Miracle-dz/UniFAR-FTUs huggingface dataset:
Bioprospecting and Functional Analysis of Neglected Environments

The global Ocean represents the worlds largest continuous ecosystem, however, little is known about the microbial functions present in the aphotic zone. The microorganisms that dwell in the deep dark waters are numerous and play key roles in the ocean carbon cycle, which is of special interest in connection to the global climate change. The polar oceans are highly affected by the temperature increase and this emphasizes the need for a better understanding of the biological processes present throughout the water column. The purpose of this study was to conduct a functional clustering of metagenome shotgun DNA libraries of samples from the Arctic Ocean and the Southern Ocean and through the water column reaching levels lower than 4,000 m. This dataset represents the deepest microbial samples from these oceans to date. Furthermore, a comparative analysis was conducted to infer the functional differences between the environments. The results indicated that the environmental factors differentiating through the first 300 m of the water column are deciding factors for shaping the functional community, rather than spatial dispersal. The mesopelagic samples were functional inseparable from the bathyand abyssopelagic samples, indicating a highly homogenous environment in the aphotic part of the ocean. Functions characterizing the aphotic zone were iron uptake and utilization, phage and bacteria interactions, adhesion and motility and others, which in general indicated a selection for copiotrophs in the deeper ocean.
A new species of sea squirt Rhopalaea bilobata (Ascidiacea: Diazonidae) from the Andaman Islands, India

Rhopalaea bilobata , a new species of the class Ascidiacea, under the family Diazonidae has been described from the Andaman Islands of Andaman & Nicobar, India. The species was found in sandy bottoms, reef areas and artificial structures at a depth range of 10–40 m. This species has bilobed anal border, six lobed branchial and atrial siphons, transparent thorax with pigmented spots at the anus, between the two siphons and at the anterior end of endostyle, and ramified basal test. The species is closely related to R. idoneta, R. macrothorax and R. tenuis in several sets of anatomical and morphological features.
There and back again – unraveling mechanisms of bacterial biogeography in the North Pacific Subtropical Gyre to and from station ALOHA

Bacterially-mediated fluxes of energy and matter are dynamic in time and space coupled with shifts in bacterial community structure. Yet, our understanding of mechanisms shaping bacterial biogeography remains limited. Near-surface seawater was collected during transits between Honolulu and Station ALOHA in the North Pacific Subtropical Gyre to examine the shape of occupancy-frequency distributions (the different number of populations occupying different number of sites) and determine bacterial metapopulation dynamics. Bacterial 16S rRNA gene amplicons were sequenced from whole seawater and filter-size fractionated plankton DNA samples while also separating the community into distinct taxonomic groups at phyla/class and analyzing these compartments separately. For the total seawater (i.e. the >0.2 μm size fraction) and picoplankton communities (i.e. the size fraction >0.2 μm and < 3.0 μm), but not the large size fraction community (i.e. the >3.0 μm size fraction), most individual operational taxonomic units (OTUs) occupied a single site and the number of OTUs occupying different number of sites followed a significant bimodal pattern with several core OTUs occupying all sites. Nevertheless, only Cyanobacteria (in particular Prochlorococcus sp.) and in a few instances also Alphaproteobacteria (in particular SAR11 clade and Aegan-169 marine group bacteria) exhibited bimodal occupancy-frequency patterns. As expected, Prochlorococcus sp. had an inversed bimodal occupancy-frequency distribution with most OTUs found at all sites. Yet, there were individual satellite OTUs affiliated with Prochlorococcus sp. that were phylogenetically distinct from the core OTUs and only found at a single site. Collectively, these findings indicate that different compartments (size fractions and taxa) have different metapopulation dynamics. Bimodal patterns among the low diversity total and picoplankton communities but not in the high diversity large size fraction suggest that positive feedbacks between local abundance and occupancy are important when environmental conditions are homogenous and diversity is low.
Taxonomic changes and an updated catalogue for the Palaearctic Sericini (Coleoptera: Scarabaeidae: Melolonthinae)

This paper presents some results of the ongoing taxonomic investigations of the Asian Sericini (Scarabaeidae: Melolonthinae) beetle fauna with an updated catalogue to the Palaearctic members of this tribe. The following new synonymies and combinations are introduced: Archeohomaloplia Nikolajev, 1982 (= Melanomaladera Miyake & Yamaya, 2001, new synonymy); Trioserica Moser, 1922 (= Sinoserica Miyake & Yamaya, 2001, new synonymy); Nipponoserica koltzei (Reitter, 1897) (= Nipponoserica opacicarina Kim & Kim, 2003, new synonymy); Maladera lignicolor (Fairmaire, 1887) (= Autoserica laboriosa Brenske, 1897, Aserica fusiana Murayama, 1934, and Serica tenebrosa Frey, 1972, new synonymy); Neosericania nitida (Kobayashi, 1985) new combination; Eumaladera subrugata (Moser, 1926) new combination; Eumaladera opaciventris (Moser, 1915) new combination (= Maladera coreana Kim & Kim, 2003, new synonymy); Maladera verticalis (Fairmaire, 1888) (= Maladera castanea koreana Kim & Kim, 2003, new synonymy); Archeohomaloplia abbreviata (Fairmaire, 1897) new combination (= Areohomaloplia potanini Nikoleav, 1982, new synonymy); Archeohomaloplia yunnana (Miyake & Yamaya, 2001) new combination; Trioserica maculipennis (Miyake & Yamaya) new combination; Serica (Taiwanoserica) anmashana (Kobayashi, 1993) new combination; S. (T.) bihluhensis (Kobayashi & Yu, 2000) new combination; S. (T.) chunlinlii (Ahrens, 2002) new combination; S. (T.) elongata (Nomura, 1974) new combination; S. (T.) gracilipes (Nomura, 1974) new combination; S. (T.) kubotai (Kobayashi, 1983) new
Spatial relationships and mechanisms of coexistence between dominant and subordinate top predators

Most forest ecosystems contain a diverse community of top-level predators. How these predator species interact, and how their interactions influence their spatial distribution is still poorly understood. Here we studied interactions among top predators in a guild of diurnal forest raptors in order to test the hypothesis that predation among competing predators (intraguild predation) significantly affects the spatial distribution of predator species, causing subordinate species to nest farther away from the dominant ones. The study analyzed a guild in southwestern Europe comprising three raptor species. For 8 years we studied the spatial distribution of used nests, breeding phenology, intraguild predation, territory occupancy, and nest-builder species and subsequent nest-user species. The subordinate species (sparrowhawk, Accipiter nisus) nested farther away from the dominant species (goshawk, A. gentilis), which preyed on sparrowhawks but not on buzzards (Buteo buteo), and closer to buzzards, with which sparrowhawks do not share many common prey. This presumably reflects an effort to seek protection from goshawks. This potential positive effect of buzzards on sparrowhawks may be reciprocal, because buzzards benefit from old sparrowhawk nests, which buzzards used as a base for their nests, and from used sparrowhawk nests, from which buzzards stole prey. Buzzards occasionally occupied old goshawk nests. These results support our initial hypothesis that interspecific interactions within the raptor guild influence the spatial distribution of predator species in forest ecosystems, with intraguild predation as a key driver. We discuss several mechanisms that may promote the coexistence of subordinate and dominant predators and the spatial assembly of this raptor guild: spatial refuges, different breeding phenology, spatial avoidance, low territory occupancy between neighboring nesting territories, nest concealment and protection, and diet segregation. This article is protected by copyright. All rights reserved.
Loss of function mutation in the S adenosylmethionine synthetase 1 gene (sams 1) increases lipogenesis, enlarges lipid droplets and reduces lipolysis efficiency in Caenorhabditis elegans

Cytosolic lipid droplets (LDs) are evolutionary conserved and versatile organelles important for storage and utilization of lipids in almost all cell types. In order to gain insights into the functional connection between LD size and lipid homeostasis we isolated, identified and finally characterized an Sadenosylmethionine synthetase (SAMS1) deficient Caenorhabditis elegans (C. elegans) mutant showing enlarged LDs throughout the life cycle. SAMS1 belongs to a family of evolutionary conserved enzymes, which catalyze the only known route of Sadenosylmethionine (SAM) synthesis. SAMdependent methylation is of quantitative importance for the synthesis of phosphatidylcholine (PC), a major phospholipid of membranes. Syntheses of PC and triacylglycerol (TAG) are intimately coupled to each other due to common intermediates, shared biosynthetic routes and mutual regulatory mechanisms. The present study shows that SAMS1 is necessary for homeostasis of PC and TAG synthesis and that SAMS1 deficiency results in excessive TAG storage in C. elegans. Thin layer chromatography based analysis of lipid extracts revealed that SAMS-1 deficiency reduces PC level but increases TAG proportions. Microarraybased expression profiling identified upregulation of several lipogenic genes due to SAMS1 deficiency, which is supposed to contribute to increased TAG proportions. Vital fat staining via BODIPY™ 493/503 revealed that increased TAG level are stored in fewer but larger LDs in sams1 mutants. A reduced surface area of few large-sized LDs is supposed to represent a mechanism to economize PC. Moreover, sams1 mutants displayed a reduced body size and an impaired reproductive capability. In summary, our data reveal a mechanism of how SAMS1 deficiency mediates increased fat storage through impaired PC synthesis, LD expansion, increased lipogenesis and reduced lipolysis efficiency.
Genetic diversity of 28 wild species of fodder legume Cassia using RAPD, ISSR and SSR markers: a novel breeding strategy

RAPD, ISSR and SSR primers were used to assess genetic diversity and phylogenetic relationships among 28 species of Cassia (2n = 16, 26, 28). RAPD, ISSR and SSR primers revealed 36.12, 42.7 and 54.4% polymorphism, respectively. The Dendograms based on RAPD, ISSR, and SSR data precisely organized 28 species of Cassia into different clusters. SSR primer could distinguish all species analyzed within the genus. Polymorphic index varied from 0.1 to 0.5 for both SSR and RAPD markers; primer index values were substantially higher for RAPD primers (0.35 – 4.65) than for SSR primers (0.35 – 1.73). It was possible to identify accessions with the help of RAPD, ISSR and SSR markers. Dendograms constructed from RAPD, ISSR and SSR data revealed DNA marker-based genetic identification in Cassia. Four groups of Cassia that were resolved corresponded to species grouped earlier taxonomically. Cassia mimosoides with a different genomic set up showed close relation to C. javanica. Cassia siamea and C. spectabilis; C. grandis and C. nodosa in a core group with close morphological similarities. Cassia artemisioides and C. covesii, both showing morphologically drought tolerance characters are closely placed, indicating that they are the wild progenitors of these species. The broad adaptation of some species of Cassia implies a large probability that nuclear DNA mutations occurred in the past and that resulted in diversification and genetic polymorphism in growth habit, vigor, and stem, leaf, seed, and pod characteristics and a physiological polymorphism, the water-use efficiency.
Analysis of Nucleosome Isolation and Recovery: From In Silico Invitrosomes to In Vivo Nucleosomes

Analysis of Nucleosome Isolation and Recovery: From In Silico Invitrosomes to In Vivo Nucleosomes Collin Brendan Skousen Department of Microbiology and Molecular Biology, BYU Master of Science There are a vast number of factors that influence nucleosome formation, and consequently gene regulation. These factors include histone modifications, nucleotide composition, transcriptional region elements, and specific nucleotide motifs, among others. Although the amount we know now is limited, we are creating new techniques and discoveries to assist us in continued understanding of chromatin. To make a significant contribution to the field of chromatin, I conducted two hypothesis driven sets of experiments that address the topic of chromatin structure. First, I created a technique for tissue specific nucleosome isolation with the goal of observing the effect of single nucleotide polymorphisms (SNPs) on nucleosome formation. Second, I created and tested a method to recover lost in vitro nucleosome reconstitution data, which can improve this type of data, commonly used for observing nucleosome positioning. The first experiment needs a more specific antibody to complete the last step and function as designed. The second experiment shows that our nucleosome recovery method, when applied conservatively, can recover 90% of the lost nucleosome data.
Ontogenetic changes in the feeding strategy of Lepidonotothen nudifrons (Pisces, Nototheniidae) off the South Shetland Islands and the Antarctic Peninsula

ABSTRACT The diet and feeding strategy of Lepidonotothen nudifrons off the South Shetland Islands and the Antarctic Peninsula, as well as their variation in relation to ontogenetic stage (juvenile–adult) and sampling area, were determined by stomach contents analysis. Additionally, the trophic level of this species was estimated to determine its position within the Antarctic food web. Out of 247 specimens with prey in their stomachs, 144 were caught near the South Shetland Islands and 103 off the Antarctic Peninsula. Ontogenetic changes in the trophic ecology of L. nudifrons were observed in both areas and were mainly related to a decrease of copepods and an increase of euphausiids in the diet. The diet of juveniles from the South Shetland Islands was characterized by the dominance of calanoid copepods, followed by isopods and amphipods, whereas diet off the Antarctic Peninsula was dominated by amphipods and cyclopoid copepods. The diet in adults was dominated by amphipods and euphausiids in both areas. The specialization of individual predators on different prey types was observed when considering the whole population of L. nudifrons, but when ontogenetic stages were considered separately it showed a more mixed feeding strategy, with different dominant prey for each class. Although the trophic level increased with fish size, L. nudifrons can be classified as secondary consumer throughout its lifespan.
Design and Synthesis of Selective Estrogen Receptor β Agonists and Their Pharmacology

DESIGN AND SYNTHESIS OF SELECTIVE ESTROGEN RECEPTOR β AGONISTS AND THEIR PHARMACOLOGY K. L. Iresha Sampathi Perera, B.Sc. (Hons), M.Sc. Marquette University, 2017 Estrogens (17β-estradiol, E2) have garnered considerable attention in influencing cognitive process in relation to phases of the menstrual cycle, aging and menopausal symptoms. However, hormone replacement therapy can have deleterious effects leading to breast and endometrial cancer, predominantly mediated by estrogen receptor-alpha (ERα) the major isoform present in the mammary gland and uterus. Further evidence supports a dominant role of estrogen receptor-beta (ERβ) for improved cognitive effects such as enhanced hippocampal signaling and memory consolidation via estrogen activated signaling cascades. Creation of the ERβ selective ligands is challenging due to high structural similarity of both receptors. Thus far, several ERβ selective agonists have been developed, however, none of these have made it to clinical use due to their lower selectivity or considerable side effects. The research in this dissertation involved the design of non-steroidal ERβ selective agonists for hippocampal memory consolidation. The step-wise process to achieve the ultimate goal of this research includes: (1) design and synthesis of (4hydroxyphenyl)cyclohexyl or cycloheptyl derivatives, (2) in vitro biological evaluation of synthesized compounds to identify highly potent and selective candidates, and (3) in vivo biological evaluation of selected candidates for hippocampal memory consolidation. Several (4-hydroxyphenyl)cyclohexyl or cycloheptyl derivatives were synthesized having structural alterations on both aromatic and cyclohexyl/heptyl ring scaffolds. ERβ agonist potency was initially evaluated in TR-FRET ERβ ligand binding assay and compounds having high potency were re-evaluated in functional cell based assays for potency and ERβ vs. ERα selectivity. Two compounds from each series, ISP 163-PK4 and ISP 358-2 were identified as most selective ERβ agonists. Both compounds revealed high metabolic stability, solubility and no cross reactivity towards other nuclear receptors. In vivo efficiency of ISP 358-2 was evaluated in ovariectomized mice (C57BL/6) with object recognition (OR) and object placement (OP) tasks. The results indicate improved memory consolidation at 100 pg/ hemisphere and 0.5 mg/Kg via DH infusion and IP injection respectively. The information learned from this project serves as a foundation for development of other cycloheptyl/hexyl based ERβ agonists or antagonists having acceptable pharmacological profiles.
Pathogenic mechanisms of Photobacterium damselae subspecies piscicida in hybrid striped bass

Photobacterium damselae subspecies piscicida, previously known as Pasteurella piscicida, is an important pathogen of hybrid striped bass and many fish species cultured in brackish water in the United States, Japan, Europe, and the Mediterranean. The purpose of this study is to investigate virulence mechanisms that contribute to the pathogenesis of this organism. The ability of P. damselae to survive/replicate within hybrid striped bass macrophages was evaluated with an in vitro killing assay. Results indicated that the numbers of bacteria recovered from macrophages at 3, 6, 12, and 18 hours of incubation increased significantly over time. In contrast, the numbers of Escherichia coli control strain recovered from macrophages declined at the same designated incubation times. Light and electron microscopy confirmed internalization, uptake, and multiplication of bacteria within spacious, clear vacuoles in the macrophages. Using acid phosphatase as a lysosomal marker, it was shown that P. damselae inhibits phagolysosomal fusion. Invasion and replication of P. damselae within epithelioma papillosum carpio (EPC), channel catfish ovary (CCO), and fathead minnow (FHM) cells lines was also evaluated using an in vitro invasion assay. All three cell lines were susceptible to invasion and supported replication of P. damselae. Fathead minnow cells were more susceptible to invasion than the other two cell lines as indicated by greater numbers of infected cells and recovered bacteria at time 0. Using light and electron microscopy, invasion of cells by bacteria was observed as early as 30 minutes after infection, and intracellular bacteria were observed in large, clear, membrane-bound vacuoles. The
Genetic variability, correlation and path analysis in wheat (Triticum aestivum L.).

A study was conducted at Agricultural Research Farm, R.B.S. College, Bichpuri, Agra (U.P.) during Rabi season 2007-08. Range, CV, genotypic, phenotypic and environment variance, genotypic and phenotypic co-efficient of variation, heritability, genetic advance, correlation co-efficient and path analysis were performed for yield and its contributing characters in 27 wheat genotypes. Analysis of variance for significant differences was among the all characters except, number of effective tillers per plant and spike length. A broad range of variation was observed for grain yield per ha-1, plant height at maturity and number of grain per spike. Phenotypic variance value for most characters was closer than the corresponding genotypic variance value showing little environment effect on the expression of these characters. The estimated value of broad sense heritability was found between 50.10 per cent (Spike length) and 97.20 per cent (grain yield ha -1 ). Heritability values were determined as 85.60 per cent, 74.80 per cent, 90.10 per cent, 96.40 per cent, 69.40 per cent, 88.10 per cent, 96.30 per cent, and 87.90 per cent, for number of effective tillers per plant, initiation of spike, days to maturity, plant height at maturity, number of spikelet's per spike, 1000 grain weight, number of grain per spike and grain yield per plant, respectively. High heritability coupled with high genetic advance as per cent over mean was observed for grain yield ha -1 , plant height at maturity, number of grain per spike and days to maturity suggesting selection for these traits would give good responses. Grain yield ha -1 showed significant positive genotypic and phenotypic correlation with grain yield per plant (rg=0.454, rp= 0.442) and spike length (rg=0.536). Grain yield ha -1 (0.938, 0.502) had highest positive direct effect on grain yield per plant followed by 1000 grain weight (0.490, 0.336). It is suggested that these characters can be considered as selection criteria in improving the grain yield.
Effects of processing and the physical form of diets on digestibility and the performance of nursery piglets

The aim of this study was to assess the influence of various diet processing methods and physical forms on digestibility and zootechnical performance parameters of nursery piglets. The study was performed in 2 phases. The first phase was performed twice with 120 piglets per experiment, for a total of 240 newly weaned piglets, in a randomized block design with 6 treatments and 5 replicates (30 pens). The following experimental diets were offered from weaning to 21 days after weaning (initial nursery phase) and included the following: mash diet (M); mash diet conditioned at 60oC (CM); diet pelleted at 60oC/matrix 2.5 mm (P2.5); diet pelleted at 60oC/matrix 2.5 mm and crumbled (P2.5C); diet pelleted at 60oC/matrix 4.75 mm (P4.75); and diet pelleted at 60oC/matrix 4.75 mm and crumbled (P4.75C). The animals’ daily weight gain (DWG), daily feed intake (DFI) and feed conversion (FC) were assessed. Phase 2 used 24 piglets (33 days old) from Phase 1, which were lodged in individual metabolic cages. The experiment employed a randomized block design with 4 treatments and 6 replicates: mash diet (M); mash diet conditioned at 60oC (CM); diet pelleted at 60oC/matrix 2.5 mm (P2.5); and diet pelleted at 60oC/matrix 4.75 mm (P4.75). Feces were collected to analyze the digestibility of and apparent digestible energy in dry matter, gross energy and ether extract. The processing and physical form of the diets did not affect the DWG and DFI of the 21- to 39-day-old piglets. The 2.5-mm-diameter pellets induced better FC compared to the crumbled and conditioned crumbled diets (P < 0.05), which might be attributed to the better digestibility of the ether extract in the pelleted diets. Pellet size had no effect on the performance parameters.