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Genomic Approaches for Improvement of Understudied Grasses

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889452422 Year: Pages: 165 DOI: 10.3389/978-2-88945-242-2 Language: English
Publisher: Frontiers Media SA
Subject: Botany --- Science (General)
Added to DOAB on : 2017-10-13 14:57:01
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Grasses are diverse, spanning native prairies to high-yielding grain cropping systems. They are valued for their beauty and useful for soil stabilization, pollution mitigation, biofuel production, nutritional value, and forage quality; grasses encompass the most important grain crops in the world. There are thousands of distinct grass species and many have promiscuous hybridization patterns, blurring species boundaries. Resources for advancing the science and knowledgebase of individual grass species or their unique characteristics varies, often proportional to their perceived value to society. For many grasses, limited genetic information hinders research progress. Presented in this research topic is a brief snapshot of creative efforts to apply modern genomics research methodologies to the study of several minor grass species.

Transcriptional Regulation: Molecules, Involved Mechanisms and Misregulation

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ISBN: 9783039212651 / 9783039212668 Year: Pages: 356 DOI: 10.3390/books978-3-03921-266-8 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology
Added to DOAB on : 2019-08-28 11:21:27
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Transcriptional regulation is a critical biological process involved in the response of a cell, a tissue or an organism to a variety of intra- and extra-cellular signals. Besides, it controls the establishment and maintenance of cell identity throughout developmental and differentiation programs. This highly complex and dynamic process is orchestrated by a huge number of molecules and protein networks and occurs through multiple temporal and functional steps. Of note, many human disorders are characterized by misregulation of global transcription since most of the signaling pathways ultimately target components of transcription machinery. This book includes a selection of papers that illustrate recent advances in our understanding of transcriptional regulation and focuses on many important topics, from cis-regulatory elements to transcription factors, chromatin regulators and non-coding RNAs, other than several transcriptome studies and computational analyses.

Keywords

major depressive disorder --- glioblastoma --- differentially expressed genes --- transcriptomics --- common pathway --- mouse --- miR-25-3p --- Akt1 --- AP-2? --- promoter --- cell metabolism --- p57Kip2 --- CDKN1C --- epigenetics --- disease --- cell differentiation --- placenta --- long non-coding RNA (lncRNA) --- human --- pregnancy --- high-throughput RNA sequencing (RNA-Seq) --- transcriptome --- Rsh regulon --- Novosphingobium pentaromativorans US6-1 --- sphingomonads --- RNA-seq --- N-acyl-l-homoserine lactone --- ppGpp --- selenium --- selenocysteine --- selenoproteins --- selenocysteine insertion sequence --- nonsense-mediated decay --- G-quadruplex --- transcriptional regulation --- promoter --- CRISPR/Cas9 --- PRDM gene family --- TCGA data analysis --- somatic mutations --- transcriptome profiling --- human malignancies --- tristetraprolin (TTP) --- tumorigenesis --- posttranscriptional regulation --- adenosine and uridine-rich elements (AREs) --- circRNA-disease associations --- pathway --- heterogeneous network --- Patau Syndrome --- cytogenetics --- FOXO1 --- transcription factor --- molecular pathways --- bioinformatics --- molecular docking --- and drug design --- transcription regulation --- gene expression --- causal inference --- enhancer activity --- insect --- transcription factors --- structures and functions --- research methods --- progress and prospects --- Pax3 --- Pteria penguin (Röding, 1798) --- tyrosinase --- melanin --- RNA interference --- liquid chromatograph-tandem mass spectrometer (LC-MS/MS) --- epigenetics --- gene expression --- nutrition --- transcription --- disorders --- mechanisms --- Crassostrea gigas --- Pacific oyster --- pediveliger larvae --- bioadhesive --- transcriptome --- gene expression --- interactome --- microscopy --- fertilization --- self-incompatibility --- transcriptome --- tea --- long non-coding RNAs --- cancer --- acute leukemia --- therapeutic targets --- Adiponectin --- cancer --- Adiponectin receptors --- obesity --- inflammatory response --- inflammation --- nutritional status --- n/a

Plant Genetics and Molecular Breeding

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ISBN: 9783039211753 / 9783039211760 Year: Pages: 628 DOI: 10.3390/books978-3-03921-176-0 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology
Added to DOAB on : 2019-08-28 11:21:27
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The development of new plant varieties is a long and tedious process involving the generation of large seedling populations for the selection of the best individuals. While the ability of breeders to generate large populations is almost unlimited, the selection of these seedlings is the main factor limiting the generation of new cultivars. Molecular studies for the development of marker-assisted selection (MAS) strategies are particularly useful when the evaluation of the character is expensive, time-consuming, or with long juvenile periods. The papers published in the Special Issue “Plant Genetics and Molecular Breeding” report highly novel results and testable new models for the integrative analysis of genetic (phenotyping and transmission of agronomic characters), physiology (flowering, ripening, organ development), genomic (DNA regions responsible for the different agronomic characters), transcriptomic (gene expression analysis of the characters), proteomic (proteins and enzymes involved in the expression of the characters), metabolomic (secondary metabolites), and epigenetic (DNA methylation and histone modifications) approaches for the development of new MAS strategies. These molecular approaches together with an increasingly accurate phenotyping will facilitate the breeding of new climate-resilient varieties resistant to abiotic and biotic stress, with suitable productivity and quality, to extend the adaptation and viability of the current varieties.

Keywords

sugarcane --- cry2A gene --- particle bombardment --- stem borer --- resistance --- NPK fertilizers --- agronomic traits --- molecular markers --- quantitative trait loci --- common wild rice --- Promoter --- Green tissue-specific expression --- light-induced --- transgenic chrysanthemum --- WRKY transcription factor --- salt stress --- gene expression --- DgWRKY2 --- Cucumis sativus L. --- RNA-Seq --- DEGs --- sucrose --- ABA --- drought stress --- Aechmea fasciata --- squamosa promoter binding protein-like --- flowering time --- plant architecture --- bromeliad --- Oryza sativa --- endosperm development --- rice quality --- WB1 --- the modified MutMap method --- abiotic stress --- Cicer arietinum --- candidate genes --- genetics --- heat-stress --- molecular breeding --- metallothionein --- Brassica --- Brassica napus --- As3+ stress --- broccoli --- cytoplasmic male sterile --- bud abortion --- gene expression --- transcriptome --- RNA-Seq --- sesame --- genome-wide association study --- yield --- QTL --- candidate gene --- cabbage --- yellow-green-leaf mutant --- recombination-suppressed region --- bulk segregant RNA-seq --- differentially expressed genes --- marker–trait association --- haplotype block --- genes --- root traits --- D-genome --- genotyping-by-sequencing --- single nucleotide polymorphism --- durum wheat --- bread wheat --- complex traits --- Brassica oleracea --- Ogura-CMS --- iTRAQ --- transcriptome --- pollen development --- rice --- OsCDPK1 --- seed development, starch biosynthesis --- endosperm appearance --- Chimonanthus praecox --- nectary --- floral scent --- gene expression --- Prunus --- flowering --- bisulfite sequencing --- genomics --- epigenetics --- breeding --- AP2/ERF genes --- Bryum argenteum --- transcriptome --- gene expression --- stress tolerance --- SmJMT --- transgenic --- Salvia miltiorrhiza --- overexpression --- transcriptome --- phenolic acids --- Idesia polycarpa var --- glycine --- FAD2 --- linoleic acid --- oleic acid --- anther wall --- tapetum --- pollen accumulation --- OsGPAT3 --- rice --- cytoplasmic male sterility (CMS) --- phytohormones --- differentially expressed genes --- pollen development --- Brassica napus --- Rosa rugosa --- RrGT2 gene --- Clone --- VIGS --- Overexpression --- Tobacco --- Flower color --- Anthocyanin --- sugarcane --- WRKY --- subcellular localization --- gene expression pattern --- protein-protein interaction --- transient overexpression --- soybean --- branching --- genome-wide association study (GWAS) --- near-isogenic line (NIL) --- BRANCHED1 (BRC1) --- TCP transcription factor --- Zea mays L. --- MADS transcription factor --- ZmES22 --- starch --- flowering time --- gene-by-gene interaction --- Hd1 --- Ghd7 --- rice --- yield trait --- Oryza sativa L. --- leaf shape --- yield trait --- molecular breeding --- hybrid rice --- nutrient use efficiency --- quantitative trait loci (QTLs), molecular markers --- agronomic efficiency --- partial factor productivity --- P. suffruticosa --- R2R3-MYB --- overexpression --- anthocyanin --- transcriptional regulation --- ethylene-responsive factor --- Actinidia deliciosa --- AdRAP2.3 --- gene expression --- waterlogging stress --- regulation --- Chrysanthemum morifolium --- WUS --- CYC2 --- gynomonoecy --- reproductive organ --- flower symmetry --- Hs1pro-1 --- cZR3 --- gene pyramiding --- Heterodera schachtii --- resistance --- tomato --- Elongated Internode (EI) --- QTL --- GA2ox7 --- n/a

Plant Innate Immunity 2.0

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ISBN: 9783038975809 Year: Pages: 386 DOI: 10.3390/books978-3-03897-581-6 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Biology --- Science (General)
Added to DOAB on : 2019-04-05 10:34:31
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Plants possess a rather complex and efficient immune system. During their evolutionary history, plants have developed various defense strategies in order to recognize and distinguishing between self and non-self, and face pathogens and animal pests. Accordingly, to study the plant innate immunity represents a new frontier in the plant pathology and crop protection fields. This book is structured in 6 sections. The first part introduces some basic and general aspects of the plant innate immunity and crop protection. Sections 2–5 focus on fungal and oomycete diseases (section 2), bacterial and phytoplasma diseases (section 3), virus diseases (section 4), and insect pests (section 5), with a number of case studies and plant–pathogen/pest interactions. The last section deals with plant disease detection and control. The book aims to highlight new trends in these relevant areas of plant sciences, providing a global perspective that is useful for future and innovative ideas.

Keywords

dieback --- disease management --- Lasiodiplodia theobromae --- mango --- pathogenicity --- Bromoviridae --- plant–virus interactions --- plant defense response --- Prune dwarf virus --- replication process --- systemic and local movement --- plant proteases --- plant immunity --- MTI --- ETI --- SAR --- ISR --- RNA silencing --- RTNLB --- Agrobacterium --- biotic stress responses --- calcium --- calcium signature --- calmodulin --- CMLs --- CDPKs --- plant immunity --- symbiosis --- cell wall --- cellulose synthase --- hypersensitive response --- pathogenesis related-protein 2 --- plant-virus interaction --- Potato virus Y --- ultrastructure --- aphid resistance --- Arabidopsis thaliana --- hydroperoxide lyase --- Macrosiphum euphorbiae --- Myzus persicae --- Solanum lycopersicum --- ?-3 fatty acid desaturase --- Arabidopsis --- azelaic acid --- glycerol-3-phosphate --- light dependent signalling --- methyl salicylate --- N-hydroxypipecolic acid --- pipecolic acid --- salicylic acid --- SAR signalling --- spectral distribution of light --- tobacco --- rice --- Chilo suppressalis --- mitogen-activated protein kinase 4 --- jasmonic acid --- salicylic acid --- ethylene --- herbivore-induced defense response --- downy mildew --- grapevine --- PRRs --- PTI --- VaHAESA --- bismerthiazol --- rice --- induced defense responses --- chemical elicitors --- Sogatella furcifera --- defense-related signaling pathways --- tomato gray mold --- tomato leaf mold --- Bacillus subtilis --- biological control --- Capsicum annuum --- Ralstonia solanacearum --- CaWRKY40b --- immunity --- negative regulator --- transcriptional modulation --- Capsicum annuum --- CaWRKY22 --- immunity --- Ralstonia Solanacearum --- WRKY networks --- metabolomics --- plant defence --- plant–microbe interactions --- priming --- pre-conditioning --- citrus decline disease --- Citrus sinensis --- Bakraee --- “Candidatus Liberibacter” --- “Candidatus Phytoplasma” --- microbiota --- innate immunity --- basal defense --- rice blast --- Magnaporthe oryzae --- proteomics --- iTRAQ --- candidate disease resistance gene --- disease resistance --- downy mildew --- garden impatiens --- leaf transcriptome --- New Guinea impatiens --- RNA-Seq --- polyphenol oxidase --- Camellia sinensis --- Ectropis obliqua --- wounding --- regurgitant --- rice --- OsGID1 --- gibberellin --- herbivore-induced plant defenses --- Nilaparvata lugens --- plant protection products --- agrochemicals --- sustainable crop protection --- food security

Salinity Tolerance in Plants

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ISBN: 9783039210268 / 9783039210275 Year: Pages: 422 DOI: 10.3390/books978-3-03921-027-5 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology --- Biochemistry
Added to DOAB on : 2019-06-26 10:09:00
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Salt stress is one of the most damaging abiotic stresses because most crop plants are susceptible to salinity to different degrees. According to the FAO, about 800 million Has of land are affected by salinity worldwide. Unfortunately, this situation will worsen in the context of climate change, where there will be an overall increase in temperature and a decrease in average annual rainfall worldwide. This Special Issue presents different research works and reviews on the response of plants to salinity, focused from different points of view: physiological, biochemical, and molecular levels. Although an important part of the studies on the response to salinity have been carried out with Arabidopsis plants, the use of other species with agronomic interest is also notable, including woody plants. Most of the conducted studies in this Special Issue were focused on the identification and characterization of candidate genes for salt tolerance in higher plants. This identification would provide valuable information about the molecular and genetic mechanisms involved in the salt tolerance response, and it also supplies important resources to breeding programs for salt tolerance in plants.

Keywords

Arabidopsis --- Brassica napus --- ion homeostasis --- melatonin --- NaCl stress --- nitric oxide --- redox homeostasis --- Chlamydomonas reinhardtii --- bZIP transcription factors --- salt stress --- transcriptional regulation --- photosynthesis --- lipid accumulation --- Apocyni Veneti Folium --- salt stress --- multiple bioactive constituents --- physiological changes --- multivariate statistical analysis --- banana (Musa acuminata L.) --- ROP --- genome-wide identification --- abiotic stress --- salt stress --- MaROP5g --- rice --- genome-wide association study --- salt stress --- germination --- natural variation --- Chlamydomonas reinhardtii --- salt stress --- transcriptome analysis --- impairment of photosynthesis --- underpinnings of salt stress responses --- chlorophyll fluorescence --- J8-1 plum line --- mandelonitrile --- Prunus domestica --- redox signalling --- salicylic acid --- salt-stress --- soluble nutrients --- Arabidopsis thaliana --- VOZ --- transcription factor --- salt stress --- transcriptional activator --- chlorophyll fluorescence --- lipid peroxidation --- Na+ --- photosynthesis --- photosystem --- RNA binding protein --- nucleolin --- salt stress --- photosynthesis --- light saturation point --- booting stage --- transcriptome --- grapevine --- salt stress --- ROS detoxification --- phytohormone --- transcription factors --- Arabidopsis --- CDPK --- ion homeostasis --- NMT --- ROS --- salt stress --- antioxidant enzymes --- Arabidopsis thaliana --- ascorbate cycle --- hydrogen peroxide --- reactive oxygen species --- salinity --- SnRK2 --- RNA-seq --- DEUs --- flax --- NaCl stress --- EST-SSR --- Salt stress --- Oryza sativa --- proteomics --- iTRAQ quantification --- cell membrane injury --- root activity --- antioxidant systems --- ion homeostasis --- melatonin --- salt stress --- signal pathway --- SsMAX2 --- Sapium sebiferum --- drought, osmotic stress --- salt stress --- redox homeostasis --- strigolactones --- ABA --- TGase --- photosynthesis --- salt stress --- polyamines --- cucumber --- abiotic stresses --- high salinity --- HKT1 --- halophytes --- glycophytes --- poplars (Populus) --- salt tolerance --- molecular mechanisms --- SOS --- ROS --- Capsicum annuum L. --- CaDHN5 --- salt stress --- osmotic stress --- dehydrin --- Gossypium arboretum --- salt tolerance --- single nucleotide polymorphisms --- association mapping. --- n/a

Evolution, Composition and Regulation of Supernumerary B Chromosomes

Authors: --- --- ---
ISBN: 9783038977865 / 9783038977872 Year: Pages: 254 DOI: 10.3390/books978-3-03897-787-2 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology
Added to DOAB on : 2019-08-28 11:21:28
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Supernumerary B chromosomes (Bs) are dispensable genetic elements found in thousands of species of plants and animals, and some fungi. Since their discovery more than a century ago, they have been a source of puzzlement, as they only occur in some members of a population and are absent from others. When they do occur, they are often harmful, and in the absence of “selfishness”, based on mechanisms of mitotic and meiotic drive, there appears to be no obvious reason for their existence. Cytogeneticists have long wrestled with questions about the biological existence of these enigmatic elements, including their lack of any adaptive properties, apparent absence of functional genes, their origin, sequence organization, and co-evolution as nuclear parasites. Emerging new technologies are now enabling researchers to step up a gear, to look enthusiastically beyond the previous limits of the horizon, and to uncover the secrets of these “silent” chromosomes. This book provides a comprehensive guide to theoretical advancements in the field of B chromosome research in both animal and plant systems.

Keywords

repetitive elements --- RNA-Seq --- genomics --- evolution --- cytogenetics --- supernumerary elements --- extra chromosomes --- B chromosomes --- transmission --- drive --- host/parasite interaction --- supernumerary chromosomes --- karyotype evolution --- genome instability --- supernumerary chromosomes --- heterochromatin --- parent-of-origin effects --- paternal X chromosome --- maternal X chromosome --- controlling element --- teleost --- population analysis --- whole genome resequencing --- DNA copy number variation --- ribosomal DNA --- B chromosomes --- FISH (fluorescence in situ hybridisation) --- GISH (genomic in situ hybridisation) --- Prospero autumnale complex --- supernumerary chromosomal segments (SCS) evolution --- tandem repeats --- Drosophila --- supernumerary --- satellite DNA --- sSMC --- B chromosomes --- dot-like (micro) Bs --- karyotypic characteristics --- ?s --- B morphotypes --- Apodemus peninsulae --- maize B chromosome --- centromere --- inactivation --- reactivation --- de novo centromere formation --- epigenetics --- supernumerary chromosomes --- additional chromosomes --- chromosome polymorphism --- evolution --- B chromosomes --- karyotypes --- genome evolution --- interphase nucleus --- mammals --- genes --- repetitive DNA --- transcription of heterochromatin --- B chromosomes --- grasshoppers --- DNA composition --- repeat clusters --- euchromatin degradation --- microdissected DNA probes --- B chromosome --- satellite DNA --- mobile element --- organelle DNA --- chromosome evolution --- fluorescent in situ hybridization --- Orthoptera --- satellite DNA --- supernumerary chromosome --- RepeatExplorer --- supernumerary chromosomes --- B chromosomes --- next-generation sequencing --- coverage ratio analysis --- n/a --- B chromosome --- transmission --- origin --- drive --- n/a

New Advances on Zika Virus Research

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ISBN: 9783038977643 Year: Pages: 552 DOI: 10.3390/books978-3-03897-765-0 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Internal medicine --- Medicine (General)
Added to DOAB on : 2019-04-05 10:34:31
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Zika virus (ZIKV) is a mosquito-borne member of the Flaviviridae family that historically has been associated with mild febrile illness. However, the recent outbreaks in Brazil in 2015 and its rapid spread throughout South and Central America and the Caribbean, together with its association with severe neurological disorders—including fetal microcephaly and Guillain-Barré syndrome in adults—have changed the historic perspective of ZIKV. Currently, ZIKV is considered an important public health concern that has the potential to affect millions of people worldwide. The significance of ZIKV in human health and the lack of approved vaccines and/or antiviral drugs to combat ZIKV infection have triggered a global effort to develop effective countermeasures to prevent and/or treat ZIKV infection. In this Special Issue of Viruses, we have assembled a collection of 32 research and review articles that cover the more recent advances on ZIKV molecular biology, replication and transmission, virus–host interactions, pathogenesis, epidemiology, vaccine development, antivirals, and viral diagnosis.

Keywords

Ziks virus --- silvestrol --- antiviral --- eIF4A --- hepatocytes --- flavivirus --- arbovirus --- Zika --- sexual transmission --- testis --- prostate --- Zika virus --- ZIKV --- rhesus macaques --- Non-human primates --- NHP --- infection --- natural history --- Asian-lineage --- African-lineage --- zika virus --- ZIKV–host interactions --- viral pathogenesis --- cell surface receptors --- antiviral responses --- viral counteraction --- cytopathic effects --- microcephaly --- ZIKV-associated neurologic disorders --- Zika virus --- serology --- flavivirus --- microsphere immunoassay --- validated --- optimised --- dengue virus --- ZIKV --- reporter virus --- cryptic promoter silencing --- full-length molecular clone --- subgenomic replicon --- plasmid toxicity --- Zika virus --- dengue viruses --- flavivirus --- ELISA --- indirect immunofluorescence --- plaque reduction neutralization test --- polymerase chain reaction --- cross-reactions --- Zika virus --- flavivirus --- infectious cDNA --- replication --- gene expression --- neuropathogenesis --- viral genetic variation --- host genetic variation --- flavivirus --- Zika virus --- therapy --- host-directed antivirals --- Aedes aegypti --- RNA-seq --- insecticide resistance --- Zika virus --- detoxification and immune system responses --- Zika virus --- mosquito-borne flavivirus --- emerging arbovirus --- outbreak control --- molecular diagnostics --- laboratory preparedness --- assay standardization --- external quality assessment --- EQA --- QCMD --- flavivirus --- eye --- zika virus --- blood-retinal barrier --- ocular --- innate response --- Zika virus --- pregnancy --- fetal infection --- congenital Zika syndrome --- Asian lineage --- Zika virus --- Full-length cDNA infectious clones --- Bacterial artificial chromosome --- NS2A protein --- Zika virus --- neural progenitor cells --- neurons --- Zika virus --- antivirals --- therapeutics --- research models and tools --- flavivirus --- Zika virus (ZIKV) --- reverse genetics --- infectious clone --- full-length molecular clone --- bacterial artificial chromosome --- replicon --- infectious RNA --- Zika virus --- flavivirus --- arbovirus --- sexual transmission --- host genetic variation --- immune response --- Zika virus --- flaviviruses --- vaccines --- virus like particles --- clinical trials --- ZIKV --- NS1 protein --- Zika virus --- diagnosis --- monoclonal antibodies --- ELISA --- zika virus --- placenta cells --- microglia cells --- siRNA --- TLR7/8 --- Zika --- viral evolution --- genetic variability --- Bayesian analyses --- Zika virus --- reverse genetics --- infectious cDNA --- Tet-inducible --- MR766 --- FSS13025 --- flavivirus --- ZIKV --- NS5 --- type I IFN antagonist --- point-of-care diagnostics --- isothermal nucleic acid amplification --- nucleic acid computation --- nucleic acid strand exchange --- zika virus --- mosquito --- mosquito surveillance --- multiplex nucleic acid detection --- boolean logic-processing nucleic acid probes --- Zika virus --- flavivirus --- astrocytomas --- dsRNA --- viral fitness --- antiviral --- heme-oxygenase 1 --- Zika virus --- viral replication --- Zika virus --- antiviral compounds --- neural cells --- viral replication --- flavivirus --- Zika virus --- viral persistence --- testicular cells --- testes --- Zika virus --- prM-E proteins --- viral pathogenicity --- virus attachment --- viral replication --- viral permissiveness --- viral survival --- apoptosis --- cytopathic effects --- mutagenesis --- chimeric viruses --- human brain glial cells --- Zika virus --- flavivirus --- microRNAs --- neurons --- neuroinflammation --- anti-viral immunity --- Zika virus --- dengue virus --- secondary infections --- cross-reactions --- IgA --- IgG avidity tests

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