Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Different Levels and Timing of Zinc Foliar Application on Growth, Yield and Quality of Sunflower Genotypes (Helianthus annuus L., Compositae

Because of the calcareous nature of soils in Mosul city and the high value of the soil pH, most micro nutrients have negligible availability in these soils, therefore an field experiment was conducted during two successive growing seasons 2009-2010 and 2010-2011 to determinate the response of growth, yield and quality of sunflower (Helianthus annuus L.) genotypes to different levels and timing of zinc foliar application. The experiment comprised of three levels of zinc sprayed on the plant leaves one dose (0, 7.5 and 15 mg.l), three sunflower genotypes (Manon, Fodak and Sunbred) and three timing of zinc application (heading stage, flowering stage and seed filling stage). It was conducted according to Randomized Completely Block Design with split split plot with three replications. The results could be summarized as: The addition of zinc sprayed on the plant leaves with concentration 7.5 mg.l led to an significant increase in characteristics: plant height, leaf area, number of seeds.head, weight of thousand seed, seed yield per plant, total seed yield, seed oil content, seed protein content and oil yield, protein yield, while increasing concentration of zinc to 15 mg.lcause a significant decrease in all investigated characteristics in the two growing seasons. Fodak genotype gave a high mean for characters: plant height, stem diameter, leaf area, number of seeds.head, seed yield per plant, total seed yield, seed oil content, seed protein content, oil yield and protein yield in both seasons 2009-2010 and 2010-2011. Delaying timing of zinc foliar application to flowering stage causes an significant increase of all investigated characteristics in both seasons 2009-2010 and 2010-2011. Received: 30/9/2012 ; Accepted: 10/1/2013
Pyramiding QTLs to improve malting quality in barley: genetic gains in phenotype and diversity.

The ability of barley breeders to deliver germplasm that combines elite malt quality characteristics, disease resistances, and important agronomic traits has been greatly enhanced by the use of molecular marker technologies. These technologies facilitate the rapid transfer of desirable traits from diverse, elite, germplasm into locally adapted varieties. This present study sought to obtain an additive genetic effect by combining the malting quality of two elite donor parents (Harrington and Morex) such that the resultant progeny would possess quality superior to either parent. Quality data from micro-malting grains showed substantial improvements in the resultant progeny, compared with the recurrent parent. Malt extract levels were increased by 1.7–4.0 %, while diastase levels increased from approximately 306 WKE to between 400– 465 WKE. Similarly, alpha-amylase levels were increased from 180 U-1 kg to between 234 and 298 U-1 kg, and wort viscosities were lowered from 2.11 cP to between 1.61 and 1.81 cP. Other quality improvements include increases in beta-glucanase levels from 386 to 492–537 units, and reductions in wort betaglucan levels by 30–60%. Whilst the genetic gains compared to the recurrent parent were impressive, quality of the derived lines were largely equivalent to the levels now available in the recently released varieties Buloke and Flagship. In a few cases, the MABC-derived lines also showed similarities to the original donors, Harrington and Morex, but in none of the cases did quality of these lines exceed those of either Harrington or Morex.
A new species of Theretra Hübner (Lepidoptera: Sphingidae) from the southern Western Ghats, India

A new species of the genus Theretra Hubner [1819], Theretra shendurneensis sp. nov., is described from Shendurney Wildlife Sanctuary, southern Western Ghats, India, based on external and internal morphology, and genetic markers. The new species is compared in external and male genital morphology, genetic divergence and geographic range with three similar and closely related species: T. boisduvalii (Bugnion, 1839) , T. sumatrensis (Joicey and Kaye, 1917) and T. rhesus (Boisduval, [1875]). Recent changes to the classification of Theretra are discussed and rejected.
IMPACT OF GASEOUS NO2 ON P. FLUORESCENS STRAIN IN THE MEMBRANE ADAPTATION AND VIRULENCE

Nowadays air pollution is increasing due to anthropogenic activity. Among all air pollutants, nitrogen oxides (NOx) such as NO 2 are predominant. It is well known that those compounds exhibit direct toxic effects on human health. However, microorganisms are also exposed to them, but the effect of NOx on the virulence of air microbiota is still poorly understood. In this study, we evaluated the impact of NO 2 on the adaptability and virulence of an airborne strain of P. fluorescens , MFA76a, by exposition of this strain to 45 ppm of NO 2 . The growth kinetics and cultivability were analysed. A decrease of cultivability coupled with an increase of the lag phase was observed suggesting a potential toxicity of NO 2 . Since NOx particularly target lipids, the membrane permeability was assessed thanks to Live Dead tests and confocal microscopy. A significant alteration of membrane permeability was observed. Furthermore, more abundant bacterial aggregates were detected compared to the control. Thus, a lipidomic study was performed using MALDI-TOF MS Imaging coupled to HPTLC. Interestingly, bacteria exposed to NO 2 were lacking one putative glycerophospholipid molecule. In agreement with a previous study from Kondakova et al., these data demonstrate the adaptation potential of P. fluorescens MFAF76a to an air pollutant such as NO 2 .
Synthetic hydrogel-based 3D culture system for maintenance of human induced pluripotent stem cell

Human induced pluripotent stem cells (hiPSCs) are generated from human somatic cells using defined transcription factors. These cells possess characteristics very similar to that of human embryonic stem cells including the ability to differentiate into cell types of all three germ layers. HiPSCs show great potential in clinical researches like drug screening and regenerative medicine, that all require large amount of cells cultured under well-defined conditions. The most common culture methods used for hiPSCs are 2D culture methods using Matrigel or vitronectin coated culture plates or flasks. 2D culture methods require large surface area to produce the same amount of cells compared to 3D methods. In addition, cells cultured in 2D culture environment are far from that in vivo. In this study, we developed a robust 3D culture condition based on hiPSC-qualified PGmatrix (PGmatrix-hiPSC) hydrogel. This 3D culture system provide hiPSCs with well-defined, more in vivo-like environment that encapsulate cells in liquid rich hydrogel with appropriate oxygen supply that resembles the hypoxia condition in vivo. Two hiPSC lines grown continuously in PGmatrix-hiPSC showed higher total population expansion and higher viability, with more consistency compared to the same cell lines grown in 2D on Matrigel or Vitronectin-XF. After grown in 3D PGmatrix-hiPSC for over 25 passages, major pluripotency markers, such as Oct4, Sox2, Nanog, and SSEA4 are expressed in most hiPSCs examined by flow cytometry. RT-qPCR also confirmed adequate expression levels of major pluripotency related genes. In addition, karyotype analysis of hiPSC after 37 passages in 3D PGmatrix-hiPSC was found normal. The same hiPSC lines cultured continuously in parallel in 2D and 3D showed differences in gene expression and surface marker TRA-1-81 expression. These results indicated the 3D PGmatrix-hiPSC system is likely superior in maintaining hiPSC growth as well as pluripotency. The findings also suggest that it is very important to study cells in 3D culture environment to better understand the mechanism of pluripotency maintenance.
Settlement, Seasonal Size Distribution, and Growth of the Invasive Bivalve Mytilopsis leucophaeata (Conrad, 1831) (Dreissenidae) in Relation to Environmental Factors

ABSTRACT Conrad's false mussel (Mytilopsis leucophaeata) is an invasive alien bivalve species causing severe biofouling problems in cooling water systems of power and industrial plants. Settlement, seasonal shell size distribution, and growth of this bivalve species were analyzed in relation to relevant environmental factors, using monitoring data from a brackish canal over a period of 4 y. Salinity at the sampling site ranged from3.2 to 9.2,water temperature from 4.5°C to 23.9°C, and chlorophyll a content from 2 to 56 µg l-1. Once a month one short-term exposed panel (1mo exposed) and one long-term exposed panel (exposed from February 1989 to the month of sampling) were collected. Settled spat and attached mussels were collected monthly from these polyvinylchloride panels and from stones in the littoral zone. The short-term exposed panels were used to determine the period of spat fall. The long-term panels were used to study growth, shell length-frequency distribution, and densities of the mussel population after settlement. To study maximum age, M. leucophaeata were kept in cages in the canal. The highest recorded settlement was 204,000 individuals/m2. The largest mussel had a shell length of 24.0 mm. Three cohorts of shell length (1–5 mm, 5–15 mm and 15–24 mm) could be distinguished. Data on survival of individual mussel size groups in cages indicated a maximum age of 4.5 y. Shell growth was very low in winter time (average growth less than 1 µm/day in the period of November to April). The average growth rate on the stones during the summer periods (3–4 mo) was 89 µm/day. On the panels, a rapid shell growth to an average shell length of 4mm was recorded in the period of July until November in their first year, followed by a period of hardly any shell growth from December until May, and a subsequently rapid shell growth to an average shell length of 13mmduring the period of May until August in the second year. Individual mussels grew up to 20.9 mm during a 13-mo period. Growth of shells was significantly correlated with water temperature. The minimum threshold temperature for shell growth stops was 9.1°C (9.1°C–10.1°C) based on monthly measurements. Growth started at a minimum temperature of 9.1°C (9.1°C–14.2°C).
Demographic analysis of sterile insect trials with the Queensland fruit fly 'Bactrocera tryoni' (Froggatt) (Diptera: Tephritidae)

Reports of 10 SIT campaigns are reviewed and compared from a demographic perspective. The campaigns ranged from treatments of 'spot' infestations, through operations in small to medium country towns to the large campaign at Perth. Conclusions are made about (a) the effective ratio of sterile to wild flies in relation to the size and potential growth rates of target populations, (b) release rates required and the distribution pattern of releases. The efficacy of pre-baiting and optimum release protocols are discussed and a new strategy for suppression in towns posing a risk to non-endemic and quarantine areas is proposed.
Coupling African elephant movement and habitat modeling for landscape availability-suitability-connectivity assessment in Kruger National park, South Africa

Making an appropriate conservation decision often requires understanding the functional connectivity of the landscape for focal species. Graph theory and continuous surface methods have become powerful tools to quantify landscape connectivity for animal movement. However, a key limitation of these methods is the use of thresholding to define either habitat patches or links between patches. We explore how to incorporate African elephants' (Loxodonta africana) movement data into an "Availability-Suitability-Connectivity (ASC)" framework which integrates habitat suitability modeling and graph-based network analysis, and how to implement connectivity results to inform conservation management that addresses locally intensive habitat utilization by elephants. In our ASC analysis, node availability was identified by satellite imagery classification and node suitability was estimated by MaxEnt model. Links were determined by effective movement between nodes in three days. Differences of Integrative Index of Connectivity (dIIC) and its fractions were calculated to prioritize patch importance, which were then used for mapping an example landscape management zones to reduce elephant local ecological impact. In total, 544 nodes and 1345 links were identified in the landscape graph. Although suitable nodes were spread across the landscape, elephants intensively used habitat at the central area. Our zone map demonstrates areas for landscape management that can facilitate elephant range expansion. The integrative framework quantified the ASC interactions between animal movement and landscape features. The results highlight the potential for coupling geographic and ecological methods to effectively identify and focus conservation efforts.
Characterization of the Neurospora Varkud Satellite Plasmid and Transcript in vivo

The Varkud satellite (VS) plasmid is found in the mitochondria of some strains of Neurospora, and exhibits properties that may allow it to be developed as a genetic transformation vector to study mitochondrial molecular biology. An ideal transformation vector would not confer a phenotype. The overall goal of my thesis was to examine interactions of VS with its Neurospora host to identify possible phenotypes, using biochemical and proteomic approaches. Biochemical experiments provided evidence consistent with the plasmid transcript, VS RNA, being present as a ribonucleoprotein particle that can be separated from ribosomal subunits by sucrose density gradient centrifugation; however, no VS-specific proteins were identified under the purification conditions examined. During the analyses of proteomic data I obtained new insights into the consequences of the statistical methods commonly used to normalize quantitative 2D gel data. However, irrespective of the method used, the fraction of the proteome amenable to 2D gelbased proteomics revealed, at most, subtle effects of VS on the abundance of a few proteins. I also observed no differences in growth rate between strains differing by the presence or absence of VS when grown in the presence of inhibitors and stressors affecting a wide range of mitochondrial and other cellular functions. Overall, despite VS RNA being as abundant as the large and small mitochondrial ribosomal RNAs, my genetic, biochemical and proteomic iii investigations of the effect of VS on its host strain provides evidence that VS is a phenotypically
Influence of ozone on carbon transformation processes in plant-soil systems: Changes in rhizosphere microbial community patterns of woody plants

Carbohydrates leaving plants contribute to the pool of dissolved organic carbon in soil, postulated as a very attractive carbon source for microbial growth. By reason of increasing concern of tropospheric ozone damage on forest trees, this study focused on European beech ( Fagus sylvatica L. ) and Norway spruce ( Picea abies (L.) Karst. ) as experimental plants, since these are common in forests of Western Europe. Using different 13C-labelling techniques, individual groups of organisms were identified to be involved in the utilization of exudates, indicating a microbial food web in the rhizosphere. Different groups of organisms within the soil microbial biomass were investigated by phospholipid fatty acid (PLFA) profiling. Investigating beech and spruce rhizosphere microbial community structures, ozone influence on plants causes changes in the microbial community structure via the carbohydrate composition within plants and rhizodeposition.
In vitro ruminal dry matter and neutral detergent fibre digestibility of common feedstuffs as affected by the addition of essential oils and their active compounds

The effects of essential oils (EO) and their active compounds (EOC) on dry matter digestibility and neutral detergent fibre digestibility (DMD and NDFD, respectively) are still not enough described since in vitro methods are limited. So, the aim of the study was to screen and compare the main effects of EO and EOC on short-term DMD and NDFD using the in vitro method. The addition of phenylpropanoid-rich cinnamon oil (CIN) and clove oil (CLO), terpenoid-rich thyme oil (THY) and oregano oil (ORG), and four EOC: cinnamaldehyde (CIN-C), eugenol (EUG), thymol (THY-C) and carvacrol (CAR) was studied at a dose of 0.5 mg · l −1 of main active compound. Products were tested on four substrates: lucerne hay, soyabean meal, maize meal and a total mixed ration (TMR). Digestibility was determined at 4 and 24 h of fermentation. Both CIN and CIN-C increased NDFD4 of lucerne and maize meal, and decreased NDFD24 of soyabean meal; while CIN-C reduced NDF24 of TMR and CIN reduced DMD of soyabean at both examined hours. CLO and EUG decreased the NDFD24 of soyabean meal improving its DMD24. Also initial DMD of lucerne was increased by both these factors. Only CLO reduced NDFD24 of maize meal. Both THY and THY-C reduced DMD4 of soyabean meal; however only THY-C improved NDF4 of lucerne and reduced NDFD24 of soyabean meal and TMR. DMD24 of most substrates (except lucerne) was reduced by ORE, but not by CAR which improved NDFD4 of lucerne. The in vitro method was sensitive to variations in digestibility caused by EO and EOC, providing a promising approach for the incorporation of EO and EOC effects in systems for cattle diet formulation.
Structural and Functional Studies of Proteins from the Agricultural Pests Tetranychus Urticae and Aspergillus Fumigatus

Agricultural pests are a worldwide problem and cause billions of dollars in crop loss. In the United States alone, an estimated $40 billion USD is lost per year due to agricultural product loss from invasive insects and pathogens. To further complicate the problem, several insects and other agricultural pests are developing resistance to currently used pesticides. Studied here are proteins from the agricultural pests Tetranychus urticae and Aspergillus fumigatus. T. urticae, or two-spotted spidermite, is a polyphagous pest, and two proteins from this pest, a cyanase and a glutathione S-transferase, are described. Cyanase is involved in the conversion of carbonate and cyanate, a toxic self-defense metabolite produced by plants, into ammonia and carbon dioxide. Glutathione S-transferases conjugate reduced glutathione to xenobiotics for detoxification and have been associated with insecticide resistance. Furthermore, A. fumigatus is a ubiquitous fungus that is not only a problem in agriculture, but also in healthcare. The mortality rate of A. fumigatus infections in immunocompromised individuals is 5085% and resistance in healthcare is becoming more prominent mainly attributed to the widespread use of fungicides in agriculture. The 2-methylcitrate cycle, which is only present in fungi, is responsible for detoxifying propionyl-CoA, a toxic metabolite produced as the fungus breaks down proteins. The enzyme responsible for this detoxification is 2-methylcitrate synthase (mcsA) and is a potential candidate for the design of new anti-fungals. However, mcsA shares a similar reaction to human citrate synthase (hCS), and both the structure and function of each enzyme is studied in parallel to find mcsA-specific inhibitors.
Isolation, characterization and expression analysis of a nutritionally enhanced α-prolamin gene and protein during developing spikes of finger millet (Eleusine coracana)

Abstract In the present study a combination of BLAST mediated homology search and 3′ RACE was utilized to isolate the full-length gene of Eleusine coracana alpha prolamin (Ec-α-prolamin) from finger millet. Phylogenetic analysis of Ec-α-prolamin along with related prolamin genes of different cereals and millets shows the clustering of Ec-α-prolamin in a separate group. Secondary structure prediction reveals 59.4% alpha helix structure, a structural hallmark of Ec-α-prolamin. Besides this, the protein also possesses a balanced proportion of all essential amino acids. Expression analysis based on qPCR shows increased accumulation of α-prolamin transcripts in developing grains of finger millet until attainment of seed maturity. Western blotting, using a monospecific anti-α-prolamin antibody, further confirmed the expression of a 22 kDa band in the S3 and S4 stages of developing spikes. The heterologous expression of isolated full-length Ec-α-prolamin could be potentially harnessed for making nutritionally enhanced functional food products and value-added industrial products.
The complete mitochondrial genome of epitokous Nereis species (Phyllodocida, Nereididae) from Dok-do, Korea

Abstract The mitogenome sequence of the epitokous Nereis species (Phyllodocida, Nereididae) was determined first in the genus Nereis. The complete mitogenome is 15,667 bp in length, containing 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs and a control region, and their gene order and structure is identical to those of other nereidid species. The mitogenome consists of 33.5% A, 20.0% C, 13.3% G, 33.1% T, showing a high content of A + T similar to the other phyllodocid polychaetes. These results will be useful for inferring the phylogenetic relationships among the members of Nereididae within the phyllodocids.
Rolling a mycobiome down a hill: endophytes in the Taiwanese Cloud Forest

Fungal endophytes of plants are ubiquitous and important to host plant health. Despite their ecological importance, landscape-level patterns of microbial communities in plant hosts are not well-characterized. Fungal wood-inhabiting and foliar endophyte communities from multiple tree hosts were sampled at multiple spatial scales across a 25 ha subtropical research plot in northern Taiwan, using culture-free, community DNA amplicon sequencing methods. Fungal endophyte communities were distinct between leaves and wood, but the mycobiomes were highly variable across and within tree species. Of the variance that could be explained, host tree species was the most important driver of mycobiome community-composition. Within a single tree species, “core” mycobiomes were characterized using cooccurrence analysis. These core groups of endophytes in leaves and wood show divergent spatial patterns. For wood endophytes, a more consistent, “minimal” core mycobiome coexisted with the host across the extent of the study. For leaf endophytes, the core fungi resembled a more dynamic, “gradient” model of the core microbiome, changing across the topography and distance of the study.
Genetic characterization of FSH beta-subunit gene and its association with buffalo fertility

Objective: To study genetic variation in buffalo follicle stimulating hormone beta-subunit (FSHB) gene and its association with fertility. Methods: In this experimental study, blood samples were collected by standard methods using EDTA anticoagulant and transrectal ultrasound examination was conducted on fertile (n=74) and infertile buffaloes with a history of anestrum (n=30) or repeat breeding (n=12). The genomic DNA was extracted for PCR followed by single strand conformation polymorphism analysis. DNA sequencing was performed for the determination of single nucleotide polymorphism of FSHB gene. Results: The study results showed that there was genetic polymorphism with two different single strand conformation polymorphism patterns, AA and AB. The former pattern was associated with fertility in Egyptian buffaloes. Pair wise alignment of the two patterns sequences revealed that FSHB pattern II (AB) has C nucleotide insertion as SNP at the site of 208 bp of sequenced fragment. Conclusions: FSHB is polymorphic in the Egyptian buffaloes, suggesting its practicability as a candidate marker for female fertility.