Miracle-dz/UniFAR-FTUs huggingface dataset:
Improved Understanding of Apoptosis and Metabolism in Chinese Hamster Ovary Cell Culture

Improved Understanding of Apoptosis and Metabolism in Chinese Hamster Ovary Cell Culture by Ruiqiang Mammalian cell culture has gained importance in biotechnology for the development of therapeutic and diagnostic agents. Among them, Chinese hamster ovary (CHO) cells are regarded as the mammalian cell "workhorse". The use ofCHO cell line for the production of recombinant proteins used in human therapy has reached a level of industrial production. However, a major problem encountered in in vitro cultures is cell death via apoptosis. Since apoptosis leads to the loss of viability of mammalian cells in vitro, especially in serum-free media. This is important and necessary to prevent the activation of apoptosis cascade and increase their cell viability and enhance their cellular robustness. The overall goal of this study is to improve our understanding of the cellular and physiological determinants of apoptosis and its relationship with other cellular functions. Apoptosis is a result of a very complex network of signaling pathways triggered from both inside and outside of the cell and a highly regulated pathway by both pro-apoptotic and anti-apoptotic proteins that promote cell survival or cell death. Although many causes of apoptotic process in mammalian cell cultures had been researched in the past and have been discussed in recent years, a lot need to be explored. In order to bring novel strategies to understand apoptosis in mammalian cell cultures, our study was not only focused on the apoptotic pathway but also expand to metabolic network to set up a link between cell growth and apoptosis. In our project, we applied systems biology methods in a mammalian cell line (CHO TF 70R), to understand the relationship between cellular metabolism and apoptosis in
Including cow information in genomic prediction of Holstein dairy cattle in the US

The number of females genotyped in the US has increased to 12,650 per month comprising 74% of the total genotypes received in 2013. The objective of this study was to evaluate the accuracy of cow and bull traditional information in the genomic evaluation system. Cutoff studies to determine gains in reliability due to the addition of genomic information were compared for three predictor populations, cows only, bulls only and cows and bulls. The addition of cow information to that of bulls increased genomic reliability by 0.4 percentage points across all traits. The use of cow information only in the predictor population can be used for genomic predictions. However, the addition of cow data to data from the large number of high reliability bulls in the US system has only a small benefit.
Human papillomavirus technologies

Currently, human papillomavirus (HPV) DNA tests validated in large trials and epidemiological studies are the hybrid capture second-generation (HC2) HPV DNA assay and a variety of polymerase chain reaction (PCR) protocolsemploying degenerate or consensus primers. This article describes the currently available technology for HPV detection and discusses novel technologies and their potential for large-scale screening. Ideally, an HPV test should allow detection of multiple HPV types, identify individual types, and provide quantitative information about the viral load of each individual type found. Moreover, it should be easy to perform, be highly reproducible, with a high specificity and sensitivity, and amenable for high throughput analysis and automation. Because we do not yet fully understand the true value of viral load and the biological relevance of the different HPV types, any HPV test should be able to detect the clinically relevant high-risk types with a sufficient sensitivity of at least 10 000 genome copies per sample. To validate the different current and future test systems and to compare inter-laboratory performance we urgently need reference samples, validated reagents, and standardized protocols.
Involvement of Nitrergic and Opioidergic Systems in the Oxidative Stress Induced by BDL Rats

the study, the literature searches and supervised the study. AHD the protocol, carried out the procedure, identified the clinical sign of the BDL model in rats and performed the experimental the ABSTRACT Aims: Liver cirrhosis is the irreversible end result of fibrous scarring and associated with prominent morbidity and mortality. We aimed to investigate the involvement of nitrergic and opioidergic systems in the oxidative stress induced by bile duct ligation (BDL) rats by evaluating the oxidative stress markers such as malondialdehyde (MDA), protein carbonyl content and total thiol in the plasma. Methodology: Rats received injections of 3 mg/kg Nω-Nitro-L-arginine methyl-ester-hydrochloride (L-NAME: a NO-synthase inhibitor), 10 mg/kg opioid-receptors antagonist naltrexone (NTX), L-NAME (3 mg/kg)+NTX (10 mg/kg) or saline once daily for 28 days after BDL or sham surgery. Oxidative stress markers and biochemical indexes were measured in plasma samples. Results: Results showed that serum levels of total bilirubin (TB) and alkaline phosphatase (ALP) to be significantly increased in BDL rats as compared with the Sham-operated (SO) group ( P <0.05). MDA level was significantly increased and plasma total thiol content was insignificantly decreased in the BDL group as compared with relevant SO control. Treatment of NTX in BDL rats could significantly decrease the MDA production ( P <0.05) as compared to BDL group. After 4 weeks of intervention, protein carbonyl content was significantly lower in BDL+L-NAME+NTX group as compared to the related SO and BDL groups ( P< 0.05). Conclusion: The results of the study showed that nitrergic and opioidergic systems have various impacts in the oxidative stress induced by BDL rats. Blockage of opioid receptors in BDL rats during the study could significantly decrease the MDA production and protein carbonyl content as compared to BDL group, therefore, could moderately prevent the severe liver injury.
A Fuzzy-Watershed Based Algorithm for Protein Spot Detection in 2DGE images

Summary An important issue in the analysis of two-dimensional electrophoresis images is the detection and quantification of protein spots. The main challenges in the segmentation of 2DGE images are to separate overlapping protein spots correctly and to find the abundance of weak protein spots. To enable comparison of protein patterns between different samples, it is necessary to match the patterns so that homologous spots are identified. In this paper we describe a new robust technique to segment and model the different spots present in the gels. The watershed segmentation algorithm is modified to handle the problem of over segmentation by initially partitioning the image to mosaic regions using the composition of fuzzy relations. The experimental results showed the effectiveness of the proposed algorithm to overcome the over segmentation problem associated with the available algorithms.
Comparative Ecomorphology of Cormorants (Phalacrocoracidae)

Abstract. Cormorants (Phalacrocoracidae) depend on their hind limbs (legs) to pursue prey underwater, rendering these structures critical for their survival. Assemblages of three or more species can be found in a variety of regions including the coasts of western USA (California), central Chile, and western South Africa. Cormorants all hunt via pursuit diving underwater while remaining close to shore, yet are able to coexist; an occurrence that is not well understood. Variation in feeding ecology within cormorant assemblages was expected to be reflected in the legs. Leg structure was examined by measurement of five leg bone characteristics from skeletal specimens of 10 species from assemblages within the aforementioned regions. Principle component analysis identified the femur and tarsometatarsus as having the highest degrees of variation. The femur was found to have the shortest length, relative to total leg length, in putative shoaling fish specialists. The tarsometatarsus was found to have the shortest length, relative to total leg length, in putative benthic fish specialists. Mantel's Test revealed that leg structures of members of the same putative feeding type were distributed closer together in Euclidean space (mean distance: 2.84) than leg structures of members of distinct putative feeding types (3.27); however, this was not significant (r = 0.138, t = 0.086, P = 0.233) indicating that similarity among assemblages is not statistically well-supported. Findings support niche differentiation within the studied regions.
Simulation of maize yield and N uptake under tropical conditions with the CERESMaize model 211

The CERES-Maize of DSSAT model (Version 3.50) was evaluated under tropical conditions using data sets obtained from field experiments carried out on an acid sulphate soil in the central region of Thailand, in 1999 and 2000. The validation parameters were crop grain yield and N uptake. Nitrogen in the form of urea was applied via sprinkler irrigation at rates of 0 kg N, 100 kg N, 150 kg N, and 200 kg N ha -1 . The soil was irrigated to field capacity based on 50% available soil moisture depletion regime throughout the season. Inputs to the model included site information, daily weather data, soil properties, soil initial conditions, irrigation and fertilizer management, and crop performance data. The weather data for 1999 and 2000 were collected from a weather station located 20 m from the field. The model performance was evaluated by comparing the observed and simulated values of grain yield and total N uptake using regression analyses and some error statistics such as average error (E) and relative error (RE). The results of the study showed that the regression coefficient (R 2 ) values were 0.97 and 0.99 in both years for maize grain yield and total N uptake, respectively. The average for the simulated maize yield across all treatments were 106.2% and 103.4% of the observed yield values in 1999 and 2000, respectively. The average of simulated total N uptake across all treatments were 110.4% and 111%, respectively, of the measured total N uptake values during 1999 and 2000. The results of the validation demonstrated agreement between the predicted and measured values. Although the study showed that the CERES-Maize of DSSAT model may be applied with confidence to study effects of N and irrigation management on maize yield and N uptake under irrigated tropical conditions, more validation under different soil and management conditions is recommended.
Growth and Carbon Metabolism of Tall Fescue and Zoysiagrass as Affected by Deficit Irrigation

Understanding turfgrass physiological responses to deficit irrigation will help explain potential effects of this practice on turf quality and subsequent stresses. The objective of this study was to investigate the influence of deficit irrigation growth and physiology of'Falcon II' tall fescue (Festuca arundinacea Schreb) and 'Meyer' zoysiagrass (Zoysia japonica Steud). Turf was subjected to deficit irrigation levels of 20%, 40%, 60%, 80%, and 100% of actual evapotranspiration (ET) from June to Sept. 2001 and 2002 in Manhattan, Kans. In an earlier study, minimum deficit irrigation levels required to maintain acceptable quality (MDIL) were determined. We compared growth and physiological parameters at these MDIL with turf irrigated at 100% ET. Tall fescue had a lower canopy vertical growth rate (30% lower), canopy net photosynthesis (P n , 14% lower), and whole-plant respiration (R w , 11% lower) in 1 of 2 years when irrigated at the MDIL compared with 100% ET; tiller number was not reduced at the MDIL. Water use efficiency (μmol CO 2 per mmol H 2 O) in tall fescue increased by 15% at the MDIL relative to turf receiving 100% ET in 1 of 2 years. In zoysiagrass, the MDIL had no effect on any of the growth or physiological parameters measured. Reductions in canopy vertical growth rate at the MDIL in tall fescue during deficit irrigation would likely reduce mowing requirements. Across all deficit irrigation levels, P n was more sensitive to deficit irrigation in both grasses than was R w , which could potentially contribute to declines in canopy vertical growth rate, tiller number, and turf quality. Zoysiagrass exhibited higher water use efficiency than tall fescue, particularly at irrigation levels 60% or more ET.
PRODUKTIVITAS TANAMAN KALIANDRA (Calliandra calothyrsus) SEBAGAI HIJAUAN PAKAN PADA UMUR PEMOTONGAN YANG BERBEDA PRODUCTIVITY OF CALLIANDRA (Calliandra calothyrsus) AS A FORAGE IN THE DIFFERENT DEFOLIATION TIME

This research aimed to determine the production and nutrient content of calliandra (Caliandra calothyrsus) as a forage for ruminant in the different defoliation time. This research was conducted for 48 weeks (June 2012–June 2013) at Kaligesing forage feed area, Animal Science Department, Purworejo, Central Java. Design of the research was Completely Randomized Block Design. Soil slope was used as block. The research treatments were 6 (P1), 8 (P2), 12 (P3) and 16 (P4) weeks of cutting age. The grass of all treatment groups were cut together at the same day prior to experiment. Caliandra calothyrsus was cut at edible portion. Parameters measured were fresh forage, dry matter, organic matter and crude protein production and also nutrient content namely dry matter, organic matter, crude protein, extract ether, crude fiber, BETN and TDN. The result showed that the highest dry matter content was found in P3 (31.25%) and was different from P1 (26.51%) and P4 (28.12%). The highest crude protein content was found in P2 (21.10%) and was not different with P1 (21.09%) and P3 (19.20%), and the lowest crude protein was found inP4 (18.04%). The highest extract ether was at P3 (2.84%) and different from P1 (1.51%). The highest crude fiber was at P4 (22.56%) different with P1 (15.80%) and P2 (18.46%). Organic matter, BETN and TDN were not different among the different defoliation time. The highest fresh forage, dry matter, organic matter and crude protein production were at P4 and different (P<0.05) from P1, P2 and P3. The lowest dry matter was at P2. It is concluded that the best quality of grass was found in P3 group and the highest harvesting quantity was found in P4 group.
Contributions of short-term flow regulation patterns to trout habitats in a boreal river

Physical habitat simulation modelling was used to evaluate the effects of flow regulation on the Siikajoki, a boreal river in Central Finland. In the modelling, the natural flow regime, the implemented regulation pattern and two alternative patterns of regulation were compared by using brown trout (Salmo trutta) as a test fish and by analysing example periods in winter and in summer. The availability of suitable habitats for brown trout (Weighted Usable Area, WUA) was clearly dependent on the flow rate. The fewest usable habitats were available for the size class fry (< 15 cm). We found only minor differences between the compared regulation patterns in terms of riverine habitats. A side channel in the test area proved to be good buffer area against flow changes, highlighting the importance of habitat diversity. In a sensitivity analysis of habitat modelling, modifications of the depth preference curve seemed to have a major influence on the WUA for young brown trout.
CYTOGEOGRAPHICAL STUDIES IN THE GENUS ARNICA

A total of 134 chromosome counts representing 21 taxa of the genus Arnica are presented. Counts are published here for the first time for A. lonchophylla (n = 38) and A. nevadensis (n = 38). Ten previously unreported counts representing 9 taxa are also presented. The basic chromosome number of the genus is x = 19. With respect to chromosome number, the genus exhibits maximum diversity in the Rocky Mountains of Colorado and Wyoming. Arnica angustifolia, A. cordifolia and A. mollis are recognized as mature polyploid complexes, containing several wide ranging polyploid races and only a few highly restricted or scattered diploid races. Within the genus in general, diploids tend to be restricted to unglaciated areas while polyploids are much wider ranging, particularly in unglaciated areas.
CLINICAL PROSPECTS OF SCALE-UP FOETAL WHARTONS JELLY DERIVED MULTIPOTENT STROMAL CELLS TO FULFIL THE THERAPEUTIC DEMANDS

Increasing clinical application of multipotent stromal cells has led to the development of large-scale manufactured of MSCs. In this context, the final cellular product should meet the various regulatory criteria, such as safety, integrity, strength, purity and quality that have been ascribed to cell therapy products. In this study, we have optimized large scale expansion of WJ-MSCs for clinical and therapeutic applications. The biologic properties of UC-MSCs, such as plastic adherence, morphology, specific surface antigens, and multipotent differentiation potential, were retained after clinical-large scale expansion. The cells formed a monolayer of homogenous spindle-like cells. Cell size underwent no obvious change, as evidenced by the consistent harvested cell density after clinical-scale expansion. We successfully up-scaled up to P2 to get as many as 5.22x10 9 cells from a single UC and also observed up to P10 with no significant change in viability, stemness and karyotyping. The growth rate were rate of WJ-MSCs as seen by CFU analysis and PD experiments. A set of typical surface phenotypic characteristics by flow cytometry confirmed that more than 95% of the cells reacted with antibodies against CD73, CD90, and CD105 and less than 1% reacted with CD45, CD34, CD79, and HLA-DR. These cells could be induced to differentiation potential of osteogenic, chondrogenic and adipogenic lineages was proved for their exploitation as a potential therapeutic tool to meet increasing therapeutic demands.
Marchantia longii (Marchantiaceae), a new species from northwestern Yunnan, China

Abstract Marchantia longii R.L. Zhu, Y.L. Xiang et L.Shu sp. nov. (Marchantiaceae) from northwestern Yunnan, China, is described as new to science. It is similar to Marchantia emarginata, but can be distinguished by the large epidermal pore ((108−)150−210 μm in diameter), the acute to obtuse inner margin of surrounding cells of pores in vertical section, the female receptacle dissected (0.2−0.4 of diameter) into 5−7 subquadrate to oblong lobes truncate or rounded apically, and the entire to weakly dentate margin of the appendage of the median scale. A phylogenetic analysis based on DNA sequences of rbcL, trnL–F and nrITS1–5.8S confirms M. longii as a sister to the clade of M. emarginata subsp. tosana + M. inflexa + M. papillata subsp. grossibarba, and this new species is placed in Marchantia subg. Clamidium.
Metabolomics approaches to decipher the antibacterial mechanisms of yerba mate ( Ilex paraguariensis ) against Staphylococcus aureus and Salmonella enterica serovar Typhimurium

The increasing prevalence of drug-resistant pathogens is an urgent problem that requires novel methods of bacterial control. Plant extracts inhibit bacterial pathogens and could contain antibacterial compounds with novel mechanisms of action. Yerba mate, a common South American beverage made from Ilex paraguariensis, has antibiotic activity against a broad range of bacterial pathogens. In this work, an attempt was first made to characterize the antibacterial source of an aqueous yerba mate extract by generating a series of extract fractions, collecting GC-MS and antibacterial activity profiles, and then ranking the hundreds of compounds by their presence in fractions with high antibacterial activity. Quinic acid, quercetin, and 5-hydroxy pipecolic acid were highly ranked, suggesting an association between the antibacterial activity of yerba mate against methicillin-resistant Staphylococcus aureus (MRSA). Next, metabolites that accumulated in the supernatants of Salmonella Typhimurium and Lactobacillus casei cultures were surveyed for decreases in phenolic compounds that might signify metabolism of bioactive yerba mate components. No decreases in phenolic compounds were observed. The hypothesis that phenolic compounds might chelate iron as a mechanism of antibacterial activity was also tested; exogenous iron sulfate stimulated the partial recovery of S. Typhimurium to the inhibitory effect of yerba mate in a milk system. Finally, an assessment of potential antibacterial mechanisms of action was undertaken by surveying the metabolites produced by Salmonella Typhimurium in the presence of yerba mate extract and conducting assays to assess cell membrane integrity and catalase activity. No effect on the cell membrane was observed while catalase activity was reduced in the presence of yerba mate extract. Metabolomics revealed significant differences in central carbon metabolism, the cell wall precursor UDP-Nacetylglucosamine, the regulatory metabolites alpha-ketoglutarate and acetylphosphate, the
A GAP in Form and Function: The Rac-GAP Alpha2-Chimaerin Regulates Dendrite Morphogenesis and Synaptic Plasticity.

Neurons possess a dynamic cellular morphology that can be modulated by synaptic transmission. In particular, dendritic spines are fine neuronal processes where spatially restricted input can induce activity-dependent changes in one spine while leaving neighboring spines unmodified. Rapid changes in spine morphology are coupled to the dynamic cycling of cell-surface receptors, which underlie aspects of synaptic plasticity. Dysregulation of synaptic receptors can result in an increase in spine density and alterations in morphology. These plastic properties of dendritic spines are considered to be compensatory mechanisms that maintain normal synaptic transmission. Importantly, alterations in dendritic spine density, morphology and function are known to be associated with cognitive pathologies and neurodevelopmental delays. From a molecular standpoint, the Rho-GTPase, Rac1 is associated with the recruitment of synaptic receptors and exerts dynamic control over dendritic spines, thus contributing to their architecture and function. However, the key molecules and mechanisms that regulate Rac1-dependent pathways at the synapse are not well understood. We have identified a Rac-GTPase activating protein, α2-chimaerin, that is a
Analysis of heteroplasmy in a cytoplasmic mutant of maize

The NCS6 mutant line of maize carries a deletion in the mitochondrial cytochrome oxidase subunit II (coxII) gene. The plant, characterized by a yellow striping of the leaves and reduced growth, is heteroplasmic. In order to analyze heteroplasmy in tissue cultures derived from NCS6 embryos the author has designed a set of three oligonucleotides that allow the amplification of sequences specific for the mutant and the normal mitochondrial genomes in a single polymerase chain reaction (PCR). Calli and suspension cells obtained from immature embryos show various degrees of heteroplasmy with a large predominance of the mutant genome. By analyzing DNA from single cells it was shown that heteroplasmic NCS6 plants and derived tissue cultures contain homoplasmic and heteroplasmic cells
Two new Indo-Pacific morays of the genus Uropterygius (Anguilliformes: Muraenidae)

Two closely-related new species of Indo-Pacific morays are described herein. Uropterygius xenodontus, from the central and western Pacific, and U. golanii, from the northern Red Sea, differ from each other in their vertebral numbers, and from all other congeners which possess a single branchial pore on the basis of their coloration, vertebral number, and dentition. The possession by the new species of wedge-shaped rather than conical jaw teeth within species of Uropterygius as well as the relationship of vomerine dentition to fish size are discussed.