Miracle-dz/UniFAR-FTUs huggingface dataset:
Defining Culture Conditions for the Hidden Nitrite-Oxidizing Bacterium Nitrolancea

Nitrification is a key process for N-removal in engineered and natural environments, but recent findings of novel nitrifying microorganisms with surprising features revealed that our knowledge of this functional guild is still incomplete. Especially nitrite oxidation – the second step of nitrification – is catalyzed by a phylogenetically diverse bacterial group, and only recently bacteria of the phylum Chloroflexi have been identified as thermophilic nitrite-oxidizing bacteria (NOB). Among these, Nitrolancea hollandica was isolated from a laboratory-scale nitrifying bioreactor operated at 35°C with a high load of ammonium bicarbonate. However, its distribution remains cryptic as very few closely related environmental 16S rRNA gene sequences have been retrieved so far. In this study, we demonstrate how such thermophilic NOB can be enriched using modified mineral media inoculated with samples from a wastewater side-stream reactor operated at 39.5°C. Distinct cultivation conditions resulted in quick and reproducible high enrichment of two different strains of Nitrolancea, closely related to Nl. hollandica. The same cultivation approach was applied to a complex nitrite-oxidizing pre-enrichment at 42°C inoculated with biomass from a geothermal spring in the Copahue volcano area in Neuquen, Argentina. Here, an additional distinct representative of the genus Nitrolancea was obtained. This novel species had 16S rRNA and nitrite oxidoreductase alpha subunit (nxrA) gene sequence identities to Nl. hollandica of 98.5% and 97.2%, respectively. A genomic average nucleotide identity between the Argentinian strain and Nl. hollandica of 91.9% indicates that it indeed represents a distinct species. All Nitrolancea cultures formed lancet-shaped cells identical to Nl. hollandica and revealed similar physiological features, including the capability to grow at high nitrite concentrations. Growth was optimal at temperatures of 35–37°C and was strongly enhanced by ammonium supplementation. Genomic comparisons revealed that the four Nitrolancea strains share 2399 out of 3387 orthologous gene clusters and encode similar key functions. Our results define general growth conditions that enable the selective enrichment of Nitrolancea from artificial and natural environments. In most natural habitats these NOB apparently are of low abundance and their proliferation depends on the balanced presence of nitrite and ammonium, with an optimal incubation temperature of 37°C.
Estimation models of variance components for farrowing interval in swine

Este trabalho teve como objetivo principal avaliar a importância da inclusao dos efeitos genetico materno, comum de leitegada e de ambiente permanente no modelo de estimacao de componentes de variância para a caracteristica intervalo de parto em femeas suinas. Foram utilizados dados que consistiam de 1.013 observacoes de femeas Dalland (C-40), registradas em dois rebanhos. As estimativas dos componentes de variância foram realizadas pelo metodo da maxima verossimilhanca restrita livre de derivadas. Foram testados oito modelos, que continham os efeitos fixos (grupos de contemporâneo e covariaveis) e os efeitos genetico aditivo direto e residual, mas variavam quanto a inclusao dos efeitos aleatorios genetico materno, ambiental comum de leitegada e ambiental permanente. O teste da razao de verossimilhanca (LR) indicou a nao necessidade da inclusao desses efeitos no modelo. No entanto observou-se que o efeito ambiental permanente causou mudanca nas estimativas de herdabilidade, que variaram de 0,00 a 0,03. Conclui-se que os valores de herdabilidade obtidos indicam que esta caracteristica nao apresentaria ganho genetico como resposta a selecao. O efeito ambiental comum de leitegada e o genetico materno nao apresentaram influencia sobre esta caracteristica. Ja o ambiental permanente, mesmo sem ter sido significativo o seu efeito pelo LR, deve ser considerado nos modelos geneticos para essa caracteristica, pois sua presenca causou mudanca nas estimativas da variância genetica aditiva.
Wound healing effect of hydroethanolic extract of Ribwort plantain leaves in rabbits.

Article history Received: 13 Feb, 2015 Revised: 15 Mar, 2015 Accepted: 23 Mar, 2015 Abstract Ribwort plantain is popularly used in the folk medicine as wound healing, antiinflammatory and for the treatment of diseases of the respiratory tract and muscular pains. In the present study, a hydroethanolic leaf extract of Ribwort plantain was evaluated for non-infected wound healing. Forty White New Zealand rabbits were divided into four groups. Full-thickness skin wounds were created on thoracolumabar region on each side of the dorsal midline in each rabbit. Groups A and B received a placebo containing 2 and 4% of hydroethanolic leaf extract of Ribwort plantain respectively, group C served as placebo (positive control) and finally group D was kept as control (negative control) receiving no application. The rate of wound size was measured at day 4, 8, 12 and 16 while histological structures were studied on days 3, 7, 14 and 20 after surgery. The wound contraction results show that Ribwort plantain hydroethanolic extract reduced wound size especially from day 6 onward. Further, Ribwort plantain hydroethanolic extract decreased poly morph nuclear cells, and increased mononuclear cells, fibroblast cell migration and new vascular formation. Thus, this study demonstrated that hydroethanolic extract of Ribwort plantain at dose rate of 2% is effective in stimulating the closure of non-infected wounds.
Isolation and identification of Streptomyces pseudogriseolus as a nominate for producing alkaline protease

Proteases are one of the most important industrial enzymes. Alkaline proteases are used in detergent industry, leathery industry, food industry and for recovery of silver from photograph films. Actinomycetes are filamentous gram positive and chemoheterotrophic bacteria that produce different materials such as antibiotics, pigments and enzymes. The aims of this study were isolation and identification of alkaline protease-producing Actinomycete spp. and determination of their enzyme activity. The soil samples were collected from Isfahan province, Iran. The samples were cultured on Yeast Extract Soluble Starch medium. The screening of alkaline protease-producing Actinomycete spp. was carried out using alkaline milk agar medium. For alkaline protease assay the lawry method was used. In this study 10 species of alkaline protease-producing Actinomycetes were isolated. The most alkaline protease activity, 180 (u/ml), after 72 hours incubation at 30°C was measured by Streptomyces psuodogriseolus. This strain could be applied for production of alkaline protease from agricultural and biotechnological cheep culture media.
The Hydraulic Architecture of Petioles and Leaves in Tropical Fern Species under Different Levels of Canopy Openness

Premise of research. Structure-function relationships of xylem in tropical fern species remain poorly explored despite the taxonomic diversity and ecological importance of ferns in tropical environments. The aim of this study is to broaden our understanding of how tropical fern morphology and anatomy are influenced by light availability. Methodology. Nine fern species, including six shade-tolerant species, two sun-exposed species, and one species with representatives in both light conditions, were studied in order to investigate the impact of light exposure on leaf morphology and xylem anatomy. Measured parameters included water potential and micromorphology based on light and electron microscopy. Pivotal results. Canopy openness was significantly correlated with specific leaf area, basic specific gravity, venation density, pit membrane area, pit aperture area, and pit membrane thickness. Intraspecific variation within Pteris quadriaurita showed that leaf morphological features such as petiole length and diameter were unaffected by light exposure, while most anatomical features of the xylem (except for conduit diameter) increased with higher light availability. Pit membrane thickness was correlated with predawn water potential, suggesting that thicker pit membranes provide higher hydraulic safety. The theoretical conduit implosion resistance was found to be surprisingly low compared to xylem of seed plants. Conclusions. Our results illustrate that the hydraulic architecture of ferns shows interesting structure-function relationships that reflect ecological adaptations for optimal growth in relation to light availability. Higher-light regimes increased the need for investment in hydraulic safety characteristics such as pit membrane thickness and diameter, while petiole length was not affected.
ANTIBACTERIAL ACTIVITY OF MARINE STREPTOMYCES SP. ISOLATED FROM ANDAMAN & NICOBAR ISLANDS, INDIA

Andaman and Nicobar Islands, considered as one of the important marine ecosystem in India and being considered as the richest source for microbial community. The marine microbial taxa and actinomycetes diversity are not been fully explored. Actinomycetes were isolated from marine soil samples and screened for antibacterial activity. Out of eight isolates, the isolate AN1 isolated from soil sample collected from Elephanta beach showed significant antibacterial activity against ATCC strains Staphylococcus aureus (19 mm), Bacillus cereus (17 mm) and Salmonella paratyphi A (16.5 mm). The ethyl acetate (EA) extract of the isolate showed increased activity against Staphylococcus aureus (22.1 mm), Bacillus cereus (19.5 mm) and Salmonella paratyphi A (19.6 mm). The standard antibiotic streptomycin disc (25µg) was used as positive control. The isolate AN1 were subjected to biochemical characterization and identified as Streptomyces species. The result of this study suggests that the Streptomyces species could be a promising source for potent antibacterial agents.
First flush pollution load of urban stormwater runoff

In a storm event, a first flush (FF) phenomenon occurs when most of the pollution load is transported in the initial part of the event discharged volume. The objectives of the study were to consider its severity for a number of pollutants as well as to recognize rainfall–runoff characteristics that influence it. The study was conducted in a semi-arid region of a mixed residential and commercial urban catchment in Iran. Ten major rainfall events were monitored for total solids (TS), total suspended solids (TSS), chemical oxygen demand (COD), total nitrogen (TN), Zn, and Pb. Total suspended solids and COD were usually above the permitted discharge. Power and polynomial functions fit well to the normalized curve of the distribution of pollutant load with volume. Discharge loads of TN, Pb, and Zn were approximately uniform. There was a relatively weak FF for TS, TSS, and COD. No correlation between FF load of TS and COD and rainfall–runoff characteristics was observed, but the amount of the FF load of TSS inc.
Bowel Movement: The Sixth Vital Sign?

Barsak hareketleri tum yas gruplarinda ozellikle de yasli bireylerde vucut fonksiyonlari ve konstipasyonun degerlendirilmesi icin oldukca onemlidir. Hemsirelik surecinde, Gunluk Yasam Aktiviteleri Modeli’ne gore 5. Sirada, Fonksiyonel Saglik Oruntuleri icerisinde 3. Sirada yer alan bosaltim aktivitesi, fizyolojik oldugu kadar fiziksel, sosyal ve psikolojik boyutlari olan bir kavramdir. Hasta/saglikli bireyin barsak hareketlerinin hemsire tarafindan tanilanmasi, sikayetlerin degerlendirilmesi, destek ve egitim gereksinimlerinin belirlenerek hemsirelik bakim planinin olusturulmasi gerekmektedir. Bu derlemede, hemsirelere barsak bosaltim aktivitesinin degerlendirilmesi ve hemsirelik bakiminin planlanmasi icin guncel literatur dogrultusunda bilimsel verilerin sunulmasi amaclanmistir.
Ethylene biosynthesis in oilseed rape pods in relation to pod shatter

ethylene to trigger the process when IAA levels are low. Ethylene production was studied during the develop- ment and senescence of seeds and pericarp tissues Key words: Oilseed rape, pod shatter, ethylene metabolism, of oilseed rape (Brassica napus L.) pods (siliquae). In aminoethoxyvinylglycine (AVG), parthenocarpy. the course of the rise to a pre-senescence climacteric, little change in 1-aminocyclopropane-1-carboxylic acid Introduction (ACC) was recorded in the seeds, indicating a rapid conversion to ethylene. In contrast, very small Seed loss from fully mature pods (pod shatter) is a amounts of ethylene were produced by the pod wall problem with monocultures of dicotyledonous crop (PW) tissues, which included the dehiscence zone (DZ), species with an extended flowering period and many- while levels of free and conjugated ACC in the PW seeded, dry fruits, such as Brassica spp. , soybean (Glycine increased consistently. As climacteric ethylene pro- max L.), and sesame (Sesame indicum L.). Pod shattering duction by the seeds declined, biosynthesis of ethy- is a particular problem in oilseed rape (Brassica napus L.) lene by the PW increased. Effects of reducing ethylene because of a marked tendency of fully mature pods to production by various means were examined in relation open. Average annual losses of about 20%, represent a to cell separation in the dehiscence zone. Amino- production eYciency that is far less than in any other ethoxyvinylglycine (AVG) applied during the pre- major arable crop. There is little variation in the suscepti- senescence climacteric reduced ACC levels and bility of current cultivars to pod shatter (Downey and ethylene production by the seeds, but did not affect Robbelen, 1989), and conventional breeding has so far subsequent values in the PW. The production of been unable to produce new cultivars which are more b-1,4-glucanase and the separation of the cells of the resistant to opening. DZ were delayed for 3-4 d by AVG, but the force The oilseed rape pod (silique or siliqua) consists of two required to open fully mature pods was unaltered. In carpels whose walls are separated by a replum containing parthenocarpic (seedless) pods, ethylene was pro- the main vascular tissue of the pod. A layer of 2-3 duced during senescence. Cell separation in the DZ parenchymatous cells between the carpel edges and the took place as in seeded pods, although it was also replum forms the separation or dehiscence zone (DZ ). delayed by 3-4 d. The results are related to changes Separation of the cells in the DZ takes place about 7 in indole-3-acetic acid (IAA) levels in oilseed rape pods weeks after anthesis, just before moisture loss is complete. which decline in PW and DZ tissues during senes- The pods open as a result of external force supplied by cence. It is concluded that separation in the cells of contact with other pods, racemes or harvesting machinery, which severs the vascular connections. the dehiscence zone requires only small amounts of
Cryptic Biodiversity in Streams: A Comparison of Macroinvertebrate Communities Based on Morphological and DNA Barcode Identifications

Abstract: Species-level identifications are difficult or impossible for many larval aquatic macroinvertebrates. We described the taxonomic composition of macroinvertebrate communities from 5 coastal streams in 3 neighboring catchments in southern California. We compared taxonomic identifications based on deoxyribonucleic acid (DNA) barcoding (cytochrome c oxidase subunit I [COI]) with morphological identifications of the same specimens. We examined 5870 individuals, and barcodes with sequence lengths >350 base pairs (bp) for 91% of those specimens. We used the naturally occurring gaps in divergence frequencies for each order (usually 2% level of genetic divergence) to delimit putative species for all taxonomic groups except Simulium (3%) and Baetis (1%). We identified 200 species across these 5 streams. We identified 104 more species via barcodes than via morphology (200 vs 96, a 108% increase). Richness increases were greatest for Chironomidae (60 more species), Ephemeroptera (10 species), Acari (10 species), and Trichoptera (6 species). Forty-five percent of the genera/species identified morphologically represented >2 species. Many (86) species identified with barcodes were represented by only 1 or 2 specimens and were found at only 1 stream. Thus, species rarity (either spatially or numerically) appears to be a common characteristic of these streams. Barcoding increased total richness at each site by 12 to 40 taxa over morphology alone, and increased the difference between reference and impact sites in terms of lost taxa. These results suggest that macroinvertebrate biodiversity in streams has been underestimated substantially in the past, as has the biodiversity lost in response to environmental stress. The potential of DNA barcoding will not be fully realized until we can assign traits, such as habitat preference, ecological function, and pollution tolerance, at the species level.
INTERACTIONS OF THE GROWTH HORMONE SECRETORY AXIS AND THE CENTRAL MELANOCORTIN SYSTEM

of Dissertation Presented to the Graduate School of the University of Florida in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy INTERACTIONS OF THE GROWTH HORMONE SECRETORY AXIS AND THE CENTRAL MELANOCORTIN SYSTEM By Amanda Marie Shaw December 2004 Chair: William J. Millard Major Department: Pharmacodynamics Ghrelin acts on the growth hormone secretagogue receptor (GHS-R) in the hypothalamus and pituitary to potently stimulate growth hormone (GH) secretion. Ghrelin also stimulates food intake and affects energy balance in part by activating neuropeptide Y (NPY) neurons containing the melanocortin receptor antagonist agouti related peptide (AGRP) in the arcuate nucleus. We therefore sought to further investigate the role of AGRP/melanocortin signaling in mediating the orexigenic effects of ghrelin by studying mice deficient in the melanocortin 3 (MC3R) and 4 (MC4R) receptors. We also sought to determine whether reduced ghrelin levels and/or an altered sensitivity to the GH-stimulating effects of ghrelin accompany the obesity syndromes of MC3R knockout (MC3R KO) and MC4R knockout (MC4R KO) mice. We measured various components of the GH axis in several age groups of male and female MC3R KO, MC4R KO and WT mice. Overall, MC4R KO mice displayed normal to elevated levels of the GH effector protein, insulin-like growth factor-I (IGF-I), in spite of reduced serum GH
5 Ribosomes and the RNA World

The hypothesis that all modern organisms are descendants of an ancient, self-replicating entity that depended on RNA both for its genetic material and for catalysis has gained a large following over the past decade, as the existence of this volume attests. This idea, also known as the RNA world hypothesis, has been around in various forms for almost 30 years, and it has been known for most of that time that RNA can serve a DNA-like function. The reason there is so much interest in the RNA world hypothesis today is that we now know something our predecessors did not, namely, that RNAs are capable of catalyzing biochemical reactions. Boiled down to its essence, the RNA world hypothesis is a proposal for the origin of life that explains why RNA is so important for gene expression in modern organisms but has no role in any other aspect of metabolism. Ribosomes are important for two reasons in this context. First, because ribosomal RNA accounts for about 80% of the RNA in most modern cells, the RNA world hypothesis either makes sense of them or fails entirely. Second, again because the ribosome contains so much RNA, information about its structure and function has to be an important part of the input used for formulating all such theories. This paper is intended to provide the reader with a broadbrush picture of the ribosome field that emphasizes the findings that bear most directly on evolutionary issues. Readers wishing to find out more about the.
Book reviews

Fastest, Highest, Strongest: A Critique of High-performance Sport represents the latest addition in the growing ‘Critical Studies in Sport’ series published by Routledge. It tackles one of the most prominent, public and polarizing sporting issues; the debate surrounding performance-enhancing drug use in modern sport. In so doing, the book connects perfectly with the broader theme of the series, which is concerned with tackling ‘some of the big questions facing sport and society, to question assumptions about sport, to critique established ideas and to explore new ones’ (Hargreaves and McDonald’s foreword, p. vii). Beamish and Ritchie challenge the dominant orthodoxy concerning the use of performanceenhancing substances and dispel many of the ideological myths which permeate this topic. They reject the common-held assumptions surrounding performanceenhancing substance use in modern sport (for example, the individualized approach to policy and punishment and the notion that drug use is a wholly modern ‘problem’). Moreover, they explicitly reject the argument that the use of performance-enhancing substances contravenes the ‘spirit of sport’. In so doing, they position the use of these substances in the very fabric of high-performance sport, its values and ideals (a point I will return to later). Utilizing the Olympic Games as a case study for their analysis, Beamish and Ritchie offer a distinctly sociological approach to the study of performance-enhancing drugs. Recalling C. Wright Mills’s (1959) ‘intellectual journey’ the text sensitizes the analysis of this topic to the broader political and social processes in which we are enmeshed. Beamish and Ritchie feverently advocate the need to locate any consideration of performance-enhancing practices in their socio-historical context in order to more adequately understand the issues at hand. The authors’ critique is structured around four central themes: i) the shift in the dynamics of Olympic sport from Coubertin’s founding principles towards high performance sport; ii) the political backdrop to the emerging ‘problem’ of performance enhancing substances; iii) the emerging ‘sport science’ movement INTERNATIONAL REVIEW FOR THE SOCIOLOGY OF SPORT 43/3(2008) 331–337 331
Mixed Inbred FVB;B6 Background Strain Attenuates Kidney Disease and Improves Survival of Gnem712t/M712T Mice

Recessive form of Hereditary Inclusion Body Myopathy (HIBM, IBM2, MIM:600737) is an adult onset muscle wasting disorders caused by hypomorphic GNE, the rate-limiting enzyme of sialic acid (Sia) biosynthesis. Unlike human patients, mice bearing the GneM712T/M712T genotype in C57BL/6 background strain suffer severe glomerular hematuria, incomplete podocyte development, and do not survive beyond the first few days of life. We crossed heterozygous mice (GneM712T/+) of B6 strain with FVB strain mice. In mixed inbred FVB;B6 background, the homozygous mice show attenuated glomerular disease and survive longer (mean survival 22±13 weeks, n=26). Paradoxically, the homozygous mice showed increased total Sia levels in serum (2x control), and Neu5Ac:Neu5Gc ratios are slightly shifted towards Neu5Ac in serum and towards Neu5Gc in muscle tissue. Increase in serum Sia levels may be caused by altered glomerular filtration. This paradoxical increase in serum Sia may contribute to Sia pools of muscle, and exert a potential beneficial effect. In summary, the background strain of mouse model can significantly affect the disease phenotype. *Corresponding author: Daniel Darvish, MD HIBM Research Group, 18341 Sherman Way #201A, Reseda, CA 91335, Tel: 818-789-1033 x 3; Fax: 818-741-3727; E-mail: ddarvish@hibm.org Received March 03, 2012; Accepted March 26, 2012; Published April 01, 2012 Citation: Valles-Ayoub Y, Haghighatgoo A, Saechao C, Khokher Z, Creencia C, et al. (2012) Mixed Inbred FVB;B6 Background Strain Attenuates Kidney Disease and Improves Survival of GneM712T/M712T Mice. Mol Biol 1:104. doi:10.4172/21689547.1000104 Copyright: © 2012 Valles-Ayoub Y, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.