Miracle-dz/UniFAR-FTUs huggingface dataset:
Increased Intake of Juniperus Phoenicea L. by Supplementation with Barley and Optigen® in Sheep

Dry littoral grasslands and rocky ground pastures throughout the Mediterranean basin are a significant source of forage for small ruminants and as such associated with traditional grazing practices. During the last decade, dissemination of terpene-rich Mediterranean shrubs, Juniperus phoenicea L. , onto pastures in Adriatic region of Croatia have caused reduction in forage production and plant diversity. In order to facilitate the intake of this new plant by small ruminants, we investigated the effects of barley and Optigen® (a source of controlled-release non-protein nitrogen) mixture to increase consumption of J. phoenicea by sheep. The preliminary results suggest that barley alone, or in combination with Optigen® enhance the intake of J. phoenicea by sheep. Furthermore, this model can be used as an environmentally safe and economically affordable approach to reduce the abundance of less palatable J. phoenicea in the environment and to increase growth of alternate, better quality forage (grasses and forbs) on Mediterranean pastures.
The evolution and diversity of the Anolis dewlap

The neotropical lizard genus Anolis is an important model system for studies of the ecology and evolution of animal diversity. One of the most striking elements of Anolis diversity is found in the morphology of the dewlap, an extensible flap of colored skin on the throat that anoles use to communicate during social interactions. The evolutionary forces that have promoted the evolution of dewlap diversity are poorly understood. A study of reproductive success in A. carolinensis showed for the first time that dewlap color is currently under selection in an anole (Chapter 1). However, this is unlikely to be a result of intrasexual competition because neither dewlap morphology nor reproductive success are related to male territory size or quality. Instead the dewlap may be under intersexual selection from female mate choice. In addition to sexual selection, the dewlap may evolve in response to a variety of other processes such as species recognition, predation, sensory drive, or a combination of these. A study of variation among populations of a single species, A. sagrei, revealed that the dewlap may be undergoing rapid adaptive diversification driven by several of these processes simultaneously (Chapter 2), while a study of variation among species in dewlap size showed that similar processes are likely shaping the evolution of the dewlap in female anoles (Chapter 3). In a case study of male-female pair formation in the Costa Rican anole A. limifrons, dewlap size or color were not good predictors of which males would form pairs and which would not, though males and females that were similar in size were found to form pairs more often than animals that were dissimilar in size (Chapter 4). Finally, a study of the correlated evolution of traits related to locomotion in anoles found that morphology, behavior, and habitat use evolve in tandem among 31 species of anoles from the Greater Antilles (Chapter 5). Together, these studies suggest that the evolutionary ecology of
Phylogeny of Hippophae (Elaeagnaceae) Inferred from Parsimony Analysis of Chloroplast DNA and Morphology

Abstract We here report the results from two parsimony analyses of all 15 recognized taxa in Hippophae (Elaeagnaceae), one based on chloroplast DNA (cpDNA), and one based on a combined data set of morphological characters and cpDNA. The genera Elaeagnus and Shepherdia were used as outgroup taxa. In general, the results are congruent with a previous RAPD study, and partly with some of the previous proposed classifications. Monophyly of Hippophae is strongly supported. The most widespread species, H. rhamnoides, is, in spite of low support, most likely monophyletic and distinguished by a single molecular synapomorphy. Due to weak internal support, we refrain from recognizing any sections within the genus. Three taxa, first published as nomina nuda but used by several authors, are here validated and/or described. These are Hippophae neurocarpa subsp. stellatopilosa, H. goniocarpa, and H. litangensis. The latter two were originally suggested to form one species with two subspecies, but they are clearly not monophyletic, a single lineage of evolution, but rather are sister to two different species in the analyses. Together with earlier information from isozymes (unpubl. data) and RAPDs, we believe they are results of two independent hybridisations and we describe them as species. In conjunction, a maternal mode of cpDNA inheritance is suggested. Communicating Editor: Alan T. Whittemore
Estimation of genetic parameters of fertility traits in Chinese Holstein cattle

Guo, G. , Guo, X. , Wang, Y. , Zhang, X. , Zhang, S. , Li, X. , Liu, L. , Shi, W. , Usman, T. , Wang, X. , Du, L. and Zhang, Q. 2014. Estimation of genetic parameters of fertility traits in Chinese Holstein cattle. Can. J. Anim. Sci. 94: 281–285. The objective of this study was to estimate genetic parameters for fertility traits in Chinese Holstein heifers and cows. Data of 20169 animals with 42106 records over a period of 10 yr (2001–2010) were collected from Sanyuan Lvhe Dairy Cattle Center in Beijing, China. Traits included age at first service (AFS), number of services (NS), days from calving to first service (CTFS), days open (DO), and calving interval (CI). Genetic parameters were estimated with multiple-trait animal model using the DMU software. Heritability estimates for AFS, NS, CTFS, DO and CI were 0.100±0.012, 0.040±0.017, 0.034±0.011, 0.053±0.019 and 0.056±0.014, respectively. Genetic correlations between traits observed ranged from −0.13 to 0.99. Genetic correlations between AFS with NS, CTFS, DO and C.
Ecological traps and behavioural adjustments of urban songbirds to fine‐scale spatial variation in predator activity

The influence of predators on bird populations is controversial and poorly understood, especially in urban areas where predator densities can be particularly high. We assessed if fine‐scale spatial variation in predator activity and proximity have direct and indirect effects on urban songbird distributions and breeding success, by testing the hypotheses that (1) songbirds that are sensitive to nest predation select territories with reduced activity of nest predators; (2) blackbird Turdus merula, a species that experiences high nest predation rates, lays smaller clutches in territories located in areas with higher numbers of nest predators as predicted by Skutch's hypothesis; (3) songbirds that are sensitive to nest predation have higher nest predation rates in areas with greater predator activity. We tested these hypotheses using two sites in urban Sheffield, UK, and focus on nest predatory corvids and grey squirrels Sciurus carolinensis. We found no evidence that songbirds that are most sensitive to nest predation adjust their territory location in response to fine‐scale spatial variation in predator distributions. It thus seems unlikely that urban predators are indirectly regulating urban bird population size by restricting habitat availability. Blackbirds did not vary their clutch size in response to predator distributions. These findings generate the potential for an ecological trap in which prey species fail to avoid areas with the highest concentrations of nest predators, or to exhibit behavioural adjustments to reduce the risk of nest predation at such sites. We find some evidence for such ecological traps as, while fine‐scale variation in grey squirrel occurrence and activity were not associated with nest predation rates, nests located in closer proximity to corvids and in areas with higher indices of corvid activity experienced slightly higher nest predation rates.
TAXONOMIC STATUS AND GEOGRAPHICAL CRANIAL VARIATION OF COMMON DOLPHINS (DELPHINUS) IN THE EASTERN NORTH ATLANTIC

The common dolphin has a widespread distribution and is relatively abundant in the temperate to subtropical waters of the eastern North Atlantic. However, it is not known whether different species, subspecies, or populations occur in this region. We examined 393 common dolphin skulls obtained from both stranded and bycaught individuals collected between 1901 and 2005. The series included skulls of 152 females and 199 males, from animals ranging in body length from 93 to 230 cm and 105 to 244 cm, respectively. The ranges of total body length, skull size, RL/ZGW ratio and maximum upper alveolar (tooth) count of common dolphins in the eastern North Atlantic overlapped with those of both short- (D. delphis) and long-beaked (D. capensis) species found off the Californian coast. However, in the absence of additional data, the common dolphin in the eastern North Atlantic is regarded here as a large form of Delphinus delphis. Sexual dimorphism and possible sex-linked characters were identified within the sample. Results of the current study
Blood Serum Protein Variations at the Species and Subspecies Level in Deer of the Genus Odocoileus

THE BLACK-TAILED DEER, Odocoileus hemionus, of the western part of North America occupy a range encompassing the widest possible climatic extremes found on the continent. In a range extending from northern Mexico to southern North West Territories and from Minnesota to the Queen Charlotte Islands there are eleven subspecies recognized on the basis of conventional characteristics of skull and external features (Cowan, 1936, 1956). These races frequently occupy discrete ecological areas, and this, taken along with structural and behavioral features, suggests that there are many adaptive characteristics involved that are not detected in museum material. For several years we have been exploring certain physiological characteristics of a selection of these subspecies in an attempt to determine the fundamental characteristics that distinguish them. It has been our aim also to determine something of the nature of the specialization that can occur at the subspecific level (Kitts et al., 1956; Bandy et al., 1957). It occurred to us that an examination of the serum proteins exhibited by different members of the species might prove useful in elucidating the extent of alteration of these basic protein elements in the evolution of the species and subspecies within this genus. Sibley (1960) has presented an excellent review of the underlying philosophy of the application of protein studies to taxonomy. Serum proteins have been shown to be reasonably conservative among the characteristics of taxonomic importance. Dessauer and Fox (1956) were able to draw up a key to some orders of reptiles based on electrophoretic characteristics. Moody, Cochran, and Drugg (1949), Moody and Doniger (1956), and Moody (1958) applied serology to the exploration of relationships between genera of hystricomorph rodents, musk ox, and lagomorphs. Johnson and Wicks (1959) have demonstrated apparently speciesconstant differences between a wide assortment of large and small mammals. These studies have all been concerned in the main with the larger taxa. The study reported here, however, sought to examine the intraspecific serum protein characteristics associated with distinctive phenotypes within the species Odocoileus hemionus as well as between this species and Odocoileus virginianus. Very little study has been devoted to intraspecific variation in serum proteins. Thompson et al. (1954), reported an inherent difference in the beta-globulin component in mice of a single strain. The difference appeared to be determined by a dominant gene or genes. Ashton (1958 a, b) has revealed a complex series of protein fraction differences within the domestic horse, including at least three distinct genotypes differing in components of a multiple allelic nature. Sibley and Johnsgard (1959b) examined the egg white proteins of twenty-three varieties of domestic fowl and found no important differences. Sibley (1960) figures electrophoretic profiles for the egg white protein of two subspecies for each of four species of birds in the orders Charadrii-
COMPUTATIONAL METHODS IN PROTEIN STRUCTURE, EVOLUTION AND NETWORKS.

Title of Document: COMPUTATIONAL METHODS IN PROTEIN STRUCTURE, EVOLUTION AND NETWORKS. Chen Cao, Doctor of Philosophy, 2013 Directed By: Professor John Moult, Institute for Bioscience and Biotechnology Research. Department of Cell Biology and Molecular Genetics, University of Maryland The advent of new sequencing technology has resulted in the accumulation of a large amount of information on human DNA variation. In order to make sense of these data in the context of biology and medicine, new methods are needed both for analysis and for integration with other resources. In this work: 1) I studied the distribution pattern of human DNA variants across populations using data from the 1000 genomes project and investigated several evolutionary biology questions from the perspective of population genomics. I found population level support for trends previously observed between species, including selection against deleterious variants, and lower frequency of variants in highly expressed genes and highly connected genes. I was also able to show that the correlation between synonymous and non-synonymous variant levels is a consequence of both mutation prevalence variation across the genome and shared selection pressure. 2) I performed a systematic evaluation of the effectiveness of GWAS (Genome Wide Association Studies) for finding potential drug targets and discovered the method is very ineffective for this purpose. I proposed two reasons to explain this finding, selection against variants in drug targets and the relatively short length of drug target genes. I discovered that GWAS genes and drug targets are closely associated in the biological network, and on that basis, developed a machine learning algorithm to leverage the GWAS results for the identification of potential drug targets, making use of biological network information. As a result, I identified some potential drug repurposing opportunities. 3) I developed a method to increase the number of protein structure models available for interpreting the impact of human non-synonymous variants, important for not only the understanding the mechanisms of genetic disease but also in the study of human protein evolution. The method enables the impact of approximately 40% more missense variants to be reliably modeled. In summary, these three projects demonstrate that value of computational methods in addressing a wide range of problems in protein structure, evolution, and networks. COMPUTATIONAL METHODS IN PROTEIN STRUCTURE, EVOLUTION AND NETWORKS
Implications of contrasting patterns of genetic variability in two vespertilionid bats from the Indonesian archipelago

Wallacean island populations of two Vespertilioninae bats, Myotis muricola and Scotophilus kuhlii, which have similar geographical ranges, showed marked contrast in the amount and pattern of genetic variation. Within islands, genetic variation was on average much higher in M. muricola but declined from west to east, whereas all populations of S. kuhlii had uniformly low levels of genetic variation by mammalian standards. S. kuhlii showed little genetic differentiation between islands and estimates of gene flow were substantial whereas island populations of M. muricola differed markedly and there was a strong isolation-by-distance effect associated with the extent of the sea crossing between islands. Furthermore, the lower mean heterozygosity and small genetic distances between eastern island populations of M. muricola is evidence that there has been a bottleneck associated with the colonization of this area. The attenuation of genetic diversity to the east is also seen in some other mammalian species and may indicate limits to dispersal and have implications for species management. The patterns of variability in S. kuhlii may be a consequence of its strong dispersal capacity and close association with human activity, which, together with other factors, suggest a panmictic population. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 83, 421–431.
Gene expression profiling and functional studies of astrocytes in SOD1-related amyotrophic lateral sclerosis

Amyotrophic Lateral Sclerosis (ALS) is the most common adult onset motor neuron (MN) disorder, characterised by muscle wasting due to MN death. Astrocytes play an important role in disease progression in the SOD1G93A transgenic mouse model and patients of ALS. Although astrocytes display a selective toxicity to MN, the toxic factor(s) have not been identified. We hypothesise that differential gene expression in SOD1-ALS astrocytes will reveal targets for therapeutic intervention. Microarray analysis was performed upon Laser Capture Microdissected astrocytes isolated from spinal cord of symptomatic (90 day) and late-stage (120 day) SOD1G93A mice and non-transgenic (NTg) littermates, and from post-mortem human SOD1-ALS and control spinal cord. Functional studies were performed using enzymatic activity assays and immunohistochemistry upon spinal cord and in vitro validation studies were performed using murine neonatal cultures of astrocytes, microglia and embryonic MNs and “i-astrocytes” directly converted from human ALS fibroblasts. In murine astrocytes annotation clustering analysis showed increased expression of lysosomal transcripts which were validated by qPCR . Using functional experiments, we have found significantly higher activity of the lysosomal enzyme β hexosamindase in the spinal cord of SOD1G93A mice. Immune response and phagocytic pathways are also enriched within both datasets, and phagocytosis assays using fluorescently labelled NSC34 cell debris show that SOD1G93A astrocytes engulf significantly higher amounts of neuronal debris compared to NTg controls, highlighting an increased reactivity of astrocytes at symptom onset. Human SOD1-astrocytes show down-regulation of transcripts involved in tight junction formation such as ZO-2, Claudin-5 and Occludin, and we hypothesise that ALS-astrocytes contribute to the breakdown in blood-brain-barrier (BBB) integrity seen in ALS. qPCR confirmed differential expression of BBB-influencing genes such as claudin-5, junctional adhesion molecule 2 and transforming growth factor beta-2. Model BBBs made with i-astrocytes from human patients co-cultured with endothelia show significantly lower transendothelial electrical resistance and dextran-permeability values pointing to an astrocyte role in increased BBB permeability during disease. These studies show the breadth of behaviours displayed by astrocytes during ALS disease progression and will provide an important guide for future therapeutic intervention.
Combretum lanceolatum flowers extract shows antidiabetic activity through activation of AMPK by quercetin

The present study evaluated the antidiabetic activity of the Combretum lanceolatum Pohl ex Eichler, Combretaceae, flowers extract (ClEtOH) in diabetic rats. Streptozotocin-diabetic rats were divided into four groups: diabetic control, diabetic treated with 500 mg/kg of metformin and diabetic treated with 250 or 500 mg/kg of ClEtOH for 21 days. The treatment of diabetic rats with 500 mg/kg of ClEtOH promoted an increase in the weight of liver, white adipose tissues and skeletal muscles, improving body weight gain. Diabetic rats treated with 500 mg/kg of ClEtOH also presented reduction in glycemia, glycosuria and urinary urea levels, and increase in liver glycogen content. HPLC chromatogram showed that quercetin is the major compound in the extract. The phosphorylation levels of adenosine monophosphate-activated protein kinase were increased in liver slices incubated in vitro with 50 µg/mL of ClEtOH, similarly to the incubation with metformin (50 µg/mL) or quercetin (10 µg/mL). The antihyperglycemic effect of ClEtOH was similar to that of metformin and appears to be through inhibition of gluconeogenesis, since urinary urea was reduced and skeletal muscle mass was increased. These data indicate that the antidiabetic activity of the Combretum lanceolatum extract could be mediated, at least in part, through activation of adenosine monophosphateactivated protein kinase by quercetin.
DNA BARCODING OF DOMESTIC SWINE BREEDS AND CROSSBREEDS (Sus scrofa) IN THE PHILIPPINES

DNA barcodes (i.e. cytochrome c oxidase subunit I or COI in the mitochondrial genome) obtained from eight domestic pig breeds and crossbreeds (Sus scrofa) in the Philippines and five swine breeds retrieved from GenBank were analyzed using Neighbour-Joining method based on Kimura 2-parameter model in MEGA5. Based on 617 COI positions, overall genetic diversity of domestic swine breeds and crossbreeds was 36.3%. Average genetic distance was highest among commercial purebred pigs (d=0.291), followed by crossbred pigs (d=0.289), native pigs (d=0.202) and smallest among GenBank-accessed breeds (d=0.008). The results indicate that DNA barcodes can be effective in differentiating between breeds sampled in the Philippines, but not among swine breeds whose COI sequences were derived from GenBank. DNA barcodes can distinguish purebred pigs sampled in the Philippines from their counterpart breed listed in GenBank. Wide genetic distances of COI sequences imply greater diversity of native genetic resources that are distinctly different from pig breeds raised locally and abroad. Genetic distances between a crossbred pig and its dam’s breed are not small. However, more COI sequences should be determined from distinct crossbred populations to improve reliability of DNA barcoding to discriminate them from their dam’s breed and to confirm breed origin of pigs. Keywords: DNA barcodes, domestic swine breeds and crossbreeds, evolutionary analysis, genetic diversity
European glacial relict snails and plants: environmental context of their modern refugial occurrence in southern Siberia

Knowledge of present‐day communities and ecosystems resembling those reconstructed from the fossil record can help improve our understanding of historical distribution patterns and species composition of past communities. Here, we use a unique data set of 570 plots explored for vascular plant and 315 for land‐snail assemblages located along a 650‐km‐long transect running across a steep climatic gradient in the Russian Altai Mountains and their foothills in southern Siberia. We analysed climatic and habitat requirements of modern populations for eight land‐snail and 16 vascular plant species that are considered characteristic of the full‐glacial environment of central Europe based on (i) fossil evidence from loess deposits (snails) or (ii) refugial patterns of their modern distributions (plants). The analysis yielded consistent predictions of the full‐glacial central European climate derived from both snail and plant populations. We found that the distribution of these 24 species was limited to the areas with mean annual temperature varying from −6.7 to 3.4 °C (median −2.5 °C) and with total annual precipitation varying from 137 to 593 mm (median 283 mm). In both groups there were species limited to areas with colder and drier macroclimates (e.g. snails Columella columella and Pupilla loessica, and plants Kobresia myosuroides and Krascheninnikovia ceratoides), whereas other species preferred areas with relatively warmer and/or moister macroclimates (e.g. snails Pupilla turcmenica and P. alpicola, and plants Artemisia laciniata and Carex capillaris). Analysis of climatic conditions also indicated that distributional shifts of the studied species during the Pleistocene/Holocene transition were closely related to their climatic tolerances. Our results suggest that the habitat requirements of southern Siberian populations can provide realistic insights into the reconstruction of Eurasian, especially central European, glacial environments. Data obtained from modern populations also highlight the importance of wet habitats as refugia in the generally dry full‐glacial landscape.