Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation and characterization of methanogenic bacteria from brewery wastewater in Kenya

The production of biogas from renewable resources is becoming a prominent feature of most developed and developing countries of the world. A study was undertaken to characterize methanogenic microbial community found in brewery waste water. Their performance with regards to methane production was also studied. Thirty-two isolates were obtained using brewer thyglycollate agar medium. Characterization of the isolates was done by culture and biochemical methods. 65% of the isolates were found to be positive with Gram staining reaction, while 35% were negative. The isolates were identified by method of polymerase chain reaction (PCR). From the phylogenetic analysis, thirteen isolates were clustered into genus Bacillus sp. , isolate 93b was closely related to Bacillus subtilis strain, while isolates 20a1, 171 and 7 closely related to Bacillus methylotrophicus isolate 10 was grouped together with Bacillus tequilensis, isolate 31 was clustered together with Bacillus licheniformis, while isolates 132, 252, 15, 262 and 182 were closely related to Lysinibacillus sp. and isolate 191 was clustered together with Lactobacillus casei. The study also shows that three isolates 32, 181 and 4 were closely related to Ralstonia pickettii, Providencia rettgeri and Myroides odoratimimus, respectively. The presence of isolates 201a, 171 and 7 with abilities to ferment different sugars, hydrolysis starch, liquefy gelatin, split amino acid tryptophan, produce catalase enzyme and hydrogen sulphide gas suggests their involvement in biogas production. The percentage methane content in the total gas produced at pH 8 varied significantly (p<0.001) for all the temperature ranges. The highest concentration of methane for most isolates was recorded at temperatures of 35 and 37°C for all the pH ranges. Key words: Biogas, characterization, methanogenic bacteria, pH, temperature, wastewater.
Sequential Herbicide Applications in Stale Seedbed Soybean (Glycine max)

Field experiments were established in 1991 and 1992 on silty clay and sandy loam soils to evaluate various split rates of early PPI and PRE (to soybean) selective herbicides with and without paraquat for sicklepod and pitted morningglory control in stale seedbed soybean. Metribuzin at 360 g ai/ha plus 60 g ai/ha chlorimuron tank-mixed with 700 g ai/ha paraquat controlled sicklepod and pitted morningglory 83 and 91%, respectively, 4 wk after planting. Without paraquat, sicklepod and pitted morningglory control was only 65% and 67%, respectively. Imazaquin at 140 g/ha PRE tank-mixed with paraquat controlled sicklepod 78% and pitted morningglory 92%. Without paraquat, control was 38% and 84%, respectively. Early PPI applications of metribuzin plus chlorimuron or imazaquin at the full rate alone or followed by paraquat at planting resulted in poor control. With sequential treatments (PPI followed by PRE) the addition of paraquat at planting did not usually improve control, and either imazaquin or metribuzin plus chlorimuron provided equivalent control when compared with the full rate of either herbicide applied PRE. Season-long weed control was not obtained with any treatment in any experiment, and the crop was not harvestable.
Thinning and Bagging Treatments and the Growing Region Influence Anthocyanin Accumulation in Red-fleshed Apple Fruit

In common apple cultivars with white flesh and red skin, it is known that fruit overload lowers fruit quality, and that skin anthocyanin concentrations are reduced by bagging treatment and warmer climatic conditions. In this study, the effects of these factors on anthocyanin accumulation in the flesh of red-fleshed apples were investigated using ‘Geneva’ and ‘Pink Pearl’ apple cultivars. Excess fruiting resulted in decreased anthocyanin concentration in the flesh and the titration acidity of the fruit in both cultivars. Fruit bagging treatments using double-layer paper bags revealed that anthocyanin was synthesized to a certain extent in the flesh under dark conditions in both cultivars. The treatment significantly reduced anthocyanin accumulation in the flesh of bagged ‘Geneva’ apples compared with unbagged fruit, but no inhibitory effect was clear in ‘Pink Pearl’ apples. In both cultivars, the anthocyanin concentration in the flesh of unbagged apples grown in sunlight was higher than that in unbagged apples grown in shade, whereas there was no difference between positions for bagged fruit. In apples grown in either sunlight or shade, no significant difference was found between anthocyanin concentrations in the sun-exposed side and shaded side of fruits. These results indicate that sunlight irradiation partially promoted anthocyanin accumulation in the flesh of unbagged ‘Geneva’ and ‘Pink Pearl’ apples and accelerated its accumulation on both the sun-exposed and the shaded side. A comparison of the fruit quality of ‘Pink Pearl’ apples grown in different climatic regions showed that apples harvested at Suzaka, a warmer region, were lower in firmness, starch index, and titration acidity and higher in soluble solids concentration compared with those from Morioka, a cooler region. The anthocyanin concentration in the flesh of ‘Pink Pearl’ apples from the trees grown at Morioka was more than ten-fold higher than that in apples from the trees grown at Suzaka. Our results suggest that an appropriate fruit load, growth in sunlight, and growth under cooler climatic conditions, may redden the flesh of red-fleshed apples, as is the case for common apples.
Drift macroalgae in the Patos Lagoon Estuary (southern Brazil): effects of climate, hydrology and wind action on the onset and magnitude of blooms

ABSTRACT Ephemeral macroalgal blooms have been increasing in frequency and abundance worldwide. We investigated the variability of drift macroalgae abundance in a shallow bay of the Patos Lagoon Estuary (PLE) in southern Brazil to determine the influence of climate and hydrology on the onset and magnitude of blooms. During the study period (January 2004 to May 2007), three growth cycles were observed and differed in timing, magnitude and persistence. Macroalgal biomass (mostly Ulva species) varied annually and interannually (3 g DW m−2 to 432.7 g DW m−2), peaking during the spring and summer. On an annual scale, macroalgal blooms occurred after reductions in freshwater discharge and associated decreases in water level and increases in salinity and retention. These hydrological parameters were influenced by precipitation which, in turn, is affected by the El Niño Southern Oscillation. On an interannual scale, the largest bloom was observed during a weak-moderate El Niño year. No direct relationship was found between biomass peaks and water nutrient concentrations, but tissue nitrogen content indicated no nitrogen limitation. However, a trend of increasing phosphorus concentration (resulting in decreased DIN:DIP ratios) may be associated with the largest bloom observed. Under favourable hydrological conditions for growth, wind action affected the algal transport in shallow areas, thereby controlling the magnitude and persistence of the blooms. The macroalgal abundance found in the PLE was comparable to that found in temperate eutrophic lagoons, highlighting an algal-dominated period triggered by the combined effects of climate and hydrological factors in a post-El Niño period.
Acanthaceae of Bolivia

Wasshausen, Dieter C. , and J. R. I. Wood. Acanthaceae of Bolivia. Contributions from the United States National Herbarium, volume 49: 152 pages (including 42 figures). —Recent fieldwork in Bolivia has resulted in the recognition of 180 species in 36 genera of Acanthaceae. The purpose of this taxonomic treatment is to discuss, in alphabetical order, all the known Bolivian species of the family, and as such, this work is a ready reference for botanists, so that they may identify their collections of acanthaceous plants or use the keys for detecting further undescribed species. Except for brief discussions to indicate possible relationships of the novelties to allied species, no phylogenetic inferences within the family have been made. A full list of synonyms for the Bolivian species and those of adjoining countries has been prepared. Keys, species descriptions, and specimen distribution data is provided. When available, illustrations, ecological and conservation data have been included. Two new species of Dicliptera, D. palmariensis and D. purpurascens are described and illustrated, and Lepidagathis alverezia is a new combination. The following 26 names are lectotypified: Ancylogyne peruviana, Aphelandra albadenia, Aphelandra simplex, Arrhostoxylum haenkeanum, Beloperone denudata, Beloperone matthewsii, Beleperone nodicaulis, Chaetochlamys ciliata, Chaetochlamys macrosiphon, Chaetothylax boliviensis, Chaetothylax tocantinus, Dicliptera pohliana, Dicliptera seriacea, Dicliptera squarrosa, Geissomeria tetragona, Justicia diamantina, Justicia dubiosa, Justicia yurimaguensis, Leptostachya parviflora, Mendoncia meyeniana, Orthotactus strobilacea, Pachystachys lutea, Porphyrocoma lanceolata, Ruellia glischrocalyx, Ruellia haenkeana, and Stephanophysum ruizianum.
Combining Ability among Inbred Onions for Resistance to Fusarium Basal Rot

Seven inbred onion (Allium cepa L.) lines representing a range of responses for resistance to Fusarium oxysporum Schlect. emend. Snyd. and Hans. f. sp. cepae, the causal agent of fusarium basal rot, were mated in a complete diallel. The resultant inbred, F1, and reciprocal F1 progenies were evaluated for resistance in a greenhouse seedling test. Mean squares for general combining ability, specific combining ability, and reciprocal effects for resistance to fusarium basal rot were significant (P = 0.000). The parent with the highest general combining ability for resistance was W404, particularly when used as a seed parent. Reciprocal differences were significant in several hybrid combinations. The greenhouse screening procedure is described.
Interaction of infectious bursal disease virus with the immune system of poultry

Shanghai Veterinary Research Institute (SHVRI), Chinese Academy of Agricultural Sciences (CAAS), 200241, China; Department of Poultry Science, Faculty of Veterinary and Animal Sciences, PMAS Arid Agriculture University, Rawalpindi, Pakistan; Department of Pathobiology, Faculty of Veterinary and Animal Sciences, PMAS Arid Agriculture University, Rawalpindi, Pakistan; National Veterinary School, Toulouse, France; Avian Innate Immunity and Host Genetic Diversity, Avian Viral Diseases Programme, The Pirbright Institute, Surrey, GU24 0NF, United Kingdom *Corresponding author: shoveldeen@shvri.ac. cn
Antilisterial Effects of a Sorbate-Nisin Combination In Vitro and on Packaged Beef at Refrigeration Temperature.

The antilisterial effects of a sorbate-nisin combination were assessed in vitro and on beef at refrigeration temperature. Three hemolytic pathogenic strains of Listeria monocytogenes , reference strain NCTC 7973, food strain L70, and clinical strain L94, were stored at 4°C in phosphate-buffered saline, pH 5.5, containing a combination of sorbate (0.2% wt/vol) and nisin (40 IU/ml). After 4 weeks, hemolysin production by the strains had ceased, their subsequent lag phases at 37°C were extended from an initial 1.23 to 1.32 h to a final 7.13 to 8.06 h and their pathogenicity for chick embryos had decreased from an initial 93.3 to 95.5% to a final 43.3 to 60.0%. Sterile beef steaks of normal pH (5.4 to 5.5) were inoculated with a cocktail of the three strains at approximately 5 log CFU/cm2 and the surface of half the steaks was treated with the antimicrobial solution 1.0% sorbate plus 1,000 IU of nisin per ml. The meat was packaged under vacuum or 100% carbon dioxide and stored at 4°C for 4 weeks. On untreated meat, L. monocytogenes grew by 1.79 log cycles in vacuum packages, but in CO2 packages the initial population decreased by 0.54 log cycle. On treated vacuum-packaged meat, L. monocytogenes decreased during storage to the extent that 96.5% of the initial pathogen load was eliminated, but the lag phase of the remaining cells at 37°C was unaffected. On treated CO2-packaged meat L. monocytogenes decreased during storage to the extent that 89.3% of the initial pathogen load was eliminated, and for surviving cells the lag phase at 37°C was extended. Treatment with the sorbate-nisin combination did not significantly affect pathogenicity of the L. monocytogenes cocktail recovered from vacuum- or carbon dioxide-packages after storage, in contrast to the in vitro study, where pathogenicity was clearly attenuated. The reason for this difference is unknown.
TriPer, an optical probe tuned to the endoplasmic reticulum tracks H2O2 consumption by glutathione

The fate of H2O2 in the endoplasmic reticulum (ER) has been inferred indirectly from the activity of ER localized thiol oxidases and peroxiredoxins, in vitro, and the consequences of their genetic manipulation, in vivo. Here we report on the development of TriPer, a vital optical probe sensitive to changes in the concentration of H2O2 in the thiol-oxidizing environment of the ER. Consistent with the hypothesized contribution of oxidative protein folding to H2O2 production, ER-localized TriPer detected an increase in the luminal H2O2 signal upon induction of pro-insulin (a disulfide bonded protein of pancreatic β-cells), which was attenuated by the ectopic expression of catalase in the ER lumen. Interfering with glutathione production in the cytosol by buthionine sulfoximine (BSO) or enhancing its localized destruction by expression of the glutathione-degrading enzyme ChaC1 in lumen of the ER, enhanced further the luminal H2O2 signal and eroded β-cell viability. Tracking ER H2O2 in live cells points to an unanticipated role for glutathione in H2O2 turnover. Significance statement The presence of millimolar glutathione in the lumen of the endoplasmic reticulum has been difficult to understand purely in terms of modulation of protein-based disulphide bond formation in secreted proteins. Over the years hints have suggested that glutathione might have a role in reducing the heavy burden of hydrogen peroxide (H2O2) produced by the luminal enzymatic machinery for disulphide bond formation. However, limitations in existing in vivo H2O2 probes have rendered them all but useless in the thiol-oxidizing ER, precluding experimental follow-up of glutathione’s role ER H2O2 metabolism. Here we report on the development and mechanistic characterization of an optical probe, TriPer that circumvents the limitations of previous sensors by retaining specific responsiveness to H2O2 in thiol-oxidizing environments. Application of this tool to the ER of an insulin-producing pancreatic b-cells model system revealed that ER glutathione antagonizes locally-produced H2O2 resulting from the oxidative folding of pro-insulin. This study presents an interdisciplinary effort intersecting cell biology and chemistry: An original redox chemistry concept leading to development of a biological tool, broadly applicable for in vivo studies of H2O2 metabolism in the ER. More broadly, the concept developed here sets a precedent for applying a tri-cysteine relay system to discrimination between various oxidative reactants, in complex redox milieux.
In vitro regeneration of chickpea (Cicer arietinum L.) via somatic embryogenesis

Somatic embryogenesis was induced from calli derived from embryonic axis explants of chickpea (Cicer arietinum L.). Five different concentrations of the auxin, 2,4- dichlorophenoxyaceticacid (2,4-D) was tested for induction of embryogenetic potential from explants. Explants cultured in modified MS (Murashige and Skoog) medium containing 3.0 mgl-1 2,4-D responded best in terms of callus induction (82%), conversion of calli to embryogenetic pathway and finally plantlet development. Developed plantlets exhibited healthy shoots and roots that could be successfully hardened in soil and established as mature fertile plants. The reported protocol can be effectively utilized for genetic improvement of chickpea.
Ecological effects and underlying molecular mechanisms of grazer-induced defenses in Fucus vesiculosus (Phaeophyceae)

This study aimed to reveal the dynamics of inducible anti-herbivory traits in the brown seaweed Fucus vesiculosus in response to grazing by the isopod Idotea baltica. As the molecular basis of defense induction in seaweeds is poorly understood, a transcriptomic approach was used in addition to gain insight into cellular processes underlying defense induction and, thus, promote the mechanistic understanding of anti-herbivory responses in seaweeds. In a 27 day feeding-assayed induction experiment, temporal patterns of the induced anti-herbivory resistance of F. vesiculosus were assessed under laboratory conditions. Feeding assays were performed in three day intervals, using fresh and reconstituted food. Moreover, microarray hybridizations investigated the expression of genes 3 days before as well as at the same time when feeding assays revealed a decreased palatability of previously grazed F. vesiculosus pieces compared to non-grazed control pieces. Despite permanent exposure to grazers, F. vesiculosus palatability varied over time. Non-grazed F. vesiculosus pieces were significantly preferred to grazed pieces after 18 and again after 27 days of previous grazing, while their relative palatability for isopods was comparable at all other times during the experiment. Relative to controls, 562/402 genes were ≥ 1.5-fold up-/down-regulated in seaweed pieces that were grazed for 18 days, i.e. when induction of defenses was detected in feeding assays. Massive reprogramming of the regulative expression orchestra (translation, transcription) as well as up-regulation of genes involved in lipid and carbohydrate metabolism, intracellular
Reciprocal contamination by invasive plants: analysis of trade exchange between Slovakia and Romania

Abstract In this work, potential contamination by invasive plant propagules as a result of trade exchange between Slovakia and Romania, was assessed. National lists, describing biology and ecology of 30 worst invasive plant taxa, were formulated, and trading in period 2006-2010 between countries analysed. Using norms for commodity impurity level, information on species habitat occupancy and literature data dealing with seed/fruit attachment on roads we calculated then potential invasive plant propagule export (PE) for each taxon. We found three fold higher total good export from Slovakia than in opposite direction, increasing export of commodities potentially containing invasive plant propagules exported from Romania to Slovakia and rise of road compared to railway transport. PEs for Slovak invasive plant taxa were one-two orders higher than those for Romanian ones. Potentially most exported taxa for Slovakia were: Amaranthus sp. , Ambrosia artemisiifolia, Galinsoga sp. , Kochia scoparia and Sorghum halepense (tens to hundreds tonnes each). And these could mostly be exported from Romania: Amaranthus sp. , Ambrosia artemisiifolia, Artemisia annua, Conyza canadensis, Cuscuta campestris, Datura stramonium, Erigeron annus, Galinsoga sp. , Iva xanthiifolia, Kochia scoparia, Lycium barbarum, Sorghum halepense, Veronica persica and Xanthium orientale subsp. italicum (units to tens tonnes each). High PE was significantly associated with cereals export. Our formula for PE is applicable for any inter- and intra-continental trade exchange.
Starvation and desiccation tolerances in Drosophila: Comparison of species from different climatic origins

Abstract:During their evolutionary history, drosophilids have been able to adapt to very diverse climatic conditions. To help explaining their geographic distribution and possibly also their cosmopolitan or endemic status, 22 species (24 strains) were investigated for their tolerance to starvation and to desiccation. Three other traits were also measured, i.e., fresh weight, water content and lipid content. For most traits, a major difference was found between temperate and tropical species, while the biogeographical status was not important. Temperate species, on average, were heavier, with more lipidic reserves and better resistance to starvation and desiccation. When the complete set of 24 strains was considered, positive correlations were found between most traits, and a negative correlation between water and lipid content. On the other hand, when the two geographic groups (tropical versus temperate) were considered separately, the correlations tended to decrease and even disappear among the less vari.
Defining deer overabundance and threats to forest communities: From individual plants to landscape structure

Abstract Changes in habitat and reduction in predation and hunting pressure are two primary causes of high-density populations of white-tailed deer (Odocoileus virginianus) in many areas of eastern North America. Despite increasing recognition of the major effects deer exert on forest communities, deciding when deer are overabundant remains a major challenge to managers charged with conserving native plant communities. In this context, we define overabundance as a condition where deer are causing the local extinction of a native plant species. Because this definition is difficult to apply from a management perspective, we outline an approach using native understory forbs. Indicator species are selected based on combined criteria of palatability to deer, leaf and flower morphology, and demographic characteristics. Four indices related to plant population viability are derived from understory survey data: flowering rate, mean stem height, stage-class distribution, and deer browsing pressure. We apply this analysis to Trillium populations from forests in Minnesota (highly fragmented agricultural landscape with varying deer densities), Pennsylvania (forested and fragmented landscape with long-term high deer densities), and New York (forested and fragmented landscape with long-term low deer densities). We observed two distinct types of deer-affected plant populations. In sites with moderate or recent increases in deer density, Trillium populations were characterized by low mean plant size, high browsing rates, intermediate flowering rates, and a size class distribution lacking large, reproductive plants. Sites affected by long-term high deer densities exhibited low browsing rates on Trillium, low Trillium flowering rates, a population structure lacking both large and small plants, and high summer browsing pressure on woody saplings. We suggest these combined indices be used to assess deer browsing impact, and we discuss the role of landscape structure and deer density in defining deer overabundance.
Carbohydrate Profile of a Dry Bean (Phaseolus vulgaris L.) Panel Encompassing Broad Genetic Variability for Cooking Time

Dry beans are typically consumed as a whole food, and cooking time is one of the most important processing quality attributes. A panel of eight dry bean entries with variability in cooking time was established, grown in three locations, and used to test the hypothesis that carbohydrate components are major underlying contributors to genetic variability in cooking time. The cooking times ranged from 17 to 160 min. In general, faster cooking bean genotypes had higher levels of soluble dietary fiber in both the raw and cooked samples. Resistant starch levels in the raw beans, although not correlated with cooking time, were of interest because of the large genotypic variability, and they ranged from 1.5 to 35%. One genotype in particular, a yellow bean from Africa, Cebo Cela, had low resistant starch levels in the raw seeds of 1.5–2.5%, whereas average resistant starch levels in the entire panel were 26–30%. Resistant starch levels (3.9–4.2%) in the cooked seed of Cebo Cela were comparable to the other genoty.