Hasil untuk "Biology (General)"

Sudhir Kumar, A. Drummond, M. Suchard et al.

L. Revell

Phylogenetic comparative methods comprise the general endeavor of using an estimated phylogenetic tree (or set of trees) to make secondary inferences: about trait evolution, diversification dynamics, biogeography, community ecology, and a wide range of other phenomena or processes. Over the past ten years or so, the phytools R package (Revell 2012) has grown to become an important research tools for phylogenetic comparative analysis. phytools is a diverse contributed R library now consisting of hundreds of different functions covering a variety of methods and purposes in phylogenetic biology. As of the time of writing, phytools included functionality for fitting models of trait evolution, for reconstructing ancestral states, for studying diversification on trees, and for visualizing phylogenies, comparative data, and fitted models, as well numerous other tasks related to phylogenetic biology. Here, I describe some significant features of and recent updates to phytools, while also illustrating several popular workflows of the phytools computational software.

B. Scholkopf, K. Tsuda, Jean-Philippe Vert

Douglas D. Thomas, L. Ridnour, J. Isenberg et al.

J. Giovannoni

Hans F. Weinberger, Mark A. Lewis, Bingtuan Li

Kenneth Haug, R. Salek, Pablo Conesa et al.

MetaboLights (http://www.ebi.ac.uk/metabolights) is the first general-purpose, open-access repository for metabolomics studies, their raw experimental data and associated metadata, maintained by one of the major open-access data providers in molecular biology. Metabolomic profiling is an important tool for research into biological functioning and into the systemic perturbations caused by diseases, diet and the environment. The effectiveness of such methods depends on the availability of public open data across a broad range of experimental methods and conditions. The MetaboLights repository, powered by the open source ISA framework, is cross-species and cross-technique. It will cover metabolite structures and their reference spectra as well as their biological roles, locations, concentrations and raw data from metabolic experiments. Studies automatically receive a stable unique accession number that can be used as a publication reference (e.g. MTBLS1). At present, the repository includes 15 submitted studies, encompassing 93 protocols for 714 assays, and span over 8 different species including human, Caenorhabditis elegans, Mus musculus and Arabidopsis thaliana. Eight hundred twenty-seven of the metabolites identified in these studies have been mapped to ChEBI. These studies cover a variety of techniques, including NMR spectroscopy and mass spectrometry.

Bin Liu, Ihtisham Bukhari, Fazhan Li et al.

Thi Thanh Nga Le, Minh Thiet Vu, Hoang Dang Khoa Do

Abstract Dicliptera tinctoria is a member of Acanthaceae, which has a wide distribution and contains potentially medicinal species, and exhibited pharmaceutical potentials. This study sequenced and characterized the complete chloroplast genome of Dicliptera tinctoria. The newly sequenced cpDNA of D. tinctoria was 150,733 bp in length and had a typical quadripartite structure consisting of a large single copy (LSC, 82,895 bp), a small single copy (SSC, 17,249 bp), and two inverted repeat (IRs, 25,295 bp each) regions. This genome also contained 80 protein-coding genes, 30 transfer RNAs, and four ribosomal RNAs, which is identical to other chloroplast genomes in Acanthaceae family. Nucleotides diversity analysis among chloroplast genomes of Acanthaceae species revealed eight hypervariable regions, including trnK_UUU-matK, trnC_GCA-petN, accD, rps12-clpP, rps3-rps19, ycf1-ndhF, ccsA-ndhD, and ycf1. Phylogenetic analysis revealed the paraphyly of Dicliptera species and monophyly in four Acanthaceae subfamilies. These results provide an overview of genomic variations in Acanthaceae chloroplast genome, which is helpful for further genomic studies.

Ya-Wen Peng, Ri Tang, Qiao-Yi Xu et al.

Background: Fibrosis is a heavy burden on the global healthcare system. Recently, an increasing number of studies have demonstrated that Extracellular vesicles play an important role in intercellular communication under both physiological and pathological conditions. This study aimed to explore the role of extracellular vesicles’ in fibrosis using bibliometric methods. Methods: Original articles and reviews related to extracellular vesicles and fibrosis were obtained from the Web of Science Core Collection database on November 9, 2022. VOSviewer was used to obtain general information, including co-institution, co-authorship, and co-occurrence visualization maps. The CiteSpace software was used to analyze citation bursts of keywords and references, a timeline view of the top clusters of keywords and cited articles, and the dual map. R package ''bibliometrix'' was used to analyze annual production, citation per year, collaboration network between countries/regions, thematic evolution map, and historiography network. Results: In total, 3376 articles related to extracellular vesicles and fibrosis published from 2013 to 2022 were included in this study, with China and the United States being the top contributors. Shanghai Jiao Tong University has the highest number of publications. The main collaborators were Giovanni Camussi, Stefania Bruno, Marta Tepparo, and Cristina Grange. Journals related to molecular, biology, genetics, health, immunology, and medicine tended to publish literature on extracellular vesicles and fibrosis. “Recovery,” “heterogeneity,” “degradation,” “inflammation,” and “mesenchymal stem cells” are the keywords in this research field. Literature on extracellular vesicles and fibrosis associated with several diseases, including “kidney disease,” “rheumatoid arthritis,” and “skin regeneration” may be the latest hot research field. Conclusions: This study provides a comprehensive perspective on extracellular vesicles and fibrosis through a bibliometric analysis of articles published between 2013 and 2022. We identified the most influential countries, institutions, authors, and journals. We provide information on recent research frontiers and trends for scholars interested in the field of extracellular vesicles and fibrosis. Their role in biological processes has great potential to initiate a new upsurge in future research.

Noorhayati Idros, Lariyah Mohd Sidek, Nur Anis Aishah M. Rahim et al.

The aim of this study is to evaluate the current water quality status of one of the urban rivers in Malaysia, called Sungai Air Hitam. The river's water supply is not only unsuitable for the inhabitants but also hazardous to the aquatic species that depend on it. In order to simulate the water quality formulation of the river, the Model for Urban Stormwater Improvement Conceptualization (MUSIC) was used. The effects of various best management practices (BMPs) components have been examined to improve the river's water quality. This study also investigated different scenarios of the expected future changes in the land cover and the quality of the river. As the proportion of impervious surfaces increases, the urban hydrology cycle can be significantly altered, resulting in an increase in volumes and peak flows, and a decrease in storage, infiltration, and interception. The MUSIC results have shown significant reductions in biochemical oxygen demand (BOD), total suspended solids (TSS), total phosphorus (TP), and total nitrogen (TN) after introducing BMPs. It was also noticed that the prediction of pollutants falls within the acceptable range set by the Urban Stormwater Management Manual for Malaysia (MSMA) 2nd edition. For the land cover, it was found that the total reduction of BOD, TSS, TP, and TN for existing land use is 92.5 %, 94.5 %, 90.7 % and 91.9 %. Meanwhile, the total reduction in future land use is 81.6 % for BOD, 86.2 % for TSS, 80.9 % for TP and 80.8 % for TN. From the simulation results, it was observed that the application of BMPs has successfully reduced the observed mean BOD concentration from 92.38 mg/L (Class V) to 6.93 mg/L (Class IV) of the national water quality standards, NWQS, water quality index. As a result, the water quality index of the overall catchment has improved from Class IV to Class III (WQ1, WQ3, and WQ4) and from Class V to IV (WQ2) with the application of the BMPs. This assessment aims to raise awareness within the Sungai Air Hitam community regarding the importance of preserving river cleanliness and understanding the long-term environmental impact of water quality. These findings underscore the importance of an integrated system in managing urban water systems, which can offer valuable insight to the decision-makers.

Scott Mastromatteo, Angela Chen, Jiafen Gong et al.

Summary: Phasing of heterozygous alleles is critical for interpretation of cis-effects of disease-relevant variation. We sequenced 477 individuals with cystic fibrosis (CF) using linked-read sequencing, which display an average phase block N50 of 4.39 Mb. We use these samples to construct a graph representation of CFTR haplotypes, demonstrating its utility for understanding complex CF alleles. These are visualized in a Web app, CFTbaRcodes, that enables interactive exploration of CFTR haplotypes present in this cohort. We perform fine-mapping and phasing of the chr7q35 trypsinogen locus associated with CF meconium ileus, an intestinal obstruction at birth associated with more severe CF outcomes and pancreatic disease. A 20-kb deletion polymorphism and a PRSS2 missense variant p.Thr8Ile (rs62473563) are shown to independently contribute to meconium ileus risk (p = 0.0028, p = 0.011, respectively) and are PRSS2 pancreas eQTLs (p = 9.5 × 10−7 and p = 1.4 × 10−4, respectively), suggesting the mechanism by which these polymorphisms contribute to CF. The phase information from linked reads provides a putative causal explanation for variation at a CF-relevant locus, which also has implications for the genetic basis of non-CF pancreatitis, to which this locus has been reported to contribute.

José C. Matos, Vanni Nicoletti, Jakub Kralovanec et al.

Europe faces many problems connected to ageing infrastructure which was built in the second half of the 20th century. Bridges are one of the crucial elements of these infrastructures. In recent years, European countries have witnessed many failures of bridges across the continent. For example, the collapse of Viadotto Polcevera in Genoa caught the attention of society regarding its tragic consequences. Therefore, engineers must deal with the assessment of existing bridges which is essential for proper decision-making. Condition rating systems for bridges vary from country to country. Consequently, these differences in the methodology can lead to different conclusions related to the future service of assessed structures. For these reasons, this paper briefly describes condition rating systems for road bridges in Italy, Slovakia, and Portugal and defines the differences in the methodology. Subsequently, the obtained conclusions are compared and discussed. The aim of the paper is to encourage standardization in the assessment of bridge health conditions within European countries, highlighting the differences in the current systems adopted by various countries.

Yunqi Zhu, Tong Liu, Yingsi Wang et al.

Chitin synthases (CHSs) are vital enzymes for the synthesis of chitin and play important and differential roles in fungal development, cell wall integrity, environmental adaptation, virulence, and metabolism in fungi. However, except for ChsC, a class III CHS, little is known about the functions of CHSs in <i>Aspergillus niger</i>, an important fungus that is widely applied in the fermentation industry and food processing, as well as a spoilage fungus of food and a human pathogen. This study showed the important functions of ChsA, a class II CHS, in <i>A. niger</i> using multi-phenotypic and transcriptional analyses under various conditions. The deletion of <i>chsA</i> led to severe defects in conidiation on different media and resulted in the formation of smaller and less compact pellets with less septa in hyphal cells during submerged fermentation. Compared with the WT, the Δ<i>chsA</i> mutants exhibited less chitin content, reduced growth under the stresses of cell wall-disturbing and oxidative agents, more released protoplasts, a thicker conidial wall, decreased production of amylases, pectinases, cellulases, and malic acid, and increased citric acid production. However, Δ<i>chsA</i> mutants displayed insignificant changes in their sensitivity to osmotic agents and infection ability on apple. These findings concurred with the alteration in the transcript levels and enzymatic activities of some phenotype-related genes. Conclusively, ChsA is important for cell wall integrity and mycelial morphology, and acts as a positive regulator of conidiation, cellular responses to oxidative stresses, and the production of malic acid and some enzymes, but negatively regulates the citric acid production in <i>A. niger</i>.

B. Boughton, Dinaiz Thinagaran, Daniel Sarabia et al.

Mass spectrometry imaging (MSI) is a developing technique to measure the spatio-temporal distribution of many biomolecules in tissues. Over the preceding decade, MSI has been adopted by plant biologists and applied in a broad range of areas, including primary metabolism, natural products, plant defense, plant responses to abiotic and biotic stress, plant lipids and the developing field of spatial metabolomics. This review covers recent advances in plant-based MSI, general aspects of instrumentation, analytical approaches, sample preparation and the current trends in respective plant research.

Juan A. Méndez-Líter, Ana Pozo-Rodríguez, Enrique Madruga et al.

Glycoside hydrolases (GHs) are enzymes that hydrolyze glycosidic bonds, but some of them can also catalyze the synthesis of glycosides by transglycosylation. However, the yields of this reaction are generally low since the glycosides formed end up being hydrolyzed by these same enzymes. For this reason, mutagenic variants with null or drastically reduced hydrolytic activity have been developed, thus enhancing their synthetic ability. Two mutagenic variants, a glycosynthase engineered from a β-glucosidase (BGL-1-E521G) and a thioglycoligase from a β-xylosidase (BxTW1-E495A), both from the ascomycete <i>Talaromyces amestolkiae</i>, were used to synthesize three novel epigallocatechin gallate (EGCG) glycosides. EGCG is a phenolic compound from green tea known for its antioxidant effects and therapeutic benefits, whose glycosylation could increase its bioavailability and improve its bioactive properties. The glycosynthase BGL-1-E521G produced a β-glucoside and a β-sophoroside of EGCG, while the thioglycoligase BxTW1-E495A formed the β-xyloside of EGCG. Glycosylation occurred in the 5″ and 4″ positions of EGCG, respectively. In this work, the reaction conditions for glycosides’ production were optimized, achieving around 90% conversion of EGCG with BGL-1-E521G and 60% with BxTW1-E495A. The glycosylation of EGCG caused a slight loss of its antioxidant capacity but notably increased its solubility (between 23 and 44 times) and, in the case of glucoside, also improved its thermal stability. All three glycosides showed better antiproliferative properties on breast adenocarcinoma cell line MDA-MB-231 than EGCG, and the glucosylated and sophorylated derivatives induced higher neuroprotection, increasing the viability of SH-S5Y5 neurons exposed to okadaic acid.

Karen Filbee-Dexter, Colette J. Feehan, Dan A. Smale et al.

Cycling of organic carbon in the ocean has the potential to mitigate or exacerbate global climate change, but major questions remain about the environmental controls on organic carbon flux in the coastal zone. Here, we used a field experiment distributed across 28° of latitude, and the entire range of 2 dominant kelp species in the northern hemisphere, to measure decomposition rates of kelp detritus on the seafloor in relation to local environmental factors. Detritus decomposition in both species were strongly related to ocean temperature and initial carbon content, with higher rates of biomass loss at lower latitudes with warmer temperatures. Our experiment showed slow overall decomposition and turnover of kelp detritus and modeling of coastal residence times at our study sites revealed that a significant portion of this production can remain intact long enough to reach deep marine sinks. The results suggest that decomposition of these kelp species could accelerate with ocean warming and that low-latitude kelp forests could experience the greatest increase in remineralization with a 9% to 42% reduced potential for transport to long-term ocean sinks under short-term (RCP4.5) and long-term (RCP8.5) warming scenarios. However, slow decomposition at high latitudes, where kelp abundance is predicted to expand, indicates potential for increasing kelp-carbon sinks in cooler (northern) regions. Our findings reveal an important latitudinal gradient in coastal ecosystem function that provides an improved capacity to predict the implications of ocean warming on carbon cycling. Broad-scale patterns in organic carbon decomposition revealed here can be used to identify hotspots of carbon sequestration potential and resolve relationships between carbon cycling processes and ocean climate at a global scale. Cycling of organic carbon in the ocean has the potential to mitigate or exacerbate global climate change, but how is this influenced by the environment? A field experiment at 35 sites spanning 12 geographic regions allows measurement of decomposition rates and changes in carbon content of kelp detritus in coastal habitats, revealing a strong influence of an ocean-temperature gradient on decomposition.

Peter S Johnstone, Maite Ogueta, Olga Akay et al.

Circadian clocks are highly conserved transcriptional regulators that control ~24 hr oscillations in gene expression, physiological function, and behavior. Circadian clocks exist in almost every tissue and are thought to control tissue-specific gene expression and function, synchronized by the brain clock. Many disease states are associated with loss of circadian regulation. How and when circadian clocks fail during pathogenesis remains largely unknown because it is currently difficult to monitor tissue-specific clock function in intact organisms. Here, we developed a method to directly measure the transcriptional oscillation of distinct neuronal and peripheral clocks in live, intact Drosophila, which we term Locally Activatable BioLuminescence, or LABL. Using this method, we observed that specific neuronal and peripheral clocks exhibit distinct transcriptional properties. Loss of the receptor for PDF, a circadian neurotransmitter critical for the function of the brain clock, disrupts circadian locomotor activity but not all tissue-specific circadian clocks. We found that, while peripheral clocks in non-neuronal tissues were less stable after the loss of PDF signaling, they continued to oscillate. We also demonstrate that distinct clocks exhibit differences in their loss of oscillatory amplitude or their change in period, depending on their anatomical location, mutation, or fly age. Our results demonstrate that LABL is an effective tool that allows rapid, affordable, and direct real-time monitoring of individual clocks in vivo.

Omayma O Abdelaleem, Olfat G. Shaker, Mohamed M. Mohamed et al.

Background: Ischemic stroke is one of the serious complications of diabetes. Non-coding RNAs are established as promising biomarkers for diabetes and its complications. The present research investigated the expression profiles of serum TUG1, LINC00657, miR-9, and miR-106a in diabetic patients with and without stroke.Methods: A total of 75 diabetic patients without stroke, 77 patients with stroke, and 71 healthy controls were recruited in the current study. The serum expression levels of TUG1, LINC00657, miR-9, and miR-106a were assessed using quantitative real-time polymerase chain reaction assays.Results: We observed significant high expression levels of LINC00657 and miR-9 in the serum of diabetic patients without stroke compared to control participants. At the same time, we found marked increases of serum TUG1, LINC00657, and miR-9 and a marked decrease of serum miR-106a in diabetic patients who had stroke relative to those without stroke. Also, we revealed positive correlations between each of TUG1, LINC00657, and miR-9 and the National Institutes of Health Stroke Scale (NIHSS). However, there was a negative correlation between miR-106a and NIHSS. Finally, we demonstrated a negative correlation between LINC00657 and miR-106a in diabetic patients with stroke.Conclusion: Serum non-coding RNAs, TUG1, LINC00657, miR-9, and miR-106a displayed potential as novel molecular biomarkers for diabetes complicated with stroke, suggesting that they might be new therapeutic targets for the treatment of diabetic patients with stroke.

Li Zhang, Bin Zhang, Anqing Liu et al.

Trust assessment is of great significance to related issues such as privacy protection and rumor transmission in online social networks. At present, there are mainly two types of trust models: discrete type and continuous, type. Little work has been done on considering distrust and trust at the same time, especially on the propagation mechanism of distrust. To this end, this paper proposes a multilevel trust model and a corresponding trust evaluation method based on a reliability model called multivalued decision diagrams (MDDs). The proposed trust model combines characteristics of both discrete and continuous trust and considers the dynamic changing mechanism of the multilevel trust. The propagation of distrust and conflicts of opinions are also handled. Experimental results show that the proposed method outperforms other existing methods.