Miracle-dz/UniFAR-FTUs huggingface dataset:
Peroxisome Proliferator‐activated Receptors: Stuctures and Function

We have been attempting to elucidate the molecular mechanisms through which peroxisome proliferators exert their pleiotropic effects, with particular emphasis on understanding why humans appear unresponsive to these compounds. There is a wealth of data to implicate the peroxisome proliferator-activated receptor alpha (PPAR alpha) in mediating these effects in rodent species; PPAR alpha is expressed in tissues that show physiological changes in response to PPs, is transcriptionally activated in vitro by a variety of PPs, and it has been recently demonstrated that mice lacking this receptor are refractory to the effects of clofibrate and Wy-14,643, at least in the short term. It is conceivable that differences in PPAR alpha between responsive rodent and unresponsive human subjects may provide the key to understanding the basis of this species variation in response, and with this in mind we have been studying the biology of PPAR alpha in humans and looking at interindividual variation. There is already published evidence, albeit on only two sequences, for structural and functional polymorphism in human PPAR alphas. We have extended these findings, and shown that: There is considerable variation in hPPAR alpha cDNAs obtained from different individuals, both at the gross structural level (lack of a coding exon) and of a more subtle nature (single base changes leading to amino acid substitutions). One such cDNA, the sequence of which differs at only three amino acids from that published, encodes a receptor that is incapable of transcriptional activation by potent PPs. The degree to which hPPAR alpha transcripts are expressed in human livers can vary by up to an order of magnitude between individuals. The tissue-specific expression profile of PPAR alpha in humans is very different from that in rat and mouse. In particular, the human liver contains generally low levels of PPAR alpha in contrast to the responsive rodents, in which potent PPs cause liver tumors. Taken together, these data suggest first that human and rodent PPAR alphas differ according to a number of molecular and biochemical criteria, and secondly that there is a degree of interindividual variation in PPAR alpha structure and function. Studies are ongoing to clarify this further, but human polymorphism may go some way towards explaining the apparent paradox that active PPAR alpha receptors can be isolated from an "unresponsive" species.
Comparative study of two plating media (PALCAM and Oxford) for detection of Listeria species in a range of meat products following a variety of enrichment procedures

Fifty‐two different varieties of sausage, salami and pâté were examined using Oxford (Oxoid) and PALCAM (Merck) listeria‐selective agars. Seven (13%) samples were positive for Listeria monocytogenes and 14 (27%) samples were positive for other Listeria species, while 31 (59%) samples were negative for Listeria species. The effectiveness of PALCAM and Oxford medium for the isolation of L. monocytogenes from the meat samples was compared. PALCAM medium was consistently more effective in suppressing other micro‐organisms thus enhancing the possibility of detecting Listeria species present in low numbers. The isolation of Listeria species for identification was also easier using PALCAM medium.
Recruitment and life-history traits of sparse plant species in subalpine grasslands

Recruitment is critical for the maintenance of plant populations and community diversity, but sexual regenera- tion is considered to be infrequent in climatically harsh habitats such as subalpine grasslands. This study examines the importance of regeneration through seed for 16 sparse herb species, and we asked whether their populations are limited by safe sites or the availability of seeds. Seedling recruitment and winter survival were recorded after sowing in an exper- imental split-plot design in (i) pasture grazed by livestock, and (ii) exclosed grassland cultivated for annual mowing. In addition we examined the effect of disturbance and local seedbank recruitment. All species were able to recruit and sur- vive the first winter in at least some of the experimental plots, although none were initially present. Recruitment mainly occurred in disturbed plots, and disturbed pasture plots had a significantly higher recruitment than disturbed exclosures for all species except Silene dioica. We further examined whether specific plant traits were related to variation in recruitment. Lower recruitment in the disturbed exclosure was associated with higher specific leaf area, leaf dry weight, and seed num- ber. In contrast, seeds sown in disturbed pasture recruited more independently of species traits. The exception was a nega- tive correlation between recruitment and leaf dry weight, and an unexpected negative correlation with seed weight. We suggest that recruitment differences among habitats mainly reflect lower humidity in the exclosure. Consequently, small stature plants with small specific leaf area should have the highest recruiting probability when exposed to drought. The almost exclusive recruitment on disturbed plots indicates a strong competitive effect on the target species in vegetated plots, and suggests that safe sites for regeneration through seed are rare in subalpine grasslands.
SEASONAL VARIATIONS IN PHOTOSYNTHESIS‐IRRADIANCE RESPONSES BY BIOFILMS IN MEDITERRANEAN STREAMS

The relationships between primary production and irradiance were analyzed over an annual cycle in natural biofilms of two undisturbed streams: La Solana (LS), an open calcareous stream, and Riera Major (RM), a shaded siliceous stream. In LS, low photosynthetic efficiency (αchl and αarea) and high values of both the light saturation parameter (Ik) and the carotenoid/chlorophyll ratio indicated adaptation to high light regimes. On the other hand, higher photosynthetic efficiency and lower Ik as well as photoinhibition at high irradiance found in the biofilms of RM indicated shade adaptation. However, the lack of correlation between light availability in nature and the photosynthetic parameters studied in the laboratory suggested that light was not the most important factor in determining seasonal changes in the photosynthetic behavior in this stream. Both in the open and shaded streams, algal patches collected simultaneously exhibited different photosynthesis‐irradiance (P‐I) curues, showing that community composition influenced the P‐I parameters. In the open stream (LS), however, significant negative correlations between αarea and chlorophyll a and between Pmaxchland chlorophyll a (r=‐0.994, P < 0.001, and r =‐0.929, P < 0.05, respectively) suggested that photosynthesis was affected by self‐shading. Due to the absence of photoinhibition in the biofilms of LS, high photosynthetic rates were maintained at the ambient high light environment, thus compensating for low photosynthesis at low irradiance. In the shaded stream (RM), because photosynthesis was saturated at low irradiances, primary production was relatively high given the low light conditions.
Monitoring of Fungi and Bacteria in the Indoor Air of Primary Schools in Edirne City, Turkey

We monitored levels of bacteria and fungi in the indoor air at selected sites of several public primary schools in the city of Edirne, Turkey. Sampling was by the Petri plate method onto both a Rose-Bengal streptomycin agar medium and a 5% sheep-blood agar medium exposed to the air for 10-minute periods. Samples were collected monthly over a period of 6 months between August 2001 and January 2002. A total of 941 microfungi and 2066 bacterial colonies were counted on 90 Petri plates. During this 6-month period, 19 bacterial genera, 15 fungal genera and 48 species of fungi were isolated from the air in the schools. Some bacteria, such as coagulase-negative Staphylococcus, Corynebacterium and Bacillus, were predominant (42.7%, 20.4% and 6.9% of the total, respectively). Penicillium, Cladosporium and Alternaria were the most common fungal genera (42.8%, 19.3% and 10.1% of the total, respectively). Staphylococcus, Acinetobacter, Corynebacterium, Propionibacterium and Pseudomonas genera were found in every month. Statistical analysis of the data showed a positive correlation between the concentrations of bacteria and air humidity (p 0.002, R2 0.726) and between bacterial concentrations and age of the schools (p 0.045, R2 0.787). Also, that there was seasonal variation since the concentrations of fungi and bacteria varied according to the months (p 0.001).
Consumptive-Competition Coefficients: An Experimental Analysis with Spiders

Data on feeding rates, dietary composition, and relative frequencies of food types in the environment for two syntopic spider species, Metepeira grinnelli and Cyclosa turbinata, were used to evaluate two consumptive-competition-coefficient formulas. The first formula, proposed by MacArthur and Levins (1967) and Levins (1968), reflects only dietary overlap between the species. The second, more complicated formula, proposed by Schoener (1974), also includes feeding rates, relative frequencies of food types in the environment, and food biomasses. The competition coefficients were computed separately for the spring and the summer. The coefficients obtained from the MacArthur-Levins formula differed dramatically from those obtained from the Schoener formula in the spring and in the summer. The coefficients obtained from the Schoener formula were asymmetrical. The larger species always had the competitive advantage, even though Cyclosa was the larger species in the spring and Metepeira was larger in the summer. Two factors caused the coefficients to be asymmetrical. First, in the spring, Cyclosa individuals consumed about 2.5 times as many prey items per day as the Metepeira individuals did. Second, in both the spring and summer, there was an overlap of the larger species' diet with the larger, more preferred prey types in the smaller species' diet, and an overlap of the smaller species' diet with the smaller, less preferred prey types in the larger species' diet. Consequently, the larger species exerted a greater per capita effect on the smaller species. To measure the effects of competition directly, I manipulated Metepeira and Cyclosa densities in the field. The experimentally determined effects of competition on spider food-consumption rates were qualitatively consistent with the Schoener formula, but not with the MacArthur-Levins formula. Hence, the extra information in the Schoener formula was crucial for estimating consumptive-competition coefficients. This formula provides a theoretical basis for asymmetrical interspecific competition.
Yield Stability of Aromatic Upland Rice with High Yielding Ability in Indonesia

Abstract Aromatic rice variety, Mentikwangi, was crossed with high-yielding upland rice variety, Poso, and the pedigree was selected to obtain lines with high yielding and aromatic characters. The objectives of the research were to study the yield stability of aromatic upland genotypes across different locations and to select aromatic upland rice genotypes having wide adaptability, and or specific location adaptability. Yield stability of genotypes was estimated by using regression lines proposed by Finlay and Wilkinson. Some genotypes showed high yield stability and wide adaptability in different locations, and others showed good adaptability to a specific location. The lines having high yield stability and wide adaptability were G10 (405 g m-2), G19 (400 g m-2), G39 (418 g m-2), and G136 (411 g m-2), which may be considered as candidates of new aromatic upland rice cultivars. Situpatenggang had specific adaptability at the fertile locations; and Poso and G13 at the infertile locations. Genotype x location interactions for the yield and its components performance were observed.
Environment rather than genetic background explains intraspecific variation in the protein-precipitating capacity of phenolic compounds in beech litter

Background: The ecological effects of phenolic compounds in plant tissues are related to their phenolic signature, i.e. the total content and structure of the phenolic compounds. Although the spatial and temporal variation of the phenolic signature within species is well documented, it remains unclear whether intraspecific variation is due to genetic differences between individuals or to environmental conditions. Aims: We aimed to disentangle the effects of the genetic background and environmental conditions on intraspecific variation in the phenolic signature of beech (Fagus sylvatica) leaf litter. Methods: In a silvicultural provenance experiment, beech populations from a wide range of the natural distribution range of the species, including different phylogeographic lineages (site of origin = genetic background), were grown in two geographically distinct common gardens (site of growth = environment). The total content and the protein-precipitation capacity of phenolic leaf litter compounds and their HPLC profile were determined as a measure of the phenolic signature of leaf litter of individual beech trees. Results: The phenolic content and the protein-precipitating capacity of methanolic litter extracts were significantly correlated. Variation in the content of phenolic compounds was largely related to genetic background and less to environment, while the reverse was true for their protein-precipitating capacity. Individuals grown in the same common garden exhibited more similar phenolic signatures than individuals from the same provenance but grown at different locations. Conclusions: We conclude that it is environmental conditions rather than the genetic background that determines the phenolic signature of leaf litter of beech individuals. It follows from our results that environmental change may in the future lead to alteration of the phenolic signatures of present beech forest ecosystems, probably with a cascading effect on ecological processes such as decomposition.
Isozyme Variation and Ploidy Levels within the Apomictic Ranunculus auricomus Complex: Evidence for a Sexual Progenitor Species in Southeastern Austria

Ranunculus notabilis R. variabilis R. auricomus R. notabilis R. variabilis R. notabilis R. variabilis R. variabilis R. notabilis R. variabilis R. notabilis R. variabilis R. notabilis R. auricomus R. variabilis.
Conservation of the Owens Pupfish: Genetic Effects of Multiple Translocations and Extirpations

Abstract The Owens Pupfish Cyprinodon radiosus represents many of the challenges of managing threatened or endangered species in fragmented refuge populations. All six extant populations of the endangered Owens Pupfish were examined to assess how management practices, including serial translocations and founder events, have influenced the genetic diversity of the species and to make recommendations for future management. Four populations were sampled twice with 3–4 years intervening; two additional populations were sampled once. Populations were genotyped at nine microsatellite loci; estimated effective population sizes ranged from 34.2 to 347.8 individuals based on the linkage disequilibrium method and from 10 to 48 using the sibship assignment method. All of the populations were estimated to have undergone severe bottlenecks, and statistically significant pairwise F ST values increased during the period between sampling. From this data we infer that the individual refuge populations have differentiated .
Molecular analysis of solute carrier family 11 member a1 (Slc11a1) gene in ruminants and non-ruminants using computational method

Solute carrier family 11 member a1 gene (Slc11a1) previously known as natural resistance-associated macrophage protein 1 (Nramp1) is a gene of member of family of metal ion-transport protein. The cellular expression is restricted to phagocytic cells. Slc11a1 delivers bivalent metal cations from the cytosol into acidic endosomal and lysosomal compartments where Fenon and Haber-Weiss reaction generates toxic antimicrobial radicals for direct antimicrobial activity against harmful microorganisms. The present study was undertaken with the objective of analyzing Slc11a1 gene to gain insight into the evolutionary proximity and divergence as well as the polymorphism of this gene in ruminants and non-ruminants including the attendant effects of the genetic variants on the function of the Slc11a1 protein. Thirty Slc11a1 gene sequences of 6 mammalian species classified as ruminant (goat, sheep, cattle, Bubalus bubalis and Bubalus carabanensis) and non-ruminant (swine and horse) animals were investigated. The length of the Slc11a1 gene varied from 448-2,357. There was substantial genetic variation and polymorphism in the aligned sequences of Slc11a1 gene within and across species. Functional analysis of non-synonymous mutations in cattle revealed that twenty five of the amino acid substitutions at the peptide binding region could be beneficial, (E36G), (T52A), (N161S) and (V248I) were likely to be beneficial while only (Q312K) was harmful. In horse, two of the amino acid mutations were harmful, two were likely to be harmful, one was undecided, four were likely beneficial and the rest twenty were beneficial. The phylogenetic trees showed some form of proximity and differentiation in Slc11a1 sequences within and across species. The present information on the polymorphism of Slc11a1 gene might be exploited in the search for association with disease resistance in Nigerian livestock species.
The presence of both recombinant and nonrecombinant strains of Tomato yellow leaf curl virus on tomato in Réunion Island

Tomato yellow leaf curl virus (TYLCV) was first detected in Reunion in 1997, based on symptoms and partial sequence data between the conserved nonanucleotide and the first 5 ′ quarter of the capsid protein (CP) gene (Peterschmitt et al ., 1999). A 516 bp portion of the C4 gene of the same isolate of TYLCV from Reunion was subsequently sequenced (Accession No. AJ842312), showing that it belonged to the mild strain (TYLCVMld[RE]) and the so-called nonrecombinant group (Navas-Castillo et al ., 2000). In April 2004, severe symptoms of stunting, yellowing and leaf curling, resembling the symptoms of tomato yellow leaf curl disease, were observed on tomato plants in Saint Gilles in the north-west region of Reunion. Twenty-two leaf samples from affected tomato plants were collected and tested for the presence of begomoviruses using a PCR assay with two sets of primers designed to amplify two regions of the A component of TYLCV: primers V2790 and C837 amplify a 800 bp fragment spanning the intergenic conserved region (IR) nonanucleotide sequence and two-thirds of the CP gene, while primers TY1944 (TTGTTTTGCCTGTTCTGCTA) and TY2460 (CATCTCCATGTGCTTATCCA) amplify a 516 bp portion of the C4 gene. The latter region was chosen to differentiate the Israeli strain (syn. TYLCV-IL Accession No. X15656) from the mild strain (TYLCVMld; Accession No. X76319). All the leaf samples produced PCR products of the expected size with both sets of primers. For three samples, a 483 bp fragment of the C4 gene was sequenced using the primer set TY1944/TY2460 (Accession Nos AJ842309, AJ842310, AJ842311) and a 685 bp fragment of IR/CP region was sequenced using the primer set V2790 (ATCCGTATAATATTACCGGATGG) and C837 GCAAATCATTCTTCACTGTTGC) (Accession Nos AJ842306, AJ842307, AJ842308). The sequences were aligned with those of known TYLCV strains using dnaman (Lynnon Biosoft, Quebec, Canada). The 685 bp fragment showed 98–99% nucleotide identity with TYLCV, TYLCV-Mld and -Mld[RE]. However, the 483 bp fragment showed a 98% nucleotide identity with TYLCV, but only 77% nucleotide identity with TYLCV-Mld and the previous Reunion isolate TYLCV-Mld[RE]. This is the first report of the presence of the Israeli strain, which belongs to the so-called recombinant group of TYLCV, from Reunion island.
Study of the Indoor Air Quality in Hospitals in South Chennai, India — Microbial Profile

A 3-month pilot study (February—April 2006) was conducted to determine the quality of indoor air in hospitals in the Tamil Nadu region of India and to characterize the predominant aerobic bacteria and fungi present. The main objectives were (1) to sample the indoor air of three different hospitals in Chennai for bioaerosols to generate baseline data using the Petri plate gravitational settling (passive) method of sampling; and (2) to isolate and identify potentially pathogenic organisms prevalent in the hospital environment. Indoor air samples were collected from various wards at the different hospitals and processed for the identification of various predominant bacteria and fungi. The overall counts of Gram-positive organisms were found to be higher than Gram-negative organisms. Of these isolates, Staphylococci and Micrococci were the predominant Gram-positive bacteria, while Klebsiella sp. and Pseudomonas sp. were the predominant potentially pathogenic Gram-negative bacteria isolated. Among yeasts and molds, Aspergillus niger and A. flavus were commonly isolated.
The early life history of two sympatric New Zealand octopuses: eggs and paralarvae of Octopus huttoni and Pinnoctopus cordiformis

This study combined morphological and morphometric information on egg clutches, egg capsules and paralarvae of two sympatric coastal octopuses from New Zealand waters, Octopus huttoni and Pinnoctopus cordiformis, to provide species-specific traits to identify their early life stages obtained from field surveys. Eggs of O. huttoni (2.5 mm length; 1 mm width) were entwined with one another forming strings that ranged from 11 to 25.8 mm in length. Eggs of P. cordiformis (6.4 mm length; 1.5 mm width) were significantly bigger than those of O. huttoni and were grouped in small clusters of about seven eggs. Paralarvae O. huttoni and P. cordiformis differed in hatching size (1.4 mm versus 3.1 mm mantle length), number of suckers per arm (four versus eight), number of lamellae per outer demibranch (five versus ten) and arrangements of chromatophores in the body surface (29 to 59 versus 91 to 179), respectively. The morphological traits described in hatchlings from the laboratory allowed comparisons with field-collected paralarvae, suggesting that such characters were reliable species-specific patterns to enable a consistent differentiation between the early life stages of these two sympatric species, even in the absence of the brooding female.
CYTOLOGY OF THE AECIOSPORES AND AECIOSPORE GERM TUBES OF PERIDERMIUM HARKNESSII AND P. STALACTIFORME OF THE CRONARTIUM COLEOSPORIOIDES COMPLEX

Cytology of aeciospores and aeciospore germ tubes of two pine rusts, Peridermium harknessii J. P. Moore and P. stalactiforme Arth. & Kern, was compared. In P. harknessii the mycelial cells giving rise to aecia were uninucleate. Young aeciospores were usually binucleate but most of them became uninucleate during maturation. Upon germination, nuclear division and septum formation occurred and germ tubes were divided into two, three, or four cells, each of which usually contained one nucleus. One to three side branches developed and nuclei migrated into them. Basidiospores were not produced. Despite the absence of basidiospores, P. harknessii is interpreted as having an endo-type life cycle with nuclear fusion and meiosis. In P. stalactiforme, aeciospores were binucleate and, upon germination, two nuclei migrated into the germ tube. The nuclei remained undivided during the formation of appressoria and infection pegs. Septa were not observed and branching was dichotomous or irregular.