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This detailed volume explores numerous multidisciplinary approaches employed to analyze the role of different molecules or strategies used by different guests to survive inside hosts. Divided into several sections, the book delves into animal-pathogen interaction, microbe-microbe interaction, as well as plant-pathogen interaction. Written for the highly successful Methods in Molecular Biology series, chapters include brief introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.uthoritative and practical, Host-Pathogen Interactions: Methods and Protocols provides many molecular and bioinformatics techniques currently in use at reputed laboratories in countries all around the world, vital for many kinds of host-pathogen interactions studies

Intro -- HOST-PATHOGEN INTERACTIONS: GENETICS, IMMUNOLOGY AND PHYSIOLOGY -- HOST-PATHOGEN INTERACTIONS: GENETICS, IMMUNOLOGY AND PHYSIOLOGY -- CONTENTS -- PREFACE -- Chapter 1 GERMS AND TISSUES: FRANK MACFARLANE BURNET, PETER BRIAN MEDAWAR, AND THE IMMUNOLOGICAL CONJUNCTURE -- ABSTRACT -- INTRODUCTION -- AGE, MICROBES, AND THE CAUSES OF INFECTIOUS DISEASE IN FRANK MACFARLANE BURNET'S RESEARCH -- GROWTH, AGING, AND TISSUE TRANSPLANTATION IN PETER BRIAN MEDAWAR'S RESEARCH -- CONCLUSION -- REFERENCES -- Chapter 2 THEORY AND EXAMPLES OF RECIPROCAL INFLUENCE BETWEEN HOSTS AND PATHOGENS, FROM SHORT-TERM TO LONG TERM INTERACTIONS: COEVOLUTION, COSPECIATION AND PATHOGEN SPECIATION FOLLOWING HOST SHIFTS -- ABSTRACT -- INTRODUCTION -- 1. RECENT ADVANCES ON COEVOLUTION: MODELS AND EXPERIMENTAL DATA -- 1.1. Coevolutionary Cycles -- 1.2. Arms Race versus Trench Warfare Models: Expectations on Genetic Diversity -- 1.3. Trench Warfare Model among Plant Hosts, Arms Race Model among Microbial Hosts and Pathogens -- 1.4. Mathematical Framework for Improved Understanding of Polymorphism Maintenance -- 2. COSPECIATION -- 2.1. Theoretical Framework and Methods to Test for Cospeciation -- 2.2. Event Based Methods -- 2.3. Topology- and Distance-Based Methods -- 2.4. Studies of Natural Associations Reveal the Prevalence of Host Shifts -- 3. FROM SHORT-TERM TO LONG-TERM HOST-PATHOGEN INTERACTIONS: TRANS-SPECIFIC GENETIC DIVERSITY AND RELATIONSHIP BETWEEN COEVOLUTION AND ECOLOGICAL SPECIATION (BUT NOT COSPECIATION) -- 3.1. Trans-Specific Polymorphism and Divergence at the Loci Involved in Coevolution -- 3.2. From Coevolution to Specialization, Models and Observations -- 3.3. Specialization and Pathogen Speciation, Theoretical Considerations -- CONCLUSION -- ACKNOWLEDGMENTS -- REFERENCES.

Front Cover -- Systems Biology Approaches for Host-Pathogen Interaction Analyses -- Copyright Page -- Dedication -- Contents -- List of contributors -- Foreword -- Preface -- Acknowledgments -- 1 Host-pathogen interactions: a general introduction -- 1.1 Introduction -- 1.1.1 Role of pathogen -- 1.1.2 Host-pathogen relationship and mechanisms -- 1.1.3 Classification of host-pathogen interactions -- 1.1.3.1 Invasion of host through breach of primary barriers -- 1.1.3.2 Evasion of host defenses by pathogens -- 1.1.3.3 Pathogen replication in host -- 1.2 Methods for prediction of host-pathogen interactions -- 1.2.1 Ortholog-based protein interaction detection -- 1.2.2 Domain-based detection of protein interaction -- 1.2.3 Biological reasoning-based prediction of host-pathogen interactions -- 1.2.3.1 Homology-based predictions -- 1.2.3.2 Structure-based predictions -- 1.2.4 Domain/motif interaction-based predictions -- 1.2.5 Machine learning-based predictions of host-pathogen interactions -- 1.3 Online repositories for host-pathogen interactions -- 1.3.1 Database of fungal virulence factors -- 1.3.2 E-fungi -- 1.3.3 Fungi DB -- 1.3.4 Ensembl genomes -- 1.3.5 EuPathDB -- 1.3.6 HPIDB -- 1.3.6.1 Pathogen portal -- 1.3.7 PLEXdb -- 1.3.8 VFDB -- 1.4 Conclusion -- Acknowledgment -- References -- 2 Host-pathogen interactions: databases and approaches for data generation -- 2.1 Introduction -- 2.2 Databases for host-pathogen interactions -- 2.3 Bioinformatic methods to discover HPI networking -- 2.3.1 Biological methods -- 2.3.2 Computational methods -- 2.4 Microscopic imaging techniques as stage of the art -- 2.5 RNA-Seq profiling: tool for determining the HPI network -- 2.5.1 Bacteria-host interactions -- 2.5.2 Virus-host interactions -- 2.5.3 Fungus-host interaction and other pathogenic interactions -- 2.5.4 Technical approach of RNA-seq and data analysis.

Invasive candidiasis is among the most life-threatening infections in patients in intensive care units. Although Candida albicans is the leading cause of candidaemia, the incidence of Candida parapsilosis infections is also rising, particularly among the neonates. Due to differences in their biology, these species employ different antifungal resistance and virulence mechanisms and also induce dissimilar immune responses. Previously, it has been suggested that core virulence effecting transcription regulators could be attractive ligands for future antifungal drugs. Although the virulence regulatory mechanisms of C. albicans are well studied, less is known about similar mechanisms in C. parapsilosis. In order to search for potential targets for future antifungal drugs against this species, we analyzed the fungal transcriptome during host-pathogen interaction using an in vitro infection model. Selected genes with high expression levels were further examined through their respective null mutant strains, under conditions that mimic the host environment or influence pathogenicity. As a result, we identified several mutants with relevant pathogenicity affecting phenotypes. During the study we highlight three potentially tractable signaling regulators that influence C. parapsilosis pathogenicity in distinct mechanisms. During infection, CPAR2_100540 is responsible for nutrient acquisition, CPAR2_200390 for cell wall assembly and morphology switching and CPAR2_303700 for fungal viability. ; The project was subsidized by the European Union and co-financed by the European Social Fund. AG was funded by NKFIH NN 113153, by GINOP-2.3.2-15-2016-00035, by GINOP-2.3.3-15-2016-00006. AG and LN were also founded by CNPq (Program Science without borders - 407380/2013-2). TN was supported by the Postdoctoral Fellowship by the Hungarian Academy of Sciences. Research at TG lab was partially funded by grants from Spanish Ministry of Economy and Competitiveness BFU2015-67107 cofounded by European Regional Development Fund (ERDF); from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreements FP7-PEOPLE-2013-ITN-606786 "ImResFun" and from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No H2020-MSCA-ITN-2014-642095. JDN is partially supported by US NIH grants R21 AI124797-02 and AI52733-06A2. We would like to thank Prof. Geraldine Butler for the KO strategy and parental strains necessary for mutant strain generation. We would like to thank Chetna Tyagi for the help with the in silico data analyses, Mónika Homolya for contributing to the chitinase and chitin synthase expression experiments, Dr. Sándor Kocsubé for the summary table and Tamás Petkovits for the help with the SEM experiments.

Penicillium digitatum and Penicillium expansum are responsible for green and blue molds in citrus and pome fruits, respectively, which result in major monetary losses worldwide. In order to study their infection process in fruits, we successfully introduced a green fluorescent protein (GFP) encoding gene into wild type P. digitatum and P. expansum isolates, using Agrobacterium tumefaciens-mediated transformation (ATMT), with hygromycin B resistance as the selectable marker. To our knowledge, this is the first report describing the transformation of these two important postharvest pathogens with GFP and the use of transformed strains to study compatible and non-host pathogen interactions. Transformation did not affect the pathogenicity or the ecophysiology of either species compared to their respective wild type strains. The GFP-tagged strains were used for in situ analysis of compatible and non-host pathogen interactions on oranges and apples. Knowledge of the infection process of apples and oranges by these pathogens will facilitate the design of novel strategies to control these postharvest diseases and the use of the GFP-tagged strains will help to determine the response of P. digitatum and P. expansum on/in plant surface and tissues to different postharvest treatments. ; The authors are grateful to the Spanish Government for its financial support with projects AGL2008-04828-C03-01 and AGL2008-04828-C03-02, for Ramón y Cajal Contract (R. Torres) and for the scholarships BES-2006-12983 (M. López) and BES-2009-027752 (G. Burón). ; Peer reviewed

Anaplasma phagocytophilum transmembrane and surface proteins play a role during infection and multiplication in host neutrophils and tick vector cells. Recently, A. phagocytophilum Major surface protein 4 (MSP4) and Heat shock protein 70 (HSP70) were shown to be localized on the bacterial membrane, with a possible role during pathogen infection in ticks. In this study, we hypothesized that A. phagocytophilum MSP4 and HSP70 have similar functions in tick-pathogen and host-pathogen interactions. To address this hypothesis, herein we characterized the role of these bacterial proteins in interaction and infection of vertebrate host cells. The results showed that A. phagocytophilum MSP4 and HSP70 are involved in host-pathogen interactions, with a role for HSP70 during pathogen infection. The analysis of the potential protective capacity of MSP4 and MSP4-HSP70 antigens in immunized sheep showed that MSP4-HSP70 was only partially protective against pathogen infection. This limited protection may be associated with several factors, including the recognition of non-protective epitopes by IgG in immunized lambs. Nevertheless, these antigens may be combined with other candidate protective antigens for the development of vaccines for the control of human and animal granulocytic anaplasmosis. Focusing on the characterization of host protective immune mechanisms and protein-protein interactions at the host-pathogen interface may lead to the discovery and design of new effective protective antigens. ; This research was partially supported by the Ministerio de Economia, Industria y Competitividad (Spain) grants AGL2014-56305 and BFU2016-79892-P, the European Union (EU) Seventh Framework Programme (FP7) ANTIGONE project number 278976, and the CSIC grant 201440E098 to Jd. MV and LM were supported by the Research Plan of the University of Castilla-La Mancha (UCLM), Spain. ; Peer Reviewed

Hematogenous dissemination followed by tissue tropism is a characteristic of the infectious process of many pathogens including those transmitted by blood-feeding vectors. After entering into the blood circulation, these pathogens must arrest in the target organ before they infect a specific tissue. Here, we describe a non-invasive method to visualize and quantify the homing of pathogens to the host tissues. By using in vivo bioluminescence imaging we quantify the accumulation of luciferase-expressing parasites in the host organs during the first minutes following their intravascular inoculation in mice. Using this technique we show that in the malarial infection, once in the blood circulation, most of bioluminescent Plasmodium berghei sporozoites, the parasite stage transmitted to the host skin by a mosquito bite, rapidly home to the liver where they invade and develop inside hepatocytes. This homing is specific to this developmental stage since blood stage parasites do not accumulate in the liver, as well as extracellular Trypanosoma brucei bloodstream forms and liver-infecting Leishmania infantum amastigotes. Finally, this method can be used to study the dynamics of tissue tropism of parasites, dissect the molecular and cellular basis of their increased arrest in organs and to evaluate immune interventions designed to block this targeted interaction. ; This work was supported by funds from the Fundacao para a Ciencia e Tecnologia (FCT)/Ministerio da Educacao e Ciencia (MEC) co-funded by FEDER (EXPL/JTAVARES-IF/00881/2012/C P0158/CT0005, EXPL/IMI-MIC/1331/2013) under the Partnership agreement PT2020, through the Research Unit No.4293, the Institut Paris - Paris, the French National Research Agency (Grant No. ANR-0-JCJC-1302-PlasmoPEP), the French Government's Investissement d'Avenir program, Laboratoire d'Excellence "Integrative Biology of Emerging Infectious Diseases" (Grant No. ANR-10-LABX-62-IBEID). JT is an Investigator FCT funded by National funds through FCT and co-funded through European Social Fund within the Human Potential Operating Programme. DC is funded by FCT (SFRH/BD/123734/2016).

Climate change is predicted to result in changes in the geographic ranges and local prevalence of infectious diseases, either through direct effects on the pathogen, or indirectly through range shifts in vector and reservoir species. To better understand the occurrence of monkeypox virus (MPXV), an emerging Orthopoxvirus in humans, under contemporary and future climate conditions, we used ecological niche modeling techniques in conjunction with climate and remote-sensing variables. We first created spatially explicit probability distributions of its candidate reservoir species in Africa's Congo Basin. Reservoir species distributions were subsequently used to model current and projected future distributions of human monkeypox (MPX). Results indicate that forest clearing and climate are significant driving factors of the transmission of MPX from wildlife to humans under current climate conditions. Models under contemporary climate conditions performed well, as indicated by high values for the area under the receiver operator curve (AUC), and tests on spatially randomly and non-randomly omitted test data. Future projections were made on IPCC 4(th) Assessment climate change scenarios for 2050 and 2080, ranging from more conservative to more aggressive, and representing the potential variation within which range shifts can be expected to occur. Future projections showed range shifts into regions where MPX has not been recorded previously. Increased suitability for MPX was predicted in eastern Democratic Republic of Congo. Models developed here are useful for identifying areas where environmental conditions may become more suitable for human MPX; targeting candidate reservoir species for future screening efforts; and prioritizing regions for future MPX surveillance efforts.