Miracle-dz/UniFAR-FTUs huggingface dataset:
First Report of Botryosphaeria parva Causing Stem Blight on Rubus crataegifolius in Korea

which is commonly found in the mountainous areas of Korea, Japan, and northeast China. R. crataegifolius has been used as food and traditional medicine for many years in this region by its various bioactivities such as immunological and antioxidant activities (Moon et al., 2011; Ni et al., 2009; Zhang et al., 2010). According to the usefulness of R. crataegifolius, the importance of disease management of R. crataegifolius has increased in Korea (Korea Forest Service, 2015). Several pathogens that infect R. crataegifolius have been reported in Korea, including Septoria rubi, Rhizopus stolonifer, Phragmidium griseum, and Phytoplasma (Kim et al., 2009). In July 2015, stem blight symptoms were observed in a field of R. crataegifolius in Pohang, Gyeongbuk province, Korea. Early in the course of the disease, plants showed dark red spots on stems; these spots expanded to black lesions associated with stem blight (Fig. 1A). As the disease progressed, pycnidia appeared on the stem lesions (Fig. 1B). The blight eventually spread to the leaves and resulted in plant death. A fungus, the presumed causal agent, was isolated from the diseased plant and designated as PPL02. The infected part of the stem was cut into small pieces and the surface of pieces was sterilized with 1% NaOCl for 1 minute and washed three times with 70% ethanol. The surface-sterilized pieces were placed onto potato dextrose agar (PDA) medium and incubated at 25C. For isolation of a pure culture, hyphal tips of mycelia on the PDA medium were cut and transferred to fresh PDA plates. Open Access Res. Plant Dis. 22(2): 116-121 (2016) http://dx.doi. org/10.5423/RPD.2016. 22.2. 116
Prevalence of Aeromonas hydrophila in relation to timing and duration of breeding in three species of ranid frogs1

Abstract: Species of temperate ranid frogs differ in ways (e.g., habitat preferences, timing and duration of their breeding seasons) that could influence their susceptibility to parasites and pathogens. In this study, we compared the prevalence of Aeromonas hydrophila in breeding adults of bull frogs (Rana catesbeiana), green frogs (R. clamitans), and leopard frogs (R. pipiens) from a region in eastern Ontario. Adult R. pipiens had a higher prevalence of A. hydrophila than either R. clamitans or R. catesbeiana, but there were no differences between sexes. There was also a trend for a decline in prevalence of A. hydrophila over the breeding seasons of all three species. Reduced immune ability soon after emergence from hibernation could explain the higher prevalence of A. hydrophila earlier in the season. The higher prevalence in R. pipiens may be a function of earlier and contracted breeding in this species. The expected high stress during breeding for this species could have implications for its relative susceptibility to other disease agents that share routes of infection with A. hydrophila or that are challenged by the same components of the immune system.
Calmodulin regulation of calcium channels and neurotransmitter release in bovine adrenal chromaffin cells

Calmodulin is a molecule implicated in regulating voltage-gated calcium channels (VGCC’s) and the exocytotic machinery to fine tune neurotransmitter release. I have investigated the role this molecule plays in stimulus-secretion coupling in bovine adrenal chromaffin cells by over-expressing either wild type (CaMwt), or a mutated calmodulin (CaMi234), rendered incapable o f binding calcium by adenoviral infection. Stimulus-evoked secretion was monitored by combined measurements o f membrane capacitance (ACm) and voltage-clamp recording o f calcium currents in single cells. Cells were clamped in either the perforated patch or whole-cell configuration and calcium-dependent exocytosis evoked by single depolarizing voltage steps or trains o f depolarisations. I show that the exocytotic efficiency, derived by dividing ACm by the integral o f the calcium current, is reduced for N-type channels compared to P/Qtype channels. Cation substitution experiments revealed that pharmacologically isolated N-type channels displayed the most profound sensitivity to calciumdependent inactivation. Studies aimed at eluding the molecular mechanisms underlying calcium-dependent inactivation show that inhibiting calcinuerin by 20 mins preincubation with lpM cyclosporine A or by introducing 30pM calmodulin inhibitory peptides through the patch pipette did not significantly reduce the level o f whole cell calcium-dependent inactivation. In contrast, adenoviral mediated expression o f a mutant calmodulin deficient in calcium binding resulted in a highly significant reduction in N-type, but not P/Q-type channel inactivation. This is the first time that calmodulin has been shown to regulate endogenously expressed N-type calcium channels. These results are consistent with calmodulin acting directly to control N-type channel inactivation and therefore limit this channels ability to couple to exocytosis during prolonged stimulation. Ca2+/calmodulin was also found to interact with the secretory machinery. Expression o f CaMi234 significantly reduced the exocytotic efficiency o f brief depolarisations (< 100ms), however the exocytotic efficiency to longer depolarisations (> 200ms) was not significantly different between cells expressing CaMj234 and CaM^. This suggests that Ca2+-Calmodulin is required for filling and/or release from a rapidly releasable pool o f vesicles which is easily depleted, but not from the slowly releasable pool which dominates exocytotic responses measured with prolonged responses. Over-expression o f CaMi234 also selectively inhibited clathrin-mediated endocytosis, leaving other endocytotic pathways unaltered. Taken together, these results place calmodulin as a central molecule that controls calcium entry (calcium channels) and the exocytotic machinery to regulate stimulus-coupled secretion.
Investigation of common disease regulatory network for metabolic disorders: A bioinformatics approach

Metabolic disorder causes the failure of metabolism process is growing concern worldwide. This research predicts a common metabolic pathway that is shared by Obesity, Type-2 Diabetes, Hypertension and Cardiovascular diseases due to metabolic disorder. A protein-protein interaction network is created to show the protein co-expression, co-regulations and interactions among gene and diseases. Genes whose are associated with metabolic diseases have been accumulated from different gene databases with verification and ‘mined’ them to establish gene interaction network models for expressing the molecular linkages among genes and diseases which affect disease progression. The number of associated genes identified for Type 2 Diabetes (T2D) is 250, Hypertension (HT) is 156, Obesity (OB) is 185 and cardiovascular disease (CVD) is 178.Among the sorted candidate gene 10 common genes are identified whose are directly or indirectly associated with four diseases by doing linkage filtering. By analysing the gene network model and PPI network a common metabolic pathway among metabolic diseases has been investigated.
Characterization and optimization of xylanase producing strain of Bacillus subtilis isolated from the Cabbage Looper (Trichoplusia ni (Hübner)) intestine

Aims: To characterize xylanolytic enzyme producing strains of Bacillus subtilis from the intestinal tract of a cabbage looper (Trichoplusia ni (Hübner)) larvae. Methodology and results: Approximately 5 g of intestinal content from the instar larvae were homogenated and serially diluted 10 -4 -10 -6 times with sterile normal saline before being spread onto duplicate tryptic soy agar plates. Every different colony was selected to test for xylanase production. Of six isolates, only one was found to be positive for xylanase production by screening agar. Biochemical characteristics and 16S rRNA gene sequencing indicated that the Bact-I was closely related to Bacillus subtilis. Optimization of xylanase enzyme production showed that Bacillus subtilis was able to produce xylanase enzymes when grown in a culture medium containing 2% (w/v) corn stover and 0.6% (w/v) yeast extract at pH 10 and 37 °C. The xylanase gene was cloned and characterized. The result revealed that the xylanase gene of Bacillus subtilis was homology to the β-1,4 endo-xylanase gene. Conclusion, significance and impact of study: A xylanase producing Bacillus subtilis was isolated from the intestinal tract of a cabbage looper (Trichoplusia ni (Hübner)) larvae. Optimization and evaluation of the xylanase activity of Bacillus subtilis indicated that it could be useful for xylanase production or as a probiotic for improving animal feed stuff.
GENETIC DIVERSITY ANALYSIS IN DATE PALM (PHOENIX DACTYLIFERA L) GERMPLASM USING MICROSATELLITE MARKERS

The Date Palm (Phoenix dactylifera L), germplasm commonly cultivated in Egypt, shows a wide range of repining periods and fruit quality and is an unexploited resource for breeding programs. The main purpose of this study was to fingerprint 45 date palm genotypes and accessions and to construct a molecular database including the cultivars commonly grown in Egypt. An analysis of thirty three microsatellite simple sequence repeat (SSR) loci out of thirty five markers was performed to define allele diversity, heterozygosity and genetic structure. The average number of alleles per locus was 32.3. Heterozygosity per locus was 0.64 (Dpalm-103) to 0.96 (Dplam-100, 256, mpdCIR08 and mpdCIR078) with an average of 0.89. The highest heterozygosity (0.768) was detected in Avanda, followed by Amhat (0.758) while Khalas had lowest heterozygosity value (0.455). The genetic similarity values ranged from 0.041 to 0.260. The obtained dendrogram showed three main clusters and generally, a good structuring of 45 genotypes and accessions. The use of 33 polymorphic microsatellite markers and the level of genetic variability detected within Egyptian date palm germplasm suggested that this is reliable, efficient and effective marker system that can be used for diversity analysis and subsequently in crop improvement programs.
Purification and characterization of extracellular α-amylase from a thermophilic Anoxybacillus thermarum A4 strain

ABSTRACT α -Amylase from Anoxybacillus thermarum A4 was purified using ammonium sulphate precipitation and Sephadex G-100 gel filtration chromatography, with 29.8-fold purification and 74.6% yield. A4 amylase showed best performance for soluble potato starch hydrolysis at 70 °C and pH 5.5-10.5. A4 amylase was extremely stable at +4 °C, and the enzyme retained over 65% of its original α - amylase activity at 70 °C and 43% at 90 °C. The enzyme’s K m values for soluble starch, amylopectin and amylose substrates were obtained as 0.9, 1.3 and 0.5 mg/mL, respectively. EDTA, Hg 2+ , B 4 O 72- , OH - , CN -, and urea exhibited different inhibition effects; their IC 50 values were identified as 8.0, 5.75, 16.5, 15.2, 8.2 and 10.9 mM, respectively. A4 amylase exhibited extreme stability toward some surfactants and perfect match for a wide variety of commercial solid and liquid detergents at 55 °C. So, it may be considered to be potential applications for detergent and other industrial uses.
Effects of gutting process on the shelf life of cultured meagre (Argyrosomus regius ASSO, 1801) stored at 4 ± 1 °C

The aim of this study was to determine chemical, nutritional and microbiological evaluation of whole or gutted meagre stored at 4 ± 1 oC. Whole ungutted (Group A), eviscerated (Group B), beheaded-eviscerated fish (Group C) and fillets (Group D) groups were created for this study. According to fatty acid analysis, it was determined that meagre is rich in PUFA content and the n3/n6 ratio is within the ideal limits. In all 4 groups, obtained from fillets values were the highest in general, quality parameters were found within acceptable limits. Psychrophilic and mesophilic aerobic bacteria counts exceeded the standards for fillet groups on 7th days of storage. According to microbiological analysis, ungutted, beheaded, eviscerated samples were not exceeded limit values on 9th day. In conclusion, whole or gutted (headed and eviscerated) storage of meagre is found to be more advantageous compared to fillets for storage at 4 ± 1 oC.
Ab initio Structural Insights and Functional Analysis of Thioredoxin GlutathioneReductase from Schistosoma japonicum

Ab initio Structural Insights and Functional Analysis of Thioredoxin Glutathione Reductase from Schistosoma japonicum Platyhelminth parasites are a major health problem in developing countries. Around the world Schistosomiasis remains a major public health concern affecting billions of people. In Schistosoma japonicum and some other platyhelminths Thioredoxin glutathione reductase (TGR) enzymes have been identified as alternative drug targets a key enzyme in the pathway of the parasite for detoxification of reactive oxygen species. In Thioredoxin glutathione reductase a C-terminal redox center containing selenocysteine (Sec) is present TGR is a homodimeric enzyme comprising a glutaredoxin domain and thioredoxin reductase (TR) domains. The secondary structural prediction of Thioredoxin glutathione reductase from Schistosoma japonicum has been done which would be useful for further analysis of this enzyme. Studies on annotating and analysing the function of (TGR) enzymes is done by using different bioinformatics tools like GRAVY, CELLO v.2. 5, and by using different expasy tools. PDB-sum a web based tools is used to analyse insights of the enzyme TGR. For treatment of human schistosomiasis praziquantel is the only drug of choice. The emergence of drug resistance to praziquantel in schistosomes makes the development of novel drugs an urgent task. The present study is designed to analyse the ab initio structural and functional insights of the TGR as a target for development of novel antischistosomal agents in Schistosoma japonicum, a platyhelminth endemic in Asia.
Unsaturation and regional influences on species richness in ecological communities: A review of the evidence

AbstractAccording to the traditional Volterra-Gause viewpoint, the number of species in ecological communities (local richness) was thought to be controlled mainly by species interactions operating within the community itself. In order for this viewpoint to be correct, communities had to be close to equilibrium, species interactions had to be intense, and local richness had to be limited by the number of resources and physical factors. Here I argue that resource limitation and other local factors often fail to set upper limits on local richness. Revised theoretical models that add realism in the form of environmental complexity and non-equilibrium population densities of the constituent species do not predict such limits. In addition, critical evidence for such limits in real communities is often lacking. Local richness frequently correlates with the number of species in the surrounding region, and does not become independent of the latter in the richest regions as would be expected if the community becam.
Improvement Fe Content of Wheat(Triticum aestivum) Grain by Soybean Ferritin Expression Cassette without Vector Backbone Sequence

Iron (Fe) is important and indispensable element for the normal physiological processes in the human body, and iron deficiency is a serious nutritional problem in the world, so it is economical and effective to breed and grow wheat cultivars with high grain iron content, especially for those population in poor-developed areas. In this paper, the soybean (Glycine max) ferritin gene was obtained by RT-PCR, and cloned into the pBAC47P vector. The soybean ferritin expression cassette without vector backbone sequence but including wheat endosperm-specific HMW-GS 1Dx5 promoter and NOS terminator was constructed by digestion and purification, and has been transformed through particle bombardment of PDS1000/He system into winter wheat(Triticum aestivum) cultivars, Jinghua No.1. After phosphinothricin (PPT) selection, differentiation and regeneration, 276 plants were regenerated from immature embryos callus. By PCR screening and PCR-Southern blot using specific primers for soybean ferritin gene 65 transgenic plants of T0 generation were selected, Among them, kernels of 29 plants of T1 generation were positive by RT-PCR on the RNA levels. The grain iron content of 8031 T1 transgenic lines have been determined. Compared to the control, there were 265 lines of them have increased iron content, ranging from 4.93 to 64.03 percent, and 22 lines of them increased significantly, which suggests that Fe content of wheat grain can be improved by the soybean ferritin expression cassette without vector backbone sequence.
Single cell analysis of lincRNA expression during human blastocyst differentiation identifies TERT (+) multi-lineage precursor cells

Chromosome instability and aneuploidies occur very frequently in human embryos, impairing proper embryogenesis and leading to cell cycle arrest, loss of cell viability, and developmental failures in 50-80% of cleavage-stage embryos. This high frequency of cellular extinction events represents a significant experimental obstacle challenging analyses of individual cells isolated from human preimplantation embryos. Here, we carried out single cell expression profiling analyses of 241 individual cells recovered from 32 human embryos during the early and late stages of viable human blastocyst differentiation. Classification of embryonic cells was performed solely based on expression patterns of human pluripotency-associated transcripts (HPAT), which represent a family of transposable element-derived lincRNAs highly expressed in human embryonic stem cells (hESCs) and regulating nuclear reprogramming and pluripotency induction. We then validated our findings by analyzing 1,708 individual embryonic cells recovered from more than 100 human embryos and 259 mouse embryonic cells at different stages of preimplantation embryogenesis. Our experiments demonstrate that segregation of human blastocyst cells into distinct sub-populations based on single-cell expression profiling of just three HPATs (HPAT-21; -2; and -15) appears to inform key molecular and cellular events of naïve pluripotency induction and accurately captures a full spectrum of cellular diversity during human blastocyst differentiation. HPAT’s expression-guided spatiotemporal reconstruction of human embryonic development inferred from single-cell expression analysis of viable blastocyst differentiation enabled identification of TERT(+) sub-populations, which are significantly enriched for cells expressing key naïve pluripotency regulatory genes and genetic markers of all three major lineages created during human blastocyst differentiation. Results of our analyses suggest that during early stages of preimplantation embryogenesis putative immortal multi-lineage precursor cells (iMPCs) are created, which then differentiate into trophectoderm, primitive endoderm and pluripotent epiblast lineages. We propose that cellular extinction events in cleavage-stage embryos are triggered by premature activation of HPAT lincRNAs reflecting failed iMPC’s creation attempts. Highlights Single cell analysis of 1,949 human & 259 mouse embryonic cells Identification of 5 most abundant HPAT lincRNAs in viable human blastocysts Expression profiling of just 3 lincRNAs captures cellular diversity of human blastocysts Identification & characterization of TERT(+) multi-lineage precursor cells MTTH/HPAT lincRNAs regulatory axis of naïve pluripotency induction in vivo
Effect of hypoxia on the composition and state of lipids and oxygen-transport properties of erythrocyte haemoglobin

ABSTRACT The aim of this study was to investigate the relationship between the composition and state of erythrocytic lipids and oxygen-binding properties of erythrocyte haemoglobin-derived haematoporphyrin under hypoxia. The results from this study showed that hypoxia causes a profound change in the composition of the lipids that form the bilayer of erythrocyte membranes, as well as in the functional characteristics of erythrocytes. The detected changes correlate with morphological reconstruction of erythrocytes and, consequently, affect the oxygen-transport properties of erythrocytes. The obtained results showed that the lipid phase plays an important role in the functioning of erythrocytes in health as well as in event of development of ischemic heart disease and other pathological processes that accompany hypoxia.
Molecular markers for germplasm identification and characterization.

Markers based on DNA polymorphism have become a common tool for genotyping individuals and inferring information on the genetic structure of germplasm collections, discovery of synonymy, and kinship. Among the numerous DNA markers (RFLP, RAPD, AFLP, SSR, ISSR, SAMPL, S-SAP, SNP, and others) proposed in the literature of the past two decades, microsatellites (or SSRs) and SNPs are the markers that are best suited for this scope, providing the robust data necessary in forensic disputes, as well as for intellectual property and patent rights. This paper is divided into three parts. The first part deals with the choice of SSR markers and protocols, with particular focus on the issues that can affect the accuracy of the analyses, such as the core repeat length, fragment binning and sizing, and allele calling. The protocols adopted for humans are used as a reference. The second part deals with the statistical analysis of identity and parentage, using once again the procedures adopted in humans as a reference, for the aspects that are common to both fields. The third part discusses several issues that are more typical of plant genotyping, such as the occurrence of chimeric tri-allelic patterns, polyploidy, and clonal variants. The last aspect, in particular, which deals with essentially derived varieties, is discussed considering the opportunity offered by the recent evolution of sequencing and genotyping platforms, and the importance of sport variants in fruit crops.
Are changes in breeding habitat responsible for recent population changes of long-distance migrant birds?

ABSTRACT Capsule: The direction and magnitude of changes in structure of UK woodlands since the 1980s, are inconsistent with them playing a causative role in the declines of four migrant bird species in upland oak woods. Aims: To investigate whether changes in woodland structure were a possible cause of population changes of four Afro-Palearctic migrants (Wood Warbler Phylloscopus sibilatrix, Tree Pipit Anthus trivialis, Pied Flycatcher Ficedula hypoleuca and Common Redstart Phoenicurus phoenicurus) in the upland oakwoods of western and northern Britain. Methods: Bird population estimates and measures of woodland structure were recorded in two time periods 1982–85 and 2003–04 across six regions of the UK. We modelled the effect of habitat change and initial habitat state on population changes between the two time periods. The predicted effects of habitat change on populations were then compared with observed population changes across the different regions. Results: All four species underwent population declines; there were also significant increases in ground cover and understorey cover. The number of birds in 2003–04 was influenced by habitat structure at this time in addition to showing regional differences. Change in bird numbers varied between regions and was affected by both the initial habitat state and change in habitat structure, with regional variation in the effect of habitat change. There was however no relationship between the predicted effect of change in habitat structure on population size and observed regional population changes. Conclusions: Changes in woodland structure are unlikely to be the main driver of population change in these four migrant bird species, and large-scale factors affecting demographics in other parts of their breeding range or in their wintering areas are likely reasons for local population declines.