Miracle-dz/UniFAR-FTUs huggingface dataset:
Contrasting patterns of diversity of abundant and rare bacterioplankton in freshwater lakes along an elevation gradient

Bacterial communities comprise large numbers of species and normally include a few abundant taxa and many rare taxa. These two subcommunities may have fundamentally different ecological roles, and it is not clear whether their diversity patterns along elevation gradients vary. In this study, we investigated the diversity of bacterioplankton and their subcommunities, i.e., abundant and rare bacterioplankton, in lakes across gradual elevations from 525 m to 4652 m at Siguniang Mountain in western China via the high‐throughput sequencing of bacterial 16S rRNA genes. Elevation showed strong influence on bacterioplankton community composition (BCC) and that the dissimilarity of BCC increased with increasing differences in elevation. However, the elevational distance‐decay rate of abundant bacterioplankton was higher than that of rare bacterioplankton. Abundant bacterioplankton were more sensitive to changes of environmental factors than rare bacterioplankton. We observed a marginal increase in alpha diversity, estimated as operational taxonomic unit richness and phylogenetic diversity, of overall bacterioplankton with increasing elevation. The alpha diversity of abundant bacterioplankton decreased monotonically with elevation; in contrast, the alpha diversity of rare bacterioplankton increased monotonically with elevation. Null model tests indicated that environmental filtering played a dominant role in overall bacterioplankton community assembly along the elevation gradient, while there was decreased contribution of environmental selection to rare bacterioplankton in smaller lakes at higher elevation. Our results revealed that abundant bacterioplankton followed the general elevation diversity theory commonly found for plants and animals in freshwater lakes, whereas rare bacterioplankton did not follow this tenet.
The Passage Effect on the Senescence Profile of Cryopreserved Bone Marrow and Adipose-Derived Mesenchymal Stem Cells

Background: Although bone marrow serves as the ‘gold standard’ MSC source, adipose tissue has become a promising alternative source. Passage and cryopreservation are two effective methods to multiply, pool, and store MSC without altering its function Aims: To investigate the passage effects on the senescence profile of cryopreserved bone marrow and adipose-derived mesenchymal stem cells (MSCs). Study Design: Analytical observational study. Methodology: We analyzed the viability, cell size, population doubling time (PDT), percentage of senescent cells, and colony forming unit. Samples were bone marrow and adipose MSCs at passage one, which was cryopreserved for the first and second time. Numerical data were analyzed using the Student’s T test and analysis of variance (ANOVA) test. Results: Both in once and twice cryopreservation group, PDT and senescent cell percentage of bone marrow and adipose tissue MSCs differed significantly, where the PDT senescent cell percentage values of bone marrow MSCs were higher in all passages compared to adipose tissue. Regarding 30% confluence cell size and viability, significant differences between once and twice cryopreservation group varied and did not show any trend. The cell size and viability were less 2500 µm2, and more than 85%, respectively. Therefore, the difference in cell size at 30% confluence and viability might be regarded as normal variations. Conclusion: Cryopreserved adipose-derived MSCs showed better results compared to cryopreserved bone marrow-derived MSCs in terms of population doubling time (PDT) and senescence.
Comparison of pregnancy rates after fresh, vitrified or cryopreserved in vitro produced embryos for direct transfer

Although over 30% conception rates have recently been achieved from embryo transfer (ET) of vitrified in vitro produced (IVP) embryos, the complex process of recovery of these embryos after vitrification remains an obstacle to commercial use of this technique, with little applicability under field conditions. The aim of this study was to compare pregnancy rates obtained after ET of fresh IVP bovine embryos, vitrified or frozen for direct transfer in the commercial routine of a big dairy farm. Oocytes (n=3171) recovered by OPU from 120 Girolando females were selected and submitted to IVM for 24 hours at 38.5°C with 5% CO2 in air and saturated humidity. The IVF was performed with sexed semen thawed from 5 Holstein bulls. After IVF, the presumptive zygotes were denuded and cultured for seven days under the same conditions for temperature and humidity as IVM and IVF, but with 5% CO2 and 5% O2. Grade I embryos in stages BL or BX were transferred to fresh, frozen or vitrified for direct transfer (DT). Embryos were transferred into previously synchronized recipients. The pregnancy rates was analyzed by Binomial Logistic Regression and the probability level of p<0.05 was considered significant. Conception rates obtained were 51.35% (133/259) for embryos transferred fresh, 34.62% (84/234) for vitrified and 42.11% (96/228) for direct transfer embryos. The rates obtained from IVP embryos vitrified and direct transfer were not different between these two groups, but they were lower than the pregnancy rates from the fresh group. These results indicate that cryopreservation of IVP embryos yields results similar to those obtained after transfer of IVP fresh embryos. These results highlight the positive aspects of the possibility of cryopreservation of IVP embryos with the convenience of direct transfer.
Étude des processus introgressifs en évolution par des méthodes de réseaux

L'evolution des organismes, des genomes et des genes n'est pas strictement arborescente; les symbioses, les transferts horizontaux de genes ou encore la fusion de genes creent des objets composites formes de parties dont les histoires evolutives sont differentes. Ces processus non arborescents sont appeles introgressifs et ont un impact non negligeable en evolution. Ils sont a l'origine de transitions evolutives majeures comme l'emergence des eucaryotes, des eucaryotes photosynthetiques ou encore de nombreux groupes d'Archaea. Dans le cas des eucaryotes, l'association et la stabilisation d'une Archaea et d'une alpha-proteobacterie a permis l'emergence d'un nouveau groupe d'organismes composites aux proprietes emergentes. L'acquisition de la photosynthese chez les eucaryotes s'est faite via l'endosymbiose d'une cyanobacterie et, bien que debattue, l'apparition des grands groupes d'Archaea semble etre concomitante avec l'acquisition de nombreux genes d'origine bacterienne. Ces superorganismes ont la particularite d'avoir des genomes composes de genes de differents partenaires symbiotiques. L'objectif de mon travail de these a constitue a etudier l'aspect introgressif de l'evolution par des methodes de reseaux de similarite de sequence et des methodes phylogenetiques. Je me suis particulierement focalise sur la detection de nouveaux genes chimeriques nommes genes symbiogenetiques (S-genes) car composes de parties originaires des differents partenaires symbiotiques. De tels genes existent dans les genomes et plusieurs regles d'association ont pu etre mises en evidence. Plus generalement, la presence de S-genes etend la notion de mosaicisme genomique au niveau infra-genique.
Transfer of Cd, Cr and Zn from zooplankton prey to mudskipper Periophthalmus cantonensis and glassy Ambassis urotaenia fishes

Assimilation efficiency (AE) of metals from ingested food is critical for understanding trace metal accumulation and trophic transfer in aquatic animals. Most recent measurements of metal AEs have been on aquatic invertebrates, whereas relatively few studies have examined metal assimilation in fishes. In this study we determined the AEs of Cd, Cr and Zn in 2 fishes (pelagic glassy Ambassis urotaenia, Ambassidae, and the intertidal mudskipper Periophthalmus cantonensis, Gobiidae) feeding on 2 zooplankton prey (brine shrimp Artemia larvae and copepods). Zooplankton were radiolabeled either by feeding on radiolabeled phytoplankton or by direct exposure to radiotracers in the dissolved phase. Fishes were then fed with radiolabeled zooplankton prey for < 1 h, and the retention of ingested metals in the fishes was followed for 2 d. The measured AEs of Cd, Cr and Zn were 14 to 33, 4 to 12, and 5 to 17% in glassy fish, and 10 to 26, 4 to 19, and 11 to 31% in mudskipper, respectively. Routes of radiolabeling in copepod prey did not affect metal AEs in either mudskipper or glassy, whereas metal AEs differed by up to 10-fold in glassy fish feeding on Artemia larvae labeled from different routes. There was little difference in the gut passage time of metals for different food types and metals or between fishes. AE was not significantly related to metal gut passage time or metal distribution in the soft tissues of zooplankton prey, for each metal. However, AE in mudskippers was significantly correlated with metal distribution in the prey's soft tissues when all 3 metals were considered. Our study demonstrated that marine fishes can appreciably assimilate trace metals, and trophic transfer should be considered as a source for metal accumulation in fishes.
Impact of Information on Northeastern U.S. Consumer Willingness to Pay for Aronia Berries

Consumption of berries has increased signiﬁcantly over the past couple of years. As such, producers and retailers are experimenting with new berry varieties to capture market share and increase their proﬁtability. We examine consumer preference and willingness to pay (WTP) for a relatively new-to-market berry (aronia: Aronia mitschurinii Skvortsov et Maitulina) compared with another relatively new berry (black currant: Ribes nigrum L.) as well as more traditional (raspberry: Rubus idaeus L., blueberry: Vaccinium corymbosum L., and blackberry: Rubus fruticosus L.) berries. Given that aronia berries have an astringent/bitter ﬂavor while having high antioxidant levels we investigate how taste and health information impact preference and WTP. Furthermore, we add to the literature by investigating the differences in WTP for locally and nonlocally (regional, the United States, and outside the United States) labeled berries across varying retail outlets (i.e., farmer’s markets, farm stands, grocery store). We ﬁnd that new berries (aronia and black currant) are heavily discounted compared with more traditional berries. Potentially negative taste information (i.e., astringent/bitter ﬂavor) has a negative impact on WTP, whereas positive health information has a positive impact on WTP. The positive effect of health information tends to offset the impact of the negative taste information. With respect to local labeling and retail outlet, locally labeled berries at a farmer’s
Molecular control of development in the reef coral, Acropora millepora

A brief overview of the embryonic and larval development of Acropora, including some previously unpublished data, provides the background for this review of our rapidly expanding knowledge of the genes that control early development in corals, with particular emphasis on Hox and Hox-like genes. Since the Phylum Cnidaria is widely accepted to be an ancient group of organisms, genes, and motifs within genes, that are shared by corals and higher metazoans are presumably ancient. Thus, shared genes allow us to study how gene structure and function have changed with time, while genes specific to higher metazoans have, presumably, evolved more recently. Anatomically, corals have many fewer cell types than higher metazoans, but it is not clear that this apparent simplicity will be reflected at the molecular level. We have already found Acropora representatives of structural genes, housekeeping genes, nuclear receptors, Hox-like genes, Pax genes and components of the dpp signalling pathway. However, thus far there is no unequivocal evidence for the cluster of Hox genes, known as the zootype genes, that is otherwise widespread among the Metazoa. As more data become available, the Cnidaria are making an increasing contribution to our knowledge of the evolution of gene structure, function, and regulation. We here illustrate the evolutionary approach that we are taking to the characterisation of coral genes with a review of our work on the Acropora Hox- like gene, cnox2-Am.
Neuroprotective Effects of Methanol Extracts of Jeju Native Plants on Hydrogen Peroxide-induced Cytotoxicity in SH-SY5Y Human Neuroblastoma Cells

Neuronal death is a common characteristic hallmark of a variety of neurodegenerative disorders including Alzheimer's disease and Parkinson's disease. However, there have been no effective drugs to successfully prevent neuronal death in those diseases, whereas oriental medicinal plants have to possess valuable therapeutic potentials to treat neurodegenerative diseases. In the present study, in an attempt to provide neuroprotective agents from natural plants, 80% methanol extracts of a wide range of medicinal plants, which are native to Jeju Island in Korea, were prepared and their protective effects on hydrogen peroxide-induced apoptotic cell death were examined. Among those tested, extracts from Smilax china and Saururus chinesis significantly decreased hydrogen peroxide-induced apoptotic cell death. The extracts attenuated hydrogen peroxide (H2O2)-induced caspase-3 activation in a dose-dependent manner. Further, plant extracts restored H2O2-induced depletion of intracellular glutathione, a major endogenous antioxidant. The data suggest that Jeju native medicinal plants could potentially be used as therapeutic agents for treating or preventing neurodegenerative diseases in which oxidative stress is implicated.
The effects of atmospheric pressure on inter-specific competition and the morphological and hematological characteristics of elevational distributions of hummingbirds

Species diversity in mountainous regions is strongly influenced elevational range limits of species, but it is generally not known which abiotic or biotic factors maintain these limits. Using Black-chinned and Broad-tailed Hummingbirds, species with offset but overlapping elevational ranges in the southwestern USA, we investigate the role barometric pressure plays in influencing these limits. In chapter one, we used a hypobaric chamber to test the effects of variable air pressures on interspecific competitive dominance. We sequenced the genes that encode the two adult isoforms of haemoglobin and measured the O2-binding affinity of each isoform. In chapter two, we explored the morphological differences between species and the haematological response of species
Signature Whistle Production during a Bottlenose Dolphin Group Integration

ii ACKNOWLEDGMENTS . iv DEDICATION . v LIST OF TABLES . xi LIST OF ILLUSTRATIONS . xii CHAPTER I INTRODUCTION . 1 Possible Origins of Delphinid Communication and Cognition . 3 Bottlenose Dolphin Society . 4 Bottlenose Dolphin Cognition . 6 Bottlenose Dolphin Vocalization . 7 Signature Whistles . 8 Signature Whistle Development and Stability . 10 Signature Whistle Copying . 11 Dolphin Group Integrations . 13 Project Overview . 14 Question 1: Does the pattern of combined whistle production increase after the new dolphin is introduced to the existing group? 15 Hypothesis: . 15
Gene regulatory mechanisms underlying the evolutionary loss of a polygenic trait

Trait loss is a pervasive phenomenon in evolution, yet the underlying molecular causes have been identified in only a handful of cases. Most of these involve loss-of-function mutations in one or more trait-specific genes. Parasitoid insects are fatty acid auxotrophs: they lost the ability to convert dietary sugars into fatty acids, a trait that is ubiquitous among non-parasitoid animals and is enabled by a highly conserved set of genes. Earlier research suggests that lack of lipogenesis is caused by changes in gene regulation, rather than gene decay. We compared transcriptome-wide responses to sugar-feeding in the non-lipogenic parasitoid species Nasonia vitripennis and the lipogenic Drosophila melanogaster. Both species adjusted their metabolism within four hours after feeding, but there was little overlap at the gene level between the responses of the two species. Even at the pathway-level, there were sharp differences between the expression profiles of the two species, especially in carbohydrate and lipid metabolic pathways. Several genes coding for key enzymes in acetyl-CoA metabolism, such as malonyl-CoA decarboxylase (MCD) and HMG-CoA synthase differed in expression between the two species. Their combined action likely blocks lipogenesis in the parasitoid species. Network analysis indicates most genes involved in these pathways to be highly connected, which suggest they have pleiotropic effects and could explain the absence of gene degradation. Our results indicate that modification of expression levels of only a few non-connected genes, such as MCD, is sufficient to enable complete loss of lipogenesis in N. vitripennis.
The influence of emrBAR efflux system on symbiosis between Medicago truncatula and Sinorhizobium meliloti

Nitrogen is an essential part of biomolecules and is needed for the metabolism and development of all plants. Symbiotic interactions between bacteria and plants have evolved in order to enable the absorption of nitrogen to plants. The main focus of this study was the effect of the EmrBAR efflux system on the symbiosis between the legume Medicago truncatula and the rhizobium Sinorhizobium meliloti. The results showed that emrA and emrR are expressed in early symbiotic interactions, during the formation of infection threads. EmrA is expressed in the infection and nitrogen-fixation zones, and emrR only in the infection zone of the nodule. Analysis of nodulation phenotype of the emrBAR deletion mutants and the wild type in sloped agar tubes might suggest that the creation of new nodules was a response to inefficient nitrogen fixation. Analysis of nodulation phenotype of the emrBAR deletion mutants and the wild type in Magenta boxes suggests that the emrBAR deletion affects symbiotic plant growth by decreasing nodule efficiency. A bacterial growth assay showed that 2-phenylphenol inhibits the growth of the two emrBAR deletion mutant strains in comparison with the wild type. This seems to indicate the importance of the EmrBAR efflux system in the extrusion of toxic substances.
Obesity and Asthma: Adiponectin Receptor 1 (Adipo R1) and Adiponectin Receptor 2 (Adipo R2) are expressed by normal human bronchial epithelial (NHBE) cells at air-liquid interface (ALI) and expression changes with IL-13 stimulation

OBESITY AND ASTHMA: ADIPONECTIN RECEPTOR 1 (ADIPO R1) AND ADIPONECTIN RECEPTOR 2 (ADIPO R2) ARE EXPRESSED BY NORMAL HUMAN BRONCHIAL EPITHELIAL (NHBE) CELLS AT AIR-LIQUID INTERFACE (ALI) AND EXPRESSION CHANGES WITH IL-13 STIMULATION By Jennifer Bradley, M.S. A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science, at Virginia Commonwealth University. Virginia Commonwealth University, 2016. Major Director: Dr. Bruce K. Rubin MD, MBA, FRCPC Affiliate Faculty of Microbiology and Immunology Professor of Biomedical Engineering Jessie Ball duPont Distinguished Professor and Chair, Dept. of Pediatrics Co-Director: Dr. Xianjun Fang PhD Associate Professor of Biochemistry and Molecular Biology Obesity is recognized as an important risk factor for the development of many chronic diseases such as hypertension, Type 2 diabetes mellitus (T2DM) cardiovascular disease, cancer, renal disease, neurologic dysfunction, metabolic syndrome and asthma (3, 4). Circulating serum adiponectin levels in obese asthmatics have been reported to be low. Therefore, we aimed to investigate the role of adiponectin in a mucus hypersecretion model and hypothesized that adiponectin would decrease IL-13 induced MUC5AC expression from differentiated NHBE cells and that increasing concentrations of IL-13 would cause a decrease in Adipo R1 and Adipo R2 expression. MUC5AC expression with exposure to adiponectin was not significant. However, mRNA expression of Adipo R1 and Adipo R2 was significantly decreased by stimulation of IL-13 for acute (24 hours) and chronic (14 days) exposure. Therefore, the obese state and specifically IL-13 concentration could play a role in Adipo R1 and Adipo R2 expression within NHBE cells.
A review of Brassica seed color

Rahman, M. and McVetty, P. B. E. 2011. A review of Brassica seed color. Can. J. Plant Sci. 91: 437-446. Canola oil has excellent fatty acid composition and low saturated fat levels, and canola meal has protein with excellent amino acid composition. Canola seed quality can be further improved by the development of higher oil, higher protein and lower fiber content germplasm through the development of yellow seeded lines. While there is no naturally occurring yellow seeded B. napus, yellow seeded mutants that have arisen in nature can be readily indentified in Brassica rapa, B. juncea and B. carinata species. Brassica napus is widely cultivated in Asia, Australia, Europe and North America. Yellow seed in Brassica species is associated with seed that has higher oil and protein content and lower fiber content. Because of these seed quality advantages of yellow seeded lines, plant breeders around the world have been attempting to develop yellow seeded B. napus genotypes using crosses involving naturally occurring yellow seeded Brassica species. Seed color in B. rapa is controlled by two genes. Two duplicate genes are responsible for seed color in B. juncea. In B. carinata, one repressor gene represses the seed color gene resulting in yellow seed, while the absence of the repressor gene results in brown seed. Several yellow seeded B. napus genotypes have been developed and in most cases three genes are reported as being are responsible for seed color. Numerous different molecular markers for seed color genes in B. rapa, B. juncea and B. napus have been developed for use in marker-assisted selection in plant-breeding programs. These molecular markers can also be used to clone the Brassica seed color gene(s) and then create transgenic yellow seeded B. napus genotypes. This review summarizes past and current research on Brassica seed color breeding, genetics and genomics/biotechnology.