Miracle-dz/UniFAR-FTUs huggingface dataset:
New Digenean Parasite Infecting the Freshwater Fish, Clarias gariepinus with Special Reference to its Tegumental Ultrastructure

The following Lepocreadiid species are described. Fifty Clarias gariepinus fish samples were collected from Giza Province, Egypt, during the period from October 2010 to January 2011. It is found that, 12 out of 50 (24.5 %) fish were found to be naturally infected with a new species (Pseudoholorchis clarii) that is named according to the host harboring this parasite which is distinguished from other species of the same genus by some interspecific variations. The tegument of the present species consists of an outer syncytial layer which is folded into a series of ridges and grooves. The syncytial layer (external layer) is connected to the nucleated internal region across the fibrous discontinuous middle layer. The folds are interrupted by numerous cuticular spins; each one is enclosed at the apex and at the base by the corresponding unit membrane. The inner nucleated layer is consisted of epidermal cells arranged in two levels. The cells are conical in shape and have a large nucleus with prominent nucleoli. Large vacuoles are also observed between the epidermal cells containing granules of different shapes and sizes.
Mapping attributes of Canada’s forests at moderate resolution through kNN and MODIS imagery

Canada’s National Forest Inventory (NFI) sampling program is designed to support reporting on forests at the national scale. On the other hand, continuous maps of forest attributes are required to support strategic analyses of regional policy and management issues. We have therefore produced maps covering 4.03 × 106 km2 of inventoried forest area for the 2001 base year using standardised observations from the NFI photo plots (PP) as reference data. We used the k nearest neighbours (kNN) method with 26 geospatial data layers including MODIS spectral data and climatic and topographic variables to produce maps of 127 forest attributes at a 250 × 250 m resolution. The stand-level attributes include land cover, structure, and tree species relative abundance. In this article, we report only on total live aboveground tree biomass, with all other attributes covered in the supplementary data (http://nrcresearchpress.com/doi/suppl/10.1139/cjfr-2013-0401). In general, deviations in predicted pixel-level values from .
The Classification of Bacillus thuringiensis

Summary. Forty-six isolates of protein crystal-forming bacteria pathogenic for insects were studied in an attempt to correlate classifications based on biochemical reactions, flagellar antigens, and esterase patterns obtained when cell extracts were analysed by electrophoresis in starch gel. Nine serotypes were represented, one being subdivided into two subtypes on the basis of secondary H antigens. There was a close correlation between the serological classification and that based on esterase analysis. The relationships between the three types of classification are described and the significance of esterase analysis in this context is discussed.
Population genetic structure of autochthonous Black Slavonian Pig

As Black Slavonian pig was forgotten and replaced by commercial hybrid pigs, after mid 1950s population declined drastically. Today’s population was founded from 46 sows and 6 boars in 1996 while currently consist of 1064 sows and 163 boars. Aim of this study was to evaluate the genetic structure and genetic variability in autochthonous Black Slavonian pig breed using pedigree. The quality of the pedigree information was evaluated by percentage of known ancestors, which was about 35.16%. Increase in pedigree completeness over the years is evident. Number of inbred Black Slavonian animals was 1695. Average inbreeding was 3.2%, with evident growth observed by year. Effective number of founders was 50.8 for males and 51.1 for females. Effective number of ancestors was, 35.8 for male and 34.8 for female animals, respectively. The proportion of the genes contributed to the reference population of males and females by the most important ancestor was 7.1% and 9.1%. The first 15 ancestors for males and 12 for females explained around 50% variability in the gene pool. Average effective population size via number of parents for the last 10 years of Black Slavonian pig is 189.2. In order to perform proper selection decisions, additional work should be done to increase the quality of pedigree data affecting the reliability of estimated parameters and genetic structure of the population.
ISOLATION AND CHARACTERIZATION OF cDNA CLONE CODING FOR LOTUS JAPONICUS NODULE SUCROSE SYNTHASE

: To study the expression of genes coding for enzymes involved in carbon metabolism, we were concerned with the isolation and characterization of cDNA clone coding for sucrose synthase. The nucleotide sequence of the cDNA clone encoding Lotus japonicus sucrose synthase was determined. The amino acid sequences of this clone were aligned with other homologous sucrose synthase sequences, derived from different organisms, in order to identify the conserved regions. The aim of the study was to describe the isolation and characterization of a cDNA clone encoding for a Lotus japonicus root nodule specific sucrose synthase, whose predicted amino acid sequence is conserved in plant kingdom.
Cloning and Expression Profiles of Myf5 Gene of Yak

To reveal the sequence characteristic and expression pattern of Myf5 gene in Jiulong yaks (Bos grunniens), a full-length cDNA of Myf5 was cloned from yak muscle tisssue by RT-PCR. The cDNA obtained was 821bp nucleotide (nt) long with an ORF of 768 bp which encoding 255 amino acids. Compared with cattle, sheep, pig, horse, human, pygmy chimpanzee, mouse, rat and dog, the homology of amino acid sequences were higher (89- 9%), but lower in Zebrafish (60%). SQ RT-PCR analysis showed that Myf5 gene expression was observed only in longissimus muscle, but not be detected in heart, liver, kidney, spleen and adipose tissues. The expression level of Myf5 gene in longissium muscle of 0.5 and over 9 years old yaks was significantly higher than those of 3.5-5.5 years old yaks (p<0.05). These results suggest that Myf5 may play an important role in the regulation of muscle growth and development of yak.
Characterizing corn hybrids (Zea mays L) for water shortage by principal components analysis.

Identifying drought tolerant genotypes is very important for increasing corn yield. Thus four simple corn hybrids were submitted to periods of water shortage, at three phenological stages of the crop, to discriminate for drought tolerance by principal components analysis and identify their main differentiating characteristics under limited water conditions. Assessments were made of the leaf water potential, gas exchange, photochemical activity, grain yield and total dry matter. Analysis of variance was carried out and the mean values were compared by the Tukey test at 5% probability. Water shortage at the three phenological stages of the corn crop reduced the leaf water potential (Ψw), stomata conductance (gs), photosynthesis (Ai), transpiration (Ei), potential quantum efficiency of the PSII (Fv/Fm), apparent rate of electron transport (ETR), photochemical dissipation coefficient (qP) and increased the non-photochemical dissipation coefficient (NPQ), mainly when there was drought at the vegetative and flower¬ing stages. The data obtained for grain yield (GY) showed that the TOL1 hybrid was outstanding for drought toler¬ance at all the phenological stages of the crop, while the SENS1 hybrid demonstrated greatest sensitivity to water shortage, proving the pattern of tolerance and sensitivity of these respective hybrids to drought. The result of the principal components analysis showed that the corn hybrids could be separated into diversity groups for irrigation treatment at the vegetative stage, and that integrated photosynthesis (Ai) was considered the best characteristic to discriminate the irrigation treatments and hybrids when submitted to water shortage at this phenological stage of the crop.
EVOLUTION AND ORIGIN OF NEUROFIBROMIN, THE PRODUCT OF THE NEUROFIBROMATOSIS TYPE 1 (NF1) TUMOR-SUPRESSOR GENE

SUMMARY Motivation: Neurofibromatosis type 1 (NF1) is a common genetic disorder, which predisposes affected individuals to a variety of clinical features including tumors of the central and peripheral nervous systems. The product of the NF1 gene, neurofibromin, is a tumor suppressor which most likely acts through the interaction of its GTPase activating protein (GAP) related domain (GRD) with RAS to regulate cellular growth. While clinical features of NF1 as well as functional activity of human neurofibromin are intensively studied now little is understood about its evolution, diversity, and overall distribution among different taxa. Results: By combining bioinformatic and phylogenetic approaches, we demonstrated that NF1 homologs are present across a wide range of eukaryotic lineages. We observed 26 similar to NF1 amino-acid sequences from Chordata, Echinodermata, Arthropoda, Platyhelmintes and Fungi taxons. Taking into account a presence of NF1 gene in fungi, we can suggest the derivation of this gene before the Metazoan origin. In this case, an absence of NF1 in Nematoda and Mollusca should be a result of this gene elimination.
Genetic analysis to find suitable parents for development of tomato hybrids.

Line × Tester analysis was used to identify the potential parents and their hybrids from a set of 12 crosses derived from three lines (LA-2661, LA-2662 and 017899) and four testers (BL-1078, BL-1079, CLN-2413 and CLN-2418-A). Results showed that parents and F1 hybrids differed significantly for general combining ability and specific combining ability effects, respectively. The values of general combining ability (GCA) and specific combining ability (SCA) variances depicted non-additive and additive gene action with predominance of non-additive gene action in the genetic determination of all characters except fruit yield per plant. Parent lines LA-2662 and CLN-2418-A provided the best general combining ability in more than one yield contributing traits. Specific combining ability effects, heterosis and heterobeltiosis in desired direction were recorded in two crosses viz. “LA-2662 × CLN-2418-A” and “LA-2662 × BL1078”. F1 hybrid “LA-2662 × CLN-2418-A” proved to be the best cross in overall performance and should be further exploited in breeding plans for hybrid vigour and commercial utilization.
Different approaches for Agrobacterium-mediated genetic transformation of Brachypodium distachyon, a new model plant for temperate grasses

Cereal crops belonging to temperate grasses are fundamental sources of human nutrition therefore their agronomical improvement is centrally important. For this purpose the establishment of an experimental model system for these monocot plants is essential in plant biology research. Considering its advantageous morphological and physiological virtues taken together with the results of the advanced genomics research the Brachypodium distachyon became the new model plant for the Poaceae. The aim of our work is to adapt and possibly improve the Agrobacterium-mediated transformation method using embryogenic callus from in vitro cultures and furthermore develop an in planta methodology via Agrobacterium tume- faciens for Brachypodium in order to simplify the transformation procedure.
Changes in population structure and body dimensions of two xanthid crabs: A long-term study in a single boulder-shore

Two xanthid crab species were studied during 29 months over a period of 14 years between 1986 and 1999 all in exactly the same boulder shore. One of the crab species studied was the xanthid, Eriphia verrucosa (Forskall, 1775) with 60 specimens, the other species, Xantho poressa (Olivi, 1792), with 155 specimens. A significant change in numbers of both males and females of E. verrucosa was noticeable between 1986 and 1996 with a marked drop in numbers between these years. In 1997 male numbers increased again to almost their previous numbers in the population during 1986. The population of X. poressa declined significantly towards the end of the study period. Numbers of both genders peaked in spring and again, in summer. There was generally a decline in numbers of both crab species during autumn and winter. Thus, the average capture during the seasons was highest in spring for males of both E. verrucosa, and X. poressa. The body dimensions: mass, carapace length (CL) and width (CW) were measured in both xanthids. The aim of this long-term study was to determine whether temporal changes in the population structure and allometric changes in the dimensions of these crabs took place. Only such long-term observations could reveal these changes in population.
A Versatile New Tactic for Fruit Tree Micrografting

Micrografting is au effective technique for elimination of viruses, early diagnosis of grafting incompatibilities, rejuvenation of mature tissue, and bypassing the juvenile phase in fruit trees. Current micrografting procedures are difficult, impractical, expensive, and generally result in an inefficient rate of successful graft production. To alleviate some of these limitations, a unique apparatus was designed to splice the in vitro-derived scion and rootstock together during the micrografting process. The dual-layer device was constructed with an outer layer of aluminum foil, with flexibility to facilitate manipulation during the grafting of micro-scale plants. A delicate, absorbent inner layer of paper toweling cushions the plant tissue. It also may be treated with hormones and other compounds. After healing, it is easy to remove the grafting apparatus from the grafted plant without damaging the tissues. This apparatus may be used to unite a scion and a rootstock with different stem diameters. Shoot-tip cultures of ‘McIntosh’ and M.7 apple and ‘North Star’ sour cherry, and in vitro seedlings of lemon, orange, and grapefruit were used as a source of in vitro scions and rootstocks. Successful graft unions were developed, and the grafted plants were transplanted into the greenhouse environment.
Aspects of the reproductive biology of dusky, spinner and sandbar sharks (Family Carcharhinidae) from the Tasman Sea

Increased harvest pressure exerted on sharks worldwide has created a necessity for more information concerning the basic biology of targeted species. This study marks the first dedicated assessment of the reproductive biology of Carcharhinus obscurus, C. brevipinna and C. plumbeus in eastern Australian waters, where these species support a demersal longline fishery. We found all three to be late maturing species of low reproductive output, suggestive of an overarching susceptibility to stock depletion in the region. Length- (L50, cm LT) and age-at-maturity (A50, years), for females and males were respectively 281.1 and 15.5, and 271.9 and 14.6 for C. obscurus; 224.9 and 10.1, and 208.9 and 8.5 for C. brevipinna; and, 174.8 and 9.5, and 164.5 and 7.0 for C. plumbeus. Uterine fecundity (i.e. litter size) was observed at 5–12 (=9.6), 5–14 (=10.6) and 3–12 (=7.8) for the same three species respectively, and increased significantly with maternal length in C. brevipinna. Length-at-birth (L0, cm LT) ranged from 92 to 96 for C. obscurus, 79–82 for C. brevipinna and 66–76 for C. plumbeus, and all three species exhibited lengthy gestation periods, overall embryonic sex ratios of 1:1 and synchronous parturition in autumn. However, given limitations with respect to sample size and temporal distribution inherent in this study, the reproductive parameters defined herein are necessarily preliminary. Nevertheless, this research challenges a range of findings emanating from other parts of the world and, in doing so, raises pertinent questions relating to the resilience to targeted fishing activities of these species in New South Wales waters compared to other oceanic regions. Moreover, it reinforces the importance of locally derived demographic parameters for population modelling and stock assessment.
Light-Regulated Transcription

This review focuses on light regulation of transcription, from light perception to changes in transcription, with an emphasis on regulatory elements in the promoters of light-regulated genes and proteins that bind to them. The abundance of over 100 mRNAs is regulated by light, and at least three photoreceptors influence transcription, but the importance of each photoreceptor may vary from gene to gene. Light-regulated promoters are composed of ubiquitous regulatory elements; the specific combination of elements appears to make a promoter light-regulated, and these combinations vary widely. Numerous proteins that bind to elements in light-regulated promoters have been identified and many have been cloned, but no cloned gene has been unequivocally assigned a function in light-regulated transcription. Substantial progress has been made in identifying steps in signal transduction from light perception to transcription, but these steps have yet to be assembled into complete pathways.
Temperature selection in wood turtles (Glyptemys insculpta) and its implications for energetics

Abstract For turtles in northern climates, the primary function of body temperature (Tb) regulation should be to maximize energy gain. The increase in energy gain with Tb is explained primarily by the increase in food consumption and passage rate, both of which have thermal reaction norms similar to that of metabolic rate. We measured Tb continuously for fed and food- deprived wood turtles (Glyptemys insculpta) in a dry thermal gradient and in an enclosure with access to water containers and infra-red radiation during the photophase. We also measured the increase in metabolic rate with Tb to estimate the increase in energy gain with increasing Tb. In the thermal gradient, fed juveniles maintained higher Tb. In the enclosure, feeding had no significant effect on Tb selection when infra-red radiation was available 10 h-d−1, but when infra-red radiation was available only 5 h-d−1 fed juveniles maintained higher Tb. Metabolic rate increased exponentially with Tb with a Q10 of 1.96 ± 0.10 (SD). We argue that, for turtles, the 95th percentile of selected Tb (Tupper) better approximates the optimal Tb for energy gain than the preferred Tb range (25th to 75th percentiles of selected Tb) commonly used in other studies. Tupper remained at 30 °C in all treatments, although Tb became increasingly skewed towards Tupper for fed turtles and when infra-red radiation was limited. We conclude that Tupper approximates the optimal Tb that fed turtles try to maintain.
In silico analysis of insect vitellogenin genes

Vitellogenins and yolk proteins are synthesized in oviparous animals to provide nutrients to the developing embryo. The complete vitellogenin gene sequences belonging to six different orders of Class Insecta have been retrieved from the GenBank to prepare a database. A comparative sequence analysis was carried out to gain better understanding of the evolution of vitellogenin genes. The conservation of residues was considerable and widespread throughout the coding region. However, the high level of divergence was observed in the size and positions of introns. This could be ascribed to the presence of repetitive DNA elements. Great sequence and structural diversity suggests that vitellogenin genes are highly evolving with selective functional constraints.
A mechanistic analysis of light and carbon use efficiencies

We explore the extent to which a simple mechanistic model of short-term plant carbon (C) dynamics can account for a number of generally observed plant phenomena. For an individual, fully expanded leaf, the model predicts that the fast-turnover labile C, starch and protein pools are driven into an approximate or moving steady state that is proportional to the average leaf absorbed irradiance on a time-scale of days to weeks, even under realistic variable light conditions, in qualitative agreement with general patterns of leaf acclimation to light observed both temporally within the growing season and spatially within plant canopies. When the fastturnover pools throughout the whole plant (including stems and roots) also follow this moving steady state, the model predicts that the time-averaged whole-plant net primary productivity is proportional to the time-averaged canopy absorbed irradiance and to gross canopy photosynthesis, and thus suggests a mechanistic explanation of the observed approximate constancy of plant lightuse efficiency (LUE) and carbon-use efficiency. Under variable light conditions, the fast-turnover pool sizes and the LUE are predicted to depend negatively on the coefficient of variation of irradiance. We also show that the LUE has a maximum with respect to the fraction of leaf labile C allocated to leaf protein synthesis ( alp), reflecting a trade-off between leaf photosynthesis and leaf respiration. The optimal value of alp is predicted to decrease at elevated [CO2]a, suggesting an adaptive interpretation of leaf acclimation to CO2. The model therefore brings together a number of empirical observations within a common mechanistic framework.
Comparative Study of Forest-Dwelling Bats' Abundances and Species Richness between Old-Growth Forests and Conifer Plantations in Nikko National Park, Central Japan

Abstract. To determine the influence of the forest type on bats in terms of roosting sites and foraging habitats, we compared species richness and abundance (total and by species) of forest-dwelling bats in old-growth forests and conifer (larch) plantations in central Japan. We also compared species richness and abundance of the bats in riparian and non-riparian habitats, and compared the old-growth forest stands with the larch plantation stands to examine differences in the forest stand structures. Species richness, total bat abundance, and the abundances of two tree-roosting specialists, the Ikonnikovi's Myotis (Myotis ikonnikovi) and the Ussurian tube-nosed bat (Murina ussuriensis), were significantly higher in the old-growth forests than in the conifer plantations. The old-growth forests contained larger trees and more snag trees, which provided roosting sites for tree-roosting species. Species richness, total bat abundance, and abundances of the two tree-roosting specialists and the Japanese large-footed bat (My. macrodactylus) were also significantly higher in the riparian habitats than in the non-riparian habitats. The riparian old-growth forest appears to be an important habitat for forest-dwelling bats. Our results suggest that a shift from old-growth forests to conifer plantations has negative effects on forest-dwelling bats, particularly tree-roosting specialists.
Occurrence of Marek's Disease in Vaccinated Poultry Flocks of Haryana (India)

Marek's Disease (MD), which is a lymphoproliferative disease of chickens, remains one of th e most important diseases. In the present study, occurrence of Marek's disease virus in ten vaccinated poultry flocks of Haryana (India) from different geographical locations was determined on the basis of clinical signs, gross and histopathology and precipitation test. The vaccines used were either HVT alone or in combination with SB-1. Samples from all the flocks had gross and histopathological lesions suggestive of Marek' s disease. Grossly, visceral tumors in liver, spleen, kidney and ovary were observed. The characteristic histopathological lesions included infiltration of pleomorphic lymphoid cells such as lymphoblasts, small and large lymphocytes, plasma cells and occasionally MD cells in different organs. The lesions were non- capsulated and infiltrative type. In immunodiffusion test, feather follicle tip samples from five flocks gave a positive precipitation reaction.