Miracle-dz/UniFAR-FTUs huggingface dataset:
Vibrissae growth rates and foraging and migration patterns for juvenile male northern fur seals (Callorhinus ursinus) from St. Paul Island, Alaska determined with stable isotope analysis

Author(s): Kelleher, Christina | Advisor(s): Kurle, Carolyn | Abstract: The causes of recent declines of the population of northern fur seals (Callorhinus ursinus) on the Pribilof Islands, Alaska are unknown. Estimations of northern fur seal migratory patterns could contribute to a better understanding of the reasons for their decline and allow for better management of their population. A method used to reconstruct marine vertebrate foraging and movement patterns is stable isotope analysis of animal tissues. Vibrissae in Otariidae grow continuously throughout their lives beginning in utero, thereby incrementally accumulating stable isotope data that reflect their food sources and migratory patterns from before birth to the time of vibrissae collection (Sherer et al. 2015). I analyzed the stable carbon (δ13C) and nitrogen (δ15N) isotope values at intervals along entire vibrissae collected from 8, known age (2, 3, and 4 year-old), juvenile male northern fur seals from St. Paul Island, Alaska. This provided the δ13C and δ15N values along a temporal scale from embryogenesis to whisker collection in August of 2014. I determined vibrissae growth rates to match stable isotope patterns to specific time periods in the animals' lives. I also analyzed the δ13C and δ15N values of the segments from the longest and shorter vibrissae from the same individuals (n=3) to determine if equivalent data were reflected in both sizes. This could allow for fewer analyses per whisker, saving resources. The mean vibrissae growth rate (±SD) per month for juvenile males (3.5 ± 1.4 mm/month) had a fairly high standard deviation. The average vibrissae growth rate per month for the first year of life (4.6 ± 1.1 mm/month) indicates a faster growth rate for young of the year animals than 1-4 year-olds (3.0 ± 1.1 mm/month). I found annual oscillations in the δ13C and δ15N values, indicating that juvenile male fur seals are traveling south of the Pribilof Islands during the non-breeding season and returning every year to the Pribilof Islands. The δ13C patterns for 0-1 year of age do not match those of older years, indicating that 1 year-olds have different seasonal foraging patterns than older animals. The δ13C oscillations seem to provide a more accurate representation of variations in foraging location over time than the δ15N values. This was expected as δ13C values more accurately reflect foraging location and δ15N values reflect animal trophic position. Shorter vibrissae matched the isotopic values of the longest vibrissae indicating full analysis of the longest whisker is unnecessary.
Functional Evolution of Solute-Binding Proteins

Solute-binding proteins (SBPs) comprise an abundant and adaptable superfamily of extracytoplasmic solute receptors involved in nutrient uptake and chemotaxis, and constitute an important component of the nutrient-scavenging arsenal in bacteria. The SBP superfamily exemplifies the power of evolution to generate functional diversity by tinkering with an existing protein fold; SBPs have evolved to recognise a wide variety of solutes with high affinity and specificity, and have also been co-opted into roles in signal transduction, transcriptional regulation and catalysis. However, the historical sequencestructure-function relationships that explain how this functional diversity could have evolved are not well understood. This thesis describes the use of ancestral protein reconstruction, a technique that leverages phylogenetic information to enable experimental characterisation of extinct proteins, to investigate two case studies of functional evolution in the SBP superfamily: the evolution of new binding specificities in the amino acid-binding protein (AABP) family, and the emergence of the enzyme cyclohexadienyl dehydratase (CDT) from a non-catalytic ancestor that belonged to the
Species delimitation in Geranium sect. Batrachioidea: morphological and molecular

Geranium subg. Robertium (Geraniaceae) comprises eight sections, of which sect. Batrachioidea contains four species centred in Eurasia, Mediterranean region and the Himalaya Mountains. Three species of Geranium pusillum, G. molle and G. pyrenaicum occur in Iran show some degree of morphological overlaps that make the species delimitation difficult. Moreover, hybrids are known to be formed between these species elsewhere. Till present time, there has been no detailed information available on molecular phylogeny and genetic structure of these species in the country. Therefore, the present study was conducted with the aim to investigate species delimitation by both morphological and molecular data and to reveal genetic diversity and population structure in these three Geranium species. For this study, 216 randomly collected plants from 30 geographical populations in three Geranium species were used. We encountered extensive within species genetic and morphological diversity. ISSR molecular markers could not .
Interactive report Cultured olfactory ensheathing cells express nerve growth factor, brain-derived neurotrophic factor, glia cell line-derived neurotrophic factor and their receptors 1

In the primary olfactory pathway axons of olfactory neurons (ONs) are accompanied by ensheathing cells (ECs) as the fibres course towards the olfactory bulb. Ensheathing cells are thought to play an important role in promoting and guiding olfactory axons to their appropriate target. In recent years, studies have shown that transplants of ECs into lesions in the central nervous system (CNS) are able to stimulate the growth ofaxons and in some cases restore functional connections. In an attempt to identify a possible mechanism underlying EC support for olfactory nerve growth and CNS axonal regeneration, this study investigated the production of growth factors and expression of corresponding receptors by these cells. Three techniques immunohistochemistry, enzyme linked immunosorbent assay (ELISA) and reverse transcriptase-polymerase chain reaction (RT-PCR) were used to assess growth factor expression in cultured ECs. Immunohistochemistry showed that ECs expressed nerve growth factor (NGF), brain derived neurotrophic factor (BDNF) and glial cell-line derived neurotrophic factor (GDNF). ELISA confirmed the intracellular presence of NGF and BDNF and showed that, compared to BDNF, about seven times as much NGF was secreted by ECs. RT-PCR analysis demonstrated expression of mRNA for NGF, BDNF, GDNF and neurturin (NTN). In addition, ECs also expressed the receptors trkB, GFRa-1 and GFRa-2. The results of the experiments show that ECs express a number of growth factors and that BDNF in particular could act both in a paracrine and autocrine manner. © 2001 Elsevier Science B.Y. All rights reserved. Theme: Development and regeneration Topic: Glia and other non-neuronal cells
Formulation of Novel Surface Sterilization Method and Culture Media forthe Isolation of Endophytic Actinomycetes from Medicinal Plants and itsAntibacterial Activity

Endophytic actinomycetes from medicinal plants were rarely reported as compared to those from soil and marine sources. The present results correlate the presence of endophytic actinomycetes in medicinal plants by isolating them from three medicinal plants i.e. Ocimum basillicum, Withania somnifera and Rauvolfia tetraphylla. In the present work surface sterilization method and media was standardized and 32 endophytic actinomycetes were isolated from three medicinal plants. We assessed the efficiency of four different surface sterilization methods and four medium for isolation of endophytic actinomycetes. The method with calcium hypochlorite, sodium hydrogen carbonate and sodium azide (New method) used was more effective in eliminating epiphytic microorganisms. Among four tested media starch casein agar (SCA) found to be best media for the isolation of endophytic actinomycetes. We succeeded in obtaining fast and luxurious growth of pure culture of endophytic actinomycetes on modified ISP-4 (M) (inorganic salt solution agar) in comparison with standard ISP-4(S). Preliminary antibacterial assay of all isolates were tested by confrontation test. The secondary screening of selected isolates were tested by disc diffusion test by using ethyl acetate extract which showed broad spectrum antibacterial activity against test human pathogens. Based on the morphological and phenotypic characters 12 isolates were identified as Streptomyces spp. Among 12 isolates A3 as a representative was characterized by SEM and identified by 16SrRNA analysis as Streptomyces flavoviridis A3WK, it showed significant antibacterial activity against test human pathogen. This is the first report of successful isolation of endophytic actinomycetes from the said medicinal plants, for using newly formulated surface sterilization method and new comparative study on ISP-4 medium.
Genetic diversity of cultivated pistachio as revealed by microsatellite molecular markers

ABSTRACT Pistacia vera L. is the only cultivated and commercially-grown species in the genus and Iran is one of the two major centers of Pistacia diversity and the main producer of pistachios in the world. Genetic diversity is crucial for sustainable use of genetic resources and conservation. To investigate the genetic diversity of pistachio (Pistacia vera), we genotyped 42 cultivars of this species using 20 polymorphic nuclear simple sequence repeat (nSSR) markers. The nSSR markers generated 3–7 alleles (102 in total) with an average of 5.10 per locus. Polymorphism information content (PIC) ranged from 0.36 to 0.86 with an average value of 0.64, while the observed heterozygosity (Ho) ranged from 0.21 to 0.79 with an average value of 0.44 and also the expected heterozygosity (He) varied from 0.11 to 0.39 with an average of 0.22. Genetic similarity values obtained from Dice's coefficient ranged from 0.08 to 0.93. The UPGMA (unweighted pair group method with arithmetic mean) dendrogram and Bayesian clustering separated the cultivars into two major clusters containing 21 and 21 cultivars, respectively, and also the neighbour-joining method revealed their phylogenetic relationships. The present results indicated the existence of wide genetic variability within the species and can be used for further research in the area of germplasm conservation and plant breeding.
Animal models of exercise therapy : mechanisms of activity-induced angiogenesis

Skeletal muscle is spatially heterogeneous in muscle fibre type composition and microvascular supply. The capacity to quantify this heterogeneity in skeletal muscle is not routinely performed for it’s a laborious and time consuming technique. We have developed a high throughput data pipeline that utilises the simultaneous immunohistochemical labelling of muscle fibre type and microvascular supply, as an input for a semi-automated analysis software package that allows for the analysis of fine morphometric indices of fibre type composition and the interactions with microvascular supply. We have successfully shown that regional variation in fibre type composition impacts the functional characteristics of a muscle. After successful characterisation of regional heterogeneity in both structure and function we sought to establish their influence in physiological (adaptive) angiogenesis. Utilising animal angiogenic models we have shown that shear stress driven angiogenesis is principally a stochastic response that does not promote improved oxygen delivery when we analyse the spatial heterogeneity of the neovasculature. Conversely, skeletal muscle overload (abluminal stretch of microvasculature) increases the homogeneity of the oxygen supply area of the capillary bed, suggesting a tissue driven angiogenic response that is not evident in shear stress. Spinal cord injury induced rarefaction of the capillary bed attempts to maintain a homogeneous distribution of fibre size and capillary supply. The combination therapy of epidural stimulation and locomotor training can ameliorate the phenotypic change and rarefied capillary bed seen with spinal cord injury to that of intact levels. Endurance and resistance exercise have a largely similar global genomic response following a chronic training regime, which we are able to replicate in animal models of exercise through indirect electrical stimulation. The shear stress and muscle overload driven angiogenic response have distinctly different angiogenic pathways that contain no commonly expressed networks.
Polymorphism of 8 X-Chromosomal STR loci in Turkish population -

In forensic sciences, X-chromosomal short tandem repeats (X-STRs), a complementary marker to the other genetic markers (autosomal, Y-chromosomal or mitochondrial), can be used in complex kinship analysis. Especially when a biological sample is not available from the putative father and samples from paternal relatives could be used instead. In this study eight X-chromosomal STR loci (DXS7132, DXS7423, DXS8378, DXS10074, DXS10101, DXS10134, DXS10135, HPRTB and Amelogenin) were investigated in population samples of 129 unrelated healthy Turkish volunteer [male (n=56), female (n=73)]. X-STRs were amplified in a multiplex PCR reaction with Mentype® Argus X-8 Kit. The separation and detection of PCR products were performed by capillary electrophoresis on a 310 Genetic Analyzer (Applied Biosystems). Statistical analysis was performed using POPgene v.1. 32. and Arlequin v3.1 softwareÂ’s. Data was compared with Turkish populations living in Europe (Germany and Denmark) and other populations (Japan, Ghana, Finland, Portugal and Germany). The high genetic distances were observed for the geographically distant populations while no significant differences found between in studied and tested Turkish populations. Results showed that eight STR loci on the X chromosome in Turkish population were found as highly polymorphic and useful for forensic applications.
Returning to Sport After Anterior Cruciate Ligament Reconstruction in Physically Active Individuals

Background Physically active individuals are susceptible to sports injuries, one of which is anterior cruciate ligament (ACL) injury. ACL injury can be managed conservatively or by surgical reconstruction. Returning to sport (RTS) after ACL injury is one of the main goals of ACL reconstruction (ACLR). However, rates of return vary and can be affected by several factors. The objectives of this study were to estimate the rate of return and to identify the factors that might affect RTS after ACLR. Methods This was a cross-sectional study, including individuals who had an ACLR. Participants were sent an online survey included questions about their injury, sport participation, International Knee Documentation Committee form (IKDC), and the Tampa Scale for Kinesiophobia (TSK-11). Participants who had their surgery in the period between January 2011 to December 2018 and participated in sports regularly were included. Descriptive statistics were performed. Chi-square and student t-tests were performed to explore the differences between participants who returned and the ones that did not. Results A total of 93 participants were included. The majority (69.9%) were playing soccer before the injury. Though more than half (61.3%) returned to sports, only 29% participated at the same level before the injury. Fear of reinjury was the most frequent reason for delaying or not returning (30%), followed by pain (29). Significantly better IKDC (p=0.002) and TSK-11 (p<0.001) scores were noted in participants who had returned to sports. On the other hand, participants’ age, body mass index (BMI), time from injury to surgery, time since surgery, and times of sports participation per week were not found to be significantly different between those who returned versus those who did not. Conclusion The participants in this study had a low rate of return with fear of reinjury being the most common reason not to return. However, a participant’s IKDC and TSK-11 scores were associated factors for RTS, thus optimizing those factors after surgery is crucial.
PHYLOGENETIC RELATIONSHIP IN FOUR ASPERGILLUS SPECIES BASED ON THE SECONDARY STRUCTURE OF INTERNAL TRANSCRIBED SPACER REGION OF rDNA

Recent studies show that, the secondary structure of the RNA transcript could provide useful information for systematic studies of fumgi. These morphological informations are not found in primary sequences. In this study, four Aspergillus species internal transcribed spacer region 1 (ITS1) secondary structure was predicted and compared. By observing the structures, some topologies were conserved in all the species and some were varied. These characters could be used for the identification fungi at generic level. Secondary structure topologies such as first stalk and junctions were varied between species. The phylogenetic trees based on both sequence and secondary structure showed similar clad in the four Aspergillus species.
Mud sticks after all: Chronically implanted microelectrodes but not electrical stimulation cause c-fos expression along their trajectory

The goal of CNS implanted devices is to build a stable brain-machine-interface. The brain tissue response to the foreign body limits the functionality and viability of this brain-machine connection. Notably the astrocytic glial scar formation and inflammation with resulting neuronal cell loss is considered to be responsible for the signal deterioration over time. We chronically implanted a polyimide microelectrode in the dorsolateral striatum of rats. First, we analyzed the c-fos immunoreactivity following high frequency stimulation (HFS) of the dorsolateral striatum and second, using GFAP and ED1 immunocytochemistry, the brain tissue response. Acute as well as chronic HFS showed no significant change of neuronal c-fos expression in the dorsolateral striatum and corresponding cortical areas. We found that the sole chronic implantation of a polyimide microelectrode leads to a reaction of the surrounding neurons, i.e. c-fos expression, along the implantation trajectory. We also observed the formation of a glial scar around the microelectrode with a low number of inflammation cells. Histological and statistical analysis of NeuN positive cells showed no ‘kill zone’, which accompanied neuronal cell death around the implantation site.
The Effects of Kiwifruit Extracts on Gene and Protein Expression Levels in In Vitro and In Vivo Mouse Models of Inflammatory Bowel Disease

Nutrigenomics is the study of interactions between diet and human genotype with the aim of understanding how food components influence gene and protein expression, and of linking this interaction to differences in individual metabolism. Inflammatory Bowel Disease (IBD) is a chronic inflammatory disorder of the gastrointestinal tract involving inappropriate immune response to commensal microorganisms in a genetically susceptible host. The principal aim of the research described here was concerned with determining if aqueous and ethyl acetate extracts of gold kiwifruit (Actinidia chinensis) or green kiwifruit (Actinidia deliciosa) had immune modulating effects against inflammatory processes known to be increased in patients with IBD. This aim involved the use of in vitro and in vivo models of IBD that were studied at the molecular level. The first part of the research examined the anti-inflammatory properties of four kiwifruit extracts (KFEs) in in vitro IBD models. These models comprised primary macrophages and intestinal epithelial cells isolated from C57BL/5J or interleukin 10 gene deficient (Il10 -/) mice and RAW 264.7, a transformed murine macrophage-like cell line. All four KFEs reduced the production of the pro-inflammatory biomarker nitric oxide and of both proand anti-inflammatory cytokines after cells were stimulated with lipopolysaccharide. Ethyl acetate extracts exhibited greater inhibitory activity compared to aqueous extracts for each type of kiwifruit. In the second part of the research, KFEs were used as a dietary intervention in Il10 -/mice, which are an in vivo model of IBD. While all Il10 -/mice developed significant colonic inflammation compared to the C57BL/6J background strain, this was not affected by the inclusion of KFE in the diet. Whole genome gene and protein expression level profiling indicated that KFEs influenced immune signalling pathways and metabolic processes within the colonic tissue; however, the effects were subtle. These findings highlight the importance of investigating food components identified by cell-based screening assays with appropriate animal models and human clinical studies to confirm and understand their activity. While KFE anti-inflammatory activity was not confirmed in our IBD mouse model, the molecular effects identified may represent immune modulating effects that are beneficial to other inflammatory disorders.
Ecological Quality Status of the Algiers coastal waters by using macroalgae assemblages as bioindicators (Algeria, Mediterranean Sea)

Macroalgae assemblages have been used as a quality element for the assessment of the Ecological Status Classes (ESC) of coastal water bodies for the implementation of the European Water Framework Directive (WFD, 2000/60/EC). To assess the suitability of this quality element in Algiers coasts, seven sampling sites with five (5) replications covering a wide range of anthropogenic pressures were studied during spring and summer 2015. Coverage data of macroalgae in each sampling site were analyzed on species, i.e., structural (species number, nMDS, clustering, K-dominance and Simper analysis on Bray–Curtis similarity) and on Ecological Status Groups, i.e., functional (nMDS, clustering, K-dominance, Ecological Evaluation Index/EEI-c) biological levels. Key water variables (temperature, salinity and pH) along with the anthropogenic stress index MALUSI were also estimated. The obtained results revealed a significant effect of anthropogenic stress in the macroalgal assemblages. The structural analysis showed: (1) species richness of 86 taxa in total, (2) dominance of Cystoseira amentacea var. stricta (late-successional) associated by Lithophyllum incrustans, and Jania rubens in non-impacted sites and of Ulva rigida, Ulva intestinalis and Caulerpa cylindracea (opportunistic) species in impacted sites, and (3) record a higher proportion of low abundance of species in polluted communities than in less polluted communities. The functional analysis showed: (1) classification of sites based on multivariate and K-dominance analyses in four groups, three in agreement with water degradation, and one for low salinity influence, (2) classification of sites into “Bad”, ”High”, “Moderate” and “Good” ESC’s by EEI-c index, (3) a strong non-linear relationship (R²=0.85) of EEI-c index with MALUSI index. Therefore, to implement a national monitoring program within the scope WFD in Algeria coasts, the EEI-c index will be a suitable tool.