Miracle-dz/UniFAR-FTUs huggingface dataset:
Insights Into Mitochondrial Genetic and Morphologic Dynamics Gained by Stochastic Simulation

MtDNA mutations in mammalian cells are implicated in cellular ageing and encephalomyopathies, although mechanisms involved are not completely understood. The mitochondrial genetic bottleneck has puzzled biologists for a long time. Approximate models of genetic bottleneck proposed in the literature do not accurately model underlying biology. Recent studies indicate mitochondrial morphology changes during cellular ageing in culture. In particular, the rates of mitochondrial fission and fusion are shown to be in tight balance, though this rate decreases with age. Some proteins involved in mitochondrial morphology maintenance are implicated in apoptosis. Hence, mitochondrial genetic and morphologic dynamics are critical to the life and death of cells. By working closely with experimental collaborators and by utilizing data derived from literature, we have developed stochastic simulation models of mitochondrial genetic and morphologic dynamics. Hypotheses from the mitochondrial genetic dynamics model include: (1) the decay of mtDNA heteroplasmy in blood is exponential and not linear as reported in literature. (2) Blood heteroplasmy measurements are a good proxy for the blood stem cell heteroplasmy. (3) By analyzing our simulation results in tandem with published longitudinal clinical data, we propose for the first time, a way to correct for the patient’s age in the analysis of heteroplasmy data. (4) We develop a direct model of the genetic bottleneck process during mouse embryogenesis. (5) Partitioning of mtDNA into daughter cells during blastocyst formation and relaxed replication of mtDNA during the exponential growth phase of primordial germ cells leads to the variation in heteroplasmy inherited by offspring from the same mother. (6) We develop a “simulation control” for experimental studies on mtDNA heteroplasmy variation in cell cultures. Hypothesis from the mitochondrial morphologic dynamics model: (7) A cell adjusts the mitochondrial fusion rate to compensate for the fluctuations in the fission rate, but not vice versa. A deterministic model for this control is proposed. Contributions: extensible simulation models of mitochondrial genetic and morphologic dynamics to aide in the powerful analysis of published and new experimental data. Our results have direct relevance to cell biology and clinical diagnosis. The work also illustrates scientific success by tight integration of theory with practice.
Special paper Heart regeneration

Heart failure is the leading cause of death worldwide and the main reason for hospitalization of patients 65-years of age and older. Current therapies only delay progression of the disease but the overall mortality remains as high as 20% per year. The underlying issue is the same whether the cause is acute damage, chronic stress from disease, or aging – progressive loss of functional cardiomyocytes and diminished hemodynamic output. Trials for regenerating cardiac muscle with cell-based therapy are ongoing for more than 10 years now. Multiple candidate cell types have been used in laboratory experiments and I generation clinical trials, including: skeletal myoblasts, bone marrow and peripheral blood mononuclear cells, endothelial progenitor cells, neonatal cardiomyocytes, mesenchymal stem cells, embryonic stem cells, induced pluripotent stem cells and cardiac stem cells. Results of these studies suggest that cell-based therapy for the failing heart can improve cardiac function. More recently, it has been shown that the heart is not terminally differentiated, and resident cardiac stem cells become a potential source for regeneration of cardiac muscle, smooth muscle and endothelium. This paper summarizes the results of I generation clinical trials and discuss prospects of regenerative therapy in the near future, especially in the context of new stem cell populations available.
Review: Breeding common bean for resistance to insect pests and nematodes

Singh, S. P. and Schwartz, H. F. 2011. Review: Breeding common bean for resistance to insect pests and nematodes. Can. J. Plant Sci. 91: 239-250. Various insect pests and nematodes cause severe losses (35-100%) globally to the yield and quality of dry and green common bean (Phaseolus vulgaris L.). The objectives of this review are to briefly describe major insect pests and nematodes in the Americas, breeding strategies and methods used, and research progress achieved. We also describe integrated genetic improvement for resistance to multiple insect pests and nematodes and cultivar development. Breeding for resistance to one insect pest or nematode at a time has been practiced in most instances. Backcross, pedigree, and bulk-pedigree breeding methods have been used. Considerable progress has been made in genetics and germplasm enhancement for resistance to bean pod weevil (Apion godmani Wagner), tropical bruchid (Zabrotes subfasciatus Boheman), leafhoppers (Empoasca kraemeri Ross and Moore), and root- knot nematode (Meloidogyne species). However, improvement in resistance to Acanthoscelides obtectus (Say), lesion (Pratylenchus species) and soybean cyst (Heterodera glycines) nematodes, and other regional insect pests has been minimal or non-existent. Furthermore, dry or green common bean cultivars with high levels of resistance to one or more insect pests and nematodes are rare. Breeding strategies for integrated and simultaneous genetic improvement of multiple qualitatively and quantitatively inherited resistances for cultivar development are briefly described.
Genetic Evaluation of GIFT and Existing Strains of Nile Tilapia, Oreochromis niloticus L., Under On-Station and On-Farm Conditions in Bangladesh

Comparative production performances of Genetically Improved Farmed Tilapia (GIFT) and existing Nile, Oreochromis niloticus L. strains were assessed in five test environments (nursery systems, cisterns, hapas, net cages, and grow-out ponds) and six multi-locational sites (Trishal, Chandina, Manikganj, Paikgacha, Jessore Sadar, and Mithapukur) under on-station and on-farm conditions in Bangladesh. The mean weight gains at harvest of the GIFT strain was significantly higher (40-57%) than the existing Nile tilapia strain in all the trials.
Impacts of land-use and management systems on organic carbon and water-physical properties of a Latossolo Amarelo (Oxisol)

O bioma Cerrado tem notavel relevância territorial no estado do Piaui, e devido as suas caracteristicas de clima, relevo e solos favoraveis tem tornado essa regiao uma referencia na producao de alimentos no estado. A partir desse estudo se objetivou avaliar as implicacoes dos diferentes sistemas de uso, manejo e tempo de adocao nos teores de carbono orgânico e em atributos fisicos do solo em um Latossolo Amarelo da regiao Sudoeste do estado do Piaui. O estudo foi realizado no municipio de Urucui, locado na regiao sudoeste do estado do Piaui. Neste estudo foram avaliados nove sistemas de producao com diferentes historicos de uso, manejo e tempo de adocao disposto da seguinte forma: areas sob sistema de plantio direto (PD3 e PD9, respectivamente com tres e nove anos de cultivo), areas sob pastagem (PA2 e PA6, respectivamente com dois e seis anos de cultivo), areas sob plantio de eucalipto (EU6 e EU12, respectivamente com seis e doze anos de cultivo), areas sob sistema de preparo convencional (PC2 e PC8, respectivamente com dois e oito anos de cultivo) e Cerrado nativo (CN), representando uma condicao de referencia. A conversao do Cerrado nativo em plantio direto e pastagem ocasionou evolucao no conteudo de carbono orgânico com o passar do tempo.
A Comprehensive and Systematic Study of Semen Quality and SpermFunctional Status in Normozoospermic Controls and Infertile Males fromSouth India

Objective: Despite, several global studies indicate the variations in semen characteristics that accounts for male infertility, the association of specific changes in semen quality and fertility status among different Indian communities are poorly investigated. With wide range of geographical locations, diverse lifestyle patterns, seasonal variations combined with heterogeneous population, India offers an excellent system to study genotype-to-phenotype correlation. Hence, the current study has been initiated in South Karnataka region of India, in order to examine the variations in semen quality and sperm functional status in infertile individuals compared with normozoospermic controls. Methods: WHO strict guidelines are followed for systematic semen analysis of 239 infertile and 244 normozoospermic control subjects. Results: Interestingly, compared to normozoospermic controls, higher percentage of physical abnormalities such as, low semen volume and reduced sperm count are observed in infertile men. Additionally, semen characteristics namely, vitality and motility values are significantly reduced in infertile than controls. Further, in sperm function test the lower scores are documented for hypo-osmotic swelling assay, but not for sperm chromatin decondensation and acrosome intactness examination, suggesting loss of sperm plasma membrane integrity in infertile men. Moreover, the observed changes in semen parameters and sperm function are also evident in different infertile sub-conditions with varied responses. Surprisingly, age wise analysis revealed reduction in sperm morphology scores, whereas, vitality, count, motility and volume remain unchanged with increasing age of infertile males. However, we recorded inverse relationship between age and sperm vitality as well as motility in normozoospermic control men. Together, though the scores for different semen parameters in normozoospermic control group are in accordance with WHO reference range, the infertile men displayed poor semen quality. Conclusion: Thus, our data establishes basic differences between infertile and normozoospermic control group in terms of semen characteristics and sperm functional status, but the cause may be attributable to genetic or environmental factors or interaction of the two, which necessitates further detailed examination in larger cohort among heterogeneous population.
Comparison of genetic values for reproductive performance in beef cattle

A simulation study was conducted to compare methods for handling censored days to calving records in beef cattle data. Days to calving was defined as the days between the time a bull is turned out in the pasture and the subsequent parturition. Simulated data were generated to have similar data structure and genetic relationships to an available field data set. Records were simulated for 33,176 daughters of 4238 sires. Data were simulated using a mixed linear model that included the fixed effects of contemporary group and sex of calf, linear and quadratic covariates for age at mating, and random effects of animal and residual error. Two methods for handling censored records were evaluated, and two censoring rates of 12 and 20% were applied to assess the influence of higher censoring rates on inferences. Censored records were assigned penalty values on a within contemporary group basis under the first method (DCPEN). Under the second method (DCSIM), censored records were drawn from their respective predictive distributions. Bayesian approach via Gibbs sampling was used to estimate variance components and predict breeding values. Posterior means (PM) and standard deviations (SD) of additive genetic variance for DCPEN at 12 and 20% censoring were 23.23 (3.72) and 21.04 (3.64), respectively, while the same estimates for DCSIM at 12 and 20% censoring were 23.65 (3.30) and 21.93 (3.42), respectively. In all cases, the true value of the genetic variance was within the high posterior density interval HPD (95%). PM (SD) of residual variance for DCPEN at 12 and 20% censoring were 415.7 (4.67) and 440.0 (4.79), respectively, while the same estimates for DCSIM at 12 and 20% censoring were 371.0 (4.31) and 365.4 (4.43), respectively. The true value of the residual variance was within the HPD (95%) for DCSIM, but it was outside this interval for DCPEN at
SWItching from malignancies to intellectual disability

Heterozygous germline mutations in components of switch/sucrose nonfermenting (SWI/SNF) chromatin remodeling complexes were recently identified in patients with non-syn dromic intellectual disability, CoffinSiris syndrome and Nicolaides-Baraitser syndrome. The common denominator of the phenotype of these patients is severe intellectual disability and speech delay. Somatic and germline mutations in SWI/ SNF components were previously implicated in tumor development. This raises the question whether patients with intellectual disability caused by SWI/SNF mutations in the germline are exposed to an increased risk of developing cancer. Here we compare the mutational spectrum of SWI/SNF components in intellectual disability syndromes and cancer, and discuss the implications of the results of this comparison for the patients.
Ecosystem variability along the estuarine salinity gradient: Examples from long‐term study of San Francisco Bay

The salinity gradient of estuaries plays a unique and fundamental role in structuring spatial patterns of physical properties, biota, and biogeochemical processes. We use variability along the salinity gradient of San Francisco Bay to illustrate some lessons about the diversity of spatial structures in estuaries and their variability over time. Spatial patterns of dissolved constituents (e.g., silicate) can be linear or nonlinear, depending on the relative importance of river‐ocean mixing and internal sinks (diatom uptake). Particles have different spatial patterns because they accumulate in estuarine turbidity maxima formed by the combination of sinking and estuarine circulation. Some constituents have weak or no mean spatial structure along the salinity gradient, reflecting spatially distributed sources along the estuary (nitrate) or atmospheric exchanges that buffer spatial variability of ecosystem metabolism (dissolved oxygen). The density difference between freshwater and seawater establishes stratification in estuaries stronger than the thermal stratification of lakes and oceans. Stratification is strongest around the center of the salinity gradient and when river discharge is high. Spatial distributions of motile organisms are shaped by species‐specific adaptations to different salinity ranges (shrimp) and by behavioral responses to environmental variability (northern anchovy). Estuarine spatial patterns change over time scales of events (intrusions of upwelled ocean water), seasons (river inflow), years (annual weather anomalies), and between eras separated by ecosystem disturbances (a species introduction). Each of these lessons is a piece in the puzzle of how estuarine ecosystems are structured and how they differ from the river and ocean ecosystems they bridge.
Growth, Water Use Efficiency and Antioxidant Defense Responses of Mycorrhizal and Non Mycorrhizal Allium sativum L. Under Drought Stress Condition

Garlic plant inoculated with Arbuscular Mycorrhizal (AM) fungi Glomus fasciculatum showed improved plant growth shoot length and biomass during drought stress condition. The mycorrhizal garlic plants were absorbing more water during drought stress condition by extraradical hyphae which were spread in soil, which helps in increasing water use efficiency of mycorrhizal garlic plants. The antioxidant defense response either increase or decrease due to response of drought stress. Proline accumulation in shoot was induced by drought stress in non AM inoculated garlic plants. But in root, proline accumulation was higher in AM garlic plants. This suggests that AM fungi help the garlic plants to greater osmotic adjustment under drought stress condition. The work suggest that AM fungi helps the garlic plants by absorbing more water and improved plant biomass by minimizing drought stress effect also activating the antioxidant and non antioxidant defense system to withstand under drought condition.
Induction of Oocyte Maturation in vitro by Steroid Hormones in the Red Sea Bream Pagrus major

Induction of Oocyte Maturation in vitro by Steroid Hormones in the Red Sea Bream Pagrus major Shinji Adachi,*1 Kazuo mi Ouchi*2 Keiji Hirose,*3 and Yoshitaka Nagahama*1 (Received January 5, 1988) A number of steroids have shown to induce o ocyte maturation in teleosts in vitro.1) Among them, 17α, 20β-dihydroxy-4-pregnen-3-one (17α, 20β-diOHprog is one of the most potent steroids.1,2) More rccently, this steroid has been identified as the natura l maturation-inducing hormone in the amago salmon Oncorhynchus rhodurus.3) These investigations, however, have been limited to several salmonid fishes and some freshwater fishes; there have been few studies on marine fishes.1,4,5) The present study used in vitro incubation techniques to determine the relative effectiveness of six steroids in inducing germinal vesicle breakdown (GVBD) in follicle-enclosed oocytes of red sea bream Pagrus major, an economically important marine teleosts in Japan. Three-year-old P. maior were held under natural ambient conditions in an indoor fiber reinforced plastic holding tank (30kl) with frce flowing sea water and an additional recilculating pump. The water temperature was approximately 16°C, similar to the natural sea water temperatures during breeding season. Under these conditions, most fish spawn in the early evening (17:00-19:00) every day during the breeding season (early April to mid-May). Fish were killed in the early afternoon and then oocytes in the tertially yolk stage with 10-20 oil droplets were isolated from ovarian pieces. Oocytes in more advanced stages had already undergone ovulation. Experiments were conducted in late April. Isolated oocytes were incubated in plastic tissue culture dishes (24 wells) (Costar) containing a L-15 (GIBCO) culturc medium (320 mOs/kg H20) (10 oocytes/ml/well). Incubates contained v arious doses of progesterone, 17α-hydroxyprogesterone ( 17α-OHprog), 17α,20β-diOHprog, testosterone, estradiol-17β and deoxycorticosterone (DOC) (Sigma). Controls consisted of groups of oocytes incubated in hormone-free media. Three replicates were made of e ach treatment。 Incubation was carried out at 18°C f or 24h. Following this incubation period, oocytes w ere transfered to a clearing solution6) and inspected for GVBD. Oocytes which had undergone GVBD w ere always transparent. In this study, the occurrence o f GVBD was used as the criterion of oocyte matura -t ion. In this study all steroids, with the exception estradiol17β, induced GVBD in vitro in follicle-enclosed oocytes of P. major. A time course study on oocyte size changes during 17α, 20β-diOHprog (0.1μg/ml)-induced oocyte maturation indicated that steroid treatment markedly increased oocyte size, probably due to hydration(Fig. 1).
Effect of Quercetin and Pectinase on Spore Germination and Hyphal Growth of Arbuscular Mycorrhizal Fungi and Biomass Production of Nicotiana tabacum L. and Calopogonium mucunoides desv

collaboration ELMN and DN designed the study. and OB the experimental design, the practical realization of RT, ABSTRACT The aim of this study was to evaluate the ability of mycorrhizal fungi to rapidly colonize roots of host plants and to predict their competitive advantage over native strains. Different concentrations of quercetin and pectinase were used to stimulate hyphal growth and to determine the germination rate of arbuscular mycorrhizal fungi (AMF) in a Petri dish. The best strains were used to inoculate two host plants under green house conditions in the presence of high concentrated polyphenol and enzyme. The essays were carried out in the laboratory of biotechnology center; University of Yaounde I. Five strains of AMF from Cameroonian’s soils were identified and compared with exotic strain. Water agar 0.7% was mixed with three different concentrations of quercetin (0, 2.5 and 5 µM) and pectinase (0, 1.6 and 3.2 units/ml). Nicotiana tabacum and Calopogonium mucunoides were used to determine the root colonisation percent of AMF and shoot biomass after inoculation. Results showed that for most species of AMF, 5% quercetin and 3.2 units/ml of pectinase significantly stimulate in vitro spore germination and hyphal growth. Treatment combining quercetin and pectinase could lead to a synergetic effect on mycorrhizal symbiosis and plant performance. These compounds which can modify the symbiosis physiology may be of great importance in the regulation of plant and soil microbe interaction. They could also contribute in stimulating the growth of these strict biotrophic fungi under in vitro culture , and to enhance an increase in plant biomass.
Redescription of Haploniscus rostratus (Menzies, 1962) (Crustacea: Peracarida: Isopoda) with observations on the postmarsupial development, size ranges and distribution

Haploniscus rostratus (Menzies, 1962) is redescribed from material obtained during deep-sea expeditions to the southeast Atlantic basins. The species is immediately recognizable by its rostrum and the unique shape of the posterior body. Specimens of all developmental stages were present in the material and are briefly described. Information on body length and body width is given and an identification key to the ontogenetic stages is provided. Development and distribution of the species are discussed. Populations of H. rostratus found north and south of the Walvis Ridge have the same morphology and do not represent cryptic species; therefore it is likely that H. rostratus is able to cross the Walvis Ridge, which has been postulated as potential barrier for benthic species by other authors.
On brazilian supratidal and estuarine snails

No litoral de Sao Paulo, Melampus coffeus (L.) vive acima da linha das mares regulares, debaixo de pedras e pedacos de madeira, entre folhas caidas no solo, assim como sobre as raizes e troncos e debaixo da casca das arvores dos manguezais. Os caracois necessitam de humidade e de protecao contra luz intensa.
Bioactivity of selected essential oils from medicinal plants found in Fiji against the Spiralling whiteflies ( Aleurodicus dispersus Russell)

The concentration of essential oil solutions [0.25%, 0.5% and 5% (v/v)] of five medicinal plants found in the South Pacific (Fiji) were subjected to the whitefly (Aleurodicus dispersus Russell) in order to assess eventual control activities, by both fumigant and repellent tests. The essential oil of Ocimum tenuiflorum L. exhibited the strongest fumigant activity against the Spiralling whiteflies with an LC50 value of 0.003% followed by the essential oil of Cymbopogon citratus (DC.) Stapf. (LC50 = 0.004%), Cananga odorata (Lam.) Hook F. and Thoms (LC50 = 0.050%), Murraya koenigii (L.) Spreng. (LC50 = 0.113%), and Euodia hortensis forma hortensis (LC50 = 0.114%). The essential oil of M. koenigii (RI=52%) and C. citratus (RI=52%) at 5% (v/v) concentration were found to have a higher repellent toxicity against the Spiralling whiteflies. The chemical composition of the selected essential oils was also determined using GC-MS. The trend in the chemical constituent of essential oils revealed that the phenolic and alcoholic compounds were the major groups of contributors to the tested activities. Thus, these data suggested that essential oils from the selected medicinal plants found in the South Pacific (Fiji) have the potential to be employed in the pesticidal activities.
A New Psammothidium Species (Bacillariophyta, Achnanthidiaceae) from Cimera Lake (Gredos Mountain Range), Central Spain

Abstract A population of an unknown Psammothidium species (Bacillariophyta, Achnanthidiaceae) was found in core sediments collected from Cimera Lake, an oligotrophic, undisturbed mountain lake in Central Spain (Gredos mountain range). The morphology and ultrastructure of this taxon is hereby documented in detail by means of light (LM) and scanning electron (SEM) micrographs. Morphologically, the closest taxon is P. levanderi, and the type of this species is analyzed here to provide a differential diagnosis. A comparison with other similar small Psammothidium species with an elliptic outline show that the combination of features exhibited by this taxon is unique and it is thus described here as Psammothidium toroi sp. nov.