Miracle-dz/UniFAR-FTUs huggingface dataset:
Assigning individual fish to populations using microsatellite DNA markers

New statistical developments combined with the use of highly polymorphic microsatellite DNA markers enable the determination of the population of origin of single fish, resulting in numerous new research possibilities and applications in practical management of fish populations. We first describe three main categories of methods available, i.e. (i) assignment tests and related methods, (ii) discriminant function analysis and (iii) artificial neural networks. In all these, individuals can be assigned to the population from which their multilocus genotypes are most likely to be derived. Assignment tests are based on calculations of the likelihood of multilocus genotypes in populations, based on allele frequencies. Discriminant function analysis is based on multivariate statistics, whereas artificial neural networks formulate predictions through exposure to correct solutions. Assignment tests are the methods of choice when considering genetic data alone, whereas discriminant function analysis and artificial neural networks may be useful when genetic data are combined with, for instance, morphological and ecological data. Assignment tests can be used to assess the genetic distinctness of populations, for discriminating among closely related species and to directly identify immigrants or individuals of immigrant ancestry, and thereby study patterns of dispersal among populations, including sex-biased dispersal. In a conservation context, assignment tests can be used to assess the genetic impact of domesticated fish on wild populations and for determining if extant fish populations are in fact indigenous or descendants from stocked fish or strayers, and they can be applied in forensics, for instance to reveal poaching. Assignment tests are at present most useful for studies of freshwater and anadromous fishes owing to stronger genetic differentiation among populations than in marine fishes. However, some genetically divergent populations of marine fishes have been discovered, which could be used as natural laboratories for studying dispersal and gene flow. It is foreseen that ongoing developments in statistical methods, combined with improved techniques for screening large numbers of loci, will permit assignment methods to become standard tools in studies on the biology of fishes.
Effects of different concentrations of ground oak acorn on growth performance, blood parameters and carcass characteristics of goat kids

The objective of the present study was to evaluate the effect of different levels of ground oak acorn on growth performance, blood parameters and carcass characteristics. Twenty-four goat kids averaging 16.93 ± 1.25 kg initial bodyweight were randomly assigned to four experimental diets in a completely randomised design for 90 days. The experimental diets consisted of (1) 0% oak acorn (control), (2) 8% oak acorn, (3) 17% oak acorn and (4) 25% oak acorn on a DM basis. The goats were slaughtered after 105 days of feeding and carcass characteristics were measured. DM intake increased linearly in small amounts as the level of acorn in the diet increased (P 0.05). There were no significant differences in blood parameters (P > 0.05). Carcass fat depth and abdominal fat weight decreased with increasing ground oak acorn in the diet. Other carcass characteristics were not affected by different levels of ground oak acorn. On the basis of the results of the present study, it may be concluded that ground oak acorn can be used up to 25% in the diets of young goats without any adverse effects on growth performance and carcass characteristics. At this level of acorns, the goats received low concentrations of hydrolysable tannins (11 g/kg DM) in their diet.
A method of estimating the slope of upper bounds of plots of body size and abundance in natural animal assemblages

Plots of species body size versus abundance in natural assemblages of animals often reveal polygonal relationships. Theory predicts that the slope of the upper bound of such polygons will approximate to -0.75, but has never been tested because of the lack of a statistical technique to estimate the slope. We present and test a method whereby the upper bound slope can be measured by dividing assemblage data into size classes, and using the highest abundance in each class to estimate the regression slope. The method accurately estimates slopes from simulated data of known upper bound, and estimates from real and simulated data vary in a similar manner when different numbers of size classes are used. We conclude that this method may be used with confidence to estimate upper bound slopes from polygonal relationships, and gives the first chance to test different hypotheses about the magnitude of such slopes.
A new taxon of birds (Aves) from the Early Cretaceous of Western Siberia, Russia

In recent decades numerous findings, mostly from the Early Cretaceous of China, have changed traditional conceptions about the diversity and evolution of the most ancient Aves. Findings of Mesozoic birds in Russia are extremely rare. Here we describe a new bird from the Lower Cretaceous (Barremian–Aptian, Ilekskaya Svita) Shestakovo-1 locality (southern Western Siberia, Russia), that has also yielded dinosaurs, mammals, crocodiles, pterosaurs and lizards. Mystiornis cyrili gen. et sp. nov. is based on an isolated metatarsus which displays a mosaic of morphological features allowing us to create a new order, Mystiornithiformes. Mystiornis has a fully consolidated (ornithurine-like) gracile metatarsus with a primitive coplanar arrangement of the metatarsals, three separate proximal articular facets, and a uniquely located distal interosseal canal. It also displays diving adaptations previously documented only in Ornithurae.
Spatial and temporal variability of picocyanobacteria Synechococcus sp. in San Francisco Bay

We collected samples monthly, from April to August 1998, to measure the abundance of autotrophic picoplankton in San Francisco Bay. Samples taken along a 160‐km transect showed that picocyanobacteria (Synechococcus sp.) was a persistent component of the San Francisco Bay phytoplankton in all the estuarine habitats, from freshwater to seawater and during all months of the spring‐summer transition. Abundance ranged from 4.6 × 106 to 5.2 ×8 cells L−1, with peak abundance during the spring bloom (April and May) and during July with a persistent spatial pattern of smallest abundance near the coastal ocean and highest abundance in the landward domains of the estuary. The picocyanobacterial component (as estimated percentage of chlorophyll a concentration) was, on average, 15% of total phytoplankton biomass during the summer–autumn nonbloom periods and only 2% of chlorophyll biomass during the spring bloom. This result is consistent with the emerging concept of a gradient of increasing importance of picocyanobacteria along the gradient of decreasing nutrient concentrations from estuaries to the open ocean.
Karyology and karyometric analysis of an Afrotropical freshwater planarian (Platyhelminthes, Tricladida)

Abstract The karyology and karyotype analysis of the Afrotropical species Dugesia aethiopica is reported. A double chromosome complement is displayed in a single individual, triploid (3n ‐ 27 + 1–2 B‐chromosomes) and diploid, (2n = 18 + 0–1 B‐chromosome) with a basic number of n = 9. The occurrence of a double chromosome number, involving both somatic and germ cell lines, fits the condition of a diffuse mosaicism or mixoploidy. The coexistence of heteromorphisms between homologous chromosomes, polysomic and monosomic conditions, and the presence of B chromosomes could be considered a condition of aneuploidy. The constant re‐occurrence of mixoploidy in D. aethiopica represents an adaptive mechanism whose persistence could be favoured by the asexual reproductive mode. The new finding confirms the existence of two different chromosomal lineages in African planarians with n = 8 and n = 9.
Influence of the genomic sequence on the primary structure of chromatin

As an important actor in the regulation of nuclear functions, the nucleosomal organization of the 10 nm chromatin fiber is the subject of increasing interest. Recent high-resolution mapping of nucleosomes along various genomes ranging from yeast to human, have revealed a patchy nucleosome landscape with alternation of depleted, well positioned and fuzzy regions. For many years, the mechanisms that control nucleosome occupancy along eukaryotic chromosomes and their coupling to transcription and replication processes have been under intense experimental and theoretical investigation. A recurrent question is to what extent the genomic sequence dictates and/or constrains nucleosome positioning and dynamics? In that context we have recently developed a simple thermodynamical model that accounts for both sequence specificity of the histone octamer and for nucleosome–nucleosome interactions. As a main issue, our modelling mimics remarkably well in vitro data showing that the sequence signaling that prevails are high energy barriers that locally inhibit nucleosome formation and condition the collective positioning of neighboring nucleosomes according to thermal equilibrium statistical ordering. When comparing to in vivo data, our physical modelling performs as well as models based on statistical learning suggesting that in vivo bulk chromatin is to a large extent controlled by the underlying genomic sequence although it is also subject to finite-range remodelling action of external factors including transcription factors and ATP-dependent chromatin remodellers. On the highly studied S. cerevisiae organism, we discuss the implications of the highlighted ‘positioning via excluding’ mechanism on the structure and function of yeast genes. The generalization of our physical modelling to human is likely to provide new insight on the isochore structure of mammalian genomes in relation with their primary nucleosomal structure.
Mechanics of the startle response in the northern pike, Esox lucius

The thrust produced during an escape response (C-start) of a northern pike, Esox lucius (0.41 m total length, 0.398 kg), an acceleration specialist, is estimated using the Weihs model for fish fast-starts. High-speed cine film records (250 Hz) of pike C-starts were digitized and the angle of attack and displacement of all body sections determined. These parameters were incorporated into the model and thrust was calculated. A comparison of model predictions with values predicted from required forces found six of eight performance parameters to be within 22% for three fast-starts. A lack of significant difference between model estimates and required forces suggests that lift and acceleration forces are the major components of total thrust during C-type fast-starts. The caudal region, including the caudal, anal, and dorsal fins, contributes the most (>90%) to positive total thrust during the propulsive stage (stage 2). High velocities, large angles of attack, and large surface areas of these sections account.
Identification of γA‐like protocadherin expressed during chick development

The protocadherins are calcium‐dependent cell adhesion molecules of the cadherin superfamily that have been described in numerous species. Although less well characterized than classical cadherins, the protocadherins are also thought to facilitate critical cell–cell interactions during embryonic development. We have cloned a novel protocadherin from the embryonic chick utilizing a monoclonal antibody produced against a peanut agglutinin‐binding fraction of cultured chick limb tissue to screen a λZAP cDNA expression library from the stage 25 limb. A 2.8 kb cDNA clone was obtained that encoded multiple cadherin‐like ectodomains. Northern blotting revealed a single 4.6 kb RNA transcript that was highly enriched in the stage 43 chick brain. Utilization of 3′ Rapid amplification of cDNA ends (RACE) identified the entire 2.4 kb reading frame. The chick protocadherin contained five cadherin‐like extracellular repeats and a highly conserved cytoplasmic domain. Amino acid alignment of the extracellular domains revealed marked identity to the human γA protocadherin subfamily. In situ hybridization showed low levels of mRNA localization in several developing chick tissues, but stronger expression in the neural tube and dorsal root ganglia at stage 27. In the stage 43 chick brain, protocadherin mRNA was noted in discrete regions, particularly within the developing optic lobe. As for protocadherins described in other species, these results suggest that this novel γA‐like protocadherin may also play a role in chick neural development. © 2003 Wiley‐Liss, Inc.
Registration of Near‐Isogenic Winter Wheat Germplasm Contrasting in Fhb1 for Fusarium Head Blight Resistance

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Comparative Study on the Synergistic Action of Garlic Synthesized and Citrate Capped Silver Nanoparticles with β-Penem Antibiotics

Resistance to antimicrobial agents by pathogenic bacteria has emerged in recent years and is a major challenge for the health care industry. For developing a cheap broad-active agent that can be applicable against different pathogens, it is necessary to develop an alternative source for normal antibacterial agents. This paper mainly focuses on the combined action of green as well as citrate synthesized silver nanoparticles and β-penem antibiotics, which are β-lactam antibiotics with penem rings. These silver nanoparticles synergistic potential helps in the enhancement of antibacterial activity of broad spectrum antibiotics. The synergistic actions of citrate capped silver nanoparticles (Ag-NPs) were compared with that of garlic (Allium sativum) synthesized silver nanoparticles together with action of antibiotics, ampicillin and amoxyclav, and some of the pathogenic organisms showed an increase in the action of antibiotics.
Mitotic Delay in Root Tips of Peas Induced by Artificial Seed Aging

Pea (Pisum sativum L. `Progress No. 9') seeds were adjusted to 7%, 13%, and 18% moisture content and stored at 10, 21, 32, and 38 C in sealed metal cans for periods of from 2 days to 6 mo. The rate of decline in germinability increased as seed moisture and storage temperature increased. As seed germinability decreased, the speed of germination decreased, and the number of abnormalities of roots and shoots increased. The abnormalities usually resulted in seedling death. The delay in the occurrence of first mitosis was correlated strongly with the decrease in germinability. The activation of cell division following the first mitosis was suppressed in aged seeds compared with unaged control seeds.
Dormancy-induced temporal up-regulation of root activity in calcium translocation to shoot in Populus maximowiczii

To explore seasonality of root functions, we analyzed the concentrations of 8 minerals in leaves of Populus maximowiczii (Japanese native poplar) by inductively coupled plasma atomic emission spectroscopy. These concentrations were used as indices of root mineral translocation activity. In leaves close to the shoot apex, dramatic increases in Ca concentration, and similar but slight increase in Mg and Mn, were observed after the onset of dormancy. Because of the constant concentration of Na, which is not essential for plant growth, the increase of Ca concentration was mainly derived from not by the increase of transpiration rate but by the enhancement of root activity of xylem loading. Leaf Ca concentration in August 2010 was approximately fivefold higher than before dormant bud formation. To investigate the shifts in Ca-translocation activity during dormancy induction, we grew saplings hydroponically under lightand temperaturecontrolled conditions and subsequently analyzed the distribution of Ca absorbed by roots using a Bio-Image Analyzer. In this pulse chase experiment, the enhancement of Ca translocation to the shoot was not observed in early dormancy. This suggested the increase of leaf Ca in early dormancy was caused by the Ca loading into root xylem vessels using the root Ca absorbed before the onset of dormancy. These changes in mineral translocation activities indicate that alterations in Ca distribution are most probably triggered by bud dormancy. Furthermore, several root functions were regulated by the dormancy induction process.
Experimental Manipulation of Wing Pigment Pattern and Survival in Western White Butterflies

Identifying the targets of natural selection in the wild is a continuing challenge for evolutionary ecologists. For quantitative (continuously varying) phenotypic traits, correlations among traits can make it difficult or impossible to determine which traits affect fitness (see, e.g., Lande and Arnold 1983; Mitchell-Olds and Shaw 1987). Many authors have concluded that experimental manipulations of phenotype provide the most direct means of identifying the targets of natural' selection (Endler 1986; Mitchell-Olds and Shaw 1987; Kingsolver and Schemske 1991), but only a handful of studies have employed such manipulations toexamine natural (nonsexual) selection in field populations (see Blest 1963; Benson 1972; Ford 1975; Endler 1978; Sinervo et al. 1992). Here I examine how experimental manipulations of wing pigment pattern affect survival rates (viability selection) in a natural population of the western white butterfly, Pontia occidentalis. I have chosen to manipulate one particular aspect of wing melanin pattern, the degree of wing melanization on the posterior half of the ventral hind wings (hereafter called pVHW melanin), for several reasons. First, previous tudies have shown that pVHW melanin can influence body temperature during basking and during heat-avoidance behaviors in this and other pierid species (Watt 1968; Kingsolver and Watt 1983; Kingsolver 1987). Second, pVHW melanin in P. occidentalis exhibits a striking developmental plasticity in which pVHW melanin is significantly reduced in the summer compared with spring generations (Shapiro 1976). This seasonal pattern suggests that reduced pVHW melanin is adaptive for avoiding deleteriously high body temperatures during hot, summer conditions (Watt 1968; Kingsolver and Wiernasz 1991a; Kingsolver, in press b). Third, mark-recapture studies show that P.: occidentalis butterflies reared under long photoperiods (and exhibiting reduced pVHW melanin) have significantly lower survival probabilities during hot, summer conditions than butterflies reared under short photoperiods (Kingsolver, in press b). However, rearing environment affects wing pattern traits, and perhaps other phenotypic traits, in addition to pVHW melanin (Kingsolver and Wiernasz 1991a). Thus in the present study I experimentally altered pVHW melanin to evaluate its direct effects on survival in hot, summer conditions.
Effect of lamb age and electrical stimulation on the colour stability of fresh lamb meat

The aim of this experiment was to compare the effects of electrical stimulation and lamb age on the retail colour stability of lamb meat. Poll Dorset Merino crossbred lambs that were 5 months ('suckers', SU) and 12 months ('carryovers', CO) finished on the same green annual pasture were slaughtered at a commercial abattoir. Half of the carcasses in each age group (10) were either electrically stimulated (ES) or not stimulated (NES) post-dressing with a commercial high voltage electrical stimulation system. Luminescence (L), hue angle (indication of redness), chroma (intensity), and oxy/met (a measure of browning) values were measured at 0 h (0 days), 21 h (0.86 days), 93 h (3.88 days), and 166 h (6.91 days) after meat had been cut 1 day after slaughter, over wrapped, and put under simulated retail display conditions. Three muscles, m. longissimus thoracis et lumborum (LL), m. gluteus medias (GM), and m. rectus femoris (RF), were measured in this way. A linear mixed model was used to fit a repeated-measurements model to the light measurements of L, hue angle, chroma, and oxy/met. Oxy/met rate of change was compared by fitting splines to predict the time required for oxy/met to reach an arbitrary benchmark value of 3. Colour and rate of colour change during display were affected by both age class and electrical stimulation but these effects depended on the muscle. The LL was the darkest (lowest L) and reddest (lowest hue angle), whilst RF was the most stable in colour (lowest rate of change for oxy/met) of the 3 muscles tested. Age class had a greater effect on oxy/met rate of change for the LL and GM compared with RF. Oxy/met of LL changed more rapidly for CO than SU lambs. ES increased the time for oxy/met to reach 3 in RF and GM for SU only but did so for both age groups in LL. ES decreased this time in RF and GM for CO. CO meat contained a higher concentration of myoglobin than SU meat. Negative effects of electrical stimulation on colour stability are more likely to occur in older lambs and in the GM and RF rather than in the LL.
Analysis and RT-PCR identification of viral sequences in peanut (Arachis hypogaea L.) expressed sequence tags from different peanut tissues.

In the Southeastern US, peanut plants are often naturally infected with different viruses resulting in economic losses. Limited information is available concerning the identification and characterization of various viruses in peanut. A collaborative effort has resulted in the production of 44,064 expressed sequence tags (ESTs) from developing seeds at three reproductive stages (R5, R6 and R7) of two peanut genotypes, Tifrunner and GT-C20 and from field collected leaf tissues using the same two genotypes. EST sequences were analyzed, assembled and putative functions were determined based on the comparison of these unique peanut sequences with the National Center of Biotechnology Information (NCBI) non-redundant (nr) database using BLASTX program. Sequences matched viral or viral associated proteins were selected for further study. We analyzed the extent of viral sequences in these peanut ESTs and detected the sequences of Peanut mottle virus (PMV), Peanut stripe virus (PStV) and Tomato spotted wilt virus (TSWV). A total of 942 sequences were identified that matched viral sequences in GenBank to PMV (606), PStV (330) and TSWV (6). We also identified peanut plant sequences with homology to pea (Pisum sativum) plant-specific Potyvirus VPg-interacting protein (PVIP), Arabidopsis thaliana tobamovirus multiplication protein 3 (TOM3) and a tobacco TMV helicase domain-binding protein. These host proteins are essential for viral multiplication and movement from cell to cell in host plants. Further study, we examined and identified the presence of these viral and plant sequences in peanut leaves, seeds and roots using RT-PCR. The potential use of these putative peanut virus host responsive proteins may lead to the development of potentially new strategies to control these virus diseases by silencing or disrupting these genes to prevent virus infection and multiplication in host plants.