Miracle-dz/UniFAR-FTUs huggingface dataset:
Leaf Area and Competition for Light between Plant Species using Direct Sunlight Transmission

A technique based on the relationship between leaf area index (LAI) and the transmittance of direct sunlight was developed for the in situ study of competition for light between plant species. Field studies were conducted in 1984 and 1985 using monocultures and mixtures of rapeseed (Brassica napus L.), wild mustard (Sinapis arvensis L. # SINAR), and common lambsquarters (Chenopodium album L. # CHEAL). LAI estimated nondestructively by this method agreed closely with LAI determined by conventional destructive techniques. Light measurements at several heights in the canopy were used to determine the vertical distribution of canopy leaf area. Combining this information with species heights allowed the separation of the canopy LAI into individual species LAI, from which light competition could be estimated by calculating the sunlit LAI of each species. The technique permits many detailed measurements in the same canopy throughout the growing season. The light sensor required is not costly and is simple to operate and to maintain.
Mycodiversity and biotechnological potential of endophytic fungi isolated from hydrophytes

Foliar endophytic fungi were isolated from regular hydrophytic plants such as Eichhornia crassipes (Pontederiaceae), Nymphaea nouchali (Nymphaeaceae), Vallisneria spiralis (Hydrocharitaceae) growing in a pond in the Anna Zoological Park, Chennai, Tamil Nadu. Five hundred leaf segments from each plant species were inoculated in Potato Dextrose Agar (PDA) medium. A total of 18 different endophytic fungi could be isolated from three host surveyed. Hyphomycetes group was the most prevalent endophyte than ascomycetes, coelomycetes, and sterile form. Nymphaea nouchali had more endophytic fungi (18 species) followed by Eichhornia crassipes (12 species), and Vallisneria spiralis (11 species). To our knowledge Vallisneria spiralis is studied for endophytic fungi diversity for the first time. Among the 18 endophytic fungi isolated, nine were present in all three hosts investigated for endophytic fungi. Curvularia lunata, Chaetomium indicum, Nigrospora oryzae, Pestalotiopsis sp. showed <5% of colonization frequency in all three host species studied. The culture filtrate of Curvularia lunata, Nigrospora oryzae, Chaetomium indicum and Pestalotiopsis microspora investigated contained alkaloids, flavonoids, terpenoids, tannins and steroids. The dominant endophytic fungi were tested for production of extracellular enzymes like amylase, cellulase, Lasparaginase, laccase and protease. Curvularia lunata, Chaetomium indicum and Pestalotiopsis microspora produced all the enzymes tested, whereas Nigrospora oryzae did not produce Lasparaginase. The culture filtrate of Chaetomium indicum and Pestalotiopsis microspora significantly increased the cell division in Allium cepa root meristem and the radical plumule length in AD8 rice variety.
Genetic diversity of characteristics in barley cultivars.

Saroei E. , K. Cheghamirza, L.Zarei (2017): Genetic diversity of characteristics in barley cultivars.Genetika, vol 49, no2, 495-510. Knowledge of the genetic diversity is important to design appropriate selection criteria in the breeding programs. In this study, the genetic diversity of 42 Iranian and European barley cultivars was investigated with morpho-agronomic traits including phenological, physiological, morphological traits, grain yield and associated traits. Analysis of variance showed high variability among cultivars. The European cultivars Panaka, Aiace and Pariglia had the highest grain yield. The results of group comparisons indicated that the European cultivars produced higher grain yield (500.57 g/m) than the Iranian cultivars (445.50 g/m), but larger genetic diversity based on morpho-agronomic traits was observed among Iranian cultivars than European cultivars. Correlation analysis revealed the high significant correlations between grain yield with biological yield (0.92), straw yield (0.77), and number of spike per square meter (0.67). Based on the factor analysis, the six factors that justified 81.63 percent of the variations were identified. The first factor having the largest eigenvalue was identified as effective factor on the vegetative and reproductive growth. In path analysis, biological yield had the greatest effect on grain yield (0.906). Cluster analysis classified the cultivars in six groups and showed that genetic variation based on the all studied traits among the barley cultivars was not related to geographical location.
DNA and Chromosomal Damage in Residents Near a Mobile Phone Base Station

Abstract Mobile phone base stations, continuously emit low-frequency radiofrequency (RF) radiations and thus are a cause of public health concern. In the present study, genetic damage in peripheral blood leukocytes (single cell gel electrophoresis/ comet assay) and buccal mucosal cells (buccal micronucleus cytome assay) of individuals residing in the vicinity of a mobile phone tower (n=50, power density 11.18±0.13 W/m2), and in healthy controls from areas with no nearby towers (n=25, power density, 0.04±0.00 W/m2), was assessed. Damage frequency, damage index, mean DNA migration length, frequencies of micronucleated, basal and pyknotic cells were significantly elevated (p=0.000) in the sample group. Age, diet, location of residences, distance from mobile phone base station and phone-set Specific Absorbance Rate values were significant predictors of genetic damage. Hence the observations indicate that 24x7 continuous exposure from base stations may pose genetic-damage threat to the populace residing nearby.
Genotypes X environment interaction effect on nutritional quality of sorghum lines in Indonesia

The adoption of sorghum as alternative souce of food in Indonesia depends on consummer acceptance of sorghum grain which is determine by the nutritional and anti-nutirtional values and the quality of sorghum grain. The objectives of this study were to obtain information on genetic variability of sorghum genotypes with diverse backgroud for nutritional values and the effect of genetic x environment on the variablity in sorghum grain nutritional values. The study was conducted on 24 sorghum lines consisted of breeding lines, introduced lines and a local variety. The lines were planted in a randomized complete block design with tree replications in two locations differing in soil fertility. The results showed that the protein, fat, amylose and tannin contents of the sorghum lines are effected by the genotype x environment interaction with different magnitutes. The presence of G X E interaction reduced the genetic variances and estimates of heritability of the characters.
Uniformity of petroleum‐derived spray oils: lethal and sublethal effects on a herbivore pest and its parasitoid

Petroleum‐derived spray oils (PDSO) are widely used and recommended in many integrate pest management programmes and in organic agriculture against several pests. However, there are numerous discrepancies in their efficacy against pests and, more interestingly, in their side effects on natural enemies. In the present study, we used the citrus key pest Aonidiella aurantii Maskell (Hemiptera: Diaspididae) and its main parasitoid Aphytis melinus DeBach (Hymenoptera: Aphelinedae) as models to evaluate both the lethal and sublethal effects of four commercial PDSO on different instars of the herbivore, as well as on the adult and immature stages of the parasitoid. The four PDSOs displayed similarly high mortalities against young instars of A. aurantii. However, most adult females survived all PDSO applications, and the fecundity of the surviving females was not altered. PDSOs were harmless to the parasitoid A. melinus because the survival (acute toxicity), longevity and fecundity of the surviving adults (sublethal effects) were not affected. Similarly, immature emergence was not affected by any of the four PDSOs after spraying the parasitized hosts. Overall, the results of the present study confirm the environmental‐friendly profile of PDSOs against natural enemies and demonstrate a similar performance for PDSOs when they were correctly sprayed under the same conditions.
Physical and Functional Characterization of the SUMO System and SUMO Chains in S. cerevisiae

The ubiquitin-like proteins (Ubls) are small polypeptides that function as post-translational modifiers. Like ubiquitin, most Ubls are covalently attached to a lysine residue on target proteins. The small ubiquitin-related modifiers (SUMO) play important roles in a number of critical biological processes, such as proliferation and regulation of the cell cycle, yet their specific cellular functions have remained poorly understood. Like ubiquitin, SUMO proteins can also form oligomeric “chains”, but the functions of these structures were even less well understood. To this end, I created the first spectral library for the identification of Ub/Ubl proteins and Ub/Ubl chain linkages in mass spectrometry experiments. This tool has dramatically improved our ability to use MS to analyze the contents of biological samples for Ub and Ubls, and to identify specific types of Ub and Ubl chains in model organisms. I also used MS to conduct the first comprehensive SUMO system protein-protein interactome in any organism. In total, 452 high confidence protein-protein interactions were detected for S. cerevisiae SUMO system proteins, encompassing a total of 321 interacting partners. Yeast SUMO system components were found to interact with proteins involved in a number of different biological processes, and my mapping effort increased the number of known SUMO system interacting partners >50-fold. This study revealed that a number of transcriptional corepressors and chromatin remodelling proteins interact physically with specific SUMO system components, with a clear division of labour between SUMO system enzymes. Finally, I conducted the first global analysis of SUMO chain function, using a combination of genetic, high-content microscopy, and high-density transcriptomics screens. Consistent with my interactomics work, this study demonstrated that inhibition of SUMO chain synthesis leads to iii severe chromatin condensation defects, which in-turn leads to chromosome missegregation, unscheduled transcription of stress-and nutrient-regulated genes, and aberrant intragenic transcription. Together, my work thus revealed a major role for the SUMO system in the maintenance of higher order chromatin structure and transcriptional repression.
Estimating Chronic Wasting Disease infectivity in cell culture

The rapid spread and high prevalence of CWD in North American cervids have raised concerns about a potential risk to human health. Experimental transmission of CWD to various species has been reported. It was demonstrated by others, that CWD is transmissible to squirrel monkey but so far not to cynomolgus macaques. We investigated prion propagation in cell lines, overexpressing transgenic PrP from humans (Homo sapiens), cynomolgus macaques (Macaca fascicularis), squirrel monkeys (Saimiri Sciureus) and white-tailed deer (Odocoileus Virginianus) to simulate interspecies transmission of CWD in vitro. The permissive HpL3-4 and SH-SY5Y cell lines were retrovirally transduced with PrP of the respective species. We characterised the produced cell lines in detail for transgene integration, transcription, protein expression and cell surface abundance of ectopically expressed PrP. The relative and absolute number of integrated genomic copies and the transcription rate of transgenic PrP were comparable among all cell lines according to quantification by qPCR. Analysis of the glycopattern of transgenic prion protein expressing cell lines confirmed that glycosylation is not dependent on PrP donor species, but on the recipient host cell line. The abundance of transgenic PrP on the cell surface was validated by FACS analysis. All generated cell lines were inoculated with different prion infections agents and tested for prion propagation in vitro. The studies showed that only HpL3-4 cell lines, expressing the prion protein of mouse or squirrel monkey, were susceptible to infection with cell culture adapted Scrapie 22L cell lysate. In comparison, the tg PrP overexpressing SH-SY5Y cell lines were not susceptible to 22L infection. Additionally, the macaque and human HpL3-4 cell lines were not susceptible to infection with CWD However, the overexpression of PrP from the squirrel monkey in HpL3-4 cell line led to permissibility of the cells to primary CWD brain inoculum. This is the first report demonstrating that a transgenic PrP overexpressing cell line could be infected with a primary inoculate derived from CWD-infected cervids. The established in vitro assay partially reflects the in vivo transmissibility of CWD, which has been successfully transmitted to squirrel monkeys, but to date infection of cynomolgus macaques or humans by CWD has not been reported. In conjunction with a high number of replicates this assay provides a powerful tool to assist in vivo experiments in non-human primates, which could lead to a reduction and refinement of animal experiments.
Significance of Wnt B catenin Signaling Pathway in the Pathogenesis of Cervical Cancer

Objective: The present study was aimed to investigate the importance of Pin1 expression in Squamous Cell Carcinoma (SCC) of cervix and to assess its level with β-catenin and APC to understand the possible involvement of Pin1 in the regulation of these proteins and subsequent activation of Wnt/β-catenin signaling. Materials and Methods: Expression of Pin1, β-catenin and APC was examined in 153 SCC patients by immunohistochemistry and revalidated by western blotting. Results: Of the 153 SCC analyzed, Pin1 was overexpressed in 73 (47.71%) cases. Loss of membranous β-catenin was noticed in 117 (76.47%) SCCs, whereas 66/153 (43.13%) and 93/153 (60.78%) cases showed its distinct cytoplasmic as well as nuclear accumulation respectively. Down regulation/loss of APC was observed in 69 (45.09%) cases, suggesting the activation of Wnt/β-catenin pathway in SCCs. Pin1 showed the significant association with nuclear β-catenin (r=.349, p<0.0001) and cytoplasmic loss of APC (r=-.287, p<0.0001). Both Pin1 as well as nuclear β-catenin were found to be associated with tumor stage (p=0.004, p=0.031) and tumor size (p=0.022, p=0.003). The Pin1 overexpression showed the significant association with disease free survival (p=0.002) but not with overall survival (p=0.421) of SCC patients. Conclusion: Current results explore the expressional relationship between Pin1, β-catenin and APC suggesting that Pin1 regulates the activation of Wnt/β-catenin pathway in SCCs via modulating the interaction between β-catenin and APC. Furthermore, the significant association of Pin1 and β-catenin with tumor variables underscores the clinical utility of these proteins in cervical cancer.
Effects of culinary treatments on lipids quality, proximate composition and mineral content of broilers meat fed with rations supplemented with powders of Camellia sinensis, Annona muricata and Zingiber officinale

This study aimed to evaluate the effects of feeding system and cooking treatments on the lipids quality, proximate composition and mineral content of broiler meat (thigh muscle) fed with powders of three natural plants. Hundred (100) twenty-one-day-old broiler chickens (Cobb 500) were randomly allocated to five (5) experimental diets with 10 replicates consisting of the basic ration (without antioxidant) from which four other feeds were obtained by adding 200 UI/kg of Vitamin E (VitE); 5 g/kg of tea leaves powder (CS); Ginger root powder (ZO) and Soursop flowers powder (AM). Feed and water were supplied ad libitum throughout the experimental period. On the 49 day, they were randomly slaughtered, and their carcasses were collected for culinary treatments. Thereafter, lipids were extracted from the meat using the method described by Bligh and Dyer. Their quality was assessed by the determination of peroxide value (PV), thiobarbituric acid reactive substances value (TBARS) and acid value (AV); while the proximate composition and mineral content were performed on meat flours. Results revealed that the treatments Raw+ZO; Fr+AM; Fr+ZO; Bo+CS; Bo+ZO and Bo+AM limited the formation of hydroperoxides. Except for the treatment Fr+AM, all the treatments significantly increased (P<0.05) the level of TBARS. Combined treatments increased AV. Plant supplementation enhances the nutritional value of broiler meat. Thus, the supplementation of broiler ration with natural powders might be a good alternative to maintain the lipids stability of broiler meat and enhance their nutritional value during cooking treatments.
Protective role of Moringa oleifera leaf-based diet on protein- energy malnutrition induced skeletal muscle degeneration

Background: Sequel to the diverse diseases resulting in muscle mass degeneration and its key role in the prognosis of the diseases. For instance, currently, only resistance exercise can be used to promote recovery of mass/strength following disuse atrophy. But in contrast, many patients are unable or unwilling to exercise at a sufficient intensity to promote muscle growth. It would therefore be of great advantage to develop natural compounds that counteract the negative effects of skeletal muscle degenerative diseases especially in the form of therapeutic feed). The present study was aimed at elucidating the mechanism by which M. oleifera ameliorates skeletal muscle degeneration caused by malnutrition. Methods: The experimental animals were malnourished with low protein iso-caloric diets for four weeks after which they were treated with 25% M. oleifera leaf – based diet, vitamin E supplemented feed and soy bean based- diet for another four weeks . Results: There was a significant reduction in the activity of calcium ATPase in the skeletal muscle of animals induced with skeletal muscle degeneration. However, this activity was significantly increased following treatments with the most significant increase observed in the skeletal muscle of animals treated with M. Oleifera leaf based diet followed by those fed with vitamin E supplemented diet. Conclusions: In summary, the study revealed that the mechanism by which M. oleifera leaf corrects muscle degeneration caused by PEM might be by increasing calcium ATPase activity and/ or its synthesis and by preventing oxidative stress due to its antioxidant properties .
The effect of diets containing raw and fermented faba beanson gut functioning and growth performance in young turkeys

Global legume production is currently on the rise due to the increasing nutritional and economic significance of legume seeds (Chandra-Hioe et al., 2016). Legume seeds have been used primarily in diets for broiler chickens (Moschini et al., 2005; Hejdysz et al., 2016), but also for turkeys (Zduńczyk et al., 2014a; Przywitowski et al., 2016) and laying hens (Drażbo et al., 2014; Zduńczyk et al., 2014b). Faba beans (FB) are among the most extensively researched legume species in Europe, due to their high content of protein (about 26%) and starch (about 30%) as well as high concentrations of amino acids, comparable with soyabean meal (SBM) (Fru-Nji et al., 2007). FB (Vicia faba L.) are considered a valuable source of protein, energy and other nutrients in poultry nutrition. However, the presence of antinutritional factors such as tannins, protease inhibitors, oligosaccharides and non-starch polysaccharides (NSP), as well as a low content of sulphur-containing amino acids reduce the nutritional value of FB, and can negatively affect nutrient utilisation and animal performance (Hejdysz et al., 2016). Oligosaccharides ABSTRACT. The aim of the study was to evaluate the effects of partial replacement of soyabean meal (SBM) with 35% of raw or fermented faba beans (RFB and FFB, respectively) on the development of the gastrointestinal tract and growth performance in young turkeys. FB were fermented with Lactobacillus plantarum. In comparison with RFB, FFB had similar crude protein content, but lower NDF and higher ADF contents. Partial replacement of SBM with FB seeds led to a decrease in wheat content, and an increase in the contents of highprotein components (by approx. 22 percentage points) and soyabean oil (by 2.5 percentage points) in turkey diets. The dietary inclusion of RFB and FFB did not affect the viscosity of small intestinal digesta. In comparison with the SBM diet, the RFB diet significantly decreased the concentrations of ammonia and butyric acid, reduced the activities of some microbial enzymes in the caecal digesta, but did not affect the concentrations of putrefactive and total short chain fatty acids (SCFAs). In comparison with the RFB diet, the FFB diet did not improve the turkey growth performance, but had a positive impact on fermentation processes in the caeca, which was reflected in an increase in the total concentrations of SCFAs and a decrease in ammonia concentration in the caecal digesta. So, dietary supplementation with 35% of FB does not compromise the growth performance of turkeys from 1 to 8 weeks of age. Fermentation of FB with Lactobacillus plantarum improves selected parameters of caecal functioning, but does not improve the growth performance of young turkeys. Received: 22 May 2017 Revised: 29 September 2017 Accepted: 15 February 2018
The emergence of compartmental organization in the olfactory bulb glomerulus

The olfactory bulb glomerulus is a discrete and heterogeneous neuropil where olfactory receptor cell axons synapse with dendrites of mitral, tufted and periglomerular neurons. In the first study, we investigated the organization of the glomerular neuropil by using antibodies to both single and double-labeled constituents for analyses with confocal microscopy. Electron microscopy was used to assess the distribution of synapses within the glomerulus. The olfactory bulbs of adult Sprague-Dawley rats were processed for immunocytochemistry with olfactory marker protein (OMP), synaptophysin, synapsin 1, glial fibrillary acidic protein (GFAP) and/or microtubule associated protein 2 (MAP2). Double labeling for OMP and MAP2 revealed two distinct subcompartments within glomeruli. Synaptophysin and synapsin 1 also showed differential labeling with the glomerulus. Electron micrograph reconstructions of glomeruli revealed interdigitating axonal and dendritic subcompartments, where primary afferent axodendritic and local circuit dendrodendritic synapses segregated within the glomerulus into the axonal and dendritic subcompartments, respectively. These results support the hypothesis of subcompartmental organization within olfactory bulb glomeruli. In the second study, we employed similar techniques to better understand the maturation of glomeruli and to examine the spatio-temporal interactions that occur during postnatal development. Sprague-Dawley rats at postnatal days 1,6, 12, and 18 were processed for single and double label immunocytochemistry for OMP, growth associated protein (GAP-43), and synaptophysin. Mature adult-like subcompartmental organization within the glomerulus emerged by postnatal day 12. Earlier in development immature axons entered the core of the glomerulus and moved to the periphery as they matured. However, beginning around 12 days postnatal, immature axons distributed in the periphery and moved toward the core as they matured. This change in the trajectories of axons into glomeruli suggests that different rules may be followed in establishing versus maintaining glomeruli.
不同林龄橡胶(Hevea brasiliensis)林土壤微生物群落和磷组分的变化

橡胶林是我国热带地区重要的经济林，而土壤磷是热带地区植物生长的重要限制因子之一，理解土壤磷转化机理对于生态系统的磷管理和可持续发展具有重要意义。 因此，以热带地区海南儋州不同林龄（4、15、31a）橡胶人工林为研究对象，采用Hedley连续浸提法研究了土壤磷组分，磷脂脂肪酸法（Phospholipid fatty acids，PLFAs）分析了土壤微生物群落。 结果表明，在橡胶林内各磷组分的相对含量大小顺序为：闭蓄态磷>中等活性态磷>活性态磷>团聚体内磷>钙磷。 随着林龄的增加，橡胶林土壤中的磷组分发生显著变化。 4、15、31a橡胶林的闭蓄态磷分别占总提取磷的52. 61%、47.17%和34. 91%，而活性态磷分别占总提取磷的6. 67%、11.32%、13.68%。 土壤总微生物、细菌、革兰氏阴性菌（G-）、革兰氏阳性菌（G+）的PLFAs含量均表现为15a > 4a > 31a，而31a橡胶林放线菌、真菌（F）和丛枝菌根真菌（AMF）的PLFAs含量均低于4a和15a。 冗余分析（RDA）显示，全氮、有机碳、pH、F、AMF、G-、G+是引起不同林龄橡胶林土壤磷组分变化的重要贡献因子。 研究表明，在橡胶林发育过程中，土壤理化性质和微生物群落发生了明显的变化，进而影响到土壤磷的转化过程。