Miracle-dz/UniFAR-FTUs huggingface dataset:
Species-specific population structure of closely related coral morphospecies along a depth gradient (5-60 m) over a Caribbean reef slope

We investigated the use of demographic characteristics to differentiate between closely related coral species that are difficult to distinguish morphologically and genetically. We looked at colony size and density in six morphospecies of the coral genus Madracis in Curacao (Netherlands Antilles). Colonies of all species (n = 1585), including individuals as small as 0.01 cm 2 , were measured in 30 x 1 m belt transects over a reef slope at 5, 10, 20, 30, 50 and 60 m depth. This resulted in a detailed description of species population structures over depth. Temperature, light, sedimentation and water movement were recorded. Our survey showed Madracis to be one of the most abundant coral genera (mean of 9.2 colonies m -2 ) at the reef slope. The size frequency distributions were species specific and provide us with a set of characteristics, in addition to traditional morphological and genetic species classifications, to distinguish between coral taxa. Species density (n m -2 ) and mortality rates differed between morphospecies and within morphospecies among depths, suggesting that population density is under environmental control (selective environment). Population structure, in terms of size frequency distribution, remained stable over depth and appears to be largely dependent on differences in species-specific life-history strategies (developmental environment). The population structure of all Madracis species changed only at the upper and lower margin of their distribution. These changes were similar in all species: (1) Densities of populations decreased, resulting in 'saw-shaped' size distributions; (2) Overall variation in un-transformed colony size distributions, expressed as coefficient of variation (CV), decreased while the variation in log-transformed size-distributions, which is indicative of the time a colony is present on the reef, increased; (3) Decreasing skewness (g 1 ) in untransformed size-distributions indicated that the proportion of smaller colonies decreased within the population; (4) The relative differences in the contribution of larger individuals to the total population surface increased, indicated by higher values for the Gini-coefficient (G); and (5) Mean colony sizes, after range standardization of size-data, became larger than 0.12. Life-history strategies partially overlap for morphospecies sharing the same colony morphology. Population turnover rates differed between species present at the same depth, ranging between >100 yrs for Madracis senaria to five yrs for Madracis decactis, which reflects species-specific susceptibility to environmentally induced mortality.
Morphometric analysis reveals a new species of Aponogeton (Aponogetonaceae) in Sri Lanka

A morphometric analysis of Sri Lankan Aponogeton was performed in order to clarify species delimitations and to facilitate their identifications by comparing states coded for 61 vegetative and reproductive characters. Both cluster analysis and principal coordinate analysis resolved five discrete phenetic groups within the genus in the island. Four of these clusters corresponded well with the four previously reported species ( A. rigidifolius , A. jacobsenii , A. crispus and A. natans ) whereas a fifth cluster delimited a new Aponogeton species, A. dassanayakei, from the wet lowland regions of Sri Lanka. These analyses have disclosed more useful characters for field identification of the species.
Above- and below-ground competition between the liana Acacia kamerunensis and tree seedlings in contrasting light

Proliferation of lianas in canopy gaps can restrict tree regeneration in tropical forests through competition. Liana effects may differ between tree species, depending on tree requirements for above- and below-ground resources. We conducted an experiment in a shade house over 12 months to test the effect of light (7 and 27% external irradiance) on the competitive interactions between seedlings of one liana species and three tree species and the contribu- tion of both above- and below-ground competition. Seedlings of the liana Acacia kamerunensis were grown with tree seedlings differing in shade toler- ance: Nauclea diderrichii (Pioneer), Khaya anthotheca (Non-Pioneer Light Demander) and Garcinia afzelii (Non-Pioneer Shade Bearer). Trees were grown in four competition treatments with the liana: no competition, root competition, shoot com- petition and root and shoot competition. Both root and root-shoot competition significantly reduced relative growth rates in all three tree species. After one year, root-shoot competition reduced growth in
Mechanisms and Dynamics of Oxidative DNA Damage Repair in Nucleosomes

DNA provides the blueprint for cell function and growth, as well as ensuring continuity from one cell generation to the next. In order to compact, protect, and regulate this vital information, DNA is packaged by histone proteins into nucleosomes, which are the fundamental subunits of chromatin. Reactive oxygen species, generated by both endogenous and exogenous agents, can react with DNA, altering base chemistry and generating DNA strand breaks. Left unrepaired, these oxidation products can result in mutations and/or cell death. The Base Excision Repair (BER) pathway exists to deal with damaged bases and single-stranded DNA breaks. However, the packaging of DNA into chromatin provides roadblocks to repair. Damaged DNA bases may be buried within nucleosomes, where they are inaccessible to repair enzymes and other DNA binding proteins. Previous in vitro studies by our lab have demonstrated that BER enzymes can function within this challenging environment, albeit in a reduced capacity. Exposure to ionizing radiation often results in multiple, clustered oxidative lesions. Near-simultaneous BER of two lesions located on opposing strands within a single helical turn of DNA of one another creates multiple DNA single-strand break intermediates. This, in turn, may create a potentially lethal double-strand break (DSB) that can no longer be repaired by BER. To determine if chromatin offers protection from this phenomenon, we incubated DNA glycosylases with nucleosomes containing clustered damages in an attempt to generate DSBs. We discovered that nucleosomes offer substantial protection from inadvertent DSB formation. Steric hindrance by the histone core in the nucleosome was a major factor in restricting DSB formation. As well, lesions positioned very close to one another were refractory to processing, with one lesion blocking or disrupting access to the second site. The nucleosome itself appears to remain intact during DSB formation, and in some cases, no DNA is released from the histones. Taken together, these results suggest that in vivo, DSBs generated by BER occur primarily in regions of the genome associated with elevated rates of nucleosome turnover or remodeling, and in the short linker DNA segments that lie between adjacent nucleosomes. DNA ligase IIIα (LigIIIα) catalyzes the final step in BER. In order to facilitate repair, DNA ligase must completely encircle the DNA helix. Thus, DNA ligase must at least transiently disrupt histone-DNA contacts. To determine how LigIIIα functions in nucleosomes, given this restraint, we incubated the enzyme with nick-containing nucleosomes. We found that a nick located further within the nucleosome was ligated at a lower rate than one located closer to the edge. This indicated that LigIIIα must wait for DNA to spontaneously, transiently unwrap from the histone octamer to expose the nick for recognition. Remarkably, the disruption that must occur for ligation is both limited and transient: the nucleosome remains resistant to enzymatic digest before and during ligation, and reforms completely once LigIIIα dissociates.
Construction and Characterization of Escherichia coli O157:H7 Strains Expressing Firefly Luciferase and Green Fluorescent Protein and Their Use in Survival Studies ‡.

The firefly ( Photinus pyralis ) luciferase (luc) gene on plasmid vector pBESTluc and the Aequorea victoria green fluorescent protein (gfp) gene on plasmid vector pGFP were introduced into strains of Escherichia coli O157:H7. The recombinant E. coli strains were indistinguishable from their parent strains in biochemical and immunological assays and in a multiplex PCR reaction. There was no significant difference in the growth kinetics of the luc-bearing recombinants and the parent strains. At 37°C all of the recombinant strains maintained the vectors and expressed luciferase and the green fluorescent protein when grown both with and without antibiotic selection. Individual colonies of luc-bearing E. coli strains were readily luminescent in the dark after being sprayed with a solution of 1 mM beetle luciferin. The recombinants containing pGFP emitted bright green fluorescence when excited with UV light and the addition of any other proteins, substrates, or cofactors was not required. The green fluorescent protein-expressing E. coli O157:H7 strains were used in studies examining the survival of the organism in apple cider and in orange juice. In apple cider the organism declined to undetectable levels in 24 days at refrigeration temperature while in orange juice the strains survived with only small decreases in number during the 24-day sampling period. These recombinant E. coli O157:H7 strains, containing readily identifiable and stable markers, could be useful as positive controls in microbial assays as well as in studies monitoring bacterial survival and the behavior of E. coli O157:H7 in foods and in a food processing environment.
Scarf skin on Rome beauty: time of origin and influence of fungicides and Ga4+7

‘Rome Beauty’ apples were enclosed in perforated polyethylene bags at various times or treated with selected fungicides, GA4+7 or nutrient sprays to determine the influence on development of scarf skin. Bagging at petal fall (PF) reduced scarf on both the green and colored sides of the fruit. The longer the bags were in place, the greater the reduction in scarf skin up to 60 days after PF. Fruit weight was reduced by as little as 10-day enclosure in bags applied at PF, and the longer the period of enclosure the greater the reduction in size. Bagging explains a decrease in the scarf skin rating which is not explained by the corresponding decrease in fruit weight. Bagging 10 days after PF reduced fruit set, but bagging at PF or 20 or 30 days after PF had no influence on fruit set. Full season fungicide programs of benomyl or dikar increased the amount of scarf skin. Nutrient dips of either solubor or CaCl2 or the insecticide dimethoate had no influence on scarf skin. GA4+7 dips during the critical period for development significantly decreased scarf skin but not to the level achievable with a polyethylene bag. Fruit samples from different orchard sites differed in the level of scarf skin present.
A simple method for immobilising small dipteran insects and its validation for Aedes aegypti

Isa ıas Cabrini*, Carlos Fernando S. Andrade, Marcelo da Costa Ferreira & Eduardo Jos e de Arruda Department of Animal Biology, Institute of Biology, State University of Campinas, Campinas, SP, Brazil, Faculty of Exact Sciences and Technology, Federal University of Grande Dourados, Dourados, MS, Brazil, and Faculty of Agricultural and Veterinary Sciences, Paulista State University, Jaboticabal, SP, Brazil
The influence of nitrogen inputs on biomass and trophic structure of ocean plankton: a study using biomass and stable isotope size-spectra

Malaspina-2010 (CSD2008-00077) funded by program CONSOLIDER-INGENIO 2010; Ministerio de Ciencia e Innovacion (Spain), project EURO-BASIN (FP7-ENV-2010 264933) of the EU; Instituto Espanol de Oceanografia (IEO); PFPI (grant of IEO) to C.M. ; FPU grant from the Spanish government (AP2010-5594) to B.F. -C.
Quantitative Analysis of the Symbiotic Nj-Eixat.ion, Non-Structural Carbohydrates and Chlorophyll Content in Sixteen Native Legume Species Collected in Different Savanna Sites

Three species of Caesalpinaceae, 8 species of Fabaceae, and 5 species of Mimosaceae, at flowering or fruiting stage, were collected during the rainy season, in 12 different savanna sites. The bulk of legume species was found in sandy soils, with pH between 4.2 to 4.6, containing low %Al saturation. Legume species were analysed in terms of their relative abundance of ureides (RAU), aamino-N (RAA-N) and nitrate (RAN) in nodules (if present), basal roots, green shoots and mature leaves. According to RAU values in shoots, nodulated native species were categorized as fairly good, intermediate, or weak N2-fixers; nodules from good N2-fixers presenting the lowest RAU. Concomitantly, an inverse relationship was recorded between RAU and RAA-N, the highest RAA-N detected in non-nodulated plants. On the other hand, RAN in nodules was significantly lower than in shoots and roots. No detectable levels of nitrate were found in leaves. All species were shown to be ureide producers, except for Sesbania sericea. This species was tentatively classified as an amino-N exporter. 0334-5114/92 /$03.50 ©1992 Balaban 294 M.L. IZAGUIRRE-MAYORAL ET AL. In ureide producer species, RAU values in shoots and roots of nodulated plants were significantly higher than those ofnon-nodulated individuals. This fact supports the use of the ureide technique for detecting and quantifying N2-fixation in native legumes. RAU in shoots was positively correlated with soil pH (r=0.667, p<0.01), and negatively correlated with soil Al contents (r=0.558, p<0.01). There was no correlation between shoot RAU values and the soil N, K, Ca, P, or Mg concentrations. RAU in shoots was also positively correlated with the leaf chlorophyll content (r=0.597, p<0.01) and inversely correlated with starch concentration in roots (r=0.443, p<0.01). In turn, no relationship was observed between leaves' or roots' total reducing sugars and the symbiotic process. The analysis of native rhizobial populations in superficial soil horizons (0-20 cm) indicated that the number of rhizobia g-1 soil was negatively correlated (p<0.01) with the% sand (r=0.784), but positively correlated (p<0.01) with soil cation exchange capacity (r=0.790) and Al contents (r=0.884). Maximum number of rhizobia was found in soils with pH 4.2, and no correlations were detected between number of rhizobia and soil N, P, K, Ca, and Mg concentrations.
High-dose Caffeine Intrauterine Exposure Altered Neuronal Morphology and Spatial Distribution in Murine Models Cerebral Cortex

Caffeine is a neurostimulant that is globally consumed with little or no restrictions by various groups of people. Though concerns have been raised over the possible effects of caffeine exposure during intrauterine life or pregnancy; there are not enough empirical evidences to establish the specific potential effects of caffeine exposure on the devolvement and the functions of the brain. The current investigation examined the possible effects of caffeine exposure at various dosages modelled after human consumption quantities in murine models. The experimental animalspregnant mice, were grouped into four and labelled A, B, C and D respectively. Anhydrous caffeine was dissolved in distilled water and administered to animals daily using oral gavages. The Control Group was labelled A and the pregnant mice were fed ad libitum throughout the experiment to serve as the reference and normal in the context of results interpretation; the Group B animals were administered the moderate caffeine dosage [10 mg/kg body weight]; Group C received moderately high dosage [50 mg/kg body weight] and the Group D received the excessively high caffeine Original Research Article Owolabi et al.; JALSI, 6(2): 1-10, 2016; Article no.JALSI. 26545 2 dosage [120 mg/kg body weight] throughout pregnancyfrom the day 1 of pregnancy to parturition. The mice litters were allowed to develop until Day 12 Postnatal life, and then sacrificed. The brain tissues were excised and processed using the Haematoxylin and Eosin histological technique. Histomorphological results showed that caffeine exposure at the excessively high dosage altered neuronal morphology and spatial distribution with evidence of limitations in dendritic and axonal development and elaboration. Caffeine at the lower dosages showed potentials to mildly influence neuronal spatial distribution; with glias not showing extensive morphological or spatial alterations.
Effect of Some Herbs in Boiler Diets on Blood Proteins and Lipids

The present study was conducted to investigate the effect of feeding some herbs on blood proteins and lipids. Sweet rush, Parsley, carrot leaves and onion were incorporated in four diets as 2% of the basal diet which were used together with a control diet (basal diet) and a diet contained antibiotic doxystin) as experimental diets. Two hundred and forty one day old (cobb) broilers were used in 6×4 design. Total protein, albumin, globulin, cholesterol, high density lipoprotein HDL, low density lipoprotein LDL, and triglyceride were measured. Results revealed that the total protein level was high (p<0.05) in the diets contained carrot leaves, Parsley (bagdonis) and those fed onion supplemented diet. Treatments significantly (P≤ 0.05) affect blood albumen the highest value for blood albumen was recorded in onion treatment whereas the lowest value was recorded in sweet rush. Globulin was not affected by different treatments. Barsely and sweet rush resulted in low cholesterol level, high level observed in Allium cepa (onion) group, antibiotic and the control group . Carrot leaves and antibiotic resulted in high level of HDL and low level HDL in bagdonis fed group. Lemongrass (Sweet rush) recorded low level of low density lipoprotein while high level was observed in the group fed Allium cepa. Triglyceride was not affected by different treatments. It is concluded that herbs had good effect on total protein, albumin, HDL, it decreases cholesterol, and LDL, but triglyceride was not affected by herbs.
Some characteristics of macrobenthic fauna from the organic-enriched sediments at Talcahuano, Chile

The community structure of the macrobenthic ( > 500 μm) fauna from organic matter enriched-soft bottom of Talcahuano Port, Concepción Bay, Chile, was studied and compared over other two sites located further away with progressively less organic content. Polychaeta was the main taxon reaching 93,9 % of the whole analyzed fauna. The numerical abundances were high (from 26.280 ind. m to 63.830 ind. m), while the number of species was low (44 species). The species diversity values calculated for the fauna were low, and the same pattern for the evenness was observed. The Talcahuano port benthic station (Cl) was dominated by the great numbers of the small opportunistic spionid polychaet Carraziella carrascoi. The nearby station C2 showed high numbers of the small polychaet Cossura chilensis and oligochaetes. The more distant site from Talcahuano port (station C3) was dominated by individuals of C. carrascoi and Owenia collaris. The stations (Cl and C2) more associated with Talcahuano port facilities, where the organic matter was important, exhibited the highest number of individuals and the lowest amount of species, which was reflected in low species diversity figures and the low slopes of the rarefaction curves. The macrobenthic fauna of station Cl (Talcahuano port) and C2, conformed a different faunal assemblage with respect to station C3, as was showed by the numerical classification. The log-normal distribution analysis of individuals among species showed a faunal transition phase to organic pollution for the two more Talcahuano port associated benthic stations. Résumé : La macrofaune benthique des fonds meubles riches en matière organique, du port de Talcahuano, dans la baie de Conception du Chili est étudiée ici. On a mené une étude comparative de ces fonds avec ceux de deux autres zones très éloignées du port et qui présentent une diminution progressive de la matière organique. Le taxon le plus nombreux, les polychètes, représente 93,9 % de la faune analysée. Les abondances numériques sont considérables (de 26 000 à 63 830 ind.m) mais le nombre d'espèces (44) est peu important. Les valeurs de différence spécifique et d'équitabilité calculées pour la faune benthique sont peu importantes. Les nombreux petits oligochètes dominant sont Carraziela carrascoi dans la zone Cl et Cossura chilensis dans la zone C2 où se trouvent également des oligochètes. Dans la zone C3, la plus éloignée du port de Talcahuano, les espèces dominantes sont C. carrascoi et Owenia collaris. C'est dans les zones les plus proches des installations du port, où les quantités de matière organique sont considérables, que le nombre d'individus est le plus important et la richesse spécifique la moins élevée. La macrofaune benthique des zones Cl et C2 est différente de celle de la zone C3 comme le démontre la classification numérique. L'analyse log-normal de la distribution des individus parmi les espèces montre une phase de transition de la faune vers une phase de pollution organique pour les deux zones les plus proches du port.
Microbiological Criteria of Random Samples of Spices and Herbs Retailed on the Austrian Market.

A total of 160 samples of 55 different spices and herbs originating from six different suppliers and retailed at outlets in Vienna were screened for their microbiological quality, based on plate count and selective identification techniques. Although maximum values of total aerobic mesophilic bacteria of >107/g could be observed with some spices such as black pepper, chillies and China spice, more than 50% of the sample material contained between 104 and 106 CFU/g. Bacilli were found in nearly all samples, showing counts >105 CFU/g in almost 40% of the products. Enterobacteria, pseudomonades and aeromonades as well as lactobacilli and enterococci were present mainly at levels of <102 CFU/g. Anaerobic sporeformers could be detected only in three products. One black pepper sample contained Salmonella arizonae . Although several samples gave colonies indicating the presence of coagulase-positive staphylococci, representative isolates were not identified as Staphylococcus aureus . Some samples, especially ginger and curry, had Bacillus cereus counts as high as 105 CFU/g, many others contained relatively low numbers of this species. On the contrary, Clostridium perfringens was detected in one caraway sample.
Substituição do fubá de milho (Zea Mays, L.) por farinha de pupunha (Bactris Gasipaes, H. B. K.) em rações para Alevinos de Tambaqui (Colossoma Macropomum, Cuvier 1818)1

Son presentados los resultados de la substitucion de la harina de maiz (Zea mays) por la harina del pijuayo (Bactris gasipaes) evaluados a traves del crecimicnto y la composicion corporal de alevinos de gamitana (Colossoma macropomum), alimentados durante 112dias con cuatro raciones, constituidas de una racion padron y tres niveles de susbtitucion gradual de la harina de maiz. Los resultados demuestran que la harina del pijuayo puede substituir completamente al maiz en las dietas para estos peces, sin afectar su ganancia de peso y su composicion corporal.