Miracle-dz/UniFAR-FTUs huggingface dataset:
A consideration of the techniques for estimation of milk yield by suckled sheep and a comparison of estimates obtained by two methods in relation to the effect of breed, level of production and stage of lactation

Summary Three techniques, lamb-suckling and test-weighing, hand- or machine-milking following administration of oxytocin, and measurements of body-water turnover, used for the estimation of milk yield in suckled sheep are discussed in relation to sources of error and comparability of estimates. Results are presented from an experiment in which the lamb-suckling and the oxytocin techniques were compared. The mean daily milk production of Scottish Blackface and East Friesland × Scottish Blackface ewes suckling single and twin lambs was measured by both methods at weekly intervals for 6 weeks. All ewes were well nourished to ensure full expression of milking capacity. Additional information from a similar experiment on Merino ewes is also presented. The oxytocin method gave higher estimates of mean daily milk yield in the first week of lactation, especially in the groups of ewes rearing single lambs and in the Blackface breed. By the second week in most groups and the third week in all groups there were no significant differences between estimates made by the two methods and the relative values of the estimates were not affected by level of milk production, number of lambs suckled or genotype of ewe and lamb.
Molecular characterization of bacteria and fungi from rice growing regions in Kenya.

The rice ecosystem provides a conducive habitat for various beneficial micro-organisms. The aim of this study was to characterize and identify soil micro-organisms from rice growing regions of Kenya using molecular approach. A total of 130 and 120 pure bacterial and fungal isolates, respectively, were used. Genomic deoxyribonucleic acid (DNA) was extracted and purified from the bacterial and fungal isolates. Universal primers were used to amplify the 16S rRNA and 18S rRNA gene regions of the bacterial and fungal isolates, respectively. Isolates sequences were identified by blastn analysis on the National Center for Biotechnology Information (NCBI) website. The known and closest match nucleotide sequences were retrieved from the GenBank database and used together with the isolates’ sequences to construct phylogenetic trees. Phylogenetic analysis was constructed using MEGA v 5.1 software. Sequence analysis of 16S rRNA gene indicated a high diversity of bacterial community belonging to the phyla Firmicutes, Proteobacteria and Actinobacteria. Majority of the isolates were closely affiliated with the genus Bacillus. All members of the fungal community belonged to the phylum Ascomycota, which was dominated by the genera Penicillium and Aspergillus. Thus, the Kenyan rice growing regions contain a relative diversity of bacteria and fungi that play important roles to the ecological health of the soil ecosystem.
An update on the COLOSS network and the “BEEBOOK: standard methodologies for Apis mellifera research”

Apis mellifera, honey bee, colony losses, monitoring, standardisation, COLOSS, BEEBOOK Journal of Apicultural Research 51(2): 151-153 (2012) © IBRA 2012 DOI 10.3896/IBRA.1. 51.2. 01 The international research network COLOSS (Prevention of honey bee COlony LOSSes)
of Serially-Sampled HIV Quasispecies

A new computational method to study within-host viral evolution is explored to better understand the evolution and pathogenesis of viruses. Traditional phylogenetic tree methods are better suited to study relation ships between contem poraneous species, which appear as leaves of a phylogenetic tree. However, viral sequences are often sampled serially from a single host. Consequently, data may be available at the leaves as well as the internal nodes of a phylogenetic tree. Recombination may further complicate the analysis. Such relations hips are not easily expr essed by traditional phylogenetic methods. We propose a new algorithm, called MinPD, based on minimum pairwise distances. Our algorithm uses multiple distance matrices and correlation rules to output a MinPD tree or network. We test our algorithm using extensive simulations and apply it to a set of HIV sequence data isolated from one patient over a period of ten years. The proposed visualization of the phylo genetic tree\network further enhances the benefits of our methods.
Glutamate-Dependent Activation of NF-κB During Mouse Cerebellum Development

NF-κB and activator protein 1 (AP-1) are dimeric transcription factors involved in transcriptional regulation in many cells, including neurons. We have examined their activity during mouse cerebellum development, a postnatal process starting just after birth and completed by the fourth postnatal (PN) week. The activity of these factors was analyzed by binding of nuclear extracts to a synthetic oligonucleotide representing the κB site of human immunodeficiency virus or the AP-1 site of the urokinase promoter. NF-κB activity was observed from 7 PN, was restricted to the developing cerebellum, and was not observed in the early postnatal neocortex and hippocampus. On the other hand, AP-1 activity was not found in cerebellum but was present in both neocortex and hippocampus. Moreover, a κB-driven transgene was found to be increasingly expressed in the cerebellum from 5 PN to 10 PN but not in the adult. The regulation of NF-κB activation in mouse cerebellum was analyzed by intraperitoneal injection of glutamate receptor antagonists to 9 PN mice, which abolished NF-κB-binding activity, suggesting an endogenous loop of glutamate receptor activation. Glutamate receptor agonists, on the other hand, induced NF-κB nuclear translocation in the cerebellum of 5 PN mice, which is a stage in which NF-κB is not yet endogenously activated. This effect was specific for NF-κB and not observed for AP-1. In adult mice, NF-κB activity was absent in the cerebellum and was not induced by intraperitoneal injection of glutamate receptor agonists. These data show that NF-κB is specifically activated during cerebellum development and indicate an important role of glutamate receptors in this process.
Molecular diversity of endobacterial communities in edible part of King oyster mushroom (Pleurotus eryngii) based on 16S rRNA

The diversity of endobacteria in the edible part (cap and stipe) king oyster mushroom (Pleurotus eryngii) was investigated using 16S rRNA sequence analysis. The bacterial 16S rRNA libraries were constructed from the body cap (BC) and the body stipe (BS) of the king oyster mushroom. The twenty sequenced BC clones were divided into four groups and the largest group was affiliated with the Firmicutes (40% of clones). While, the twenty sequenced BS clones could be divided into six groups and the largest group was affiliated with the Actinobacteria (40% of clones). The predominant bacterial family from both the cap and stipe of the mushroom was corresponded with the Gram positive bacteria (62.5%).
Transient Gene Expression in Plant Cells Mediated by Agrobacterium tumefaciens: Application for the Analysis of Virulence Loci

Yasushi Yoshioka, Yoshito Takahashi \ Ken Matsuoka, Kenzo Nakamura, Jun Koizumi, Mineo Kojima and Yasunori Machida 1 Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-01 Japan 2 Laboratory of Biochemistry, Faculty of Agriculture, Nagoya University, Chikusa-ku, Nagoya, 464-01 Japan 3 Department of Applied Biology, Shinshu University, Tsuneta 3-15-1, Ueda, Nagano, 386 Japan
APPLICATION OF RAPD AND ISSR MARKERS TO ANALYSES MOLECULAR RELATIONSHIPS IN AZERBAIJAN WHEAT ACCESSIONS (TRITICUM AESTIVUM L.)

Sadigova, S. , H. Sadigov, R. ESHgHi, S. SalayEva and J. oJagHi, 2014. application of Rapd and iSSR markers to analyses molecular relationships in azerbaijan wheat accessions (triticum aestivum l.). Bulg. J. Agric. Sci., 20: 87-95 To estimate genetic relationships of 33 wheat accessions originating from different regions of azerbaijan Republic, Rapd and iSSR analysis was performed with 22 and 20 primers, respectively. The most discriminating primers were opg-20, opH-01, opE-02 and opg-08 for Rapd and iSSR-8, iSSR-11, iSSR-19 for iSSR which showed the highest values of genetic diversity. a high level of polymorphism was found with both Rapd and iSSR markers, and the mean genetic diversity values were 0.789 and 0.863 for Rapd and iSSR markers, respectively. in Rapd analyses, 319 out of 374 bands (84.89%) were polymorphic. The number of alleles ranged from 8 to 30 per primer, with an average of 17 per primer. in iSSR analyses, a total of 350 alleles were detected, among which 318 alleles (90.85%) were polymorphic. The number of alleles per primer ranged from 10 to 26 with an average of 17.5 alleles per iSSR primer. Cluster analyses indicated that both Rapd and iSSR markers could distinguish all 33 wheat accessions. although the analysis of Rapd and iSSR markers could successfully be used to investigate the genetic diversity of the wheat accessions, the iSSR markers were superior to Rapd markers in the capacity of revealing more informative bands in a single amplification. In addition, ISSR analyses are more specific than RAPD analyses, due to the longer SSR-based primers with higher primer annealing temperature, which enable higher-stringency and greater band reproducibility amplifications.
OSNABRÜCK NET PRIMARY PRODUCTIVITY DATA SET

An extensive compilation of nearly 700 field estimates of net primary productivity of natural and agricultural ecosystems worldwide was synthesized in Germany in the 1970s and early 1980s. The literature cited dates from 1869 to 1982, with the majority of references from the 1960s and 1970s. Although the Osnabruck data set has not been updated since the 1980s, it represents a wealth of information for use in model development and validation. This data paper documents the development of this data set, its contents, and its recent availability on the Internet, both in Ecological Archives on the Ecological Society of America's web site, and in a “mirror” copy at the Oak Ridge National Laboratory Distributed Active Archive Center for Biogeochemical Dynamics. The version presented here (version 2.0) incorporates amendments suggested by data users over the past two years. Caution is advised in using these data, which necessarily include assumptions that may not be universally applicable to all study sites and records. Nevertheless, we consider these “Class III” data to be useful, even though they may not meet the “Gold Standards” which are being developed for this type of data (mainly because the documentation may be incomplete, not because the numbers themselves are of poor quality).
Effect of phosphorus sources and mycorrhizal inoculation on root colonization and phosphorus uptake of barley (Hordeum vulgare L.)

The majority of land plants (more than 90% all species) form a symbiotic association with soil fungi called mycorrhiza (myco = fungus, rhiza = root) (Sylvia, 1999). Mycorrhizae are a form of fungi that are able to grow and survive colonized with the host green plants. Both the fungus and the plant benefit from the association. Mycorrhizae take carbohydrates (sugars) from the plant in return for improving the supply of plant nutrients and water from the soil. In this relationship, mycorrhizae take over the role of the plant s root hairs and actions as an extension of the root system (Jakobsen and Abbott, 1992; Pellerin et al., 2007).
Extraction and Purification of Mycobacterial Mycolic Acids

[Abstract] Mycolic acids are major long-chain fatty acids, containing up to 80-90 carbon atoms that represent essential components of the mycobacterial cell wall (Pawelczyk and Kremer, 2014). Each mycobacterial species possesses a specific mycolic acid profile characterized by various chemical modifications that decorate the lipid. Mycolic acids play a critical role in the architecture and impermeability of the cell envelope, hence the natural resistance of mycobacteria to most antibiotic treatments. They are also key determinants of virulence in pathogenic species, including Mycobacterium tuberculosis (M. tuberculosis), the causative agent of tuberculosis. In addition, they are known as the primary target of several first-line and second-line antitubercular drugs. Thus, the unique enzymes involved in the mycolic acid biosynthetic pathway represent an attractive reservoir of targets for future chemotherapy whose developments are particularly warranted in the context of multi-drug-resistant and extensively-drug-resistant strains of M. tuberculosis. Herein, we describe a protocol to extract the mycolic acids from mycobacteria. Purification of the various subspecies may be particularly useful for subsequent structural studies involving mass spectrometry or NMR. The qualitative and quantitative biochemical characterization of the mycolic acid pattern by thin layer chromatography can be used to address how drugs alter mycolic acid biosynthesis (Alahari et al., 2007, Hartkoorn et al., 2012), to study the phenotypes of genetically modified mutants affected in this metabolic pathway (Bhatt et al., 2007) or to unravel new mycolic acid regulatory mechanisms (Vilcheze et al., 2014). The same protocol can be applied to all mycobacteria, including environmental and pathogenic species.
A revision of genus Toxorhynchites Theobald, 1901, in the South-East Asian countries, with description of a new species Toxorhynchites (Toxorhynchites) darjeelingensis from West Bengal, India (Diptera, Culicidae)

The genus Toxorhynchites (Tribe Toxorhynchitini), comprising 89 species worldwide which are organized under four subgenera (Afrorhynchus, 19 species; Ankylorhynchus, 4 species; Lynchiella, 16 species and Toxorhynchites, 50 species), is characterized by mosquitoes that do not feed on blood; instead they subsist on variety of plant juices and have their mouth parts commensurately designed. Globally there are about 3,543 species of mosquitoes (Family: Culicidae), of which nearly 3,061 species are culicines under Subfamily Culicinae that is further divided into eleven tribes one of which is Toxorhynchitini Lahille, 1904, represented by a solitary genus Toxorhynchites Theobald, 1901. Species of the subgenus Toxorhynchites alone are prevalent in the southeastern Asian countries (Indonesia, 12 species; India, 9 species; Thailand, 8 species; Bangladesh, 2 species; Sri Lanka, 2 species; DPR Korea, 1 species; Myanmar, 1 species; and Nepal, 1 species). A taxonomic comparison is made amongst all taxa endemic to these countries. Ironically no species of Toxorhynchites has ever been reported from Bhutan, Maldives and Timor-Leste. Toxorhynchites (Tox.) splendens is the most common species amongst all and has so far been recorded from only seven countries including India which is a home for as many as ten species, including the current Tx. (Tox.) darjeelingensis sp. n. collected from the foothills of Darjeeling Himalayan Mountains in the West Bengal State. Toxorhynchites (Tox.) darjeelingensis sp. n. is described, with a comparison offered with its closest allies, i.e., Tx. bengalensis, Tx. splendens and Tx. tyagii.
Generalized Transduction in Rhizobium leguminosarum

Generalized transduction in Rhizobium leguminosarum by two virulent bacteriophages, RL38 and RL39, is described. The transduction frequency was increased by ultraviolet irradiation of phage lysates. Cotransduction of auxotrophic and antibiotic resistance markers was shown, as was transduction of two PI group R plasmids. Transduction between strains of Rhizobium trifolii and interspecific transduction from R. leguminosarum to R. trifolii occurred but no transduction from R. trifolii to R. leguminosarum was detected.
An energy‐biochar chain involving biomass gasification and rice cultivation in Northern Italy

The competing demand for food and bioenergy requires new solutions for the agricultural sector as, for instance, the coupling of energy production from gasification technology and the application of the resulting biochar as soil amendment. A prerequisite for the implementation of this strategy is the scale‐specific assessment of both the energetic performance and of the impacts in terms of greenhouse gases (GHG) emission and crop responses. This study considered the gasification process developed by Advanced Gasification Technology (AGT, Italy), which is a fixed‐bed, down‐draft, open core, compact gasifier, having 350 kW of nominal electric capacity (microgeneration); this gasifier uses biomass feedstock deriving from agricultural/forest products and byproducts. In this study, the resulting biochar, derived from conifer wood chips of mountain forestry management in North‐western Italy, was applied to a nearby paddy rice field, located in the largest rice agricultural area of Europe. We performed a Life Cycle Analysis (LCA) adapting the BEAT2 model specifically focusing on the GHG balance of the supply chain, from the forestry management to the field distribution of the resulting biochar. The results indicated that the gasification stage had the highest impact in the supply chain in terms of emissions, but net emissions allocated to biochar were always negative (ranging between −0.54 and −2.1 t CO2e t−1 biochar), hypothesizing two scenarios of 32% and 7.3% biochar mineralization rate in soil, over a time period of 100 years. Finally, biochar had a marginal but positive effect on rice yield, thus increasing the sustainability of this energy‐biochar chain.
Habitat use patterns by ground beetles (Coleoptera: Carabidae) of northeastern Iowa

Summary Ground beetle assemblages were monitored in six different habitats (tallgrass prairie, oats, corn, soybean, old-field, woods) at four sites in northeastern Iowa from 1994 to 1998. The objective of this study was to quantify the influence of habitat type on the activity and distribution of ground beetles. Over five years, 13,654 ground beetles representing 107 different species were captured. Of these, 14 species represented 85% of the captured beetles. Based on habitat use, we categorized 24 as generalist species, 14 as agricultural species, 12 as grassland species, 39 as prairie specialists, and 19 as woodland species. Tallgrass prairie hosted a significantly more (P
International Journal of Food Science, Nutrition and Dietetics (IJFS) ISSN 2326-3350

The enzyme linked immunosorbent assay (ELISA) is a potential tool for the determination of dextran. In this study, dextran-BSA antigens were prepared by Reductive amination method, and were confirmed by SDS-PAGE and free amino detection. The effects of coupled reac- tion conditions such as different oxidation degree of dextran, the reaction time were investigated and the immunity of the resulting dextran- BSA neoglycoprotein antigens were evaluated through the interaction with standard dextran antibody. The immunogen was immunized with white rabbits to obtained polyclonal antibody respectively. A general and broad class-specific Elisa detection method was developed according to Elisa theory. The method was put to use for quantitative analysis of dextran in practical saccharose samples.
Determination of PNEC for selected decontaminants based on seed germination and vigor indexes of terrestrial plants / Wyznaczenie wartości PNEC dla wybranych odkażalników w oparciu o indeksy kiełkowania i wigoru roślin lądowych

Abstract Due to the existing threat of use of CWA, many countries developed special chemical formulations dedicated to remove CWA - the so-called military decontaminants. The function of the decontaminant is to neutralize the toxic properties of the contaminant through chemical reactions: oxidation and nucleophilic substitution. The decontaminants released to the environment may transform to toxic products which have a harmful impact on plants and other soil biota. To evaluate the impact of these chemicals on plants phytotoxicity, early growth tests with Sinapis alba, Lepidium sativum and Sorghum saccharatum were used. Parallely with standard toxkit endpoints (seed germination and root elongation, data not presented here), seed vigor indexes and germination indexes were calculated. GI is a more sensitive endpoint in phytotoxicity testing than SVI. The EC50-72h values based on GI are about 2-3 times lower than those based on SVI. Very low PNEC soil values indicate that wide usage of such compositions in case of CWA release will cause damage to vegetation in the environment. Streszczenie W związku z nieustannie istniejącym zagrożeniem użycia bojowych środków trujących, wiele państw Świata wprowadziło w wyposażenie armii specjalnie przygotowane formulacje chemiczne - tzw. odkażalniki wojskowe. Zadaniem odkażalników jest neutralizacja toksycznych właściwości bojowych środków trujących, poprzez reakcje utleniania oraz substytucję nukleofilową. Odkażalniki te, po przedostaniu się do środowiska naturalnego, mogą tworzyć produkty o wysokiej toksyczności w stosunku do składowych ekosystemu, w tym organizmów roślinnych. W celu oceny fitotoksyczności badanych odkażalników wojskowych, przeprowadzony został krótkoterminowy test Phytotoxkit z Sinapis alba, Lepidium sativum oraz Sorghum saccharatum. Oprócz standardowych punktów końcowych (kiełkowanie nasion i wydłużanie korzeni, dane nieprezentowane w artykule) w teście oznaczony został indeks kiełkowania oraz indeks wigoru nasion. Wartości uzyskane dla indeksu kiełkowania nasion były ponad 2-3 razy niższe niż analogiczne wartości uzyskane dla indeksu wigoru. Obliczone w pracy wartości PNEC wskazują na możliwość wystąpienia znacznego zagrożenia dla ekosystemów glebowych w przypadku masowego zastosowania badanych odkażalników wojskowych w celu dekontaminacji skażonego terenu.
Two New Species of Cnemidophorus (Squamata: Teiidae) from Islands of the Northeastern Coast of Venezuela

Abstract We describe two new whiptail lizard species, previously assigned to Cnemidophorus lemniscatus, from islands of the state of Nueva Esparta and Los Frailes Archipelago, off the northeastern coast of Venezuela. The two new species differ from C. lemniscatus in color, pattern, and squamation. The species from the islands of Margarita and Cubagua can be distinguished from the one of Los Frailes Archipelago in having the circumorbital semicircles extending further anteriorly, more scales between supraocular and supraciliaries, and a larger number of scales of a smaller size between the preanal shield and anal spurs. The two new species also differ conspicuously in color and pattern of both sexes and all age classes. Additionally, we comment on the status of the population of Cnemidophorus of Los Testigos Archipelago, discuss the morphological and color variation observed in C. lemniscatus from northern Venezuela and restrict the distribution of the latter species in the country to the mainland.
ETIOLOGY AND EVALUATION OF SPERM CHROMATIN ANOMALIES

Evidence suggests that human sperm chromatin anomalies adversely affect reproductive outcomes and infertile men possess substantially amount of sperm with chromatin anomalies than fertile men. Routine semen analysis evaluates parameters such as sperm motility and morphology, but does not examine the nuclear DNA integrity of spermatozoa. It has been suggested that altered nuclear chromatin structure or damaged DNA in spermatozoa could modify the special cellular functions of human spermatozoa, and thereby affect the fertility potential. Intra-cytoplasmic sperm injection (ICSI) bypass the barriers to fertilization for such a sperm, then the effect of chromatin anomalies on the development remains a concern. Therefore, it is essential to develop and use accurate diagnostic tests, which may provide better prognostic capabilities than the standard sperm assessments. This review discusses our current understanding of the structure and organization of sperm DNA, the different procedures for assessment of sperm chromatin anomalies including comet assay, Chromomycin A3 (CMA3), sperm chromatin structure assay (SCSA), acridine orange test (AOT), terminal TdT-mediated dUTP-nick-end labelling (TUNEL) assay, aniline blue and sperm chromatin dispersion (SCD) test and the impact of chromatin anomalies on reproductive outcome.