Miracle-dz/UniFAR-FTUs huggingface dataset:
First evidence of the Jurassic thalattosuchian (both teleosaurid and metriorhynchid) crocodylomorphs from Slovakia (Western Carpathians)

Abstract We report here finds of thalattosuchians from Western Carpathians. The material consists of two isolated teeth from two different localities of the Pieniny Klippen Belt. The material represents the first evidence of the occurrence of both clades Teleosauridae and Metriorhynchidae in Slovakia. The first, a small tooth comes from the locality Beňatina and is dated early Middle Jurassic (Aalenian). Identification of the specimen shows it belongs to a longirostrine teleosaurid, possibly to Steneosaurus. Teleosaurids were largely restricted to lagoonal/near-shore environments. Their limbs allow them to support and walk on land. Regarding that fact, the presence of this taxon in Beňatina might be an indication of terrestrial land in the nearby area and shows a location of epicontinental seaways. A second larger tooth was found in the Upper Jurassic (Tithonian) sediments of the locality Kyjov, and is tentatively allocated in the genus Plesiosuchus. The members of Plesiosuchina are known in England, France, Portugal and Sicily. Our findings indicate a much wider spatial distribution of this clade in Europe and it fits well with the previous interpretation of sediments of the locality Kyjov as deep-water pelagic deposits.
The effect of a high forage diet and different oil blends on rumen fermentation in vitro

The experiment was carried out in a Rusitec system. The effect of diet (control-fresh lucerne plus maize, 60:40%) and fat sources (linseed LO, rapeseed RO, fish FO oils) as oil blends (LO+RO, FO+LO, FO+LO+RO, 5%wt.wt-1) on rumen fermentation was studied. The experiment lasted 13 days. To ensure a steady state within the Rusitec vessels a 7-day adaptation period preceded a 6-day collection period. The diet with a 5% addition of oil blends, LO+RO, LO+FO, LO+FO+RO, was added to the fermentation vessels daily. Supplementation with blends (LO+RO, LO+FO, LO+FO+RO) did not affect some basal parameters of rumen fermentation (pH, total VFA production, dry matter digestibility) in comparison with the control. Detergent fibre digestibility was significantly reduced, mainly with LO+RO+FO (NDF,ADF, cellulose) and LO+RO (ADF). The oil blends significantly reduced the mol% of acetate, n-butyrate, A/P ratio, and increased the mol% of propionate. The oil blends supplemented to the high forage diet significantly (P<0.005) decreased the efficiency of microbial protein synthesis.
Breeding program for indigenous chicken in Kenya

Abstract Ngeno, K. (2015). Breeding program for indigenous chicken in Kenya. Analysis of diversity in indigenous chicken populations. PhD thesis, Wageningen University, the Netherlands The objective of this research was to generate knowledge required for the development of an indigenous chicken (IC) breeding program for enhanced productivity and improved human livelihood in Kenya. The initial step was to review five questions; what, why and how should we conserve IC in an effective and sustainable way, who are the stakeholders and what are their roles in the IC breeding program. The next step of the research focused on detecting distinctive IC ecotypes through morphological and genomic characterization. Indigenous chicken ecotypes were found to be populations with huge variability in the morphological features. Molecular characterization was carried out using microsatellite markers and whole genome re-sequenced data. The studied IC ecotypes are genetically distinct groups. The MHC-linked microsatellite markers divided the eight IC ecotypes studied into three mixed clusters, composing of individuals from the different ecotypes whereas non-MHC markers grouped ICs into two groups. Analysis revealed high genetic variation within the ecotype with highly diverse MHC-linked alleles which are known to be involved in disease resistance. Whole genome re-sequencing revealed genomic variability, regions affected by selection, candidate genes and mutations that can explain partially the phenotypic divergence between IC and commercial layers. Unlike commercial chickens, IC preserved a high genomic variability that may be important in addressing present and future challenges associated with environmental adaptation and farmers’ breeding goals. Lastly, this study showed that there is an opportunity to improve IC through selection within the population. Genetic improvement utilizing within IC selection requires setting up a breeding program. The study described the systematic and logical steps in designing a breeding program by focusing on farmers’ need, how to improve IC to fit the farming conditions, and management regimes.
Molecular Cloning and Characterization of an Anthocyanidin Synthase Gene in Prunus persica (L.) Batsch

To elucidate the effect of anthocyanidin synthase (ANS) gene on anthocyanin accumulation in fruit skin of Prunus persica (L.) Batsch cv. 'Chunmei', this study cloned and characterized an ANS gene ( PpANS ) from peach. PpANS (GenBank accession No. KX760117) was encoded by a 1074 bp-long open reading frame (ORF) corresponding to a polypeptide consisting of 358 amino acids with a molecular mass of 40.45 kD and an isoelectric point of 5.46. PpANS contains a conserved 2-oxoglutarate- and iron-dependent dioxygenases and non-haem dioxygenase binding regions. PpANS shared high similarities to angiosperm ANS and displayed the closest genetic relationship to Prunus domestica . Real-time PCR analysis indicated that PpANS was highly expressed in fruit skin, flesh and flowers, and peach fruit skin showed the highest transcript level of PpANS . Anthocyanin accumulation analysis indicated that it was highly accumulated in fruit skin and flesh of peach. Changes in the transcript level were highly correlated with anthocyanin content in the different tissues of peach. Prokaryotic expression analysis showed PpANS that protein can be expressed correctly in E. coli , and the size of PpANS recombinant protein was consistent with its predicted size. In vitro enzyme activity assay revealed that recombinant PpANS protein could catalyze the formation the cyanidin from leucocyanidin. These results indicated that PpANS was responsible for anthocyanin accumulation in P. persica .
Measuring Mating Success Of Transgenic Versus Wild-Type Male Medaka To Help Estimate The Risk Of Gene Flow To Wild Populations

Abstract Genetically engineered fish are likely to become the first transgenic animal approved for commercial farming for human food. Transgenic fish escaping from fish farms could interbreed with wild relatives. This raises the need to assess whether their transgenes would spread into the wild populations or be purged by natural selection [5, 7, 10, 11, 13]. A net fitness model can be used to estimate the fate of a transgene. I examined mating advantage, one of six net fitness traits in the model, and tested the hypothesis that growth-enhanced transgenic male medaka have a mating advantage over wild-type males [10, 13]. I used one line of medaka ( Oryzias latipes ) bearing a salmon growth hormone gene construct that enhances growth rate and final size. I randomly selected five pairs of wild-type and transgenic males competing for five wild-type females and recorded which male attained the first successful mating in each of five trials, of five copulations each. I then placed the fish together according to a Latin Square Design (Table 1) and rotated each male accordingly to encounter with a different male and female [1]. Statistical analyses of these results indicate that there is no difference (p 0.30) between the mating advantage of transgenic and wild-type males in this line, a result that reinforces the need to test each transgenic line before drawing conclusions.
The primary motor cortex is critical for the retention of implicit sensorimotor adaptation

Sensorimotor adaptation, or adaptation of movements to external perturbations, is thought to involve the primary motor cortex (M1). In addition to implicit error-driven remapping, explicit re-aiming strategies also contribute to sensorimotor adaptation. However, no studies to date have examined the role of M1 in implicit learning in isolation from explicit strategies. Because the application of explicit strategies requires time, it is possible to emphasise implicit learning by controlling the time available to prepare movement. Here, we examined the role of M1’s role in implicit adaptation to rotated visual feedback whilst suppressing the use of explicit re-aiming strategies by limiting movement preparation times to less than 350ms. Perturbing M1 activity via single-pulse TMS during adaptation to a 30 ° rotation of visual feedback did not alter the rate or extent of error compensation, but elicited poorer retention in post-adaptation trials with no perturbation. This work shows that M1 is critical in the retention of new visuomotor maps as a result of implicit adaptation to a perturbation in sensory feedback when strategic error correction processes are suppressed. Highlights Adaptation of movements to perturbations occurs through explicit and implicit processes. Here, explicit strategies were suppressed by shortening movement preparation time. Perturbing motor cortex (M1) with TMS selectively impaired retention but not acquisition of sensorimotor adaptation. M1 plays a crucial role in retention of sensorimotor adaptation obtained via implicit learning.
Seasonal Variations in the Content of Nutrient Elements in the Leaves of Fig (Ficus carica L. Yesilguz)

Seasonal variations of N, P, K, Na, Ca, Mg, Fe, Zn, Mn and Cu contents in the leaves of fig were studied. Samples were taken from the 10 years old trees of fig (Ficus carica L. cv. Yesilguz). Leaf sampling was carried out on the third node, which was counted from the base of the shoots from April to November. The purpose of the present experiment is to find seasonal changes in macro and micro nutritive elements in the leaves at different phenological periods. According to results, the N, P, K, Na, Ca and Mg contents varied between 1.71-5.45 %, 0.05-0.34 %, 0.35-1.15 %, 0.02-0.04 %, 0.68-2.98 % and 0.38-0.68 %, respectively. Micro nutrient elements content, which were Fe, Zn, Mn and Cu varied between 65.58-89.43 ppm, 11.57-34.98 ppm, 24.10-46.53 ppm, 2.93-8.45 ppm, respectively. The nutrient status of leaf samples was low in terms of K, Ca, Mg, Fe, Mn and Cu.
Oviposition site selection by a lepidopteran leafminer in response to heterogeneity of leaf surface conditions: structural traits and microclimates

1. Leafminer larvae are sedentary and make feeding tracks called mines. Their spatial distribution in trees affects their growth and survival through interaction with the heterogeneity of environments, such as leaf traits and microclimate. Lepidopteran leafminers that mine lower leaf surfaces have shown evolutionary radiation, suggesting that lower surfaces improve leafminer performance.
Quantitative Determination of Benzoic Acid, Sorbic Acid and Saccharin in Preserved Fruits

The recovery test of benzoic acid, sorbic acid and saccharin added in preserved fruit by high performance liquid chromatography was studied. The percentage of recovery found at the concentration levels 10-30 mg/kg was 94-101. It can be modified to determine these food additives in sour preserved fruit (pH<3). This method consumes less time but provides better precision than the Association of Official Analytical Chemists' method which determines the additives individually. Key words: Preservatives, Sweetener, Benzoic acid, Sorbic acid, Saccharin
Characterization of Macrophomina phaseolina isolates affecting sunflower growth in El-Behera Governorate, Egypt

Thirty three Macrophomina phaseolina isolates were recovered from different regions where sunflower was grown in ElBehera governorate during the 2003 and 2004 growing seasons. Housh Eisa and Abo El-Matameer were the most affected regions as 33.3% and 30.3% of the total isolates were recovered, respectively. This was followed by Etay El-Barood, where 12.1% of the isolates were recovered. Occurrence of M. phaseolina in rest of the surveyed regions i.e., El-Dalangat, Kafr ElDawar and El-Mahmoudia was less than 10%. The recovered M. phaseolina isolates were characterized for pathogenicity, colony phenotype, protein banding pattern and the random amplified polymorphic DNA (RAPD). All the recovered isolates were pathogenic to both of the tested sunflower cultivars, H11-008 and H11-009, in the pathogenicity test. However, 27.8% of the isolates (combined data) were identified as highly, 28.1% intermediately and 44.1% lowly pathogenic phenotype. Five color phenotypes and six growth patterns were recognized on PDA, Czapek-Dox and Chlorate media. These were white, grey, black, dark green and brown colony color phenotypes; grey being the most frequent (30.3%). Colony growth patterns recognized were the dense, light, sparse dense, sparse, restricted and shy growth; dense being the most frequent (40.3%). Eleven isolates i.e., 33.3% of the total 33 M. phaseolina isolates analyzed, were Chlorate sensitive, while rest were Chlorate resistant. All the isolates showed the expression of 8 100 kDa polypeptides with 78.4% mean content and exhibited 6 20 polypeptide bands in this kDa range with 34.5% of the isolates were differentiated with unique bands. At the higher 101 300 kDa protein analysis, 27.4 51.3% of the isolates only contained polypeptides of this kDa range with little variation (2 6 bands) and less differentiation (6.7 21.7%). Moreover RAPD-PCR analysis using eight random oligonucleotide primers revealed DNA fingerprints 2 9 bands ranging from 350bp to 3kbp. However, no variations were revealed for number of bands between isolates with primers OPS-16 or OPA-2, while more variations were revealed with OPA-1, OPA-4, OPA-5, OPA-8, OPA-13 and OPR-14 primers. The stem type of M. phaseolina isolates exhibited higher pathogenicity as revealed from size of the lesions incited, plant death and plant head reduction in the pathogenicity tests as compared to the root type of isolates showing these values as 6.1 cm, 37.9% and 37.4%. However, no distinct colony phenotype or protein banding pattern was linked to any of the both types of isolates or even any of the high, intermediate and the low pathogenic phenotypes. However, the RAPD-PCR phylogenetic analysis did not reveal known genetic entities for the stem type and the root type of isolates, since it did revealed two clusters for the high pathogenic isolates and the low pathogenic isolates in the Dendrogram of the tested M. phaseolina isolates.
Determination of optimal harvest boundaries for Honeycrisp™ fruit using a new chlorophyll meter

DeLong, J., Prange, R. , Harrison, P., Nichols, D. and Wright, H. 2014. Determination of optimal harvest boundaries for Honeycrisp™ fruit using a new chlorophyll meter. Can. J. Plant Sci. 94: 361-369. In this study, a new chlorophyll measurement tool [the delta absorbance (DA) meter] was used to develop an optimal harvest maturity model for Honeycrisp™ fruit. Apples from nine commercial orchards in the Annapolis Valley, Nova Scotia, Canada, were sampled over 11 consecutive weekly harvests during the 2010, 2011 and 2012 growing seasons. At each harvest, a sample of fruit was measured for its DA (IAD) values, firmness, titratable acidity (TA),% soluble solids content (SSC), red skin coloration and internal core ethylene. Following approximately 3 mo of storage at 3.5°C, samples were removed and assessed for disorder incidence. The optimal harvest period was identified by aligning all “at harvest” IAD values, fruit quality measurements and “post-storage” disorder data with the corresponding harvest week. Then, the IAD values associated with the harvests having high commercial fruit quality and the least collective expression of disorders, delineated the optimal harvest boundaries. As IAD units declined during fruit maturity, the upper boundary value of 0.59 was deemed “when to begin” harvest, while the lower boundary value of 0.36 was deemed “when to end” harvest for long-term storage. The use of the DA model approach for optimal harvest delineation is potentially applicable to all commercial apple cultivars, but should be developed for each within a distinct growing region.
Pneumolysin as a vaccine and study of structure and function

Streptococcus pneumoniae is a Gram-positive bacterium capable of causing the life threatening invasive diseases pneumonia, septicemia and meningitis. It can also cause the highly prevalent, but less serious diseases, acute otisis media (AOM) and sinusitis. Pneumolysin, a 52Kda protein toxin, is not only an important virulence factor of Streptococcus pneumoniae but toxoid versions can be protective immunogens, although they suffer from residual activity. The toxin is produced by all serotypes and has very limited structural variation. Structurally pneumolysin consists of four domains. The mechanism of action of pneumolysin has been proposed to involve binding to the cell surface via its domain 4, then the toxin monomers oligomerize on the cell surface and finally structural changes in domain 3 results alpha helices being converted into beta hairpins that insert into the membrane to form a pore. To understand how the structure explains this function of pneumolysin, two sets of mutants were constructed to investigate the role of individual amino acids in these events. In one set, cystine bridges were introduced to lock different domains; C262+C278 was found to have locked TMH2. In the second set, mutants were made to test hypotheses on which amino acids took part in oligomerization, a double mutant 18A: 84A was found to be inactive. Currently the available pneumococcal vaccines are polysacchride based (Pneumovax) and a protein conjugate vaccine (Prevenar). The problem with Pneumovax is that it does not elicit protection in people at high risk and it covers only 23 serotypes. Prevenar is expensive and has even more limited serotype coverage. An ideal vaccine solution would be a molecule with little or no variation among different serotypes and capable of inducing a T-cell dependent response. The functionally important C-terminal domain of pneumolysin (D4) was investigated for its immunogenicity as a protective antigen and as an adjuvant. Domain 4 (D4) of pneumolysin elicits antibody response and boost it as an adjuvant but didn’t provide protection on its own. Domain 4 mixed in equimolar amounts with domains 1-3 was nontoxic and it provided protection against a lethal dose of S. pneumoniae.
Adult-specific trimethylation of histone H3 lysine 4 is prone to dynamic changes with aging in C. elegans somatic cells

Tri-methylation on histone H3 lysine 4 (H3K4me3) is associated with active gene expression but its regulatory role in transcriptional activation is unclear. Here we used Caenorhabditis elegans to investigate the connection between H3K4me3 and gene expression regulation during aging. We uncovered around 30% of H3K4me3 enriched regions to show significant and reproducible changes with age. We further showed that these age-dynamic H3K4me3 regions largely mark gene-bodies and are acquired during adult stages. We found that these adult-specific age-dynamic H3K4me3 regions are correlated with gene expression changes with age. In contrast, H3K4me3 marking established during developmental stages remained largely stable with age, even when the H3K4me3 associated genes exhibited RNA expression changes during aging. Moreover, we found that global reduction of H3K4me3 levels results in significantly decreased RNA expression of genes that acquire H3K4me3 marking in their gene-bodies during adult stage, suggesting that altered H3K4me3 levels with age could result in age-dependent gene expression changes. Interestingly, the genes with dynamic changes in H3K4me3 and RNA levels with age are enriched for those involved in fatty acid metabolism, oxidation-reduction, and stress response. Therefore, our findings revealed divergent roles of H3K4me3 in gene expression regulation during aging, with important implications on physiological relevance.
Aeration rate effect on the growth kinetics, phytase production and plasmid stability of recombinant Escherichia coli BL21 (DE3)

Phytase production using Escherichia coli BL21 (DE3), a recombinant strain harboring a plasmid encoding thermostable Bacillus phytase, in semi-industrial scale was studied in this work. Among the factors needed to be considered in order to achieve high enzyme yield, aeration rate plays an important role. Suitable aeration is required to supply cells with sufficient amount of air for cell and phytase production. The effect of different aeration rates, (1.0, 2.0 and 3.0 vv-1min-1), on the kinetics of cell growth and phytase production by the recombinant E. coli BL21 (DE3) in 16-L pilot scale stirred tank bioreactor was investigated. The highest cell concentration of 3.81 gL-1 concomitant with the maximal total phytase production of 15.63 UmL-1 were obtained in a bioreactor of aeration rate 3.0vv-1min-1. At this high aeration rate, a maximal specific growth rate (μmax) and the maximal specific phytase production of 0.33 h-1 and 4102Ug-1, respectively, were achieved.
Suitability of cover crop monocultures for late-season forage in South Dakota

Hansen, M. J., Owens, V. N. , Beck, D. and Sexton, P. 2013. Suitability of cover crop monocultures for late-season forage in South Dakota. Can. J. Plant Sci. 93: 589-597. Cover crops provide many agronomic benefits and can produce large amounts of forage that is suitable for grazing. The objectives of this study were to determine (1) suitable cover crop forages based on yield and nutrient values; and (2) changes in feed value and yield of these crops through the late fall. Five cover crop monocultures consisting of lentil (Lens culinaris Medikus), cowpea (Vigna unguiculata L.), foxtail millet (Setaria italica L.), oats (Avena sativa L.), forage radish (Raphanus sativus L.), and a mixture of these crops were planted after winter wheat (Triticum aestivum L.) harvest in 2010 and 2011 in central and southeastern South Dakota. Forage data were collected on approximately Oct. 01, Nov. 01, and Dec. 01 each year. Yields increased after the first harvest date at both sites, both years. Oats, radish, and the cover crop mixture all yielded >4000 kg of dry matter per hectare on the second harvest date in 2011 in central South Dakota and radish and oats yielded >4000 kg ha-1 in southeastern South Dakota on the second and third harvest dates, respectively. Forage quality tended to decrease after each harvest date. Radish in central South Dakota in 2010 had the highest protein values for the study (194-313 g kg-1) whereas oats in southeastern South Dakota had the lowest protein concentrations (63-108 g kg-1), both years. All cover crops except cowpea were viable forages through the late fall when they had good establishment with the potential need for protein supplementation with oats, foxtail millet, and the cover crop mixture, depending on animal requirements.
HPLC Profiling and Evaluation of In-vitro Antioxidant Activity of Cirsium arvense L. (Family: Asteraceae)

This study evaluated HPLC analysis and in-vitro antioxidant activity of Cirsium arvense commonly known as Canada thistle that has been used to treat various diseases as traditional medicine. The different antioxidant assays such as DPPH free radical scavenging, nitric oxide scavenging, hydrogen peroxide scavenging, superoxide radical scavenging, reducing power, ferrous ions chelating ability, total phenolic, flavonoids and tannin contents were studied. Moreover, high performance liquid chromatography (HPLC) coupled with diode-array detection was used to identify and quantify the phenolic compounds present in C. arvense. The ethanol extract of Cirsium arvense showed dose-dependent antioxidant activity compared to the standard in different antioxidant activity tests. P-coumaric acid, rutin hydrate, quercetin and kaemferol were identified in the extract. Among the phenolic compounds, quercetin was abundantly present in the extract. Our exploration suggests that C. arvense contains high amount of phenolic compounds which may be responsible for its biological activities in folkloric medicine.