Miracle-dz/UniFAR-FTUs huggingface dataset:
On the maintenance and origin of alternative strategies in the Ruff Philomachus pugnax

This paper has tried to answer the question of how the independent and the satellite strategy of the Ruff originated and has been maintained during evolution. It is not intended as a report of a piece of completed research but gives a number of tentative, but testable hypotheses. Data are presented that independent males and satellites are equally successful in copulating, provided that almost all copulations occur on leks, and independent males and satellites spend an equal proportion of their time on leks. The extent that males with the different strategies are attached to leks is analysed. Within the group of independent males, considerable differences exist: a resident male is strongly attached to only one particular lek and a marginal male seems to sample many leks. A satellite male behaves intermediately: he is attached to a limited number of leks. The mechanism for the maintenance of both strategies could not be explained by competition for resources (copulations). Contests between independent males and satellites are asymmetric, the satellite being the weaker contestant. The mechanism seems to be due to enlarging the accessibility of the resource by cooperation between both strategies. The ideas on the origin of the system are based mainly on the behaviour of females. There is no relation between the distribution of leks and the size of a female's foraging area, except that most leks are situated along the migration route. It further seems that the number of copulating females in the Netherlands is larger than the number of males on leks, but the number of breeding females is much lower. It is suggested that many females copulate on migration, which is related to extreme breeding conditions in the north of the range. Apart from a change in the sex ratio from south to north, a change in the proportion of satellites is also predicted. The origin of the system is ascribed to the incompatibility between favourable food conditions for chicks and further possibilities for inter-male competition on leks in the same area. The satellite strategy is considered as being derived from a non-competitive strategy accompanying females on migration. In the phase of cooperation between resident and satellite males, individual recognition became important. This could be the factor underlying the evolution of white plumages in satellites and the extreme plumage diversity in independent males.
Volatile odour components and sensory quality of fresh and processed mandarin juices

Twelve volatile compounds were quantified by gas chromatography/mass spectrometry in juices from two Spanish mandarin varieties, Fortuna and Clemenules. Fresh Clemenules juice contained a higher amount of total volatile compounds (61.1 ± 1.1 mg L−1) than fresh Fortuna juice (48.8 ± 2.5 mg L−1), with D-limonene (97.1%), myrcene (1.7%), sabinene (0.5%), α-pinene (0.3%) and linalool (0.3%) being the predominant compounds. Pasteurisation of the mandarin juices (20 s at 98 °C) caused a significant reduction (∼12%) in vitamin C concentration. On the other hand, vitamin C was stable during storage of the juices for 60 days in aseptic tanks at 2 °C. Volatile compounds, however, were more affected by storage in aseptic refrigerated tanks (2 °C) than by heat treatment. Pasteurisation caused a mean decrease in the total concentration of volatile compounds of about 18%, while, after a storage time of 60 days, 36% of total volatiles present in the juices after pasteurisation were lost from both Fortuna and Clemenules juices. Significant reductions in the concentrations of D-limonene, myrcene, sabinene, α-pinene and linalool were found, while those of α-terpineol and terpinen-4-ol increased. Copyright © 2006 Society of Chemical Industry
SYNTHESIS, IN VITRO ANTIBACTERIAL, TOXICITY AND MOLECULAR DOCKING ANTICANCER ACTIVITY OF NOVEL N-[(2-CHLOROQUINOLIN-3-YL) METHYLIDENE]-2-ANILINE SCHIFF'S BASES

Objective: Synthesis of N -[(2-chloroquinolin-3-yl) methylidene]-2-aniline schiff bases (3a-j) and to study their in vitro antibacterial activity and in silico study towards cancer and malarial proteins. Methods: Various N -[(2-chloroquinolin-3-yl) methylidene]-2-aniline schiff bases ( 3a-j) were synthesized by using 2-chloro-3-formyl quinoline and different anilines in presence of acetic acid as catalyst. All the new compounds were characterized by 1 H-NMR, [13]C-NMR and LCMS analysis. The compounds 3a-j was subjected to antibacterial activity. In silico molecular properties were predicted using various online cheminformatic tools, the binding interactions with Human DNA topoisomerase I and Plasmodium falciparum lactate dehydrogenase proteins was studied through molecular docking and Irinotecan and mefloquine were used as reference drugs. Results: Fairly good yield of N -[(2-chloroquinolin-3-yl) methylidene]-2-aniline schiff bases (3a-j) were synthesized by convenient and economical procedure. The preliminary in silico pharmacokinetics study reveals that the compounds 3a-j shows excellent drug like property. The toxicity profile of compounds 3a-h was found safe. The compounds 3a-j was exhibited promising MIC values against the both S. aureus and E. coli . Similarly the docking results predict that the compound 3d shown highest interaction by forming two hydrogen bonds against the cancer protein with the interaction energy-20.696 kcal/mol. Compound 3c exhibits highest dock score of-45.703 kcal/mol with two hydrogen bonds against malarial protein. Conclusion: From the results of docking studies of N -[(2-chloroquinolin-3-yl) methylidene]-2-aniline schiff bases (3a-j), it has been concluded that the compounds were found to exhibit multifunctional lead property, hence these compounds are worth to be considered as potential lead molecules for further study. Keywords: N -[(2-chloroquinolin-3-yl) methylidene]-2-aniline, 2-chloro-3-formyl quinoline, antibacterial, Molecular docking, ADMET
ArgR–promoter interactions in Corynebacterium glutamicum arginine biosynthesis

Arginine biosynthesis in Corynebacterium glutamicum is currently poorly understood. A better understanding of its regulation will aid in the engineering of overproducing strains. A transcriptional analysis of the argCJBDFRGH genes and construction of argR deletion mutant confirmed the role of ArgR as a negative regulator of arginine biosynthesis. Increasing the copy number of the argC promoter region caused arginine levels to increase twofold. Electrophoretic mobility shift assays using recombinant ArgR revealed in vitro binding with dissociation constants between 200 and 250 nM to the putative promoter regions of argC and carAB. In contrast, ArgR did not bind in vitro to the putative argG promoter region. Binding of ArgR to the argC and carA promoter regions was prevented by double‐stranded competitor oligonucleotides containing motifs resembling the universal ARG box consensus sequence (two in the case of the argC promoter region and one in the case of the carA promoter region). A single ARG box was identified in the carA promoter region. The consensus sequence for the three C. glutamicum ARG box motifs was 5′‐HMT GMA TSW ADW WTW TDY‐3′ and the core sequence (underlined) is well conserved throughout the C. glutamicum genome and located preceding several putative ArgR targets.
Molecular characterization of the sheep mitochondrial genome

Summary Mitochondrial DNA (mtDNA) from 240 sheep of 10 breeds and several wild sheep was analysed in an RFLP study with 14 restriction enzymes. Phylogenetic analyses revealed two major domestic sheep mtDNA lineages, and the mitochondrial genome of one sheep from each lineage was mapped and cloned. The complete nucleotide sequence of one of these mtDNAs, which comprises 16616 bp, was determined and 7160 bp were comparatively sequenced. The D-loop region and the genes encoding Cyt. b, ND 3, CO III, 8 tRNAs (Ala, Arg, Asn, Gln, Gly, Ile, Met, Trp) as well as the origin of L-strand replication were completely characterized. Partial sequence data were obtained from ND1, ND2, ND41, ND5, ATPase 6, 12s RNA and 5 tRNA (Cys, Glu, Phe, Pro, Thr) genes. Several nucleotide substitutions, some of which cause changes in the predicted amino acid sequences, were observed. Statistical analysis showed significant mtDNA effects on birthweight of lambs, but maternal contributions could not be completely separated from cytoplasmic effects. Zusammenfassung Molekulare Analyse des mitochondrialen Genoms von Schafen Die mitochondriale DNA (mtDNA) von 240 Schafen aus 10 Rassen sowie verschiedener Wildschafe wurde in einer RFLP-Studie mit 14 Restriktionsenzymen untersucht. Die phylogenetische Analyse zeigte zwei Haupt-mtDNA-Linien beim Hausschaf auf. Die mitochondrialen Genome von einem Schaf aus jeder dieser Linien, wurden kartiert und kloniert. Die Nukleotidsequenz einer mtDNA, die 16616 bp umfast, wurde vollstandig bestimmt und 7160 bp vergleichend sequenziert. Die D-Loop-Region sowie die Gene fur Cyt. b, ND 3, CO III, 8 tRNAs (Ala, Arg, Asn, Gln, Gly, Ile, Met, Trp) und der L-Strang-Replikationsursprung wurden vollstandig verglichen. Teilsequenzvergleiche konnten im Bereich der ND 1-, ND 2-, ND 4L-, ND 5-, ATPase 6-, 12s RNA-Gene sowie verschiedener tRNA-Gene (Cys, Glu, Phe, Pro, Thr) durchgefuhrt werden. Dabei wurden Nukleotidsubstitutionen beobachtet, die teilweise Veranderungen in den abgeleiteten Aminosauresequenzen zur Folge haben. Die statistische Analyse ergab signifikante mtDNA-Effekte auf das Merkmal Geburtsgewicht, die jedoch nicht vollstandig von anderen maternalen Einflussen getrennt werden konnten.
Propriedades físico-mecânicas de painéis LVL produzidos com três espécies amazônicas

This work aimed to evaluate the physical-mechanical performance of laminated veneer lumber (LV) produced with different compositions of tropical Amazonian species and Pinus oocarpa. Three tropical species were used: Cordia goeldiana Huber. (Freijo), Parkia gigantocarpa Ducke (Faveira) and Brosimum parinarioides Ducke (Amapa doce). For comparison, Pinus oocarpa wood obtained from an experimental stand was used. Three types of veneer combination were evaluated: (i) one species; (ii) the three Amazonian species combination and (iii) combination of Amazonian species with Pinus oocarpa. The acoustic propagation velocity was also evaluated with the stress wave timer for correlation between dynamic modulus of elasticity (MOEd) and static modulus of elasticity (MOEs) of the panel. Panels produced with Amazonian species presented lower water absorption than Pinus oocarpa panels. Regarding the mechanical properties, the lowest strength was verified for "faveira" panels. There was no statistical difference among panels in glue line shear strength. The stress wave timer could be used for prediction of MOEs by using MOEd.
Effet du stress salin sur la croissance, l'accumulation de la proline et des sucres solubles sur des plantules porte-greffe de Pistacia atlantica Desf. subsp. atlantica

L'effet du stress salin sur quelques parametres physiologiques et biochimiques des plantules de Pistacia atlantica Desf. subsp. atlantica a ete etudie sous conditions controlees. Les plantules ont ete cultivees dans des pots et irriguees avec la solution nutritive de Hoagland durant 120 jours. Ensuite, les plantules ont ete separees et traitees a 100, 200 et 400 meq·l-1 de NaCl + CaCl2 pendant 10 jours. Les sels sont rajoutes a la solution nutritive de Hoagland. Il a ete etabli que l'application de ces concentrations de sels cause un stress aux plantules de pistachier qui s'exprime par la reduction de croissance au niveau des tiges et des racines. La teneur en proline des feuilles croit significativement avec la concentration du milieu en sels pour tous les traitements. La teneur maximale de l'acide amine est observee sous le traitement a 400 meq·l-1 pour l'ensemble des plantules. Par ailleurs, une difference significative pour la teneur relative en eau (RWC) est enregistree sous l'effet 400 meq·l-1 de NaCl + CaCl2 ; en revanche, les plantules stressees a 100 meq·l-1 ne manifestent aucune influence du sel sur la teneur relative en eau. L'accumulation des sucres solubles pour le lot stresse a 100 meq·l-1 est superieure a celle du lot stresse a 200 meq·l-1. Aussi, l'effet de la concentration de 400 meq·l-1 de NaCl + CaCl2 provoque une accumulation de ces composes glucidiques. On constate qu'apres sept jours de stress, la concentration en sucres solubles croit en fonction de la concentration saline. Le taux de proline et de sucres reducteurs chez le porte-greffe P. atlantica subsp. atlantica est tres eleve. Les resultats obtenus au terme de cette etude montrent que P. atlantica subsp. atlantica peut etre utilise comme porte-greffe de Pistacia vera, car il est tolerant a la salinite.
Animal Models for Tumor Immunology

D uring most of the past century, promises of cancer immunotherapy were often regarded as fanciful fictionalization, due to the lack of molecular characterization of putative tumor antigens. This view seems painfully old-fashioned now, as so many tumor antigens have been molecularly defined over the past decade, due to technical advances such as expression cloning and the identification of immuno-dominant antigenic epitopes through biochemical means. A paucity of tumor antigens is therefore not the bottleneck for the development of immunotherapeutical procedures, as so pointedly phrased by Boon and Old (1997) when they lamented in the title of a review on tumor immunology: “A wealth of tumor antigens recognized by T cells—and now what? ”. Indeed, identification of antigenic epitopes on neoplastic cells represents only a beginning, be it by T cells or by B cells. Nevertheless, it is an important beginning which points the way towards the future: rather than continuing to wonder whether tumors express potential targets for the immune system, tumor immunologists can now legitimately dedicate their efforts to resolving why anti-tumor immunity so often fails. Also, there can be little doubt that attempts to immunize patients against defined antigens or nonspecifically improve the immune system’s functioning in cancer patients may be valuable, and a number of different interventions aimed towards that end are currently in progress (reviewed in Pardoll, 1998). In addition, since it is not for lack of antigenicity that most tumors fail to trigger the immune system, much effort is devoted to seeking a better understanding of the regulation of both T cell and B cell mediated anti-tumor immunity, as well as of the role of the innate immune system, and of the regulation of antigen-presenting cell function. It is in this context that a chapter on animal models for studying anti-tumor immunity is appropriate at this time.
Analysis of sequence variations of Calpastatin gene of inhibitory region in Cyprinus carpio var. communis

Calpastatin gene, an endogenous inhibitor of calpain enzyme, is important for maintaining muscle texture and postmortem degradation of myofibrils. Present study was carried out for the identification of SNPs in the inhibitory region of calpastatin gene in common carp Cyprinus carpio var. communis for genetic improvement of genotypes. Primers were designed from cDNA sequences of Atlantic salmon (AFV08638.1), Rainbow trout (NP_001118010.1) and cDNA as well as genomic DNA sequences of Zebra fish (NM_001130591.2) to amplify the CAST gene in Common carps. Four exons (13, 14, 19 and 20) and intervening introns demarcated by zebrafish genomic data base of 316 and 311 base pairs were amplified. The sequencing and insilico translation was done for the identification and characterization calpastatin. The results showed that Cyprinus carpio var. communis have two highly conserved sequence motifs DTLPP, GYR repeats in the inhibitory domain which corresponds to the exon-14 and exon-20 of Zebra fish. The single amino acid change in the inhibitory motif G (GGT)/X (X = Q 394aa (CAA) in Danio rio , Sequence ID: ref|NP_001124063. 2, E 491aa (GAG) in Salmo salar , Sequence ID: ref|NP_001167162. 1, K 223aa (AAG) in Onchorhyncus mykiss long isoform, Sequence ID: ref|NP_001118010. 1, and E 54aa (GAG) in Onchorhyncus mykiss short isoform, Sequence ID: ref|NP_001118117. 1) have role in the diversification of inhibitory activity of the protein due to species diversification. Another interesting characteristic feature of the inhibitory motif of exon-20 in Common carps having Glysine (GGT) amino acid and rest instead of Glutamic acid (GAG) at 548 th aa in Danio rio and 689 th aa Salmo salar . It was also observed that Common carp shear (94-95%) CAST gene sequence with Zebra fish while as only (52-54%) sequence homology was observed with Atlantic salmon and Rainbow trout due to species divergence. Phylogenetic analyses of different species revealed telosts are more primitive than tetrapods. Variations observed in inhibitory domain play important role in postmortem proteolysis. Development of markers for meat tenderness and fillet quality based on the mutations in the inhibitory region will help in selecting genotypes of better fillet/texture quality.
Nonkin Associations in Wild Boar Social Units

Abstract We investigated the social organization of wild boars (Sus scrofa) using genetic and spatial data from a study population in Tuscany, Italy. In total, 120 wild boars of different sexes and age classes were captured and monitored from 2002 to 2006. All of them were genetically analyzed by using 10 polymorphic microsatellites (HE = 0.693, k = 6.6) and a matrix of pairwise relatedness was calculated. In addition, a reference sample of fully related individuals was created by genotyping 11 adult females and their fetuses (n = 56). Spatial data were gathered for 65 animals that had been fitted with either radiocollars or ear transmitters. Sixteen social units were identified by capture data and confirmed by observations and telemetry. A correlation between interindividual spatial distance and relatedness was observed only in summer–early autumn and seemed to be associated to the presence of piglets. The prediction of matrilinearity in wild boar social units was not confirmed, because a low degree of relatedness among boars was observed within groups. Aggregations of unrelated adult females (with their litters) were detected in the study population. The high turnover in the population due to human-caused mortality seems to be the main factor responsible for this altered social structure. Accordingly, we suggest that the observed social organization would result from grouping of unrelated survivors that is promoted by the presence of wolves in the area.
Precision and accuracy of flyout counts of the common bent-wing bat (Miniopterus schreibersii)

ABSTRACT Visual flyout count data for the common bent-wing bat Miniopterus schreibersii, collected by a team of observers over two seasons at a disused mine in the Kinglake National Park, south-eastern Australia, was compared with infra-red video footage, collected simultaneously, in order to quantify the precision and accuracy of the observer counts. Bayesian statistical models were used to evaluate the relationship between observer counts and the actual number of bats emerging from the cave, as determined by analysis of the infra-red video footage of the flyout. The accuracy of flyout counts was found to decline with increasing flyout rates, with observers' counts becoming increasingly negatively biased as the rate of bat emergence from the mine increased. In addition, there was evidence of inter-observer variation in the accuracy of the counts. Although the bias in observer counts was relatively small, caution needs to be exercised in interpreting the results of visual flyout counts. We conclude that the use of infra-red video footage for determining numbers is preferable to visual observer counts. The major difficulty in using flyout counts for monitoring is the considerable night-to-night variation in numbers of bats emerging, which could be attributed to variation in the proportion of bats emerging to forage, or to the use of alternative roosting sites by individual bats on successive nights. Both observer error and short-term temporal variation in numbers of emerging bats have the potential to bias population estimates of bats, and need to be properly accounted for if flyout counts are to be used as a tool for population assessment and monitoring.
Evidence for Topographic Control of Tree Spatial Patterning in an Old-growth, Mixed Mesophytic Forest in Southeastern Ohio, USA1

Abstract Analyzing the spatial pattern of individuals within a plant community is useful for inferring the underlying mechanisms and processes governing community organization. Aggregated patterns can be caused by habitat-specificity or dispersal limitation, while overdispersed patterns are often caused by competition or predatory host-specificity. However, few studies have looked at how abiotic influences might drive spatial patterning. Here, we address how topography might lead to differences in tree spatial patterning on a north- and south-facing slope at Dysart Woods. We also look at how species identity, canopy position, and sampling year affect spatial patterning. We found that the spatial distribution of trees was highly aggregated on a south-facing plot, but did not differ from random on a north-facing plot. We attribute these differences largely to the differential dominance of Acer saccharum and Fagus grandifolia on the north and south plots, respectively. Acer saccharum individuals were largely randomly distributed, while Fagus grandifolia individuals were highly aggregated. We also found differences between understory and overstory individuals, with smaller individuals being more aggregated, likely due to life-history or competitive self-thinning processes. Lastly, we observed a surprising change in the scale that aggregation occurred at from 1996 to 2011 on the south plot. In 1996, stems on the south plot were aggregated at distances >3 meters, but only at distances >10 meters in 2011. We found that this reduction in aggregation was largely due to the unusually high mortality rates of Cornus florida and Prunus serotina. We conclude that topography can greatly influence spatial patterning, and that this and other abiotic variables should be taken into consideration in future studies on community structure.
Genome-wide association study of the backfat thickness trait in two pig populations

Backfat thickness is a good predictor of carcass lean content, an economically important trait, and a main breeding target in pig improvement. In this study, the candidate genes and genomic regions associated with the tenth rib backfat thickness trait were identified in two independent pig populations, using a genome-wide association study of porcine 60K SNP genotype data applying the compressed mixed linear model (CMLM) statistical method. For each population, 30 most significant single-nucleotide polymorphisms (SNPs) were selected and SNP annotation implemented using Sus scrofa Build 10.2. In the first population, 25 significant SNPs were distributed on seven chromosomes, and SNPs on SSC1 and SSC7 showed great significance for fat deposition. The most significant SNP (ALGA0006623) was located on SSC1, upstream of the MC4R gene. In the second population, 27 significant SNPs were recognized by annotation, and 12 SNPs on SSC12 were related to fat deposition. Two haplotype blocks, M1GA0016251MARC0075799 and ALGA0065251-MARC0014203M1GA0016298-ALGA0065308, were detected in significant regions where the PIPNC1 and GH1 genes were identified as contributing to fat metabolism. The results indicated that genetic mechanism regulating backfat thickness is complex, and that genome-wide associations can be affected by populations with different genetic backgrounds.