Miracle-dz/UniFAR-FTUs huggingface dataset:
Maternal and genetic contributions to geographical variation in Rana temporaria larval life-history traits

The relative importance of genetic, environmental, and maternal effects as determinants of geographical variation in vertebrate life-histories has not often been explored. We examined the role of genetic and maternal effects as determinants of population divergence in survival and three important larval life-history traits (growth rate, age, and size at metamorphosis) using reciprocal crosses between two latitudinally separated populations of the common frog (Rana temporaria Linnaeus). Genetic effects were important in all three traits as indicated by the significant effect of male origin, but there was also evidence for nonadditive genetic contributions on metamorphic size and growth rate. Likewise, maternal effect contributions to population divergence were large, partially environment dependent, and apparently acting primarily through egg size in two of three traits. These results suggest that both genetic and maternal effects are important determinants of geographical variation in amphibian life-histories, and that much of the differentiation resulting from maternal effects is mediated through variation in egg size.
In Silico Study of Leishmania donovani α-β Tubulin and Inhibitors

Leishmania donovani is a parasite that causes visceral leishmaniasis, a severe form of leishmaniasis that affects vital organs. An important target for the treatment of this disease is the protein α-β tubulin, which was modeled in this paper and proposed as a target for the treatment of visceral leishmaniasis. Two classes of compounds were studied, dinitroanilines and oxadiazoles. According to the docking results, dinitroanilines interact better with the L loop domain and oxadiazoles interact better with the colchicine domain.
Quantification in tissue near–infrared spectroscopy

In near–infrared spectroscopy (NIRS) of tissue, light attenuation is due to: (i) absorption from chromophores of fixed concentration, (ii) absorption from chromophores of variable concentration, and (iii) light scatter. NIRS is usually concerned with trying to quantify the concentrations of chromophores in category (ii), in particular oxy– and deoxyhaemoglobin (HbO2 and Hb) and cytochrome oxidase. In the absence of scatter the total light absorption in the medium is a linear sum of that due to each chromophore. In a scattering medium like tissue, this linear summation is distorted because the optical path length at each wavelength may differ. This distorted spectrum is then superimposed upon a further wavelength–dependent attenuation arising from light loss due to scatter, which is a complex function of the tissue absorption and scattering coefficients ( μ a and μ s), scattering phase function, and tissue and measurement geometry. Consequently, quantification of NIRS data is difficult. Over the past 20 years many differing approaches to quantification have been tried. The development of methods for measuring optical path length in tissue initially enabled changes in concentration to be quantified, and subsequently methods for absolute quantification of HbO2 and Hb were developed by correlating NIRS changes with an independent measurement of arterial haemoglobin saturation. Absolute determination of tissue optical properties, however, requires additional information over and above the detected intensity at the tissue surface, which must then be combined with a model of light transport to derive μ a and μ s. The additional data can take many forms, e.g. the change in intensity with distance, the temporal dispersion of light from an ultrashort input light pulse, or phase, and modulation depth changes of intensity–modulated light. All these approaches are now being actively pursued with considerable success. However, all the approaches are limited by the accuracy of the light transport models, especially in inhomogeneous media.
KINETIKA REAKSI FERMENTASI GLUKOSA HASIL HIDROLISIS PATI BIJI DURIAN MENJADI ETANOL

Ethanol can be produced by glucose fermentation process using Saccharomyces cerevisiae . The potential source of glucose is starch of durian seed. This research studies about determine the kinetics model of ethanol fermentation of glucose and to identify the physical properties of ethanol produced. Glucose fermentation using Saccharomyces cerevisiae for 72 hours at various initial concentrations of 20, 40, 60 and 80 ppm has been conducted. After ethanol produced was reacted with potassium dichromate using Conway crucible. It was then analyzed by UV-Vis spectrophotometer at 605 nm. The physical properties of ethanol determined were density and refraction index. The result showed that the kinetics model of ethanol fermentation obtained was accordance with = -0,0011 + 0,0002 equation. As for Michaelis-Menten (K m ) constant was 5,5 ppm -1 and maximum velocity (V max ) 5000 ppm.hour -1 . In addition, its physical properties i.e. density and refractive index were in the range of 0,9767-0,9809 g/mL and 1,3347-1,3365 respectively.
Field and Laboratory Methods in Primatology: Field endocrinology: monitoring hormonal changes in free-ranging primates

Field endocrinology can be considered as the application of non-invasive methodologies to examine behavioural endocrine interactions in primates living in natural conditions and social settings. In bringing together laboratory and field-based research methods, the discipline provides new and exciting opportunities for developing a more integrated approach to studies of primate behavioural ecology. Traditionally, field studies have relied mainly on visual measures, such as behaviour and/or morphology. Although this has generated a great deal of essential information, its limitation is that interpretation of the observations is often based on assumptions concerning the physiological context inwhich theyweremade. The availability of non-invasive methodologies based on measurement of hormones in either urine or faeces now provides us with quantitative measures of physiological status by which the significance of observational data can be gauged. This greatly facilitates the testing of hypotheses concerning the adaptive significance of behavioural and morphological traits and mating systems and is helping to provide new insights into reproductive processes in an evolutionary context. Field endocrinology also facilitates a better understanding of the impact of anthropogenic activities on primate physiology. In combination with studies of the health status of wild primates (Chapter 8), this can help to elucidate the link between environmental stress, health and reproductive parameters and thus to estimate the viability of threatenedpopulations (Pride, 2005;Chapman et al., 2007). In this chapter, we review the most important aspects fieldworkers need to be aware of when planning and carrying out
Studies of the world Gyponinae (Homoptera, Cicadellidae): The genus Polana

Eighty seven species are placed in Polana DeLong, 11 previously described (including 3 synonyms) and 13 described as new. These species are placed in ten subgenera as follows: Subgenus Declivella, subgen. n. , with one species danesa, sp. n. ; subgenus Bohemanella, subgen. n. , with 14 species, chelata, sp. n. , resupina, sp. n. , bohemani (Stal) (Type-species) (= praeterita (Fowler), = draba Evans, new synonyms), alia, sp.n. , retenta, sp.n. , assula, sp. n. , resilara, sp.n. , celsa, sp. n. , chifama, sp.n. , orbita, sp.n. , macula, sp.n. , elabora, sp.n. , scela, sp.n. , and ardua, sp.n. ; Subgenus Angusana, subgen.n. , with one species exornata (Fowler); Subgenus Bulbusana, subgen.n. with 13 species, villa, sp.n. , pendula, sp.n. , plumea, sp.n. (Type-species), bruneola (Osborn), nida, sp.n. , vana, sp.n. , extranea (Fowler), dispara, sp.n. , quatora, sp.n. , piceata (Osborn), laca, sp.n. , inclinata, sp.n. , and obtecta, sp.n. ; Subgenus Polana DeLong, with 24 species, ocellata (Spangberg), quadrinotata (Spangberg) (Type-species), unca, sp.n. , pensa, sp.n. , aspersa, sp.n. , principia, sp.n. , spindella, sp.n. , gelera, sp.n. , optata, sp.n. , mala, sp.n. , nidula, sp.n. , peda, sp.n. , bulba sp.n. , lanara, sp.n. , inimica, sp.n. , merga, sp.n. , flectara, sp.n. , coresa, sp.n. , squalera, sp.n. , scuta, sp.n. , ruppeli, sp.n. , parca, sp.n. , fusconotata (Osborn), and alitera, sp.n. ; Subgenus Parvulana, subgen.n. , with 4 species, tulara, sp.n. , bidens, sp.n. , pandara, sp.n. , and alata, sp.n. (Type-species); Subgenus Largulara, subgen.n. , with 2 species, fantasa, sp.n. (Type-species), and elera, sp.n. ; Subgenus Nihilana, subgen.n. , with 13 species, icara, sp.n. nisa, sp.n. , fetera, sp.n. , celeta (Fowler) (=resima (Fowler)), obtusa (Spangberg), rixa, sp.n. , scina, sp.n. , pressa, sp.n. , bena, sp.n. , aneza, sp.n. , fina, sp.n. , agrilla, sp.n. , and obligua, sp.n. ; Subgenus Polanana, subgen.n. , with 8 species, falsa, sp.n. , venosa (Stal) (Type-species), sereta, sp.n. , truncata, sp.n. , quadrilabes, sp.n. , mella, sp.n. , macuella, sp.n. , and parvula, sp.n. ; and Subgpnus Polanella, subgen.n. , with 3 species, cupida, sp.n. (Type-species), helara, sp.n. , and randa, sp.n. The genus Polana is distributed from the southern states of the United States through Central America and the Caribbean Islands, to the greater part of South America. Very little is known of their host plants.
Ultrastructural Studies on the Behavior of Centrioles during Meiosis of Starfish Oocytes

The behavior of centrioles and ultrastructural changes of the nucleus were observed in maturing oocytes of the starfishes, Asterina pectinifera and Asterias amurensis. Observations were focused on the number and behavior of centrioles during two successive meiotic divisions. Examination of serial sections revealed that in meiosis I each division pole has a pair of centrioles, whereas in meiosis II each has only one centriole, confirming the observations by Sluder et al. (1989) on oocytes of Pisaster ocraceus and Asterias forbesi. The first polar body had two centrioles and the second polar body had only one. These results indicate that no duplication of centrioles occurs during the two successive meiotic divisions, and that the egg inherits one centriole from a primary oocyte.
Detection of bias in animal model pedigree indices of heifers

Tutkimuksen tavoitteena oli tutkia ovatko hiehojen odotusarvot (PI) harhaisia ja jos ovat, onko harha eri suuruinen eri hiehoryhmissa. Harhan arvioimiseksi laskettiin kahdetelainmalliarvostelut kahden eri aineiston perusteella. Ensimmainen aineisto kasitti kaikki 1978-94 poikineiden lehmien kolmen ensimmaisen tuotantovuoden 305 paivan maito- ja valkuaistuotostiedot. Toisesta tiedostosta poissuljettiin tuotantotiedot lehmilta, jotka poikivat ensimmaisen kerran maaliskuun 1993 jalkeen, jolloin niiden jalostusarvoiksi muodostui isan ja eman arvosteluihin perustuva odotusarvo (PI). Arvostelujen jalkeen kertyi 51 744 Ayrshire-lehmaa, joilta oli seka ensimmaisen tuotantovuoden tietoihin perustuva jalostusarvon ennuste (EBV), etta karsitusta aineistosta laskettu PI. Tarkasteltavat elaimet jaettiin kolmeen eri kohderyhmaan vanhempiensa perusteella: jalkelaisarvosteltujen keinosiemennyssonnien (valiosonnien) tyttaret, arvostelemattomien sonnien (nuorsonnien) tyttaret ja sonninematasoisten emien tyttaret. Arvostelujen tuloksien testaamiseen kaytettiin kolmea eri menetelmaa: t-testia, lineaarista regressiota EBV:sta PI:lle ja polynomiaalista regressiota, jossa harhaa EBV-PI selitettiin PI:lla. Kaytannossa merkittavasti harhaisia olivat vain nuorsonnien tyttarien odotusarvot. Keskimaarin niiden odotusarvot olivat vaaristyneet ylospain 0,20 keskihajonnan yksikkoa eli 78,8 kg maitotuotoksessa, ja 0,21 keskihajonnan yksikkoa eli 2,2 kg valkuaistuotoksessa. Harhan oletettiin johtuvan nuorsonnien emien jalostusarvojen yliarvioinnista, joka aikaisemmissa tutkimuksissa on havaittu elainmalliarvosteluille tyypilliseksi. Sonninematasoisiksi luokiteltujen lehmien tyttarien odotusarvot tuntuivat ennustavan tyttarien tulevia jalostusarvosteluja melko luotettavasti. Taman arveltiin saattavan johtua erityishuomiosta, jota karjanomistajat voivat antaa parhaiden lehmiensa tyttarille. Polynomiaalisen regression erittely osoitti, etta keskimaarainen harhaisuuden aste muuttui hieman odotusarvon suuruuden mukaan, joskin ko. mallin antaman alhaisen selitysasteen perusteella PI:n suuruus ei kaytannossa anna merkittavaa lisatietoa odotusarvon luotettavuudesta.
Genetic map of a basidiomycete fungus, Lentinula edodes (shiitake mushroom), constructed by tetrad analysis

We constructed a framework map of the edible mushroom Lentinula edodes (shiitake mushroom) using tetrad analysis. The map is based on the segregation of 264 randomly amplified polymorphic DNA (RAPD) markers, 14 structural genes, 1 expressed sequence tag (EST) marker, 2 mating factors (matA and matB), and 8 sequence-characterized amplified regions (SCARs) among 92 basidiosporic strains in 23 tetrads. We identified 11 linkage groups on a support interval of a minimal LOD score of 3.0 and a maximum distance of 25 centimorgans (cM). The length of the 11 linkage groups (LGs) ranged from 157.2 cM to 24.4 cM, and they covered a distance of 908.8 cM. One of the quantitative trait loci controlling the vegetative growth rate on potato dextrose agar (PDA) for L. edodes was detected between the markers D18CCA-360t and S08-1000c on LG2.
Chronological Study on Changes in Luteinizing Hormone Release during Fasting and Refeeding in Ovariectomized Estrogen-primed Rats

To investigate the effect of food manipulation on luteinizing hormone (LH) secretion, changes in pulsatile release of the hormone during the periods of 48h fasting and subsequent 24h refeeding, both started at noon, were examined chronologically in ovariectomized estrogen-primed rats fed in 14L-10D (lights on at 0500h) lighting condition, by taking plasma samples at intervals of 10 min for 6h in each animal. Diurnal pattern of LH secretion, being high in the afternoon and low in the morning, was observed in the free feeding group rats. The plasma concentration of LH started to decrease from 6-12h after the food deprivation and was kept low thereafter throughout the fasting period. Refeeding caused the prompt recovery of pulsatile release of LH and frequent occurrence of LH pulses which lasted for 6h or a little more. Frequent LH pulses were observed again on the morning of the next day in the refed rats, while the hormone release remained low at the same clock time in the freely fed animals. Suppression of the LH secretion by fasting seemed to be slightly alleviated on the third day of fasting. The sensation from digestive organs associated with fasting and refeeding may be the primary factor responsible for the change in LH secretion, and also the intervention of light-dark cycle in the mechanism was suggested. Animal Science Journal 71 (3): 239-249, 2000
Plant Transposable Elements and Their Application to Genetic Analysis via High-throughput Sequencing Platform

Transposable elements (TEs) are mobile genetic elements in the eukaryotic genome. They are divided into two classes (class I: retrotransposons and class II: DNA transposons) based on their structure and manner of transposition. TEs are major components of the eukaryotic genome and retrotransposons are especially abundant in higher-plant genomes. As retrotransposon insertions with high copy numbers are dispersed throughout the genome and are inherited genetically, insertion polymorphisms among crop cultivars have been used as molecular markers. Recently, we developed an efficient method for screening the long terminal repeats (LTRs) of retrotransposon families that exhibit high levels of insertion polymorphisms among crop cultivars using a next-generation sequencing (NGS) platform. This method focuses on the primer binding site (PBS) that is adjacent to the 5' LTR and has a conserved DNA sequence among different LTR retrotransposon families. Construction of a sequencing library through PCR amplification using the PBS conserved sequence allowed us to acquire a large number of LTR sequences and their insertion sites throughout the genome. From our data analysis, we screened the LTR sequences that showed high levels of insertion polymorphism among closely related cultivars. In addition, we identified the insertion sites of these identified LTR retrotransposon families at the genome-wide scale in a number of cultivars with an NGS platform, which enabled us to reveal the genetic relationships among the cultivars and acquire a number of molecular markers for cultivar screening. Our results indicated that the target sequencing of these retrotransposon insertion sites was highly effective for DNA genotyping and marker development without requiring any whole-genome sequence information. This review describes the genomic structure and evolutionary aspects of TEs and discusses the development of molecular markers based on retrotransposon insertion polymorphisms.
Effects of thinning and nitrogen fertilization on growth of Douglas-fir: relative contribution of foliage quantity and efficiency

The aboveground biomass of Douglas-fir (Pseudotsugamenziesii (Mirb.) Franco) and annual production over 7 years was studied in relation to thinning and nitrogen fertilization. Biomass yield of both treatments increased during the first 3–4 years then decreased for fertilization but not with thinning. Treatments doubled biomass production of individual trees over the study period when applied separately and quadrupled it when combined. Annual biomass production per unit of foliage (E) increased during the first 3–4 years, but was at or below control level after 7 years. The increased E accounted for 20, 37, and 27% of the stemwood dry matter response to thinning, fertilization and the combined treatments, respectively; the remainder was attributed to an increase in foliage biomass. Thinning, but not fertilization, influenced distribution of radial growth along the stem, increasing growth only below the top one-third of the stem. This pattern was related to crown development.
Water quality, production parameters and nutritional condition of Litopenaeus vannamei (Boone, 1931) grown intensively in zero water exchange mesocosms with artificial substrates

The effect of artificial substrates on the water quality, production parameters and nutritional condition was assessed in experimental intensive cultures of Litopenaeus vannamei grown in mesocosm units with zero water exchange. The initial stocking densities in triplicate 1000 L tanks were 600 and 800 g of juvenile shrimp (2.7 g) per unit, with (W) and without (WO) artificial substrates. There were no significant differences between the water quality parameters of the four treatments. In the tanks with the lower stocking biomass, the best survival (96.7% vs. 87.0%), growth rate (1.69 vs. 1.35 g week−1), final biomass (1969.6 vs. 1516.0 g m3) and feed conversion ratio (1.30 vs. 1.90) were obtained with artificial substrates. Similar results were observed for the higher stocking biomass (90.9% vs. 74.5%, 1.50 vs. 1.13 g week−1, 2221.6 vs. 1560.8 g m3, and 1.50 vs. 2.60 respectively). The nutritional condition of shrimp was improved using artificial substrates. The protein content in muscle was higher (21.6% and 20.4%) in ponds with substrates as compared with the control (21.2% and 15.9%).
Simulation of Peroxiredoxin II and Brain-type Creatine Kinase protein-protein interaction using the on-line docking server ClusPro 2.0 -

Article history: Received on: 28/04/2015 Revised on: 17/05/2015 Accepted on: 22/06/2015 Available online: 28/08/2015 Importance of dedicated web servers and specialized software for simulations of protein-protein interactions is well established. The purpose of our study was to examine the protein-protein interaction that occurred under physiological and stress conditions between peroxiredoxin II and the creatine kinase brain-type using proteindocking server ClusPro 2.0. To predict the particular site of amino acid docking, computer software analyzes various protein conformations and chooses the most profitable energy state, therefore selecting a number of possible combinations that would fit the correct profile. By co-immunoprecipitation assay, we demonstrated that two molecules Prx II and CKBB have interacted with further attenuation of this specific binding by pretreatment with selected stress factors. In previous study, we showed that the enzymatic activity of CKBB was recovered by different concentration ratios of Prx II. The specific binding models were generated by ClusPro 2.0 protein docking server and studied using PyMol software. It was shown that a number of amino acid residues including Lys 11, Arg 13, Ala 204, Arg 209for creatine kinase, and Asp 181, Glu 192, Lys 196, Glu 162, Gln 163 for Prx II have participated in the complex formation throughout the first ten conformations.
Response of Rabbiteye Blueberry (Vaccinium ashei Reade) to the Growth Regulators CPPU and Gibberellic Acid

Experiments were conducted during 1999 and 2000 at Griffin, Ga. , with rabbiteye blueberries (Vaccinium ashei Reade) to determine how the growth regulator CPPU affected fruit set, berry size, and yield. CPPU (applied at two different timings) was used alone, and in conjunction with GA 3 on mature, field-grown 'Tifblue' plants. A control treatment without either growth regulator was also included. The CPPU concentration used was 10 mg.L -1 (a single application per treatment), and the GA 3 concentration used was 200 mg.L -1 (two applications per treatment). Results from both years showed a positive benefit of CPPU with respect to fruit set and berry size, especially in the absence of GA 3 . Depending on timing, berry number per plant was increased by more than 200% in 1999 using CPPU. Berry size increases of more than 30% occurred in 2000 when CPPU alone was applied at 17 d after flowering (DAF). CPPU did not increase berry size of GA 3 -treated plants in either year. Total yield per plant during 2000 was 5.0, 7.1, and 8.3 kg for control, CPPU applied 7 DAF, and CPPU applied 17 DAF treatments, respectively, without GA 3 . While CPPU did substantially increase fruit set, berry size, and yield of 'Tifblue', there was a notable delay in fruit ripening. These results suggest that CPPU may be useful for increasing yield of rabbiteye blueberries under conditions of inadequate fruit set (such as occurs in much of the Southeast), but a delay in ripening will likely result. Chemical names used: N-(2-chloro-4-pyridyl)-N'-phenylurea (CPPU); gibberellic acid (GA 3 ).
UP-PCR genotyping and rDNA analysis of Ascochyta pisi Lib

Isolates of Ascochyta pisi, previously identified as separate pathotypes, were genotyped by rDNA-RFLP and UP-PCR using 8 UP-primers and 2 arbitrary primers individually or in pair-wise combinations. The appearance of polymorphic UP-PCR products for all studied isolates facilitated their differentiation. The markers were suitable in identifying isolates, and may be useful for developing isolate- or pathotype-specific PCR-based diagnostic assays. In studying genetic relatedness by UP-PCR among A. pisi isolates, two distinct clusters were revealed. rDNA analysis of the isolates based on endo-ntjclease digestion of amplified ITSl and 1TS2-25S nuclear rDNA regions did not separate the isolates, whereas the variabihty of the isolates using UP-PCR was more than 40%. Zusammenfassung Die Genotypen von Ascochyta pisi-Isolaten, die unter-schiedliche Pathotypen reprasentierten, wurden mittels rDNA-RFLP und UP-PCR untersucht, wobei 8 UP-Primer und 2 willkurliche Primer einzeln oder paarweise verwendet wurden. Bei allen untersuchten Isolaten traten polymorphe UP-PCR-Produkte auf, was die Unterscheidung vereinfachte. Die Marker eigneten sich zur Identifizierung der Isolate und konnten fur die Entwicklung isolat- oder pathotypspezifischer, auf PCR basierender diagnostischer Tests nutzlich sein. Bei der Untersuchung der genetischen Verwandtschaft zwischen den Isolaten mittels UP-PCR ergaben sich zwei verschiedene Cluster. Die rDNA-Analyse der Isolate nach Endonuclease-Spaltung der amplifizierten ITS1- und ITS2-25S-Regionen der Kern-rDNA fuhrte nicht zu einer Trennung der Isolate. Bei UP-PCR betrug die Variabilitat der Isolate himgegen mehr als 40%.