Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of SSR and RAPD markers linked to a resistance allele for angular leaf spot in the common bean (Phaseolus vulgaris) line ESAL 550

The objective of this study was to identify RAPD and SSR markers associated with a resistant allele for angular leaf spot (Phaeoisariopsis griseola) from the line 'ESAL 550', derived from the Andean 'Jalo EEP 558' cultivar, to assist selection of resistant genotypes. The resistant line 'ESAL 550' and the susceptible cultivar 'Carioca MG' were crossed to generate F1 and F2 populations. One hundred and twenty F2:3 families were evaluated. The DNA of the 12 most resistant families was bulked and the same was done with the DNA of the 10 most susceptible, generating two contrasting bulks. One RAPD and one SSR marker was found to be linked in coupling phase to the resistant allele. The SSR marker was amplified by the primer PV-atct001282C, and its distance from the resistant allele was 7.6 cM. This is the most useful marker for indirect selection of resistant plants in segregating populations. The RAPD marker was amplified by the primer OPP07857C linked in coupling phase to the resistant allele, and distant 24.4 cM. Therefore, this RAPD marker is not so useful in assisting selection because it is too far from the resistant allele.
Micropropagation of Maclura tinctoria L.: an endangered woody species

Algumas especies nativas produzem sementes com baixa porcentagem de germinacao e, na maioria dos casos, dormencia que pode dificultar o aparecimento de novos individuos, por meio da propagacao sexuada. A Maclura tinctoria tem sido considerada como ameacada de extincao devido ao uso indiscriminado de sua madeira e a baixa taxa de germinacao de suas sementes. Nesse contexto, o objetivo deste estudo foi estabelecer uma metodologia de propagacao in vitro para a especie. Combinacoes de ANA + BAP, diferentes concentracoes de GA3 e combinacoes de AIB + carvao ativado foram avaliadas na inducao de brotacoes, alongamento caulinar e inducao de enraizamento, respectivamente. Os resultados indicaram que a maxima formacao de brotacoes foi obtida quando 5,37 mM NAA + 4,45 mM BAP foram utilizados. O crescimento das brotacoes foi observado com 5,48 mM GA3. Para a formacao de raizes, foi indicado o uso do meio WPM, com pH ajustado para 7,0, suplementado com 23,62 mM AIB e 4,7 g L-1 de carvao ativado. O uso de sombrite 70% por sete dias, seguido da utilizacao de sombrite 50 e 30%, tambem por sete dias cada, promoveu 97% de sobrevivencia de plantas.
Partitioning of river metabolism identifies phytoplankton as a major contributor in the regulated Murray River (Australia)

Summary 1. River metabolism was measured over an annual cycle at three sites distributed along a 1000 km length of the lowland Murray River, Australia. 2. Whole system metabolism was measured using water column changes in dissolved oxygen concentrations while planktonic and benthic metabolism were partitioned using light-dark bottles and benthic chambers. 3. Annual gross primary production (GPP) ranged from 775 to 1126 g O2 m−2 year−1 which in comparison with rivers of similar physical characteristics is moderately productive. 4. Community respiration (CR) ranged from 872 to 1284 g O2 m−2 year−1 so that annual net ecosystem production (NEP) was near zero, suggesting photosynthesis and respiration were balanced and that allochthonous organic carbon played a minor role in fuelling metabolism. 5. Planktonic rates of gross photosynthesis and respiration were similar to those of the total channel, indicating that plankton were responsible for much of the observed metabolism. 6. Respiration rates correlated with phytoplankton standing crop (estimated as the sum of GPP plus the chlorophyll concentration in carbon units), yielding a specific respiration rate of −1.1 g O2 g C−1 day−1. The respiration rate was equivalent to 19% of the maximum rate of phytoplankton photosynthesis, which is typical of diatoms. 7. The daily GPP per unit phytoplankton biomass correlated with the mean irradiance of the water column giving a constant carbon specific photon fixation rate of 0.35 gO2 g Chl a−1 day−1 per μmole photons m−2 s−1 (ca. 0.08 per mole photons m−2 on a carbon basis) indicating that light availability determined daily primary production. 8. Annual phytoplankton net production (NP) estimates at two sites indicated 25 and 36 g C m−2 year−1 were available to support riverine food webs, equivalent to 6% and 11% of annual GPP. 9. Metabolised organic carbon was predominantly derived from phytoplankton and was fully utilised, suggesting that food-web production was restricted by the energy supply.
Ethiopian coffee cultivation—Implications for bird conservation and environmental certification

Coffee cultivation plays a role in biodiversity alteration and conservation in much of the tropics. This is particularly so in Ethiopia, where coffee is an indigenous shrub and a major commodity in national and local trade. In southwestern Ethiopia, coffee (Coffea arabica, “highland coffee”) is harvested from both forests (its natural habitat) and from within farmland where it is grown in small patches under isolated shade trees. We investigated the effects of management practices on bird assemblages in each of these systems. We found that bird assemblages in the forest remnants were distinct from those in the farmland even if many species were regularly found in both habitats. Coffee cultivation in open farmlands promoted bird species diversity through the retention of forest trees, while coffee cultivation in forests reduced bird diversity. Forest coffee management may, however, ensure that forest remnants are not converted to other forms of more open agriculture. Certification standards for “ecologically friendly” coffee in Ethiopia need to take this complexity into account.
FINE-SCALE POPULATION STRUCTURE IN THE WOOD FROG (RANA SYLVATICA) IN A NORTHERN WOODLAND

We investigated the genetic structure of wood frog (Rana sylvatica) populations in a woodland habitat around Lake Itasca, Minnesota, USA. Based on published studies of wood frog movement patterns, we expected to find genetic differentiation at inter-population distances exceeding a few kilometers. We sampled 10 populations separated by 95 m to 9.6 km. Of five microsatellite loci developed for a study of R. sylvatica in North Dakota, only three were polymorphic in the Itasca sample. We found some evidence for statistically significant differences among populations, with the greatest magnitude estimates of FST derived from comparisons involving the most isolated populations. The smallest geographic distance associated with a statistically significant genetic difference was 1070 m, but most populations were very similar in allele frequencies, even at distances greater than several kilometers. Small sample sizes and the small number of loci limited the strength of any conclusions regarding fine-scale population structure. Itasca populations were significantly different than populations from Nelson County, North Dakota, a distance of over 200 km, with FST estimated at about twice the largest pairwise estimates among Itasca samples. Even at this distance, however, there were substantial similarities in the overall pattern of allele frequencies at four of the five loci.
Measuring culturable microbial populations and filamentous microbial growth in soil of wheat plots subjected to crop rotation and monoculture.

Crop management practices, including the addition of fertilisers, often lead to different microbial communities in agricultural soils. Soil dilution plates were used to enumerate yeasts, basidiomycetous fungi, general heterotrophic microbes, as well as actinomycetes in soils sampled at three times (winter, spring, early summer) within and between rows of plots planted to a wheat monoculture and wheat-legume rotation. An adapted version of the buried slide technique was used to measure the numbers of filamentous microbes in the soil. Seasonal changes (July - November) were evident in all measured microbial populations in both plots sampled. Whereas most microbe populations showed similar or declining numbers from winter (July) to spring (September), gen-eral heterotrophic counts increased slightly in the monoculture plot, while filamentous growth increased within crop rows in the monoculture plot. Biolog EcoPlatesTM were used to give an indication of spatio-temporal changes in the soil bacterial metabolic profile. A seasonal shift occurred in the ability of the bacterial community to assimilate carbon sources with more organic acids utilised in November than in July. Fungi, capable of anaerobic growth, occurred more abundantly in the soil of the monoculture plot. This study indicated the efficacy of using simple culture methods, in combination with the buried slide method, to detect fine-scale and short-term temporal changes in the abundance and metabolic activity of important microbial populations in soils subjected to different agronomic practices.
Histochemical studies in the leaves of some Dioscorea L. (Dioscoreaceae) and the taxonomic importance

Histochemical studies on the localization of calcium oxalate crystals and other ergastic substances in the leaf of ten species of Dioscorea L. (Discoreaceae) were carried out. There are clear variations both in the positions and shapes (types) of calcium oxalate crystals and other ergastic substances found in the leaf of these Dioscorea species. D. rotundata POIR. have highly elongated, missile-like raphides in addition to their calcium oxalate crystals. D. minutiflora ENGL. is diagnostic in possessing raphide even at the base of the trichome whereas D. odoratissima PAX has ‘needle-like’ raphide in addition to crystals. ‘Barrel-shaped’ raphide bundles were localized in the leaf of D. smilacifolia DEWILD. and D. minutiflora. In the same vein, D. esculenta (LOUR.) BURKILL, and D. bulbifera L. have crystals and raphides even inside the chloroplasts. Apart from the crystals and raphides, most of these Dioscorea species are also taninferous as can be seen in the leaves of D. preussii PAX, D. rotundata, D. esculenta and D. bulbifera. The presence of raphides and crystals at the base of trichome and inside chloroplasts are being reported for the first time in these taxa. Moreover, variation in the localization of the crystals and the raphides in different parts of the leaf suggests other role of these ergastic substances in the taxa other than storage.
Decomposing diversity patterns of a soft-bottom macroinvertebrate community in the tropical eastern Pacific

Diversity is one of the most frequently used attributes of ecological communities, and there is a long-standing discussion about their adequate use, calculus and interpretation. One of the most conspicuous and simple diversity estimators is species richness, but it has been criticized by recurrent pitfalls, which has biased comparisons and the testing of hypotheses. Otherwise, synthetic ecological indices of diversity are difficult to interpret due to the underlying complex or cryptic concepts. Most of the studies in soft-bottom macroinvertebrate communities trying to estimate species richness, have actually quantified species diversity as species density; the number of species per unit area. In the present study, the diversity of a tropical Pacific soft bottom community is analytically decomposed using two null models to assess species richness and evenness, and the slope of species–area curves to estimate species density. A declining trend of species richness was observed along a 2-year period and could be related to the cumulative effects of interannual environmental variability and fishing disturbance. The species–area relationship could be considered a good indicator of spatial heterogeneity, specifically to illustrate the depth gradient. Local abundance was negatively correlated with evenness, showing that high-density communities are the result of increases in abundance of a few dominant species. Here we demonstrate that seasonality, depth and abundance could explain diversity in soft-bottom macroinvertebrate communities of coastal waters and propose a robust procedure to survey diversity as a part of monitoring programmes of coastal management.
Expected future performance of salmon abundance forecast models with varying complexity

We evaluated the scope for improving abundance forecasts for fishery management using Sacramento River fall Chinook salmon (Oncorhynchus tshawytscha) as a case study. A range of forecast models that related the Sacramento Index (SI; an index of adult ocean abundance) to jack (estimated age 2) spawning escapement the previous year were considered. Alternative models incorporated effects of density dependence, local environmental conditions, the abundance of the previous cohort, and trends or autocorrelation in the jack-to-SI relationship. Forecast performance was assessed in terms of bias, accuracy, ability to track trends in the SI, and management objectives. Several models achieved higher accuracy than the model used for management, but no single model performed best across all criteria, and substantial forecast error remained across all approaches considered. Environmental models generally performed better than the management model, but there were differences in the relative importance of individual env.
In‐situ remediation of contaminated farmland by horizontal transfer of degradative plasmids among rhizosphere bacteria

Horizontal transfer of catabolic genes for pollutant degradation among rhizobacteria plays an important role in environmental bioremediation, but lacks support from field trial data. To address this problem, Pseudomonas fluorescens strain TP13 was inoculated into the soils of a phenol‐contaminated farmland on which tomato seedlings were growing in April 2009, 2010, 2011 and 2012. Results consistently showed that introduction of TP13 strain significantly reduced phenol content and increased plant biomass after 20 days, compared with controls. Strain TP13 was able to colonize the plant rhizosphere and the number of rhizosphere bacteria which were grown on phenol and contained the plasmids containing the gene encoding for catechol 2, 3‐dioxygenase (C23O) increased gradually in the later stages of the experiment. The increase in magnitude of the plasmid‐containing rhizosphere bacteria correlated well with plant biomass, while the number of plasmid‐containing rhizosphere bacteria and phenol content was strongly negatively correlated. Furthermore, six strains (T1‐T6) of rhizosphere bacteria were isolated and found to possess large plasmids containing identical C23O genes and similar HindIII restriction patterns. Sequence alignment showed that the C23O genes from strains T1‐T6 contained almost identical sequences and the sequence of the C23O of strain T1 was the same as that of strain TP13. These data indicated that the plasmids were transferred from strain TP13 to these rhizosphere bacteria and that horizontal gene transfer stimulated phenol degradation and plant growth in the contaminated farmland. This is an important finding for in situ remediation of contaminated farmland.
Effects of conjugated linolenic acid and conjugated linoleic acid on lipid metabolism in mice.

The effects of two isomers of conjugated linolenic acid (CLnA), α-eleostearic acid (α-ESA) and punicic acid (PA), on body fat and lipid metabolism were investigated, compared with a conjugated linoleic acid (CLA) mixture (primarily cis9,trans11- and trans10,cis12-18:2) and α-linolenic acid (ALA), a non-conjugated octadecatrienoic acid, in the present study. ICR mice were fed either a control diet or one of four experimental diets supplemented with 1 % α-ESA, 1 % PA, 1 % CLA mixture and 1 % ALA in the form of triacylglycerols (TAG) for 6 weeks. The weights of perirenal and epididymal adipose tissues were significantly decreased while the liver weight was significantly increased in mice fed CLA, compared with the control. In contrast to CLA, the tissue weights in α―ESA-, PA- and ALA-fed mice were not affected. No significant differences were observed in TAG, total cholesterol, high-density lipoprotein and low-density lipoprotein cholesterol levels among the five groups. The liver TAG level was significantly decreased in mice fed α-ESA and PA while it was significantly increased in mice fed the CLA mixture. These results indicate that CLnA and CLA have differential effects on body fat mass and liver TAG levels in mice.
Isolation and identification of an effective fibrinolytic strain Bacillus subtilis FR-33 from the Chinese doufuru and primary analysis of its fibrinolytic enzyme

Fibrinolytic microorganisms were screened from the Chinese soy cheese doufuru as well as Japanese natto and Chinese douchi. Initially, 16 isolates with fibrinolytic activity were selected based on activity and cultural characteristics for further characterization. An exponential standard curve, covering 39 to 2500 IU/mL of urokinase activity, was well established with urokinase through the fibrin plate method. With fermentation and preliminary purification, the fibrinolytic activities of the crude enzymes of these isolates were estimated to range across 142 to 1833 IU/mL of urokinase through the standard curve using the thrombolytic area on the fibrin plate. The strain FR-33 from doufuru was chosen based on the maximum activity 1833 IU/mL and better reproducibility. Further purification of its crude enzyme through Sephadex G-50 gel filtration increased the enzyme activity to 2474 IU/mL, and the SDS-PAGE performance indicated that its molecular weight is approximately 30 kDa. The 16S rDNA of the isolate FR-33 was sequenced and analyzed, and the strain was identified as Bacillus subtilis based on the sequence combined with morphological, cultural, physiological and biochemical characteristics. However, in contrast to the typical B. subtilis, the strain FR-33 could grow in 9 and 12% NaCl, but could not secret pyruvate dehydrogenase and urease, nor ferment lactose, sucrose and maltose. The crude enzyme of the isolate showed stronger activity than those reported from natto and douchi, and this makes it an attractive agent as a biomaterial for health-producing foods.
EVOLUTION OF THE MATING SEASON IN THE PITVIPERS OF NORTH AMERICA

Abstract In the majority of temperate zone snakes, the mating season is temporally dissociated from the time of fertilization. Similarly, in males, the mating season is often temporally dissociated from spermatogenesis. In temperate zone pitvipers of North America, estrus, the time when females signal that they are receptive to males, occurs at some time during vitellogenesis. In these pitvipers, vitellogenesis is initiated in the late summer or fall. The vitellogenic follicles overwinter at an intermediate size, resume development in the spring, and culminate with ovulation in the spring. The seasonal patterns of estrus (late summer/fall or spring or both seasons) vary among species and rarely among populations within a species. In our model, we assume (i) that females determine the mating season, (ii) that there are significant costs to females during estrus, and (iii) that males adapt their mating season to the combined time when females enter estrus. We propose that the vitellogenic cycle of temperate zone pitvipers is simply a modification of the vitellogenic cycle seen in tropical pitvipers. The major difference being the interruption of vitellogenesis in temperate species by cold temperatures. In tropical pitvipers the vitellogenic cycle is continuous (no winter pause) and the mating season occurs at some time during vitellogenesis. As populations of pitvipers evolved into temperate climates, due to range expansion into temperate regions or climate change in existing ranges, the seasonal vitellogenic cycle was interrupted by winter. Since the mating season occurs during vitellogenesis, having a summer/fall and spring mating season is consistent with the tropical pattern. The different mating patterns we see today reflect a loss of either the summer/fall or the spring mating season. The reason for the loss may be due to the success of one mating season (all the females being fertilized) and the costs associated with having a redundant mating season. Since males also have significant costs associated with being prepared to mate, the loss of the female mating season would result in a corresponding loss of that season in males.
The Genus Fejervarya (Anura: Ranidae) in Central Western Ghats, India, with Descriptions of Four New Cryptic Species

ABSTRACT We compared six taxa of the genus Fejervarya from central Western Ghats, southwestern India, including F. rufescens, F. sahyadris, and four taxa that possess distinct mtDNA haplotypes as demonstrated by our previous studies. Morphological comparisons with F. brevipalmata, F. keralensis, F. nilagirica, and F. syhadrensis on the basis of literature descriptions and museum specimens revealed that the four haplotypes do not correspond to any of the previously described species. Therefore, they are named herein as new species. Although each of these new species was separated clearly by discriminant analyses, two large-bodied species, as well as two small-bodied species, occurring sympatrically or parapatrically in many collecting sites, were very similar to each other in external appearance. Acoustic characteristics available for five of the six species were most conspicuous and diagnostic features. This study revealed the occurrence of active speciation in Fejervarya in the Western Ghats, one of the hot spots of biodiversity in the world.
Genetic analysis of physical grain quality characters in sorghum

Sorghum is grown the world over for both human and animal consumption. Recently, the increase in grain production has slowed; simultaneously, its marketability has declined. Grain size is one of the most important determinants of grain yield and market price in India. One important factor responsible for the decline in consumption of sorghum in India is the inferior quality of rainy season produce. Consumers prefer post rainy season sorghums as the grains are bold, round and lustrous in appearance. Any improvement in the quality of rainy season sorghum grain would help it to fetch higher market prices. In the present study, the genetics of important grain quality characteristics such as grain size, grain shape and lustre were studied using two crosses based on elite sorghum lines 463B and AKMS 14B, and a germplasm line, IS 17600, during 2001 at the National Research Centre for Sorghum, Hyderabad, India. Generation mean analysis and frequency distribution studies revealed that grain size is governed by dominant genes that are polygenic in nature. Predominance of dominance and epistatic interactions in both crosses indicates that selection for higher grain size would be more effective if the dominance and epistatic effects are first reduced by a few generations of selfing. Biparental mating is suggested for developing homozygous bold grain lines. Round grain shape is governed by a single dominant gene and grain lustre by two complementary recessive genes. The study suggested that developing a sorghum hybrid with bold, round grain is feasible provided either of the parents has bold and/or round grain. However, for the hybrid to be lustrous, both parents need to be lustrous and homozygous for the alleles conferring grain lustre at a common locus. With the possibility of development of sorghum hybrids with bold, round and lustrous grain, there is scope for improvement in consumer preference of rainy season sorghum grain.
Upshot of the ripening time on biological activities, phenol content and fatty acid composition of Tunisian Opuntia ficus-indica fruit

−1 DW) with a stronger antioxidant activity. Bianca fruit collected in August exhibited a lower phenolic content (3.13 mg GAE g −1 DW) together with the stronger antiradical activity (96.14%). The advantage of this ecotype was more discernible as compared to positive controls butylated hydroxytoluene (BHT, 79.75%). Likewise, CpG chromatogram identification revealed also an important difference between the ecotypes on oleic and linoleic acids.