Miracle-dz/UniFAR-FTUs huggingface dataset:
Ribosomal (rDNA) Variation in a Deep Sea Hydrothermal Vent Polychaete, Alvinella Pompejana, From 13°N on the East Pacific Rise

The rDNA repeat-unit of the vent polychaete Alvinella pompejana was investigated using restriction analysis. Mapping revealed evidence of rDNA polymorphism within and between individuals which was due to individual restriction site variation and sequence rearrangements involving spacer regions. The size of the repeat unit was 10.5 kb with virtually no evidence of length variation. Sequence inversions indicated the presence of two spatially-distinct subfamilies of repeats, probably on different chromosome pairs. Animals from contrasting vent habitats with respect to age and chemical emissions (young vs old chimneys and white vs black smokers) from within the 13°N/EPR (East Pacific Rise) vent sector were analysed for evidence of population differentiation. Based on individual restriction site variation, average FST estimates across neighbouring populations were in the region of ~0.05 and differed significantly from zero. This level of genetic differentiation is comparable to values reported previously for allozymes. Spatial and temporal allelic frequency variances estimated from pairwise combinations (i.e. s2S and s2T) strongly suggested that differences in allelic frequency were the result of repeated extinction/recolonization events associated with the vent instability. Estimates of the effective population size derived from standardized temporal allelic frequency variances Fks were very low compared to actual population size indicating great temporal fluctuations in the former. Theoretically, such an effective population size is not sufficient to maintain the observed level of polymorphism within the 13N/EPR vent sector. Results are therefore consistent with a ‘propagule’ colonization-type model in which extinction/recolonization rates are high. In Alvinella, planktonic larval dispersal appears sufficient to overcome any genetic differentiation resulting from drift, but these findings also indicate that propagules may only be capable of dispersing a few tens of kilometres per generation.
MERCURY VAPOUR: A HEALTH HAZARD IN HERBARIA

SUMMARY Metallic mercury vapour is released from herbarium specimens poisoned with mercuric chloride, in quantities which might constitute a health hazard. By increasing the ventilation in the Cambridge University Herbarium, the concentration of mercury vapour in the air has been reduced to a safer level. Even if herbaria no longer use mercuric chloride to protect specimens against insect attack, botanists might wish to consider the health hazard involved by release of mercury from older herbarium specimens which might have been poisoned in the traditional manner.
Bacteriological study of catfish, Claria gariepinus, from fish pond sources in Akungba-Akoko community, Nigeria.

Aim: To determine the microbiological quality of catfish meant for public consumption in the university community, Akungba-Akoko. Study design: Cross-sectional study. Place and Duration of Study: Department of Microbiology, Adekunle Ajasin University, P.M. B. 01, Akungba-Akoko, Nigeria, between May 2010 and June 2011. Methodology: Fresh catfish, Claria gariepinus, sample obtained from typical fish pond in Akungba-Akoko was subjected to microbiological Investigation in the Laboratory. Nutrient Agar, Eosine Methylene Blue Agar and Man Rogosa Sharpe Agar were generally used for isolation and maintenance of cultures during the study. Moreover a pour plate technique was used for the estimation of the total bacterial and coliform counts. Results: The total plate count of fish skin samples gave high bacterial count of 65 x 10 2 cfu/ml, the coliforms count was 7.0 x 10 1 cfu/ml, while the anaerobic organisms encountered gave a value of 20 x 10 1 cfu/ml. Similarly, bacterial count of 2.25 x 10 7 cfu/ml coliform count of 1.35 x 10 4 cfu/ml and 6.5 x 10 4 cfu/ml anaerobic organisms were obtained from gills. The isolated bacteria species identified were Bacillus spp, Staphylococcus spp, Streptococcus spp, Microcococcus spp, and members of enterobacteriaceae which include Escherichia coli and Klebsiella spp were found in the skin of the fresh fish. Other complex forms of bacterial species were also encountered in the gills of catfish sample used for this study. This includes S. aureus, E. coli, Bacillus spp. The total aerobic counts of the Clarias gariepinus (Catfish) sample were determined and the results of this study shows that the largest numbers of anaerobic microbes were found in gills. Conclusion: The study suggests adequate monitoring of our fish ponds with a view of adding some antibiotics to their feeds to reduce infectious agents from this source. Research Article British Microbiology Research Journal, 2(1): 1-9, 2012 2
Revision of the species group Napaeus variatus (Gastropoda, Pulmonata, Buliminidae) from the Canary Islands, with description of five new species *

The Napaeus variatus (Webb & Berthelot, 1833) species group from the Canary Islands is reviewed from literature information, types, other museum specimens, and newly collected material. Anatomy data is newly provided for six species. Five new species are described: N. elegans and N. esbeltus from Tenerife, N. orientalis and N. beguirae from La Gomera, and N. exilis from Gran Canaria. Eight species lack a diverticulum and are referred to the subgenus Napaeus (Napaeus) Albers, 1850, whereas five species are provided with a diverticulum and arc referred to Napaeus (Napaeinus) Hesse, 1933. Four species cannot be assigned to a subgenus due to a lack of information. Keys of species from the different islands are provided.
Kinetics of Douglas-fir (Pseudotsuga menziesii) somatic embryo development

Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) is one of the most economically important softwood species in the Pacific Northwest region. Somatic embryogenesis is a potential mass propagation technology for increasing the productivity of existing forest acreage. Combined with traditional breeding methods and recent advances of genetic engineering in plant species, somatic embryos can shorten the elite clone selection process significantly. Somatic embryo culture of Douglas-fir involves three stages: maintenance, abscisic acid (ABA) singulation, and maturation. At the beginning of all stages of culture, the population of cells with embryogenic potential is increased through the weekly subcultured maintenance stage; transfer into the ABA singulation stage initiates embryo development, while cotyledonary embryos are formed in the maturation state. The first two stages were carried out in submerged suspension culture, while during the maturation stage the developing embryos were placed on a polyester pad.
HISTOCHEMICAL DEMONSTRATION OF HUMAN LIVER HEXOKINASE USING NITRO-BLUE TETRAZOLIUM

Histochemical demonstration of human liver hexokinase, low Km hexokinase, Km for glucose 10-4M or less (HK), and glucokinase, Km for glucose 10-1M(GK), was described in control and liver disease patients. The method was essentially an application of kinetic assay system of HK and GK established by Vinuela et al. The activities of HK and GK were demonstrated as a dark blue deposit of formazan, which produced by the reduction of nitro blue tetrazolium (nitro-BT) with NADPH, an intermediate in the HK reaction coupled to the oxidation of glucose-6-phosphate (G6P). The specificity of present method was indicated by the lack of color development in the absence of either ATP or glucose. The intensity of formazan deposition appeared to represent the activity of HK and GK in the human liver tissue. HK was demonstrated when stained with 0.5mM glucose concentration and HK and GK was demonstrated with 100mM glucose concentration.
Fish in the Structure and Function of Freshwater Ecosystems: A "Top-down" View

The role of fish in regulation of the structure and function of freshwater ecosystems (lakes and streams) is examined with respect to effects resulting directly from their feeding activity, indirectly from size or other forms of prey selectivity, and from influences on nutrient cycling and transport. That fish have long had a legitimate place in limnological research is documented by a review of limnological books, texts, and journals. Recognition of their "top-down" effects, started largely from Czechoslovakian research (Hrbacek and others) in the mid-1950's, was popularized by American and German research (Brooks, Jacobs, and others) in the mid-1960's and has enjoyed a remarkable upsurge in the 1970's, continuing into the 1980's. Although size-selective predation has been an important phenomenon in stimulating widespread research on effects of fish on freshwater communities and their function, the importance of other mechanisms in such regulation is considered.
APLICACIÓN DE RIEGO LOCALIZADO PARA AUMENTAR LA RETENCIÓN DE FRUTOS DE Vanilla planifolia EN EL TOTONACAPAN, VERACRUZ, MÉXICO

El objetivo del presente estudio fue evaluar el efecto de riego en la retencion de frutos de Vanilla planifolia Andrews. Se diseno y probo un sistema de riego localizado en huertos con tres tipos de manejo en el Totonacapan, Veracruz, Mexico. Durante 2000 y 2001 se seleccionaron en huertos tecnificados (Te), semitecnificados (St) y tradicional (Tr) 40 tutores con plantas de vainilla por tutor y divididos en grupos de 10 individuos. Se suministro riego diariamente a las 18:00 h durante la temporada seca (mayo-junio) en cuatro tratamientos: 1) 1.0 L m 2 de agua; 2) 0.5 L m 2 ; 3) 0.25 L m 2 ; 4) un grupo testigo sin riego. Mensualmente se cuantifico la permanencia de los frutos de vainilla en las plantas y se midio la cobertura arborea en cada tipo de parcela para obtener el porcentaje de sombra. Se midieron el pH del suelo, temperatura, precipitacion y humedad atmosferica. La retencion de frutos no vario entre los anos, la cual fue de 45 a 70 % y equivalente a 0.44 t ha 1 , este resultado es superior a la media nacional (0.22 t ha 1 ). El huerto con manejo semitecnificado presento una retencion de 69.5 % de frutos, atribuible al riego y a las caracteristicas del sistema de cultivo. La combinacion de humedad del suelo y el manejo de los vainillales parece tener una fuerte influencia sobre la retencion de frutos, lo cual mejora la condicion del cultivo
Neofabraea populi in Hybrid Aspen Stands in Southern Finland

Symptoms typical of Neofabraea populi infection were identified from seven hybrid aspen (Populus tremula L. 2 P. tremuloides Michx.) stands in southern Finland. Morphology of the fungal isolates in vitro and ascospores released from apothecia on cankers was compared with reference isolates and the literature, respectively. A damage inventory was compiled in five stands. The percentages of healthy, diseased and dead stems per stand were calculated. The disease caused remarkable losses within stands (up to 53% mortality). Random amplified microsatellite markers were amplified from single-ascospore isolates, isolates from wood tissue and three reference isolates of N. populi. Both morphological and molecular analyses confirmed that the causal agent was N. populi, as suspected. The results imply that this fungus may become a major problem in hybrid aspen plantations in southern Finland.
Enriched atmospheric CO2 and defoliation: effects on tree chemistry and insect performance

We examined the effects of CO2 and defoliation on tree chemistry and performance of the forest tent caterpillar, Malacosoma disstria. Quaking aspen (Populus tremuloides) and sugar maple (Acer saccharum) trees were grown in open‐top chambers under ambient or elevated concentrations of CO2. During the second year of growth, half of the trees were exposed to free‐feeding forest tent caterpillars, while the remaining trees served as nondefoliated controls. Foliage was collected weekly for phytochemical analysis. Insect performance was evaluated on foliage from each of the treatments. At the sampling date coincident with insect bioassays, levels of foliar nitrogen and starch were lower and higher, respectively, in high CO2 foliage, and this trend persisted throughout the study. CO2‐mediated increases in secondary compounds were observed for condensed tannins in aspen and gallotannins in maple. Defoliation reduced levels of water and nitrogen in aspen but had no effect on primary metabolites in maple. Similarly, defoliation induced accumulations of secondary compounds in aspen but not in maple. Larvae fed foliage from the enriched CO2 or defoliated treatments exhibited reduced growth and food processing efficiencies, relative to larvae on ambient CO2 or nondefoliated diets, but the patterns were host species‐specific. Overall, CO2 and defoliation appeared to exert independent effects on foliar chemistry and forest tent caterpillar performance.
Effect of interannual climate variations on radial growth of jack pine provenances in Petawawa, Ontario

Effect of interannual climate variations on radial growth was compared among jack pine (Pinus banksiana Lamb.) of diverse geographical origins in a 41-year-old common-garden experiment in Petawawa, Ontario. Provenance ex- periments established from seeds transferred from different parts of a species range (from the northern United States to northern Canada) to the same environment might be considered as a simulation model of climate change and a shift of cli- mate zones. The following questions are addressed: Did the response of growth to interannual climate variations differ among the provenances transferred within the experimental site? What climatic factors affect interannual growth variations of jack pine provenances? Tree-ring chronologies for 16 populations were developed for the period 1970-2004. The best climate predictors of radial growth were precipitation of June and March of the current year and precipitation of December of the previous year. Although, climatic factors affecting growth were similar between the provenances, absolute radial growth was proportional to the growth potential of the provenances. We conclude that variability due to seeds origins is not a significant source of variation for dendroclimatic studies of jack pine. Increased frequency of summer droughts might result in a growth decrease of jack pine. Resume´ : Nous avons etudieles relations entre le climat et la croissance radiale annuelle de provenance de pin gris (Pinus banksiana Lamb.) etablis depuis 41 ans dans un jardin commun a Petawawa en Ontario. Des tests de descendance etablis dans des conditions similaires a partir de graines provenant de differentes parties de l'aire de distribution de l'espece (depuis le Nord des Etats-unis jusqu'au nord du Canada) simulent des changements climatiques et des transitions entre differentes zones bioclimatiques. Nous avons tentesd e repondre aux questions suivantes : Est-ce que la relation entre la croissance radi- ale interannuelle et le climat varie en fonction des provenances? Quelles sont les facteurs climatiques qui controlent la crois- sance radiale des differentes provenances. Des chronologies de la croissance radiale couvrant la periode 1970-2004 ont ete ´ developpees pour 16 provenances. Les facteurs climatiques les plus correles avec la croissance radiale sont les precipitations pour juin et mars de l'annee en cours et les precipitations de decembre pour l'annee precedente. Bien que les facteurs clima- tiques controlant la croissance sont les memes pour toutes les provenances, la croissance absolue variait en fonction du po- tentiel de croissance de chaque provenance. Nous concluons que la variabilitedue a la provenance des graines ne constitue pas une source importante de variation dans la reponse dendroclimatique chez le pin gris. Une augmentation de la frequence des secheresses durant la periode estivale pourrait entraoˆner une diminution de la croissance du pin gris.
Seasonal patterns in community composition of bats in forest fragments of the Alto Rio Paraná, southern Brazil

We studied seasonal patterns in richness and abundance in bat communities in Atlantic Forest fragments along the Paraná River in Brazil. There were differences in species composition among fragments but these appear more related to habitat quality than to fragment size. All fragments had high rates of captures of generalist frugivores and a scarcity of species known to be susceptible to disturbance. Richness and abundance were slightly lower during the dry season, but differences were significant only in the most degraded fragment.
Semi‐strong Hybrid Scaling, a new ordination algorithm

There is a small group of association measures that appear optimal for comparing sites on the basis of their species composition. These measures can accurately estimate affinity between sites when they are ecologically similar. Once sites share few or no species, these measures always under-estimate the ‘ecological distance’ between them. A new ordination algorithm called Semi-strong Hybrid Scaling, SHS, uses these features in an attempt to provide a better configuration of the sites. The new method is evaluated by a direct comparison of the structure in simulated data with the Hybrid method of Faith, Minchin & Belbin (1987). To evaluate SHS and compare it with Hybrid Scaling, 3240 datasets were generated using the COMPAS simulator (Minchin 1987). The data were designed to simulate as closely as possible, what is known of the distribution of species on environmental gradients. The factors included the dimensionality of the data, the number of sites and species, the shape of the species response surfaces, positioning of the sites in the simulation space, carrying capacity and level of noise. Recovery of the simulated site positions by SHS and Hybrid Scaling was evaluated using Procrustes rotation. SHS produced a better recovery in 88% of the datasets.
Fjärilsmyggfaunan i ett hagmarksområde och en ladugård i östra Blekinges skogsland. Med en översikt av familjen Psychodidae:s morfologi, systematik och utforskande, samt särskilt de svenska Psychoda s.l.-arternas biologi.

Svensson, B.W. Fjärilsmyggfaunan i ett hagmarksområde och en ladugård i östra Blekinges skogsland. Med en översikt av familjen Psychodidae:s morfologi, systematik och utforskande, samt särskilt de svenska Psychoda s.l. -arternas biologi. [The moth fly fauna in a pasturewoodland area and a barn in the eastern part of the province Blekinge, SE Sweden. Insecta: Diptera, Psychodidae, with a review of the morphology, ecology and research history of the family Psychodidae, and especially the biology of the Swedish Psychoda s.l. species. ] – Entomologisk Tidskrift 130 (3-4): 185-208. Uppsala, Sweden 2009. ISSN 0013-886x.
An MPN method for the enumeration of marine hydrocarbon degrading bacteria.

An MPN method for the counting of marine hydrocarbon degrading bacteria was developed. The medium in this method contained small amounts of yeast extract in order to support the growth of hydrocarbon degrading bacteria that require other organic nutrients in addition to hydrocarbons. Surveys of hydrocarbon degrading bacteria in sea water and beach sand showed that the incorporation of 0.05% (w/v) yeast extract in the enumeration medium resulted in increases of up to 100 times in the number of hydrocarbon degrading bacteria. The growth of hydrocarbon degrading bacteria in the medium could be detected either by an increase in turbidity or a decrease in pH, or by a combination of the two. During the course of the study, we found that some samples of hydrocarbon fractions, especially some kerosene samples, were toxic to the growth of marine hydrocarbon degrading bacteria.
Mitochondrial DNA divergence between wild and laboratory populations of Anopheles albimanus Wiedemann (Diptera: Culicidae)

Studies of insect vectors may be facilitated by using laboratory colonies. However, it has been suggested that the colony insects are not representative of natural populations, sometimes yealding to erroneous interpretations of the intraspecific genetic variation between the individuals. In the present study the variability of the mitochondrial gene cytochrome b was evaluated among a closed laboratory colony of Anopheles albimanus that was founded 20 years ago and the field population from which it was derived. The analyses revealed the presence of five and three nucleotide haplotypes in the wild and colony populations, respectively. Wild individuals presented greater variability than those of the colony based on the number of polymorphic sites, haplotype diversity, nucleotide diversity and mean values of nucleotide differences. The mean and net numbers of nucleotide substitutions per site between populations and the significant FST value calculated (0,37179, P = 0.05) indicate that there is a considerable degree of genetic differentiation between them. The phylogenetic tree showed that the colony haplotypes appear to be derived from the wild population. These results suggest a great genetic variability in wild specimens compared with the laboratory ones as a consequence of a long time of colonization.
Differential accumulation of phenolic compounds in potato in response to weakly and highly aggressive isolates of Verticillium dahliae

Abstract Verticillium wilt, caused by the soilborne pathogen Verticillium dahliae (Kleb.), is an important disease affecting more than 400 plant species, including many economic crops. This study explored differential accumulation of phenolic compounds in potato in response to weakly and highly aggressive isolates of this pathogen. After phenolic compounds were extracted from roots, stems and leaves of inoculated plants, those showing differential accumulation were identified using high performance liquid chromatography (HPLC) equipped with a photodiode array detector, a fluorescence detector, and co-elution with commercial standards. Profiling of phenolic compounds during the potato–V. dahliae interaction confirmed previous observations on rutin accumulation in response to infection and showed differential accumulation of hydroxycinnamic acids in different tissues in response to two isolates possessing different levels of aggressiveness. In particular, differential accumulation of caffeic and ferulic acids was recorded in the roots and stems after inoculation, especially with the highly aggressive isolate. In the stems, the accumulation of rutin in response to inoculation was inhibited by the highly aggressive isolate, as compared with the weakly aggressive one.