXTH activities were regulated by Al or F via controlling the expressions of CsXTH genes and the content of xyloglucan oligosaccharide in C. sinensis roots was affected by Al or F, which might finally influence the elongation of roots and the growth of plants.

Description: Background Salicornia europaea is a halophyte that has a very pronounced salt tolerance. As a cell wall manipulating enzyme, xyloglucan endotransglycosylase/hydrolase (XTH) plays an important role in plant resistance to abiotic stress. However, no systematic study of the XTH gene family in S. europaea is well known. PacBio Iso-Seq transcriptome sequence data were used for bioinformatics and gene expression analysis using real-time quantitative polymerase chain reaction (RT-qPCR). Results Transcriptome sequencing (PacBio Iso-Seq system) generated 16,465,671 sub-reads and after quality control of Iso-Seq, 29,520 isoforms were obtained with an average length of 2112 bp. A total of 24,869 unigenes, with 98% of which were obtained using coding sequences (CDSs), and 6398 possible transcription factors (TFs) were identified. Thirty-five (35) non-redundant potential SeXTH proteins were identified in S. europaea and categorized into group I/II and group III based on their genetic relatedness. Prediction of the conserved motif revealed that the DE(I/L/F/V)DF(I)EFLG domain was conserved in the S. europaea proteins and a potential N-linked glycosylation domain N(T)V(R/L/T/I)T(S/K/R/F/P)G was also located near the catalytic residues. All SeXTH genes exhibited discrete expression patterns in different tissues, at different times, and under different stresses. For example, 27 and 15 SeXTH genes were positively expressed under salt stress in shoots and roots at 200 mM NaCl in 24 h, and 34 SeXTH genes were also positively regulated under 48 h of drought stress in shoots and roots. This indicates their function in adaptation to salt and drought stress. Conclusion The present study discovered SeXTH gene family traits that are potential stress resistance regulators in S. europaea, and this provides a basis for future functional diversity research.

Description: Background The 26S proteasome, canonically composed of multi-subunit 19S regulatory (RP) and 20S core (CP) particles, is crucial for cellular proteostasis. Proteasomes are re-modeled, activated, or re-localized and this regulation is critical for plants in response to environmental stresses. The proteasome holoenzyme assembly and dissociation are therefore highly dynamic in vivo. However, the stoichiometric changes of the plant proteasomes and how proteasome associated chaperones vary under common abiotic stresses have not been systematically studied. Results Here, we studied the impact of abiotic stresses on proteasome structure, activity, and interacting partners in Arabidopsis thaliana. We analyzed available RNA expression data and observed that expressions of proteasome coding genes varied substantially under stresses; however, the protein levels of a few key subunits did not change significantly within 24 h. Instead, a switch in the predominant proteasome complex, from 26S to 20S, occurs under oxidative or salt stress. Oxidative stress also reduced the cellular ATP content and the association of HSP70-family proteins to the 20S proteasome, but enhanced the activity of cellular free form CP. Salt stress, on the other hand, did not affect cellular ATP level, but caused subtle changes in proteasome subunit composition and impacted bindings of assembly chaperones. Analyses of an array of T-DNA insertional mutant lines highlighted important roles for several putative assembly chaperones in seedling establishment and stress sensitivity. We also observed that knockout of PBAC1, one of the α-ring assembly chaperones, resulted in reduced germination and tearing of the seed coat following sterilization. Conclusions Our study revealed an evolutionarily conserved mechanism of proteasome regulation during oxidative stress, involving dynamic regulation of the holoenzyme formation and associated regulatory proteins, and we also identified a novel role of the PBAC1 proteasome assembly chaperone in seed coat development.

Description: Background One of the important components of the health system is the emergency medical services (EMS) system. The EMS system was implemented at Kerman University of Medical Sciences teaching hospitals to communicate the situation of patients being transferred to the hospital by EMS and to provide facilities tailored to the patient's condition. The objective of this study was to investigate the impact of the EMS system on the patient care process and the workflow of users. Methods The hospital information system (HIS) report was used to investigate the impact of the EMS system on the patient care process and a questionnaire was distributed among 244 participants to determine its impact on the workflow of the users. Mann–Whitney U was used to analyze HIS reports, and Chi-square was used to analyze the data collected by questionnaires. Results The EMS system reduced the patient's stay in hospital by an average of 3 h and 45 min. It also increased the number of patients' discharge from the emergency room to 2.2% and reduced the death rate by 1.3% (p 

Description: Background Effective and applicable predictors of non-alcoholic fatty liver disease (NAFLD) are needed for the non-obese Chinese population. This study was undertaken to investigate: whether serum gamma-glutamyl transferase (GGT) was associated with incident NAFLD in the non-obese Chinese population. Methods This was a retrospective cohort study that enrolled 33,153 initially NAFLD-free individuals who underwent a health examination in Wenzhou Medical Center of Wenzhou People’s Hospital from January 2010 to December 2014. Serum GGT levels at the time of enrollment were evaluated in 11,906 persons who follow-up. The relationship between GGT levels and incident NAFLD was analyzed using Cox regression and generalized additive models after adjusting for demographic and clinical variables. In addition, Subgroup analysis was conducted, which was explored by Cox proportional hazard models. It was stated that the data had been downloaded from the DATADRYAD website. Results Multivariable Cox regression models were used to estimate the hazard ratio (HR) for GGT with incident NAFLD after adjusted demographic and clinical variables (HR, 1.010; 95% CI, 1.007–1.012; P 

Description: Background Salt stress is one of the main constraints determining crop productivity, and therefore one of the main limitations for food production. The aim of this study was to characterize the salt stress response at the physiological and molecular level of different Broccoli (Brassica oleracea L. var. Italica Plenck) cultivars that were previously characterized in field and greenhouse trials as salt sensitive or salt tolerant. This study aimed to identify functional and molecular traits capable of predicting the ability of uncharacterized lines to cope with salt stress. For this purpose, this study measured different physiological parameters, hormones and metabolites under control and salt stress conditions. Results This study found significant differences among cultivars for stomatal conductance, transpiration, methionine, proline, threonine, abscisic acid, jasmonic acid and indolacetic acid. Salt tolerant cultivars were shown to accumulate less sodium and potassium in leaves and have a lower sodium to potassium ratio under salt stress. Analysis of primary metabolites indicated that salt tolerant cultivars have higher concentrations of several intermediates of the Krebs cycle and the substrates of some anaplerotic reactions. Conclusions This study has found that the energetic status of the plant, the sodium extrusion and the proline content are the limiting factors for broccoli tolerance to salt stress. Our results establish physiological and molecular traits useful as distinctive markers to predict salt tolerance in Broccoli or to design novel biotechnological or breeding strategies for improving broccoli tolerance to salt stress.

Description: Background Plants grown under shade are exposed to low red/far-red ratio, thereby triggering an array of altered phenotypes called shade avoidance syndrome (SAS). Shade negatively influences plant growth, leading to a reduction in agricultural productivity. Understanding of SAS is crucial for sustainable agricultural practices, especially for high-density indoor farming. Brassicaceae vegetables are widely consumed around the world and are commonly cultivated in indoor farms. However, our understanding of SAS in Brassicaceae vegetables and their genome-wide transcriptional regulatory networks are still largely unexplored. Results Shade induced common signs of SAS, including hypocotyl elongation and reduced carotenoids/anthocyanins biosynthesis, in two different Brassicaceae species: Brassica rapa (Choy Sum and Pak Choy) and Brassica oleracea (Kai Lan). Phenotype-assisted transcriptome analysis identified a set of genes induced by shade in these species, many of which were related to auxin biosynthesis and signaling [e.g. YUCCA8 (YUC8), YUC9, and INDOLE-3-ACETIC ACID INDUCIBLE (IAAs)] and other phytohormones signaling pathways including brassinosteroids and ethylene. The genes functioning in plant defense (e.g. MYB29 and JASMONATE-ZIM-DOMAIN PROTEIN 9) as well as in biosynthesis of anthocyanins and glucosinolates were repressed upon shade. Besides, each species also exhibited distinct SAS phenotypes. Shade strongly reduced primary roots and elongated petioles of B. oleracea, Kai Lan. However, these SAS phenotypes were not clearly recognized in B. rapa, Choy Sum and Pak Choy. Some auxin signaling genes (e.g. AUXIN RESPONSE FACTOR 19, IAA10, and IAA20) were specifically induced in B. oleracea, while homologs in B. rapa were not up-regulated under shade. Contrastingly, shade-exposed B. rapa vegetables triggered the ethylene signaling pathway earlier than B. oleracea, Kai Lan. Interestingly, shade induced the transcript levels of LONG HYPOCOTYL IN FAR-RED 1 (HFR1) homolog in only Pak Choy as B. rapa. As HFR1 is a key negative regulator of SAS in Arabidopsis, our finding suggests that Pak Choy HFR1 homolog may also function in conferring higher shade tolerance in this variety. Conclusions Our study shows that two Brassicaceae species not only share a conserved SAS mechanism but also exhibit distinct responses to shade, which will provide comprehensive information to develop new shade-tolerant cultivars that are suitable for high-density indoor farms.

Description: Background Soil salinization is causing ecosystem degradation and crop yield reduction worldwide, and elucidation of the mechanism of salt-tolerant plants to improve crop yield is highly significant. Podocarpus macrophyllus is an ancient gymnosperm species with a unique environmental adaptation strategy that may be attributed to its lengthy evolutionary process. The present study investigated the physiological and molecular responses of P. macrophyllus plants to salt stress by analyzing its photosynthetic system and antioxidant enzyme activity. We also analyzed the differentially expressed genes (DEGs) in P. macrophyllus under salt stress using RNA sequencing and de novo transcriptome assembly. Results Salt treatment significantly affected the photosynthetic system in P. macrophyllus seedlings, which decreased chlorophyll content, altered chloroplast ultrastructure, and reduced photosynthesis. The activities of antioxidant enzymes increased significantly following salt stress treatment. Transcriptome analysis showed that salt stress induced a large number of genes involved in multiple metabolic and biological regulation processes. The transcription levels of genes that mediate phytohormone transport or signaling were altered. K+ and Ca2+ transporter-encoding genes and the MYB transcription factor were upregulated under salt stress. However, the genes involved in cell wall biosynthesis and secondary metabolism were downregulated. Conclusion Our research identified some important pathways and putative genes involved in salt tolerance in P. macrophyllus and provided clues for elucidating the mechanism of salt tolerance and the utilization of the salt tolerance genes of P. macrophyllus for crop improvement.

Description: Phytopathogenic bacteria are economically important because they affect crop yields and threaten the livelihoods of farmers worldwide. The genus Xanthomonas is particularly significant because it is associated with some plant diseases that cause tremendous loss in yields of globally essential crops. Current management practices are ineffective, unsustainable and harmful to natural ecosystems. Bacteriophage (phage) biocontrol for plant disease management has been of particular interest from the early nineteenth century to date. Xanthomonas phage research for plant disease management continues to demonstrate promising results under laboratory and field conditions. AgriPhage has developed phage products for the control of Xanthomonas campestris pv. vesicatoria and Xanthomonas citri subsp. citri. These are causative agents for tomato, pepper spot and speck disease as well as citrus canker disease.Phage-mediated biocontrol is becoming a viable option because phages occur naturally and are safe for disease control and management. Thorough knowledge of biological characteristics of Xanthomonas phages is vital for developing effective biocontrol products. This review covers Xanthomonas phage research highlighting aspects of their ecology, biology and biocontrol applications.

Description: Background Graph-based analysis (GBA) of genome-scale metabolic networks has revealed system-level structures such as the bow-tie connectivity that describes the overall mass flow in a network. However, many pathways obtained by GBA are biologically impossible, making it difficult to study how the global structures affect the biological functions of a network. New method that can calculate the biologically relevant pathways is desirable for structural analysis of metabolic networks. Results Here, we present a new method to determine the bow-tie connectivity structure by calculating possible pathways between any pairs of metabolites in the metabolic network using a flux balance analysis (FBA) approach to ensure that the obtained pathways are biologically relevant. We tested this method with 15 selected high-quality genome-scale metabolic models from BiGG database. The results confirmed the key roles of central metabolites in network connectivity, locating in the core part of the bow-tie structure, the giant strongly connected component (GSC). However, the sizes of GSCs revealed by GBA are significantly larger than those by FBA approach. A great number of metabolites in the GSC from GBA actually cannot be produced from or converted to other metabolites through a mass balanced pathway and thus should not be in GSC but in other subsets of the bow-tie structure. In contrast, the bow-tie structural classification of metabolites obtained by FBA is more biologically relevant and suitable for the study of the structure-function relationships of genome scale metabolic networks. Conclusions The FBA based pathway calculation improve the biologically relevant classification of metabolites in the bow-tie connectivity structure of the metabolic network, taking us one step further toward understanding how such system-level structures impact the biological functions of an organism.

Description: Background This study focuses on the task of supervised prediction of aging-related genes from -omics data. Unlike gene expression methods for this task that capture aging-specific information but ignore interactions between genes (i.e., their protein products), or protein–protein interaction (PPI) network methods for this task that account for PPIs but the PPIs are context-unspecific, we recently integrated the two data types into an aging-specific PPI subnetwork, which yielded more accurate aging-related gene predictions. However, a dynamic aging-specific subnetwork did not improve prediction performance compared to a static aging-specific subnetwork, despite the aging process being dynamic. This could be because the dynamic subnetwork was inferred using a naive Induced subgraph approach. Instead, we recently inferred a dynamic aging-specific subnetwork using a methodologically more advanced notion of network propagation (NP), which improved upon Induced dynamic aging-specific subnetwork in a different task, that of unsupervised analyses of the aging process. Results Here, we evaluate whether our existing NP-based dynamic subnetwork will improve upon the dynamic as well as static subnetwork constructed by the Induced approach in the considered task of supervised prediction of aging-related genes. The existing NP-based subnetwork is unweighted, i.e., it gives equal importance to each of the aging-specific PPIs. Because accounting for aging-specific edge weights might be important, we additionally propose a weighted NP-based dynamic aging-specific subnetwork. We demonstrate that a predictive machine learning model trained and tested on the weighted subnetwork yields higher accuracy when predicting aging-related genes than predictive models run on the existing unweighted dynamic or static subnetworks, regardless of whether the existing subnetworks were inferred using NP or the Induced approach. Conclusions Our proposed weighted dynamic aging-specific subnetwork and its corresponding predictive model could guide with higher confidence than the existing data and models the discovery of novel aging-related gene candidates for future wet lab validation.

Description: Background Cholesterol accumulation and calcium depletion induce hepatic injury via the endoplasmic reticulum (ER) stress response. ER stress regulates the calcium imbalance between the ER and mitochondria. We previously reported that phosphatase of regenerating liver-1 (PRL-1)-overexpressing placenta-derived mesenchymal stem cells (PD-MSCsPRL−1) promoted liver regeneration via mitochondrial dynamics in a cirrhotic rat model. However, the role of PRL-1 in ER stress-dependent calcium is not clear. Therefore, we demonstrated that PD-MSCsPRL−1 improved hepatic functions by regulating ER stress and calcium channels in a rat model of bile duct ligation (BDL). Methods Liver cirrhosis was induced in Sprague–Dawley (SD) rats using surgically induced BDL for 10 days. PD-MSCs and PD-MSCsPRL−1 (2 × 106 cells) were intravenously administered to animals, and their therapeutic effects were analyzed. WB-F344 cells exposed to thapsigargin (TG) were cocultured with PD-MSCs or PD-MSCsPRL−1. Results ER stress markers, e.g., eukaryotic translation initiation factor 2α (eIF2α), activating transcription factor 4 (ATF4), and C/EBP homologous protein (CHOP), were increased in the nontransplantation group (NTx) compared to the control group. PD-MSCsPRL−1 significantly decreased ER stress markers compared to NTx and induced dynamic changes in calcium channel markers, e.g., sarco/endoplasmic reticulum Ca2+ -ATPase 2b (SERCA2b), inositol 1,4,5-trisphosphate receptor (IP3R), mitochondrial calcium uniporter (MCU), and voltage-dependent anion channel 1 (VDAC1) (*p 

Description: Background Soil organic carbon (SOC) affects essential biological, biochemical, and physical soil functions such as nutrient cycling, water retention, water distribution, and soil structure stability. The Andean páramo known as such a high carbon and water storage capacity ecosystem is a complex, heterogeneous and remote ecosystem complicating field studies to collect SOC data. Here, we propose a multi-predictor remote quantification of SOC using Random Forest Regression to map SOC stock in the herbaceous páramo of the Chimborazo province, Ecuador. Results Spectral indices derived from the Landsat-8 (L8) sensors, OLI and TIRS, topographic, geological, soil taxonomy and climate variables were used in combination with 500 in situ SOC sampling data for training and calibrating a suitable predictive SOC model. The final predictive model selected uses nine predictors with a RMSE of 1.72% and a R2 of 0.82 for SOC expressed in weight %, a RMSE of 25.8 Mg/ha and a R2 of 0.77 for the model in units of Mg/ha. Satellite-derived indices such as VARIG, SLP, NDVI, NDWI, SAVI, EVI2, WDRVI, NDSI, NDMI, NBR and NBR2 were not found to be strong SOC predictors. Relevant predictors instead were in order of importance: geological unit, soil taxonomy, precipitation, elevation, orientation, slope length and steepness (LS Factor), Bare Soil Index (BI), average annual temperature and TOA Brightness Temperature. Conclusions Variables such as the BI index derived from satellite images and the LS factor from the DEM increase the SOC mapping accuracy. The mapping results show that over 57% of the study area contains high concentrations of SOC, between 150 and 205 Mg/ha, positioning the herbaceous páramo as an ecosystem of global importance. The results obtained with this study can be used to extent the SOC mapping in the whole herbaceous ecosystem of Ecuador offering an efficient and accurate methodology without the need for intensive in situ sampling.

Description: Background Current alignment tools typically lack an explicit model of indel evolution, leading to artificially short inferred alignments (i.e., over-alignment) due to inconsistencies between the indel history and the phylogeny relating the input sequences. Results We present a new progressive multiple sequence alignment tool ProPIP. The process of insertions and deletions is described using an explicit evolutionary model—the Poisson Indel Process or PIP. The method is based on dynamic programming and is implemented in a frequentist framework. The source code can be compiled on Linux, macOS and Microsoft Windows platforms. The algorithm is implemented in C++ as standalone program. The source code is freely available on GitHub at https://github.com/acg-team/ProPIP and is distributed under the terms of the GNU GPL v3 license. Conclusions The use of an explicit indel evolution model allows to avoid over-alignment, to infer gaps in a phylogenetically consistent way and to make inferences about the rates of insertions and deletions. Instead of the arbitrary gap penalties, the parameters used by ProPIP are the insertion and deletion rates, which have biological interpretation and are contextualized in a probabilistic environment. As a result, indel rate settings may be optimised in order to infer phylogenetically meaningful gap patterns.

Description: Objective To develop a collision engine (haptic force feedback simulator) compatible with a 5-degrees-of-freedom (DOF) haptic wand. This has broad applications such as telerobotic ultrasound systems. Integrating force feedback into systems is critical to optimize remote scanning. A collision engine compatible with a 5-DOF haptic wand was developed based on the Gilbert–Johnson–Keerthi algorithm. The collision engine calculated force during collision between the wand and a virtual object based on code developed using MATLAB. A proportional force was subsequently returned to a user via the haptic wand, thereby simulating the collision force for the user. Three experiments were conducted to assess the accuracy of the collision engine on curved and flat surfaces. Results The average errors in calculation of distances between the wand and virtual object were 2.1 cm, 3.4 cm, and 4.2 cm for the model of the human hand, cylinder, and cuboid, respectively. The collision engine accurately simulated forces on a flat surface, though was less accurate on curved surfaces. Future work will incorporate haptic force feedback into a telerobotic ultrasound system. The haptic force simulator presented here may also be used in the development of ultrasound simulators for training and education.

Description: Objective In previous studies using Illumina Infinium methylation arrays, we have identified DNA methylation marks associated with cancer predisposition and progression. In the present study, we have sought to find appropriate technology to both technically validate our data and expand our understanding of DNA methylation in these genomic regions. Here, we aimed to assess the repeatability of methylation measures made using QIAseq targeted methyl panel and to compare them with those obtained from the Illumina HumanMethylation450 (HM450K) assay. We included in the analysis high molecular weight DNA extracted from whole blood (WB) and DNA extracted from formalin-fixed paraffin-embedded tissues (FFPE). Results The repeatability of QIAseq-methylation measures was assessed at 40 CpGs, using the Intraclass Correlation Coefficient (ICC). The mean ICCs and 95% confidence intervals (CI) were 0.72 (0.62–0.81), 0.59 (0.47–0.71) and 0.80 (0.73–0.88) for WB, FFPE and both sample types combined, respectively. For technical replicates measured using QIAseq and HM450K, the mean ICCs (95% CI) were 0.53 (0.39–0.68), 0.43 (0.31–0.56) and 0.70 (0.59–0.80), respectively. Bland–Altman plots indicated good agreement between QIAseq and HM450K measurements. These results demonstrate that the QIAseq targeted methyl panel produces reliable and reproducible methylation measurements across the 40 CpGs that were examined.

Description: Background Archival formalin-fixed, paraffin-embedded (FFPE) tissue samples with clinical and histological data are a singularly valuable resource for developing new molecular biomarkers. However, transcriptome analysis remains challenging with standard mRNA-seq methods as FFPE derived-RNA samples are often highly modified and fragmented. The recently developed 3′ mRNA-seq method sequences the 3′ region of mRNA using unique molecular identifiers (UMI), thus generating gene expression data with minimal PCR bias. In this study, we evaluated the performance of 3′ mRNA-Seq using Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit FWD with UMI, comparing with TruSeq Stranded mRNA-Seq and RNA Exome Capture kit. The fresh-frozen (FF) and FFPE tissues yielded nucleotide sizes range from 13 to 〉 70% of DV200 values; input amounts ranged from 1 ng to 100 ng for validation. Results The total mapped reads of QuantSeq 3′ mRNA-Seq to the reference genome ranged from 99 to 74% across all samples. After PCR bias correction, 3 to 56% of total sequenced reads were retained. QuantSeq 3′ mRNA-Seq data showed highly reproducible data across replicates in Universal Human Reference RNA (UHR, R 〉 0.94) at input amounts from 1 ng to 100 ng, and FF and FFPE paired samples (R = 0.92) at 10 ng. Severely degraded FFPE RNA with ≤30% of DV200 value showed good concordance (R 〉 0.87) with 100 ng input. A moderate correlation was observed when directly comparing QuantSeq 3′ mRNA-Seq data with TruSeq Stranded mRNA-Seq (R = 0.78) and RNA Exome Capture data (R 〉 0.67). Conclusion In this study, QuantSeq 3′ mRNA-Seq with PCR bias correction using UMI is shown to be a suitable method for gene quantification in both FF and FFPE RNAs. 3′ mRNA-Seq with UMI may be applied to severely degraded RNA from FFPE tissues generating high-quality sequencing data.

Description: Background Several computational tools for predicting protein Ubiquitylation and SUMOylation sites have been proposed to study their regulatory roles in gene location, gene expression, and genome replication. However, existing methods generally rely on feature engineering, and ignore the natural similarity between the two types of protein translational modification. This study is the first all-in-one deep network to predict protein Ubiquitylation and SUMOylation sites from protein sequences as well as their crosstalk sites simultaneously. Our deep learning architecture integrates several meta classifiers that apply deep neural networks to protein sequence information and physico-chemical properties, which were trained on multi-label classification mode for simultaneously identifying protein Ubiquitylation and SUMOylation as well as their crosstalk sites. Results The promising AUCs of our method on Ubiquitylation, SUMOylation and crosstalk sites achieved 0.838, 0.888, and 0.862 respectively on tenfold cross-validation. The corresponding APs reached 0.683, 0.804 and 0.552, which also validated our effectiveness. Conclusions The proposed architecture managed to classify ubiquitylated and SUMOylated lysine residues along with their crosstalk sites, and outperformed other well-known Ubiquitylation and SUMOylation site prediction tools.

Description: Objectives Financial protection mechanisms are in place to overcome the costs of a few diseases in India. Our objective was to estimate the costs incurred due to Oral Potentially Malignant Disorders (OPMD) and to determine predictors of such costs. Results We found that the median (Interquartile range IQR) total costs of OPMD was Indian Rupees (INR) 500 (350–750), direct medical costs was INR 0 (0–50), direct non-medical costs was INR 150 (40–200) and indirect costs was INR 350 (250–500). The travel cost to attend the health facilities [INR 100 (40–150)] and the patient’s loss of wages [INR 200 (150–400)] mainly accounted for the direct non-medical and indirect costs respectively. The median expenditure on smokeless and smoking forms of tobacco was INR 6000 (5400–7200) and INR 2400 (1800–3600) respectively. On multiple linear regression analysis, rural residence, belonging to below poverty line family, being a sole earner in the family, number of months since diagnosis and first visit at a private provider were found to be the significant predictors of total costs of OPMD. Financial protection mechanisms are needed for covering the direct non-medical and indirect costs. Early management of OPMD might mitigate the costs of OPMD.

Description: Objective Near visual impairment (VI) is a common disability in an aging population. Near vision is crucial in activity of daily living including reading, smartphone and computer use and meal preparation. This study was conducted to determine the association between near visual acuity (VA) and contrast sensitivity (CS) with activity of daily living (ADL) among visually impaired older adults. Results A total of 208 participants aged  ≥  60 were recruited from the population-based longitudinal study on neuroprotective model for healthy longevity. Habitual near VA and CS were measured using Lighthouse near VA chart and Pelli-Robson CS chart, respectively. Lawton instrumental activities of daily living (IADL) was used to assess ADL. There are 41.8% participants with near visual impairment and 28.7% among them had IADL disability. Independent t test showed significant lower mean IADL score among visually impaired participants [t(206)  =  2.03, p  =  0.04]. IADL score significantly correlated with near VA (r  =   − 0.21, p  =  0.05) but not with CS (r  =   − 0.14, p = 0.21). Near VA (B  =   − 0.44, p  =  0.03) and age (B  =   − 0.07, p  =  0.01) significantly predicted IADL. The findings show poorer VA renders higher IADL disability, which may necessitate interventions to improve ADL among visually impaired older adults.

Description: Background Undernutrition is the main cause of child death in developing countries. This paper aimed to explore the efficacy of machine learning (ML) approaches in predicting under-five undernutrition in Ethiopian administrative zones and to identify the most important predictors. Method The study employed ML techniques using retrospective cross-sectional survey data from Ethiopia, a national-representative data collected in the year (2000, 2005, 2011, and 2016). We explored six commonly used ML algorithms; Logistic regression, Least Absolute Shrinkage and Selection Operator (L-1 regularization logistic regression), L-2 regularization (Ridge), Elastic net, neural network, and random forest (RF). Sensitivity, specificity, accuracy, and area under the curve were used to evaluate the performance of those models. Results Based on different performance evaluations, the RF algorithm was selected as the best ML model. In the order of importance; urban–rural settlement, literacy rate of parents, and place of residence were the major determinants of disparities of nutritional status for under-five children among Ethiopian administrative zones. Conclusion Our results showed that the considered machine learning classification algorithms can effectively predict the under-five undernutrition status in Ethiopian administrative zones. Persistent under-five undernutrition status was found in the northern part of Ethiopia. The identification of such high-risk zones could provide useful information to decision-makers trying to reduce child undernutrition.

Description: Background Mammalian mandible and cranium are well-established model systems for studying canalization and developmental stability (DS) as two elements of developmental homeostasis. Nematode infections are usually acquired in early life and increase in intensity with age, while canalization and DS of rodent skulls could vary through late postnatal ontogeny. We aimed to estimate magnitudes and describe patterns of mandibular and cranial canalization and DS related to age and parasite intensity (diversity) in adult yellow-necked mice (Apodemus flavicollis). Results We found the absence of age-related changes in the levels of canalization for mandibular and cranial size and DS for mandibular size. However, individual measures of mandibular and cranial shape variance increased, while individual measures of mandibular shape fluctuating asymmetry (FA) decreased with age. We detected mandibular and cranial shape changes during postnatal ontogeny, but revealed no age-related dynamics of their covariance structure among and within individuals. Categories regarding parasitism differed in the level of canalization for cranial size and the level of DS for cranial shape. We observed differences in age-related dynamics of the level of canalization between non-parasitized and parasitized animals, as well as between yellow-necked mice parasitized by different number of nematode species. Likewise, individual measures of mandibular and cranial shape FA decreased with age for the mandible in the less parasitized category and increased for the cranium in the most parasitized category. Conclusions Our age-related results partly agree with previous findings. However, no rodent study so far has explored age-related changes in the magnitude of FA for mandibular size or mandibular and cranial FA covariance structure. This is the first study dealing with the nematode parasitism-related canalization and DS in rodents. We showed that nematode parasitism does not affect mandibular and cranial shape variation and covariance structure among and within individuals. However, parasite intensity (diversity) is related to ontogenetic dynamics of the levels of canalization and DS. Overall, additional studies on animals from natural populations are required before drawing some general conclusions.

Description: Background Vancomycin-resistant enterococci (VRE) are successful nosocomial pathogens able to cause hospital outbreaks. In the Netherlands, core-genome MLST (cgMLST) based on short-read sequencing is often used for molecular typing. Long-read sequencing is more rapid and provides useful information about the genome’s structural composition but lacks the precision required for SNP-based typing and cgMLST. Here we compared prophages among 50 complete E. faecium genomes belonging to different lineages to explore whether a phage signature would be usable for typing and identifying an outbreak caused by VRE. As a proof of principle, we investigated if long-read sequencing data would allow for identifying phage signatures and thereby outbreak-related isolates. Results Analysis of complete genome sequences of publicly available isolates showed variation in phage content among different lineages defined by MLST. We identified phage present in multiple STs as well as phages uniquely detected within a single lineage. Next, in silico phage typing was applied to twelve MinION sequenced isolates belonging to two different genetic backgrounds, namely ST117/CT24 and ST80/CT16. Genomic comparisons of the long-read-based assemblies allowed us to correctly identify isolates of the same complex type based on global genome architecture and specific phage signature similarity. Conclusions For rapid identification of related VRE isolates, phage content analysis in long-read sequencing data is possible. This allows software development for real-time typing analysis of long-read sequencing data, which will generate results within several hours. Future studies are required to assess the discriminatory power of this method in the investigation of ongoing outbreaks over a longer time period.

Description: Background The carcass value of cattle is a function of carcass weight and quality. Given the economic importance of carcass merit to producers, it is routinely included in beef breeding objectives. A detailed understanding of the genetic variants that contribute to carcass merit is useful to maximize the efficiency of breeding for improved carcass merit. The objectives of the present study were two-fold: firstly, to perform genome-wide association analyses of carcass weight, carcass conformation, and carcass fat using copy number variant (CNV) data in a population of 923 Holstein-Friesian, 945 Charolais, and 974 Limousin bulls; and secondly to perform separate association analyses of carcass traits on the same population of cattle using the Log R ratio (LRR) values of 712,555 single nucleotide polymorphisms (SNPs). The LRR value of a SNP is a measure of the signal intensity of the SNP generated during the genotyping process. Results A total of 13,969, 3,954, and 2,805 detected CNVs were tested for association with the three carcass traits for the Holstein-Friesian, Charolais, and Limousin, respectively. The copy number of 16 CNVs and the LRR of 34 SNPs were associated with at least one of the three carcass traits in at least one of the three cattle breeds. With the exception of three SNPs, none of the quantitative trait loci detected in the CNV association analyses or the SNP LRR association analyses were also detected using traditional association analyses based on SNP allele counts. Many of the CNVs and SNPs associated with the carcass traits were located near genes related to the structure and function of the spliceosome and the ribosome; in particular, U6 which encodes a spliceosomal subunit and 5S rRNA which encodes a ribosomal subunit. Conclusions The present study demonstrates that CNV data and SNP LRR data can be used to detect genomic regions associated with carcass traits in cattle providing information on quantitative trait loci over and above those detected using just SNP allele counts, as is the approach typically employed in genome-wide association analyses.

Description: Background This study aims to observe and analyze the effect of diffusion weighted magnetic resonance imaging (MRI) on the patients with locally advanced breast cancer undergoing neoadjuvant chemotherapy. Methods Fifty patients (mean age, 48.7 years) with stage II–III breast cancer who underwent neoadjuvant chemotherapy and preoperative MRI between 2016 and 2020 were retrospectively evaluated. The associations between preoperative breast MRI findings/clinicopathological features and outcomes of neoadjuvant chemotherapy were assessed. Results Clinical stage at baseline (OR: 0.104, 95% confidence interval (CI) 0.021–0.516, P = 0.006) and standard apparent diffusion coefficient (ADC) change (OR: 9.865, 95% CI 1.024–95.021, P = 0.048) were significant predictive factors of the effects of neoadjuvant chemotherapy. The percentage increase of standard ADC value in pathologic complete response (pCR) group was larger than that in non-pCR group at first time point (P 

Description: Background GROWTH-REGULATING FACTORs (GRFs), a type of plant-specific transcription factors, play important roles in regulating plant growth and development. Although GRF gene family has been identified in various plant species, a genome-wide analysis of this family in lettuce (Lactuca sativa L.) has not been reported yet. Results Here we identified 15 GRF genes in lettuce and performed comprehensive analysis of them, including chromosomal locations, gene structures, and conserved motifs. Through phylogenic analysis, we divided LsaGRFs into six groups. Transactivation assays and subcellular localization of LsaGRF5 showed that this protein is likely to act as a transcriptional factor in the cell nucleus. Furthermore, transgenic lettuce lines overexpressing LsaGRF5 exhibited larger leaves, while smaller leaves were observed in LsaMIR396a overexpression lines, in which LsaGRF5 was down-regulated. Conclusions These results in lettuce provide insight into the molecular mechanism of GRF gene family in regulating leaf growth and development and foundational information for genetic improvement of the lettuce variations specialized in leaf character.

Description: Background Light quality significantly affects plant growth and development, photosynthesis, and carbon and nitrogen metabolism. Apple (Malus domestica Borkh.) is a widely cultivated and economically important fruit crop worldwide. However, there are still few studies on the effects of different light qualities on the growth and development of apple seedlings. Results In this study, we explored the effects of blue and red light treatments on the growth and development, photosynthetic characteristics, leaf chloroplast ultrastructure, and carbon and nitrogen metabolism of apple seedlings. Blue light significantly inhibited apple plant growth and leaf extension, but it promoted the development of leaf tissue structures and chloroplasts and positively affected leaf stomatal conductance, the transpiration rate, and photosynthetic efficiency. The red light treatment promoted apple plant growth and root development, but it resulted in loosely organized leaf palisade tissues and low chlorophyll contents. The blue and red light treatments enhanced the accumulation of ammonium nitrogen in apple seedlings. Moreover, the blue light treatment significantly promoted nitrogen metabolism. Additionally, an RNA-seq analysis revealed that both blue light and red light can significantly up-regulate the expression of genes related to carbon and nitrogen metabolism. Blue light can also promote amino acid synthesis and flavonoid metabolism, whereas red light can induce plant hormone signal transduction. The expression of a gene encoding a bHLH transcription factor (MYC2-like) was significantly up-regulated in response to blue light, implying it may be important for blue light-mediated plant development. Conclusions Considered together, blue and red light have important effects on apple growth, carbon and nitrogen metabolism. These findings may be useful for determining the ideal light conditions for apple cultivation to maximize fruit yield and quality.

Description: Background Asian cultivars were predominantly represented in global rice panel selected for sequencing and to identify novel alleles for drought tolerance. Diverse genetic resources adapted to Indian subcontinent were not represented much in spite harboring useful alleles that could improve agronomic traits, stress resilience and productivity. These rice accessions are valuable genetic resource in developing rice varieties suited to different rice ecosystem that experiences varying drought stress level, and at different crop stages. A core collection of rice germplasm adapted to Southwestern Indian peninsular genotyped using SSR markers and characterized by contrasting water regimes to associate genomic regions for physiological, root traits and yield related traits. Genotyping-By-Sequencing of selected accessions within the diverse panel revealed haplotype variation in genic content within genomic regions mapped for physiological, morphological and root traits. Results Diverse rice panel (99 accessions) were evaluated in field and measurements on plant physiological, root traits and yield related traits were made over five different seasons experiencing varying drought stress intensity at different crop stages. Traits like chlorophyll stability index, leaf rolling, days to 50% flowering, chlorophyll content, root volume and root biomass were identified as best predictors of grain yield under stress. Association mapping revealed genetic variation among accessions and revealed 14 genomic targets associated with different physiological, root and plant production traits. Certain accessions were found to have beneficial allele to improve traits, plant height, root length and spikelet fertility, that contribute to the grain yield under stress. Genomic characterization of eleven accessions revealed haplotype variation within key genomic targets on chromosomes 1, 4, 6 and 11 for potential use as molecular markers to combine drought avoidance and tolerance traits. Genes mined within the genomic QTL intervals identified were prioritized based on tissue specific expression level in publicly available rice transcriptome data. Conclusion The genetic and genomic resources identified will enable combining traits with agronomic value to optimize yield under stress and hasten trait introgression into elite cultivars. Alleles associated with plant height, specific leaf area, root length from PTB8 and spikelet fertility and grain weight from PTB26 can be harnessed in future rice breeding program.

Description: Background The origin is the starting site of DNA replication, an extremely vital part of the informational inheritance between parents and children. More importantly, accurately identifying the origin of replication has great application value in the diagnosis and treatment of diseases related to genetic information errors, while the traditional biological experimental methods are time-consuming and laborious. Results We carried out research on the origin of replication in a variety of eukaryotes and proposed a unique prediction method for each species. Throughout the experiment, we collected data from 7 species, including Homo sapiens, Mus musculus, Drosophila melanogaster, Arabidopsis thaliana, Kluyveromyces lactis, Pichia pastoris and Schizosaccharomyces pombe. In addition to the commonly used sequence feature extraction methods PseKNC-II and Base-content, we designed a feature extraction method based on TF-IDF. Then the two-step method was utilized for feature selection. After comparing a variety of traditional machine learning classification models, the multi-layer perceptron was employed as the classification algorithm. Ultimately, the data and codes involved in the experiment are available at https://github.com/Sarahyouzi/EukOriginPredict. Conclusions The prediction accuracy of the training set of the above-mentioned seven species after 100 times fivefold cross validation reach 92.60%, 90.80%, 91.22%, 96.15%, 96.72%, 99.86%, 96.72%, respectively. It denotes that compared with other methods, the methods we designed could accomplish superior performance. In addition, our experiments reveals that the models of multiple species could predict each other with high accuracy, and the results of STREME shows that they have a certain common motif.

Description: Background The wealth of biological information available nowadays in public databases has triggered an unprecedented rise in multi-database search and data retrieval for obtaining detailed information about key functional and structural entities. This concerns investigations ranging from gene or genome analysis to protein structural analysis. However, the retrieval of interconnected data from a number of different databases is very often done repeatedly in an unsystematic way. Results Here, we present TAxonomy, Gene, Ontology, Protein, Structure INtegrated (TAGOPSIN), a command line program written in Java for rapid and systematic retrieval of select data from seven of the most popular public biological databases relevant to comparative genomics and protein structure studies. The program allows a user to retrieve organism-centred data and assemble them in a single data warehouse which constitutes a useful resource for several biological applications. TAGOPSIN was tested with a number of organisms encompassing eukaryotes, prokaryotes and viruses. For example, it successfully integrated data for about 17,000 UniProt entries of Homo sapiens and 21 UniProt entries of human coronavirus. Conclusion TAGOPSIN demonstrates efficient data integration whereby manipulation of interconnected data is more convenient than doing multi-database queries. The program facilitates for instance interspecific comparative analyses of protein-coding genes in a molecular evolutionary study, or identification of taxa-specific protein domains and three-dimensional structures. TAGOPSIN is available as a JAR file at https://github.com/ebundhoo/TAGOPSIN and is released under the GNU General Public License.

Description: Purpose Some predictive systems using machine learning models have been developed to predict sepsis; however, they were mostly built with a low percent of missing values, which does not correspond with the actual clinical situation. In this study, we developed a machine learning model with a high rate of missing and erroneous data to enable prediction under missing, noisy, and erroneous inputs, as in the actual clinical situation. Materials and methods The proposed artificial neural network model was implemented using the MATLAB ANN toolbox, based on stochastic gradient descent. The dataset was collected over the past decade with approval from the appropriate institutional review boards, and the sepsis status was identified and labeled using Sepsis-3 clinical criteria. The imputation method was built by last observation carried forward and mean value, aimed to simulate clinical situation. Results The mean area under the receiver operating characteristic (ROC) curve (AUC) of classifying sepsis and nonsepsis patients was 0.82 and 0.786 at 0 h and 40 h prior to onset, respectively. The highest model performance was found for one-hourly data, demonstrating that our ANN model can perform adequately with limited hourly data provided. Conclusions Our model has the moderate ability to predict sepsis up to 40 h in advance under simulated clinical situation with real-world data.

Description: Background Rhinoviruses (RVs) cause more than half of common colds and, in some cases, more severe diseases. Functional genomics analyses of RVs using siRNA or genome-wide CRISPR screen uncovered a limited set of host factors, few of which have proven clinical relevance. Results Herein, we systematically compare genome-wide CRISPR screen and surface protein-focused CRISPR screen, referred to as surfaceome CRISPR screen, for their efficiencies in identifying RV host factors. We find that surfaceome screen outperforms the genome-wide screen in the success rate of hit identification. Importantly, using the surfaceome screen, we identify olfactomedin-like 3 (OLFML3) as a novel host factor of RV serotypes A and B, including a clinical isolate. We find that OLFML3 is a RV-inducible suppressor of the innate immune response and that OLFML3 antagonizes type I interferon (IFN) signaling in a SOCS3-dependent manner. Conclusion Our study suggests that RV-induced OLFML3 expression is an important mechanism for RV to hijack the immune system and underscores surfaceome CRISPR screen in identifying viral host factors.

Description: Background Much of the complex anatomy of a holometabolous insect is built from disc-shaped epithelial structures found inside the larva, i.e., the imaginal discs, which undergo a rapid differentiation during metamorphosis. Imaginal discs-derived structures, like wings, are built through the action of genes under precise regulation. Results We analyzed 30 honeybee transcriptomes in the search for the gene expression needed for wings and thoracic dorsum construction from the larval wing discs primordia. Analyses were carried out before, during, and after the metamorphic molt and using worker and queen castes. Our RNA-seq libraries revealed 13,202 genes, representing 86.2% of the honeybee annotated genes. Gene Ontology analysis revealed functional terms that were caste-specific or shared by workers and queens. Genes expressed in wing discs and descendant structures showed differential expression profiles dynamics in premetamorphic, metamorphic and postmetamorphic developmental phases, and also between castes. At the metamorphic molt, when ecdysteroids peak, the wing buds of workers showed maximal gene upregulation comparatively to queens, thus underscoring differences in gene expression between castes at the height of the larval-pupal transition. Analysis of small RNA libraries of wing buds allowed us to build miRNA-mRNA interaction networks to predict the regulation of genes expressed during wing discs development. Conclusion Together, these data reveal gene expression dynamics leading to wings and thoracic dorsum formation from the wing discs, besides highlighting caste-specific differences during wing discs metamorphosis.

Description: Background Poultry is the major reservoir of Campylobacter that contributes to human campylobacteriosis and threatens food safety. Litter contact has been linked to Campylobacter colonization, but the gut microecological impact underlying this link remains not fully clear. Here, we sought to investigate the impact of the gut microecology on the presence of Campylobacter by examining the microbiota in the duodenum, jejunum, ileum, ceca, and feces from chickens raised on commercial litter and in individual cages at 0–57 days of age. Results Through litter contact, the presence of Campylobacter was found to benefit from microecological competition among Lactobacillus, Helicobacter, and genera that are halotolerant and aerobic or facultatively anaerobic in the upper intestine, such as Corynebacterium and Brachybacterium. The presence was also promoted by the increased abundance in obligate anaerobic fermentation microbes, especially members of the orders Clostridiales and Bacteroidales. The longitudinal analysis supported the vertical or pseudo-vertical transmission but suggested that colonization might occur immensely at 7–28 days of age. We observed a host genetic effect on the gut microecology, which might lead to increased heterogeneity of the microecological impact on Campylobacter colonization. Conclusions The findings advance the understanding of the gut microecological impact on Campylobacter presence in the chicken gut under conditions of litter contact and suggest that manipulations of the gut microecology, as well as the microbes identified in the Campylobacter association networks, might be important for the development of intervention strategies.

Description: Background Extremophiles have attracted much attention in the last few decades, as they possess different properties by producing certain useful metabolites. However, the secondary metabolism of the extremophiles of Antarctic krill has received little attention. Results In this study, a new bacterial strain MSAK28401T from Antarctic krill was isolated and identified. The results of analysis on phenotypic, chemotaxonomic, and genomic characteristics showed that the strain MSAK28401T belongs to the genus Planococcus. Cells of this strain were coccoid (0.89–1.05 μm) and aerobic. The majority of the fatty acid content was C15:0 anteiso (37.67 ± 0.90%) followed by C16:1 ω7c alcohol (10.37 ± 1.22%) and C16:0 iso (9.36 ± 0.71%). The calculated average nucleotide identity and DNA–DNA hybridization values between the strain MSAK28401T and type strains P. citreus DSM 20549T and P. rifietoensis M8T were lower than 91 and 70%, respectively. The strain MSAK28401T (=KCTC 43283T and MCCC 1k05448T) represented a new member of the genus Planococcus and was named P. alpniumensis sp. nov. Moreover, genes involved in the degradation of aromatic compounds (e.g., salicylate, gentisate, and quinate) were found in the genome, implying that strain MSAK28401T has an aromatic compound as its potential metabolite. This work will help us understand the genomic characteristics and potential metabolic pathway of Planococcus from Antarctic krill. Conclusions This study reported the genomic information and phenotypic characteristics of the new strain P. alpniumensis MSAK28401T isolated from Antarctic krill, and provided the genome information of Planococcus strains for further studying the function roles in aromatic compound metabolism.

Description: Background Finding significant genes or proteins from gene chip data for disease diagnosis and drug development is an important task. However, the challenge comes from the curse of the data dimension. It is of great significance to use machine learning methods to find important features from the data and build an accurate classification model. Results The proposed method has proved superior to the published advanced hybrid feature selection method and traditional feature selection method on different public microarray data sets. In addition, the biomarkers selected using our method show a match to those provided by the cooperative hospital in a set of clinical cleft lip and palate data. Method In this paper, a feature selection algorithm ILRC based on clustering and improved L1 regularization is proposed. The features are firstly clustered, and the redundant features in the sub-clusters are deleted. Then all the remaining features are iteratively evaluated using ILR. The final result is given according to the cumulative weight reordering. Conclusion The proposed method can effectively remove redundant features. The algorithm’s output has high stability and classification accuracy, which can potentially select potential biomarkers.

Description: Background Opportunity and challenges of the agriculture scenario of the next decades will face increasing demand for secure food through approaches able to minimize the input to cultivations. Large panels of tomato varieties represent a valuable resource of traits of interest under sustainable cultivation systems and for genome-wide association studies (GWAS). For mapping loci controlling the variation of agronomic, fruit quality, and root architecture traits, we used a heterogeneous set of 244 traditional and improved tomato accessions grown under organic field trials. Here we report comprehensive phenotyping and GWAS using over 37,300 SNPs obtained through double digest restriction-site associated DNA (dd-RADseq). Results A wide range of phenotypic diversity was observed in the studied collection, with highly significant differences encountered for most traits. A variable level of heritability was observed with values up to 69% for morphological traits while, among agronomic ones, fruit weight showed values above 80%. Genotype by environment analysis highlighted the strongest genotypic effect for aboveground traits compared to root architecture, suggesting that the hypogeal part of tomato plants has been a minor objective for breeding activities. GWAS was performed by a compressed mixed linear model leading to 59 significantly associated loci, allowing the identification of novel genes related to flower and fruit characteristics. Most genomic associations fell into the region surrounding SUN, OVATE, and MYB gene families. Six flower and fruit traits were associated with a single member of the SUN family (SLSUN31) on chromosome 11, in a region involved in the increase of fruit weight, locules number, and fruit fasciation. Furthermore, additional candidate genes for soluble solids content, fruit colour and shape were found near previously reported chromosomal regions, indicating the presence of synergic and multiple linked genes underlying the variation of these traits. Conclusions Results of this study give new hints on the genetic basis of traits in underexplored germplasm grown under organic conditions, providing a framework for the development of markers linked to candidate genes of interest to be used in genomics-assisted breeding in tomato, in particular under low-input and organic cultivation conditions.

Description: Background Seed sanitization via chemical processes removes/reduces microbes from the external surfaces of the seed and thereby could have an impact on the plants’ health or productivity. To determine the impact of seed sanitization on the plants’ microbiome and pathogen persistence, sanitized and unsanitized seeds from two leafy green crops, red Romaine lettuce (Lactuca sativa cv. ‘Outredgeous’) and mizuna mustard (Brassica rapa var. japonica) were exposed to Escherichia coli and grown in controlled environment growth chambers simulating environmental conditions aboard the International Space Station. Plants were harvested at four intervals from 7 days post-germination to maturity. The bacterial communities of leaf and root were investigated using the 16S rRNA sequencing while quantitative polymerase chain reaction (qPCR) and heterotrophic plate counts were used to reveal the persistence of E. coli. Result E. coli was detectable for longer periods of time in plants from sanitized versus unsanitized seeds and was identified in root tissue more frequently than in leaf tissue. 16S rRNA sequencing showed dynamic changes in the abundance of members of the phylum Proteobacteria, Firmicutes, and Bacteroidetes in leaf and root samples of both leafy crops. We observed minimal changes in the microbial diversity of lettuce or mizuna leaf tissue with time or between sanitized and unsanitized seeds. Beta-diversity showed that time had more of an influence on all samples versus the E. coli treatment. Conclusion Our results indicated that the seed surface sanitization, a current requirement for sending seeds to space, could influence the microbiome. Insight into the changes in the crop microbiomes could lead to healthier plants and safer food supplementation.

Description: Calling fusion genes from RNA-seq data is well established, but other transcriptional variants are difficult to detect using existing approaches. To identify all types of variants in transcriptomes we developed MINTIE, an integrated pipeline for RNA-seq data. We take a reference-free approach, combining de novo assembly of transcripts with differential expression analysis to identify up-regulated novel variants in a case sample. We compare MINTIE with eight other approaches, detecting 〉 85% of variants while no other method is able to achieve this. We posit that MINTIE will be able to identify new disease variants across a range of disease types.

Description: Background Intercropping, especially with legumes, as a productive and sustainable system, can promote plants growth and improves the soil quality than the sole crop, is an essential cultivation pattern in modern agricultural systems. However, the metabolic changes of secondary metabolites and the growth in tea plants during the processing of intercropping with soybean have not been fully analyzed. Results The secondary metabolomic of the tea plants were significant influence with intercropping soybean during the different growth stages. Especially in the profuse flowering stage of intercropping soybean, the biosynthesis of amino acids was significantly impacted, and the flavonoid biosynthesis, the flavone and flavonol biosynthesis also were changed. And the expression of metabolites associated with amino acids metabolism, particularly glutamate, glutamine, lysine and arginine were up-regulated, while the expression of the sucrose and D-Glucose-6P were down-regulated. Furthermore, the chlorophyll photosynthetic parameters and the photosynthetic activity of tea plants were higher in the tea plants-soybean intercropping system. Conclusions These results strengthen our understanding of the metabolic mechanisms in tea plant’s secondary metabolites under the tea plants-soybean intercropping system and demonstrate that the intercropping system of leguminous crops is greatly potential to improve tea quality. These may provide the basis for reducing the application of nitrogen fertilizer and improve the ecosystem in tea plantations.

Description: Background Catechins are crucial in determining the flavour and health benefits of tea, but it remains unclear that how the light intensity regulates catechins biosynthesis. Therefore, we cultivated tea plants in a phytotron to elucidate the response mechanism of catechins biosynthesis to light intensity changes. Results In the 250 μmol·m− 2·s− 1 treatment, the contents of epigallocatechin, epigallocatechin gallate and total catechins were increased by 98.94, 14.5 and 13.0% respectively, compared with those in the 550 μmol·m− 2·s− 1 treatment. Meanwhile, the photosynthetic capacity was enhanced in the 250 μmol·m− 2·s− 1 treatment, including the electron transport rate, net photosynthetic rate, transpiration rate and expression of related genes (such as CspsbA, CspsbB, CspsbC, CspsbD, CsPsbR and CsGLK1). In contrast, the extremely low or high light intensity decreased the catechins accumulation and photosynthetic capacity of the tea plants. The comprehensive analysis revealed that the response of catechins biosynthesis to the light intensity was mediated by the photosynthetic capacity of the tea plants. Appropriately high light upregulated the expression of genes related to photosynthetic capacity to improve the net photosynthetic rate (Pn), transpiration rate (Tr), and electron transfer rate (ETR), which enhanced the contents of substrates for non-esterified catechins biosynthesis (such as EGC). Meanwhile, these photosynthetic capacity-related genes and gallic acid (GA) biosynthesis-related genes (CsaroB, CsaroDE1, CsaroDE2 and CsaroDE3) co-regulated the response of GA accumulation to light intensity. Eventually, the epigallocatechin gallate content was enhanced by the increased contents of its precursors (EGC and GA) and the upregulation of the CsSCPL gene. Conclusions In this study, the catechin content and photosynthetic capacity of tea plants increased under appropriately high light intensities (250 μmol·m− 2·s− 1 and 350 μmol·m− 2·s− 1) but decreased under extremely low or high light intensities (150 μmol·m− 2·s− 1 or 550 μmol·m− 2·s− 1). We found that the control of catechin accumulation by light intensity in tea plants is mediated by the plant photosynthetic capacity. The research provided useful information for improving catechins content and its light-intensity regulation mechanism in tea plant.

Description: Background Both underground rhizomes/buds and above-ground Moso bamboo (Phyllostachys heterocycla) shoots/culms/branches are connected together into a close inter-connecting system in which nutrients are transported and shared among each organ. However, the starch storage and utilization mechanisms during bamboo shoot growth remain unclear. This study aimed to reveal in which organs starch was stored, how carbohydrates were transformed among each organ, and how the expression of key genes was regulated during bamboo shoot growth and developmental stages which should lay a foundation for developing new theoretical techniques for bamboo cultivation. Results Based on changes of the NSC content, starch metabolism-related enzyme activity and gene expression from S0 to S3, we observed that starch grains were mainly elliptical in shape and proliferated through budding and constriction. Content of both soluble sugar and starch in bamboo shoot peaked at S0, in which the former decreased gradually, and the latter initially decreased and then increased as shoots grew. Starch synthesis-related enzymes (AGPase, GBSS and SBE) and starch hydrolase (α-amylase and β-amylase) activities exhibited the same dynamic change patterns as those of the starch content. From S0 to S3, the activity of starch synthesis-related enzyme and starch amylase in bamboo rhizome was significantly higher than that in bamboo shoot, while the NSC content in rhizomes was obviously lower than that in bamboo shoots. It was revealed by the comparative transcriptome analysis that the expression of starch synthesis-related enzyme-encoding genes were increased at S0, but reduced thereafter, with almost the same dynamic change tendency as the starch content and metabolism-related enzymes, especially during S0 and S1. It was revealed by the gene interaction analysis that AGPase and SBE were core genes for the starch and sucrose metabolism pathway. Conclusions Bamboo shoots were the main organ in which starch was stored, while bamboo rhizome should be mainly functioned as a carbohydrate transportation channel and the second carbohydrate sink. Starch metabolism-related genes were expressed at the transcriptional level during underground growth, but at the post-transcriptional level during above-ground growth. It may be possible to enhance edible bamboo shoot quality for an alternative starch source through genetic engineering.

Description: Objective Although perceived neighbourhood environment is considered a predictor of leisure-time physical activity (LTPA), evidence for this is limited in South Asia. Thus, the aim was to determine the association between neighbourhood social and built environment features in carrying out LTPA among adults in Colombo District, Sri Lanka. A cross-sectional study among 1320 adults was carried out using validated questionnaires for physical activity (PA) and built environment data collection. Multiple logistic regression analysis was conducted to assess the associations between environment characteristics and LTPA after adjusting for gender, age, employment status, income level and sector of residence. Results A total of 21.7% of adults participated in some LTPA. The commonest type of LTPA was walking; carried out by 14.5%. Moderate and vigorous activity at leisure was carried out by 10.3% and 3.9% respectively. Perceived social acceptance for PA was positively associated with LTPA. Out of the built environment characteristics perceived infrastructure for walking, and recreational facilities for PA were negatively associated with LTPA. Self-efficacy emerged as an important positive correlate of LTPA. The participants were positively influenced by the self-efficacy and perceived social environment which should be addressed when promoting LTPA.