The molecular basis of host specialization in bean pathovars of Pseudomonas syringae

Biotrophic phytopathogens are typically limited to their adapted host range. In recent decades, investigations have teased apart the general molecular basis of intraspecific variation for innate immunity of plants, typically involving receptor proteins that enable perception of pathogen-associated molecular patterns or avirulence elicitors from the pathogen as triggers for defense induction. However, general consensus concerning evolutionary and molecular factors that alter host range across closely related phytopathogen isolates has been more elusive. Here, through genome comparisons and genetic manipulations, we investigate the underlying mechanisms that structure host range across closely related strains of Pseudomonas syringae isolated from different legume hosts. Although type III secretion-independent virulence factors are conserved across these three strains, we find that the presence of two genes encoding type III effectors (hopC1 and hopM1) and the absence of another (avrB2) potentially contribute to host range differences between pathovars glycinea and phaseolicola. These findings reinforce the idea that a complex genetic basis underlies host range evolution in plant pathogens. This complexity is present even in host-microbe interactions featuring relatively little divergence among both hosts and their adapted pathogens.     

Logistic Bayesian LASSO for identifying association with rare haplotypes and application to age-related macular degeneration

Rare variants have been heralded as key to uncovering "missing heritability" in complex diseases. These variants can now be genotyped using next-generation sequencing technologies; nonetheless, rare haplotypes may also result from combination of common single nucleotide polymorphisms available from genome-wide association studies (GWAS). The National Eye Institute's data on age-related macular degeneration (AMD) is such an example. Studies on AMD had identified potential rare variants; however, due to lack of appropriate statistical tools, effects of individual rare haplotypes were never studied. Here we develop a method for identifying association with rare haplotypes for case-control design. A logistic regression based retrospective likelihood is formulated and is regularized using logistic Bayesian LASSO (LBL). In particular, we penalize the regression coefficients using appropriate priors to weed out unassociated haplotypes, making it possible for the rare associated ones to stand out. We applied LBL to the AMD data and identified common and rare haplotypes in the complement factor H gene, gaining insights into rare variants' contributions to AMD beyond the current literature. This analysis also demonstrates the richness of GWAS data for mapping rare haplotypes-a potential largely unexplored. Additionally, we conducted simulations to investigate the performance of LBL and compare it with Hapassoc. Our results show that LBL is much more powerful in identifying rare associated haplotypes when the false positive rates for both approaches are kept the same.     

Retinoid Binding Properties of Nucleotide Binding Domain 1 of the Stargardt Disease-associated ATP Binding Cassette (ABC) Transporter,ABCA4

The retina-specific ATP binding cassette transporter, ABCA4 protein, is associated with a broad range of inherited macular degenerations, including Stargardt disease, autosomal recessive cone rod dystrophy, and fundus flavimaculatus. In order to understand its role in retinal transport in rod out segment discs, we have investigated the interactions of the soluble domains of ABCA4 with both 11-cis- and all-trans-retinal. Using fluorescence anisotropy-based binding analysis and recombinant polypeptides derived from the amino acid sequences of the four soluble domains of ABCA4, we demonstrated that the nucleotide binding domain 1 (NBD1) specifically bound 11-cis-retinal. Its affinity for all-trans-retinal was markedly reduced. Stargardt disease-associated mutations in this domain resulted in attenuation of 11-cis-retinal binding. Significant differences in 11-cis-retinal binding affinities were observed between NBD1 and other cytoplasmic and lumenal domains of ABCA4. The results suggest a possible role of ABCA4 and, in particular, the NBD1 domain in 11-cis-retinal binding. These results also correlate well with a recent report on the in vivo role of ABCA4 in 11-cis-retinal transport.     

CD16 regulates TRIF-dependent TLR4 response in human monocytes and their subsets

Blood monocytes recognize Gram-negative bacteria through the TLR4, which signal via MyD88- and TRIF-dependent pathway to trigger an immune-inflammatory response. However, a dysregulated inflammatory response by these cells often leads to severe pathologies such as sepsis. We investigated the role of CD16 in the regulation of human monocyte response to Gram-negative endotoxin and sepsis. Blood monocytes from sepsis patients demonstrated an upregulation of several TRIF-dependent genes as well as a selective expansion of CD16-expressing (CD16(+)) monocytes. Gene expression and biochemical studies revealed CD16 to regulate the TRIF-dependent TLR4 pathway in monocytes by activating Syk, IFN regulatory factor 3, and STAT1, which resulted in enhanced expression of IFNB, CCL5, and CXCL10. CD16 also upregulated the expression of IL-1R-associated kinase M and IL-1 receptor antagonist, which are negative regulators of the MyD88-dependent pathway. CD16 overexpression or small interfering RNA knockdown in monocytes confirmed the above findings. Interestingly, these results were mirrored in the CD16(+) monocyte subset isolated from sepsis patients, providing an in vivo confirmation to our findings. Collectively, the results from the current study demonstrate CD16 as a key regulator of the TRIF-dependent TLR4 pathway in human monocytes and their CD16-expressing subset, with implications in sepsis.     

Cutting edge: impaired MHC class I expression in mice deficient for Nlrc5/class I transactivator

MHC class I and class II are crucial for the adaptive immune system. Although regulation of MHC class II expression by CIITA has long been recognized, the mechanism of MHC class I transactivation has been largely unknown until the recent discovery of NLRC5/class I transactivator. In this study, we show using Nlrc5-deficient mice that NLRC5 is required for both constitutive and inducible MHC class I expression. Loss of Nlrc5 resulted in severe reduction in the expression of MHC class I and related genes such as β(2)-microglobulin, Tap1, or Lmp2, but did not affect MHC class II levels. IFN-γ stimulation could not overcome the impaired MHC class I expression in Nlrc5-deficient cells. Upon infection with Listeria monocyogenes, Nlrc5-deficient mice displayed impaired CD8(+) T cell activation, accompanied with increased bacterial loads. These findings illustrate critical roles of NLRC5/class I transactivator in MHC class I gene regulation and host defense by CD8(+) T cell responses.     

Diverse viscerotropic isolates of Leishmania all express a highly conserved secretory nuclease during human infections

Previously, we characterized a gene encoding the unique nuclease (LdNuc(s)) from a Sudanese isolate of the human pathogen Leishmania donovani. This parasite secretory enzyme is involved in the salvage of host-derived purines and is constitutively expressed by both developmental forms of the parasite. Currently, we assessed whether an LdNuc(s)-like nuclease was conserved among other geographically disparate isolates of L. donovani and whether this enzyme was produced by intracellular amastigotes during human infections. Using RT-PCR and Southern blotting, we showed that LdNuc(s) gene homologs were present in each of the viscerotropic Leishmania tested (i.e., L. donovani isolates from the Sudan, Ethiopia and India as well as L. infantum). Further results of in situ enzyme activity gel analyses showed that each of these parasite isolates also expressed a released/secreted LdNuc(s)-like nuclease activity. In Western blots, our anti-LdNuc(s) (Sudan) peptide-specific antibody reacted with only a single ~35 kDa protein in each of the viscerotropic Leishmania isolates. Further, the ~35 kDa nuclease secreted by each of these isolates was specifically immunoprecipitated by the anti-LdNuc(s) antibody above. In situ gel analyses showed that each of these immunoprecipitates had LdNuc(s)-like nuclease activity. Moreover, sera from acute visceral leishmaniasis patients from India, Sudan and Brazil all immunoprecipitated an LdNuc(s)-HA expressed nuclease demonstrating, that these patients possessed antibodies against this parasite secretory enzyme. Cumulatively, these results showed that the LdNuc(s) homologs were functionally conserved among geographically disparate visceral Leishmania spp. and that amastigotes of these parasites must produce this nuclease enzyme during the course of human disease.     

Quantitative analysis of the mechanism of DNA binding by Bacillus DnaA protein

DnaA protein has the sole responsibility of initiating a new round of DNA replication in prokaryotic organisms. It recognizes the origin of DNA replication, and initiates chromosomal DNA replication in the bacterial genome. In Gram-negative Escherichia coli, a large number of DnaA molecules bind to specific DNA sequences (known as DnaA boxes) in the origin of DNA replication, oriC, leading to the activation of the origin. We have cloned, expressed, and purified full-length DnaA protein in large quantity from Gram-positive pathogen Bacillus anthracis (DnaA_BA). DnaA_BA was a highly soluble monomeric protein making it amenable to quantitative analysis of its origin recognition mechanisms. DnaA_BA bound DnaA boxes with widely divergent affinities in sequence and ATP-dependent manner. In the presence of ATP, the K_D ranged from 3.8 × 10⁻⁸ M for a specific DnaA box sequence to 4.1 × 10⁻⁷ M for a non-specific DNA sequence and decreased significantly in the presence of ADP. Thermodynamic analyses of temperature and salt dependence of DNA binding indicated that hydrophobic (entropic) and ionic bonds contributed to the DnaA_BA·DNA complex formation. DnaA_BA had a DNA-dependent ATPase activity. DNA sequences acted as positive effectors and modulated the rate (V_max) of ATP hydrolysis without any significant change in ATP binding affinity.     

Exploiting BAC-end sequences for the mining,characterization and utility of new short sequences repeat (SSR) markers in Citrus

The aim of this study was to develop a large set of microsatellite markers based on publicly available BAC-end sequences (BESs), and to evaluate their transferability, discriminating capacity of genotypes and mapping ability in Citrus. A set of 1,281 simple sequence repeat (SSR) markers were developed from the 46,339 Citrus clementina BAC-end sequences (BES), of them 20.67% contained SSR longer than 20 bp, corresponding to roughly one perfect SSR per 2.04 kb. The most abundant motifs were di-nucleotide (16.82%) repeats. Among all repeat motifs (TA/AT)n is the most abundant (8.38%), followed by (AG/CT)n (4.51%). Most of the BES-SSR are located in the non-coding region, but 1.3% of BES-SSRs were found to be associated with transposable element (TE). A total of 400 novel SSR primer pairs were synthesized and their transferability and polymorphism tested on a set of 16 Citrus and Citrus relative’s species. Among these 333 (83.25%) were successfully amplified and 260 (65.00%) showed cross-species transferability with Poncirus trifoliata and Fortunella sp. These cross-species transferable markers could be useful for cultivar identification, for genomic study of Citrus, Poncirus and Fortunella sp. Utility of the developed SSR marker was demonstrated by identifying a set of 118 markers each for construction of linkage map of Citrus reticulata and Poncirus trifoliata. Genetic diversity and phylogenetic relationship among 40 Citrus and its related species were conducted with the aid of 25 randomly selected SSR primer pairs and results revealed that citrus genomic SSRs are superior to genic SSR for genetic diversity and germplasm characterization of Citrus spp.     

Improved efficiency in cryo-em secondary structure topology determination from inaccurate data

The determination of the secondary structure topology is a critical step in deriving the atomic structure from the protein density map obtained from electron cryo-microscopy technique. This step often relies on the matching of two sources of information. One source comes from the secondary structures detected from the protein density map at the medium resolution, such as 5-10 ?. The other source comes from the predicted secondary structures from the amino acid sequence. Due to the inaccuracy in either source of information, a pool of possible secondary structure positions needs to be sampled. This paper studies the question, that is, how to reduce the computation of the mapping when the inaccuracy of the secondary structure predictions is considered. We present a method that combines the concept of dynamic graph with our previous work of using constrained shortest path to identify the topology of the secondary structures. We show a reduction of 34.55% of run-time as comparison to the na?ve way of handling the inaccuracies. We also show an improved accuracy when the potential secondary structure errors are explicitly sampled verses the use of one consensus prediction. Our framework demonstrated the potential of developing computationally effective exact algorithms to identify the optimal topology of the secondary structures when the inaccuracy of the predicted data is considered.     

Gender discrimination in undernutrition with mediating factors among Bengalee school children from Eastern India

This study was undertaken to determine age and sex variations in the prevalence of underweight and stunting, and to assess the impact of some socio-economic variables on undernutrition among 6–16 year old school children of Bengalee ethnicity in Chapra, West Bengal, India. The subjects were selected randomly from various schools and madrassas of the Chapra Block. A total of 725 children (342 boys and 383 girls) aged 6–16 years were measured and data on their socio-economic status were collected. Age and sex combined rates of underweight and stunting were 44.40% and 37.20%, respectively. Weight-for-age Z-score (WAZ) showed significant association with per-capita income (PCI) among boys (F = 5.45) and girls (F = 8.14). Height-for-age Z-score (HAZ) has also shown the association with per-capita income among boys (F = 4.43) and girls (F = 9.69). The WAZ was significantly associated with fathers’ educational status (FOS) (t = ?2.95) and the number of living rooms (NLR) (t = ?2.91) among girls. The HAZ showed significant association with number of siblings (NS) among girls (F = 4.25). Linear regression analyses revealed that NLR (t = 2.04) and NS (t = 1.95) had a significant impact on HAZ among boys. Among girls, PCI (t = 3.38), FOS (t = 2.87) and NLR (t = 2.81) had a significant impact on WAZ and also PCI (t = 3.28) and FOS (t = 2.90) had a significant impact on HAZ. NLR had significant associations with underweight (χ² = 3.59) and stunting (χ² = 4.20) among boys. Among girls, PCI had significant associations with underweight (χ² = 11.15) and stunting (χ² = 11.64). FOS also showed significant associations with underweight (χ² = 8.10) as well as stunting (χ² = 8.28) among girls. NLR showed a significant association with underweight (χ² = 7.75). Logistics regression analyses revealed that FOS (Wald = 8.00) and NLR (Wald = 4.09) were significant predictors of stunting among boys. Among girls, PCI was a significant predictor of underweight (Wald = 10.95) as well as stunting (Wald = 10.45). FOS, NLR and NS were also significant predictors of stunting (Wald = 8.16), underweight (Wald = 7.68) and stunting (Wald = 6.97) respectively. The present study revealed that the nutritional status of the children was unsatisfactory and it is of paramount importance not only to increase the amount of food supplementation given but also to promote gender equality.