200 research outputs found
Investigation of the domestication of common bean (Phaseolus vulgaris) using multilocus sequence data
No full textMultilocus sequence data collected from domesticated and related wild relatives provides a rich source of information on the effect of human selection on the diversity and adaptability of a species to complex environments. To evaluate the domestication history of common bean (Phaseolus vulgaris L.), multilocus sequence data from landraces representing the various races within the Middle American (MA) and Andean gene pools was evaluated. Across 13 loci, nucleotide diversity was similar between landraces and wild germplasm in both gene pools. The diversity data were evaluated using the approximate Bayesian computation approach to test multiple domestication models and estimate population demographic parameters. A model with a single domestication event coupled with bidirectional migration between wild and domesticated genotypes fitted the data better than models consisting of two or three domestication events in each genepool. The effective bottleneck population size was ~50% of the base population in each genepool. The bottleneck began ~8200 and ~8500 years before present and ended at ~6300 and ~7000 years before present in MA and Andean gene pools respectively. Linkage disequilibrium decayed to a greater extent in the MA genepool. Given the (1) geographical adaptation bottleneck in each wild gene pool, (2) a subsequent domestication bottleneck within each gene pool, (3) differentiation into gene-pool specific races and (4) variable extents of linkage disequilibrium, association mapping experiments for common bean would more appropriately be performed within each genepool.</jats:p
Syntenic relationships among legumes revealed using a gene-based genetic linkage map of common bean (Phaseolus vulgaris L.)
No full textMolecular linkage maps are an important tool for gene discovery and cloning, crop improvement, further genetic studies, studies on diversity and evolutionary history, and cross-species comparisons. Linkage maps differ in both the type of marker and type of population used. In this study, gene-based markers were used for mapping in a recombinant inbred (RI) population of Phaseolus vulgaris L. P. vulgaris, common dry bean, is an important food source, economic product, and model organism for the legumes. Gene-based markers were developed that corresponded to genes controlling mutant phenotypes in Arabidopsis thaliana, genes undergoing selection during domestication in maize, and genes that function in a biochemical pathway in A. thaliana. Sequence information, including introns and 3’ UTR, was generated for over 550 genes in the two genotypes of P. vulgaris. Over 1,800 single nucleotide polymorphisms and indels were found, 300 of which were screened in the RI population. The resulting LOD 2.0 map is 1,545 cM in length and consists of 275 gene-based and previously mapped core markers. An additional 53 markers that mapped at LOD <1.0 were placed in genetic bins. By screening the parents of other mapping populations, it was determined that the markers were useful for other common Mesoamerican x Andean mapping populations. The location of the mapped genes relative to their homologs in Arabidopsis thaliana (At), Medicago truncatula (Mt), and Lotus japonicus (Lj) were determine by using a tblastx analysis with the current pseduochromosome builds for each of the species. While only short blocks of synteny were observed with At, large-scale macrosyntenic blocks were observed with Mt and Lj. By using Mt and Lj as bridging species, the syntenic relationship between the common bean and peanut was inferred
Signaling crosstalk between TGFβ and Dishevelled/Par1b
No full textCrosstalk of signaling pathways is critical during metazoan development and adult tissue homeostasis. Even though the transforming growth factor-beta (TGF beta) transduction cascade is rather simple, in vivo responsiveness to TGF beta ligands is tightly regulated at several steps. As such, TGF beta represents a paradigm for how the activity of one signaling system is modulated by others. Here, we report an unsuspected regulatory step involving Dishevelled (Dvl) and Par1b (also known as MARK2). Dvl and Par1b cooperate to enable TGF beta/bone morphogenetic protein (BMP) signaling in Xenopus mesoderm development and TGF beta responsiveness in mammalian cells. Mechanistically, the assembly of the Par1b/Dvl3/Smad4 complex is fostered by Wnt5a. The association of Smad4 to Dvl/Par1 prevents its inhibitory ubiquitination by ectodermin (also known as transcriptional intermediary factor 1 gamma or tripartite motif protein 33). We propose that this crosstalk is relevant to coordinate TGF beta responses with Wnt-noncanonical and polarity pathways. Cell Death and Differentiation (2012) 19, 1689-1697; doi:10.1038/cdd.2012.50; published online 11 May 201
DOMESTICATION HISTORY IN COMMON BEAN (PHASEOLUS VULGARIS L.): INFERENCES FROM MULTILOCI SEQUENCE DATA
No full textINVESTIGATION OF THE DOMESTICATION PROCESS IN COMMON BEAN (PHASEOLUS VULGARIS L.) USING MULTILOCI SEQUENCE DATA
No full textEfficacy of certain yogic and naturopathic procedures in premature ejaculation: A pilot study
No full textContext: Premature ejaculation (PE) is the most common sexual disorder of young males. Even though there are number of treatment options available for PE, patient′s satisfaction and drug side effects remain to be a problem. Non-pharmacological treatment options like Yoga and Naturopathy have been implicated in sexual fulfillment, pleasure and efficacy of some of these approaches has been established in previous studies.
Aim: To assess the efficacy of certain yogic and naturopathic procedures in the management of PE.
Materials and Methods: A total of 12 patients with PE satisfying the DSM IV TR diagnostic criteria were selected and allotted into two groups, Yoga group and Naturopathic group by following the randomization method. In the Yoga group, various asanas, mudra, bandha and pranayama were practiced 1 hour daily for 21 days. In the Naturopathy group, lower abdomen massage and steam bath, hip bath and lingasnana, mud pack on lower abdomen, and acupressure were done 1 hour daily for 21 days. Criteria of assessment were based on the scoring of Premature Ejaculation Severity Index (PESI). Statistical analysis was done by using paired and unpaired " t" tests.
Results: In the Yoga group ( n = 6), 7.3% relief was observed ( P 0.05) on the total score of PESI. There was no significant difference ( P > 0.05) found in between the two groups.
Conclusion: Both Yoga and Naturopathic procedures didn′t provide relief (<25%) on total score of PESI
USP15 is a deubiquitylating enzyme for receptor-activated SMADs.
No full textThe TGFβ pathway is critical for embryonic development and adult tissue homeostasis. On ligand stimulation, TGFβ and BMP receptors phosphorylate receptor-activated SMADs (R-SMADs), which then associate with SMAD4 to form a transcriptional complex that regulates gene expression through specific DNA recognition. Several ubiquitin ligases serve as inhibitors of R-SMADs, yet no deubiquitylating enzyme (DUB) for these molecules has so far been identified. This has left unexplored the possibility that ubiquitylation of R-SMADs is reversible and engaged in regulating SMAD function, in addition to degradation. Here we identify USP15 as a DUB for R-SMADs. USP15 is required for TGFβ and BMP responses in mammalian cells and Xenopus embryos. At the biochemical level, USP15 primarily opposes R-SMAD monoubiquitylation, which targets the DNA-binding domains of R-SMADs and prevents promoter recognition. As such, USP15 is critical for the occupancy of endogenous target promoters by the SMAD complex. These data identify an additional layer of control by which the ubiquitin system regulates TGFβ biology
Automated Carotid IMT Measurement and Its Validation in Low Contrast Ultrasound Database of 885 Patient Indian Population Epidemiological Study: Results of AtheroEdge® Software
No full textThis chapter demonstrates the usage of an automated computer-based IMT measurement system called CALEX 3.0 (a class of patented AtheroEdge® software) on a low contrast and low-resolution image database acquired during an epidemiological study from India. The overall purpose of this chapter is to show that fully automated methods nowadays have accuracy and reproducibility suitable to epidemiological studies. The image contrast was very low resolution, with pixel density of 12.7 pixels/mm. The accuracy and reproducibility of the AtheroEdge® software system were compared with that of the manual tracings of a vascular surgeon—considered as a gold standard. We automatically measured the IMT value of 885 common carotid arteries in longitudinal B-Mode images. CALEX 3.0 consisted of a stage for the automatic recognition of the carotid artery and an IMT measurement modulus made of a fuzzy K-means classifier. Performance was assessed by measuring the system accuracy and reproducibility against manual tracings by experts. Results were very encouraging: CALEX 3.0 processed all the 885 images of the dataset (100% success). The average automated obtained IMT measurement by CALEX 3.0 was 0.407 ± 0.083 mm compared with 0.429 ± 0.052 mm for the manual tracings, which led to an IMT bias of 0.022 ± 0.081 mm. The IMT measurement accuracy (0.022 mm) was comparable to that obtained on high-resolution images and the reproducibility (0.081 mm) was very low and suitable to clinical application. The Figure-of-Merit defined as the percent agreement between the computer-estimated IMT and manually measured IMT for CALEX 3.0 was 94.7%. CALEX 3.0 had a 100% success in processing low contrast/low-resolution images. CALEX 3.0 is the first technique, which has led to high accuracy and reproducibility on low-resolution images acquired during an epidemiological study. We propose CALEX 3.0 as a generalized framework for IMT measurement on large dataset
Demographic factors shaped diversity in the two gene pools of wild common bean Phaseolus vulgaris L.
No full textFAM/USP9x, a deubiquitinating enzyme essential for TGFbeta signaling, controls Smad4 monoubiquitination.
No full textThe assembly of the Smad complex is critical for TGFbeta signaling, yet the mechanisms that inactivate or empower nuclear Smad complexes are less understood. By means of siRNA screen we identified FAM (USP9x), a deubiquitinase acting as essential and evolutionarily conserved component in TGFbeta and bone morphogenetic protein signaling. Smad4 is monoubiquitinated in lysine 519 in vivo, a modification that inhibits Smad4 by impeding association with phospho-Smad2. FAM reverts this negative modification, re-empowering Smad4 function. FAM opposes the activity of Ectodermin/Tif1gamma (Ecto), a nuclear factor for which we now clarify a prominent role as Smad4 monoubiquitin ligase. Our study points to Smad4 monoubiquitination and deubiquitination as a way for cells to set their TGFbeta responsiveness: loss of FAM disables Smad4-dependent responses in several model systems, with Ecto being epistatic to FAM. This defines a regulative ubiquitination step controlling Smads that is parallel to those impinging on R-Smad phosphorylation
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