Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequence analysis and expression patterns of two nifA genes from Frankia EuIK1

Two nifA genes were cloned from Frankia EuIK 1 strain, a symbiont of Elaeagnus umbellata Thunb. and analysed on the basis of their deduced amino acid sequences and expression patterns. The complete nucleotide sequence of 1926 bp of nifA1 and 1524 bp of nifA2 was determined, respectively. A putative NifA-binding site was found -95 to about -80 bp upstream of start codon for nifA 1 ORF as TGT-N 10 -ACA, but the clpB ORF was followed by nifA2 ORF with 15 bp of intergenic sequence. Deduced amino acid sequence showed that two nifA genes encode typical NifA, having three major domains and two linkers, and their central domains of NifAl and NifA2 showed sequence similarity of 70-75% with those from other NifA proteins. However, entire NifA2 ORF is more similar to alternative NifA (60%) than to typical NifA (53%). Conserved amino acid sequence in helix-turn-helix motif of typical NifA was also found in NifA1, but it was not conserved in NifA2, which is also common in alternative NifA proteins. Moreover, the expression of nifA1 during nodule development was similar to that of Rhizobium meliloti in that it was expressed at low level constitutively, while that of nifA2 was similar to the pattern of nifH, structural gene for nitrogenase reductase, in that its transcripts level was changed in accordance with nitrogenase activity. These results indicate that nifA 1 and nifA2 might be classified into typical nifA and alternative nifA, respectively. This is the first report on the presence of two nifA genes in Frankia.
Characterization Of The Mamu-A*01-Restricted Cd8-Positive T Lymphocyte Immunodominance Hierarchy In Simian Immunodeficiency Virus-Infected Rhesus Monkeys

CD8 cytotoxic T lymphocytes (CTLs) play a critical role in controlling human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) replication. The CTL responses that are thought to be the most protective against HIV and SIV are those that are of high frequency, recognize multiple epitopes, and perform multiple antiviral functions. Therefore, current vaccines aim to elicit CTLs possessing these characteristics. However, the phenomenon of immunodominance likely limits the potential of vaccines from generating such CTL responses by restricting the breadth of epitopes recognized by CTLs and the frequency and functionality of these CTL responses. In this dissertation, we explored the relationship between SIV epitope dominance and the functionality of the epitope-specific CTL populations. We also examined factors that contribute to the development of SIV epitope immunodominance hierarchies. We initially investigated the relationship between SIV epitope dominance and the antiviral functionality of the epitope-specific CTL populations in rhesus monkeys. We performed a gene expression analysis in dominant and subdominant epitope-specific CTLs during the acute phase of SIV infection and observed differential expression of a number of genes during this time. Subsequent in vitro functional studies of these epitope-specific CTL populations during the chronic phase of infection confirmed the presence of differences in maturation phenotype
An annotated list of mammal specimens in the collections of the former Zoological Museum of the University of Amsterdam (1890-2010)

Mammal type specimens in the former Zoological Museum in Amsterdam, The Netherlands, are listed and, where necessary and possible, annotated. The collection held 123 type specimens including 10 holotypes, 91 paratypes, 2 lectotypes, and 20 paralectotypes, together representing 6 orders, 15 families, 22 genera, and 26 species and subspecies.
Effect of Deltamethrin and a Neem Based Pesticide Achook on Some Biochemical Parameters in Tissues Liver, Ovary and Muscle of Zebrafish Danio rerio (Cyprinidae)

The present study is aimed to evaluate the changes in total protein, total free amino acid content and nucleic acids (DNA and RNA) in the liver, ovary and muscle of Zebrafish after exposure to 96 h LC 5, LC 10 and LC 20 of Deltamethrin and neem based pesticide Achook. It was found that the protein content was reduced to 45, 68, 65% (after Deltamethrin exposure) and 54, 81, 85% (after Achook exposure) as compared to the controls (100%) after 16 days in the liver, ovary and muscle, respectively at LC 20 exposure. The total free amino acid contents in liver were enhanced to 146 and 142% of controls (100%) after exposure to LC 20 of Deltamethrin and Achook respectively. However, in the ovary of treated fishes the total free amino acid content was significantly (P<0.05) reduced. In addition, DNA content was reduced to 26, 40 and 38% of controls (100%) in liver, ovary and muscle respectively after 16 days exposure to LC 20 of Deltamethrin. The reduction in DNA content from the control was 37, 46 and 44% in liver, ovary and muscle respectively due to Achook at the same concentration and exposure period as that of Deltamethrin. Similarly, RNA contents were also reduced in the liver, ovary and muscle significantly after Deltamethrin and Achook exposure. It was observed that all the changes were concentration as well as time dependent. This study will reflect the potential role of these biochemical parameters for assessment of aquatic pollution as far as the natural pesticides are concerned.
Acidification of Soil Associated with Lupins Grown in a Crop Rotation in North-eastern Victoria

Soil pH decline and net acidification inputs were determined for a long-term crop rotation experiment at Rutherglen in north-eastern Victoria. The rotations utilized were continuous wheat (WW), a 1 : 1 wheat-lupin sequence (WL) and continuous lupins (LL), and each rotation was cropped from 1975-1989. The soil at the site had an initial pH (0.01 mol/LCaCl2) of 6.0 (0-10 cm depth), sandy loam texture, and had a past use of grape vines and then lucerne pasture. The soil pH (0-10 cm) declined for each rotation with time (1977/78-1988/89), decreasing by about 0.8 units for WW and further decreasing with the inclusion of lupin in the rotation. Compared with the WW soil, the WL soil pH was 0.7 and 0.4 units lower at 5-10 cm and 10-15 cm depth and the LL soil pH was 1.0 and 0.8 units lower at 5-10 and 10-15 cm depth. There was no difference in pH between WW and WL below 20 cm depth, but the LL soil had a significantly lower pH to 40 cm depth. Acidification rates were calculated for the period of cropping and for the 3 rotations, with rates of 3.22, 4.11 and 5.26 kmols H+/ha.yr as net acid input for WW, WL and LL rotations. These values represent a rapid rate of soil acidification. The removal of alkalinity in grain accounted for between 15-21% of the overall calculated acidification rate for the 3 rotations. Therefore, it is likely in this cropping system that the acidification largely results from progressive nitrate leaching.
Influence of combined usage of garlic powder and copper on egg yolk cholesterol concentration in laying hens

A research was conducted to evaluate the effects of combined usage of garlic powder (GP) and cupric sulfate pentahydrate (CS) as two different cholesterol-lowering supplements on blood serum and egg yolk cholesterol concentration in laying hens. A total of one-hundred ninety two 40-wks-old Single Comb White Leghorn (SCWL) laying hens were selected in a completely randomized designed to four diets that included unsupplemental basal diet as control diet (CO), the basal diet supplemented with either 15 g/kg GP, 200 mg/kg CS, or both 15 g/kg GP and 200 mg/kg Cs for a period of 6 weeks. During the experimental period hens performance traits included body weight gain, egg production, egg and yolk weights, egg mas, feed consumption, and feed conversion ratio were recorded. For statistical analysis, data were averaged by replicate for 6 wks period. At the end of the experimental period blood serum and egg yolk samples were collected for cholesterol analysis. Supplementation of GP or CS to the basal diet had no significant (p>0.05) effect on overall performance in laying hens. A decrease in blood serum and egg yolk cholesterol concentration was found (p<0.01) in birds fed GP, CS, and GP/CS diets in comparison with the unsupplemented diet birds (CO diet). Serum cholesterol levels were reduced by feeding GP, CS, or both by about 14, 20, and 28% respectively (p<0.01). Feeding GP or CS decreased egg yolk cholesterol about 6 and 12.5%, respectively (p<0.01), but feeding both GP and CS diet/ supplements had no further beneficial effect on egg yolk cholesterol.
In-vitro Assessment of Probiotic Potential of Lactic acid Bacteria

"Lactic Acid Bacteria (LAB) are the major constituents of the human intestinal micro flora. These have been considered as the major microbial group having probiotic potential. They are able to exert a wide range of beneficial health promoting effects that include inhibition of pathogen growth and production of antimicrobials and vitamins. In food industry, LAB have received considerable attention due to their probiotic activities. The probiotic strain’s ability to resist unfavorable physiological conditions of the gastrointestinal tract (GIT) depends on various factors like tolerance to bile secretion and lysozyme resistance. The present study was conducted with the objectives of in-vitro screening of various indigenous LAB strains isolated from milk and yogurt in order to evaluate their probiotic potential. For probiotic potential, the pH sensitivity, bile resistance, H2O2 and lysozyme resistance of LAB strains will be determined. Our in-vitro studies concluded that PL5 ( Lactobacillus paracasei), PL8 (Enterococcus faecium), PL13 (L. delbrueckii) and PL14 (L. saekei) proved to be most promising LAB strains among all that exhibited a high resistance towards low pH, bile, lysozyme and H2O2. In future, these in-vitro studies will facilitate scientists to select suitable LAB strains and evaluate their probiotic properties in-vivo to understand how they affect human host and cope with adverse conditions in human GI tract. In future, more potential properties of these strains may be checked, like folate & oxalate production, adhesion to mucin, production of β- galactosidase, cholesterol reduction mechanisms on LAB strains. It will be helpful to design new protocols for in-depth studies related to their potentia"
A review of factors influencing key biological components of maternal productivity in temperate beef cattle

Cow–calf efficiency or maternal productivity is highly correlated with total system efficiency of beef production. Balancing the needs of the cow herd with other production components is a daily challenge beef producers address to maximise the number of calves born and raised to weaning and, in turn, maximise maternal productivity. Pressure to satisfy modern consumer needs has shifted selection emphasis to production traits at the expense of fitness traits allowing adaptability to decline. Balancing the needs of the cow herd with production objectives presents cow–calf producers with the challenge of genetically tailoring their cattle to modern needs, while sustainably managing these cattle and natural resources. This balancing act is highlighted by the debate surrounding the application of residual feed intake to reduce costs associated with provision of feed for beef production. Some uncertainty surrounds the relationships between efficiency, production and maternal productivity traits. This review examines key components and definitions of maternal productivity. Management decisions as well as cow and calf traits have important interacting impacts on maternal productivity. Achieving a calving interval of 365 days represents the single most important production issue affecting maternal productivity and is dependent on heifer development during early life and energy reserves (i.e. body condition score) in subsequent years. Management issues such as calving date and selection decisions interact with environmental factors such as photoperiod and production traits such as feed intake, and previous production levels, to influence heifer development and cow body energy reserves. Some proposed definitions of maternal productivity simply include weaning weight per cow mated which can be averaged over all progeny weaned during a cow’s lifetime. Ideally, a definition should include the inputs and outputs of maternal productivity. Some definitions express maternal productivity over large time scales, e.g. a cow’s productive lifetime. Most definitions focus on the cow–calf unit, while some include progeny growth and feed intake to slaughter. This review recommends a definition that focuses on the cow–calf unit, as follows: (weight of calf weaned and cow weight change)/(metabolisable energy intake per cow and calf unit). This definition has the capacity to be scaled up, to include progeny postweaning production, as well as being applicable over varying time scales (e.g. 1 year to a cow’s whole productive life). Improvements in all facets of maternal productivity using this definition can be expected to improve beef-production efficiency.
Resource depletion by active suspension feeders on tidal fiats: Influence of local density and tidal elevation1

Sampling at two elevations from a tidal flat on the Shark Bay (Western Australia) shoreline at Monkey Mia revealed abundant suspension-feeding bivalves of numerous (> 17) species. Their total density increased by 3 x up the tidal elevation gradient from the subtidal margin of the flat to intertidal sites -97 cm higher. Factorial field experiments were used to test the effect of site (tidal elevation), local bivalve density, and their interaction on growth and survivorship of three species of suspension-feeding bivalves. Survivorship was high and did not vary significantly with site or local density. Individual growth was generally lower at higher density for both AnomaZocardia squamosus and Circe lenticularis, but growth of CaZZista impar never responded significantly to local density. Site effects on individual growth were far stronger than density effects and operated on all three species: growth at the intertidal site was substantially lower than at the subtidal site. The intensity of the site effect on individual growth about doubled from the first (February-June) to the second (June-December) experimental interval, probably because average daily exposure to air also doubled. Despite the success of tidal exposure in explaining seasonal variation in growth differences between sites, at a given season clams at the intertidal site grew substantially less than predicted from duration of aerial exposure and density. We hypothesize that density effects estimated locally within 1 -m2 areas fail to assess the full magnitude of food depletion that occurs over broader scales and that suspension feeders low on the flat deplete suspended foods in incoming tidal flows before they ever reach clams at higher elevations.
An assessment of British farmers’ and gamekeepers’ experiences, attitudes and practices in relation to the European Polecat Mustela putorius

Postal questionnaires were distributed to farmers and gamekeepers within the Polecat’s Mustela putorius main range in Britain. Only 11% of responding farmers had ever experienced damage by Polecats; 28% regarded the species as a threat to livestock. Conversely 53% of farmers believed Polecats control Rabbits Oryctolagus cuniculus, and 39% believed they control rodents on the farm. Two-thirds of responding gamekeepers had experienced Polecat predation of penned game, with the commonest access routes via ‘pop-holes’ and beneath the perimeter wire. Most gamekeepers (68%) regarded the Polecat as a minor pest, but ranked it as a less serious threat to game than predators such as the Fox Vulpes vulpes, Feral Cat Felis catus, Stoat Mustela erminea, corvids and Mink Mustela vison. Majorities of both farmers and gamekeepers would be concerned about an increase in the numbers of Polecats, and most wished to be free to control the species. Trapping was regarded as the main defence against Polecat predation of game; 91% of gamekeepers had trapped Polecats over the preceding 5 years. A minority of farmers carried out Polecat control; this activity was more prevalent on farms near the fringe of the species’ range. Pest-control practices likely to impact accidentally or indirectly upon Polecats, such as rodenticide use, fumigation (‘gassing’) of Rabbit burrows and ferreting, were also more prevalent on farms towards the fringe of the species’ range. These findings are discussed in the light of the Polecat’s status as a Scheduled species recovering its range in Britain. In anticipation of the species’ further spread into areas where game shooting is prevalent, recommendations are made regarding the need to improve game husbandry and to modify trapping practice. In particular, the night-time closure of pop-holes and the effective exclusion of Polecats from tunnel traps are suggested as a means of promoting greater tolerance of Polecats and compliance with the law.
The epiphyte vegetation of Annona glabra on Barro Colorado Island, Panama

Aim Information on the community composition, structure, and dynamics of epiphyte vegetation is scarce. A survey of the epiphytes occurring on all individuals of one particular host tree species in a well‐studied neotropical research site allowed us a comparison of the epiphyte flora of this tree with the local epiphyte flora, the analysis of spatial distribution patterns and the use of these patterns as indications for changes in time. In the future, our results can be used as a baseline data‐set for the direct observation of the long‐term dynamics in epiphyte communities.
Writing Scientific Papers in English

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RECOGNIZING DINOFLAGELLATE SPECIES USING ITS rDNA SEQUENCES 1

Dinoflagellate taxonomy is based primarily on morphology and morphometric data that can be difficult to obtain. In contrast, molecular data can be rapidly and cost‐effectively acquired, which has led to a rapid accumulation of sequence data in GenBank. Currently there are no systematic criteria for utilizing taxonomically unassigned sequence data to identify putative species that could in turn serve as a basis for testable hypotheses concerning the taxonomy, diversity, distribution, and toxicity of these organisms. The goal of this research was to evaluate whether simple, uncorrected genetic distances (p) calculated using ITS1/5.8S/ITS2 (ITS region) rDNA sequences could be used to develop criteria for recognizing putative species before formal morphological evaluation and classification. The current analysis used sequences from 81 dinoflagellate species belonging to 14 genera. For this diverse assemblage of dinoflagellate species, the within‐species genetic distances between ITS region copies (p=0.000–0.021 substitutions per site) were consistently less than those observed between species (p=0.042–0.580). Our results indicate that a between‐species uncorrected genetic distance of p≥0.04 could be used to delineate most free‐living dinoflagellate species. Recently evolved species, however, may have ITS p values <0.04 and would require more extensive morphological and genetic analyses to resolve. For most species, the sequence of the dominant ITS region allele has the potential to serve as a unique species‐specific “DNA barcode” that could be used for the rapid identification of dinoflagellates in field and laboratory studies.
Long-term genetic contributions : Prediction of rates of inbreeding and genetic gain in selected populations

This dissertation focuses on the prediction of long-term genetic contributions, rates of inbreeding and rates of gain in artificially selected populations. The long-term genetic contribution ( r i ) of ancestor i born at time t 1 , is defined as the proportion of genes from i that are present in individuals in generation t 2 deriving by descent from i , where ( t 2 - t 1 )→∞. The long-term genetic contribution of an individual was predicted by linear regression on the selective advantage of the individual. With overlapping generations, long-term genetic contributions were predicted using a modified gene flow approach. A novel definition of generation interval was introduced, which states that the generation interval is the length of time in which long-term genetic contributions sum to unity. It was shown that the rate of inbreeding is proportional to the sum of squared of expected long-term genetic contributions and that the rate of genetic gain is proportional to the sum of cross products of long-term genetic contributions and Mendelian sampling terms. Accurate predictions of rates of inbreeding were obtained for populations with discrete or overlapping generations undergoing either mass selection or selection on Best Linear Unbiased Prediction of breeding values. The method was applied to crossbreeding systems, which showed that the use of crossbred information may increase the rate of genetic gain, but measures to restrict the rate of inbreeding are required.
Insect Seasonal Cycles: Genetics and Evolution

The cyclic changes associated with seasonal progression probably constitute the most important and all-encompassing set of environmental variables that organisms encounter. Therefore, a fundamental and unifying aspect of each species' or population's life history is the adaptations that determine its seasonal cycle-i.e. the timing of the periods of development, reproduction, dormancy, and migration in relation to seasonal changes in biotic and abiotic factors. Such coordinated sets of seasonal adaptations are popularly referred to as seasonal "strategies. " Insects occur all over the world, and they encounter an extraordinary variety and range of seasonal conditions. Although insects that experience similar environmental changes sometimes show similar patterns in their seasonal responses, each species appears to have a unique set of eco-physiological adaptations that underlie its seasonal cycle. Moreover, seasonal adaptations vary within species. This great interand intraspecific diversity in seasonal adaptations subserves the broad geographic distribution of the Insecta and enables insects to utilize diverse, often ephemeral, biotic and abiotic resources and unpredictable habitats. Seasonal cycles also strongly influence interactions between organisms, the major example being the seasonal synchrony between host and parasite (sensu lato). Moreover, in some instances species utilizing a single resource reduce competition by the seasonal partitioning of that resource (e.g. 129). Asynchronous seasonal cycles can also serve as important reproductive isolating mechanisms between both sympatrically and allopatrically derived species (96, 137, 138). Knowledge of the evolution of seasonal cycles thus provides a key to understanding how organisms exploit their environment, how they interact,
Morphological and Anatomical Characteristics of Cichorium intybus L., Tragopogon latifolius Boiss. and Tussilago farfara L. (Asteraceae)

Edible and medicinal parts of Cichorium intybus L. Tragopogon latifolius Boiss. and Tussilago farfara L. (Asteraceae) were investigated morphologically and anatomically. These plants are used as food and folk medicines. Plant samples were collected from different locations in the West and Central Black Sea regions. The stem and leaf of C. intybus, the leaf of T. latifolius and the leaf and petiole of T. farfara were used for anatomical investigation. The stomata index and stomata index rate of three species were calculated. C. intybus had secretory structure in the cortex of stem and little glandular hairs on the upper and lower epidermis of leaves. T. latifolius and C. intybus had equifacial and T. farfara had bifacial mesophyll. T. latifolius had anomocytic and anisocytic stomata. C. intybus and T. farfara had anomocytic stomata.