Miracle-dz/UniFAR-FTUs huggingface dataset:
Towards Navigating the Minotaur's Labyrinth: Cryptic Diversity and Taxonomic Revision within the Speciose Genus Hipposideros (Hipposideridae)

Recent molecular evidence has shown that the largest genus of the family Hipposideridae, Hipposideros, is paraphyletic with respect to H. commersonii sensu lato and H. vittatus, both belonging to a species complex referred to as the commersonii group. The taxonomic issues at the generic level of certain species of Hipposideros remain unresolved in part related to insufficient material in previous molecular studies. Herein, we expand sampling of the commersonii group and include H. commersonii sensu stricto from its type locality, Madagascar. Our phylogenetic analysis revealed that the commersonii group forms a highly supported monophyletic clade with H. cyclops, which is sister taxa to Aselliscus and Coelops. A combination of phylogenetic and comparative morphological analyses, as well as divergence time estimates, were used to provide compelling evidence to support the placement of the clade containing the commersonii group and that with H. cyclops in two resurrected genera, Macronycteris and Doryrhina, respectively. Divergence time estimates indicated that Macronycteris and Doryrhina diverged 19 mya and separated from Coelops and Aselliscus in the Oligocene, about 31 mya. The commersonii group underwent a rapid radiation as recently as 3 mya likely in response to favourable climatic conditions during the Late Pliocene in Africa. Phylogenetic analysis of Cyt-b could not resolve relationships within this morphologically conserved complex. Further sampling is necessary to fully elucidate the evolutionary history of Doryrhina. Given that cryptic species are widespread among bats, including within the genus Hipposideros, this study highlights the shortcomings of current chiropteran taxonomy to describe hidden diversity.
The use of visual marker genes for investigation of regeneration pathway and development of transformation system for wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.)

Recent advancements in molecular biology, genetic modification technology and genomics platforms will greatly enhance plant breeding practices for meeting global demand for food, feed, fibre, fuel and even biological drugs. Development of such plant biotechnology will transform modem agriculture into sustainable, low input, high and diverse output businesses. Although the most important cereal crops, including wheat and barley, have proven to be transformable, the existing transformation methods are not yet efficient to meet the needs for research and product development. This thesis describes effort to contribute to wheat and barley transformation method development and optimisation by: (1) investing plant regeneration pathways; (2) exploiting new visual marker genes as early reporters for screening transformed cells and plants; (3) testing Agrobacterium-mediated wheat transformation as an alternative DNA delivery method to the current method. Understanding of plant regeneration pathway is an intriguing scientific topic in its own right. It is also a pre-request for developing an efficient transformation method. The wheat regeneration pathway was studied after introducing foreign genes into cultured immature zygotic embryos of wheat (Triticum aestivum L.) by microprojectile bombardment. Three reporting systems, gusA, ClILc and gfp, were used. The results suggested clearly that regenerated wheat plants originated from single cell sources of scutellar tissue via a typical somatic embryogenesis. New vital visual markers allows for refinement of transformation permutations and possibly for replacing negative selectable markers. A synthetic green fluorescent protein gene, sgfp (S65T), was used during studies of wheat transformation. Another visual marker, the firefly luciferase gene, luc, was used during studies of barley (Hordeum vulgare L.) transformation, together with a selectable marker, the bar gene, and a target, the dapA gene. The expression of the sgfp (S65T) gene in regenerating cultures was followed using epifluorescence microscopy. Green fluorescence was detected within multicellular structures as early as 12 days after microprojectile bombardment. The sequential epifluorescent screens allowed detection of the GFP signal within early embryogenic structures without the aid of a selectable marker; thus, this gene can be used as an independent co-transformation marker.
Habitat diversification promotes environmental selection in planktonic prokaryotes and ecological drift in microbial eukaryotes

Whether or not communities of microbial eukaryotes are structured in the same way as prokaryotes is a basic and poorly explored question in ecology. Here we investigated this question in a set of planktonic lake microbiotas in Eastern Antarctica that represent a natural community ecology experiment. Most of the analysed lakes emerged from the sea during the last 6,000 years, giving rise to waterbodies that originally contained marine microbiotas and that subsequently evolved into habitats ranging from freshwater to hypersaline. We show that habitat diversification has promoted environmental selection driven by a salinity gradient in prokaryotes and ecological drift in microeukaryotes. Nevertheless, we detected also a number of microeukaryotes with specific responses to salinity, indicating that albeit minor, environmental selection has had a role in the assembly of their communities. Altogether, we conclude that habitat diversification can promote contrasting responses in planktonic microeukaryotes and prokaryotes belonging to the same communities.
Screening of Rice Varieties for Bacterial Leaf Blight Resistance by Using SSR Markers

Genetic variations of seventeen rice germplasms were studied using two SSR markers (RM122 and RM390) linked to the rice bacterial leaf blight (BLB) resistance genes.The average number of allele per locus was 10, with a range of 7 (RM122) to as many as 13 (RM390). The highest level of gene diversity value (0.9135) was observed in loci RM390 and the lowest level of gene diversity value (0.7059) was observed in loci RM122 with a mean diversity of 0.8097. The PIC values ranged from a low of 0.6715 (RM122) to a high of 0.9069 (RM390) and averaged of 0.7892. A dendrogram based on genetic distance using UPGMA, indicates segregation of the 17 rice varieties in six major clusters, BR10 and Binadhan 5, which were single variety formed cluster-1 and cluster-2 respectively. BRRIdhan 38, Malshira, Binadhan 7, BRRIdhan 29, BRRIdhan 31 were grouped in cluster-3, in which sub cluster-I include BRRIdhan 38, Malshira and sub cluster-II includes Binadhan 7, BRRIdhan 29, BRRIdhan 31. Cluster-4 was the largest cluster comprised of seven rice varieties. These are Iratom 24, BRRIdhan 34, Binasail, Binadhan 4, BR 26, BR 16 and Binadhan 6. Only BRRIdhan 33 was formed cluster-5. BR 14 and BRRIdhan 32 formed cluster-6. Thus, using the same linked marker RM122, BR 14 and BR 10 might be resistant to BLB diseases. SSR markers offer a potential, simple, rapid and reliable method in marker assisted breeding.
A new generic key to the New Zealand cave weta genera Orthoptera Rhaphidophoridae

Ward, D.F. (1997). A new generic key to the New Zealand cave weta genera (Orthoptera: Rhaphidophoridae). New Zealand Natural Sciences Volume 23:13-17. A revised generic key to the cave weta genera (Rhaphidophoridae) of New Zealand is presented based on published descriptions. Taxonomic characters used to identify each genera are also listed in table form in an attempt to clarify the confusion about the identification of specimens.
Effect of Butylated Hydroxytoluene on Acrosome Integrity and Viability of Crossbred Bull Spermatozoa

The present study was conducted to observe the effect of Butylated hydroxytoluene (BHT) on acrosomal integrity of crossbred bovine bull spermatozoa. Total eighteen ejaculates from two crossbred bulls were collected and extended with egg yolk tris dilutor along with addition of different concentrations of BHT i.e. 0.0mM (Control), 0.5mM (T 1 ) and 1.0mM (T 2 ), respectively. Acrosome integrity was assessed by Trypan blue giemsa staining during post dilution (Stage I), post equilibration (Stage II) and post thaw (Stage III). Mean percent of AIL spermatozoa were significantly (p<0.05) higher in group T 2 compared to T 1 and control at stage I and II. At stage III, T 1 and T 2 showed significantly (p<0.05) higher AIL sperms compared to control. Mean percent of AID spermatozoa were significantly (p<0.05) higher in control compared to T 1 and T 2 at Stage I, II and III. T 2 showed significantly lower ALL and ALD spermatozoa compared to control at stage III. The study indicates that 1mM BHT increased the cryosurvival i.e., (higher acrosomal integrity and viability) i.e. higher AIL and lower AID, ALL and ALD spermatozoa. Effect Butylated Acrosome Viability Crossbred Bull
Evaluation of Chemical Characterization, Antioxidant Activity and Oxidative Stability of Some Waste Seed Oil

In this study, fatty acid composition, antioxidant activity, total phenolic compounds (TPC) and oxidative stability of cherry seed (SCO), sweet cherry seed (SCSO), mulberry seed (MSO) and plum seed oil (PSO) were determined. Oleic acid was determined as primary fatty acid (42.9-67.3%), and followed by linoleic acid (23.4-41.8%) for SCO, SCSO and PSO. Linoleic acid was determined as primary fatty acid in MSO. γ-tocopherol was determined the main and highest tocopherol isomers varied from 579.9 to 605 mg/kg oil in SCO, SCSO and PSO, whereas δ-tocopherol was determined main tocopherol isomer with 1354mg/kg oil value in MSO. Plum seed oil (PSO) was the highest antioxidant activity values in both 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azino-bis-(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) assays. There was no significant differences in lipid hydroperoxide and TBARS (2-thiobarbituric acid-reactive substance) formation among SCO, SCSO and MSO. PSO had the highest induction period (15.1 h), followed by MSO (1.4 h), SCSO (1.5 h), SCO(1.3 h). PSO was oxidatively more stable than the other oil samples. This research shows that these waste seed oils have high antioxidant capacity and tocopherol content, so they could be used in food industry.
Inhibitory activity of Harpullia arborea (Blanco) Radlk. and Hydnocarpus pentandra (Buch.-Ham.) Oken against seed-borne fungi

Seed-borne fungi are of much significance for crop production as they are known to reduce germination and cause huge crop loss. Botanicals are shown to be effective in the management of seed associated pathogenic fungi. The present study was performed to investigate antifungal potential of methanolic extract obtained from leaves of two plants viz. Harpullia arborea (Blanco) Radlk. (Sapindaceae) and Hydnocarpus pentandra (Buch.-Ham.) Oken (Achariaceae) against a total of 7 seed-borne fungi. Maceration process was used to obtain extracts from the shade dried and powdered leaf material of selected plants. Poisoned food technique was used to determine antifungal activity. Both extracts were effective in causing mycelial growth inhibition in a concentration dependent manner. Marked antifungal activity was displayed by H. arborea when compared to H. pentandra. Among fungi, Aspergillus niger and Penicillium sp. was inhibited to highest and least extent respectively by both extracts. The plants selected in this study are promising in terms of their potential to inhibit seed mycoflora. In suitable formulation, these plants can be used against mycoflora associated with seeds for the management of seed-borne fungal diseases of plants.
CD44 Expression in Microglia of the Retina and Cerebellum of Developing and Adult Chicken

CD44 is a transmembrane protein that acts as a receptor for an adhesion molecule, hyaluronic acid. The type of cells expressing CD44 and roles of CD44 are still controversial and need to be elucidated. The aim of the present study was to examine the type of cells expressing CD44 and the changes in their distribution in the retina and the cerebellum of the developing and adult chicken. Embryonic day 14 (E14) and post-hatch day 90 (P90) chickens were used in this study. CD44-immunoreactive (ir) cells were observed both in the retina and the cerebellum of the two developmental stages examined. In the retina of E14, CD44-ir cells were mainly located in the nerve fiber layer. In adults, most of the CD44-ir cells were in the nerve fiber layer and some were dispersed in other layers of the retina. In the cerebellum of E14, CD44-ir cells were distributed throughout the cerebellar cortex, including the external and internal granular layers. CD44-ir cells were more frequently found in the cerebellum of P90 adult chickens than in that of E14 embryos. At higher magnification, CD44-ir cells showed ramified cytoplasmic processes irradiating from their cell bodies. In the retina and in the cerebellum of all ages examined, double staining showed that most of the CD44-ir cells also expressed RCA-1, a marker of microglia. In contrast to that, at the same locations, GFAP and CD44 were not co-expressed in cells. When the adult retina was stimulated by LPS, CD44 immunoreactivity increased, and CD44-ir cells were also RCA-1-positive. The present results indicated that CD44 was expressed in microglia of the retina and the cerebellum of the developing and adult chicken even in normal conditions, and microglial CD44 expression was increased upon LPS stimulation.
Do extended incubation recesses carry fitness costs in two cavity-nesting birds?

Because extended incubation recesses, where incubating songbirds are away from nests for periods much longer than usual, occur infrequently, they have been treated as outliers in most previous studies and thus overlooked. However, egg temperatures can potentially fall below the physiological zero temperature during extended recesses, potentially affecting developing embryos. As such, evaluating extended recesses in an ecological context and identifying their possible fitness effects are important. With this aim, we used iButton data loggers to monitor the incubation behavior of female Blue Tits (Cyanistes caeruleus) and Great Tits (Parus major) during two breeding seasons in central Spain. We classified incubation recesses as extended if they were more than four times the mean recess duration for each species. Extended incubation recesses occurred more frequently in 2012 when females exhibited poorer body condition. Female Blue Tits had more extended incubation recesses than female Great Tits and, for both species, more extended recesses occurred at the beginning of the breeding season. Both nest attentiveness and average minimum nest temperature decreased when at least one extended recess occurred. Incubation periods averaged 4 d longer for nests where females had at least one extended recess, potentially increasing predation risk and resulting in lower-quality nestlings. Overall, our results suggest that extended recesses may be more common among songbirds than previously thought and that, due to their effects on egg temperatures and attentiveness, they could impose fitness costs.
Spatio-temporal structure of the jellyfish community in the transition zone of cold and warm currents in the northwest Pacific

: Species composition, diversity and biomass of jellyﬁsh (Cnidaria and Ctenophora), with their spatio-temporal distributions, were analyzed in the upper 1500 m of the Oyashio front, the Transition zone and the Kuroshio extension, off Tohoku, northeastern Japan, between May 2005 and March 2006. Species composition and abundance differed remarkably between the shallower layer and the deeper layer at the boundary of 300–500 m depth, where water density was within the range of the North Paciﬁc Intermediate Water. In the deeper layer, diversity reached its peak with the appearance of 27 taxa common in all the regions throughout the year, though abundance was low. Pantachogon haeckeli and Crossota rufobrunnea were dominant in the deeper layer. The possibility of diel vertical migration was suggested in two midwater species: Euphysa japonica and Atolla vanhoeffeni . In the Oyashio waters, jellyﬁsh abundance was much higher than in the Transition waters and Kuroshio-derived waters, but with low diversity, dominated by large numbers of Aglantha digitale and Dimophyes arctica . High values of diversity were found in the Kuroshio-derived waters with various tropical and warm-water species, especially calycophoran siphonophores being present. In the Transition waters, diversity was relatively high, with co-occurrence of warm-water species and cold-wa-ter species. Jellyﬁsh biomass tended to be high in the midwater zone due to the occurrence of large species, particularly Scyphozoa. Carbon-based jellyﬁsh biomass calibrated with other studies exceeded that of other organism groups. the deeper layer of the Oyashio area, the Transition zone of cold waters, the Transition zone of warm waters and the Kuroshio area in this study, with their distributions worldwide.
First Documented Records of White Plumage Aberration in the White-necked Thrush (Turdus albicollis)

ABSTRACT Aberrations of plumage coloration are caused by hereditary and environmental factors and are not rare in wild birds, but few studies have estimated their frequency in natural populations. Here, we provide the first report of a white plumage aberration in an insular population of the White-necked Thrush (Turdus albicollis) on Ilha Grande, in southern Rio de Janeiro state, Brazil. Four (two males and two females) of the 123 individuals examined in 2013–2015 presented unusual white feathers on some part of the body (especially the hindneck), which may represent progressive graying or the result of injury. The frequency of the white plumage aberration recorded in our study (3.25%) is approximately three times higher than that expected in natural bird populations, and three of the four aberrant individuals were captured in the most disturbed forest site sampled. Further studies will be necessary to identify the true causes of the high frequency of white plumage aberrations detected in the study population, which may include diet, longevity, behavior, parasitism or other environmental factors.
Genetic Variation in Chum Salmon in the Sanriku Region, Japan, Inferred from Mitochondrial DNA Analysis

Genetic variation in about 500 chum salmon (Oncorhynchus keta) representing seven populations in the Sanriku region and one population in Fukushima, on the Pacifi c coast of northern Honshu, Japan, was estimated by mitochondrial DNA analysis. A total of nine haplotypes of 479–481 bp in the 5’ fi rst half of the control region were found in the chum populations examined. The observed haplotype diversity ranged from 0.424 ± 0.084 to 0.805 ± 0.056, which was lower than previously reported diversity in Japan’s Hokkaido populations, but higher than Russian and North American populations. AMOVA suggested moderate genetic diff erentiation among local populations within Sanriku and Fukushima, but no large-scale regional diff erences were detected.
Construction of a live attenuated Salmonella strain expressing FanC protein to prevent bovine enterotoxigenic Escherichia coli and evaluation of its immunogenicity in mice

: To construct a novel vaccine candidate against bovine enterotoxigenic Escherichia coli (ETEC), FanC, the major subunit of K99 fimbriae adhesion, was inserted into secretion plasmid pYA3560 containing a β -lactamase secretion system. This was then transformed into Δ asd Δ crp Salmonella ( S .) Typhimurium and designated as JOL950. Secretion of recombinant fanC fimbrial antigens was confirmed by immunoblot analysis. Groups of mice were inoculated with single or double doses of JOL950. Another group was used as a negative control. Compared to control mice, all immunized mice had significantly higher levels ( p < 0.05) of serum immunoglobulin (Ig)G, and secretory IgA against FanC. The IgG2a and IgG1 titer assays revealed that immunization highly induced IgG2a compared to that of IgG1, indicating that T helper-1- related cell-mediated immune responses may be elicited by JOL950. The results show that both systemic and mucosal immunities against selected fimbrial antigens of bovine ETEC expressed by a live attenuated S . Typhimurium strain are prominently produced in mice immunized with JOL950 via an oral route.
Protein network reconstruction of CHO cell secretory pathway

Proteins associated or linked to early secretion pathway were identified by manually literature on mouse models and cell lines. The proteins found were used to identify CHO-K1 genes of the ERAD and protein folding pathway. Introduce a more systematic approach in improv-ing the protein production in CHO cell lines Employ a guided approach that integrates protein function interaction network, gene expression and comparative studies of mouse and CHO cells. Identify functional gene targets within the secretory pathway for modification in order to increase protein production.
DIVERSITY OF APHYLLOPHORALES FUNGI ISOLATED FROM TANJUNG PUTING NATIONAL PARK, CENTRAL KALIMANTAN AND ITS POTENTIALITY FOR LIGNIN DECOMPOSITION

A total of fifty-three samples of fungal basidiocarp were collected from peat area in Tanjung Puting National Park, Central Kalimantan, Indonesia. These samples are mostly determined to genus until more studies are available.The fungi were isolated on CMA medium then the isolated strains were purified on PDA medium. The fungi belong to at least 3 families of Aphyllophorales, however there were a wide diversity in the genus with respect to macroscopic examination.An agar plate screening procedures was developed for the rapid selection of fungi and estimation of their capacity for lignin-decomposer. The test is based on the visualization and interpretation of the formation of halo zone or decolourization process in well-defined agar medium containing Poly R-478. The selected isolates were also tested in to rhemazol brilliant blue R salt (RBBR) medium. Five isolates had the ability to decolourize either Poly R-478 or RBBR. These isolates showed a qualitative lignin decomposition although a comparative study of selected fungi revealed the difference potentiality. The highest loss of lignin was 28.18% and attempts have been made to determine the unidentified fungi, which is resupinate type, by direct sequencing of 18s ribosomal DNA (rDNA).