Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel organelle anion channels formed by chromogranin B drive normal granule maturation in endocrine cells

All endocrine cells need an anion conductance for maturation of secretory granules. Identity of this family of anion channels has been elusive for forty years. We now show that a family of granule protein, CHGB, serves the long-sought conductance. CHGB interacts with membranes through two amphipathic helices, and forms a chloride channel with large conductance and high anion selectivity. Fast kinetics and high cooperativity suggest that CHGB tetramerizes to form a functional channel. Nonfunctional mutants separate CHGB’s function in granule maturation from that in granule biogenesis. In neuroendocrine cells, CHGB channel and a H+-ATPase drives normal insulin maturation inside or dopamine loading into secretory granules. CHGB’s tight membrane-association after exocytotic release of secretory granules separates its intracellular function from extracellular functions of its proteolytic peptides. CHGB-null mice show consistent impairment of granule acidification in pancreatic beta-cells. These findings together support that the phylogenetically conserved CHGB proteins constitute a new family of organelle chloride channels in the regulated secretory pathway among various endocrine cells.
Stabilization of Alliinase from Garlic by Osmolytes and the Mannose-Specific Lectin ASAI

Objectives: Alliinase is a pyridoxal-5’-phosphate (PLP)-dependent enzyme responsible for the production of diallyl thiosulfinate (allicin), the biologically active component of garlic, from alliin. The use of allicin for treatment of various diseases has been proposed but it is very unstable in the blood stream. This difficulty can be overcome by administration of alliin, together with a conjugate of alliinase directed towards the target cells. This, in turn requires a stable and active form of the enzyme. In this study we evaluate the stability of alliinase itself, in the presence and absence of osmolytes, as well as that of its catalytically active complex with a mannose-specific lectin, ASAI (Allium sativum agglutinin I), also presents in garlic. Methods: Alliinase, and ASAI were both purified from garlic cloves. Thermal stability of alliinase itself, and of its complexes with PLP and ASAI, in the presence and absence of osmolytes, was analyzed by monitoring enzymic activity, and using DSC (differential scanning calorimetry). Key findings: PLP exerts only a minor influence on alliinase structure and stablity. But both osmolytes and ASAI stabilize the enzyme considerably. Conclusions: The principle finding is that ASAI greatly stabilizes alliinase. Thus, the lectin-enzyme complex, which can be lyophilized and stored until used, provides an effective formulation of alliinase for generation of allicin from alliin in vivo.
miR-21-5p and miR-30a-5p are identical in human and bovine, have similar isomiR distribution, and cannot be used to identify xenomiR uptake from cow milk

microRNAs (miRNAs) are often highly conserved across species, but species-specific sequences are known. In addition, miRNA “isomiRs” arise from the same precursor molecule but differ in post-processing length and modification, usually at the 3’ end. A recently published feeding study reported the intriguing result that two bovine milk-specific miRNAs were taken up into human circulation after ingestion of bovine milk. Unfortunately, this interpretation is based on annotation errors in a public microRNA database. Reanalysis using databses including the MirGeneDB database reveals that the miRNAs in question, miR-21-5p and miR-30a-5p, arise from 100% identical 5’ precursor sequences in human and bovine, and the putative bovine-specific isomiRs appear to be depleted, not enriched, in bovine milk. Thus, enrichment of these isomiRs in human blood is inconsistent with uptake of xenomiRs and likely betrays endogenous miRNA regulation in response to diet or technical artifact.
Peel and pulp of baru (Dipteryx Alata Vog.) provide high fiber, phenolic content and antioxidant capacity

, 2014). No scientific study about the proximate composition of baru peel, separated from the pulp, has been found in the literature up to now. Studies have shown that phenolic compounds have anti-inflammatory, anti-proliferative and anti-infectious properties, as well as exerting a protective effect against oxidative stress related to diabetes, cancer, cardiovascular and neurodegenerative diseases (Del Rio et al., 2013). Considering the applicability of baru peel and pulp in processed foods for human consumption and the health-benefits of phenolic compounds, it is worth studying the nutrients and phenolic content of the whole baru fruit, including its peel and pulp. The chemical characterization of peel and pulp, compared to the almond, can stimulate the consumption of whole fruit and the economic investments on processed foods with baru. Thus, the aim of this study was to evaluate the proximate composition, the total phenolic contents and the antioxidant capacity of the peel and pulp of baru fruit compared to raw and roasted baru almonds.
Donor effect on cultured pearl nacre development and shell matrix gene expression in Pinctada margaritifera reared in different field sites

: Understanding the respective roles played by donor and recipient pearl oysters in pearl quality determination in relation to the environment In most Pinctada species, pearl size is mainly related to recipient oyster growth performance, but also relies to some extent on the biomineralisation activity of the pearl sac, a tissue that originates from the donor oyster mantle. We examined donor effect on pearl size in response to culture in the lagoons on Arutua and Apataki atolls. Overall nacre weight and thickness were greater in Arutua than in Apataki, but sensitivity to the environment differed between donors. Some donors were associated with significantly heavier and thicker nacre in Arutua (I group), while others had similar results at the two sites (NI group). On average, up to 20% of the pearl size could be attributed to the donor but, in group I, donor effect was responsible for up to 36% of nacre weight determination. Additionally, a real-time PCR expression study of eight matrix protein genes related to biomineralisation in the pearl sac showed that MSI60 , pearlin and pif177 were significantly and positively correlated with nacre weight and thickness, with the latter two genes explaining the larger pearl size observed in Arutua. Donor oysters in P. margaritifera therefore play a key role in pearl size improvement, related to the role of the shell matrix protein genes. Understanding such contributions could help in the design of genetic selection plans for specific and adapted donor oyster lines.
Transcriptional regulation of a pea vicilin gene

· ·· ······················ ·· ··· ············· ···· ··· ··· ······· ·············· ················ ······ ······ ······· ···· ····· vii Abbreviations . ix Chapter 1. Literature review. 1 1.
Development of a high-throughput PCR & sequencing approach for SNP identification in Leguminosae species

9 Abstract in het Nederlands . 11in het Nederlands . 11 1 Eurolegume . 13 2 Leguminosae . 15 2.1 Biological nitrogen fixation . 15 2.2 Glycine max (soybean) . 17 2.3 Pisum sativum and Vicia faba . 18 3 Quantitative genetics and molecular markers . 19 3.1 Quantitative genetics . 19 3.2 Molecular markers . 19 3.3 SNP’s. 19 3.4 SNP’s as molecular markers . 20 4 Goals . 21 5 Materials and methods . 23 5.1 Design primers and optimization of PCR conditions . 23 5.1. 1 Primer design . 23 5.1. 2 Optimization of PCR conditions . 24 5.2 PCR . 28 5.2.1 Genomic PCR . 28 5.2.2 Barcoding PCR . 30 5.3 DNA Sequencing . 33 5.3.1 Library preparation. 33 5.3.2 Emulsion PCR . 34 5.3.3 DNA sequencing . 37 6 Results and discussion . 41 6.1 Experiment design . 41 6.1. 1 Primer design . 41 6.1. 2 PCR kit . 41 6.1. 3 Thermocycler . 44 6.2 Genomic PCR . 49 6.2.1 Results & discussion . 50 6.3 Barcoding PCR . 53 6.3.1 Results & discussion . 55 6.4 DNA-sequencing . 58 6.4. 1 Library preparation. 58 6.4. 2 Emulsion PCR . 61 7 Conclusion . 63 Bibliography . 65 Appendix A: Designed primers . 71 Appendix B : Melting curves genomic PCR. 79 Appendix C : Melting curves barcoding PCR. 85 Appendix D: Primers that worked in genomic PCR and barcoding PCR . 91
Diseases on Christmas trees in southern Sweden and western North Carolina - with emphasis on Phytophthora root rot and Neonectria canker

Surveys and inoculation experiments were conducted in Sweden and North Carolina to investigate diseases of Christmas trees, focusing on Phytophthora root rot and Neonectria canker. Christmas tree production is a significant business in North Carolina and for individual growers in Sweden. In North Carolina, six Phytophthora species were discovered on symptomatic Fraser fir (Abies fraseri), three of which were new to the region (P. europaea, P. citrophthora, and P. sansomeana). Phytophthora cinnamomi was the dominating species causing disease, but P. cryptogea also contributed significantly to Fraser fir loss. According to a questionnaire survey, 88% of Christmas tree growers had Phytophthora root rot in their fields. To combat Phytophthora root rot in North Carolina eastern white pine is planted on heavily infested sites as an alternative to Fraser fir. After screening eastern white pine families for P. cinnamomi tolerance, it is evident that families specifically selected for tolerance will reduce problems with Phytophthora root rot. In Sweden, 16 disease-causing pathogens and six pests were discovered in a survey of Christmas tree plantations. Further studies focused on Phytophthora root rot and Neonectria canker. Five identified Phytophthora species were isolated from waterways and soil samples. In addition, P. megasperma was isolated from a young diseased Norway spruce (Picea abies). Inoculation tests with P. cryptogea, P. megasperma, P. plurivora showed minor disease development. The Phytophthora species found were not widespread and it is currently a minor problem for Swedish Christmas tree growers. From Norway spruce trees with top-dieback, Neonectria fuckeliana was commonly isolated. On Nordmann fir, Neonectria neomacrospora was found. Inoculation studies using N. fuckeliana and N. neomacrospora on Norway spruce and Nordmann fir, respectively, demonstrated that both pathogens caused disease, while a second N. fuckeliana inoculation study found symptom development to be minor. For rapid and reliable identification of N. fuckeliana in northern Europe, a species-specific PCR-based test was developed.
Preliminary study on character associations, phenotypic and genotypic divergence for yield and related quantitative traits among cowpea landraces (Vigna unguiculata) from the Western Highland Region of Cameroon

Abstract Cowpea (Vigna unguiculata) is an important tropical legume crop contributing significantly to food security in tropical regions. The present study was carried out to determine the extent of genetic variation, to estimate character associations, heritability and genetic advance of 25 quantitative traits in 30 genotypes of cultivated Vigna unguiculata from the western highland region of Cameroon. These quantitative traits were selected among cowpea descriptor lists. For all these traits, the analysis of variance showed significant difference among genotypes, highlighting the existence of important genetic divergence among the studied accessions. The highest phenotypic and genotypic coefficient of variation was observed in grain yield, pod yield and 100 seed weight. Genetic advance of these three characters was also the highest. Broad sense heritability was high in general, with 20 traits out of 25 having heritability values greater than 70%. This high heritability indicates little influence of the environment on these characters in cowpea. The highest heritability was recorded for 100 seed weight (98.15%) and the lowest for shoot weight (41.38%). At 0.05 probability level, grain yield correlated significantly with 21 out of the 24 other quantitative traits. Among others, grain yield correlated positively and significantly with 100 seed weight, number of pods per plant, number of branches per plant, number of nodes per plant, plant height, plant width, pod length, pod width, seed length, seed width and number of seeds per pod. These positive correlations between grain yield and many other traits indicate that a selection program based on any of these traits will result in increasing yield. Cluster analysis using UPGMA method revealed five distinct clusters. Genotypes named KEBCP025, KEB-CP006, KEB-CP098, KEB-CP070, and more importantly KEB-CP054 and KEB-CP004, were grouped in a single cluster and were characterized by a significantly higher grain yield, pod yield, number of pods per plant, number of seed per pod, plant height, pod length and pod width compared to other clusters. Accessions KEB-CP036 and KEB-CP031 produced significantly more important fresh biomass. These genotypes could be used as parents in genetic improvement programs aiming to increase yield and fresh biomass in cowpea.
Cyanobacteria reduce quagga mussel (Dreissena rostriformis bugensis) spawning and fertilization success

Quagga mussels (Dreissena rostriformis bugensis) are highly fecund broadcast spawners invasive to freshwaters of North America and western Europe. We hypothesized that environmental cues from phytoplankton can trigger gamete release in quagga mussels. Nutritious algae may stimulate dreissenid spawning, but less palatable food, such as bloom-forming cyanobacteria, could be a hindrance. The objective of our study was to test whether exposure to cyanobacteria can inhibit quagga mussel spawning and fertilization. We assessed spawning in the presence of serotonin, a known spawning inducer, where adult quagga mussels placed in individual vials were exposed to 13 cyanobacteria cultures and purified algal toxin (microcystin-LR) with artificial lake water as the control. Fertilization success was evaluated by combining eggs with sperm in conjunction with cyanobacteria, and enumerating zygote formation marked by cellular cleavage. Several cyanobacterial strains reduced spawning and fertilization success, but microcystin-LR had no effect. Fertilization was more sensitive to cyanobacteria than gamete release. Only 1 culture, Aphanizomenon flos-aquae, inhibited spawning, whereas 6 cultures consisting of Anabaena flos-aquae, Dolichospermum lemmermanii, Gloeotrichia echinulata, Lyngbya wollei, and 2 Microcystis aeruginosa isolates reduced fertilization rates by up to 44%. The effects of cyanobacteria on reproduction in invasive freshwater mussels in the wild have not yet been identified. However, our laboratory studies show that concentrations of cyanobacteria that are possible during bloom conditions probably limit reproduction. Reproductive consequences on wild populations may become more prevalent as cyanobacteria blooms occur earlier in the year, making overlap between blooms and mussel spawning more common. Describing the mechanism by which cyanobacteria inhibit spawning and fertilization could reveal novel control methods to limit reproduction of this invasive species.
Distinctions in proteomics among developmental stages of dengue vector (Aedes albopictus) mosquitoes

The embryonic proteomics that drift in the adult stage and responsible for performing visual activities including, biting and maintaining the vectorial life of dengue vector Aedes albopictus is not projected earlier. In a series of experiments we have indicated the concentration and extension of early proteomic cursors in the latter stages of life cycle up to the early emerging adult. We noticed about 70% gain of protein during larval developmental stages, until pupation. Newly emerged adult mosquitoes lost about 12% of protein than the pupal stage. In case of peptides, we observed 14-26 polypeptide bands during immature and early adult stages by using 12% of separating gel in ID SDS-PAGE. The bands in early larval stages up to 4th instar larvae were in the range of approximately ~58 to ~7 kDa, while in pupal and adult stages they were between ~200 and ~7 kDa. Newly emerged bands in pupal (i and ii) and adult (iii-vi) stages could be identified as stage specific peptides. The band number 10, which migrated at the same position in the PAGE with equal strength in all stages was identified as an essential peptide. Characterization of the above peptides might help in the pin pointing to possible virus transmission blocking mechanism of this vector insect. Bangladesh J. Zool. 45 (2): 171-183, 2017
circuitSNPs: Predicting genetic effects using a Neural Network to model regulatory modules of DNase-seq footprints

Motivation Identifying and characterizing the function of non coding regions in the genome, and the genetic variants disrupting gene regulation, is a challenging question in genetics. Through the use of high throughput experimental assays that provide information about the chromatin state within a cell, coupled with modern computational approaches, much progress has been made towards this goal, yet we still lack a comprehensive characterization of the regulatory grammar. We propose a new method that combines sequence and chromatin accessibility information through a neural network framework with the goal of determining and annotating the effect of genetic variants on regulation of chromatin accessibility and gene transcription. Importantly, our new approach can consider multiple combinations of transcription factors binding at the same location when assessing the functional impact of non-coding genetic variation. Results Our method, circuitSNPs, generates predictions describing the functional effect of genetic variants on local chromatin accessibility. Further, we demonstrate that circuitSNPs not only performs better than other variant annotation tools, but also retains the causal motifs / transcription factors that drive the predicted regulatory effect. Contact fluca@wayne.edu, rpique@wayne.edu Availability http://github.com/piquelab/circuitSNPs
Does current climate explain plant disjunctions? A test using the New Zealand alpine flora

More than 90% of plant species found in New Zealand's alpine environment are endemic to New Zealand. Two particularly species‐rich regions of high endemism are located at the northern and southern ends of the South Island and several vascular alpine plant species show clear disjunct distributions between these two regions. The aim of this study was to test the ability of a climatic hypothesis to explain these disjunct distributions and to identify if the central South Island acts as a climatic barrier.
The genomic landscape of recombination rate variation in Chlamydomonas reinhardtii reveals a pronounced effect of linked selection

Recombination confers a major evolutionary advantage by breaking up linkage disequilibrium (LD) between harmful and beneficial mutations and facilitating selection. Here, we use genome-wide patterns of LD to infer fine-scale recombination rate variation in the genome of the model green alga Chlamydomonas reinhardtii and estimate rates of LD decay across the entire genome. We observe recombination rate variation of up to two orders of magnitude, finding evidence of recombination hotspots playing a role in the genome. Recombination rate is highest just upstream of genic regions, suggesting the preferential targeting of recombination breakpoints in promoter regions. Furthermore, we observe a positive correlation between GC content and recombination rate, suggesting a role for GC-biased gene conversion or selection on base composition within the GC-rich genome of C. reinhardtii. We also find a positive relationship between nucleotide diversity and recombination, consistent with widespread influence of linked selection in the genome. Finally, we use estimates of the effective rate of recombination to calculate the rate of sex that occurs in natural populations of this important model microbe, estimating a sexual cycle roughly every 770 generations. We argue that the relatively infrequent rate of sex and large effective population size creates an population genetic environment that increases the influence of linked selection on the genome.
Reproductive Pattern of the Silky Short-Tailed Bat Carollia brevicauda (Chiroptera: Phyllostomidae) in the Andes of Colombia

Abstract. The silky short-tailed bat (Carollia brevicauda) is common and widely distributed in the Neotropic; however, data on reproductive biology is scarce. Here, we present the results of a monitoring of two colonies in the Andes of Colombia. The high recapture rate allowed us to estimate the length of pregnancy, lactation, and between-births interval. Results showed that this species reproduced with low synchrony throughout the year and may exhibit a polyoestry reproductive pattern with oestrous postpartum that lasts around eight months. The pregnancy length was two and a half months to three months and lactation length was one and a half month to two months. Males also showed reproductive activity throughout the year. The asynchronous reproduction of this species at the study area suggests that factors related to body condition may be more important for timing of reproduction than environmental cues. The reproductive life-history traits of this species are similar to other species of the genus Carollia and Phyllostomidae family.
1 IP 3 R 2-independent Ca 2 + release from the endoplasmic reticulum in astrocytes

Department of Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo 133-0033, Japan Department of Cellular and Molecular Pharmacology, Nihon University School of Medicine, Tokyo 173-8610, Japan. Department of Physiology, University of California at San Francisco, San Francisco, CA 94143, USA Section of Viral Vector Development, National Institute for Physiological Sciences, Okazaki 444-8585, Japan. The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193, Japan. Department of Neurobiology, Graduate School of Medicine, The University of Tokyo, Tokyo 133-0033, Japan
Analisis Pengaruh Kepuasan Pelanggan KRL Komuter terhadap Adopsi Inovasi Sistem Tiket Tunggal Elektronik Smart Card untuk Mendukung Integrasi Moda Transportasi Massal di Jakarta

Masalah transportasi di Jakarta adalah kompleks karena tingkat pertumbuhan jalan tidak sebanding dengan peningkatan jumlah kendaraan. Untuk mengantisipasi terjadinya kemacetan yang cukup parah diperlukan pembangunan moda transportasi massal busway yang terintegrasi, sehingga kekhawatiran akan terjadinya “Stagnan Transportasi” tidak terjadi. Penelitian ini bertujuan menganalisa hubungan antara kepuasan pelanggan busway dan adopsi inovasi penggunaan sistem tiket tunggal elektronik smart card di moda transportasi busway untuk mendukung integrasi antar moda. Data dikumpulkan dari responden busway dan diolah menggunakan SEM dengan program Amos dengan metode SERVQUAL dan Adopsi Inovasi. Berdasarkan hasil analisis terhadap model penelitian yang diuji menunjukkan bahwa model dapat diterima berdasarkan indeks indeks model seperti Chi-Square= 1371,726 P=0.000, TLI=0.875, CFI=0.881, CMIN/DF=1.336, RMSEA=0.047, GFI=0.733, dan AGFI=0.706, sehingga dapat disimpulkan bahwa model memenuhi kriteria goodness of fit.