Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative diversity at the major histocompatibility complex in two dolphin species

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The characterization of repetitive DNA elements in the genome of Atlantic Salmon (Salmo salar)

Unrelated families of repetitive DNA were identified in the genome of Atlantic salmon (Salmo salar) and characterized. -- 1) A segment of DNA containing a single Bg/I repeat tandem array was isolated from a genomic library. Bg/I repeats comprise 2.3% of the S, salar genome and were found in the vicinity of rDNA genes. Southern blot hybridization detects a homologue of the Atlantic salmon Bg/I repeat in the brown trout (Salmo truita) genome but not in other salmonids. However, a DNA fragment with sequence homology to part of the Bg/I repeat has been isolated from Arctic charr (Hartley and Davidson 1994). The Bg/I repeat also detects RFLPs in Atlantic salmon. -- 2) Tel transposon-like sequences are present in salmon, trout, and charr species and may belong to several families that do not follow phylogenetic lines. As many as 15,000 copies reside in the Atlantic salmon haploid genome. The complete DNA sequence of one transposon-like element (SALT1) in Atlantic salmon is 1535 base pairs long. It contains terminal inverted repeats and a degenerate open reading frame of 1273 nucleotides whose inferred amino acid sequence shares homology with transposases from Caenorhabditis sp. and Drosophila sp. Zoo blot analysis indicates that Tel transposon-like sequences are present in other lower vertebrates including several fish species and amphibians but the copy number can vary significantly in different lineages. -- 3) Members of the NheI family share a great deal of sequence similarity with one another and with corresponding elements present in brown trout (over 95% identity). These elements, which comprise more than 1.2% of the Atlantic salmon genome, do not exist in long tandem arrays as is typical of satellite DNA. Subfamily structure exists and there is evidence that members of the same subfamilies are found in both Salmo species. Sequences homologous to the NheI repeat are located within a 1424-bp segment inserted immediately downstream of the 5' end of a Tc1 transposon-like sequence isolated from Atlantic salmon (Radice et al. 1994). -- 4) Various minisatellite and other short tandem repeat loci were characterized. Southern blot analysis of the phylogenetic distribution of a subset of the minisatellites indicates one sequence to be pervasive among vertebrates, others present only in Salmoninae or Salmonidae species, and one selectively amplified in Atlantic salmon. Their value as probes for detecting variable number tandem repeat loci is assessed. Evidence exists for coevolution of microsatellite and minisatellite arrays at some loci.
Exploring the impact of heterogeneities on HIV dynamics within host

This thesis is concerned with exploring how cell heterogeneity and drug resistance can cause long term persistence of HIV. We examine models of multiple viral strains to assess the impact of drug resistance on viral persistence and extend our cell heterogeneity models to include multiple strains. Chapter 1 summarises the nature of HIV infection within host. The key barriers to HIV eradication within host and the role of mathematical models to help understand these issues are discussed. In Chapter 2 we analyse models that include cell heterogeneity. We find robust long term viral persistence is possible on therapy and differences in viral load between body compartments explained by cell heterogeneity. The inclusion of a drug sanctuary also allows low level viral load on treatment. Competition and evolutionary models of wildtype and drug resistant strains of virus are described in Chapter 3. We analyse two models containing three strains of virus with different mutation mechanisms. We find that the proportion of the minority strains of virus is determined by the number of mutations away from the dominant strain. In Chapter 4 we extend our cell heterogeneity models from Chapter 2 to include a drug resistant strain of virus. We find that when a drug sanctuary is present coexistence is possible in the absence of an evolutionary mechanism. The two compartment model also shows differential dominance whereby a different strain is dominant in each compartment. within the host. We find the latent cell reservoir acts as an archive for previously dominant viral strains when there is a mechanism for latent cell maintenance and that the balance between ongoing viral and latent cell replication determines the longevity of the archive.
The Effect of the Modified Munson Training System on Uneven Ripening, Soluble Solids and Yield of ‘Concord’ Grapes1

‘Concord’ grape vines trained to the Modified Munson and 4-arm Kniffin systems were sampled, at weekly intervals, beginning approximately one month before harvest and continuing to harvest. The fruit were categorized for evenness of ripening and analyzed for total pigment content and per cent soluble solids. Total yield, and components of yield were compared under the 2 training systems. Fruit harvested from the Modified Munson trained vines ripened more evenly, contained more anthocyanin pigments, soluble solids, and produced greater yields than did vines trained to the 4-arm Kniffin system. The yield increase was due to increases in the percentage of fruiting shoots, clusters per shoot, and cluster weights on vines trained to the Modified Munson system. The increase in cluster weight was due to increases in berry weight and berries per cluster.
Early Events in Monocot Evolution: A well-supported phylogenetic framework for the monocot order Alismatales reveals multiple losses of the plastid NADH dehydrogenase complex and a strong long-branch effect

The order Alismatales is a cosmopolitan and enormously diverse clade of monocotyledons, comprising ~4500 extant species in 13 families, as currently defined (Stevens, 2001þ; Janssen and Bremer, 2004; APG III, 2009). Some of the oldest monocot fossils (late Barremian and early Albian; 125–112 Ma) have been assigned to this lineage (Friis et al., 2004, 2010), and most phylogenetic studies (e.g. Chase et al., 2006; Givnish et al., 2006, 2010; Graham et al., 2006) resolve Alismatales as the sister group of all monocots except Acorus (Acorales: Acoraceae). Refining our understanding of the phylogenetic backbone of Alismatales will therefore be important for understanding the early evolutionary history of the monocots. The overall composition of Alismatales remained relatively constant until a recent expansion to include Araceae and Tofieldiaceae (e.g. Dahlgren and Clifford, 1982; Tomlinson, 1982; Les et al., 1997; APG I, 1998; APG II, 2003; APG III, 2009;
Expressed Sequence Tags of the Wheat-rye Translocation Line Possessing 2BS/2RL

Hamlet (PI549276) possessing 2RL was obtained by cross between a wheat cultivar ND7532 (Froid/Centurk) and a rye cultivar Chaupon. Chaupon was known to have resistant gene to biotype L of Hessian fly [Mayetiola destructor (Say)] larvae. The wheat-rye translocation line (Coker797*4/Hamlet) was also known to be resistant to biotype L of Hessian fly larvae. We analysed a set of 96 ESTs from the wheat-rye translocation line (2BS/2RL). ESTs were classified by various physiological processings, such as primary metabolism, secondary metabolism, transcription, translation, transport, signal transduction, defense, transposable element, and others. Three sequences encoding thioredoxin peroxidase, 26S rRNA, and rubisco small subunits were homologous to registered genes in rye. Although limited number of clones were used to develop ESTs, these clones and their sequence information may be useful for researchers studying general physiology and molecular biology on the translocation line.
Improvement of the reproductive efficiency for the development of the Sardinian sheep breeding

Reproductive activity of the sheep bred at temperate latitude is conditioned by photoperiodic trend. Melatonin haematic levels are considered the biological informer of photoperiodic trend. The action of melatonin on reproductive activity is carried on through receptors present at hypothalamic level. Polymorphism of receptor MT1 gene in several sheep breeds resulted involved in the regulation of reproductive seasonality. Then, the study of this gene even in the Sarda breed sheep can give the possibility of a better rationalization of the reproductive activity. With this purpose, blood samples from 1000 sheep from different farms were taken. Age, sex and lambing date of the animals were recorded during at least 3 years. The DNA obtained from each blood sample was used for the typication of the MT1 receptor gene. Finally, the obtained genetic and reproductive data were subjected to statistical analysis to show the probable link between them. The confirmation of a relationship between genetic variants and reproductive activity more or less connected to photoperiod can supply a new approach both to selection and management of Sarda breed sheep. In fact, the animals less bound to photoperiod could be used for the deseasoning of lambing and consequently of productions. On the contrary, animals with a reproductive activity deeply linked with photoperiod could be directed to obtain spring lambing. All that, undoubtedly, can produce a great development of the Sardinian ovine sector according to the trend of product demands of market, bound to the tourist vocation of the island.
Microbial transformation of alpha-naphthol by Aspergillus niger -PTCC 5011

The metabolism of α-naphthol by Aspergillus niger PTCC 5011, a fungi isolated in Ardebil, Iran, from industrial wastewater, was studied. A niger metabolized approximately 80% of α-naphthol within 5 days. The identification and quantification of degradation products using GC-MS demonstrated that approximately 41% of the parent compound was converted into 1-ethyl-2-methyl benzene, 7.43% was converted into acetonaphthone, 5.55% was transformed into 4-hydroxy-1-naphthyl sulfate, 3% into 1,4-naphthoquinone, and about 6.68% into 2-phenyl-1,2,3-tetrahydro-1-naphthol. These results support a role for A niger in affecting the environmental fat of pollutants in ecosystems.
Baetis khakassikus n. sp., a new species of the subgenus Rhodo- baetis JACOB, 2003 from Middle Siberia, Russian Federation (Ephemeroptera: Baetidae)

A new species Baetis khakassikus n. sp. belonging to the subgenus Rhodobaetis J ACOB, 2003 is described and illustrated at larval stage from material collected in West Sayan Mountains (1332 m a.s.l.), Republic of Khakassia, Middle Siberia, Russian Federation. Critical characters distinguishing it from other representa- tives of Rhodobaetis are presented.
Effect of Paecilomyces fumosoroseus SFP-198 on greenhouse whitefly, Trialeurodes vaporariorum in greenhouse

For the control of the greenhouse whitefly, Trialeurodes vaporariorum entomopathogenic fungi were isolated from forest soils and infected insects. We selected three strains, which showed high pathogenicity and named as SFB-582(Beauveria sp.), SFP-198(Paecilomyces fumosoroseus) and SFV-1053(Verticillium sp.) respectively. Particularly, at the concentration of conidia/ml, P. fumosoroseus SFP-198 had the highest pathogenicity, in laboratory. In glasshouse application, SFP-198 showed high protective values() regardless of developmental stages, which were similar with that of Verticillium lecanii F-903 already reported. Four kinds of formulations of entomopathogenic fungi were developed, formulation with surfactant Silwet L-77 gave best control of greenhouse whitefly(over 90%). These results suggest that P. fumosoroseus SFP-198 is a promising candidate as a microbial pesticide for the control of T. vaporariorum.
Testing for quantitative trait loci for lactation persistency in dairy cattle

Lactational persistency has not been selected for in New Zealand dairy populations. Existing milk production data and pedigrees from New Zealand Holstein-Friesian cattle at pasture, recorded in the Livestock Improvement Corporation database were utilized with a grand-daughter design, for a genome-wide search for a quantitative trait locus for persistency of lactation. Persistency was defined as a weighted sum of test-day yields. A significant region was identified in one grandsire family on Chromosome 3 at microsatellite marker position AGLA247 (chromosomal position 67cM; P <0.05). To verify this result, data from a research dairy herd defining persistency as the mean of three weekly tests of daily yield in March (late lactation) divided by the equivalent daily yields in October (early lactation)) for three seasons beginning in 1997/98 were used in a phenotypic association study on Chromosome 3 only. One allele of marker HUJ246, close to the original region appeared to show an additive effect. The maximal difference between this genotype and the others at this marker locus was 12.3 ± 4.4% of the mean persistency. The potential use of this marker in the New Zealand dairy cattle population depends on the current allele frequencies in the industry.
The biology and ecology of six rare plants from Plumas National Forest, Northern California, USA

THE BIOLOGY AND ECOLOGY OF SIX RARE PLANTS FROM PLUMAS NATIONAL FOREST, NORTHERN CALIFORNIA, USA by Suzie Woolhouse The majority of our knowledge about the natural world has come from the study and observation of common species, yet a significant portion of species in the world are rare. In this study, biological and ecological data was collected for six rare taxa from Plumas National Forest. The taxa were Monardella stebbinsii, Monardella follettii (Lamiaceae), Lewisia cantelovii (Montiaceae), Cypripedium californicum, Cypripedium fasciculatum (Orchidaceae) and Clarkia mildrediae subsp. mildrediae (Onagraceae). The two Monardella’s and Cypripedium californicum are serpentine endemics, and the Lewisia is found growing both on and off serpentine. Five sites were visited per species, and soil samples and leaf tissue were collected to examine elemental concentrations in the soil and respective ion uptake. Detailed studies were conducted on the three rarest taxa, including comparative ecology and reproductive biology of the two congeners and a reciprocal transplant to assess the extent of local adaptation to substrate in L. cantelovii. Significant differences were found in the study of the two Monardella’s and Lewisia cantelovii showed early evidence for local adaptation to substrate. Gaining a better understanding of the biology and ecology of these rare plants will increase the efficacy of management practices as well as provide data in order to inform a multispecies conservation approach.
Main driving factors influencing passage kinetics in ruminants

Mean retention time (MRT) is a key step in feed evaluation. Passage rate (kp) and MRT can be affected by several factors. In general, they can be classified as animal or diet-dependent factors. Furthermore, the markers and methods are central aspects of discrepancy regarding the procedures used to estimate kp and MRT in ruminants. Therefore, the primary objective of this paper was to review the main factors and the current knowledge regarding markers and the direct method used to determine kp and MRT in ruminants. Key-words: Markers, methods, ruminants, passage rate, mean retention time. RESUMO Tempo médio de retenção (TMR) é um ponto chave na avaliação de alimentos. Taxa de passagem (kp) e TMR pode ser afetada por diversos fatores. Em geral, pode ser classificada como fatores dependente do animal ou da dieta. Além disso, marcadores e métodos são aspectos centrais de divergência com relação ao procedimento para estimar kp e TMR em ruminantes. Portanto, o objetivo desse artigo foi revisar os principais fatores e o conhecimento atual relacionado aos marcadores e ao método direto usado para determinar kp e MRT em ruminantes. Palavras-chave: Marcadores, métodos, ruminantes, taxa de passagem, tempo médio de retenção.
Dementia, awareness and depression

We examined 170 outpatients, 103 with Alzheimer's disease, 43 with vascular dementia and 24 with various other causes, in order to investigate whether or not depressive symptoms were more likely to occur in dementia patients who had some degree of awareness of their cognitive deterioration. Awareness was rated on a four‐point scale that assessed discrepancies between the patient's and the caregiver's history. The level of awareness was significantly related to the severity of dementia but not to depression or to the score on Hamilton's depression scale. However, the score from the item “psychic anxiety” showed a weak but significant correlation with the level of awareness of one's deficits. It is concluded that intact awareness of deterioration was not clearly related to the development of depression or depressive symptoms in dementia.
Utilization of grape seeds in ruminant nutrition:effects of this by-product on health conditions, milk production and quality, and ruminal metabolism in Sarda dairy sheep

Grape seed is a by-product derived from winery and distillery industries, containing relevant concentrations of polyphenolic compounds. The use of this by-product in ruminant nutrition had not been evaluated yet. The present work studied the effects of dietary inclusion of grape seed, alone or in combination with linseed, as source of PUFA, on immune response, liver and kidney metabolic activity, ruminal metabolism, and milk yield, composition, fatty acid profile and oxidation stability in Sarda dairy sheep. It was demonstrated that grape seed and linseed can be included, alone or in combination, in dairy ewes diet without adverse effects on milk production traits and health status; in addition, an immunomodulatory effect of this residue was evidenced. Grape seed was not effective in reducing PUFA ruminal biohydrogenation; however, it increased the ruminal accumulation of CLA cis -9, trans -11 when used alone, and of vaccenic acid when combined with linseed, manly due to its high content in linoleic acid. Milk quality was improved, in term of FA composition, by the inclusion of grape seed and linseed, especially when used in combination. Moreover, dietary grape seed improved oxidative stability of milk, by reducing the accumulation and formation of lipid hydroperoxides and volatile secondary lipid oxidation products, i.e., hexanal and benzaldehyde, after light exposure. In conclusion, the inclusion of grape seeds in the diet of dairy ewes is an alternative use of this by-product.
Welche Rolle spielt die endozoochore Ausbreitung von Pflanzen durch wildlebende Säugetiere? - Untersuchungen in zwei brandenburgischen Waldgebieten

HEINKEN, T. ; HANSPACH, H. ; SCHAUMANN, F. : How important is endozoochorous seed dispersal by wild mammals in centrat European forests? - Hercynia N.F. 34 (2001): 237-259. In two forest areas in Brandenburg (NE Germany) endozoochorous dispersal of plants by wild herbivorous and omnivorous mammals with a ! arge home range was investigated. Feces of roe deer (Capreolus capreolus), fallow deer (Cervus dama), hare (Lepus europaeus) and wild boar (Sus scrofa) were collected throughout a vegetation period. Seeds from the feces collected each month were germinated in a greenhouse. The results were compared with the forest vegetation of both investigated areas. The mean contents of germinable seeds within the feces of herbivorous mammals were 20 to 40 times higher than those of wild boar, which apparently ingest only small amounts of seeds in their diet. Taking the population densities and defecation rates into consideration, it is evident that roe and fallow deer disperse high numbers of seeds, whereas wild boar and hare only carry small amounts. Altogether, 65 plant species were detected endozoochorously, 13 of these (among others Milium effusum, Moehringia trinervia and Ranunculus ficaria) for the first time. Due to their choice of diet, the spectrum of species dispersed by roe deer was smaller than the spectra of the other animals investigated. Though the investigated feces were collected within the forest areas, feces of roe deer contained no characteristic forest species, and only small amounts were detected in those of the other wild mammals. In the mesic forest habitat of the Brieselang, the herbivores dispersed almost exclusively annual species from ruderal vegetation, arable land and trampled areas. In the acidic forest habitat of the Kramer, they dispersed in particular species which occur both in oligotrophic grasslands and forests. In general, almost all diaspores dispersed by the herbivorous mammals were small ( <1mg), as they are less likely to be damaged during the chewing procedure. Wild boar also defecate live seeds of ! arger diaspores, among them several cultivated plants. Several of the species dominating the acidic, and most dominating the mesic, forest stand are obviously dispersed endozoochorously either only very seldom or not at all by the investigated mammals. This is probably because their diaspores arenot able to survive the passage through the gut, due to their )arge size as weil as the fact that they are only produced in small numbers. The results confirm the assumption of low dispersal potentials of forest floor species and may be generally applied to centrat European forest habitats. Thus, at least by endozoochory, roe and fallow deer, hare and wild boar play only a small roJe in long-distance dispersal of forest species. Their importance may be greater in the dispersal of plant species of the open landscape. Keywords: dispersal, endozoochory, forest, ! arge mammals, NE Germany, phanerogams
Isolation of a vicilin gene from pea (Pisum sativum L.), and nuclease sensitivity of seed storage protein genes in pea chromatin

A library of pea genomic DNA in the bacteriophage vector EMBL3 was screened by hybridisation to cDNAs encoding vicilin, a major storage protein of pea (Pisum sativum L.) seeds. A vicilin gene, vic A, was isolated and characterised by restriction mapping and DNA sequencing. The nucleotide and predicted amino acid sequences of vic A were compared to those of vicilin cDNAs, and the gene was found to encode a 50,000M(_r) non-glycosylated vicilin subunit that does not undergo post-translational proteolytic cleavage. The introns in vic A were typical of those in plant genes, being small and high in A+T content, and the nucleotide sequences at the splice sites showed good homology to the plant consensus. The positions of the introns in vic A were similar to those in a gene encoding a subunit of phaseolin, a related protein from French bean (Phaseolus vulgaris). Methods were developed for the analysis of nuclease sensitivity of specific genes in pea chromatin. The DNAase I sensitivity of the seed storage protein genes was found to be greater in developing cotyledons, where the genes were transcriptionally active, than in leaves, where they were inactive. The pea ribosomal genes showed relative resistance to DNAase I in both tissues. The nucleosome repeat length, determined by digestion of chromatin with micrococcal nuclease, was similar in both tissues. No evidence was obtained for DNAase I hypersensitive sites in pea chromatin. This result supports the findings of two other studies, and suggests that such sites are absent from plant chromatin.