Rapeseed (Brassica napus), an important oilseed crop, has adapted to diverse climate zones and latitudes by forming three main ecotype groups, namely winter, semi-winter, and spring types. However, genetic variations underlying the divergence of these ecotypes are largely unknown. Here, we report the global pattern of genetic polymorphisms in rapeseed determined by resequencing a worldwide collection of 991 germplasm accessions. A total of 5.56 and 5.53 million singlenucleotide polymorphisms (SNPs) as well as 1.86 and 1.92 million InDels were identified by mapping reads to the reference genomes of ''Darmor-bzh'' and ''Tapidor,'' respectively. We generated a map of allelic drift paths that shows splits and mixtures of the main populations, and revealed an asymmetric evolution of the two subgenomes of B. napus by calculating the genetic diversity and linkage disequilibrium parameters. Selective-sweep analysis revealed genetic changes in genes orthologous to those regulating various aspects of plant development and response to stresses. A genome-wide association study identified SNPs in the promoter regions of FLOWERING LOCUS T and FLOWERING LOCUS C orthologs that corresponded to the different rapeseed ecotype groups. Our study provides important insights into the genomic footprints of rapeseed evolution and flowering-time divergence among three ecotype groups, and will facilitate screening of molecular markers for accelerating rapeseed breeding.

Toxoplasma gondii, a significant public health risk, is able to infect almost all warm-blooded animals including humans, and it results in economic losses in production animals. In the last three years, a large number of vaccination experiments have been performed to control T. gondii infection, with the target of limiting the acute infection and reducing or eliminating tissue cysts in the intermediate hosts. In this paper, we summarize the latest results of the veterinary vaccines against T. gondii infection since 2013. Immunization with live-attenuated whole organisms of non-reverting mutants has been shown to induce remarkably potent immune responses associated with control of acute and chronic toxoplasmosis. The non-cyst-forming mutants are promising new tools for the development of veterinary vaccines against T. gondii infection.

This paper analyzes the phase error for a three-dimensional (3D) shape measurement system that utilizes our recently proposed projector defocusing technique. This technique generates seemingly sinusoidal structured patterns by defocusing binary structured patterns and then uses these patterns to perform 3D shape measurement by fringe analysis. However, significant errors may still exist if an object is within a certain depth range, where the defocused fringe patterns retain binary structure. In this research, we experimentally studied a large depth range of defocused fringe patterns, from near-binary to near-sinusoidal, and analyzed the associated phase errors. We established a mathematical phase error function in terms of the wrapped phase and the depth z. Finally, we calibrated and used the mathematical function to compensate for the phase error at arbitrary depth ranges within the calibration volume. Experimental results will be presented to demonstrate the success of this proposed technique. Disciplines Computer-Aided Engineering and Design | Mechanical Engineering CommentsThis article is from Applied Optics 50 (2011) This paper analyzes the phase error for a three-dimensional (3D) shape measurement system that utilizes our recently proposed projector defocusing technique. This technique generates seemingly sinusoidal structured patterns by defocusing binary structured patterns and then uses these patterns to perform 3D shape measurement by fringe analysis. However, significant errors may still exist if an object is within a certain depth range, where the defocused fringe patterns retain binary structure. In this research, we experimentally studied a large depth range of defocused fringe patterns, from near-binary to near-sinusoidal, and analyzed the associated phase errors. We established a mathematical phase error function in terms of the wrapped phase and the depth z. Finally, we calibrated and used the mathematical function to compensate for the phase error at arbitrary depth ranges within the calibration volume. Experimental results will be presented to demonstrate the success of this proposed technique.

Objective To investigate immune responses of peptide-specific CD4+ and CD8+ T cells, and nonpeptide-specific Vγ2Vδ2+ T cells during clinical quiescence of latent Mycobacterium tuberculosis coinfection in HIV-1-infected humans. Methods One hundred HIV-1-infected individuals who had HIV infection only [HIV+tuberculosis−(TB−)], latent Mycobacterium tuberculosis coinfection (HIV + LTB), LTB), or active tuberculosis (HIV + TB) were recruited to measure mycobacterium purified protein derivative (PPD)-specific IFNγ+ CD4+ and CD8+ T cells, and phospho-antigen HMBPP-specific IFNγ+ Vγ2Vδ2+ T cells using enzyme-linked immunospot and intracellular cytokine staining assays. Results Both HIV + TB and HIV + LTB groups had low levels of PPD-specific IFNγ + CD4+ T cells regardless of CD4+ peripheral blood lymphocytes counts. However, numbers of PPD-specific IFNγ +CD8+ T cells in the HIV +LTB group were significantly greater than those in the HIV +TB group. Surprisingly, numbers of phosphoantigen hydroxy-3-methyl-but-2-enyl pyrophosphate-specific IFNγ + Vγ2Vδ2+ T cells in the HIV + LTB group were much greater than those in the HIV + TB group (P < 0.001). This difference was present in the subgroups of HIV + LTB whatever the levels of CD4+ T-cell counts more than 200/μl or less than 200/μl. Numbers of hydroxy-3-methyl-but-2-enyl pyrophosphate-specific IFNγ+ Vγ2Vδ2+ T cells were even five times greater than those of PPD-specific IFNγ+ CD8 T cells within the HIV + LTB group. Conclusion Potent immune responses of hydroxy-3-methyl-but-2-enyl pyrophosphate-specific IFNγ+ Vγ2Vδ2+ T cells and PPD-specific IFNγ+ CD8+ T cells were detected in HIV + LTB persons but not HIV + TB patients. The robust immune responses of Vγ2Vδ2+ and CD8+ T effector cells were associated with the latent stage of Mycobacterium tuberculosis coinfection in HIV-1-infected humans.

Background: An accurate test for Mycobacterium tuberculosis infection is urgently needed in immunosuppressed populations. The aim of this study was to investigate the diagnostic power of enzymelinked immunospot (ELISPOT)-based IFN-γ release assay in detecting active and latent tuberculosis in HIVinfected population in bacillus Calmette-Guerin (BCG)-vaccinated area. A total of 100 HIV-infected individuals including 32 active tuberculosis patients were recruited. An ELISPOT-based IFN-γ release assay, T-SPOT.TB, was used to evaluate the M. tuberculosis ESAT-6 and CFP-10 specific IFN-γ response. Tuberculin skin test (TST) was performed for all recruited subjects.

Microbiome research is a quickly developing field in biomedical research, and we have witnessed its potential in understanding the physiology, metabolism and immunology, its critical role in understanding the health and disease of the host, and its vast capacity in disease prediction, intervention and treatment. However, many of the fundamental questions still need to be addressed, including the shaping forces of microbial diversity between individuals and across time. Microbiome research falls into the classical nature vs. nurture scenario, such that host genetics shape part of the microbiome, while environmental influences change the original course of microbiome development. In this review, we focus on the nature, i.e., the genetic part of the equation, and summarize the recent efforts in understanding which parts of the genome, especially the human and mouse genome, play important roles in determining the composition and functions of microbial communities, primarily in the gut but also on the skin. We aim to present an overview of different approaches in studying the intricate relationships between host genetic variations and microbes, its underlying philosophy and methodology, and we aim to highlight a few key discoveries along this exploration, as well as current pitfalls. More evidence and results will surely appear in upcoming studies, and the accumulating knowledge will lead to a deeper understanding of what we could finally term a “hologenome”, that is, the organized, closely interacting genome of the host and the microbiome.

BackgroundToxoplasma gondii is an obligate intracellular parasite which can infect almost all mammalian animals, leading to toxoplasmosis. T. gondii rhoptry protein 38 (TgROP38) is an active rhoptry protein kinase which is involved in the inhibitory effect on host cell transcription by down-regulating the MAPK signaling track.MethodsTgROP38 gene was amplified and inserted into eukaryotic vector pVAX I and formed the DNA vaccine pVAX-ROP38. Mice in the experimental group were intramuscularly immunized with pVAX-ROP38 and those injected with pVAX I, PBS or nothing were treated as controls. After three injections at two week intervals, all mouse groups were challenged intraperitoneally with 1000 tachyzoites of the virulent T. gondii RH strain (Type I, ToxoDB #10) and 10 cysts of the PRU strain (Type II, ToxoDB #1), respectively.ResultsMice inoculated with pVAX-ROP38 vaccine had a higher level of IgG antibodies (P < 0.01) and T lymphoproliferative response. The high ratio of IgG2a/IgG1 and the increasing levels of IFN-γ and IL-2 (P < 0.05) indicated an activated Th1 cell-mediated immune responses. Furthermore, the CD4+ and CD8+ proportions in vaccinated mice were also increased significantly compared with that in mice of the three control groups (P < 0.01). In the model of acute infection, the average survival time of mice in the pVAX-ROP38 group (8.1 days ± 0.75) was no statistically different compared to that in the PBS, pVAX I and blank control groups which died within 7 days. However, in the model of chronic infection, the brain cyst reduction in the pVAX-ROP38 group reached 76.6%, compared to controls (P < 0.01).ConclusionsThe present study revealed that the pVAX-ROP38 vaccine could elicit strong humoral and cell immunity response against chronic T. gondii infection in mice, resulting in the reduction of the brain cyst formation effectively, which suggests that TgROP38 is a desirable vaccine candidate against chronic T. gondii infection.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2334-14-525) contains supplementary material, which is available to authorized users.

Drought stress results in significant crop yield losses. Comparative transcriptome analysis between tolerant and sensitive species can provide insights into drought tolerance mechanisms in jute. We present a comprehensive study on drought tolerance in two jute species—a drought tolerant species (Corchorus olitorius L., GF) and a drought sensitive species (Corchorus capsularis L., YY). In total, 45,831 non-redundant unigenes with average sequence length of 1421 bp were identified. Higher numbers of differentially expressed genes (DEGs) were discovered in YY (794) than in GF (39), implying that YY was relatively more vulnerable or hyper-responsive to drought stress at the molecular level; the two main pathways, phenylpropanoid biosynthesis and peroxisome pathway, significantly involved in scavenging of reactive oxygen species (ROS) and 14 unigenes in the two pathways presented a significant differential expression in response to increase of superoxide. Our classification analysis showed that 1769 transcription factors can be grouped into 81 families and 948 protein kinases (PKs) into 122 families. In YY, we identified 34 TF DEGs from and 23 PK DEGs, including 19 receptor-like kinases (RLKs). Most of these RLKs were downregulated during drought stress, implying their role as negative regulators of the drought tolerance mechanism in jute.