Miracle-dz/UniFAR-FTUs huggingface dataset:
Brook Trout Population Genetic Tools for Natural Barriers in Fragmented Subwatersheds

Barriers to fish movement can cause aquatic habitat fragmentation by reducing the amount of available habitat. The primary goal of my research was to investigate applications of population genetic analysis tools as indicators of barrier effects on brook trout populations in fragmented subwatersheds. In chapter1, I tested the hypothesis that brook trout population genetic differentiation (FST) above and below barriers will differ in relation to barrier height and gradient. I also tested the hypothesis that average gene diversity per locus (H) and the numbers of alleles (A) differed between samples below and above each barrier. There was no significant difference in average number of alleles (A) or average gene diversity per locus (H) between the aboveand belowbarrier samples, but linear regression identified a statistically significant relationship between barrier height and FST values. Unrooted neighbor-joining consensus trees of Cavalli-Sforza and Edwards (1967) chord distances provided evidence of genetic differentiation between samples of resident brook trout above and below natural barriers. Additionally, average total allelic diversity (A), average gene diversity per locus (H), average number of private alleles per locus per sample, and total alleles per sample differed between Level III Ecoregions. In chapter 2 I tested the hypothesis that the presence of a barrier, total habitat potentially isolated above a barrier (km), road density, and percent forest cover within a subwatershed (USGS 6 th -level Hydrologic Units) were significant habitat iii fragmentation factors affecting the effective population size (Ne) of brook trout in the Blue Ridge Level III Ecoregion. Multivariable linear regression indicated that total habitat above the barrier (km) and road density were significant variables retained in the model to predict Ne. In chapter 3, the objective of the study was to infer relationships between barriers and family structure in brook trout populations. Maximum likelihood analysis of pairwise kinship relationships between aboveand below-barrier individuals indicated the presence of parent-offspring relationships between aboveand below-barrier individuals at six sites in the Blue Ridge Level III Ecoregion and five sites in the Northern Lakes and Forests Level III Ecoregion, which indicated movement of individuals between the aboveand below-barrier locations.
A checklist of Asteraceae from Pedra do Lagarto, Santa Maria, Rio Grande do Sul, Brazil

1 Laboratório de Estudos em Vegetação Campestre, Instituto de Biociências, Universidade Federal do Rio Grande do Sul. Av. Bento Gonçalves, 9500, Prédio 43431, Agronomia, Porto Alegre, RS, Brazil. 2 Laboratório de Taxonomia Vegetal, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Avenida Roraima, 1000, prédio 16, Camobi, Santa Maria, RS, Brazil. Corresponding author: Juliana Schaefer, julianaschaeferbio@gmail.com
Bioerosion: the other ocean acidification problem: Towards a Broader Perspective on Ocean Acidification Research Part 2 A special issue of the ICES Journal of Marine Science

&NA; Bioerosion of calcium carbonate is the natural counterpart of biogenic calcification. Both are affected by ocean acidification (OA). We summarize definitions and concepts in bioerosion research and knowledge in the context of OA, providing case examples and meta‐analyses. Chemically mediated bioerosion relies on energy demanding, biologically controlled undersaturation or acid regulation and increases with simulated OA, as does passive dissolution. Through substrate weakening both processes can indirectly enhance mechanical bioerosion, which is not directly affected by OA. The low attention and expert knowledge on bioerosion produced some ambiguous views and approaches, and limitations to experimental studies restricted opportunities to generalize. Comparability of various bioerosion and calcification rates remains difficult. Physiological responses of bioeroders or interactions of environmental factors are insufficiently studied. We stress the importance to foster and advance high quality bioerosion research as global trends suggest the following: (i) growing environmental change (eutrophication, coral mortality, OA) is expected to elevate bioerosion in the near future; (ii) changes harmful to calcifiers may not be as severe for bioeroders (e.g. warming); and (iii) factors facilitating bioerosion often reduce calcification rates (e.g. OA). The combined result means that the natural process bioerosion has itself become a “stress factor” for reef health and resilience.
Predator foraging response to a resurgent dangerous prey

Summary Prey switching occurs when a generalist predator kills disproportionately more of an abundant prey species and correspondingly spares a rarer species. Although this behaviour is a classic stabilizing mechanism in food web models, little is known about its operation in free-living systems which often include dangerous prey species that resist predation. We used long-term (1995–2015) data from a large mammal system in northern Yellowstone National Park, USA, to understand how prey preference of a wild, generalist predator (Canis lupus) responds to a shift in prey species evenness involving rising numbers of dangerous prey (Bison bison) and dropping numbers of relatively safer prey (Cervus elaphus). Contrary to the prey switching hypothesis, wolves attacked and killed disproportionately more of the rarer, but safer, species. Wolves maintained a strong preference against bison even when this species was nearly twice as abundant as elk. [Correction added after online publication on 26 April 2017: ‘more than’ changed to ‘nearly’]. There was also evidence that wolves were increasingly averse to hunting bison as relative bison abundance increased. Wolves seldom hunted bison because capture success was limited to a narrow set of conditions: larger packs (>11 wolves) chasing smaller herds (10–20 bison) with calves. Wolves scavenged bison carrion instead and did so more frequently as bison abundance increased. Our study demonstrates the overarching importance of prey vulnerability to understanding the prey preferences of generalist predators in ecological communities with dangerous prey. The formidable defences of such prey diminish the potential for switching and its stabilizing influence on population dynamics. In these communities, shifts from hunting to scavenging are perhaps more likely than shifts in prey preference. The assumption of switching may therefore overestimate the stability of multi-prey systems that include dangerous prey species. A lay summary is available for this article.
A review of the biology and status of Cape Fold Ecoregion freshwater fishes

Mediterranean climate regions are globally recognized as hotspots of endemism in fishes; however, these unique assemblages are increasingly threatened by human mediated impacts including water abstraction, damming and non-native species introductions. The Cape Fold aquatic ecoregion (CFR) of South Africa supports an assemblage of range-restricted endemic freshwater fishes, the majority of which are conservation priorities because they are under severe threat of extinction. Effective conservation and management are constrained by the lack of readily available information on this imperilled group of fishes because research efforts over the last century have been temporally disjointed and relatively uncoordinated. This review provides an exhaustive appraisal of published literature on the taxonomy, biogeography, life history, ecology and physiology of freshwater fishes in the CFR, and the human impacts that affect them. Its aim is to direct future research needs for effective management and conservation of this imperilled group. Only 103 peer-reviewed articles on CFR fishes were recorded and the majority of available research is on taxonomy and biogeography (40.8%), followed by ecological investigations (22.3%), conservation (19.4%) and human impacts (17.5%). Despite a plethora of studies on taxonomy and biogeography, recent genetic evidence suggests that fish diversity in the CFR has been severely underestimated and requires urgent attention. Human impacts severely threaten the existence of many native CFR fishes and require further study. Information on the biology and ecology of CFR fishes is limited to studies on selected species; of particular note is the lack of physiological information which is particularly pertinent given projected climate change scenarios.
Basidiocarps of ectomycorrhizal fungi inEucalyptus urograndisplantation at the Zona da Mata de Minas Gerais: main genera and seasonal distribution

Spore inoculation is a low cost alternative to produce seedlings of ectomycorrhizal plants to degraded lands. The objective of this work was to identify and evaluate the occurrence of ectomycorrhizal fungi basidiocarps in a Eucalyptus urograndis plantation in Rio Pomba. We identified fungi belonging to the genera Pisolithus sp. and Scleroderma sp. The highest production of basidiocarps was observed 40 to 60 days after the beginning of the raining period. Most part of basidiocarps was observed in sites with direct incidence of the sun light in soil. This information will subsidize strategies of basidiocarps collection in order to obtain spores to inoculation programs in nurseries.
Alzheimer's disease decreases surface glutamate receptors by regulating actin stabilization

The early stage cognitive deficits in Alzheimer's disease (AD) have been attributed to soluble, oligomeric forms of Amyloid [Beta] (sA[Beta]) and its effect on synaptic structure, function glutamate receptor content. Excitatory synapses in the brain mainly reside on dendritic spines. Their synaptic activity involves ionic currents that are mediated by glutamate receptors. Dendritic spines are rich in the cytoskeletal component actin, which mediates spine stability and morphology as well as anchors receptors to the spine surface. We observe that sA[Beta} reduces the expression of total and surface glutamate receptors through a mechanism that involves an increase in the activity of cofilin, an actin severing protein. In addition, we show that inhibition of cofilin's F-actin severing activity prevents the decrease in surface glutamate receptor expression witnessed in the presence of sA[Beta]. This provides a novel mechanism behind sA[Beta]- induced synaptic dysfunction in Alzheimer's Disease
Gas chromatography-mass spectrometry analysis and in vitro antioxidant potential of ajwain seed (Trachyspermum ammi L.) essential oil and its extracts

The aim was to study the composition of ajwain seed oil by gas chromatography-mass spectrometry (GC-MS) and to evaluate antioxidant activity of ajwain seed oil, its fractions, extracts, thymol, and its derivatives. GC-MS analysis of ajwain seed essential oil showed the presence of 47 compounds. Thymol (31.40%) was found to be the major component while γ-terpinene, isobornyl isobutyrate, and p-cymene were minor compounds. The antioxidant potential of selected components was evaluated using 2, 2-diphenyl-1-picrylhydrazyl, hydroxyl, nitric oxide radical scavenging and ferric reducing antioxidant power assays. Results demonstrated that methanol extract exhibited higher antioxidant activity in 2,2-diphenyl-1-picrylhydrazyl (IC50 value 130 µg/mL), Hydroxyl radical (IC50 value 120 µg/mL), nitric oxide (IC50 value 90 µg/mL) scavenging assays, and highest ferric reducing antioxidant power (FRAP) value (780 µg Fe (II)/g dry weight) as compared to hexane and dichloromethane extracts. Total phenolic (16.52 mg gallic acid equivalents/g) and flavonoid contents (3.89 mg quercetin equivalent/g) were also found to be higher in methanol extract compared to other extracts and ajwain oil. Practical applications Degradation of food materials by oxidation and its prevention during production, storage, and distribution is an important issue in the food industry. Due to the potential carcinogenic effect of some synthetic antioxidants, much attention has been paid to naturally-derived compounds having potential to act as antioxidants. The present study revealed that the methanol extract of ajwain seeds which contained terpenoids, phenols, and flavonoids as essential phytochemicals have high antioxidant properties, which can provide opportunities for use in pharmaceutical, nutraceutical, and food industries.
Effect of modulating S. Epidermidis biofilms dormancy in the biofilm physiology and host immune response

XI List of Abbreviations . XVII List of Figures . XIX List of Tables . XXI CHAPTER 1. General Introduction. 1 1.1. Staphylococcus epidermidis. 3 1.2. Staphylococcus epidermidis biofilms . 4 1.3. The interaction of biofilms with the host immune system. 7 1.4. Heterogeneity of cells within a biofilm . 10 1.5. Staphylococcus epidermidis biofilm dormancy model . 15 1.6. Proteomic and transcriptomic crosstalk to disclose molecular pathways in bacterial dormancy . 18 1.7. Goals . 23 CHAPTER 2. Dormancy within S. epidermidis biofilms: a transcriptomic analysis by RNASeq . 25 2.
Haplotype Effects on Human Survival: Logistic Regression Models Applied to Unphased Genotype Data

Haplotype based linkage disequilibrium (LD) mapping exhibits higher power than the single locus approach because it makes use of the LD information contained in the flanking markers. New statistical methods have been proposed to help to infer haplotype effects on human diseases using multi‐locus genotype data collected from unrelated individuals. In this paper, we introduce a statistical procedure for measuring haplotype effects on human survival using the popular logistic regression model with haplotype based parameterizations. By modeling haplotype frequency as a function of age, our model infers haplotype effects by estimating and testing the slope parameters under different genetic mechanisms (multiplicative, dominant, or recessive). In addition, by estimating the sex‐specific slope parameters, our model allows the detection of sex‐specific haplotype effects or haplotype‐sex interactions. As an example, we apply our model to an empirical dataset on a stress related gene, interleukin‐6, to look for haplotypes that affect individual survival and for haplotype‐sex interactions. We show that our logistic regression based haplotype model can be a helpful tool for researchers interested in the genetics of human aging and longevity.
Genomic analysis of human polymorphisms affecting drug-protein interactions

Human genetic variability is thought to account for a substantial fraction of individual biochemical characteristics – in biomedical sense, of individual drug response. However, only a handful of human genetic variants have been linked to medication outcomes. Here, we combine data on drug-protein interactions and human genome sequences to assess the impact of human variation on their binding affinity. Using data from the complexes of FDA-drugs and drug-like compounds, we predict SNPs substantially affecting the protein-ligand binding affinities. We estimate that an average individual carries ~6 SNPs affecting ~5 different FDA-approved drugs from among all of the approved compounds. SNPs affecting drug-protein binding affinity have low frequency in the population indicating that the genetic component for many ADEs may be highly personalized with each individual carrying a unique set of relevant SNPs. The reduction of ADEs, therefore, may primarily rely on the application of computational genome analysis in the clinic rather than the experimental study of common SNPs.
Characteristics of 22 cassava (Manihot esculenta Crantz) genotypes from Riau Province, Indonesia.

1Department of Biology, Faculty of Mathematics and Natural Sciences, Riau University, Kampus Binawidya Km 12.5, Jl. HR Soebrantas, Panam, Pekanbaru 28293, Indonesia 2Agency for the Assessment and Application of Technology (BPPT), Gedung 630, Kawasan Puspiptek Serpong, Tangerang 15314, Indonesia *Corresponding author’s email: dewiindriyaniroslim@gmail.com Co-authors’ email addresses: hermansyahdan@unri.ac. id, nery_yusuf@yahoo.com, chanivat@yahoo.com, ini.rezty@yahoo.com, adnil_bio@yahoo.com
Phylogeny and systematics of the tribe Thlaspideae (Brassicaceae) and the recognition of two new genera

Thlaspideae is an Old World tribe of Brassicaceae centered in SW Asia. Thirty-seven of 42 species (ca. 88%) in 13 genera of the tribe were analyzed using nuclear ITS and chloroplast trnL-F markers in a family-wide context. Both singlemarker and concatenated phylogenies corroborated Thlaspideae as a well-supported monophyletic clade. With the exception of polyphyletic Alliaria and Parlatoria and paraphyletic Thlaspi and Didymophysa, the remaining genera were monophyletic. Alliaria petiolata comprised diploid and hexaploid populations in two well-resolved clades. The non-weedy diploid and hexaploid populations are restricted to SW Asia, and together with diploid A. taurica (formerly P. taurica), formed a sister clade to well-resolved Sobolewskia (3 spp.) and P. rostrata (now treated as the new monospecific genus Lysakia) clades. By contrast, the European and North American weedy and invasive hexaploid A. petiolata populations clustered with the diploid P. cakiloidea. Polyphyletic Thlaspi formed two distinct clades easily distinguished morphologically, and two of its six species are segregated into the new genus Mummenhoffia. Elburzia is reduced to synonymy of Didymophysa, and the new combinations D. fenestrata, Lysakia rostrata, Mummenhoffia alliacea, and M. oliveri are proposed and a diagnostic key for determination of Thlaspideae genera is presented. Age estimations based only on calibration by the controversial fossil Thlaspi primeavum resulted in unrealistic old age estimates. Chromosome counts are reported for 16 species.
An Evaluation of Interstate Efforts to Re-Introduce Paddlefish to the Upper Ohio River Basin

Abstract Historically, Polyodon spathula (American Paddlefish) occurred within the Mississippi River Basin's large rivers, traversing hundreds of kilometers to complete their life cycle. However, populations declined in response to the installation of lock and dam (L/D) structures, declining water quality, and the loosely regulated harvest of the species. By the late 1800s, American Paddlefish were extirpated from many portions of their historic range. In response, federal and state agencies sought to restore inter-jurisdictional populations of this fish. Our objective was to assess reintroduction efforts in the northeastern-most portion of its range. Using a combination of gill nets, boat electrofishing, and larval drift nets, populations were sampled in Pennsylvania and New York over a 10-year-period, post-stocking. Although American Paddlefish were at large in navigable waters of the upper Ohio River Basin, free-flowing and tail-water areas below L/D structures appeared to hold more fish than impounded reaches. The presence of L/D structures and fixed-crest dams may inhibit upstream passage of fish and reduce the availability of forage, as reflected in reduced condition-index scores. Although gravid fishes were captured in Pennsylvania and New York, little evidence exists to suggest the presence of self-sustaining populations, as only one larval American Paddlefish was captured. The recovery of this species to its historic northeast range may hinge on continuing stocking efforts, development of fish-passage structures, conservation lockages, and improvement and protection of suitable spawning habitats.
Évaluation de la contamination bactériologique des eaux usées des stations d’épuration du Grand Agadir : isolement, caractérisation moléculaire et antibiorésistance des espèces du genre Vibrio

In countries such as Morocco, characterized by scarce rainfall, lack of freshwater resources and high groundwater salinity where agriculture reuse of municipal wastewater is becoming a compulsory choice for water resources management. This study evaluated the efficiency of the three wastewater treatment plants (WTPs) for the removal of physico-chemical and microbiological contaminants. Resistance to antibiotics, pulsed field gel electrophoresis and MALDI-TOF mass spectrometry were used to characterize Vibrio isolates. Mean values were used to determine treatment performances of the 3 WTPs, electric conductivity didn’t showed any difference between raw and treated wastewater and the mean values varying from 2900 μS/cm to 3300, the pH varying from 6,66 to 8,6, and the temperature varying between 16°C and 26. 4°C. Removal efficiencies of fecal coliforms, enterococci and spores of sulphite reducing anaerobic bacteria were betwenn 3 and 4 log unit for the 3WTPs. 4 species of Vibrio were identified, among the 58 Vibrio sp. Isolated, 53,44% were identified as V. Cholerae, 29,31% as V. Alginolyticus, 17,78% as V. Fluvialis and 1,74% as V. Metschnikovii. Of the total 58 Vibrio isolates, 53,44% were susceptible to all antibiotics. Of the resistant (46,56%) Vibrio strains, 39,83% were resistant against one to three antibiotics. PFGE with NotI digestion produced patterns with higher level of heterogeneity, and about 31% of Vibrio isolates were untypeable. MALDI-TOF-MS-based fingerprinting of Vibrio isolates has potential as a rapid for identification and finest differences between strains can readily be evaluated by the dendrogram based on percentage identity of MALDI-TOF mass spectra of Vibrio isolates, but requires further development for database of BioTyper.
Motor nuclei innervating eye muscles spared in mouse model of SOD1-linked ALS

The eye muscles of humans with either inherited or sporadic forms of ALS are relatively unaffected during disease progression, a function of sparing of the cranial nerve motor neurons supplying them. Here we observe that cranial nerve nuclei are also spared in a mouse model of inherited SOD1-linked ALS. We examined the cranial nerve motor nuclei in a mouse strain, G85R SOD1YFP, which carries a high copy transgene encoding a mutant human SOD1-YFP fusion protein, that exhibits florid YFP-fluorescent aggregates in spinal cord motor neurons and paralyzes by 6 months of age. We observed in the cranial nerve nuclei that innervate the eye, 3N (oculomotor), 4N (trochlear), and 6N (abducens), that there was little (4N, 6N) or no (3N) aggregation, in comparison with other motor nuclei, 5N (trigeminal), 7N (facial), and 12N (hypoglossal), in the latter two of which florid aggregation was observed. Correspondingly, the number of ChAT positive motor neurons in 3N of G85R SOD1YFP relative to that in 3N of ChAT-EGFP mice showed that there was no loss of motor neurons over time, whereas in 12N there was progressive loss of motor neurons, amounting to a loss of ∼30% from G85R SOD1YFP by end-stage. Thus, the sparing of extraocular motor neurons as occurs in humans with ALS appears to be replicated in our SOD1-linked ALS mouse strain, supporting the validity of the mouse model for studying this aspect of selective motor system loss in ALS. Comparisons of extraocular motor neurons (e.g., from 3N), resistant to ALS pathology, with other cranial motor neurons (e.g., from 12N), sensitive to such pathology, may thus be of value in understanding mechanisms of protection vs. susceptibility of motor neurons.