Miracle-dz/UniFAR-FTUs huggingface dataset:
The physiology and molecular biology of peptide transport in seeds

Abstract Peptide transport plays a major role in the nitrogen nutrition of the cereal embryo during germination. During germination, enzymatic hydrolysis of storage proteins in the cereal grain endosperm forms a reservoir of small peptides and amino acids which are translocated across the scutellum to supply organic nitrogen to the growing embryo. Uptake of these solutes by the scutellum, a modified cotyledon which functions in nutrient transport, is mediated by carriers localized to the plasma membrane of the scutellar epithelium. To date the peptide transporter HvPTR1 is by far the best characterized example of a nutrient transporter involved in reserve mobilization during germination. Peptide transport in the barley scutellum has been relatively well-characterized biochemically, and in recent years the barley scutellar peptide transporter HvPTR1 has been cloned and characterized at the molecular level. Here, we review the physiological role and importance of peptide transport in germination, focusing on recent characterization of the barley peptide transporter HvPTR1. In barley, the uptake of small peptides by the scutellum appears to be mediated by a proton-coupled peptide transport system capable of handling peptides 2–4 amino acid residues in length.
AN EVALUATION OF THE FUNGAL INOCULATION METHOD OF DETERMINING THE RESISTANCE OF LODGEPOLE PINE TO MOUNTAIN PINE BEETLE (COLEOPTERA: SCOLYTIDAE) ATTACKS

Abstract Field tests were made of the fungal inoculation method of Reid et al. which assesses the potential of individual lodgepole pine trees (Pinus contorta Dougl var. latifolia Engelm.) to resist attacks by mountain pine beetle (Dendroctonus ponderosae Hopk.). Four hundred and eighty-four trees were inoculated with one of the beetle’s mutualistic blue-staining fungi (Europhium clavigerum Robinson and Davidson), tree responses were determined, and the potential of each tree to resist D. ponderosae was predicted. Two months later, after mountain pine beetles had attacked some of these same trees, most of the predictions based on the fungal assay system proved to be incorrect. Most of the trees which were attacked and which had been rated potentially resistant did not prevent successful bark beetle reproduction. These results, contrary to those of Shrimpton and Reid, suggest that some improvement is needed in the fungal assay method of assessing resistance of lodgepole pine to mountain pine beetle. Measures of tree resistance based on success of mountain pine beetle reproduction showed no difference in the proportion of non-resistant trees between epidemic and endemic areas.
Effect of Probiotic on Beneficial and Pathogenic Microorganisms in the Gastrointestinal Tract of Commercial Broiler with BCRDV Vaccine

The present study was conducted to determine the effect of probiotic on beneficial and pathogenic microorganisms in the gastrointestinal tract of Commercial Broiler. A total of 80 day-old broiler chicks were divided into two main groups I and II with 40 chicks in each. Group I was supplemented with Probiotic ( Saccharomyces cerevisiae 2 gm/kg feed) containing feed and chicks of group II was supplemented with conventional feed. Group I and II was again subdivided into two subgroups as group A, B and C, D respectively on 6 days of age. Birds of subgroups A and C were vaccinated with ND vaccine (BCRDV) and birds of subgroups C and D were kept as unvaccinated. The result evidenced the following information: (a) The total viable count (TVC) and total coliform count (TCC) were significantly (P<0.01) lower in experimental birds as compared to control at 14, 28 and 32 days of age both in vaccinated and non-vaccinated birds. It was always found that the lower TVC in probiotic fed broilers as compared to conventional fed broilers (b) The total lactobacilli count (TLC) was significantly (P<0.01) higher in experimental birds as compared to control at 14, 28 and 32 days of age both in vaccinated and non-vaccinated birds. So it can be said that Saccharomyces cerevisiae supplementation can reduce the pathogenic microorganism and increase the growth of beneficial microorganism. DOI: http://dx.doi. org/10.3329/pa.v24i1-2.19111 Progress. Agric. 24(1&2): 107 - 115, 2013
Effects of Dietary Protein Level on Growth Performance, Muscle Composition, Blood Composition, and Digestive Enzyme Activity of Wuchang Bream (Megalobrama amblycephala) Fry

The purpose of this study was to determine the dietary protein requirement and effects of dietary protein level on growth performance, muscle composition, blood composition, and digestive enzyme activity in Wuchang bream fry. Five isoenergetic and isolipidic semi-purified diets were formulated to contain 28%, 30%, 32%, 34%, or 36% (dry matter) dietary protein. Diets were fed to triplicate groups of 25 fishes (16.08±0.03 g) to near satiation three times a day in a closed recirculation system for 10 weeks. Weight gain, specific growth rate, and feed conversion ratio significantly improved as the dietary protein content increased up to 34%. The protein efficiency ratio, hepatosomatic index, and viscerosomatic index significantly dropped as the dietary protein rose while the Fulton condition factor was positively correlated to the dietary protein level. Increased dietary protein resulted in increased muscle protein content and decreased lipid content. Red blood cell, hemoglobin, and hematocrit counts increased significantly with the increase in dietary protein. Serum triiodothyronine and thyroxine significantly rose as the dietary protein rose but serum aspartate aminotransferase significantly dropped. Intestinal protease and amylase activity rose significantly with the increase in dietary protein while lipase tended to drop. On the basis of broken-line regression analysis of weight gain and FCR, the dietary protein requirement of Wuchang bream fry is 32-33%.
Behavioral reactions of free-ranging harbor porpoises Phocoena phocoena encountering standard nylon and BaSO4 mesh gillnets and warning sound

Field tests suggest that high-density nets can reduce harbor porpoise Phocoena pho- coena by-catch in demersal gillnet fisheries. However, it is not clear whether acoustic reflectivity or twine stiffness are responsible for this. We conducted sonar tests in a tank in the frequency range of 110 to 190 kHz and found that the target strength of the high-density BaSO4 net was 7.2 dB higher at 150 kHz than that of the standard nylon net. In a fjord on Vancouver Island, Canada, we investigated porpoise surfacing and echolocation behavior as they encountered 2 surface gillnets (45 × 9 m, 165 mm mesh size) made of (1) standard 100% nylon and (2) a mix of BaSO4 and nylon. The distrib- ution of click intervals shifted to longer intervals when the BaSO4 net was used (median = 51 ms vs. 45.2 ms for the standard net; Kolmogorov-Smirnov test, p < 0.001), indicating a greater target dis- tance. We estimated that porpoises are able to detect BaSO4 nets 4.4 m in advance of standard nylon nets. However, an unexpected low percentage of echolocating porpoise groups within 50 m of the center of nets (standard 30.6%, BaSO4 19.3%) indicates that additional measures may be necessary to reduce by-catch. A subsequent experiment showed that transmission of 2.5 kHz tones as a warn- ing sound increased biosonar use by a factor of 4 compared to controls (16.7% for controls vs. 71.4% for groups during ensonification; chi 2 -test, p < 0.001). The combination of reflective nets and warning sounds may be a promising mitigative tool.
Correlation Between the Content of Biogenic Amines and Other Wine Compounds

To investigate the source (origin) of biogenic amines, 135 wines of various origins were initially analyzed to determine their content of amino acids and biogenic amines. Of these wines, 58 containing varying concentrations of biogenic amines then underwent a complete analysis. Amino acids and biogenic amines were quantified by HPLC with fluorescence detection. The results of the study indicate that a large number of amines can be formed from their precursor amino acids. This occurs primarily during and after the spontaneous malolactic fermentation process. Moreover, the presence of amines is linked to substances characteristic of wine spoilage. Therefore, the type of lactic acid bacteria should be controlled, and all microbiological action after completion of malolactic fermentation should be halted.
Soil water effect on crop growth, leaf gas exchange, water and radiation use efficiency of Saccharum spontaneum L. ssp. aegyptiacum (Willd.) Hackel in semi-arid Mediterranean environment

Great effort has been placed to identify the most suited bioenergy crop under different environments and management practices, however, there is still need to find new genetic resources for constrained areas. For instance, South Mediterranean area is strongly affected by prolonged drought, high vapour pressure deficit (VPD) and extremely high temperatures during summertime. In the present work we investigated the soil water effect on crop growth and leaf gas exchange of Saccharum spontaneum L. ssp. aegyptiacum (Willd.) Hackel, a perennial, rhizomatous, herbaceous grass. Furthermore, the net increase of biomass production per unit light intercepted [radiation use efficiency (RUE)] and per unit water transpired [water use efficiency (WUE)] was also studied. To this end a field trial was carried out imposing three levels of soil water availability (I 100 , I 50 and I 0 , corresponding to 100%, 50% and 0% of ETm restutition) under a semi-arid Mediterranean environment. Leaf area index (LAI), stem height, biomass dry matter yield, CO 2 assimilation rate, and transpiration rate resulted significantly affected by measurement time and irrigation treatment, with the highest values in I 100 and the lowest in I 0 . RUE was the highest in I 100 followed by I 50 and I 0 ; on the other hand, WUE was higher in I 0 than I 50 and I 100 . At LAI values greater than 2.0, 85% photosynthetically active radiation was intercepted by the Saccharum stand, irrespective of the irrigation treatment. Saccharum spontaneum spp. aegyptiacum is a potential species for biomass production in environment characterized by drought stress, high temperatures and high VPD, as those of Southern Europe and similar semi-arid areas.
Larval development of theterebellid polychaete Eupolymnia nebulosa (Montagu) in the Mediterranean Sea

The morphology of young stages of Eupolymnia nebulosa (Montagu, 1818) is observed using SEM. Significant changes occur at several times after egg laying. The transition from endotrophy to exotrophy takes place when the larvae are about 13–15 days old. At the same time, the primary tentacle appears as a hemispherical bud; the first setae to emerge are transitory and club‐shaped. They are shed when the larvae are about 50 days old. Observations on the development of the uncinigerous torus of the 11th segment (the first one bearing uncini with the main fang in an alternated direction) indicate that the uncini appear at the dorsal extremity of the torus and then move toward the medio‐ventral axis as they increase in size. The uncini are shed when they reach the ventral extremity of the torus. These changes may result in taxonomic confusions unless the complete sequence of development is known.
A conifer–angiosperm divergence in the growth vs. shade tolerance trade‐off underlies the dynamics of a New Zealand warm‐temperate rain forest

A central tenet of forest ecology is that succession and regeneration dynamics are driven by an interspecific trade‐off between juvenile growth rates in high light and shade tolerance. There is evidence, however, that a single trade‐off axis may fail to explain the dynamics of mixed conifer–angiosperm rain forests in the Southern Hemisphere, especially in New Zealand. We tested for growth vs. shade tolerance trade‐offs by measuring juvenile growth of five podocarps and five broadleaved canopy angiosperms across a wide range of light environments in a New Zealand warm‐temperate rain forest. The light compensation point of growth was used as a measure of species light requirements, which we then compared with height growth in 10% light, approximating the environments encountered beneath small treefall gaps. Despite considerable overlap between the ranges of both growth rates and compensation points found in the two lineages, major axis tests showed that the growth vs. shade tolerance trade‐off differed significantly between podocarp and angiosperm species. At a common compensation point, angiosperms were faster growing than podocarps in 10% light. However, juveniles of these angiosperm species were notably scarce in the more open environments associated with forest margins. Synthesis. A conifer–angiosperm divergence in the growth vs. shade tolerance trade‐off may explain long‐standing problems of the dynamics of these forests. Although juveniles of most lowland podocarps can tolerate considerable shade, the more vigorous response of broadleaved angiosperms to small canopy openings enables them to out‐compete podocarps in old‐growth stands. The greater abundance of podocarp juveniles on forest margins cannot be attributed to them out‐competing angiosperm species where light is abundant and is likely to reflect superior resistance to frost and/or drought. The drivers of the dynamics of New Zealand's podocarp–broadleaved forests therefore differ appreciably from those ascribed to tropical and north‐temperate forests.
Meiofauna enhances organic matter mineralization in soft sediment ecosystems

We investigated the influence of meiofauna on the benthic decomposition of a radiolabeled diatom bloom by measuring the production of 14CO2 in a laboratory microcosm. Mineralization of the diatom bloom material in the sediment was significantly enhanced in the treatment with high meiofauna abundance, with cumulative mineralization values, on average, 50% greater in the treatment with high meiofaunal abundance after 17 d, compared to sediments with low meiofauna abundance. In addition, bacteria species composition in the treatment with high meiofauna abundance was significantly different from the treatment with low meiofauna abundance, indicating that the activities of meiofauna in the sediments had an effect on the bacterial community composition. Meiofauna can enhance the mineralization of organic matter, probably by stimulating the activity of sediment bacterial community, indicating that positive biological interactions such as facilitation from meiofauna are important for ecosystem processes in soft sediments.
α- and β-Proteobacteria Control the Consumption and Release of Amino Acids on Lake Snow Aggregates

ABSTRACT We analyzed the composition of aggregate (lake snow)-associated bacterial communities in Lake Constance from 1994 until 1996 between a depth of 25 m and the sediment surface at 110 m by fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes of various specificity. In addition, we experimentally examined the turnover of dissolved amino acids and carbohydrates together with the microbial colonization of aggregates formed in rolling tanks in the lab. Generally, between 40 and more than 80% of the microbes enumerated by DAPI staining (4′,6′-diamidino-2-phenylindole) were detected asBacteria by the probe EUB338. At a depth of 25 m, 10.5% ± 7.9% and 14.2% ± 10.2% of the DAPI cell counts were detected by probes specific for α- and β-Proteobacteria. These proportions increased to 12.0% ± 3.3% and 54.0% ± 5.9% at a depth of 50 m but decreased again at the sediment surface at 110 m to 2.7% ± 1.4% and 41.1% ± 8.4%, indicating a clear dominance of β-Proteobacteria at depths of 50 and 110 m, where aggregates have an age of 3 to 5 and 8 to 11 days, respectively. From 50 m to the sediment surface, cells detected by aCytophaga/Flavobacteria-specific probe (CF319a) comprised increasing proportions up to 18% of the DAPI cell counts. γ-Proteobacteria always comprised minor proportions of the aggregate-associated bacterial community. Using only two probes highly specific for clusters of bacteria closely related toSphingomonas species and Brevundimonas diminuta, we identified between 16 and 60% of the α-Proteobacteria. In addition, with three probes highly specific for close relatives of the β-Proteobacteria Duganella zoogloeoides (formerly Zoogloea ramigera),Acidovorax facilis, and Hydrogenophaga palleroni, bacteria common in activated sludge, 42 to 70% of the β-Proteobacteria were identified. In the early phase (<20 h) of 11 of the 15 experimental incubations of aggregates, dissolved amino acids were consumed by the aggregate-associated bacteria from the surrounding water. This stage was followed by a period of 1 to 3 days during which dissolved amino acids were released into the surrounding water, paralleled by an increasing dominance of β-Proteobacteria. Hence, our results show that lake snow aggregates are inhabited by a community dominated by a limited number of α- and β-Proteobacteria, which undergo a distinct succession. They successively decompose the amino acids bound in the aggregates and release substantial amounts into the surrounding water during aging and sinking.
Predation by Coccinellid beetles : experiments on switching

The predatory behavior of a ladybird, Coccinella, was examined as it preyed upon varying ratios of two aphid species, Acrythosiphon pisum and Aphis fabae. Experiments were done in petri dishes and on bean plants. The ladybirds attacked the two prey species in direct proportion to their relative abundance. There was little variability among predators in a given treatment. Training had no effect on the subsequent diets of the predators, and all treatments provided a very good fit to a simple no—switching" model. Predation on each species was density independent. This simple type of predation contrasts markedly with the results of earlier experiments on predatory snails in which variability among predators and a strong training effect produce switching. See full-text article at JSTOR
FRUIT DEVELOPMENTAL STAGES EFFECTS ON BIOCHEMICAL ATTRIBUTES IN DATE PALM

Some date palm cultivars grown in Pakistan were biochemically characterized and the effect of fruit maturity on radical scavenging capacity (DPPH), total phenolic contents (TPC), specific activity of antioxidant enzymes, sugars profile and soluble protein contents was assessed. Higher range of differences in composition of studied phytochemicals was recorded among different cultivars. Antiradical efficiency (AE), TPC, antioxidant enzymes and soluble protein contents were recorded higher at khalal stage thereafter, declined at rutab then finally at tamar stage. The amount of glucose (11.32-32.50%) and fructose (10.95-32.41%) started accumulation from khalal stage and were in higher composition at tamar stage due to hydrolysis and inversion of sucrose (10.82-3.1%) contents. The results concluded that variation in biochemical attributes primarily influenced by type of cultivars and different fruit developmental stages.
MICROBIAL CONTAMINATION OF BIVALVE MOLLUSKS USED FOR HUMAN CONSUMPTION

We studied 127 samples of bivalve mollusks (Mediterranean mussel, Mytilus galloprovincialis; smooth clam, Callista chione; grooved carpet-shell clam, Tapes decussatus; and striped venus clam, Chamelea gallina) obtained in the winter and spring of 2009 from retail fish and shellfish vendors in Granada, Spain. Samples were analyzed (raw and after steaming) to determine the prevalence of Escherichia coli, mesophilic aerobes, Staphylococcus aureus and the disease-causing microorganisms Salmonella spp. , Listeria monocytogenes and Vibrio parahaemolyticus. E. coli was found in 25% of raw samples and 4% of cooked samples. Aerobes were found in 89% of raw samples (more than 1,000 cfu/g), and S. aureus was found in 37.0%. Only one raw sample was positive for V. parahaemolyticus. The percentage of positive findings was fourfold as high in the spring sample as in the winter sample. Contamination was most frequent in the smooth clam, and samples obtained on Mondays were more frequently contaminated than those obtained on other days of the week. PRACTICAL APPLICATIONS Current Spanish legislation establishes that all bivalve mollusks intended for commercial sale and human consumption must be treated at a detoxification center. The application of detoxification is of fundamental importance because it constitutes a barrier against the transmission of bacterial and viral diseases of aquatic origin. We analyzed possible differences in contamination parameters in this type of shellfish, indicated characteristics that may be affected by alterations in quality, and discussed the potential effects of these alterations on human health.
Phylogenetic and biogeographic relationships of gerbil mice Eligmodontia (Rodentia, Cricetidae) in South America, with a description of a new species

We present a systematic study of the genus Eligmodontia (sigmodontine rodents of the tribe Phyllotini) from Argentina, Bolivia, and Chile, based on molecular data. Phylogenetic relationships among 49 individuals were examined using nucleotide sequence data from the entire 1143 bp of the mitochondrial cytochrome-b gene. Unweighted parsimony, minimum evolution, maximum-likelihood (TrN+I+G), and Bayesian analyses revealed 2 major clades, representing Andean and non-Andean groups, and 6 minor clades, representing E. typus (lowland), E. typus (highland), E. morgani, E. puerulus, E. moreni, and E. hirtipes. E. typus (highland) is described as a new species based on combined data from the cytochrome-b gene, morphology, and karyology. The results indicate that the genus Eligmodontia is composed of a complex of species, most of which correspond to taxa that were described originally and each of which shows molecular cohesion within a limited geographic range. This species complex has relevance to current theories regarding the speciation patterns and the historical biogeography of South American sigmodontine rodents. The biogeographic history of the genus also is outlined.
Association of genetic variants in UGT1A6 genes and non-genetic variant with valproic acid doses and plasma concentration in Thai epileptic patients

The aim of this study was to investigate the association of genetic variants in UGT1A6 19T>G, 541A>G and 552A>C together with non-genetic variant with VPA dose and plasma concentrations in Thai epileptic patients. Eighty four Thai epileptic patients who were treated with VPA maintenance dose at Phramongkutklao Hospital were enrolled to this study. Three candidates single nucleotide polymorphisms (SNPs), including UGT1A6 19T>G, 541A>G and 552A>C were genotyped by using Taqman SNP genotyping assay. Non-genetic factor, co-medication, was divided into three categories including drug inducer, drug inhibitor and drug with no effect. Nonparametric methods (Mann-Whitney U and Kruskal-Wallis test) were used to identify the association of genetic and nongenetic variants, drug interaction, with VPA maintenance dose and steady state trough plasma concentration. The three candidate SNPs of 84 patients were genotyped. All of the genotypic distributions were consistent with HardyWeinberg equilibrium. For co-medication, only drug inducer and drug with no effect which were 37 and 47 respectively were found. Results of this study demonstrated that UGT1A6 541A>G and 552A>C variants were associated with lower VPA dose (p-value = 0.037, 0.031, respectively). Whereas, non-genetic factor, drug inducer tended to be associated with higher VPA dose. In line with this, drug inducer was found to be associated with lower VPA plasma concentration (p-value = 0.002) while UGT1A6 polymorphisms were shown a tendency of association with higher VPA plasma level. The present study demonstrated that genetic variants in UGT1A6 influenced variability in VPA dose while drug interaction had an impact on VPA plasma concentration in Thai epileptic patients. These finding suggested that genetic variants in gene encoding drug metabolizing enzyme and non-genetic factor, drug inducer, could explain in part the inter-individual variability in VPA maintenance dose and blood levels.