bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Sequence-Anchored Linkage Map of the Plant–Parasitic Nematode Meloidogyne hapla Reveals Exceptionally High Genome-Wide Recombination
Authors: Thomas Varghese P , Fudali Sylwia L , Schaff Jennifer E , Liu Qingli , Scholl Elizabeth H , Opperman Charles H , Bird David McK , Williamson Valerie M 
Published: July 2012

Abstract
Root-knot nematodes (Meloidogyne spp.) cause major yield losses to many of the world’s crops, but efforts to understand how these pests recognize and interact with their hosts have been hampered by a lack of genetic resources. Starting with progeny of a cross between inbred strains (VW8 and VW9) of Meloidogyne hapla that differed in host range and behavioral traits, we exploited the novel, facultative meiotic parthenogenic reproductive mode of this species to produce a genetic linkage map. Molecular markers were derived from SNPs identified between the sequenced and annotated VW9 genome and de novo sequence of VW8. Genotypes were assessed in 183 F2 lines. The colinearity of the genetic and physical maps supported the veracity of both. Analysis of local crossover intervals revealed that the average recombination rate is exceptionally high compared with that in other metazoans. In addition, F2 lines are largely homozygous for markers flanking crossover points, and thus resemble recombinant inbred lines. We suggest that the unusually high recombination rate may be an adaptation to generate within-population genetic diversity in this organism. This work presents the most comprehensive linkage map of a parasitic nematode to date and, together with genomic and transcript sequence resources, empowers M. hapla as a tractable model. Alongside the molecular map, these progeny lines can be used for analyses of genome organization and the inheritance of phenotypic traits that have key functions in modulating parasitism, behavior, and survival and for the eventual identification of the responsible genes.
Impact of Sampling Schemes on Demographic Inference: An Empirical Study in Two Species with Different Mating Systems and Demographic Histories
Authors: St. Onge K R , Palmé A E , Wright S I , Lascoux M 
Published: July 2012

AbstractMost species have at least some level of genetic structure. Recent simulation studies have shown that it is important to consider population structure when sampling individuals to infer past population history. The relevance of the results of these computer simulations for empirical studies, however, remains unclear. In the present study, we use DNA sequence datasets collected from two closely related species with very different histories, the selfing species Capsella rubella and its outcrossing relative C. grandiflora, to assess the impact of different sampling strategies on summary statistics and the inference of historical demography. Sampling strategy did not strongly influence the mean values of Tajima’s D in either species, but it had some impact on the variance. The general conclusions about demographic history were comparable across sampling schemes even when resampled data were analyzed with approximate Bayesian computation (ABC). We used simulations to explore the effects of sampling scheme under different demographic models. We conclude that when sequences from modest numbers of loci (&lt;60) are analyzed, the sampling strategy is generally of limited importance. The same is true under intermediate or high levels of gene flow (4Nm &gt; 2–10) in models in which global expansion is combined with either local expansion or hierarchical population structure. Although we observe a less severe effect of sampling than predicted under some earlier simulation models, our results should not be seen as an encouragement to neglect this issue. In general, a good coverage of the natural range, both within and between populations, will be needed to obtain a reliable reconstruction of a species’s demographic history, and in fact, the effect of sampling scheme on polymorphism patterns may itself provide important information about demographic history.
A Noncomplementation Screen for Quantitative Trait Alleles inSaccharomyces cerevisiae
Authors: Kim Hyun Seok , Huh Juyoung , Riles Linda , Reyes Alejandro , Fay Justin C 
Published: July 2012

AbstractBoth linkage and linkage disequilibrium mapping provide well-defined approaches to mapping quantitative trait alleles. However, alleles of small effect are particularly difficult to refine to individual genes and causative mutations. Quantitative noncomplementation provides a means of directly testing individual genes for quantitative trait alleles in a fixed genetic background. Here, we implement a genome-wide noncomplementation screen for quantitative trait alleles that affect colony color or size by using the yeast deletion collection. As proof of principle, we find a previously known allele of CYS4 that affects colony color and a novel allele of CTT1 that affects resistance to hydrogen peroxide. To screen nearly 4700 genes in nine diverse yeast strains, we developed a high-throughput robotic plating assay to quantify colony color and size. Although we found hundreds of candidate alleles, reciprocal hemizygosity analysis of a select subset revealed that many of the candidates were false positives, in part the result of background-dependent haploinsufficiency or second-site mutations within the yeast deletion collection. Our results highlight the difficulty of identifying small-effect alleles but support the use of noncomplementation as a rapid means of identifying quantitative trait alleles of large effect.
Development of a 10,000 Locus Genetic Map of the Sunflower Genome Based on Multiple Crosses
Authors: Bowers John E , Bachlava Eleni , Brunick Robert L , Rieseberg Loren H , Knapp Steven J , Burke John M 
Published: July 2012

AbstractGenetic linkage maps have the potential to facilitate the genetic dissection of complex traits and comparative analyses of genome structure, as well as molecular breeding efforts in species of agronomic importance. Until recently, the majority of such maps was based on relatively low-throughput marker technologies, which limited marker density across the genome. The availability of high-throughput genotyping technologies has, however, made possible the efficient development of high-density genetic maps. Here, we describe the analysis and integration of genotypic data from four sunflower (Helianthus annuus L.) mapping populations to produce a consensus linkage map of the sunflower genome. Although the individual maps (which contained 3500–5500 loci each) were highly colinear, we observed localized variation in recombination rates in several genomic regions. We also observed several gaps up to 26 cM in length that completely lacked mappable markers in individual crosses, presumably due to regions of identity by descent in the mapping parents. Because these regions differed by cross, the consensus map of 10,080 loci contained no such gaps, clearly illustrating the value of simultaneously analyzing multiple mapping populations.
Mutations in the pqe-1 Gene Enhance Transgene Expression in Caenorhabditis elegans
Authors: Yamada Koji , Tsuchiya Jun-ichi , Iino Yuichi 
Published: July 2012

Abstract
Although various genetic tools have been developed and used as transgenes, the expression of the transgenes often is hampered by negative regulators. Disrupting such negative regulators of gene expression is potentially a way to overcome the common problem of low expression of transgenes. To find such regulators whose mutations enhance transgene expression in Caenorhabditis elegans, we took advantage of a newly developed reporter transgene, lin-11pAΔ::venus. This transgene induces expression of a fluorescent protein, Venus, in specific neurons including AIZ, where the expression was stochastic. The frequency of reporter expression in AIZ seemed to be correlated with the strength of transgene expression. By using this system, in which a moderate increase of expression was converted to all-or-none expression states, we describe here a forward genetic screen for mutations that enhance the expression of transgenes. Through the screen, we found that mutations in the pqe-1 gene, which encodes a Q/P-rich nuclear protein with an exonuclease domain, increase the chance of reporter expression in AIZ. The fluorescence intensity in RIC, in which all lin-11pAΔ::venus animals show reporter expression, was increased in pqe-1 mutants, suggesting that pqe-1 reduces the expression level of the transgene. Expression of transgenes with other promoters, 3′UTR, or reporter genes was also enhanced by the pqe-1 mutation, suggesting that the effect was not specific to a particular type of transgenes, whereas the effect did not seem to extend to endogenous genes. We propose that pqe-1 mutants can be used to increase the expression of various useful transgenes.
A Genome-Wide Screen Identifies Genes That Affect Somatic Homolog Pairing inDrosophila
Authors: Bateman Jack R , Larschan Erica , D’Souza Ryan , Marshall Lauren S , Dempsey Kyle E , Johnson Justine E , Mellone Barbara G , Kuroda Mitzi I 
Published: July 2012

AbstractIn Drosophila and other Dipterans, homologous chromosomes are in close contact in virtually all nuclei, a phenomenon known as somatic homolog pairing. Although homolog pairing has been recognized for over a century, relatively little is known about its regulation. We performed a genome-wide RNAi-based screen that monitored the X-specific localization of the male-specific lethal (MSL) complex, and we identified 59 candidate genes whose knockdown via RNAi causes a change in the pattern of MSL staining that is consistent with a disruption of X-chromosomal homolog pairing. Using DNA fluorescent in situ hybridization (FISH), we confirmed that knockdown of 17 of these genes has a dramatic effect on pairing of the 359 bp repeat at the base of the X. Furthermore, dsRNAs targeting Pr-set7, which encodes an H4K20 methyltransferase, cause a modest disruption in somatic homolog pairing. Consistent with our results in cultured cells, a classical mutation in one of the strongest candidate genes, pebble (pbl), causes a decrease in somatic homolog pairing in developing embryos. Interestingly, many of the genes identified by our screen have known roles in diverse cell-cycle events, suggesting an important link between somatic homolog pairing and the choreography of chromosomes during the cell cycle.
Impact of Loci Nature on Estimating Recombination and Mutation Rates in Chlamydia trachomatis
Authors: Ferreira Rita , Borges Vítor , Nunes Alexandra , Nogueira Paulo Jorge , Borrego Maria José , Gomes João Paulo 
Published: July 2012

Abstract
The knowledge of the frequency and relative weight of mutation and recombination events in evolution is essential for understanding how microorganisms reach fitted phenotypes. Traditionally, these evolutionary parameters have been inferred by using data from multilocus sequence typing (MLST), which is known to have yielded conflicting results. In the near future, these estimations will certainly be performed by computational analyses of full-genome sequences. However, it is not known whether this approach will yield accurate results as bacterial genomes exhibit heterogeneous representation of loci categories, and it is not clear how loci nature impacts such estimations. Therefore, we assessed how mutation and recombination inferences are shaped by loci with different genetic features, using the bacterium Chlamydia trachomatis as the study model. We found that loci assigning a high number of alleles and positively selected genes yielded nonconvergent estimates and incongruent phylogenies and thus are more prone to confound algorithms. Unexpectedly, for the model under evaluation, housekeeping genes and noncoding regions shaped estimations in a similar manner, which points to a nonrandom role of the latter in C. trachomatis evolution. Although the present results relate to a specific bacterium, we speculate that microbe-specific genomic architectures (such as coding capacity, polymorphism dispersion, and fraction of positively selected loci) may differentially buffer the effect of the confounding factors when estimating recombination and mutation rates and, thus, influence the accuracy of using full-genome sequences for such purpose. This putative bias associated with in silico inferences should be taken into account when discussing the results obtained by the analyses of full-genome sequences, in which the “one size fits all” approach may not be applicable.
Genetic Variability and Character Association in Some Native Orchid Species (<i>Dendrobium spp.</i>)
Authors: Moniruzzaman M. , Zaman M. A. , Hossain M. Earshad , Bhuiyan M. M. H. , Rahman M. Z. 
Published: July 2012

An experiment was carried out using 20 native Dendrobium orchids in Completely Randomized Design (CRD) with three replications at the Orchidarium of Landscape, Ornamental and Floriculture Division, HRC, BARI, Gazipur during the period January 2007 to June 2007 to estimate genetic variability, genetic parameters and correlation coefficient among different flower components. Highly significant variations were observed among the genotypes for all the characters. High broad sense heritability with high genetic advance was observed in spike length (94.00% and 98.29), rachis length (95.34% and 93.85), flower durability (94.00% and 89.00) and floret number (70.50% and 65.47) indicating additive gene action, suggesting the possibility of improvement of these traits through selection. Other characters exhibited moderate broad sense heritability with low genetic advance. The number of florets per spike recorded a highly significant association with flower durability, rachis length and spike length. Durability of flower had significant positive correlation with rachis length, flower size and spike length at both genotypic and phenotypic level. Highly significant positive correlation was also found between rachis length and spike length. However, the correlation study revealed that selection of parents should be done based on characters such as floret number, rachis length and flower durability which would be useful in a breeding program. The path analysis revealed that rachis length, durability of flower and number of flowers per spike had contributed maximum direct effects on flower yield, indicating the importance of these three characters as selection criteria for native Dendrobium orchid. DOI: http://dx.doi.org/10.3329/agric.v10i1.11058 The Agriculturists 2012; 10(1): 1-9
Effect of Organic Manures on Growth, Rhizome Yield and Quality Attributes of Turmeric (<i>Curcuma longa</i> L.)
Authors: Kamal M. Z. U. , Yousuf M. N. 
Published: July 2012

The investigation was carried out to evaluate the effect of different organic manures on turmeric with reference to vegetative growth, biomass production, rhizome yield and its attributes of turmeric (Curcuma longa L.). Turmeric showed better response to the application of organic manures. Plant with neem cake application had the taller plant (79.30 cm), maximum number of tillers per plant (5.40), leaf number (5.40), leaf area (44.09) leaf area index (0.429), fresh weight of halum ( 190.05g), fresh weight of root (49.13 g), fresh weight of rhizome per plant (256.21 g) and dry weight of halum (15.21g), dry weight of root (7.32 g), dry weight of rhizome per plant (40.35 g), total dry matter yield (6.85 t ha-1) than those received other types of manures. Moreover, yield attributes such as number of mother rhizomes per plant-1 (1.75), more number of primary rhizomes per plant-1 (5.19), secondary rhizomes per plant-1 (18.03) and tertiary rhizomes per plant (7.69) were also highly accelerated by neem cake application. Similarly, the same treatment expressed the best in terms of size of mother rhizome (7.69 cm), primary rhizome (21.86 cm) and secondary rhizomes (7.05 cm).All these parameters in cumulative contributed to produce the highest estimated fresh rhizomes yield & cured rhizomes yield (29.48 t ha-1, 5.59 t ha-1 respectively). The highest curing percentage (20.28) was observed in T3 treatment having mustard cake@ 2.0 t/ha. Thus, organic manure like neem cake was best fitted natural fertilizer for turmeric cultivation.DOI: http://dx.doi.org/10.3329/agric.v10i1.11060The Agriculturists 2012; 10(1): 16-22
Effect of Phosphate Rock on the Growth and Yield of Wheat (<i>Triticum aestivum</i> L.) under Old Brahmaputra Floodplain Soils
Authors: Al Mamun Md. Nurul Huda , Rahman Md. Safinur , Jahangir N. M. , Moula M. Safiqul , Islam Kazi Nazrul 
Published: July 2012

A study was conducted to determine the direct and residual effects of phosphate rock (PR) on the growth and yield of wheat cv. Kanchan during Rabi season of 2004-2005 at the Bangladesh Agricultural University farm, Mymensingh. The experiment was designed with four treatments and was laid out in a Randomized Complete Block Design (RCBD) with four replications. The treatments were: T1: control (0 kg P ha-1), T2: PR (26 kg P ha-1), T3: TSP (26 kg P ha-1), and T4: PR (210 kg P ha-1 applied in previous crop to cover 6 succeeding crops). Dry matter yield at panicle initiation (PI) stage was significantly influenced by the treatments. Effective tillers hill-1 and grains panicles-1 varied significantly with P treatments. The highest grain yield (3.10 t ha-1) and straw yield (5.54 t ha-1) were found in T3 treatment. Economic analysis demonstrated that the highest net benefit of Tk. 24,788 ha-1 was obtained in T3 treatment which was followed by Tk. 22,964 ha-1 and Tk.12,292 ha-1 in T4 and T2, respectively. The highest net benefit was obtained from T3 treatment due to higher grain and straw yields.DOI: http://dx.doi.org/10.3329/agric.v10i1.11062The Agriculturists 2012; 10(1): 31-37
Effects of Garlic Extract, Allamanda Leaf Extract and Provax -200 on Seed Borne Fungi of Rice
Authors: Yeasmin F. , Ashrafuzzaman M. , Hossain I. 
Published: July 2012

Seeds of rice were treated with Garlic (Allium sativum) clove extract @ 1:0, 1:1, 1:2 dilutions in water, allamanda (Allamanda cathartica) leaf extract @ 1:1, 1:2, 1:3 dilutions in water and Provax-200 @ 0.3% for controlling seed borne fungi, where the seed samples of three rice varieties viz. Katharee, Gutee Aus and Kalijira were collected from farmers storages of Bangladesh. The seed germination under control ranged from 64 to 77%, where treatments resulted up to 100% germination. The identified seed borne fungi of rice were Bipolaris oryzae, Curvularia oryzae, Fusarium oxysporum, F. moniliforme, Nigrospora oryzae, Aspergillus flavus, Aspergillus niger and Penicillium sp., where prevalence of Bipolaris oryzae (7.5%) and Fusarium moniliforme (8.3%) were the maximum. All the treatments significantly reduced the seed borne fungi up to 100% over the control, where Provax was found best and was statically similar to garlic (1:1) extract against seed borne pathogen of rice.DOI: http://dx.doi.org/10.3329/agric.v10i1.11064The Agriculturists 2012; 10(1): 46-50
Characterization of Chittagong Aerosol by PCA Modeling
Authors: Begum Bilkis A , Biswas Swapan K , Nasiruddin M 
Published: July 2012

Black carbon and other selected trace elements concentrations in aerosol samples collected at the Continuous Air Monitoring Station (CAMS) in Chittagong, the second largest city in Bangladesh, were investigated for possible source contributions. The particulate matter (PM) sampling was done from end of winter to middle of rainy season (February and July, 2007) using dichotomous sampler. The samples collected in two fractions of <2.5 ?m (fine) and 2.5 to 10 ?m (coarse) were analyzed for elemental concentrations by proton induced X-ray emission (PIXE), hydrogen by proton elastic scattering analysis (PESA), and black carbon by reflectance measurement. The elemental data sets together with black carbon were analyzed by principal component analysis method to identify the possible sources contributing to the mass concentration of coarse and fine particulate matter (FPM) fractions. The best solutions were found to be six and seven factors for coarse and fine fractions respectively, which could explain more than 90% of the variance in the data set. The sources were identified as biomass burning/brick kiln, soil dust, road dust, Zn source, Pb source, motor vehicle, CNG (compressed natural gas) vehicle and sea salt. It was found that in coarse fraction, the sea salt is mixed with Zn source and in fine fraction, the road dust factor is mixed with CNG vehicle source. DOI: http://dx.doi.org/10.3329/jbas.v36i1.10907 Journal of Bangladesh Academy of Sciences, Vol. 36, No. 1, 19-31, 2012
Genetic Polymorphism Based on &beta;-napthyl Acetate in Different Age Group of Gambusia Affinis in Bangladesh
Authors: Ahasan Md Monjurul , Rahman Md Anisur , Uddin AFM Jamal 
Published: July 2012

Genetic polymorphism of esterase isozymes was examined in different developmental stages of Gambusia affinis after staining with ?-napthyl acetate as substrate by 7.5% polyacrylamide gel electrophoresis. Samples were just after birth, seven, 14 days old fry, 21, 28, 35, 42, 49 days old male and female. Altogether three esterase bands named as Est-1, Est-2 and Est-3 were observed. Est-1 was absent in seven samples out of 13, Est-2 was absent only in just after birth, Est-3 was absent in seven different samples out of 13 samples. This result indicates that Est-1 and Est-3 were less active and Est-2 was very active at ? napthyl acetate. DOI: http://dx.doi.org/10.3329/jbas.v36i1.10917 Journal of Bangladesh Academy of Sciences, Vol. 36, No. 1, 39-44, 2012
Some Features &alpha;-T<sub>0</sub> Spaces in Supra Fuzzy Topology
Authors: Hoque MF , Hossain MS , Ali DM 
Published: July 2012

Four concepts of T0 supra fuzzy topological spaces are introduced and studied in this paper. The workers also established some relationships among them and studied some other properties of these spaces. DOI: http://dx.doi.org/10.3329/jbas.v36i1.10921 Journal of Bangladesh Academy of Sciences, Vol. 36, No. 1, 61-69, 2012
Assessment of Radiological Significance of the Wastes Generated from the Triple Super Phosphate (TSP) Fertilizer Factory, Chittagong, Bangladesh
Authors: Samad MA , Ali MI , Paul D , Islam SMA 
Published: July 2012

The activity concentration of 226Ra, 232Th and 40K was determined in solid and liquid samples collected from the TSP Fertilizer Factory, Chittagong, Bangladesh. A total of 18 samples of seven different kinds (including liquid and solid wastes) were collected and analyzed by gamma ray spectrometry technique using a high purity germanium (HPGe) detector of 40% relative efficiency. The analysis of the liquid waste samples showed that the average activity concentrations of 226Ra and 232Th were 6.26 ± 0.63 and 10.01 ± 1.39 Bq/L, respectively and no 40K was detected in any of the liquid samples. In the solid waste samples the average value of activity concentrations of 226Ra, 232Th and 40K were 187.49 ± 4.88, 70.06 ± 11.76 and 655.94 ± 110.24 Bq/kg, respectively. Considering the stored wastes as a part of the ambient environment of the factory, radium equivalent activity, radiation hazard index and external annual effective dose to the worker and public due to these wastes were also calculated and compared with world average values. DOI: http://dx.doi.org/10.3329/jbas.v36i1.10923 Journal of Bangladesh Academy of Sciences, Vol. 36, No. 1, 79-88, 2012