Miracle-dz/UniFAR-FTUs huggingface dataset:
Cytological and Bioinformatical Analysis of SPE-26, a C. elegans Kelch-like Protein that Functions during the Karyosome Stage of Spermatogenesis

4 Chapter 1: Introduction . 5 Figure 1-1: Comparison of Mitosis and Meiosis . 19 Figure 1-2: Schematics of C. elegans Spermatogenesis . 20 Chapter 2: SPE-26, a C. elegans Kelch-like protein, concentrates in the nucleus of karyosome-stage spermatocytes and is required for normal meiotic chromosome segregation. 23 Figure 2-1: Specific microtubule defects in spe-26 mutants. 41 Figure 2-3: WT SPE-26 concentrates in the nucleus during the karyosome stage, while spe26(it112) SPE-26 remains diffuse. 46 Figure 2-4: M-phase signal is late entering the nucleus spe-26 spermatocytes. 47 Figure 2-5: Synaptonemal complex breakdown occurs normally, while karyosome cells accumulate in spe-26 mutants. 50 Figure 2-6: Chromosome detachment and compaction occurs normally in spe-26 mutants. 51 Figure 2-8: Transcriptional termination occurs normally in spe-26 mutants. 52 Figure 2-9: Summary of Cytological Markers Before and After the Karyosome Stage. 54 Chapter 3: Investigation of SPE-26 Structure and Function Using Bioinformatics . 55 Figure 3-1: Venn Diagram Comparison of Number of BTB, BACK, and/or Kelch-containing proteins in several representative organisms. 67 Figure 3-2: Structural Diagrams of SPE-26 protein. 68 Figure 3-3: Bioinformatics results. 69 Table 3-1: Top 10 BLAST hits. 70 Table 3-2: Non-nematode BLAST hits. 71 Table 3-3: Top I-TASSER Templates . 71 Table 3-4: UbPred Data: Condensed . 72 Table 3-6: NetPhosK Phosphorylation site predictions . 76 Chapter 4: Future Directions . 77 Figure 4-1: Chromatin colocalization of SPE-26 during meiotic divisions observed in WT and spe-26 (hc139). 85 Chapter 5: Materials and Methods . 86 Table 5-1: Antibody incubation and wash conditions. 88 References . 91
Inheritance of height in sorghum.

SORGHUM varieties range in height from 2 to 15 feet. Tall varieties predominate in much of the world where sorghum is grown and are usually preferred for forage because fodder yields are almost directly proportional to plant height. Except in the United States and Australia, dwarfness is not considered generally advantageous even in grain varieties because the stalks usually are needed for fodder or for building purposes. However, dwarf varieties of kafir, durra, hegari, kaoliang, and broomcorn have come to America from Africa, Asia, or Europe. Several mutations to dwarfness have occurred in this country since sorghums were introduced, and fully 95% of the sorghum grain produced in the United States now is grown on short-stalked varieties that are harvested with a combine. These short varieties, except for Double Dwarf milo 38, resulted from combining dwarfness from more than one source. This paper reports on the inheritance of height in sorghum, and lists the genetic factors for height among varieties grown in the United States, or that have been used as parents to produce new varieties. A knowledge of the height factors carried by varieties is now of added importance because of the possibility of hybrid sorghum production and of the consequent breeding work necessary to obtain parental lines
Does circadian regulation lead to optimal gas exchange regulation?

Optimal stomatal theory is an evolutionary model proposing that leaves trade-off Carbon (C) for water to maximise C assimilation (A) and minimise transpiration (E), thereby generating a marginal water cost of carbon gain (λ) that remains constant over short temporal scales. The circadian clock is a molecular timer of metabolism that controls A and stomatal conductance (gs), amongst other processes, in a broad array of plant species. Here, we test whether circadian regulation contributes towards achieving optimal stomatal behaviour. We subjected bean (Phaseolus vulgaris) and cotton (Gossypium hirsutum) canopies to fixed, continuous environmental conditions of photosynthetically active radiation, temperature and vapour pressure deficit over 48 hours. We observed a significant and self-sustained circadian oscillation in A and in stomatal conductance (gs) which also led to a circadian oscillation in λ. The lack of constant marginal water cost indicates that circadian regulation does not directly lead to optimal stomatal behaviour. However, the temporal pattern in gas exchange, indicative of either maximizing A or of minimizing E, depending upon time of day, indicates that circadian regulation could contribute towards optimizing stomatal responses. More broadly, our results add to the emerging field of plant circadian ecology and show that molecular controls may partially explain leaf-level patterns observed in the field.
Tef ( Eragrostis tef ) variety Kora

Tef [ Eragrostis tef (Zucc.) Trotter], is a staple food crop of Ethiopians that originated and diversified in Ethiopia. It has existed in Ethiopia throughout recorded history. Annually, it occupies 3.02 million hectares thereby ranking first among all cereals cultivated in the country. However, the national average yield of tef is low 1.6 t ha -1 . The use of unimproved local cultivars and biotic and abiotic stresses are partially attributed to the low yield of the crop. Thus, the experiment was designed to develop high yielding and desirable quality improved varieties of tef suitable for diverse agro-ecologies, farming systems and purposes. Fourteen tef genotypes including two checks were laid out in randomized complete block design using four replications for two years (2012 and 2013) at eight locations. The combined data analysis across locations and over the years indicated that candidate variety Kora (DZ-Cr-438 (RIL No. 133B) performed better than the two checks and other test genotypes. Consequently, Kora was identified and approved for large scale production.
Behaviorally active substances affecting reproductive success of the fungus gnat, Lycoriella ingenua, a pest of white button mushrooms, Agaricus bisporus

Little is known about the host seeking and courtship behaviors of the fungus gnat, Lycoriella ingenua (Diptera: Sciaridae), one of the most severe insect pests of cultivated white button mushrooms, Agaricus bisporus. Published works concerning L. ingenua focus primarily on aspects of control including: insecticide susceptibility, insecticide resistance, viability of biological control agents, and determining damage thresholds. The work presented in this dissertation examines the host seeking behavior of female flies and the copulatory behavior of male flies. Host seeking and copulatory behaviors in insects involve a complex series of events beginning with signal acquisition, signal transduction, and signal processing. Signal molecules provide the searching insect with information about the quality and location of the host material or potential mate. In this dissertation I present work showing that gravid L. ingenua female flies are attracted the composted substrate that mushrooms are grown on, not the mushrooms themselves, and to the mycoparasitic green mold, Trichoderma aggressivum. Fungi including Penicillium citrinum, Mycothermus thermophilium, and several Aspergillus sp. present in mushroom compost, may be responsible for the initial attraction to female L. ingenua flies. We also isolated a single female produced pheromone component, a germacradienol, that attracts male L. ingenua flies and elicits copulatory behavior including wing fanning and abdomen curling. Ultimately the work presented in this dissertation may provide growers with new tools to manage and control L. ingenua populations in mushroom houses.
Seasonal Incidence of mustard flea beetle, Phyllotreta cruciferae on Brassica species in relation to weather parameters at different dates of sowing

The present field experiment was carried out to study the incidence of flea beetle on Brassica species in different dates of sowing at Norman E. Borlaug Crop Research Center of G.B. Pant University of Agriculture and Technology, Pantnagar, India during Rabi 2015-16 and 2016-17. Eight Brassica species including B. rapa cv. BSH-1and YST-151, B. alba, B. carinata, B. nigra, E. sativa cv. T-27, B. juncea cv. Varuna and B. napus cv. GSC-6 were sown on five dates of sowing starting from October 3 to December 3, 2015 and 2016 at fifteen days interval. The results showed that E. sativa harboured highest population of P. cruciferae (5.79 and 19.2 bettles/ m2) while it was lower on B. carinata (2.08 and 6.1 bettles/ m2) during consecutively for two years, 2015-16 and 2016-17. the population of flea beetle recorded on different brassica species in present study different significantly with respect to different dates of sowing in both the years. regarding the date of sowing, overall mean population of P. cruciferae was found maximum in first, second and third sowing date of sowing while minimum in fourth and fifth date of sowing during 2015-16. however, the flea beetle population was found higher in fourth and fifth date of sowing during 2016-17.
Complete mitochondrial genome of Pallas’s Leaf Warbler (Phylloscopus proregulus)

Abstract In the present study, the complete mitochondrial DNA sequence of Pallas’s Leaf Warbler (Phylloscopus proregulus) was determined for the first time. The mitochondrial genome of Pallas’s Leaf Warbler is a circular molecule of 16,880 bp in size and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 control regions. The base composition is 32.7% for C, 14.3% for G, 30.0% for A and 23.0% for T. These data will be useful for studying the genetic diversity within the species of Pallas’s Leaf Warbler and phylogenetic relationships among different Phylloscopidae species.
Morphological ontogeny of Protoribates dentatus (Acari, Oribatida, Haplozetidae)

Abstract The morphological ontogeny of Protoribates dentatus (Berlese, 1883) is described and illustrated. The juveniles of P. dentatus are elongated, oval in cross section, and their prodorsal, gastronotal setae and most setae on the legs are thin, smooth or with short barbs, which is typical of xylophages. Typical for this group is also a posterior position of the anal opening and relatively thick leg segments and claws, especially on leg I. The larva of P. dentatus has 11 pairs of gastronotal setae, including h2; and setae c2, la and lm are with excentrosclerites. The nymphs have 15 pairs of setae, of which c2 l- and h-series are with excentrosclerites. The adult of this species has a long seta ad1 (which is short in most congeners) and the number of claws varies on all leg tarsi.
Relative impacts of light, temperature, and reactive oxygen on thaumarchaeal ammonia oxidation in the North Pacific Ocean

Thaumarchaeota are implicated as the major ammonia oxidizers in the ocean. However, the influence of various abiotic factors in determining their distribution and activity in the upper ocean remain largely unclear. Here, we examined the influence of light, hydrogen peroxide (H2O2), and temperature on ammonia oxidation rates for communities dominated by Thaumarchaeota at the nitrite maximum across two North Pacific transects. In situ ammonia oxidation was almost exclusively driven by Thaumarchaeota, as inferred from ammonia monooxygenase subunit A (amoA) genes, amoA transcripts, and inhibitor studies. A major shift in population structure near the eastern North Pacific Subtropical Front was revealed by sequence variation of amoA genes, showing different Thaumarchaeota community structure in oligotrophic gyre and temperate regions. While the most dominant OTUs were closely related, we found significant differences in physiological responses to light and temperature of incubation. At four stations in different biogeochemical regimes, the impact of sunlight intensity and temperature on activity was evaluated using 15 NH4+ ‐spiked whole seawater collected from the nitrite maximum and incubated at different depths on a free floating in situ array. Ammonia oxidation was usually completely inhibited by PAR at the surface and 21–45% inhibited at 1% surface PAR, whereas a temperature effect on ammonia oxidation was observed at only two of four stations. While inhibition due to H2O2 cannot be ruled out in surface waters, our findings show that below the mixed layer, photoinhibition, and not H2O2 toxicity, had a greater influence on ammonia oxidation.
System-wide analysis of manganese starvation-induced metabolism in key elements of Lactobacillus plantarum

To analyze the response mechanisms of Lactobacillus plantarum against manganese starvation stress, different metabolisms from physiology, proteomics and transporters aspects in L. plantarum CCFM 436 were systematically investigated. The kinetics of cell growth (μmax) decreased from 0.310 to 0.256 h−1, while thinner cell morphology was observed by transmission electron microscopy under Mn-starvation conditions. Gas chromatography-mass spectrometry analysis indicated that membrane mobility and compactness increased, with a higher proportion of unsaturated fatty acids and cyclopropane fatty acids. High-performance liquid chromatography analysis showed that intracellular Asp, Glu, and Arg contents, closely related to energy metabolism, were significantly increased. Fourier transform infrared spectroscopy proved that some functional groups (N–H and OC–OH) were significantly affected by Mn starvation. Comparative two-dimensional proteomic analysis identified 73 proteins that differed significantly under Mn starvation conditions. These differentially expressed proteins involved in carbohydrate, amino acid and transcription/translation metabolisms and stress response were categorized as crucial components required to resist manganese starvation stress. Moreover, qRT-PCR analysis proved that MntH 1–5, negatively regulated by MntR, acted as potential Mn importers under Mn starvation conditions. The proposed coordinated mechanism model provides a reference for, and insight into, the intracellular metabolism of LAB strains.
Genetic diversity of Kelampayan using dominant DNA markers based on inter-simple sequence repeats (ISSRs) in Sarawak

Neolamarckia cadamba (Roxb.) Bosser, or locally known as kelampayan, is a fast-growing timber species which produces one of the best sources of raw material for the plywood industry and also for the pulp and paper industry. It has been selected as one of the promising plantation tree species for large-scale planted forest development in Sarawak. Therefore, the molecular characterization of this indigenous tropical tree species is needed to maintain its high quality. Intersimple sequence repeats (ISSR) markers were used in this study to determine the genetic diversity of kelampayan in three progeny trial blocks at the Landeh Nature Reserve, Semengok, Sarawak. The seeds were collected from the selected mother trees located at the Pasai Bon, Niah and Lawas seed production areas (SPAs) in Sarawak. Three ISSR primers, namely (GTG)6, (AG)10 and (AC)10, that yielded reproducible, informative and scorable fragments were chosen for ISSR analysis. A total of 64 loci were generated of which 45.3–74.6% of the loci were identified as polymorphic bands with the size ranging from 500 bp to 2 kb among 247 kelampayan progenies selected in the present study. Molecular diversity based on Shannon’s diversity indices (I) among 247 trees ranged from 0.268 to 0.350. In general, the kelampayan trees in the three progeny trial blocks exhibited a high level of molecular diversity and DNA polymorphism compared with its natural populations. This preliminary information will form the base for kelampayan tree improvement and conservation programmes.
Biology, ecology and demography of the tropical treehopper Ennya maculicornis (Hemiptera: Membracidae): relationships between female fitness, maternal care and oviposition sites

1. Treehoppers (Hemiptera: Membracidae) exhibit a wide range of social behaviours related to maternal care and nymphal aggregation. Maternal care represents an investment in terms of time and energy leading to trade‐offs which bear a strong relationship with parity and can thus affect population dynamics. These trade‐offs can be modulated by biotic and abiotic features of the oviposition site.
Identification de marqueurs épidémiologiques par spectrométrie de masse de type MALDI-TOF : application aux principales espèces bactériennes responsables d'infections nosocomiales

Le typage bacterien est une mesure de controle essentielle pour lutter contre la diffusion des bacteries multiresistantes, mais les techniques actuelles sont longues et couteuses. L'objectif de cette these etait d'evaluer la capacite de la technique MALDI-TOF MS a typer les 3 principales especes bacteriennes responsables d'infections nosocomiales - Escherichia coli, Staphylococcus aureus et Pseudomonas aeruginosa. L'analyse par MALDI-TOF MS permet d'identifier les souches de E. coli appartenant au phylogroupe B2, souches les plus virulentes parmi les souches extra-intestinales, et au STI 31, clone tres implique dans la dissemination des P-lactamases a spectre etendu. Chez S. aureus, cette technique reconnait les souches appartenant au CC398, impliquees dans une proportion importante d'infections graves chez des personnes fragiles. La technique MALDI-TOF MS identifie egalement cinq clones de P. aeruginosa a haut risque epidemique - STI 11, STI 75, ST235, ST253, ST395. Si nous avons confirme des pics caracteristiques du phylogroupe B2 decrit egalement par d'autres auteurs, les pics biomarqueurs identifiant E. coli ST131 ou des clones epidemiques de S. aureus varient suivant les etudes. Differents parametres peuvent influencer les resultats de typage par MALDI-TOF MS et doivent donc etre standardises. La technique MALDI-TOF MS permet d'identifier certains clones epidemiques. En gardant a l'esprit que le choix d'une methode de typage doit etre fait en fonction des objectifs mais aussi des performances des differents systemes disponibles, la technique MALDI-TOF MS pourrait se positionner comme un outil de typage de premiere ligne.
Soil compaction caused by harvest and logging operations in eucalyptus forests in coarse-textured soils from northeastern Brazil

Planted forests occupy more than 6.5 million ha in Brazil, where harvest and logging operations are performed with increasingly heavier machinery, increasing the risk of soil compaction. Soil compaction can be avoided if soil load bearing capacity is not exceeded, what makes it important to assess both the soil strength and the impact of different operations. The aim of this study was to evaluate the load bearing capacity of some coarse textured soils (two Hapludult and one Haplorthod) in two soil horizons (BA and B), from northeastern Brazil; and to assess the impact of harvest and logging operations performed with harvester and forwarder. Although the Haplorthod presented higher load bearing capacity in both the BA horizon (for the whole moisture range) and the B horizon (for higher water contents), it suffered the greatest soil compaction. Traffic with the harvester resulted in soil compaction in both the BA and the B horizons, but the increase in bulk density was higher on the later, reaching 18.7% in the Haplorthod. The forwarder traffic intensity and the presence of plant residue cover significantly affected the occurrence of soil compaction. In the BA horizon, the increase in soil bulk density for different forwarder traffic intensities was 3 passes ~ 6 passes < 12 passes ~ 16 passes. The increase in bulk density was higher in the Haplorthod, reaching 32% after 16 forwarder passes over bare soil. Significant linear regressions were obtained from the number of forwarder passes and the increase in bulk density.
Evaluation of Zn Bioavailability and Metallothionein Expression by RT-PCR in Zinc Sulphate and Zinc Proteinate Fed Chickens -

The present study was conducted to evaluate the bioavailability of different forms and concentration of Zinc (Zn) incorporated into diets of chicken and to find out Metallotheionein (MT) expression by Real time Polymerase Chain Reaction (RT-PCR). In this study broiler birds were fed with corn-soya based basal diet (BD) as control (T1), BD with ZnSO4@ 80 ppm (T2) and BD with 40 and 80 ppm of Znproteinate (T3 and T4) respectively, for a period of 42 days. At day 42, six birds from each treatment were slaughtered, liver and duodenal scrapings were collected for MT expression, whereas tibia and serum were collected for Zn estimation. On comparison of treatments and control group for Zn bioavailability and MT mRNA expression, treatment groups showed significantly higher levels of Zn in tibia and serum and also up regulation of MT mRNA. But, birds fed with Zn-proteinate exhibited MT mRNA expression significantly greater than all other treatments, suggesting that Zn-proteinate form is more bioavailable than ZnSO4. Subsequent commercial trails with reduced (50 %) mineral inputs via Zn-proteinate revealed equal performance characteristics as compared to inorganic Zn feeding at 100 % level.
Antimalarial Activity of Ethanolic Leaf Extract of Maesobotrya barteri and Effects on Some Hematological and Biochemical Parameters of Mice

Aim: This study was conducted to determine the antimalarial activity of ethanolic leaf extract of Maesobotrya barteri, and effects on some hematological and biochemical parameters. techniques in order to generate permanently stained sections. Results: Maesobotrya barteri showed a significant parasitemia reduction. For all three doses of the extract administered to infected mice, there was a significant reduction in the mean number of parasitized red blood cells during the four days of treatment. The concentration of 1000 mg/kg body weight of the plant extract had the highest antimalarial activity with a parasite inhibition of 97.2%. There was a significant increase in PCV level and haemoglobin concentration. The WBC count showed an increase which was not statistically significant. The ESR level was lowered for the treated groups when compared to the negative control. The liver markers assay revealed a significant lowering in the levels of ALT, AST, ALP and total bilirubin for all treated groups when compared to the negative control. The levels of the liver enzymes for the positive control was similar to the values obtained for the extract treated groups. The histology of the infected, untreated group showed endothelial cell derangement in the central vein (CV) and hepatic necrosis. The histological section of groups treated with standard drugs and 1000 mg/kg bwt extract showed the impression of normal histology. Conclusion: This study has established the antiplasmodial activity of Maesobotrya barteri . The study also confirmed that the plant has hematopoietic potential and hepato-enhancing property. These findings support the folkloric use of the plant in the treatment of malaria.
A Global Assessment of Inland Wetland Conservation Status

&NA; Wetlands have been extensively modified by human activities worldwide. We provide a global‐scale portrait of the threats and protection status of the world's inland wetlands by combining a global map of inundation extent derived from satellite images with data on threats from human influence and on protected areas. Currently, seasonal inland wetlands represent approximately 6% of the world's land surface, and about 89% of these are unprotected (as defined by protected areas IUCN I‐VI and Ramsar sites). Wetland protection ranges from 20% in Central and 18% in South America to only 8% in Asia. Particularly high human influence was found in Asia, which contains the largest wetland area of the world. High human influence on wetlands even within protected areas underscores the urgent need for more effective conservation measures. The information provided here is important for wetland conservation planning and reveals that the current paradigm of wetland protection may be inadequate.