Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenetic relationships and evolution of reproductive modes within flattened syllids (Annelida : Syllidae) with the description of a new genus and six new species

Abstract. Syllid annelids from the so-called ‘ribbon clade’ are flattened, ribbon-shaped worms of the genera Parahaplosyllis Hartmann-Schröder, 1990, Eurysyllis Ehlers, 1864, Xenosyllis Marion & Bobretzky, 1875, Trypanosyllis Claparède, 1864, Ramisyllis Glasby, Schroeder & Aguado, 2012, Trypanobia Imajima & Hartman, 1964, Plakosyllis Hartmann-Schröder, 1956, Pseudosyllis Grube, 1863 and Trypanedenta Imajima & Hartman, 1964. Some species possess a remarkable reproductive strategy using multiple stolons that has been recently suggested to be ancestral to the group. Here, to evaluate the evolution of reproductive modes in the group, we assess, for the first time, the phylogenetic relationships within the ribbon clade and related genera. We collected new material of Trypanobia and Trypanosyllis from Japan, Spain, Philippines and Indonesia and sequenced it for the nuclear markers 18S rRNA and the mitochondrial markers 16S rRNA and cytochrome c oxidase I for phylogenetic inference and also performed ancestral character reconstruction for the reproductive strategy in the entire group. Formal taxonomic descriptions of a new genus and six new species are provided. The new genus, Trypanospina, gen. nov., is characterised by the spines that cover its surface. Most genera within the ‘ribbon clade’ are monophyletic and the relationships appeared well supported in most cases. However, our phylogenetic hypotheses are not conclusive in regard to the relationships of the genera Trypanedenta and Trypanobia, nor to the status of those to genera as distinctive, since they seem to be paraphyletic and they appear in low-supported clades. In contrast, our results shed light on the evolution of the reproductive modes within the group, showing that scissiparity (development of a single stolon each time) is the ancestral character for the entire group and gemmiparity (development of more than one stolon at the same time) then appeared twice in two independent clades.
Expression of cucumber LOX genes in response to powdery mildew and defense-related signal molecules

Oh, S. -K. , Jang, H. A. , Kim, J., Choi, D. , Park, Y. -I. and Kwon, S. -Y. 2014. Expression of cucumber LOX genes in response to powdery mildew and defense-related signal molecules. Can. J. Plant Sci. 94: 845-850. The cucumber genome contains 23 lipoxygenase (LOX) genes. The expression of seven type-I and six type-II LOX genes was induced when cucumber leaves were challenged with Sphaerotheca fuliginea and treated with salicylic acid, methyl jasmonate, and abscisic acid. These 13 CsLOX genes were differentially regulated during biotic and abiotic stresses.
Determination of optimum maturity of north Sri Lankan KilichondanMangofruits (Mangifera indica L.) based on their biochemical properties

Mangoes (Mangifera indica, L.) produced in Northern Sri Lanka, are lost due to poor transportation and storage facilities. Optimum date for harvesting was determined to extend the postharvest life. Harvest maturity of Kilichondan mango cultivars grown in Northern Sri Lanka between April and January, were studied to reduce such losses. Though Kilichondan mangoes are delicious and economically positive for the poor, the maturity index of this variety has not been determined yet. Therefore this study was aimed at recommending proper maturity indices for Kilichondan mango and to analyze the physical and chemical properties of this fruit during ripening. Time after the full bloom stage, the colour of the skin, floating / sinking ability, total soluble solids (TTS), titratable acidity (TTA), moisture content, dry matter, TTS/TTA ratio were measured. Most fruits sank in water. TSS, pH, dry matter content increased rapidly, whereas TTA and moisture content percentage decreased rapidly towards maturity. Fruits harvested up to 93 days from full bloom stage, showed significant differences in the above mentioned values than the fruits harvested after 93 days from full bloom stage. 90 percent of fruits ripened on the tree after 97 and 98 days from full bloom stage where as fruits harvested after 98 days from full bloom stage were over-ripened and of poor quality. Since a non-destructive method reduces loss of yield, the study recommends the slightly yellow colour patchon the green shoulder, is an acceptable maturity index that appears on the 93rd day from full bloom stage for Kilichondan mango variety. Testing panel results confirmed the acceptable eating quality of these fruits after being ripened
Regulation of Pluripotency and Differentiation by Chromatin Remodeling Factors

Central to the control of virtually all cellular activity is the regulation of gene expression. In eukaryotes, this regulation is greatly influenced by chromatin structure, which is itself regulated by numerous chromatin-remodeling complexes. These are typically large protein complexes with interchangeable subunits that allow for highly specialized functions in different cell types. Moreover, additional specificity can be gained through complexes formed from different subunit isoforms. Histone modifications also regulate chromatin by recruiting remodeling complexes to particular genomic regions. In this thesis we characterize MBD3C, an isoform of the Nucleosome Remodeling and Deacetylase (NuRD) complex subunit MBD3. MBD3 is essential for pluripotency and development, but MBD3C appears to be expressed only in embryonic stem cells (ESCs), and whether it forms a distinct NuRD complex, how its expression is regulated, and its precise function(s) remain unknown. We show that MBD3C forms a complete NuRD complex that functions redundantly with the other MBD3 isoforms in ESC gene regulation. Furthermore, MBD3C binds the SET/MLL complex subunit WDR5 through a conserved motif within its unique N-terminal region, and this interaction is necessary for the regulation of >2,000 ESC genes. Together, these findings indicate that ESCs can utilize isoforms of the same protein to achieve similar functions through diverse mechanisms. The second part of this thesis focuses on the role of the histone modification H3.3K56ac in pluripotency and differentiation. Although H3K56ac is well-studied in yeast, in mammalian cells it is far less abundant and its functions
Glucocorticoid Regulation of the Leptin Receptor Signaling System in the Rat.

Obesity, a recognized health problem, is associated with cardiovascular disease, diabetes and hypertension. Removal o f adrenal steroids by adrenalectomy (ADX) slows the development of obesity. Leptin decreases food intake through effects initiated by activation o f the JAK-STAT pathway. Defects in leptin signaling lead to obesity, which is associated with hyperleptinemia and leptin resistance. In chapter 4, leptin induces phosphoewo/pyruvate carboxykinase (PEPCK) mRNA expression and increases glucose production in hepatocytes from lean but not obese Zucker rats. This suggests that hyperleptinemia in obesity causes hyperglycemia. In chapter 5, ADX decreased the levels o f PEPCK mRNA, and increased leptin receptor mRNA expression o f obese Zucker rats. The decrease in PEPCK mRNA is presumed to correct the hyperglycemia in these rats. ADX decreases leptin levels and increases leptin receptor (OBR) mRNA in obese Zucker rats, suggesting that leptin downregulates OBR. ADX was reported to increase sensitivity to leptin treatment. I hypothesized that high glucocorticoids in obesity impaired OBR signaling, and removal thereof will activate this pathway. In chapter 6, ADX increased the expression o f leptin receptor mRNA in Sprague Dawley rats. ADX increased STAT-3 mRNA and protein levels, and induced constitutive STAT-3 phosphorylation and DNA binding activity. ADX also reduced SOCS-3 mRNA and protein levels. ADX and leptin treatment increased STAT-3 phosphorylation, but with no concomitant increase in DNA binding activity. We speculate that PIAS-3, a protein inhibitor o f activated STAT-3, inhibited DNA binding o f the activated STAT-3 as a protective measure of cytokine hypersensitivity in the absence of SOCS-3. Leptin and ADX decreased NPY mRNA expression, but their combination did not further decrease NPY mRNA. In conclusion,
Bacteria as Normal Flora in Postmortem Body Fluid Samples

Bacterial culture and identification are useful in the clinical and forensic field [1], although there are many concerns regarding postmortem bacterial culture and identification. Furthermore, there are no specific guidelines, recommendations, or checklists that address the standards for performing that type of testing [1]. The Human Microbiome Project has revealed that an adult body contains approximately ten times more microbial cells than human cells [2], although it is unclear what happens to these microbial cells after a person dies. During the antemortem period, the immune system ensures that bacteria are not present in most internal organs and body fluids (e.g., the blood and cerebrospinal fluid). However, the immune system fails Korean J Leg Med 2017;41:87-93 https://doi.org/10.7580/kjlm.2017. 41.4. 87
A Phylogenetic Perspective on the Influence of Ecological Attributes on Selected Species of Astragalus

ABSTRACT The use of phylogeny in ecology has gained attention due to its benefits in understanding biological diversity and adaptation processes. In this study, phylogenetic positions of 12 Astragalus taxa were evaluated by comparing with 419 Astragalus taxa sequences in a database. Additionally, the influence of ecological traits on morphology was assessed. Although the samples were grouped according to subgenera or sections they belong to, this division was not striking. The phylogenetic relationships of the nine endemic and three common Astragalus taxa based on nrDNA region sequences and morphological features as well as their interplay with the environment were examined. Furthermore, soil characteristics of the fields where each Astragalus taxon grows were determined. Analysis of the sequences revealed that the 12 taxa were grouped into three clades using the Bayesian Inference method. A cladogram of 431 Astragalus taxa showed that the samples were divided into ten major clades. Morphological traits were found to be correlated with soil properties, which could indicate adaptation to environmental conditions of these taxa.
Mitochondrial genome of Sitona callosus (Coleoptera: Curculionidae) and phylogenetic analysis within Entiminae

Abstract In this study, we sequenced and annotated the nearly complete mitochondrial genome (mitogenome) of Sitona callosus (Coleoptera: Curculionidae). This mitogenome was 14,333 bp long and encoded 13 protein-coding genes, 19 transfer RNA genes (tRNAs), and two ribosomal RNA unit genes. Gene rearrangements were presented in a tRNA cluster of six tRNAs between nad3 and nad5, i.e. the ancestral order ARNSEF was changed to be RNSAEF. All tRNAs had a typical secondary cloverleaf structure, except for trnS1 which lacked the dihydrouridine arm. The Bayesian phylogenetic tree of 11 Entiminae species based on the concatenated nucleotide sequences of 13 PCGs showed that S. callosus and S. lineatus formed a clade which was at the basal position in the Entiminae phylogeny.
Rumen fermentation characteristics of West African Dwarf goats fed enzyme supplemented total mixed ration in the dry season.

The study was conducted to investigate the effect of exogenous enzyme additive on rumen environment parameters of West African Dwarf (WAD) goats fed total mixed ration (TMR) for a period of 70 days. Four experimental diets were formulated with enzyme included at 0.0, 0.2, 0.4 and 0.6 g/kg dry matter to constitute treatments 1,2, 3 and 4 respectively. Sixteen growing WAD goats were subjected to the four dietary treatments in a completely randomized design. Rumen fluid was collected from the goats before the commencement and at the end of the feeding trial. Data were collected on rumen pH, ammonia nitrogen, volatile fatty acids (VFAs) production and microbial population. Enzyme additive significantly (p<0.05) affect the total VFAs, propionic acid and butyric acid production with the highest values (86.23, 26.17, 14.87 Mm/100ml) for the three respectively obtained at T4(0.6g/kg). The bacteria count was significantly highest (5.20 × 10 6 cfu/ml) at T3 although not statistically different from what was obtained at T4. A total of 5 bacteria (Bacteroides, Clostridium, Fusobacterium, Streptococcus and Peptococcus spp.), 1 fungus (Aspergillus spp.) and 2 protozoa (Holotrich spp. and Trichuris spp.) species were isolated from the rumen at the end of the study. It was therefore concluded that exogenous enzyme containing cellulase, xylanase and beta glucanase can be included in a TMR for WAD goats at 0.4g/kg for increased bacteria count and total VFAs production.
Disentangling the relative merits and disadvantages of parentage analysis and assignment tests for inferring population connectivity

Accurately estimating patterns of population connectivity in marine systems remains an elusive goal. Current genetic approaches have focused on assigning individuals back to their natal populations using one of two methods: parentage analyses and assignment tests. Each of these approaches has their relative merits and weaknesses. Here, we illustrate these tradeoffs using a forward-time agent-based model that incorporates relevant natural history and physical oceanography for 135 Kellet’s whelk (Kelletia kelletii) populations from Southern California. Like most marine organisms, Kellet’s whelks live in large meta-populations where local populations are connected by dispersive larvae. For estimating population connectivity, we found parentage analyses to be relatively insensitive to the amount of genetic differentiation among local populations, but highly sensitive to the proportion of the meta-population sampled. Assignment tests, on the other hand, were relatively insensitive to the proportion of the meta-population sampled, but highly sensitive to the amount of genetic differentiation found among local populations. Comparisons between the true connectivity matrices (generated by using the true origin of all sampled individuals) and those obtained via parentage analyses and assignment tests reveal that neither approach can explain >26% of the variation in true connectivity. Furthermore, even with perfect assignment of all sampled individuals, sampling error alone can introduce noise into the estimated population connectivity matrix. Future work should aim to improve the number of correct assignments without the expense of additional incorrect assignments, perhaps by using dispersal information obtained from related individuals as priors in a Bayesian framework. These analyses dispel a number of common misconceptions in the field and highlight areas for both future research and methodological improvements.
“To Sartaba, From Sartaba” A New Proposal to Identify the Location of the Second Station on the Beacon Line from Jerusalem to Babylon

Abstract The Hebrew calendar is a lunisolar calendar. Its months are based on the revolution of the moon about the Earth, as it is said: This is the burnt offering of every new moon throughout the months of the year1 (Num. 28:14) At the present time the moment of the true new moon is approximated mathematically. However during the Second Temple period, the beginning of the new lunar month had to be observed and certified by witnesses. Then the Sanhedrin Court was to make a public proclamation on the first day of the lunar month (ראש חודש). In Mishnah, Tractate Rosh Hashana, Chapter 2 describes the process of communicating the information about the beginning of new month through the chain of beacon fires: “From the Mount of Olives to Sartaba, and from Sartaba to Grofina, and from Grofina to Hauran, and from Hauran to Bet Biltin. From Bet Biltin they did not move, but rather waved back and forth and up and down until he saw the whole of the diaspora before him lit up like one bonfire. ”2 Questioning of reliability of the quoted above description, its completeness and exclusiveness of the delineated in the Mishnah route is beyond the scope of the presented research. In this article we’ll apply methods of the geographic information systems (GIS) analysis in order to examine the existed theories regarding localization of Sartaba - the second mentioned station in the chain of beacon fires, reveal their discrepancies and propose an innovative, albeit rather technical, solution for long-known problem.
Development of an Endothelial Cell Niche in Three-dimensional Hydrogels

Three-dimensional (3D) tissue models have significantly improved our understanding of structure/function relationships and promise to lead to new advances in regenerative medicine. However, despite the expanding diversity of 3D tissue fabrication methods, in vitro approaches for functional assessments have been relatively limited. Herein, we describe the guidance of primary endothelial cells (ECs) in an agarose hydrogel scaffold that is chemically patterned with an immobilized concentration gradient of vascular endothelial growth factor 165 (VEGF165) using multiphoton laser patterning of VEGF165. This is the first demonstration of this patterning technology to immobilize proteins; and the first demonstration of immobilized VEGF165 to guide endothelial cell growth and differentiation in 3D environments. It is particularly compelling that this 3D hydrogels provide an excellent biomimetic environment for stem cell niche, thereby offering a new approach to study stem cell biology. In this thesis, we focused on the retinal stem cell niche, investigating cellular interactions between retinal stem and progenitor cells (RSPCs) and endothelial cells (ECs). By using this 3D in vitro model, we demonstrated the synergistic interactions between RSPCs and ECs wherein RSPCs migrated into 3D gels only in the presence of ECs and RSPCs stabilized EC tubular-like formations. Moreover, we
Impact of Harvesting Time and Length of Cold Storage Period On Physiological and Quality Traits of Four Quince Genotypes (Cydonia Oblonga Mill.)

Abstract The investigation was conducted to determine the best harvesting time and the storage period of some quince cultivars and promising genotypes from the collection of quince germplasm in the Horticultural Research Station of Isfahan, Iran. For this study, fruits of ‘Vidoja’ and ‘Isfahan’ cultivars as well as promising genotypes PH2 and NB4 were harvested on 6, 14 and 21 October 2015 and 2016 and then stored at 0 ± 1 °C with 90 ± 5% R.H. for five months. Weight loss, firmness, total soluble solids (TSS), titrable acids (TA), taste index, pectin, total phenols, and percent of decay and surface browning of fruits were measured immediately after harvest and one-month intervals after storage in a factorial experiment based on a completely randomized design with three replications and 10 fruits per each replication. The results showed that ‘Isfahan’ cultivar had the highest TSS (18.83%), total phenols and weight loss. The least weight loss was observed in the ‘Vidoja’ cultivar. NB4 genotype showed the least taste index and pectin, while the most pectin and firmness was related to PH2 genotype. Generally, the delay in harvesting and prolongation of storage led to increasing of TSS and weight loss and declining of firmness and phenols, TA, and pectins. Until the third month of storage, there was no surface browning. Browning symptoms were observed from the fourth month of storage and increased in the fifth month up to 1.72%. Generally, the best harvesting time for ‘Vidoja’ was 185 days and for the rest of the genotypes, it was 193 days after full bloom. Fruit storage for four months in cold is advisable for these cultivars and genotypes.
Identifying the autoantigen of a diabetogenic CD8 T cell clone isolated from young NOD mice

Defining the autoantigenic targets of T cells involved in insulindependent diabetes mellitus (IDDM) is essential for understanding the pathogenesis of diabetes. IDDM results from the autoimmune destruction of the pancreatic islet (3 cells. The non-obese-diabetic (NOD) mouse is a murine model for spontaneous IDDM. T cells play an important role in the pathogenesis of diabetes, and CD8 T lymphocytes may be critical initiators of diabetes. Several [3-cell specific autoantigens of CD4 T cells have been identified. However, the autoantigens of CD8 T cells, which are likely to play an important role in the induction of diabetes, have not yet been identified. In this thesis we describe the application of a single-cell T cell assay, which takes advantage of a lacZ reporter construct, as a means to identify the target antigen of a diabetogenic CD8 T cell clone isolated from young NOD mice. Indicator cells are lacZ -inducible T-cell hybrids specific for the unknown antigen, and are shown here to turn blue in the presence of NOD mouse islets and the chromogenic substrate X-gal. These T cell hybrids, and COS-7 cells transfected with the murine MHC class I molecule as antigen-presenting cells, have been used to screen a NOD mouse islet cDNA library for the target antigen of the diabetogenic CD8 T cell clone. Our findings suggest that increasing the sensitivity and specificity of the lacZ assay may be necessary for detecting autoantigenic cDNA when it exists at very low frequencies in the cDNA library.
PHYLOGENETIC RELATIONSHIP BETWEEN FOUR SPECIES USING DIVERGENT DOMAIN D9 AND D11 IN FAMILY: SILURIDAE (PISCES)

Molecular characterization and assessment of genetic variation in 28S region especially divergent domain D9 and D11 ribosomal DNA in fresh water catfish Ompok pabda, O. pabo, O. bimaculatus and Wallago attu was carried out. The nucleotide sequences and GC% of divergent domains of 28S ranged from 419-427 bp and 61% in D9 region and 686-688 bp and 55% in D11 region. In D9 region, O. pabda and O. bimaculatus were 100% similar, whereas other species were found 99% similar. In D11 region, O. pabda with O. pabo and O. bimaculatus were 100% similar and other species were 99% similar. After sequence analysis, Ompok species exhibited more variability from W. attu. DNA sequence data play an essential role in the reconstruction of evolutionary relationships among the organisms, resulting in insights in genetic affinities that may confirm or conflict with traditional taxonomy because of attractive properties, the rDNA is popular for examine phylogenetic relationships and for studying genetic variability and divergence within and between species.