Miracle-dz/UniFAR-FTUs huggingface dataset:
A repository of ENU mutant mouse lines and their potential for male fertility research

Many of the proteins and their encoding genes involved in spermatogenesis are unknown, making the specific diagnosis and treatment of infertility in males difficult and highlighting the importance of identifying new genes that are involved in spermatogenesis. Through genome-wide chemical mutagenesis using N-ethyl-N-nitrosourea (ENU) and a three-generation breeding scheme to isolate recessive mutations, we have identified mouse lines with a range of abnormalities relevant to human male fertility. Abnormal phenotypes included hypospermatogenesis, Sertoli cell-only (SCO) seminiferous tubules, germ-cell arrest and abnormal spermiogenesis and were accompanied, in some, with abnormal serum levels of reproductive hormones. In total, from 65 mouse lines, 14 showed a reproductive phenotype consistent with a recessive mutation. This study shows that it is feasible to use ENU mutagenesis as an effective and rapid means of generating mouse models relevant to furthering our understanding of human male infertility. Spermatozoa and genomic DNA from all mouse lines, including those with abnormal reproductive tract parameters, have been cryopreserved for the regeneration of lines as required. This repository will form a valuable resource for the identification and analysis of key regulators of multiple aspects of male fertility.
SELECTIVE KNOCKDOWN OF THE TRYPANOSOMA BRUCEI FLA GENES AND DEVELOPMENT OF A CHEMOTAXIS ASSAY

Sleeping sickness, or African trypanosomiasis, is a disease found in Sub-Saharan Africa caused by the Trypanosoma brucei parasite that affects hundreds of thousands of people each year. The trypanosome parasites are highly evolved to survive both in their vector, the tsetse fly, and in mammalian hosts. Trypanosomes move around within flies and mammals by use of their single flagellum. Their flagellum is unique in that it emerges from a flagellar pocket, and is attached down the length of the cell. Within the flagellar pocket, the flagellum is attached to the cell in what is known as the flagellar attachment zone (FAZ). I have chosen to study two proteins, FLA1, a homolog of a Trypanosoma cruzi protein that has been localized to the FAZ, and FLA 2, a closely related gene. It has previously been shown that RNAi suppression of both of these gene products simultaneously leads to a phenotype where the flagellum detaches from the cell. The first objective of this project is to suppress the product of each FLA gene individually in order to observe and compare the resulting phenotypes to each other, as well as to the results of previous experiments.
By how much does dietary salt reduction lower blood pressure? II--Analysis of observational data within populations.

OBJECTIVE--To determine whether the estimates of the size of the association between blood pressure and sodium intake derived from studies of individuals within populations can be quantitatively reconciled with our estimates derived from comparisons of the average blood pressure and sodium intake between different populations. DESIGN--Examination of data from 14 published studies that correlated blood pressure recordings in individuals against measurements of their 24 hour sodium intake (within population studies). MAIN OUTCOME MEASURE--Comparison of observed differences in blood pressure per 100 mmol/24 h difference in sodium intake in each within population study with predicted differences calculated from the between population data, after allowing for the underestimation of the true association of blood pressure with sodium intake caused by the large day to day variation in 24 hour sodium intake within individuals. RESULTS--The underestimation bias inherent in the within populations studies reduced the regression slope of blood pressure on single measures of 24 hour sodium intake to between a half and a quarter of the true value (for example, in one study from 6.0 to 2.4 mm Hg/100 mmol/24 h). Estimates from between population comparisons of the regression slope of blood pressure on sodium intake, after adjustment to take this underestimation bias into account, were similar to the values actually observed in the within population studies. CONCLUSION--The within population studies confirm our estimates from between population comparisons of the magnitude of the association between blood pressure and sodium intake.
DIEL CHANGES IN THE COMPOSITION OF PHOTOSYNTHETIC PIGMENTS AND CELLULAR CARBON AND NITROGEN IN PYRAMIMONAS PARKEAE (PRASINOPHYCEAE) 1

Diel changes in mean cell volume, cellular carbon (carbon content per cell), cellular Chl a, C/N ratio, Chl a/carbon ratio and pigment composition were determined for an axenic clonal culture of Pyramimonas parkeae Norris et Pearson through three 12:12 h LD cycles in a laboratory culture tank of 1 m3. Mean cell volume and cellular C, N and most pigments increased during the light period as a result of photosynthesis and decreased with an increase in cell density by phased cell division during the dark period. Chi a and Chi b increased in a parallel manner during the light period. Increases in the diel synthesis pattern of carotenoids varied. Violaxanthin and lutein content increased for a few hours at the beginning of the light period and preceeded that of neoxanthin. The diel synthesis pattern of neoxanthin was similar to that of Chi a. Increases of loroxanthin and its ester form were slower than that of Chi a at the beginning of the light period. A net increase of α‐carotene was observed during the dark period. Mass spectroscopy of carotenoid structure showed a new xanthophyll, loroxanthin dodecenoate, in this species.
A long‐standing Pleistocene refugium in southern Africa and a mosaic of refugia in East Africa: insights from mtDNA and the common eland antelope

Aim Previous genetic studies of African savanna ungulates have indicated Pleistocene refugial areas in East and southern Africa, and recent palynological, palaeovegetation and fossil studies have suggested the presence of a long‐standing refugium in the south and a mosaic of refugia in the east. Phylogeographic analysis of the common eland antelope, Taurotragus oryx (Bovidae), was used to assess these hypotheses and the existence of genetic signatures of Pleistocene climate change.
Two Novel IL-1 Family Members, IL-1δ and IL-1ε, Function as an Antagonist and Agonist of NF-κB Activation Through the Orphan IL-1 Receptor-Related Protein 21

IL-1 is of utmost importance in the host response to immunological challenges. We identified and functionally characterized two novel IL-1 ligands termed IL-1δ and IL-1ε. Northern blot analyses show that these IL-1s are highly abundant in embryonic tissue and tissues containing epithelial cells (i.e., skin, lung, and stomach). In extension, quantitative real-time PCR revealed that of human skin-derived cells, only keratinocytes but not fibroblasts, endothelial cells, or melanocytes express IL-1δ and ε. Levels of keratinocyte IL-1δ are ∼10-fold higher than those of IL-1ε. In vitro stimulation of keratinocytes with IL-1β/TNF-α significantly up-regulates the expression of IL-1ε mRNA, and to a lesser extent of IL-1δ mRNA. In NF-κB-luciferase reporter assays, we demonstrated that IL-1δ and ε proteins do not initiate a functional response via classical IL-1R pairs, which confer responsiveness to IL-1α and β or IL-18. However, IL-1ε activates NF-κB through the orphan IL-1R-related protein 2 (IL-1Rrp2), whereas IL-1δ, which shows striking homology to IL-1 receptor antagonist, specifically and potently inhibits this IL-1ε response. In lesional psoriasis skin, characterized by chronic cutaneous inflammation, the mRNA expression of both IL-1 ligands as well as IL-1Rrp2 are increased relative to normal healthy skin. In total, IL-1δ and ε and IL-1Rrp2 may constitute an independent signaling system, analogous to IL-1αβ/receptor agonist and IL-1R1, that is present in epithelial barriers of our body and takes part in local inflammatory responses.
Recycle Bioreactor for Bioethanol Production from Wheat Starch II. Fermentation and Economics

Bioethanol has been produced using sugars from cold hydolysis of pure wheat starch, sterile wheat flour, and unsterile wheat flour. The conversion of sugars to ethanol from pure starch reached 96% of the theoretical maximum while that from sterile wheat flour was 69% and from unsterile wheat flour only 35%. These data indicate that sequential hydrolysis and fermentation of wheat flour is not feasible. However, the simultaneous cold hydrolysis and fermentation of both wheat starch and wheat flour proved successful. Both sugar sources produced 95% of the theoretical maximum amount of ethanol. The process could be repeated in a sequential batch fashion for over 110 h of operation, achieving high ethanol yields in each run. A scale-up design of bioethanol production using sequential batch, simultaneous cold starch hydrolysis, and fermentation indicates that this process would be economically feasible. High levels of revenue are generated from both the bioethanol and the byproduct: food-grade wheat gluten. The payback period is predicted to be < 2 years with a discounted cash flow rate of return of 46%.
ENZYMES OF AMMONIUM ASSIMILATION IN THE MYCORRHIZAL FUNGUS PEZIZELLA ERICAE READ

Summary Growth of Pezizella ericae Read in solution culture with ammonium (NH4+) as the primary nitrogen source was accompanied by decrease in pH and ammonium concentration. Both glutamate dehydrogenase (GDH) and glutamine synthetase (GS) were involved in ammonium assimilation. Activities of these enzymes changed during the time course of the experiment (28 d). Maximum GDH activity [0.35 μol NAD(P)H oxidized min−1 mg protein−1] occurred when external NH4+ concentration was high (5 to 10 mM). Maximum GS activity (0.2 μol of γ-glutamyl hydroxamate min−1 mg protein1) occurred when external NH4+ concentration was low (1 mM). L-Methionine DL sulphoximine (MSX), a specific inhibitor of GS, inhibited uptake of 15NH4Cl in 13-d-old mycelium of P. ericae. The nitrogen nutrition of the fungus and the host in the soil environment is discussed.
(Environmental Entomology,23:535-542)Periodic mass rearing and harvesting based on the theories of both the age-specific life table and the age-stage, two-sex life table

Periodic mass rearing and harvesting of specific life stages are analyzed based on the theories of both the age-specific life table and the age-stage, two-sex life table. Formulae for the calculations of the optimal discard age and harvest rate are derived. For practical applications, the use of thermal summation to manipulate the developmental time of specific life stage is suggested. The model is demonstrated using life table data of Ostrinia furnacalis (Guenee).
Biological control of fusarium wilt of tomato by antagonist fungi and cyanobacteria

Biological control of Fusarium oxysporum f. sp . lycopersici (FOL) causing wilt disease of tomato was studied in vitro as well as under pot conditions. Dual culture technique showed that Aspergillus niger, Penicillium citrinum, Penicillium sp. and Trichoderma harzianum inhibited the radial colony growth of the test pathogen. Methanol extract of Nostoc linckia and Phormidium autumnale showed moderate and minor zone of inhibition. Maximum seed germination was observed in seeds treated with N. linckia (93%), whereas, T. harzianum, P. autumnale, P. citrinum showed 80% seed germination, while A. niger treated seeds showed 50% germination. Under pot conditions, the plant heights, fresh and dry weight of plants were found to be increased significantly (p ≤ 0.05) in all treatments except in P. autumnale amended soil. Similar results were observed in chlorophyll (a+b) content of treated plants. Maximum control of wilt disease was observed with T. harzianum (44.4%) treated plants as compared to FOL inoculated plants. Whereas, effectiveness of the other antagonists were recorded in the following order: A. niger (35.6%), N. linckia (33.3%), P. citrinum (24.4%), and P. autumnale (0.9 %). Key words : Biological control, fusarium wilt, tomato, antagonist fungi, cyanobacteria
A molecular approach to the phylogenetic status of the aeolid genus Babakina Roller, 1973 (Nudibranchia)

Leila Carmona1, Terrence M. Gosliner2, Marta Pola3 and Juan Lucas Cervera1 Departamento de Biologia, Facultad de Ciencias del Mar y Ambientales, Universidad de Cadiz, Poligono Rio San Pedro s/n, Ap.40, 11510 Puerto Real (Cadiz), Spain; Department of Invertebrate Zoology, California Academy of Sciences, 55 Music Concourse Drive, Golden Gate Park, San Francisco, CA 94118, USA; and Laboratorio de Biologia Marina, Departamento de Biologia, Edificio de Biologia, C/ Darwin, 2, Universidad Autonoma de Madrid, 28049 Madrid, Spain
Ethylene biosynthesis in peach fruitlet abscission

Ethylene biosynthesis was studied in the peach (Prunus persica L. Batsch) fruitlet abscission zone (AZ), located between pedicel and pericarp and responsible for the shedding of the fruit. Explants, made up of the abscission layer and small parts of pedicel and pericarp, were flushed with air or air + propylene (500 cm 3 m -3 ) for up to 72 h. Parameters of ethylene biosynthesis were monitored in excised zone and non-zone tissues. Both treatments induced an increase of ethylene biosynthesis in all tissues examined and a climacteric-like behaviour was observed: ethylene evolution peaked at 12 and 48 h in air + propylene and air, respectively. The activity of 1-aminocyclopropane-1-carboxylate oxidase (ACO) and related transcript accumulation paralleled ethylene evolution. Furthermore a decreasing gradient, in terms of ethylene production, ACO activity and mRNA accumulation was in general observed moving from the distal (pericarp side) to the proximal (pedicel side) non-zone, through the abscission zone. The content of 1-aminocyclopropane-1-carboxylate (ACC) showed significant difference among treatments only at 12 h of air + propylene flushing in AZ3 and non-zones, but no difference in terms of ACC synthase transcript and related polypeptide accumulation was observed. Endo-β-1,4-glucanase (EG), the cell wall hydrolase involved in cell separation, appeared to be up-regulated by propylene and its activity was almost exclusively confined to the abscission layer. Similarly, EG transcript accumulation occurred in zone but not in non-zone tissues. In air-treated and air + propylene-treated explants the ethylene climacteric preceded the increase of EG activity and the cell separation at the level of the abscission zone.
Anti‐diabetic effect of an α‐glucan from fruit body of maitake (Grifola frondosa) on KK‐Ay mice

We have evaluated the anti‐diabetic effect of a α‐glucan (MT‐α‐glucan) from the fruit body of maitake mushrooms (Grifola frondosa) on KK‐Ay mice (a kind of genetical type 2 diabetes animal model). The effects of MT‐α‐glucan (450 or 150 mg kg−1) on diabetic mice were investigated by observing the changes in body weight, the level of fasting plasma glucose, glycosylated serum protein (GSP), hepatic glycogen, serum insulin, triglycerides, cholesterol, free fatty acid, liver superoxide dismutase (SOD), glutathione peroxidase (GSHpx), reduced glutathione (GSH) and malondialdehyde (MDA). Moreover, the binding capacity of insulin receptors on liver crude plasma membranes was assayed and histopathological changes in the pancreas were observed. Treatment with MT‐α‐glucan significantly decreased the body weight, level of fasting plasma glucose, GSP, serum insulin, triglycerides, cholesterol, free fatty acid and MDA content in livers. Treatment with MT‐α‐glucan significantly increased the content of hepatic glycogen, GSH and the activity of SOD and GSHpx. Moreover, the insulin binding capacity to liver crude plasma membranes increased and histopatho‐logical changes in the pancreas were ameliorated in the treatment group. These data suggest that MT‐α‐glucan has an anti‐diabetic effect on KK‐Ay mice, which might be related to its effect on insulin receptors (i.e., increasing insulin sensitivity and ameliorating insulin resistance of peripheral target tissues).
Defoliation and site differences influence vegetative spread in grassland

Summary • Plants spread vegetatively at rates that depend on both their own and their neighbours’ traits. We tested hypotheses that such rates also interact with defoliation intensity and differ between sites. • Well-established monoculture patches (20 × 20 cm) of five grass species were arranged in plots so that every species patch had all the remaining species as neighbours. Sites were in central Scotland, UK, and at a drier location in eastern Scotland. Plots were cut at 3 cm (‘short’) or 6 cm (‘tall’), either uniformly or in a chessboard pattern. • Invasiveness and resistance to invasion followed the transitive hierarchy, Agrostis capillaris > Festuca rubra > Lolium perenne = Holcus lanatus > Poa trivialis , except that P. trivialis strongly invaded H. lanatus at the damper, more fertile site. ‘Tall’ patches spread and intermixed most, independent of species. The effects of cutting neighbouring patches depended on both invading and invaded species’ traits. • Thus, defoliation altered the relationships between species, as did differences between sites, influencing both the speed and direction of species replacement.
Cloning and characterization of the 14-3-3 protein gene from Ipomoea batatas (L.) Lam

The 14-3-3 proteins are a group of highly conserved and widely distributed eukaryotic proteins with diverse functions. In plants, it regulates basal metabolism, ion transport, cell passage, enzyme activity and gene expression, and it is also important in disease resistance, anti-oxidation and drought resistance. Based on assembled sequences of sweet potato (Ipomoea batatas L. Lam) transcriptome, 14-3-3 protein cDNAs were cloned for the first time, and the sequencing analysis revealed the presence of three highly homologous isoforms of 14-3-3 protein cDNAs, designated as Ib14-3-3a, Ib14-3-3b and Ib14-3-3c. Three cDNA isoforms are all 1176 bp in length with 7 mutation sites and have a 789 bp of open reading frame encoding a polypeptide of 262 amino acids. The results from digital gene expression (DGE) profiling showed that the expression levels of 14-3-3 genes are different among tissues, predominantly in harvested tuberous roots (223.08 TPM) and very low in mature leaves (85.07 TPM) , which were also confirmed by semi-quantitative Reverse transcription polymerase chain reaction (RT-PCR) analysis.
Assessing abundance of populations with limited data: Lessons learned from data-poor fisheries stock assessment

Estimation of population abundances in the absence of good observational data are notoriously difficult, yet urgently needed for biodiversity conservation and sustainable use of natural resources. In the field of fisheries research, management regulations have long demanded population abundance estimates even if data available are sparse, leading to the development of a range of fish stock assessment methods designed for data-poor populations. Here, we present methods developed within the context of fisheries research that can be applied to conduct population abundance estimations when facing data-limitations. We begin the review from the less data-demanding approaches and continue with more data-intensive ones. We discuss the advantages and caveats of these approaches, the challenges and management implications associated with data-poor stock assessments, and we propose the implementation of the Bayesian hierarchical framework as the most promising avenue for future development and improvement of the cur.
Evaluation of the CONSUME and FOFEM fuel consumption models in pine and mixed hardwood forests of the eastern United States

Reliable predictions of fuel consumption are critical in the eastern United States (US), where prescribed burning is frequently applied to forests and air quality is of increasing concern. CONSUME and the First Order Fire Effects Model (FOFEM), predictive models developed to estimate fuel consumption and emissions from wildland fires, have not been systematically evaluated for application in the eastern US using the same validation data set. In this study, we compiled a fuel consumption data set from 54 operational prescribed fires (43 pine and 11 mixed hardwood sites) to assess each model's uncertainties and application limits. Regions of indifference between measured and predicted values by fuel category and forest type represent the potential error that modelers could incur in estimating fuel consumption by category. Overall, FOFEM predictions have nar- rower regions of indifference than CONSUME and suggest better correspondence between measured and predicted consump- tion. However, both models offer reliable predictions of live fuel (shrubs and herbaceous vegetation) and 1 h fine fuels. Results suggest that CONSUME and FOFEM can be improved in their predictive capability for woody fuel, litter, and duff consumption for eastern US forests. Because of their high biomass and potential smoke management problems, refining estimates of litter and duff consumption is of particular importance.
Improvement of the Biochemical Properties of Watermelon Rinds Subjected to Saccharomyces cerevisae Solid Media Fermentation

2 Abstract: Improvement of the nutritional quality of watermelon rinds was attempted by Saccharomyces cerevisae solid media fermentation. The fermented rinds were analyzed with regard to proximat e composition, antinutrient contents and phytonutrient properties and compared to unfermented watermelon rinds. Results revealed a significant increase (p 0.05) in the antinutrient contents of the fermented watermelon rinds. Significant increases (p 0.05) of the alkaloid and saponin contents. These results indicate that Saccharomyces cerevisae, a cheap, non-pathogenic and saprophytic fungus, would efficiently improve the nutritional qualities of watermelon rinds and reduce the antinutrition levels.
A New Storm-Petrel Species from Chile

ABSTRACT. We describe a new species of storm-petrel, Oceanites pincoyae (Pincoya Storm-Petrel), from the Puerto Montt and Chacao channel area, Chile. The description is based on 1 specimen collected at sea in Seno Reloncavi on 19 February 2011 and 11 other individuals that were caught, examined, and released. The new taxon's foraging ecology and behavioral habits are unique among the southern Oceanitinae, including “mouse-runs” and repeated diving beneath the surface to retrieve food items. Its distinctive appearance includes bold white ulnar bars, extensive white panels to the underwing, and white to the lower belly and vent. Among species of Oceanites, it is unique in showing white outer vanes to the outer two pairs of rectrices. It further differs from all other storm-petrels in having a distinctive juvenile plumage. Morphometrically it is distinct from Oceanites gracilis gracilis (Elliot's Storm-Petrel) and smaller than O. oceananicus chilensis (the Fuegian form of Wilson's Storm-Petrel), having a shorter tarsus and longer middle toe. There also appear to be differences in the timing of breeding and molt between the new taxon and both O. o. chilensis and O. g. gracilis. We estimate the population size of the new species as ∼3,000 individuals.