Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies

Background

The sinorhizobia are amongst the most well studied members of nitrogen-fixing root nodule bacteria and contribute substantial amounts of fixed nitrogen to the biosphere. While the alfalfa symbiont Sinorhizobium meliloti RM 1021 was one of the first rhizobial strains to be completely sequenced, little information is available about the genomes of this large and diverse species group.

Results

Here we report the draft assembly and annotation of 48 strains of Sinorhizobium comprising five genospecies. While S. meliloti and S. medicae are taxonomically related, they displayed different nodulation patterns on diverse Medicago host plants, and have differences in gene content, including those involved in conjugation and organic sulfur utilization. Genes involved in Nod factor and polysaccharide biosynthesis, denitrification and type III, IV, and VI secretion systems also vary within and between species. Symbiotic phenotyping and mutational analyses indicated that some type IV secretion genes are symbiosis-related and involved in nitrogen fixation efficiency. Moreover, there is a correlation between the presence of type IV secretion systems, heme biosynthesis and microaerobic denitrification genes, and symbiotic efficiency.

Conclusions

Our results suggest that each Sinorhizobium strain uses a slightly different strategy to obtain maximum compatibility with a host plant. This large genome data set provides useful information to better understand the functional features of five Sinorhizobium species, especially compatibility in legume-Sinorhizobium interactions. The diversity of genes present in the accessory genomes of members of this genus indicates that each bacterium has adopted slightly different strategies to interact with diverse plant genera and soil environments.     

Clostridium difficile 027/BI/NAP1 Encodes a Hypertoxic and Antigenically Variable Form of TcdB

The Clostridium difficile exotoxin, TcdB, which is a major virulence factor, varies between strains of this pathogen. Herein, we show that TcdB from the epidemic BI/NAP1/027 strain of C. difficile is more lethal, causes more extensive brain hemorrhage, and is antigenically variable from TcdB produced by previously studied strains of this pathogen (TcdB₀₀₃). In mouse intoxication assays, TcdB from a ribotype 027 strain (TcdB₀₂₇) was at least four fold more lethal than TcdB₀₀₃. TcdB₀₂₇ caused a previously undescribed brain hemorrhage in mice and this correlated with a heightened sensitivity of brain microvascular endothelial cells to the toxin. TcdB₀₀₃ and TcdB₀₂₇ also differed in their antigenic profiles and did not share cross-neutralizing epitopes in a major immunogenic region of the protein. Solid phase humoral mapping of epitopes in the carboxy-terminal domains (CTD) of TcdB₀₂₇ and TcdB₀₀₃ identified 11 reactive epitopes that varied between the two forms of TcdB, and 13 epitopes that were shared or overlapping. Despite the epitope differences and absence of neutralizing epitopes in the CTD of TcdB₀₂₇, a toxoid form of this toxin primed a strong protective response. These findings indicate TcdB₀₂₇ is a more potent toxin than TcdB₀₀₃ as measured by lethality assays and pathology, moreover the sequence differences between the two forms of TcdB alter antigenic epitopes and reduce cross-neutralization by antibodies targeting the CTD.     

Unusual Secondary Metabolites from Astragalus halicacabus Lam.

From the whole plant of Astragalus halicacabus (Sect. Halicacabus), a new cycloartane‐type glycoside, (20R,24S)‐3‐O‐[α‐L ‐arabinopyranosyl‐(1→2)‐β‐D ‐xylopyranosyl]‐20,24‐epoxy‐16‐O‐β‐D ‐glucopyranosyl‐3β,6α,16β,25‐tetrahydroxycycloartane, and a new glycoside, 3‐O‐[β‐D ‐apiofuranosyl‐(1→2)‐β‐D ‐glucopyranosyl]maltol were isolated together with seven known cycloartane‐type glycosides, i.e., cyclocanthoside D, askendosides D, F, and G, cyclosieversioside G, cyclostipuloside A, elongatoside, and a known maltol glucoside, 3‐O‐β‐D ‐glucopyranosylmaltol. The structures were elucidated by means of high‐resolution mass spectrometry, and extensive 1D‐ and 2D‐NMR spectroscopic analysis. This is the first phytochemical work on A. halicacabus, and a maltol glycoside was encountered for the first time in the Leguminosae family.     

The Dot and Line Method: A Long Range Correction to Coulomb Interaction in a Cylindrical Pore

The charge line (CL) method had been used in the past to represent the periodic charges in Monte Carlo simulations of ions in a cylindrical pore. In this method, there exists a possible singularity when the edge of the image line overlaps with an ion in the central cylinder. This singularity is more problematic for molecular dynamics when the force is evaluated. Molecular dynamics simulations with the CL method have not been reported in the literature. By replacing the first section of the image charge line with an image point, we show that the CL method can be improved and be applicable in the molecular dynamics simulation of electrolytes in a cylindrical geometry. The modified method is demonstrated to be effective by simulations of a high packing primitive model electrolyte, representing the state of a molten salt.     

Identification of benzofuran central cores for the inhibition of leukotriene A4 hydrolase

Leukotrienes (LT’s) are known to play a physiological role in inflammatory immune response. Leukotriene A₄ hydrolase (LTA₄H) is a cystolic enzyme that stereospecifically catalyzes the transformation of LTA₄ to LTB₄. LTB₄ is a known pro-inflammatory mediator. This paper describes the identification and synthesis of substituted benzofurans as LTH₄H inhibitors. The benzofuran series demonstrated reduced mouse and human whole blood LTB₄ levels in vitro and led to the identification one analog for advanced profiling. Benzofuran 28 showed dose responsive target engagement and provides a useful tool to explore a LTA₄H inhibitor for the treatment of inflammatory diseases, such as asthma and inflammatory bowel disease (IBD).     

Neuromechanical control of the forearm muscles during gripping with sudden flexion and extension wrist perturbations

The purpose of this study was to investigate how gripping modulates forearm muscle co-contraction prior to and during sudden wrist perturbations. Ten males performed a sub-maximal gripping task (no grip, 5% and 10% of maximum) while a perturbation forced wrist flexion or extension. Wrist joint angles and activity from 11 muscles were used to determine forearm co-contraction and muscle contributions to wrist joint stiffness. Co-contraction increased in all pairs as grip force increased (from no grip to 10% grip), corresponding to a 36% increase in overall wrist joint stiffness. Inclusion of individual muscle contributions to wrist joint stiffness enhanced the understanding of forearm co-contraction. The extensor carpi radialis longus (ECRL) and brevis had the largest stiffness contributions (34.5 ± 1.3% and 20.5 ± 2.3%, respectively), yet muscle pairs including ECRL produced the lowest co-contraction. The muscles contributing most to wrist stiffness were consistent across conditions (ECRL for extensors; Flexor Digitorum Superficialis for flexors), suggesting enhanced contributions rather than muscular redistribution. This work provides investigation of the neuromuscular response to wrist perturbations and gripping demands by considering both co-contraction and muscle contributions to joint stiffness. Individual muscle stiffness contributions can be used to enhance the understanding of forearm muscle control during complex tasks.     

Identification of Chromosomal Errors in Human Preimplantation Embryos with Oligonucleotide DNA Microarray

A previous study comparing the performance of different platforms for DNA microarray found that the oligonucleotide (oligo) microarray platform containing 385K isothermal probes had the best performance when evaluating dosage sensitivity, precision, specificity, sensitivity and copy number variations border definition. Although oligo microarray platform has been used in some research fields and clinics, it has not been used for aneuploidy screening in human embryos. The present study was designed to use this new microarray platform for preimplantation genetic screening in the human. A total of 383 blastocysts from 72 infertility patients with either advanced maternal age or with previous miscarriage were analyzed after biopsy and microarray. Euploid blastocysts were transferred to patients and clinical pregnancy and implantation rates were measured. Chromosomes in some aneuploid blastocysts were further analyzed by fluorescence in-situ hybridization (FISH) to evaluate accuracy of the results. We found that most (58.1%) of the blastocysts had chromosomal abnormalities that included single or multiple gains and/or losses of chromosome(s), partial chromosome deletions and/or duplications in both euploid and aneuploid embryos. Transfer of normal euploid blastocysts in 34 cycles resulted in 58.8% clinical pregnancy and 54.4% implantation rates. Examination of abnormal blastocysts by FISH showed that all embryos had matching results comparing microarray and FISH analysis. The present study indicates that oligo microarray conducted with a higher resolution and a greater number of probes is able to detect not only aneuploidy, but also minor chromosomal abnormalities, such as partial chromosome deletion and/or duplication in human embryos. Preimplantation genetic screening of the aneuploidy by DNA microarray is an advanced technology used to select embryos for transfer and improved embryo implantation can be obtained after transfer of the screened normal embryos.     

Assessment of Global and Regional Diffusion Changes along White Matter Tracts in Parkinsonian Disorders by MR Tractography

Purpose

The aim of the study was to determine the usefulness of diffusion tensor tractography (DTT) in parkinsonian disorders using a recently developed method for normalization of diffusion data and tract size along white matter tracts. Furthermore, the use of DTT in selected white matter tracts for differential diagnosis was assessed.

Methods

We quantified global and regional diffusion parameters in major white matter tracts in patients with multiple system atrophy (MSA), progressive nuclear palsy (PSP), idiopathic Parkinson’s disease (IPD) and healthy controls). Diffusion tensor imaging data sets with whole brain coverage were acquired at 3 T using 48 diffusion encoding directions and a voxel size of 2×2×2 mm³. DTT of the corpus callosum (CC), cingulum (CG), corticospinal tract (CST) and middle cerebellar peduncles (MCP) was performed using multiple regions of interest. Regional evaluation comprised projection of fractional anisotropy (FA), mean diffusivity (MD), radial diffusivity (RD) and the apparent area coefficient (AAC) onto a calculated mean tract and extraction of their values along each structure.

Results

There were significant changes of global DTT parameters in the CST (MSA and PSP), CC (PSP) and CG (PSP). Consistent tract-specific variations in DTT parameters could be seen along each tract in the different patient groups and controls. Regional analysis demonstrated significant changes in the anterior CC (MD, RD and FA), CST (MD) and CG (AAC) of patients with PSP compared to controls. Increased MD in CC and CST, as well as decreased AAC in CG, was correlated with a diagnosis of PSP compared to IPD.

Conclusions

DTT can be used for demonstrating disease-specific regional white matter changes in parkinsonian disorders. The anterior portion of the CC was identified as a promising region for detection of neurodegenerative changes in patients with PSP, as well as for differential diagnosis between PSP and IPD.     

An Evaluation of Association between a Novel Hippocampal Biology Related SNP (rs7294919) and Schizophrenia

Recent genetic analyses have implicated several candidate susceptibility variants for schizophrenia. The single nucleotide polymorphism (SNP) rs7294919 is likely a schizophrenia-susceptibility variant according to its significant association with hippocampal volume, hippocampus function, and cognitive performance as well as the nominal association with schizophrenia. However, all previous analyses were conducted only in Europeans, and whether rs7294919 is associated with schizophrenia in other populations are yet to be tested. Here, we conducted a case-control analysis of rs7294919 with schizophrenia in six independent Chinese (N = 3) and Japanese (N = 3) samples, including a total of 7,352 cases and 10,824 controls. The results of our association analysis were not able to confirm the association of rs7294919 with schizophrenia (p = 0.51 in total samples, odds ratio = 1.02 for allele[C]). The absence of rs7294919’s association in Chinese and Japanese suggest a potential genetic heterogeneity in the susceptibility of schizophrenia on this locus and also demonstrate the difficulties in replicating associations of schizophrenia across different ethnic populations.