Miracle-dz/UniFAR-FTUs huggingface dataset:
Mass Upstream Dispersal of Pelagic-Broadcast Spawning Cyprinids in the Rio Grande and Pecos River, New Mexico

Abstract. Pelagic-broadcast spawning minnows are a reproductive guild of fishes, of which several species occur in the American Great Plains and Southwest. The eggs and larvae of these species drift laterally and downstream, with drift distances varying depending on channel conditions and flow. Persistence or recolonization of these species in upstream reaches must depend on retention of eggs and larvae or upstream dispersal of later life stages, otherwise net downstream displacement of eggs and larvae would result in upstream extirpations. However, only a few individuals of several species have been observed dispersing. Here, we describe 2 direct visual observations of the young-of-year of 4 species of pelagic-broadcast spawning minnows dispersing upstream en masse. In August 2009, we observed Plains Minnow (Hybognathus placitus), Speckled Chub (Macrhybopsis aestivalis), and Rio Grande Shiner (Notropis jemezanus) dispersing upstream. The continuous shoal of fish was >200 m in length and was dispersing upstream at a rate of >1000 fish/min. In July 2017, we observed a continuous shoal of Rio Grande Silvery Minnow (Hybognathus amarus) approximately 1.9 km in length dispersing upstream at a rate between 350 and 1500 fish/min. While such dispersal events are rarely observed, they may be important for maintenance of populations in upstream areas.
Kinetic, Metabolic and Macromolecular Response of Bacteria to Antimicrobial Agents

Bacteria have the extraordinary capability to modify their phenotype in response to stress agents. Response mechanisms to stressor (such as nanoparticles or light treatments) are the result of an evolutionary process in which bacteria can become resistant, or adapt to the stressor. Therefore, it is essential to elucidate the bacterial adaptation mechanisms to metal nanoparticles or pulse ultraviolet light since these processes not only can compromise the efficacy of these treatment methods but also has implications to public health issues. Silver nanoparticles (AgNPs) are one of the most commonly used nanomaterials in consumer products and medical applications due to their antimicrobial properties. Also, pulsed lights (PL) applications for water treatment purposes are gaining increasing attention. PL has showed higher inactivation of microorganisms and degradation of PAHs, because of its rich and broad-spectrum UV content, high energy peaks and predictable treatment outcomes. However, the fate of microorganisms after exposure to AgNPs and pulsed lights as well as their negative impacts possible on the environment and public health are growing concerns. There are knowledge gaps related to: the studying molecular level change of microorganism after exposure to AgNPs by Fourier-transform infrared spectroscopy (FTIR); Bacterial adaptation to chronic exposure to nanoparticles in continuous culture: kinetic and macromolecular response; and the effect of pulsed ultraviolet light system for removal of polycyclic aromatic hydrocarbon and disinfection of pathogens in drinking water. In this study, Escherichia coli K-12 MG1655 (E. coli) responses to AgNPs was assessed under batch and continuous conditions. Further, we investigated the response of the same bacteria to PL. In detail, we evaluated antimicrobial agent’s impacts on metabolic functions and cell structure such as, colony formation units, membrane permeation, respiration, growth, gene regulation and changes in cellular composition. The results of batch culture for AgNPs toxicity test showed that bacteria developed resistance toward AgNPs and resulted in changes in the genotype and expression in the phenotype. Moreover, in continuous culture, results showed that culture growth conditions significantly affect bacterial response to nanoparticle exposure. Finally, from PL exposure to bacteria we obtained that the antimicrobial efficiency of PL depends on the PL lamp cut-off. This study provides data that have a predominant role to determine the performance of toxicological tests. Hence, the knowledge of nanoparticles fate in different growth condition minimizes the upcoming environmental and public health issues due to releasing nanoparticles release on the ecosystems. Also, understanding the bacterial responses to antimicrobial agents help us to select the more sensible agents for antimicrobial purposes.
Partial genetic characterization of a closed bovine herd produced in Canada, called “Lynch Lineback”

The Lynch Lineback is a Canadian landrace breed of cattle, originating in Eastern Canada. Developed by a Canadian family (Lynch), this breed has been a closed herd for almost a century. This study provides a partial characterization of the genetic diversity of this breeds in comparison with 10 beef, dairy, and dual purpose breed produced in Canada. A total of 21 microsatellite markers were used to evaluate the genetic profile of the different samples collected for this study. Basic statistical, cluster, and structure analyses were performed to determine the current genetic diversity and the genetic relation with other bovine breeds. Our results revealed that individuals assigned to Lynch Lineback clustered together and this cluster was isolated from all other breeds included in this study. Basic molecular analyses revealed a lower presence of alleles per locus and a lower heterozygosity for this breed. This partial genetic characterization demonstrated that Lynch Lineback breed is a unique population and it could have an impact in the production of beef or dairy cattle.
Effect of NaCl and Sorbitol on the Production of Some Alkaloids of Fenugreek Cotyledons Derived Callus

Alkaloids often had pharmacological effects. The aim at this study is to increase some alkaloids in fenugreek. Callus induction occurred on cotyledon segments 5 mm long. Murshige and Skoog medium (MS) supplied with 1 mg. lˉ¹ of 2, 4 – D and 0.4 mg. lˉ¹ of kinetin was prepared. The best medium maintained callus was using MS medium supplied with 0.5 mg. lˉ¹ 2, 4-D and 0.5 mg. lˉ¹ kinetin. Callus formation was allowed to take place for a period of thirty days in the dark at 25°C±2. Calli were analyzed using high performance liquid chromatography (HPLC). Methanol callus extract showed high concentrations of some alkaloids compared to the methanol extract of cotyledons. For increasing, the concentration of secondary metabolites, NaCl was added at concentrations 0, 1, 1.5 or 2 g. lˉ¹, sorbitol at concentrations 0, 7, 8 or 9 g. lˉ¹. NaCl at 2 g. lˉ¹ led to significant increase in trigonelline reaching 1354.72 µg per 100 mg fresh weight of callus. NaCl at 1g. lˉ¹ increased choline and carpaine reached 400.82, 483.92 µg. mlˉ¹ per 100 mg respectively. Treatment with 9 g. lˉ¹ sorbitol increased trigonelline and carpaine reached 1666.41, 742.67 µg per 100 mg respectively, while treatment 8 g. lˉ¹ sorbitol significantly increased in choline recorded 588.87 µg per 100 mg.
Effects of Oxytetracycline Antibiotic on GST Enzyme Activity and Gene Expression Levels in Rainbow Trout

In this study, effects of oxytetracycline on glutathione s-transferase enzyme activity and gene expression levels in rainbow trout (Oncorhynchus mykiss) liver were investigated. For this purpose, liver tissues from rainbow trout exposed to oxytetracycline application were collected at third, sixth and 12th hours. The group not exposed to oxytetracycline was assigned as control. While the lowest enzyme activity of GST was at 12th, the highest enzyme activity was observed in control. While compared with the control group, enzyme activity at 12th hour was highly significant (p <0.001), the third and sixth hours groups were significant (p<0.05). The lowest gene expression level was found in 12th group and the highest level was the third. While compared with the control group, difference at the third hour of gene expression level was highly significant (p <0.001), at the sixth and 12th hours groups was not significant. As a result, there was understand that no correlation between gene expression levels and GST enzyme activity. Keywords— Oncorhynchus mykiss, Liver, Glutation STransferase, Oxytetracycline, Enzyme Activity.
Chromatin at X-linked repeats that guide dosage compensation in Drosophila melanogaster is modulated by the siRNA pathway

Many heterogametic organisms adjust sex chromosome expression to accommodate differences in gene dosage. This requires selective recruitment of regulatory factors to the modulated chromosome. How these factors are localized to a chromosome with requisite accuracy is poorly understood. Drosophila melanogaster males increase expression from their single X chromosome. Identification of this chromosome involves cooperation between different classes of X-identity elements. The Chromatin Entry Sites (CES) recruit a chromatin-modifying complex that spreads into nearby genes and increases expression. In addition, a family of satellite repeats that is enriched on the X chromosome, the 1.688X repeats, promotes recruitment of the complex to nearby genes. The 1.688X repeats and CES are dissimilar, and appear to operate through different mechanisms. Interestingly, the siRNA pathway and siRNA from a 1.688X repeat also promote X recognition. We postulate that siRNA-dependent modification of 1.688X chromatin contributes to recognition of nearby genes. In accord with this, we found enrichment of the siRNA effector Argonaute2 (Ago2) at some 1.688X repeats.Mutations in several proteins that physically interact with Ago2, including the histone methyltransferase Su(var)3-9, enhance the lethality of males with defective X recognition. Su(var)3-9 deposits H3K9me2 on some 1.688X repeats, and this mark is disrupted upon ectopic expression of 1.688X siRNA. Furthermore, integration of 1.688X DNA on an autosome induces local H3K9me2 deposition, but enhances expression of nearby genes in a siRNA-dependent manner. Our findings are consistent with a model in which siRNA-directed modification of 1.688X chromatin contributes to recognition of the fly X chromosome by the MSL complex.
Potential of Telfairia occidentalis leaf extract as boar semen extender

The preservation of semen for Artificial insemination (AI) required the use of extender, which served as a buffer media to keep the sperm cell in good condition for fertilization. In this study, fluted pumpkin Telfairia occidentalis leaf extract (TOLE) potential as an unconventional boar semen extender was compared to Beltsville thawing solution (BTS), a conventional semen extender over a 48hr storage period. Aqueous solution of TOLE was prepared at three (3) concentration levels (25, 50 and 75%). Fresh ejaculates from boar were extended at (1:4) in TOLE solutions and BTS extender in a completely randomized design; treatments were replicated four (4) times. Extended semen was stored at 17C and evaluated for semen qualities which include pH, dead/live ratio (%) and sperm cell concentration at time intervals (0, 12, 24, 36 and 48) hrs. Extended semen was significantly (P < 0.05) affected by semen extenders and storage periods for pH, and dead/live ratio (%) but sperm cell concentration (10/cm) not (P > 0.05) affected. The pH values for BTS was significantly (P < 0.05) higher as compared to TOLE extenders. 75% TOLE extender had highest value (43.89%), and BTS had lowest value (12.15%) for dead/live ratio significantly (P < 0.05). The pH and dead/live ratio (%) values increased over storage time in all extender. The optimum performance of TOLE as compared to BTS extender was recorded at 50% concentration of TOLE extender. TOLE showed a potential as boar semen extender, but further studies are required to validate and improve its application.
Cellular uptake and actions of bilberry anthocyanins in retinal pigment epithelial cells

Inflammation and oxidative stress play a significant role in the pathogenesis of age-related macular degeneration (AMD). In AMD, retinal pigment epithelium (RPE) cells are damaged by oxidative stress and die via the process of apoptosis. Anthocyanins from fruits and berries, such as bilberry (Vaccinium myrtillus), possess significant antioxidant activity in vitro and have been used in "traditional medicine" to treat AMD. It is not clear whether intracellular concentrations of anthocyanins are sufficient to quench radical species and mitigate oxidative stress in vivo. In this research project, human RPE cells in vitro were used to establish an oxidative stress model in which the effects of anthocyanin and phenolics from a bilberry extract could be tested for their antioxidant potential and ability to inhibit hydrogen peroxide-induced apoptosis. Highpressure liquid chromatography with ultraviolet, electrochemical, and mass spectroscopic detection was used to characterize the bilberry extract and to measure uptake, transport, and metabolism in RPE cells. Results suggest that RPE cells internalize and metabolize anthocyanins. Although ineffective in preventing apoptosis, bilberry extract inhibited intracellular radical generation by as much as 60%. Western blot analysis revealed that physiological concentrations of bilberry anthocyanins up-regulate the oxidative stress protective enzymes heme oxygenase-1 (HO-1) and glutathione S-transferase (GSTP1) proteins in RPE cells by 1.5to 2-fold over untreated cells in 6 hours and, at pharmacologic doses, up-regulate HO-1 as much as 10-fold over a 24-hour period. Bilberry anthocyanins and phenolics were shown to induced increases in HO-1 and GSTP1 messenger RNA. The observed increases were similar to that observed for protein. Bilberry anthocyanin induction of phase II detoxifying and oxidative stress protective enzymes suggest more significant protective effects than direct radical quenching suggesting these phytochemicals may thus enhance glutathione levels or altered cellular redox states.
Copy Number Variation in Neuropsychiatric Disorders

Author(s): Huang, Alden Yen-Wen | Advisor(s): Coppola, Giovanni | Abstract: In this thesis, I characterize the contribution of rare copy number variation (CNV) to the genetic etiology of Tourette syndrome (TS) and bipolar disorder (BP). I accomplish this using several different study designs and various methods for CNV detection. As array data was widely available for the majority of samples evaluated, I make extensive use of this technology throughout this project and first provide an overview of the technical challenges involved and describe the analytical pipeline I developed to produce reliable CNV calls from such data.Then, in the largest TS CNV study conducted to date, I report the discovery of the first two genome-wide significant CNVs associated with the disorder, and demonstrate an increased global burden of large, singleton events and CNVs at known, pathogenic loci. Conditioned on this latter observation, I perform an exploratory analysis aimed at gene discovery through the identification of de novo copy number variants from whole-exome sequencing in a sample of affected proband, unaffected parent trios in TS.I then describe a CNV study of 26 large, multigenerational families with a high incidence of BP from two population isolates, using both microarray and whole-genome sequencing data. While thorough examination of these extended BP pedigrees revealed no segregating variants of large effect, I observe a significant increase in CNV burden across a subset of BP-related genes. Finally, I explore this notion further in a larger North American sample of unrelated individuals ascertained for BP. I demonstrate that although BP cases show no observable differences in the rate or size of rare CNVs, case CNVs affect more highly constrained, brain-expressed genes, and I provide evidence for an increased female CNV burden for BP.
Evaluation of character state polarity of Conus radular tooth characters.

EnglishThe character state polarity of fifteen characters of Conus radular teeth is evaluated by analysing a large data set (1400 radular teeth from 450 Conus populations of specific and subspecific rank) from previously published as well as unpublished results. A selected sample of radular teeth in different developmental stages is employed here to exemplify the characters and the results of the analysis. The selected sample is representative of putative primitive, generalist, vermivorous, molluscivorous and piscivorous type of teeth occurring in species of the genus Conus and includes radular teeth information for some species of older and more recent turrids that likely represent out-group and/or sister groups. Based on the state of the characters in putative ancestral species and, where available, on the evidence provided from the intra-specific ontogenetic change observed, plesiomorphy or apomorphy of each character are determined. italianoViene analizzato lo stato di quindici caratteri del dente radulare del genere Conus L. Lo studio di oltre 1400 radule da 450 popolazioni (species e subspecies) di Conus costituisce l'ampia base di dati indispensabile per tale analisi. Per esemplificare i caratteri e riepilogare i risultati di questa analisi, viene utilizzata una selezione di denti radulari in differenti stadi di sviluppo. Il campione e rappresentativo dei diversi tipi morfologici osservati in Conus spesso correlabili alla specializzazione trofica specifica e qui classificati come “primitivo”, “generalista”, “vermivoro”, “molluscivoro”. Il campione include il dente radulare di alcune specie di turridi, potenziale out-group e/o sister groups in una analisi cladistica. Lo stato plesiomorfico o apomorfico di ciascun carattere viene infine determinato confrontando lo stato del carattere in specie ritenute ancestrali in base ad altri caratteri morfologici, al record fossile dove noto e sull'evidenza fornita dalle modificazioni ontogenetiche osservate a livello intraspecifico.
SOME EFFECTS OF CRUDE AND NO 2 FUEL OIL ON THE CHROMOSOMES OF THE SMOOTH FLOUNDER, LIOPSETTA PUTNAMI (GILL)

An analysis was conducted on the genotoxic effects of water soluble fractions (WSF) of Venezuelan crude and No. 2 fuel oil on the chromosomes of smooth flounder (Liposetta putnami) gill cells. Both static and flow-through in-lab exposures were used to determine the effects of long-term low-level WSF exposure (7%, 4%, and 2% WSF) on adult L. putnami. The long-term exposures were of 96 and 99 days for the No. 2 fuel and crude static systems respectively, and 137 days for the flow-through systems. Chromosome aberrations scored include: fragments, chromatid deletions, complex rearrangements, rings, and translocations. Chromosome count variations were also analyzed. Water samples were examined for hydrocarbon content with fluorescent spectroscopy. Of the long-term exposures, significant increases in chromosome breakage occurred in the No. 2 fuel static experiment. The crude static and flow-through exposures resulted in a less dramatic, but significant increase in chromosome fragments. Additionally, a short-term exposure to 7% WSFs of both oil types proved significantly (P (LESSTHEQ) 0.01) more toxic (via larval mortality) than 0, 2, and 4% WSF to L. putnami sac fry when exposed for 10 days. It is hypothesized that the smooth flounder possesses an active mixed function oxidase enzyme system which may transform certain hydrocarbons into active mutagenic forms, and also may depurate hydrocarbons. The studies reported here are the first known to directly address the impacts of WSFs of oil upon the chromosome morphology of a marine species.
Investigation of the cellular tropism and in vivo distribution of HIV-1

Since its discovery in 1983, HIV-1 has spread rapidly resulting in a global pandemic. Currently an estimated 40 million people are infected with the virus. Infection leads eventually to the acquired immunodeficiency syndrome (AIDS) and death. The symptoms of the syndrome are largely due to the devastating effect HIV has on the immune system. HIV has been the focus of an unprecedented amount of research however there are still many aspects of HIV pathogenesis which remain incompletely characterized. One area which continues to attract attention is HIV tropism. HIV requires two receptorsCD4 and a co-receptorfor infection. In vivo, HIV variants mainly use either CCR5 or CXCR4 as co-receptors and thus variants can be classified as either R5 (CCR5 using), X4 (CXCR4 using) or (R5X4) (dual tropic). However these classifications do not fully explain the differing abilities of variants to infect particular cell types. It is thought that other factors, such as receptor density or alternative receptors, may underlie observed differences in tropism. In addition to studying viral variants to investigate determinants of tropism, it is also possible to investigate post-mortem material from HIV infected individuals to characterize nature and cellular location of HIV variants. HIV can infect cells in the brain and this leads in some cases to HIV associated dementia (HAD). The presence of HIV in the brain poses a challenge to attempts to eradicate the virus as many drugs have poor CNS penetration. There have been concerns that sub-optimal levels of drugs in the CNS may support the evolution of drug resistant variants. Alternatively, low levels of drugs may allow growth of drug sensitive variants which could reseed the periphery if the drug regime was halted. Characterisation of the provirus present in post mortem brain material could lead to a better understanding of this issue. The virus in the brain appears to mainly infect microglia and macrophages however it is not clear to what extent other brain cells might be infected. Conflicting reports have emerged regarding the infection of astrocytes and neurons. Thus a method for separating the various brain cells which allows them to be tested for HIV could be valuable.
Electrical-charge accumulation enables integrative quality control during B. subtilis sporulation

Quality control of offspring is important for the survival of cells. However, the mechanism by which quality of offspring cells may be monitored while running genetic programs of cellular differentiation remains largely unclear. Here we investigated a quality control system during Bacillus subtilis spore formation by combining single-cell time-lapse microscopy, molecular biology and mathematical modelling. Our results revealed that the quality-control system via premature germination is coupled with the accumulation of cations on the surface of developing forespores. Specifically, the forespores accumulating less cations on their surface are more likely to be aborted. This charge accumulation system enables the projection of multidimensional information about the external environment and morphological development of the forespore onto a one-dimensional information of cation accumulation. Based on the insight we gain, we propose a novel use of Nernstian chemicals for reducing the yield and quality of Bacillus endospores.