Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi-locus genotyping of cattle genomes on the bases of the region homology to retrotransposons

Abstract Intensification in livestock has led to necessity of developing methods which allows to es-timate animal genomic breeding values (GBV). In this, an approach was based on identifying asso-ciation of animal production traits’ variability to polymorphism in different genome elements, from microsatellite loci to millions of single nucleotide polymorphisms (SNPs), in genome-wide sequenc-ing. Despite numerous accumulated data, the development of relatively simple, fast and affordable to interpretation methods of polyloci genotyping (genome scan) for assessing breed «gene pool stan-dard» or genomic selection is still actual. The mobile genetic elements, being high polymorphic ge-nomic sites, can serve as anchors in a multi-locus genotyping. The species-specific retrotransposons such as L1_BT LINE which present in the bovine genome with high frequency and the endogenous retrovirus ENV1_BT are of particular interest. In this regard, the aim of this work was the compara-tive analysis of polymorphism in genomic DNA fragments flanked by inverted repeats of nucleotide sequences homologous to fragments of these retrotransposons in genomes of specialized dairy Ayr-shire and Black and White Holstein breeds and the Kalmyk beef breed. A recombination between L1_BT LINE and ENV1_BT we reported earlier turned out to be conservative in studied breeds. This apparently indicated it to be old in appearance. Since the genetic relationships identified from distribution patterns and length polymorphisms of DNA flanked by ENV1_BT inverted repeats dif-fered significantly between specialized dairy breeds and local meat breed but were low variable within the breeds, this allowed to conclude about its relatively low transposition activity. The PIC values (polymorphic information content) for spectra produced in PCR with the endogenous retrovirus ERV1_BT fragment as a primer ranged from 0.075 to 0.089 for studied breeds. Distribution of in-verted repeats homologous to L1_BT was different in character and varied among breeds and within breeds, the PIC values were substantially higher and ranged from 0.062 to 0.260. Thus, the use of multi-locus genotyping of transposable elements is effective for the purposes of animal genetics and breeding but their application depends on transposition activity. Our data showed that the ENV1_BT inverted repeats seem to be convenient marker in genetic differentiation among breeds and revealing «gene pool standard», whereas more transposable L1_BT elements are more relevant in indicating individual variability within a breed. Keywords: multi-locus genotyping, retrotransposons, inverted repeats, genomic scan-ning, breed, cattle.
Importance of Proximity to Foraging Areas for the Pacific Great Blue Heron (Ardea herodias fannini) Nesting in a Developed Landscape

Abstract. Habitat loss due to human development is a threat to colonial waterbird species, which require nesting habitat in proximity to productive aquatic foraging areas to ensure reproductive success. When development of habitat occurs, waterbirds must either tolerate the changes or relocate nesting colonies to habitat elsewhere. Land cover and nesting colony data were used to study the implications of development for the Pacific Great Blue Heron (Ardea herodias fannini). Colonies were closer to major foraging areas than expected by chance, but were not farther from human development than expected by chance, suggesting that Pacific Great Blue Herons will tolerate some development to remain close to major foraging areas. There was no relationship between distance to human development and colony productivity; however, distance to major foraging area was a significant predictor of productivity, which suggests Pacific Great Blue Herons may prioritize proximity to foraging areas because it is critical for reproductive success. Given their demonstrated preference for proximity to foraging areas, and high levels of development near these areas, relocation away from human development may not be an option for nesting Pacific Great Blue Herons in south coastal British Columbia, Canada, because potential nesting habitat availability was most restricted within 5 km of major foraging areas. Future management strategies for this species, and colonial waterbirds in general, should prioritize conservation of nesting habitat near major foraging areas to maximize future reproductive success.
Genetic Variation Among Crocus L. Species from Western Turkey as Revealed by RAPD and ISSR Markers

Crocus L. is of interest to the horticultural, culinary and pharmacological fields. Our aims herein are to obtain information based on genetic diversity and to investigate existing levels of genetic variation within and among the Crocus species sampled. Since the classification of this species has not been clarified to date, this research may shed some more light on methods for classification of Crocus L. RAPD and ISSR markers systems were used to estimate genetic diversity of 56 individuals representing 19 Crocus taxa from Western Turkey. RAPD and ISSR banding matrix were calculated to construct a dendrogram (Ward) by a cluster analysis performed by JMP software. High level of genetic variation detected among sampled Crocus species. Genetic distance (GD) values ranged between 0.06 and 0.52 GD. DNA markers based clustering of Crocus L. did not coincide with morphological classifications. This taxon should be reconsidered in terms of classification at the DNA-based level using nuclear, mitochondrial, and chloroplast DNA, as well as more types of robust DNA markers such as AFLP and SSR. The existing high level of genetic variation shows that Turkey could be one of the centers of origin for Crocus L.
Discrimination with Light Stimuli and a Lever-Pressing Response in Melipona Rufiventris

SummaryAfter a long period of training, the worker bee studied was able to discriminate (in 76% of 140 trials) between “light on” and “light off” stimuli presented simultaneously. The bee was required to press one of two small levers to obtain a reward for a correct choice. The experimental apparatus is shown to need some changes: enlargement of the light sources to improve their visibility, and an increased distance between the levers to prevent superfluous responses.
An investigation on DNA polymorphism of the cattle breeds in the province of Kars by RAPD-PCR technique

Une analyse genetique utilisant des marqueurs RAPD a ete realisee afin de determiner les amorces specifiques, les empreintes RAPD et la diversite genetique des races bovines (Rouge Anatolien Est, Zavot, Brown Swiss et Simmenthal) dans Kars une province importante pour l'elevage bovin. Les echantillons d'ADN ont ete isoles a partir de 91 animaux issus des quatre races et dix-huit amorces aleatoires ont ete examinees. Des relations genetiques entre les races ont ete determinees par l'analyse des polymorphismes par RAPD obtenus a partir d'un total de 89 loci. L'analyse statistique des donnees a permis d'evaluer les distances genetiques entre les races et de construire les arbres de faisceau par la methode d'UPGMA. L'evaluation des rapports genetiques entre les races a mis en evidence deux groupes de races clairement distincts : un groupe compose des races Rouge Anatolien Est et Simmenthal, et un deuxieme groupe comprenant les races Brown Swiss et Zavot. Aucune bande RAPD specifique de la race ou du sexe n'a ete detectee. L'etude a montre que l'evaluation des polymorphismes par RAPD-PCR permet de determiner les relations genetiques et les empreintes digitales des races bovines de la province de Kars.
Regulation of Ethylene Biosynthesis and Action in Cut Carnation Flower Senescence by Cytokinins

Cytokinins delay the onset of senescence in cut carnation flowers (Dianthus caryophyllus) by affecting the biosynthesis and action of ethylene in the tissue. The onset of senescence is marked by an increase in ethylene sensitivity and production by the tissue. A characteristic rise in 1-aminocyclopropane-1-carboxylic acid (ACC), the immediate precursor of ethylene, accompanies the initial stages, but the greatest increases in ACC are associated with the decline in ethylene production during the later stages of senescence. Cytokinins delay the onset of senescence and reduce ethylene sensitivity and production. Benzyladenine (BA), a cytokinin, prevents the rise in endogenous ACC levels and reduces the capacity of the tissue to convert ACC to ethylene. The effects of other anti-senescence agents, aminoethoxy vinylglycine (AVG), silver ions and cobalt ions, are compared with those of BA on ethylene sensitivity and production. The mechanism of action of BA in the delay in flower senescence is discussed.
Enumeration of Escherichia coli O157:H7 by using immunomagnetic separation and ATP bioluminescence in buffer solution

Escherichia coli O157:H7, (EHEC), is associated with consumption of ground beef or raw milk. Illnesses caused by EHEC infections can range from self-limited watery diarrhea to life-threating manifestations such as haemolytic-uraemic syndrome (HUS) and thrombotic thrombocytopenic purpura (TTP). The lack of efficient selective enrichment medium for EHEC, reduces the sensitivity and specificity of the conventional cultural method (CCM). Immunomagnetic separation (IMS) using Dynabeads® anti-E. coli O157:H7 represents the selective enrichment procedure needed to improve the CCM. On the other hand, measuring the light given off by the reaction of ATP with luciferase+luciferin reagent in relative light units (RLU), indicates the count of EHEC. In this study, the combination of immunomagnetic separation and ATP bioluminescence methods were used in the detection and enumeration of EHEC in buffer solution, respectively. As a result, correlation coefficient between EHEC count obtained by CCM and ATP bioluminescence method is found as r = 0.8308 which is an acceptable value for such a study. La separation immunomagnetique avec les Dynabeads® anti-E.coli O157 :H7 (enrichissement) suivie de la mesure de la bioluminescence de l'ATP permettent de detecter et de denombrer les E.coli O157:H7 enterohemorrhagiques dans une solution tampon.
A guide to the nomenclature of heterochrony

Since Haeckel's Biogenetic Law (‘ontogeny recapitulates phylogeny’) fell into disrepute early in the twentieth century, there has been intermittent debate, particularly in recent years (de Beer, 1958; Gould, 1977; Alberch et al., 1979; Alberch, 1980; Bonner, 1982; McNamara, 1982a), on the nature of the relationship between an individual's development and phylogenetic history. Important questions under discussion include the following: If a strong causal relationship does exist, what is its nature? How does it work? What is its importance in evolution? How can it be recognized in the fossil record?
Herbicide Programs for Red Rice (Oryza sativa) Control in Soybean (Glycine max)

A study was conducted in 1994 and 1995 at two Mississippi locations to evaluate preplant incorporated (PPI) and preemergence (PRE) applications of alachlor, clomazone, SAN 582, metolachlor, pendimethalin, and trifluralin, and postemergence (POST) applications of AC 263,222 and imazethapyr alone or followed by clethodim late postemergence (LPOST) for red rice control in soybean. Applications of 110 g ai/ha clethodim increased red rice control when following any earlier herbicide application at one location that harbored a high natural infestation. In 1 yr at one location, red rice seedhead suppression from PPI and PRE herbicide applications alone was greater than 95% due to high activity from herbicides and drought conditions during red rice seedhead development. Early postemergence (EPOST) applications of 30 g ae/ha AC 263,222 suppressed at least 95% of red rice seedheads, regardless of year, location, or clethodim LPOST application. At one location, any treatment where 110 g/ha clethodim followed an earlier herbicide application suppressed red rice seedheads at least 95%. Compared to the nontreated control, only AC 263,222 injured soybean (30%) and reduced soybean yield (200 kg/ha).
Transhumance of dairy cows to highland summer pastures interacts with breed to influence body condition, milk yield and quality

Abstract This paper aimed at testing the differences of adaptability of bovine dairy, dual purpose and local breeds during the summer transhumance to highland pastures (summer farms), evaluating temporal variations of body condition and of milk yield and quality. Data were from 799 dairy cows of specialised (Holstein Friesian and Brown Swiss), dual purpose (Simmental) and local (mostly Rendena and Alpine Grey) breeds, and were collected before and after the transhumance in 109 permanent dairy farms, and during transhumance in 15 summer farms of the Autonomous Province of Trento, north-eastern Italy. Body Condition Score (BCS), milk production and quality (fat, protein, casein, lactose, urea, SCS) were analysed for the fixed effects of breed, parity, days in milk, month, supplementary concentrate level, and for the random effects of summer farm and individual cow. Body condition score was influenced by transhumance to summer farms, with low values in July and a recovery at the end of the period. This pattern was particularly marked in the specialised breeds. Similarly, also milk production declined, especially for Holstein Friesian and Brown Swiss, so that towards the end of transhumance all breeds had similar milk productions. Returning to permanent farms did not compensate the specialised breeds for the production loss experienced at the beginning of the grazing season. In conclusion, local and dual purpose breeds adapt better than specialised breeds to the summer pastures, and this results into an important reduction of their productive gaps (with lower variations of milk quality) and in maintaining body fat reserves.
Impacts of bottom fishing on the sediment infaunal community and biogeochemistry of cohesive and non‐cohesive sediments

Bottom‐trawl fisheries are wide‐spread and have large effects on benthic ecosystems.We investigate the effect of scallop dredging on sand and otter trawling on mud by measuring changes in the infaunal community and the biogeochemical processes which they mediate. We hypothesize that changes in biogeochemistry due to fishing will be larger in mud where macrofauna‐mediated processes are expected to play a greater role, than in sand where hydrodynamics mediate the redox system. We sampled benthic infauna, sediment pore‐water nutrients, oxygen, chlorophyll a (Chl a), apparent redox potential discontinuity layer, organic carbon and nitrogen content over a gradient of fishing intensity in sand and mud. The effects of fishing on biogeochemistry were stronger on mud than on sand, where biogeochemistry appeared to be more strongly influenced by tidal currents and waves. On mud, trawling increased sediment‐surface Chl a and ammonium concentration beyond 5 cm depth, but decreased ammonium and silicate concentration in the upper sediment layers. The effects of fauna and bioturbation potential on biogeochemistry were very limited in both mud and sand habitats. Our results suggests that otter trawling may be affecting organic‐matter remineralization and nutrient cycling through sediment resuspension and burial of organic matter to depth rather than through the loss of bioturbation potential of the benthic community. In conclusion, our hypothesis that the effects of trawling on biogeochemistry are larger in mud is supported, but the hypothesis that these effects are mediated by changes in the infauna is not supported. These results imply that management of trawling on muddy sediments should have higher priority.
Benthic harpacticoid copepods of the Yenisei Gulf and the adjacent shallow waters of the Kara Sea

ABSTRACT The harpacticoid fauna was studied at 16 stations in the Yenisei Gulf (the Kara Sea) and the adjacent shallow-water open-sea area. The total harpacticoid abundance was relatively low (an average of 64.4 individuals/10 cm2). Thirty-three species (including putative species) from 13 families were recorded; the Ameiridae, Miraciidae and Pseudotachidiidae were the most diverse families. Most of the species identified were new for the Kara Sea, several were found for the first time after their original description, and seven forms were presumably new to science. The updated list of the Kara Sea harpacticoids has twice as many species in common with the White and Barents Seas than with the eastern Arctic/northern Pacific seas, presumably indicating the asymmetry in the Trans-Arctic fauna exchange. Species diversity increased significantly with increasing distance from the freshwater section seawards. Four assemblages were distinguished based on their taxonomic composition, one in the riverine part and three seaward. Canonical correspondence analysis indicated the salinity, depth, type of sediments and chlorophyll a content in the water column as the main factors affecting the community structure. By contrast with macrofauna, harpacticoid distribution in the Yenisei Gulf did not show a wide transition area with predominance of brackish-water forms. The harpacticoid fauna of the Kara Sea is most likely not impoverished compared with other Arctic seas, but it is greatly under-explored and remains a ‘blank spot’ in this respect.
Cloning of red-spotted grouper TSHβ promoter and its localization expression in primitive gonad and pituitary of zebrafish embryos.

Thyroid-stimulating hormone(TSH) regulates the growth and function of thyroid for formation of thyroid hormones,which are involved in regulation of growth,development,metabolism and reproduction. TSHβ and their thyroidal receptors have been investigated extensively in mammals,but comparative studies were considerably less in lower vertebrates.Our lab had cloned and characterized the full-length cDNA encoding thyroid-stimulating hormone β-subunit(TSHβ) from orange-spotted grouper(Epinephelus coioides),and first reported TSHβ expressed in the gonads of any vertebrates in addition to the expected expression in the pituitary.Further analysis found that TSHβ also expressed in the gonads of the red-spotted grouper(Epinephelus akaara). To elucidate the mechanisms regulating TSHβ expression,we isolated a 5.1kb fragment of the 5'-flanking region of TSHβ promoter from red-spotted grouper by Genome walking.1. 8 kb of this upstream region was used to produce GFP reporter construct(pBK-TOL2) for analysis of tissue-specific expression in zebrafish embryos.During 12—30hpf stage,GFP expressed in the PGC;36hpf—7dpf stage,GFP expressed not only in the PGC but also in pituitary.Western blot analysis showed that GFP protein was detected early in the 10hpf stage embryos.
The complete mitochondrial genome of squat lobster, Munida gregaria (Anomura, Galatheoidea, Munididae)

Abstract We determined the mitogenome sequence of Munida gregaria (Fabricius 1793) (Anomura, Galatheoidea, Munididae), which is the first complete mitogenome sequence in the family Munididae Ahyong et al., 2010. The mitogenome of M. gregaria is 16 326 bp in length and contains 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs) and two control regions (CRs). Mitogenome analysis of M. gregaria showed an extra copy of the CR and rearrangements of two PCGs (nad2 and nad3) compared to the arthropod ground pattern. Additionally, it contains a tRNA (trnY) inversion and rearrangements of two PCGs (nad1 and nad3) when compared with that of Neopetrolisthes maculatus and Shinkaia crosnieri, respectively. The phylogenetic tree confirmed that M. gregaria belongs to the superfamily Galatheoidea within Anomura. Our results will be useful for the detailed study of mitogenome evolution and the phylogenetic relationships among the superfamily in the infraorder Anomura.
IDENTIFICATION OF SINGLE NUCLEOTIDE POLYMORPHISMS ON CATTLE BREEDS IN INDONESIA USING BOVINE 50K

Single nucleotide polymorphisms (SNPs) abundant in bovine genome influence genetic variation in biological mechanism. The study aimed to identify SNPs on Indonesian cattle breeds and analyze their genetic diversity using Bovine 50K SNP chip. Twenty eight "Ongole Grade" (OG) beef cattle and 20 "Holstein Friesian" (HF) dairy cattle were used for the Infinium II assay test. This assay included amplification of genomic DNA, fragmenta-tion, precipitation, resuspension, hybridization, processing bead chip for single-base extension, and imaging at iScan. Data and clusters were analyzed using GenomeStudio software. The Bovine 50K SNP chip containing 54,609 SNPs was observed spanning all chromosomes of bovine genome. Genotyping for the total SNPs was successfull based on Call Rate, GeneCall and GeneTrain scores. Most SNP markers had alleles that shared among the individuals or breeds, or had specific alleles at distinctive frequencies. Minor allele frequency (MAF) spreads equally with intervals of 0-0.5. The breeds of OG and HF tended to be separated in different clusters without considering their genetic history and twin or normal. This result suggests that most individuals are closely related to one another, regardless of the same breed. Some genes identified on chromosomes 3, 4, 5, 7, 13, 17 and 18 were located in the loci/regions that contained SNPs with specific alleles of either HF or OG breed. These SNPs were more powerful for differentiation of beef cattle and dairy cattle than among individuals in the same breed. These SNP variations and genetic relatedness among individuals and breeds serve basic information for cattle breeding in Indonesia.
Chick conditions in first and second broods in the Pallid Swift Apus pallidus

In 1999-2000 we investigated chick condition of first and second broods in the Pallid Swift Apus pallidus in Sofia city, Bulgaria. Data on nine variables characterising chick conditions were collected from post-hatching day 15 to fledging. First and second broods differed in the amount of mass loss. Second brood chicks lost twice as much weight (10.5 ′ 3.05 g) as first brood chicks (5.5 ′ 3.82 g). This difference is supposed to be due mainly to reduced fledging masses in second broods (39.7 ′ 3.06 vs. 42.4 ′ 5.36 g), since peak weights did not differ significantly. Chicks in second broods also reached their peak weights significantly later in the nestling period (34.2 ′ 5.75 vs. 31.4 ′ 5.12 d), and had significantly lower wing loading. Differences in wing loading probably reflect different selective pressures acting during immediate post-fledging periods in mid-summer and late autumn. Hatching asynchrony was more marked in second clutches and was reflected in more pronounced effects of brood hierarchy. Within second broods early hatched chicks had a longer nestling period, reached peak body mass significantly earlier, had longer slimming periods and fledged longer-winged than late-hatched siblings. None of the variables characterising chick condition differed significantly among siblings within first broods. This was supposed to be due to the more plentiful and stable food supply in summer when first broods are raised. Chicks growing in second broods with singletons were of poorer condition than both early hatched and late hatched chicks in second broods with two chicks.
Phytoplankton periodicity: its motivation, mechanisms and manipulation

This review summarizes some recent work to find a generalized explanation of phytoplankton periodicity in lakes. Much of the observational and experimental evidence is drawn from work centred on the large enclosures (Lund Tubes) installed in Blelham Tarn, English Lake District. Observations on the phytoplankton in the tubes are related to the periodic changes that occur in natural lakes and it is suggested that such changes have common patterns, that they are due to common causes, that they are affected by similar processes and that they are therefore predictable and, potentially, manipulable.