scholarly journals Dual RNA-seq provides insight into the biology of the neglected intracellular human pathogen Orientia tsutsugamushi

2019 ◽  
Author(s):  
Bozena Mika-Gospodorz ◽  
Suparat Giengkam ◽  
Alexander J. Westermann ◽  
Jantana Wongsantichon ◽  
Willow Kion-Crosby ◽  
...  
Keyword(s):  
Infection Model ◽  
Neglected Diseases ◽  
Orientia Tsutsugamushi ◽  
Rna Seq ◽  
Sequencing Technologies ◽  
Mouse Infection Model ◽  
Vector Borne ◽  
Antisense Regulation ◽  
Responsible Pathogen ◽  
Insight Into

SummaryEmerging and neglected diseases pose challenges as their biology is frequently poorly understood, and genetic tools often do not exist to manipulate the responsible pathogen. Organism agnostic sequencing technologies offer a promising approach to understand the molecular processes underlying these diseases. Here we apply dual RNA-seq to Orientia tsutsugamushi (Ot), an obligate intracellular bacterium and the causative agent of the vector-borne human disease scrub typhus. Half the Ot genome is composed of repetitive DNA, and there is minimal collinearity in gene order between strains. Integrating RNA-seq, comparative genomics, proteomics, and machine learning, we investigated the transcriptional architecture of Ot, including operon structure and non-coding RNAs, and found evidence for wide-spread post-transcriptional antisense regulation. We compared the host response to two clinical isolates and identified distinct immune response networks that are up-regulated in response to each strain, leading to predictions of relative virulence which were confirmed in a mouse infection model. Thus, dual RNA-seq can provide insight into the biology and host-pathogen interactions of a poorly characterized and genetically intractable organism such as Ot.

Detecting differentially expressed genes by smoothing effect of gene length on variance estimation

2015 ◽  
Vol 13 (06) ◽  
pp. 1542004 ◽  
Author(s):  
Jinyang Tang ◽  
Fei Wang
Keyword(s):  
Variance Estimation ◽  
Differentially Expressed ◽  
Smoothing Effect ◽  
Gene Length ◽  
Rna Seq ◽  
Genome Research ◽  
Sequencing Technologies ◽  
Long Genes ◽  
Insight Into ◽  
Generation Sequencing

Next-generation sequencing technologies are widely used in genome research, and RNA sequencing (RNA-Seq) is becoming the main application for gene expression profiling. A large number of computational methods have been developed for analyzing differentially expressed (DE) genes in RNA-Seq data. However, most existing algorithms prefer to call long genes as DE. Short DE genes are rarely detected. In this work, we set out to gain insight into the influence of gene length on RNA-Seq data analysis and to figure out the effect of gene length on variance estimation of RNA-Seq read counts, which is important for statistic test to identify DE genes. We proposed a balanced method of hunting for short DE genes with significance by smoothing a gene length factor. Computational experiments indicate that our method performs well. Software available: http://www.iipl.fudan.edu.cn/lenseq/ .

scholarly journals An epitope-based malaria vaccine targeting the junctional region of circumsporozoite protein

npj Vaccines ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Lucie Jelínková ◽  
Hugo Jhun ◽  
Allison Eaton ◽  
Nikolai Petrovsky ◽  
Fidel Zavala ◽  
...  
Keyword(s):  
Mouse Model ◽  
Malaria Vaccine ◽  
High Titer ◽  
Circumsporozoite Protein ◽  
Infection Model ◽  
Vaccine Platform ◽  
Junctional Region ◽  
Mouse Infection Model ◽  
Virus Like Particle ◽  
Major Surface

AbstractA malaria vaccine that elicits long-lasting protection and is suitable for use in endemic areas remains urgently needed. Here, we assessed the immunogenicity and prophylactic efficacy of a vaccine targeting a recently described epitope on the major surface antigen on Plasmodium falciparum sporozoites, circumsporozoite protein (CSP). Using a virus-like particle (VLP)-based vaccine platform technology, we developed a vaccine that targets the junctional region between the N-terminal and central repeat regions of CSP. This region is recognized by monoclonal antibodies, including mAb CIS43, that have been shown to potently prevent liver invasion in animal models. We show that CIS43 VLPs elicit high-titer and long-lived anti-CSP antibody responses in mice and is immunogenic in non-human primates. In mice, vaccine immunogenicity was enhanced by using mixed adjuvant formulations. Immunization with CIS43 VLPs conferred partial protection from malaria infection in a mouse model, and passive transfer of serum from immunized macaques also inhibited parasite liver invasion in the mouse infection model. Our findings demonstrate that a Qβ VLP-based vaccine targeting the CIS43 epitope combined with various adjuvants is highly immunogenic in mice and macaques, elicits long-lasting anti-CSP antibodies, and inhibits parasite infection in a mouse model. Thus, the CIS43 VLP vaccine is a promising pre-erythrocytic malaria vaccine candidate.

scholarly journals Scrub Typhus and Molecular Characterization of Orientia tsutsugamushi from Central Nepal

Pathogens ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 422
Author(s):  
Rajendra Gautam ◽  
Keshab Parajuli ◽  
Mythili Tadepalli ◽  
Stephen Graves ◽  
John Stenos ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Scrub Typhus ◽  
Febrile Illness ◽  
Acute Febrile Illness ◽  
Limited Information ◽  
Orientia Tsutsugamushi ◽  
Health Measures ◽  
Central Nepal ◽  
Vector Borne

Scrub typhus is a vector-borne, acute febrile illness caused by Orientia tsutsugamushi. Scrub typhus continues to be an important but neglected tropical disease in Nepal. Information on this pathogen in Nepal is limited to serological surveys with little information available on molecular methods to detect O. tsutsugamushi. Limited information exists on the genetic diversity of this pathogen. A total of 282 blood samples were obtained from patients with suspected scrub typhus from central Nepal and 84 (30%) were positive for O. tsutsugamushi by 16S rRNA qPCR. Positive samples were further subjected to 56 kDa and 47 kDa molecular typing and molecularly compared to other O. tsutsugamushi strains. Phylogenetic analysis revealed that Nepalese O. tsutsugamushi strains largely cluster together and cluster away from other O. tsutsugamushi strains from Asia and elsewhere. One exception was the sample of Nepal_1, with its partial 56 kDa sequence clustering more closely with non-Nepalese O. tsutsugamushi 56 kDa sequences, potentially indicating that homologous recombination may influence the genetic diversity of strains in this region. Knowledge on the circulating strains in Nepal is important to the development of diagnostic tests and vaccines to support public health measures to control scrub typhus in this country.

scholarly journals A Cronobacter turicensis O1 Antigen-Specific Monoclonal Antibody Inhibits Bacterial Motility and Entry into Epithelial Cells

2014 ◽  
Vol 83 (3) ◽  
pp. 876-887 ◽  
Author(s):  
Kristina Schauer ◽  
Angelika Lehner ◽  
Richard Dietrich ◽  
Ina Kleinsteuber ◽  
Rocío Canals ◽  
...  
Keyword(s):  
Monoclonal Antibody ◽  
Epithelial Cells ◽  
Foodborne Pathogen ◽  
Antimicrobial Effect ◽  
Infection Model ◽  
Cell Agglutination ◽  
Content Type ◽  
O Antigen ◽  
Lethal Infection ◽  
Insight Into

Cronobacter turicensisis an opportunistic foodborne pathogen that can cause a rare but sometimes lethal infection in neonates. Little is known about the virulence mechanisms and intracellular lifestyle of this pathogen. In this study, we developed an IgG monoclonal antibody (MAb; MAb 2G4) that specifically recognizes the O1 antigen ofC. turicensiscells. The antilipopolysaccharide antibody bound predominantly monovalently to the O antigen and reduced bacterial growth without causing cell agglutination. Furthermore, binding of the antibody to the O1 antigen ofC. turicensiscells caused a significant reduction of the membrane potential which is required to energize flagellar rotation, accompanied by a decreased flagellum-based motility. These results indicate that binding of IgG to the O antigen ofC. turicensiscauses a direct antimicrobial effect. In addition, this feature of the antibody enabled new insight into the pathogenicity ofC. turicensis. In a tissue culture infection model, pretreatment ofC. turicensiswith MAb 2G4 showed no difference in adhesion to human epithelial cells, whereas invasion of bacteria into Caco-2 cells was significantly inhibited.

scholarly journals RNA-Seq Approach for Genetic Improvement of Meat Quality in Pig and Evolutionary Insight into the Substrate Specificity of Animal Carbonyl Reductases

PLoS ONE ◽  
2012 ◽  
Vol 7 (9) ◽  
pp. e42198 ◽  
Author(s):  
Won Yong Jung ◽  
Seul Gi Kwon ◽  
Minky Son ◽  
Eun Seok Cho ◽  
Yuno Lee ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Meat Quality ◽  
Genetic Improvement ◽  
Rna Seq ◽  
Insight Into

scholarly journals The zinc transporter ZnuABC is critical for the virulence of Chromobacterium violaceum and contributes to diverse zinc-dependent physiological processes

2021 ◽  
Author(s):  
Renato E. R. S. Santos ◽  
Waldir P. da Silva Júnior ◽  
Simone A. Harrison ◽  
Eric P Skaar ◽  
Walter J. Chazin ◽  
...  
Keyword(s):  
Mutant Strain ◽  
Zinc Uptake ◽  
Chromobacterium Violaceum ◽  
Host Protein ◽  
Infection Model ◽  
Uptake System ◽  
Environmental Bacterium ◽  
Mouse Infection Model ◽  
Synthetic Metal

Chromobacterium violaceum is a ubiquitous environmental bacterium that causes sporadic life-threatening infections in humans. How C. violaceum acquires zinc to colonize environmental and host niches is unknown. In this work, we demonstrated that C. violaceum employs the zinc uptake system ZnuABC to overcome zinc limitation in the host, ensuring the zinc supply for several physiological demands. Our data indicated that the C. violaceum ZnuABC transporter is encoded in a zur-CV_RS15045-CV_RS15040-znuCBA operon. This operon was repressed by the zinc uptake regulator Zur and derepressed in the presence of the host protein calprotectin (CP) and the synthetic metal chelator EDTA. A ΔznuCBA mutant strain showed impaired growth under these zinc-chelated conditions. Moreover, the deletion of znuCBA provoked a reduction in violacein production, swimming motility, biofilm formation, and bacterial competition. Remarkably, the ΔznuCBA mutant strain was highly attenuated for virulence in an in vivo mouse infection model and showed a low capacity to colonize the liver, grow in the presence of CP, and resist neutrophil killing. Overall, our findings demonstrate that ZnuABC is essential for C. violaceum virulence, contributing to subvert the zinc-based host nutritional immunity.

scholarly journals Spatial metabolomics identifies localized chemical changes in heart tissue during chronic cardiac Chagas Disease

2021 ◽  
Vol 15 (10) ◽  
pp. e0009819
Author(s):  
Danya A. Dean ◽  
Gautham Gautham ◽  
Jair L. Siqueira-Neto ◽  
James H. McKerrow ◽  
Pieter C. Dorrestein ◽  
...  
Keyword(s):  
Chagas Disease ◽  
Neglected Tropical Diseases ◽  
Clinical Manifestations ◽  
Parasite Burden ◽  
Heart Tissue ◽  
Cardiac Symptoms ◽  
Heart Region ◽  
Contaminated Food ◽  
Vector Borne ◽  
Insight Into

Chagas disease (CD), caused by the parasite Trypanosoma cruzi, is one of nineteen neglected tropical diseases. CD is a vector-borne disease transmitted by triatomines, but CD can also be transmitted through blood transfusions, organ transplants, T. cruzi-contaminated food and drinks, and congenital transmission. While endemic to the Americas, T. cruzi infects 7–8 million people worldwide and can induce severe cardiac symptoms including apical aneurysms, thromboembolisms and arrhythmias during the chronic stage of CD. However, these cardiac clinical manifestations and CD pathogenesis are not fully understood. Using spatial metabolomics (chemical cartography), we sought to understand the localized impact of chronic CD on the cardiac metabolome of mice infected with two divergent T. cruzi strains. Our data showed chemical differences in localized cardiac regions upon chronic T. cruzi infection, indicating that parasite infection changes the host metabolome at specific sites in chronic CD. These sites were distinct from the sites of highest parasite burden. In addition, we identified acylcarnitines and glycerophosphocholines as discriminatory chemical families within each heart region, comparing infected and uninfected samples. Overall, our study indicated global and positional metabolic differences common to infection with different T. cruzi strains and identified select infection-modulated pathways. These results provide further insight into CD pathogenesis and demonstrate the advantage of a systematic spatial perspective to understand infectious disease tropism.

scholarly journals Population Genomic- and Phylogenomic-Enabled Advances to Increase Insight Into Pathogen Biology and Epidemiology

2021 ◽  
Vol 111 (1) ◽  
pp. 8-11
Author(s):  
Remco Stam ◽  
Pierre Gladieux ◽  
Boris A. Vinatzer ◽  
Erica M. Goss ◽  
Neha Potnis ◽  
...  
Keyword(s):  
Population Genetics ◽  
Population Genomics ◽  
Cost Effective ◽  
Whole Genome ◽  
Genome Data ◽  
Sequencing Technologies ◽  
Population Genomic ◽  
High Throughput Dna Sequencing ◽  
Opening Up ◽  
Insight Into

Population genetics has been a key discipline in phytopathology for many years. The recent rise in cost-effective, high-throughput DNA sequencing technologies, allows sequencing of dozens, if not hundreds of specimens, turning population genetics into population genomics and opening up new, exciting opportunities as described in this Focus Issue . Without the limitations of genetic markers and the availability of whole or near whole-genome data, population genomics can give new insights into the biology, evolution and adaptation, and dissemination patterns of plant-associated microbes.

scholarly journals A Transcriptomic Analysis of Gonads from the Low-Temperature-Induced Masculinization of Takifugu rubripes

Animals ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 3419
Author(s):  
He Zhou ◽  
Yuqing Sun ◽  
Xin Li ◽  
Ziyu Zhou ◽  
Kexin Ma ◽  
...  
Keyword(s):  
Low Temperature ◽  
Transcriptome Sequencing ◽  
Average Length ◽  
Gonadal Development ◽  
Temperature Treatment ◽  
Takifugu Rubripes ◽  
Rna Seq ◽  
Low Temperature Treatment ◽  
Cultured Fish ◽  
Insight Into

The phenotypic sex of fish is usually plastic. Low-temperature treatment induces the masculinization of Takifugu rubripes, resulting in pseudo-males (PM) with the physiological sex of a male (M) and genetic sex of a female (F). For a comparison of gonadal transcriptomes, we collected gonads from three groups of T. rubripes (F, M, and PM) for high-throughput transcriptome sequencing. The results provided 467,640,218 raw reads (70.15 Gb) and a total of 436,151,088 clean reads (65.43 Gb), with an average length of 150 bp. Only 79 differentially expressed genes (DEGs) were identified between F and PM, whereas 12,041 and 11,528 DEGs were identified between F and M, and PM and M, respectively. According to the functional annotation of DEGs, 13 DEGs related to gonadal development were screened (LOC101066759, dgat1, limk1, fbxl3, col6a3, fgfr3, dusp22b, svil, abhd17b, srgap3, tmem88b, bud4, and mustn10) which might participate in formating PM. A quantitative PCR of the DEGs confirmed the reliability of the RNA-seq. Our results provide an important contribution to the genome sequence resources for T. rubripes and insight into the molecular mechanism of masculinization in a cultured fish subject to low-temperature treatment.

scholarly journals The infection-tolerant mammalian reservoir of Lyme disease and other zoonoses broadly counters the inflammatory effects of endotoxin

2020 ◽  
Author(s):  
Gabriela Balderrama-Gutierrez ◽  
Ana Milovic ◽  
Vanessa J. Cook ◽  
M. Nurul Islam ◽  
Youwen Zhang ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Laboratory Model ◽  
Infection Model ◽  
Rna Seq ◽  
Acute Phase Reactants ◽  
Macrophage Response ◽  
Reactive Protein ◽  
Arginase 1 ◽  
The Difference ◽  
The Cost

ABSTRACTAnimals that are competent natural reservoirs of zoonotic diseases commonly suffer little morbidity from the pathogens they persistently harbor. The mechanisms of this infection tolerance and the trade-off costs are poorly understood. We used exposure to a single dose of lipopolysaccharide (LPS) endotoxin as an experimental model of inflammation to compare the responses of the cricentine rodent Peromyscus leucopus, the white-footed deermouse, to that of Mus musculus, the standard laboratory model for pathogenesis studies. Four hours after injection with either LPS or saline, blood and spleen and liver tissues were collected postmortem and subjected to RNA-seq, untargeted metabolomics, and specific RT-qPCR. This was followed by analysis of differential expression at the gene, pathway, and empirical network levels. The deermice showed the same signs of sickness as the mice with LPS exposure, and in addition demonstrated comparable increases in levels of corticosterone and expression of interleukin (IL)-6, tumor necrosis factor, IL-1β, and acute phase reactants, including C-reactive protein. But whereas the M. musculus response to LPS was best-characterized by network analysis as cytokine-associated, the P. leucopus response was dominated by pathway terms associated with neutrophil activity. Dichotomies between the species in expression profiles of arginase 1 and nitric oxide synthase 2, as well as the ratios of IL-10 to IL-12, were consistent with a type M1 polarized macrophage response in the mice and a type M2 or alternatively-activated response in the deermice. Analysis of metabolites in the plasma and RNA in the tissues revealed differences between the two species in tryptophan metabolism during response to LPS. Two up-regulated genes in particular signified the difference between the species: Slpi (secretory leukocyte proteinase inhibitor) and Ibsp (integrin-binding protein sialoprotein). The latter was previously unrecognized in the context of inflammation or infection. Key RNA-seq findings in P. leucopus were replicated in a second LPS experiment with older animals, in a systemic bacterial infection model, and with cultivated fibroblasts. Taken together, the results indicate that the deermouse possesses several adaptive traits to moderate effects of inflammation and oxidative stress ensuing from infection. This seems to be at the cost of infection persistence and that is to the benefit of the pathogen.

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