Miracle-dz/UniFAR-FTUs huggingface dataset:
Landscape and microenvironmental conditions influence over regeneration dynamics in old-growth Nothofagus betuloides Southern Patagonian forests

Abstract Old-growth forests present a mosaic of different conditions resulting from the natural forest structure of the stands. Nothofagus betuloides forests have high spatial variability in regeneration without a clear correlation with overstory, and could be related to location of the stands in the landscape. The objective was to evaluate the influence of macro- and micro-variables over regeneration dynamics in old-growth N. betuloides forests, considering the effect of landscape (altitude and influence of the sea) and microenvironment conditions in the forest floor (closeness to trees, pits, understory cover type and bare soil). A total of four sites and 24 stands were sampled including forest structure, regeneration, understory cover and microclimate variables. Macro- (landscape) and micro- (microenvironment conditions in the forest floor) variables influenced over regeneration dynamics. Natural regeneration values (0.17 million ha−1 in the drier site vs. >4.52 million ha−1 in the other sites) not greatly depended on forest structure variables, but they were related to soil moisture (14% vs. 29–36% volumetric soil water content). Microenvironment conditions in the forest floor determined the recruitment as well as regeneration density, age and distribution of seedlings, whereas different soil moisture were related to each microenvironment type, generating positive (bare soil, ferns and mosses growing in turfs) or negative (mosses growing in mats, pits and proximity of the overstory trees) effects over regeneration, according to the soil moisture levels. These findings can be used to understand the functional integrity of the old-growth forest ecosystems and to propose silvicultural prescriptions to ensure regeneration recruitment and maximize growth potential in N. betuloides forests.
Effect of Dietary Lactosucrose on Faecal Flora and Faecal Metabolites of Dogs

The effects of lactosucrose on faecal flora and faecal metabolites, were studied in eight shepherd dogs fed 1.5 g of lactosucrose/each/day for 2 wk. During lactosucrose administration, the levels of bifidobacteria expressed as log 10 no./ g of stool were increased significantly ( P < 0.05) from 8.9 ± 0.5 to 9.4 ±0.4 (mean ± SD), while the levels of Clostridium perfringens decreased significantly ( P < 0.05) from 6.0 ± 1.2 to 4.4 ± 1.1 and 3.1 ± 0.8. No detectable change occurred in the levels of other organisms throughout the experimental periods. Faecal concentrations of ammonia, phenol, indole, skatol, ethylphenol and butyric acid were significantly ( P < 0.05) reduced from 427.4 ± 288.6 μg/g to I72.5 ± 84.5 μg/g, from 49.2 ± 25.7 μg/g to 25.9 ± 8.3 μg/g, from 34.4 ± 16.0 μg/g to 18.9 ± 9.2 μg/g, from 3.0 ± 2.1 μg/g to 1.3 ± 0.5 pg/g, from 8.5 ± 9.3 μg/g to 0 μg/g, and from 2.56 ± 0.98 mg/g to 1.53 ± 0.78 mg/g respectively on day 14 of lactosucrose administration compared to pre-administration. The water content of the faeces increased significantly ( P < 0.05) from 74.3 ± 2.8 per cent to 77.8 ± 1.2 per cent and 76.9 ± 1.5 per cent during administration, but the pH values decreased only slightly. The odour of the faeces decreased remarkably during lactosucrose administration. Keywords: Ammonia; Dog; Intestinal flora; Lactosucrose; Metabolic products.
Some Characteristics of Simple Types of Predation and Parasitism

In an earlier study (Holling, 1959) the basic and subsidiary components of predation were demonstrated in a predator-prey situation involving the predation of sawfly cocoons by small mammals. One of the basic components, termed the functional response, was a response of the consumption of prey by individual predators to changes of prey density, and it appeared to be at least theoretically important in population regulation: Because of this importance the functional response has been further examined in an attempt to explain its characteristics.
NAD+-malic enzyme affects nitrogenase activity of Mesorhizobium loti bacteroids in Lotus japonicus nodules

A gram-negative bacterium, Mesorhizobium loti, contains a NADP+-malic enzyme (mlr5329) and a malate oxidoreductase (mlr0809) in the genome. We have screened transposon-induced mutants from the signature-tagged mutant library to survey their roles in nodule nitrogenase activity. The nodules induced by malate oxidoreductase mutants failed to fix N2, although NADP+-malic enzyme (NADP+-ME) mutants induced nodules exhibiting no change in nodule nitrogenase activity. When malate-degrading enzyme activities were compared between malate oxidoreductase mutants and wild-type M. loti, NAD+-malic enzyme (NAD+-ME) activity was decreased significantly in malate oxidoreductase mutants, suggesting it is an NAD+-ME mutant. We found that NADP+-ME was not required for N2 fixation. The fact that significant accumulations of sucrose, starch granules and malate were observed in the nodules induced by malate oxidoreductase mutant suggests that low nitrogenase activity of the nodules resulted in photosynthate accumulation. These data suggest that this malate oxidoreductase has a similar function to NAD+-ME in both Bradyrhizobium japonicum and Sinorhizobium meliloti.
CLN3P, the Batten's disease protein, is a novel palmitoyl‐protein Δ‐9 desaturase

Batten's disease, one of the most common recessively inherited, untreatable, neurodegenerative diseases of humans, is characterized by progressive neuronal loss and intraneuronal proteolipid storage. Although the gene for the disorder was cloned more than a decade ago, the function of the encoded protein, CLN3P, has not been defined thus far.
Mycobacteria Induce IFN-γ Production in Human Dendritic Cells via Triggering of TLR21

IFN-γ is of central importance for the induction of robust cell-mediated immunity and for the activation of APC. Recent studies using experimental murine systems have now suggested a fundamental role for APC-derived IFN-γ during infection with intracellular pathogens. It is currently unknown whether human dendritic cells (DC) can respond to bacterial stimulation with production of IFN-γ. To test this question, we used human monocyte-derived DC stimulated by Mycobacterium bovis bacillus Calmette-Guérin as a model system. We demonstrate production of IFN-γ mRNA and protein on the single cell level. IFN-γ in DC cultures was not simply produced by contaminating lymphocytes because production of DC-IFN-γ could also be demonstrated in highly purified DC cultures containing virtually no T, B, and NK cells. TLR2 was identified as a key receptor involved in triggering production of DC-IFN-γ. Interestingly, DC-IFN-γ seems to participate in an autocrine DC activation loop, and production of DC-IFN-γ could be enhanced by costimulation of DC with IL-12/IL-15/IL-18. In conclusion, we have demonstrated production of IFN-γ by human DC on the single cell level, identified TLR2 as a pattern recognition receptor involved in this process, and elucidated some of the functional consequences of autocrine IFN-γ production by human DC.
Characterisation of 57 novel microsatellite markers from the goose (Anser cygnoides) genome

Fifty-seven polymorphic loci were isolated from a microsatellite-enriched goose (Anser cygnoides) genomic library. The number of alleles per locus ranged from 2 to 10. The expected and observed heterozygosities ranged from 0.05 to 0.95 and from 0.04 to 1.00, respectively. Forty-seven out of 57 loci conformed to the Hardy–Weinberg equilibrium, and no significant linkage disequilibrium was found in the pairwise comparisons among the 57 loci. The microsatellite markers isolated and characterised in this study will contribute to the construction of a genetic map and mapping of quantitative trait loci in geese, as well as to phylogenetic studies of this species.
Greenhouse Assessment of Seedling Reaction to Tan Spot in Synthetic Hexaploid Wheat

Decreased tillage combined with limited use of rotation crops in the southern Great Plains has led to an increase in the incidence and severity of tan spot of winter wheat (Triticum aestivum L.). This has prompted an aggressive germplasm search for resistance to tan spot, caused by Pyrenophora tritici-repentis (Died.) Drechs. Although genetic resistance is used to help control tan spot, few commercial lines in the southern Great Plains contain highly effective resistance. Here, we report on a greenhouse assay appropriate for quantitative and precise assessment of tan spot reaction, with application to a novel collection of synthetic materials. Our objectives were to (i) identify new sources of resistance and partition the phenotypic variation in tan spot reaction and (ii) validate the quantitative visual assay using digital methods. More than one-half of the 94 synthetic hexaploid wheat accessions assayed showed a percentage leaf infection level not significantly different from that of the resistant check, 'Red Chief' (20%). Visual estimates of infected leaf area were highly correlated with digital estimates (r = 0.90, P < 0.01). Repeatability on an accession-mean basis was moderately high (0.81), but not without rigorous sampling from 10 replicates, two plants per replicate, and three leaves per plant. Using the described assay, a large amount of genetic material can potentially be discarded for undesirable susceptibility to tan spot as a prelude to more costly field discrimination for varying levels or types of resistance.
Phylogenetic Relationships between Ulva conglobata and U. pertusa from Jeju Island Inferred from nrDNA ITS 2 Sequences

In this study the length of ITS2 from four species of the Ulvaceae in Jeju Island varied between 167 and 203 bp. The resuits of this investigation showed that two genus, Ulva and Enteromorpha are grouped in a monophyletic assemblage with 100% bootstrap support in all phylogenetic trees. However, a thorough eamination of these characters from representatives does not provided a way to identify any unique morphological features of clasdes in this tree. This study reveals that Ulva conglobata and Ulva pertusa belong to one clade in the phylogenetic tree with the samples from Jeju Island, Korea.
Qualitative and quantitative analysis of the ovarian maturation process of Penaeus vannamei after a production cycle

Summary The present study analyzes the longitudinal and transversal organization of ovaries of Penaeus vannamei during maturation. For this purpose, oocyte diameter and proportion of area occupied by each oocyte class were quantified on the left and right sides and on five zones of the ovaries: anterior lobe, thoracic lobe, first abdominal segment, middle part of the abdominal lobe, and distal part of the abdominal lobe. Ovaries in vitellogenic (early and late) and cortical ovarian stages were considered for this analysis. The qualitative and quantitative analysis revealed that there were no differences in the left or right side and that only the zone of the first abdominal segment was clearly different from the other ones. When grouping data in cephalothoracic and abdominal regions, several differences were found, indicating a more advanced vitellogenic development in the cephalothoracic region. Thus, the homogeneous development of ovaries that is generally assumed in penaeid shrimps could have some limitations if a detailed analysis of oocyte development is needed.
ALLOZYME SURVEY AND RELATIONSHIPS OF LIMNOPORUS STÅL SPECIES (HETEROPTERA: GERRIDAE)

Abstract Five species of Limnoporus Stål (L. canaliculatus [Say], L. dissortis [Drake and Harris], L. nearcticus [Kelton], L. notabilis [Drake and Hottes], and L. rufoscutellatus [Latreille]) were each sampled at 20 electrophoretic loci. Twofold differences among species in mean heterozygosity appear to be unrelated to presence of wing dimorphism. Low heterozygosity in some populations within species may reflect geographic isolation. There were substantial differences in allele frequency among, but not within, species. Limnoporus rufoscutellatus from western Europe and L. nearcticus from Alaska were the most similar pair of species, with a Nei’s standard genetic identity that is generally found only between populations of the same species. Limnoporus canaliculatus was the most divergent species, and the relationship among L. dissortis, L. notabilis, and the L. rufoscutellatus – L. nearcticus pair is resolved as a trichotomy. Résumé Cinq espèces de Limnoporus Stål (L. canaliculatus [Say], L. dissortis [Drake et Harris], L. nearcticus [Kelton], L. notabilis [Drake et Hottes] et L. rufoscutellatus [Latreille]) ont été échantillonnées à 20 loci. Des différences interspécifiques de l’ordre du double existant au niveau de l’hétérozygosité n’ont pas pu être imputées au dimorphisme alaire. Au niveau intraspécifique, l’isolation géographique de certaines populations pourrait expliquer leur faible degré d’hétérozygosité. On a noté des différences substantielles concernant la fréquence de certains allèles au niveau interspécifique, mais pas au niveau intraspécifique. Limnoporus rufoscutellatus d’Europe occidentale et L. nearcticus d’Alaska constituent la paire d’espèces les plus semblables, avec une valeur du standard d’identité génétique de Nei caractéristique de populations d’une même espèce Limnoporus canaliculatus était l’espèce la plus divergente, et la parenté entre L. dissortis, L. notabilis, et la paire L. rufoscutellatus – L. nearcticus se résout à une trichotomie.
The Effect of Temperature On Larval Fishes

The influence of temperature on fish eggs and larvae is briefly described from an autecological viewpoint. Temperature may have lethal or sub-lethal effects as well as pacing metabolism, other physiological responses and behaviour. It influences body size, growth, differentiation of muscle and meristic characters. Increase of temperature, as would occur with global warming, will change the timing of ecological events such as the spring plankton outburst so influencing the match or mismatch of larvae with their food supply and their predators.
Summary of findings from a participant country pollen beetle questionnaire

Un questionnaire a ete envoye a tous les pays participants pour rassembler des informations de base sur la culture du colza et sur les meligethes (Meligethes aeneus). Le but etait de trouver des informations sur l'utilisation de seuils, la disponibilite de substances actives et, le cas echeant, sur l'annee ou la resistance a ete observee la premiere fois. Un resume des principales conclusions du questionnaire est presente. Au total 20 pays ont repondu et la resistance des meligethes a ete signalee dans 12 de ces pays. Les informations presentees montrent la gamme des substances actives et les doses recommandees, la frequence de l'utilisation des insecticides sur colza et l'annee de signalement de la resistance.
A novel method, based on lithium sulfate precipitation for purification of chicken egg yolk immunoglobulin Y, applied to immunospecific antibodies against Sendai virus.

Egg-laying hens were immunized with Sendai virus (SV) that had been grown in chicken embryos. TheÂ titres of immunospecific SV antibodies varied from log212 to log216 during the 5-month immunizationÂ period and total immunoglobulin Y (IgY) concentrations varied from 1.6 to 4.0 mg per ml of egg yolk. Â Two IgY purification methods based on salt precipitation using lithium sulfate or sodium citrate wereÂ developed. These methods were compared with two other purification methods based on polyethylene glycolÂ (PEG) precipitation and chloroform extraction, respectively in terms of yield, total protein content, IgYÂ concentration and immunospecific anti Sendai IgY activity. The total protein and IgY contents when purifiedÂ by chloroform were 1.4-2.8 times and 1.3-2.3 times higher, respectively than in corresponding preparationsÂ purified by the other methods. However, the proportion of nonsense proteins was approximatelyÂ 10% higher in the IgY preparation purified by chloroform than in those purified by salt precipitation. TheÂ immunospecific IgY activity recorded in the preparations from the new salting out methods was lowerÂ compared with the PEG and chloroform purification methods. However, the purity analysis of IgY by sodiumÂ dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) demonstrated that IgY purified withÂ lithium sulfate contained only two major components with molecular weights of 40 kDa and 66 kDa andÂ one minor protein component of 45 kDa. By contrast, IgY extracted with ammonium sulfate, which is aÂ classical method used to obtain purified IgY, contained two major protein of 40 kDa and 66 kDa and atÂ least three less intense protein bands corresponding to proteins of molecular weights 31.4 kDa, 33.5 kDaÂ and 45 kDa. The results indicate that the purification of IgY by lithium sulfate results in very pure IgY inÂ high quantities (94% +/- 5% of total egg yolk protein). Â
Competitive Nucleation in Nanoclusters

Nucleation is the primary mechanism by which systems change phase and it plays a major role in the formation of new materials in nature and industrially. In particular, experiments and molecular dynamic simulations have shown that nanoclusters, at the same initial conditions, freeze to different structures through a competitive process. Understanding the mechanism of nucleation requires a knowledge of the reaction coordinate, which consists of a set of variables that accurately describe the formation of the critical nucleus. In classical nucleation theory (CNT), the embryo size is solely used as the reaction coordinate, but this does not capture the formation of different structures in a competitive nucleation event. Competitive nucleation is modeled using a two dimensional Potts model undergoing heterogeneous nucleation on to a nanoscale impurity. The rates of formation of the different stable phases are calculated using transition state theory and compared with the rates obtained from the mean first passage time and survival probability methods. Transition state theory is shown to predict the rates to the different structures under various condition when the nucleation barrier is correctly normalized relative to the metastable state. A multiple paths maximum likelihood analysis, (MPMLA), is developed to extract accurate reaction coordinates to the different phases. The results show that the linear combination of size and surface area of a given component is the accurate variable that describes the transition to the phase. Molecular dynamics simulations are used to study the competitive freezing of gold nanoclusters for a range of cluster sizes and temperatures. Measuring the probability of observing each cluster type in an ensemble of freezing events, along with the overall rate at which liquid drops freeze to any structure, allows the rate of formation for each structure to be calculated. The rate of formation of icosahedral structures is about an order of magnitude higher than the rates for other structures. Also, as the size of the cluster increased, the rate of formation of icosahedral structure decreased while that of decahedral and FCC structures increases. The MPMLA is applied to the transition path ensembles to obtain the best reaction coordinate for the different transitions. Order parameters such as size, the Steinhardt bond orientational parameters, local order parameters such as Qe, ratio of local atom type in the largest embryo, and structural order parameters are tested as reaction coordinates. A linear combination of
Testes size, ejaculate quality and sperm competition in birds

The relationship between testes size, ejaculate quality (volume, sperm concentration, number of sperm per ejaculate) and sperm competition in birds was analysed using data collected in artificial insemination studies. I hypothesized that ejaculate quality, because of natural selection, should be superior in species with intense sperm competition compared with other species. In regression analyses, testes weight increased with body weight, with an exponent less than one, and ejaculate volume increased with testes weight with an exponent not significantly different from one, whereas sperm number per ejaculate increased with testes weight with an exponent larger than one. Species with relatively large testes also produced ejaculates with a high sperm concentration. Monogamous species with a relatively low intensity of sperm competition copulate rarely, but deliver ejaculates with a relatively large number of sperm. Monogamous species with a high intensity of sperm competition copulate frequently, but produce ejaculates with a relatively small number of sperm. Males of polygynous species, which also experience intense sperm competition, copulate rarely with specific females, but produce many ejaculates per male each with a relatively small number of sperm.
Genomic organization and promoter characterization of RANTES, MIP-1β like and MCP-like CC chemokines of domestic duck (Anas platyrhynchos).

The duck immunology is gaining more interest in recent years since ducks have been identified as “Trojan horse” of highly pathogenic avian influenza. In the present study, we characterize the gene and promoter regions of three CC chemokines from domestic duck. Analysis of the gene revealed significant similarity with chicken and mammalian chemokine genes with three coding exon and two intron pattern. Though the exons are highly conserved with respect to corresponding chicken chemokine genes, introns revealed low identity. Promoter regions of duck RANTES and MCP-like chemokines were amplified by Genome walking method. Analysis of the 500 bp upstream nucleotide sequences of ATG (translational start site) of RANTES and MCP-like chemokine revealed a number of putative binding sites for transcription factors. Comparative analysis of RANTES promoter with human and chicken sequences revealed conserved TATA box, NFkB binding site and transcription start site. The predicted transcription start site and TATA box are also conserved in duck and chicken MCP-like chemokine sequences. The present study shows that the over all organization of gene and putative transcription factor binding sites in the promoter regions of these three chemokines were conserved with respect to chicken and human sequences indicating these molecules of innate immune system is conserved in the process of evolution.
Life History Studies on the Genus Trillium (Liliaceae) VI. Life History Characteristics of Three Western North American Species and Their Evolutionary‐Ecological Implications

Life history characteristics of three western North American Trillium species, i. e. , T. ovatum (Pedicellate-group), T. albidum and T. petiolatum (both Sessile-group), were critically investigated and compared. The stage-class structure, based upon leaf area, of populations of the three species all were indicative of stable populations, even though the species occurred in contrastingly different habitat conditions. Trillium ovatum occurred in the deep shade of mesic coniferous forests on mountain ridges or slopes. Trillium albidum was found in exceedingly damp sandy-loam soils in deciduous forests developed on the lowland flood plains. Trillium petiolatum occurred on dry rocky or gravelly shrub-dominant areas. There was a gradual but conspicuous decrease in the number of individuals in the early juvenile stages, followed by similar numbers of plants in the intermediate stages and mature flowering stages. Recruitment of offspring appears to be exclusively dependent upon sexual reproduction in all three species, since none of the species formed vegetative offshoots as found in some sessile group species occurring in eastern as well as western North America. Analysis of spatial distributions within the populations of T. ovatum and T. petiolatum revealed successive changes from aggregated (juveniles) to random (intermediate stages), and overdis-persed (flowering plants) distributions. The evolutionary-ecological relationships of these three species are compared with those of 27 other Trillium species.