Solanum section Petota are complicated and the section seems overclassified. Many of the presumed (sub)species from South America are very similar and they are able to exchange genetic material. We applied a population genetic approach to evaluate support for subgroups within this material, using AFLP data. Our approach is based on the following assumptions: (i) accessions that may exchange genetic material can be analyzed as if they are part of one gene pool, and (ii) genetic differentiation among species is expected to be higher than within species.The taxonomy and systematic relationships among species of Petota could be arranged in 16 clusters of various size and composition. Next, the accessions within the clusters were grouped by maximizing the partitioning of genetic diversity among subgroups  for all available individuals of the accessions (2767 genotypes). This two-step approach produced an optimal partitioning into 44 groups.A dataset of 566 South-American accessions (encompassing 89 species and subspecies) was analyzed in two steps. First, with the program STRUCTURE 2.2 in an 'unsupervised' procedure, individual accessions were assigned to inferred clusters based on genetic similarity. The results showed that the South American members of section Some of the species clustered as genetically distinct groups, either on their own, or combined with one or more other species. However, accessions of other species were distributed over more than one cluster, and did not form genetically distinct units.We could not find any support for 43 species . For 28 species some level of support could be found varying from good to weak. For 18 species no conclusions could be drawn as the number of accessions included in our dataset was too low. These molecular data should be combined with data from morphological surveys, with geographical distribution data, and with information from crossing experiments to identify natural units at the species level. However, the data do indicate which taxa or combinations of taxa are clearly supported by a distinct set of molecular marker data, leaving other taxa unsupported. Therefore, the approach taken provides a general method to evaluate the taxonomic system in any species complex for which molecular data are available. Petota of the genus Solanum, is known to be problematic [Solanum species he recognized, had arisen from hybrid speciation. A quote from Correll [Tuberarium being roughly equivalent to the current section Petota).The taxonomy of wild potato species, belonging to section blematic -3. Identblematic . Hawkes blematic  hypothes Correll   in the STRUCTURE analyses, accessions of certain species may already start to be assigned to different clusters before accessions of other species would be separated from each other. When large datasets are analyzed convergence problems for the Gibbs sampler algorithm used in STRUCTURE software may occur ,28. TherPisum. The advantage is that an a priori grouping is made and accessions formerly classified under the same name may end up in different groups. An alternative option was to optimize the grouping of accessions by maximizing the Fst among the species or among combinations of species. This has two important advantages: (1) all plants within an accession can be included in this computationally simple analysis, and (2) even if several rounds of grouping are performed, it is still much faster than optimizing and performing a STRUCTURE analysis on each of the 16 clusters. A disadvantage is that accessions of the same name remain together, which may mean that in theory the best solution is less optimal than obtained with the nested STRUCTURE approach.The second level (nested) analyses could be done again by STRUCTURE for each group separately, as e.g. Jing et al.  did in PAs a pilot experiment, we performed a nested STRUCTURE analysis on a few clusters and compared the results to an Fst analysis of the same clusters. The results were compared by calculating the Fst among groups for the nested STRUCTURE analysis and for the optimized Fst approach. The optimized Fst approach always resulted in a higher value for the Fst among the groups within the cluster (not shown). We therefore decided to continue with the Fst analysis. This combination is a novel approach.The partitioning of genetic variation (Fst) among STRUCTURE clusters or among new groups within a cluster was computed using AFLP-SURV 1.0 . The allWithin each of the 16 STRUCTURE clusters we calculated Fst based on the species present using AFLP-Surv. Subsequently, combinations of accessions with different species labels were made and the overall Fst value and pairwise Fst values between the groups within a cluster were computed. We performed several rounds of grouping. Each time the accessions of those species or groups that showed a pairwise Fst of less than the observed overall Fst of the groups within the cluster were combined. This process was repeated, merging species and species groups, until further merging of groups did not increase the overall Fst value significantly.The 566 South-American accessions were analyzed using STRUCTURE, testing various numbers of groups, from K = 1 to K = 30. Figure S. okadae, S. raphanifolium, S. verrucosum, and S. macropilosum occupy exclusively one cluster, while many other accessions are found to share a cluster with accessions from one or more other species, for instance S. huancabambense with S. sogarandinum. Many accessions labeled with the same species name are distributed over two clusters, e.g. the accessions of S. maglia, S. gourlayi, S. tarijense. Finally, there is a number of species whose accessions show membership to more than two clusters. Additional file The estimated population structure of one run at K = 16 is shown in Figure The partitioning of genetic variation among the clusters (Fst) in the 16 cluster arrangement represented 31% of the genetic variation  we obtained support for additional groups within these clusters, up to a total of 44 units (or 48 units including the unknown species accessions) (Table Many described species in section s) Table . This doIf not all accessions of a species are in one cluster but one or a few are present in different clusters, this may indicate misclassification. Occurrence of different species labels intermingled within one cluster points at overclassification. From both situations we see examples in our dataset and these may have consequences for the (sub) species status of the present taxa.S. microdontum, S. vernei, S. boliviense and S. megistacrolobum. Only one of the recognized subspecies was supported in our analysis: S. commersonii subsp. malmeanum could be differentiated genetically from S. commersonii subsp. commersonii  species have been extensively studied previously, using morphology. The subspecies rodontum  and shoucal data  and withcal data . Based or et al.  studied S. raphanifolium, S. verrucosum (with S. macropilosum as synonym), S. microdontum, S. commersonii, S. okadae (only the seven accessions in cluster 15), S. huancabambense, and S. sogarandinum. The seven S. okadae accessions that appear in cluster 3 together with S. venturii accessions turned out to be mislabeled and have been corrected as being S. venturii accessions . The accessions labeled S. microdontum, S. huancabambense and S. sogarandinum share their cluster with accessions from other species, but the optimal partitioning of genetic variation within the cluster shows that they represent distinct genetic units. This is consistent with the results from Jacobs et al. [The following species are supported as genetically distinct units: s et al.  and mosts et al. ,32,36,37S. verrucosum and S. macropilosum in cluster 2, of S. kurtzianum and S. maglia in cluster 3, of S. venturii and S. okadae in cluster 3, of S. sandemanii, S. weberbauerii, and S. medians in cluster 5. Some of these combinations have already been recognized in the literature, e.g. S. macropilosum is considered a synonym of S. verrucosum [Some species are assigned to one STRUCTURE cluster, but their accessions do not form distinct genetic units within the cluster on their own, but combined with accessions from another species they do Table . These arrucosum .S. medians and S. sandemanii, but not S. weberbauerii, which name they apparently considered as a synonym . Spooner et al. [S. sandemanii and S. weberbaueri under S. medians.Spooner and Salas  recognizr et al.  synonymiS. maglia, S. doddsii, S. chacoense, S. gourlayi, S. virgultorum, S. hoopesii, S. augustii, S. tarijense S. vernei, S. infundibuliforme, S. alandiae, S. neorosii, S. sucrense, S. pachytrichum, and S. violaceimarmoratum. A major cause for this situation is probably mislabeling of accessions, although some of these species may be the product of hybridization events that occurred a long time ago. For instance, Solanum doddsii from Bolivia has been hypothesized to be a hybrid between S. alandiae and S. chacoense [The analysis showed that accessions from some species were scattered across two or even three clusters. This was the case for the accessions with the following species labels: hacoense .Misclassifications do occur since identification is often problematic due to ambiguous species characteristics. Problems with the identification of species were already addressed by Spooner and Salas  and SpooSolanum sect. Petota are the results of hybridization. Recent hybridizations can readily be recognized from the STRUCTURE analysis by the probability with which they are assigned to a particular cluster. While most accessions have a very high probability  to belong to one cluster, hybrid individuals tend to have a much lower probability (< 0.5) and have a, often only slightly lower, probability to belong to another cluster. Schulte et al. [Many authors ,4,41,42 e et al.  also argS. spegazzinii and S. gourlayi, which co-occur in northern Argentina. The S. spegazzinii accession SPG386 was assigned to cluster 3 with a probability of 0.459 and with 0.262 to cluster 16. Another example of recent hybridization is NRS737 which shows probabilities of 0.435 and 0.434 with the clusters 13 and 15, respectively. However, in all cases the actual parents are unknown.To practically present our results, we have assigned all accessions to the cluster to which it had the highest probability, but Additional file S. mochiquense, S. immite, S. chancayense in cluster 7, S. canasense, S. bukasovii, S. candolleanum, S. coelestipetalum, S. pampasense, S. ambosinum, S. marinasense, S. multidissectum, S. velardei in cluster 10, S. arnezii, S. yungasense, in cluster 12, S. incamayoense in cluster 13, S. tarijense, S. berthaultii in cluster 14, S. arac-pappa, S. leptophyes, S. ugentii, S. oplocense, S. sparsipilum, and S. brevicaule in cluster 16.Some species do appear in one cluster in the STRUCTURE analysis, but their accessions do not form a separate group in the Fst analysis, not even as part of a fixed combination with another species label. This concerns the following species: S. canasense S. bukasovii, S. candolleanum, S. coelestipetalum, S. pampasense, S. ambosinum, S. marinasense, S. velardei, S. incamayoense, S. leptophyes, S. ugentii and S. sparsipilum. Ugent [Solanum oplocense was shown to be a well-defined species using morphological data [S. berthaultii and S. tarijense should be combined. The species in cluster 7 were studied morphologically by Ames and collaborators [Solanum immite and S. chancayense among the 6 distinctive species in a group of 29 species, the remainder of which were 'difficult to distinguish'.Many species mentioned in this category are part of what is termed the 'brevicaule complex' ,8,44: S.m. Ugent  already cal data  and molecal data  nor in ocal data  and a mocal data  had alreborators , who plahttp://www.solanaceaesource.org), where Spooner and his collaborators maintain two species, S. candolleanum for the northern representatives, and S. brevicaule for the southern representatives. Cluster 7 contains almost exclusively Peruvian accessions, and some species labels in cluster 7  are associated with series Piurana [Many accessions within a cluster come from the same geographical region  exchange(d) genetic material. For exchange of genetic material at least the accessions with the different species labels should have overlapping or adjacent geographical areas, at present or in the recent past.Cluster 14 contains all Petota given in Hijmans et al. [S. augustii, S. immite and S. dolichocremastrum in cluster 7, and S. berthaultii and S. tarijense in cluster 14.Indeed, information on the distribution areas of the species of sect. s et al.  confirmsSolanum section Petota. The approach taken in the present paper was to determine the genetic distinctiveness of these species. The outcome questions the species and subspecies status of more than half of the taxonomic labels used in South American part of Solanum section Petota. The genetically distinct clusters and groups within clusters resulting from our analysis can be used as a basis for recognizing groups of species and for an evaluation of species status .Click here for file


This problem is further compounded by the fact that prostate cancer has become a major public health problem in developing countries. Thereby, global collaborations among prostate cancer scientists, clinicians, survivors and advocates are important to better understand the etiology of prostate cancer among at-risk Black men, and develop effective interventions to address these disparities.Prostate cancer continues to be the most significant cancer proven to disproportionately overburden men of African descent, especially United States (US) Black men. Unfortunately, African American race/ethnicity is one of the three primary non-modifiable risk factors confirmed for prostate cancer.Science of Global Prostate Cancer Disparities in Black Men conference was organized to:The 1. Provide opportunities for mutual learning, knowledge transfer, and collaborations among prostate cancer scientist clinicians, survivors and advocates.2. Promote trans-disciplinary and multi-disciplinary prostate cancer research globally;3. Facilitate networking among individuals involved in all aspects of prostate cancer control, education and research in Black men.4. Facilitate the development of a global community of practice to address common challenges in prostate cancer, including prevention, detection, diagnosis, treatment and survivorship.5. Contribute to a global impact against prostate cancer through research training and education programs for low-resource countries.The primary goals for participants were to:• Learn - Learn from internationally renowned speakers recognized in prostate cancer disparities and survivorship research.• Discover - Discover the latest research findings on prostate cancer Prevention, Early Detection, Diagnosis, Treatment, Survivorship and End-of-Life.• Connect - Connect with other Researchers, Clinicians, Patients, Advocates and Policy makers from North America, South America, Europe, Africa, and the Caribbean.• Share - Share ideas with other conference delegates involved in all aspects of prostate cancer control and research in Black Men.• Explore - Explore the world of trans-disciplinary prostate cancer research.• Develop - Develop a global community of practice to address common challenges in prostate cancer disparities.st Biennial Science of Global Prostate Cancer Disparities in Black Men Conference was held in the heart of downtown Jacksonville, Florida on August 27-29, 2010. A total of 96 delegates participated in the conference, including 21 patient/survivors, family, and friends. There were 15 international delegates from Africa, the Caribbean, and United Kingdom.The 1Prostate Cancer Treatment & Outcomes. The second workshop was chaired by Dr. Durado Brooks. Dr. Brooks and Dr. Kevin Stein discussed Prostate Cancer Prevention, Early Detection, and Survivorship. Dr. Brian Cleaver chaired the third workshop and discussed Research Ethics: Protection of Human Subjects in Research, a session mostly attended by international delegates. The afternoon concurrent workshops were chaired by Dr. Diane Woods, Dr. R. Renee Reams and Dr. Titilola Akinremi (Nigeria). The session chaired by Dr. Woods focused on Tools for Low Resource Countries. She presented Community-based Participatory Research and Ms. Tara Hylton discussed Cancer Registration. For the fifth workshop, Dr. Reams (chair), Dr. Yehia Daaka and Dr. Jong Park presented Tools for Molecular Basis. The last pre-conference workshop was on Research Collaboration with Low Resource Countries: Overcoming the Challenges, and was presented by Dr. Akinremi (chair) and Dr. Folakemi Odedina.There were a total of six pre-conference workshops, with three concurrent sessions in the morning and three concurrent sessions in the afternoon. Dr. Philipp Dahm chaired the first workshop. Dr. Dahm and Dr. Isaac Powell, presented the latest findings on Opening Plenary Session took place on Saturday, August 28 with opening remarks by Dr. Folakemi Odedina (Conference Chair) and program overview provided by Mr. Virgil Simons. The conference was officially opened by Senator Anthony Hill Sr . Dr. Vickie L.. Shavers  and Col. Robert E. Porter (100 Black men Jacksonville) welcomed all conference delegates, and Dr. Paul Okunieff (UF Shands Cancer Center Director) gave the Welcome Address. The key note speaker was introduced by Dr. Rick Kittles (Scientific Program Committee Co-Chair).The PSA Testing in Black Men Across the Globe: Policy Implications. This session was moderated by Dr. Charles Rosser and Mr. Anthony Grissett. The speakers/panelists were Dr. Frank Chinegwundoh ( UK), Dr. Femi Ogunbiyi (Nigeria), Dr. Robin Roberts (Bahamas) and Dr. Curtis Pettaway (USA).A Community-Academic Town Hall Forum was held on Saturday, August 28 on The key note speaker was Dr. John Carpten, PhD. Dr. Carpten is Professor and Director of Integrated Cancer Genomics Division, and Head of the Cancer Gene Discovery and Molecular Validation Unit at the Translational Genomics Research Institute. Dr. Carpten delivered an outstanding lecture on the status of the African American Hereditary Prostate Cancer Study Network. This multicenter collaboration has recruited a large number of African American families with men who have a high risk of developing prostate cancer to identify the genetic risk factors for prostate cancer.Epidemiology and Genetics and was led by Dr. Rick Kittles who presented along with Dr. Tim Rebbeck. Mr. Theodies Mitchell, Jr. chaired plenary session two, with Dr. Alexander Asea, Dr. Richard Ablin, and Dr. Philipp Dahm presenting on Prevention and treatment.Nationally and internationally renowned experts were invited to present the latest findings on prostate cancer research for the conference plenary sessions. The first plenary session focused on Psychosocial and Behavioral Factors was the focus of plenary session three which was chaired by Dr. Carole Kimberlin, and included presentations from Dr. Folakemi Odedina, as well as Dr. V. Diane Woods. Dr. Rich Segal chaired plenary session four with presentations from Dr. Isaac Powell and Dr. Camille Ragin which focused on Geographical and Outcome Variations.The Translation Continuum: Innovative Research Approaches to Addressing Prostate Cancer Disparities from Bench to Bedside to Community. Plenary session six focused on Funding Opportunities for Prostate Cancer Disparities. The session was chaired by Dr. Frank Chinegwundoh (UK) with presentations by Dr. Alexis Bakos , Dr. Carolyn Best (Department of Defense), and Dr. Ronilt Elk (American Cancer Society). The final plenary session was From Community to Bench: Researchable Community Issues on Prostate Cancer by Mr. Jim West (chair) and Dr. Willie Kimmons.Dr. Vickie L. Shavers chaired plenary session five with Dr. Rick Kittles, Dr. Femi Ogunbiyi (Nigeria), and Dr. Robin Roberts (Bahamas) presenting on Prevention & Early Detection or Prostate Cancer – Protective and Risk factors. Dr. Richard Segal and Dr. Robin Roberts (Bahamas) moderated the poster sessions. The posters presentations were Histopathological Review of Prostate Cancer in Lokoja, Nigeria by Dr. Olabode Oluwole; The Role of Dietary Fat in Prostate Cancer Risk in Jamaican Men: A Pilot Study by Dr. Ayokunle Osho; Correlation Between Gleason Grade And Age At Presentation Of Prostate Cancer in Black Men in Abeokuta, Nigeria by Dr. A. Olutunde; and Prostate Cancer: Histopathological Analysis of 66 cases by Dr. Olabode OluwoleA total of 13 abstract submissions were accepted for presentation at the conference. Four posters were presented during a 3-hour poster session on Saturday afternoon. The poster abstracts were placed in either of two categories, Prognostic Factors for Prostatic Carcinoma Among Men in Lagos, Nigeria; Dr. V. Diane Woods who discussed African American Men’s Response to Prostate Cancer Prevention and Early Detection: The Pcap Toolkit; and Dr. Kabore Aristide (Burkina Faso) who gave a presentation on Prostate Cancer Outcome in Burkina Faso.There were nine oral podium presentations. Dr. B. Lee Green was the moderator for the first oral presentation session. The presenters were Dr. M. Tokunboh Odubanjo (Nigeria) who presented on the Detecting Gene-Gene Interactions in CaP Disease in African American. During the same session, Ms. Jennifer Green presented a study on The Efficacy and Toxicity of Selective Estrogen Receptor Modulators in the LNCaP Cell Line; Dr. Rose Mary Stiffin provided an overview on The Presence of Megakaryocytes in Cancerous Prostate Cancer Tissue; and Dr. Hernan Flores-Rozas discussed the Differential Contribution of Mismatch Repair Genes in the Processing of DNA Damage.The second oral presentation session was led by Dr. R. Renee Reams, who also gave an overview of Review of Prostate Cancer Research in Nigeria and Dr. Belinda Morrison (Jamaica) gave an overview of her work on Bone Mineral Density in Jamaican Men on Androgen Deprivation Therapy for Prostate Cancer.Dr. Jong Park moderated the third oral presentation session, in which Dr. Titilola Akinremi (Nigeria) gave a presentation on the The patient and provider symposium was organized by the Prostate Net and chaired by Mr. Virgil Simons, Founder and President of Prostate Net. This symposium was a unique experience allowing patients to learn with and learn from prostate cancer providers and researchers.Patient/Survivor Track. The Patient/Survivor track was moderated by Dr. Brian Stone. He gave a presentation on the Prevention and Diagnosis of Prostate Cancer. Following Dr. Stone’s presentation , a joint session on Prostate Cancer Treatment: What’s Best for You was led by Dr. Winston Tan, Dr. Stephen Ko, and Dr. David Theil. Dr. Paul Godley presented next on Efficacy of PSA Screening for Prostate Cancer among Elderly African Americans: A Case-Control Study.Emerging Trends, Issues & Treatment in Late-Stage Disease. For the afternoon session, Dr. Brian Stone and Dr. Elisabeth Heath discussed the Treatment of Advanced Stage Disease followed by a presentation on Controlling Therapeutic Side Effects/Pain Management and by Dr. Stephen Ko and Dr. David Theil.The Keynote Luncheon was given by Dr. Oliver Sartor who discussed the Provider Track. The provider track targeted clinicians and offered CME provided by the University of Florida. Dr. Stephen Ko and Dr. David Theil opened this track with a presentation on Managing Hormone Sensitive, Non-Metastatic Relapse Prostate Cancer. The next presentation was Managing Castrate-Resistant, Metastatic Prostate Cancer by Dr. Winston Tan (chair) and Dr. Elisabeth Heath.The Prostate Cancer Patient and Provider Symposium concluded with a Joint Provider-Patient Symposium session discussing the Future of Prostate Cancer Research and How to Address Clinical Trial Barriers. This session was moderated by Dr. Elisabeth Heath and Mr. Virgil SimonsMeet the Clinical Experts session was held on Saturday, August 28 presided by Dr. Christopher Williams. Six breakfast round table discussions were held on diverse prostate cancer topics led by Dr. Christopher Williams, Dr. Durado Brooks, Dr. Chidiebere Ogo (Nigeria), Dr. Adeteru Ayoade (Nigeria), Dr. Curtis Pettaway, and Dr. Charles Rosser.To foster dialogue between patients and leading prostate cancer clinicians, a “Science of Global Prostate Cancer Disparities in Black Men” will be held biennially. The next conference will be in The Bahamas and will focus on the “Global Burden of Prostate Cancer: Economic, Clinical and Humanistic Outcomes of Prevention, Detection & Treatment”.Global collaborations are essential to better understand and effectively address the disproportionate burden of prostate cancer seen in Black men. To foster global collaborations and accelerate prostate cancer control and cure, the


Molecular Pathogenesis of Virus Infections describes our current understanding of the pathogenesis of selected virus and prion infections. The innate response is an early barrier to virus spread. In this context, O. Haller et al. describe the antiviral activity of type I interferons and the various virus-encoded countermeasures. R.P. van Rij and R. Andino review the role of RNAi as a therapeutic antiviral agent and its use by the host and virus during viral infections. J.L. Whitton gives an overview of the adaptive CD8+ T-cell immune response in the context of virus infections. G. Screaton and J. Mongkolsapaya explain potential roles of T-cell responses in dengue hemorrhagic fever. E. Turnbull and P. Borrow provide a detailed description of the ineffectual roles of the innate and immune responses in the control of HIV and the long road ahead for development of either a prophylactic or therapeutic vaccine.Transmissible spongiform encephalopathies have perhaps the most unconventional natural history of any infectious agent. J.C. Manson and R.M. Barron describe the diagnosis of transmissible spongiform encephalopathies, the appearance of new strains, and the nature of host susceptibility to disease. C.M. Dixon et al. depict the special problems presented to the host by certain RNA viruses that are maintained and persist in human populations through avoidance or inhibition of apoptosis, innate immune response, and adaptive immune response.Other viruses infect humans only as incidental hosts and cause epizootics of varying degrees. A.L. Hartman et al. review our current understanding of the pathogenesis of Ebola and Marburg filoviruses, paying particular attention to the factors that contribute to lethal disease. C. Dye and S. Siddell discuss the pathogenesis of feline coronavirus, an animal disease model that has provided insights into the study of the newly recognized disease, severe acute respiratory syndrome. R.G. Webster et al. enumerate the key influenza genes responsible for human pathogenicity, their roles in past pandemics, and the potential of avian influenza virus strains to evolve into highly pathogenic and transmissible viruses for human populations.Many viruses modify host metabolism and innate/immune responses to their own ends. L. Gray et al. describe the impact of human papillomaviruses on cell cycle and apoptosis. S.M. Lemon and K. Li review the data documenting hepatitis C virus disruption of innate intracellular antiviral defenses, including interferons and toll-like receptors. M.B. Ruiz-Arguello et al. enumerate the multiple, distinct receptor homologs and binding proteins encoded by poxviruses that target tumor necrosis factor. L.K. Dixon summarizes the multiple host pathways that are targeted at multiple levels by African swine fever virus. J.P. Stewart et al. describe the pathogenesis of murid herpesvirus 4 that supports its use as model for gammaherpesviruses. M.L. Freeman et al. provide an overview of the potential role of the immune system in the latency of the alphaherpesvirus, herpes simplex virus 1. This book is suitable for the serious student and professional and is well referenced for further reading.


Leishmania (L.) major, L. tropica and L. aethiopica. L. tropica can also visceralize and cause VL. In India, the large epidemics of VL are caused by L. donovani and cases of CL are caused by L. major and L. tropica. However, strains of L. tropica have also been isolated from Indian cases of VL.Leishmaniases are divided into cutaneous (CL) and visceral leishmaniasis (VL). In the Old World, CL is caused by L. tropica isolated from human cases of CL are genetically identical to or different from Indian strains of L. tropica isolated from human cases of VL and to see if any genetic differences found correlated with clinical outcome presenting as either CL or VL.This study was done to see if Indian strains of L. tropica, was used to characterize and identify eight strains of L. tropica isolated from human cases of CL examined in clinics in Bikaner City, Rajasthan State, north-west India. Their microsatellite profiles were compared to those of 156 previously typed strains of L. tropica from various geographical locations that were isolated from human cases of CL and VL, hyraxes and sand fly vectors.Multilocus microsatellite typing (MLMT), employing 12 independent genetic markers specific to L. tropica from Bikaner isolated from human cases of CL fell into one of the subpopulations in the population India/Asia together with strains from other Asian foci. Indian strains isolated from human cases of VL fell into the same sub-population but were not genetically identical to the Bikaner strains of L. tropica.Bayesian, distance-based and factorial correspondence analyses revealed two confirmed populations: India/Asia and Israel/Palestine that subdivided, respectively, into two and three subpopulations. A third population, Africa/Galilee, as proposed by Bayesian analysis was not supported by the other applied methods. The strains of It seems that the genetic diversity encountered between the two groups of Indian strains is mainly owing to their geographical origins rather than their different times of isolation. Also, the genetic differences seen between the dermatotropic and viscerotropic strains might be connected with the difference in pathogenicity. The leishmaniases have been divided into cutaneous (CL) and visceral leishmaniases (VL), and each of the two basic types of clinical conditions has its particular causative agents. In the Old World, CL is caused by Leishmania major, L. tropica and L. aethiopica, and VL by L. donovani and L. infantum.The leishmaniases are endemic to 98 countries in the world. With 278,000 counted cases they are one of the most neglected tropical diseases. Alvar et al.  estimateL. donovani and L. infantum can also cause CL without patent signs of visceral disease; bearing in mind that post-kala azar dermal leishmaniasis (PKDL) is a sequel to VL and not just a form of CL, and L. tropica can also visceralize and cause VL without patent cutaneous symptoms [However, it has long since been recorded that symptoms ,3. This symptoms -6.L. donovani, is of major concern since more than 100,000 cases are said to occur annually, most of them in Bihar State, north-eastern India [Leishmania have been found to cause CL in India: L. major, L. tropica and L. donovani[L. tropica and the vector of the sand fly species Phlebotomus (P.) (Paraphlebotomus) sergenti[P. sergenti is ubiquitous and the main vector for L. tropica. A strain of L. tropica was also isolated from a dog, the 'Bikaner dog strain' MCAN/IN/1971/DBKM [et al. [L. tropica was identified as the species causing the cases. Interestingly, Sharma et al. [L. tropica and, also, L. donovani among 161 cases of CL from a new epidemic focus in Himachal Pradesh, northern India. In the same focus, they also found a case of VL caused by L. tropica[L. tropica was described [P. argentipes, which is considered to be the vector of L. donovani in India, one might surmise that these cases of CL were caused by L. donovani. In Sri Lanka, strains isolated from human cases of CL were identified as L. donovani[In India, human VL caused by rn India . Human Crn India , Himacharn India , and Ker donovani where th donovani and wher sergenti,13. P. s971/DBKM ,15. Aara [et al.  have sum. tropica. More reescribed ,19. Seve donovani. Sri LanLeishmania are associated with more than one clinical condition, forming a clinical syndrome, e. g., L. tropica being associated with simple CL, leishmaniasis recidivans (LR) and VL, L. donovani with VL, CL, and oro-nasal leishmaniasis, L. aethiopica with CL, diffuse cutaneous leishmaniasis (DCL) and rare cases of mucocutaneous leishmaniasis (MCL), and L. braziliensis with CL and MCL, the human hosts are considered to be the varying part of the host-parasite relationship where the hosts' immunological status determines the clinical outcome and the parasites are considered a uniform unvarying entity. However, various means, including serological, biochemical and molecular genetic methods have shown that the different strains constituting the different leishmanial species vary, of course, among the species and also among the strains within each species, the strains of the species L. tropica particularly so [It has generally been thought that where species of larly so -23.L. tropica isolated from human cases of CL are genetically identical to or different from Indian strains of L. tropica isolated from human cases of VL; and, if they are different, how different. In doing this, the Indian strains were compared to other strains of L. tropica from many other places, isolated from cases of CL and VL from those places.The interest in this study was to see if Indian strains of L. tropica isolated from human cases of CL, secondly, their own genetic interrelationship and, then, their genetic relationship to Indian strains of L. tropica isolated from human cases of VL and many other strains of L. tropica from human cases and some from sand flies and animal hosts  was applied to determining, firstly, the microsatellite profiles of Indian strains of L. tropica is intrinsically very variable. Extensive genetic variation was confirmed by a study that investigated variation in 21 microsatellite markers of 117 strains of L. tropica from different African and Asian foci that identified ten different genetic groups [L. tropica isolated from cases of VL from Bihar State grouped in one cluster together with other strains from the Asian continent.Serological -23, biocc groups . In thatThis study was approved by the Ethics Committees of the “S.P. Medical College and associated group of hospitals” in Bikaner Rajasthan State, India.L. tropica typed genetically by MLMT were isolated in 2006 and 2007 from human cases of CL presenting at clinics in the City of Bikaner, Rajasthan State, north-west India. Their WHO codes are given in Additional file The eight strains of L. tropica of widely distributed geographical origins, most of which were isolated from human cases of CL, some of which were isolated from human cases of VL and a few of which were isolated from sand fly vectors and hyrax hosts, are also given in Additional file MLMT genotypes and genetic population affiliations of 156 strains of L. tropica used in a previous study [et al. [et al. [et al. [The number of markers for the species us study  was redu [et al.  and Jamj [et al. . Further [et al. , were moEach PCR reaction was done in a volume of 25 μl that contained 1× PCR buffer, 200 μM dNTP mix, 5 pmol fluorescence-labelled forward and unlabelled reverse primer, 1 unit Taq polymerase , and 20 ng genomic DNA. PCRs started with denaturation for 5 min at 95°C, followed by 35 cycles  was used for the subsequent analysis of the peaks. The resulting microsatellite profiles were summarized in an excel file. Strains missing data for more than two microsatellite markers were excluded from the analyses and, thus, are not listed in Additional file Fragment lengths had to be normalized for several reasons. Two different sequencers and different fluorescence dyes were used in each of two studies, this one and a previous one , which uL. tropica from Bikaner was determined and compared with the microsatellite profiles of the 156 strains typed previously.Variation in the 12 independent microsatellite markers in the eight strains of Once the input file was created with MSA version 4.05 , the BayAs an additional statistical approach based on allele frequencies, the data were processed by factorial correspondence analysis (FCA) as implemented in Genetix 4.05 . The conhttp://bioinformatics.org/~tryphon/populations/) was applied to calculate the genetic distances, using the shared alleles distance measure (DAS). The Neighbour Joining (NJ) tree based on these data was visualized by MEGA 5.1 [POPULATIONS software version 1.2.34 , and of mean number of alleles (A), observed (Ho), expected (He) heterozygosity, and the inbreeding coefficient (FIS) were performed with MSA 4.05 and GDA 1.1 [Calculations of  GDA 1.1 , respectThe whole set of samples comprised 97 different genotypes, of which 75 were unique to individual strains within the set. Six of the eight strains from Bikaner, BKC-1; -2; -10; -11; -15; -28, were of identical genotype, one, BCK-3 differed from the others in a single microsatellite marker, LIST7040, and in one strain, BCK-5, amplification failed for one marker, GA1.LtroMS 030, 031, 032) when compared to those of the four Indian strains isolated from cases of VL between 1979 and 1997 . Compared with the eight Indian strains isolated from cases of CL from Bikaner, the DNA from all four older Indian strains isolated from cases of VL showed different repeat lengths in three of the microsatellite markers, GA2, LIST7033, and LIST7040. Four other microsatellite markers, GA9n, LIST7010, LIST7027, and LIST7039, were different in at least one of the strains  values between the populations ranged from 0.30 to 0.65 , ranging from 0.06 to 0.814, was generally higher than the observed heterozygosity (Ho), ranging from 0.000 to 0.402. The inbreeding coefficients per locus (FIS) showed more positive than negative values, indicating a large number of homozygotes among these strains. The FIS value of the population Asia/India, 0.091, indicated nearly random mating  to 16 (LIST7039), with an average of 7.42  arabicus[P. (Paraphlebotomus) sergenti, which is the vector in the other Israeli foci [L. tropica. Also, it was in this focus that a strain of L. tropica was isolated from a hyrax of the species Procavia capensis and hyraxes are thought to be the animal reservoir of L. tropica[P. capensis is found all along the Great Rift Valley, which stretches from northern Syria via the Jordan Valley that separates Israel and Jordan then through East Africa to end in central Mozambique in southern Africa.A group of strains isolated in Israel formed a distinct subpopulation within the essentially African population Africa/Galilee. They came from a focus on the northern side of the Sea of Galilee and were previously shown to be genetically  and anti arabicus,44 ratheeli foci  and, in L. tropica isolated from human cases of CL, which were examined at clinics in Bikaner City. The MLMT profiles of these strains showed genetic similarities to and, also, differences from those of older Indian strains of L. tropica isolated from human cases of VL. However, all the different analyses applied to these dermatotropic and the viscerotropic strains consigned them to the same main genetic population, together with strains of L. tropica from other Asian foci. It is assumed that the genetic diversity seen among the Indian strains of L. tropica examined is not only owing to their different geographical origins but also to their different times of isolation; however, we cannot exclude the possibility of genetic differences underlying the different genotypes of Indian strains of L. tropica being responsible for their difference in pathogenicity. This might be resolved if more strains of L. tropica from different foci of CL and VL would be included in the study, including those from the focus in Himachal Pradesh where cases of both CL and VL have been caused by L. tropica.Microsatellite typing was used to genotype eight Indian strains of L. tropica from other countries, three main genetic populations, Asia/India, Israel/Palestine and Africa/Galilee, were discerned, the strains of which separated into subpopulations with some geographical anomalies occurring. Genetic changes occur in a given place at a given time for whatever reason and spread in a population from that place during more time. One can assume that genotypes that appear to be out of geographical synchronization have been imported in some way. Animals, most insects and humans travel, including animal hosts and vectors. Humans are particularly well-travelled, more so today than ever before, and their parasites go with them wherever they go. Only where suitable hosts, animal or human, and vectors are available, zoonotic or anthroponotic leishmaniases will establish themselves.In comparing the Indian strains with the strains of The authors declare that they have no competing interests.LK carried out the microsatellite typing, conducted the data analysis, and wrote the manuscript. RAB collected the samples. KA, JW, and MDM carried out microsatellite typing. LS and PS isolated the sample DNA and participated in writing the manuscript. GS designed the study, participated in data analysis and writing the manuscript. All authors have read and approved the final manuscript.Ltro indicates L. tropica and MS microsatellite, in an attempt to initiate a standardized nomenclature and identification system for microsatellite profiles and their corresponding genotypes. Doc = documentation: *cited in Schwenkenbecher et al., 2006; **this study, ***own unpublished data. The fragment lengths are given in bp and were normalized to the reference strain MHOM/PS/2001/ISL590 as mentioned in the methods section.Strains used in this study. Doubled strains in the table represent different clones of the same strain received from different laboratories. In the genotype designations Click here for fileA: calculation for all strains in this study to specify the number of main populations, B-D: sub-structuring of the proposed populations .Calculation of the most probable number of populations, ∆K, based on the results of Bayesian statistics. Click here for fileFST values calculated for the three main populations identified by Bayesian analyses. FST estimates describe the genetic distances resulting from pairwise comparison of the distinct populations. Values are categorized into little (<0.05), moderate (0.05-0.15), great (0.15-0.25), and very great (>0.25) genetic differentiation.Click here for file


Epicrates (Boidae) presented only one continental species, Epicrates cenchria, distributed in Central and South America, but after a taxonomic revision using morphologic characters five species were recognized: E. cenchria, E. crassus, E. maurus, E. assisi, and E. alvarezi. We analyzed two independent data sets, environmental niche models and phylogeny based on molecular information, to explore species delimitation in the continental species of this genus. Our results indicated that the environmental requirements of the species are different; therefore there are not evidences of ecological interchangeability among them. There is a clear correlation between species distributions and the major biogeographic regions of Central and South America. Their overall distribution reveals that allopatry or parapatry is the general pattern. These evidences suggest that habitat isolation prevents or limits gene exchange among them. The phylogenetic reconstruction showed that the continental Epicrates are monophyletic, being E. alvarezi the sister species for the remaining two clades: E. crassus - E. assisi, and E. maurus - E. cenchria. The clade grouping the continental Epicrates is the sister taxon of the genus Eunectes and not of the Caribbean Epicrates clade, indicating that the genus is paraphyletic. There is a non-consistent pattern in niche evolution among continental Epicrates. On the contrary, a high variation and abrupt shifts in environmental variables are shown when ancestral character states were reconstructed on the sequence-based tree. The degree of genetic and ecological divergence among continental Epicrates and the phylogenetic analyses support the elevation to full species of E. cenchria, E. crassus, E. maurus, E. assisi, and E. alvarezi.Until recently, the genus  Accurate species delimitation is one of the most basic tasks in systematic research. However, lineages separation is a temporally extended process that may result in populations with all or some of the following features: reciprocal monophyly, reproductive isolation, ecological divergence, and morphological distinctiveness Epicrates, nine insular species distributed in the region of the Great Antilles and the Bahamas have been recognized, and until recently only one continental species, Epicrates cenchriaE. c. cenchria, E. c. maurus, E. c. alvarezi, E. c. gaigei, E. c. crassus, E. c. barbouri, E. c. polylepis, E. c. hygrophilus and E. c. assisiE. cenchria, covering areas with very different environmental conditions and the fact that some morphotypes present an important degree of differentiation in color patterns and meristic characters E. c. cenchria, E. c. maurus and/or E. c. crassus to the rank of full species Epicrates cenchria complex based on an analysis of the morphological variation in meristic, color pattern and morphometric characters proposed a new taxonomic arrangement, which comprises the species E. cenchria , E. crassus (including E. c. polylepis), E. maurus (including E. c. barbouri), E. assisi, and E. alvareziEpicrates group.In the genus Ecological divergence is an important step in the process of speciation The use of molecular markers also contributes to establish species limits since they provide solid information about the phylogenetic relationships among the taxa and/or individuals. Moreover, levels of genetic divergence among closely related recognized species can serve to systematists to infer, by comparison, the status of the evolutionary independent lineages observed in groups presenting a controversial taxonomy Epicrates combining two independent data sets, environmental niche models and phylogeny based on molecular information. We also compared our results with the previously obtained from morphological data, predicting that morphologically distinctive species will also be ecologically and genetically divergent. Additionally, we assessed whether the genetic variation across lineages is associated with divergence in the ecological niche.The aim of this study was to explore species delimitation in the continental forms of the genus E. maurus (5.8%). On the other hand, annual precipitation makes a large contribution only to the E. cenchria model. The assessment of the Maxent models accuracy by “receiver operated characteristics” (ROC) plots indicates that the models predicted for each continental species of the genus Epicrates are robust, with high values of “area under the curve” (AUC)  .E. alvarezi, E. crassus, E. assisi, E. cenchria and E. maurus are shown in The predicted distribution for each species was nearly identical in Maxent and GARP. The areas of probable occurrence determined by their respective models for E. alvarezi , in Central and East of Bolivia and West of Brazil. Epicrates alvarezi distributes allopatrically with respect to all the other members of the genus Epicrates.The overall distribution of the five species reveals that allopatry or parapatry is the general pattern. Small or none overlapping zones between species were detected , except P≤0.001). Furthermore, the statistically significant separation among species occurs along the three PC axes .The PCA analysis revealed three components that collectively explain more than the 84% of the variation, with each PC responsible for 51%, 22% and 11% of the variation, respectively. The PC1 depicts a gradient from subtropical sites with a marked cold and dry winter, to tropical sites with higher temperatures . The PC2The MP and BI phylogenetic trees of each partition produced highly congruent estimates of phylogenetic relationships among the taxa; in general, the nodes received less support in the MP analyses .Epicrates, the second clade groups those of the genus Eunectes and the third clade clusters all the sequences of the continental Epicrates. Within this last clade, E. alvarezi is recovered as the sister taxon of the rest of the lineages of the continental Epicrates. Epicrates crassus appears as the sister taxa of E. assisi and E. cenchria, of E. maurus. In this last clade, one sequence of Epicrates cenchria  to 13.9% . Epicrates alvarezi is the most genetically divergent of the continental clade. The sequence U69777 presents similar levels of genetic distance with E. cenchria and with E. maurus (2.6% and 2.7% respectively); given the uncertainty about the taxonomy of the specimen, this sequence was not considered in the genetic distance analysis. Among the Caribbean Epicrates the values of genetic distances are the highest, 14.2% on average, ranging from 6.0% (E. crisogaster-E. exsul) to 17.5% (E. angulifer-E. striatus). Between the species of the genus Eunectes the genetic distance was 12.1%. Within species, the genetic distances are, on average, 0.8% and 1.4% for the continental and Caribbean Epicrates, respectively . Sister species pairs showed different trends: E. maurus presents little divergence in genetic and moderate divergence in ecological distances with E. cenchria , but it is ecologically more similar to E. assisi despite their genetic differences .A non directional niche evolution is observed in the continental Epicrates are shown in the reconstruction of ancestral character states of environmental variables on the sequence-based tree  The environmental niche models obtained from our data are in agreement with the known distribution of each species Epicrates. This is shown by the fact that the relative contribution of each environmental parameter is taxon specific  to clarify the relationships among the population of this area and the continental species of Epicrates.In accordance with the new taxonomic arrangement Epicrates that includes all continental species and the majority of the Caribbean ones. The phylogenetic trees obtained with MP and BI show three well supported clades: the Caribbean Epicrates, the species of the genus Eunectes and the continental Epicrates. The three clades are grouped in a polytomy in the mtDNA tree, but in the nDNA+mtDNA analyses, this polytomy is resolved indicating that the Caribbean Epicrates are the sister taxon of the clade formed by the continental Epicrates and by the species of the Eunectes genus. This clearly indicated that the genus Epicrates is not monophyletic. The paraphyly of the genus was suggested in previous phylogenetic analyses of Boinae. Burbrink, using cytochrome b gene as molecular marker, recovered the continental Epicrates as the sister taxon of the Caribbean Epicrates and the Eunectes clade Epicrates outside the cluster grouping the continental Epicrates and Eunectes murinusEpicrates, E. cenchria, since they were performed before the new taxonomic arrangement Epicrates, eight of the nine species of the Caribbean Epicrates and two of the three species of Eunectes, which greatly increases the reliability of the phylogenetic outcome obtained. Besides, the basal position of the clade grouping the insular Epicrates supports the hypothesis of a divergence between the South American Epicrates and Eunectes, posterior to the split of the Caribbean group.This is the first molecular phylogenetic analysis of the genus Epicrates, it was suggested that speciation could have been inhibited because of the high levels of gene flow that kept the populations connected Epicrates are lower than those found among Caribbean species, they are similar to those obtained between the two well recognized species of the genus Eunectes here analyzed, thus confirming that lineage diversification has also occurred in the continental species.Regarding the speciation pattern in the continental Epicrates. Epicrates alvarezi is recovered as the sister taxon of the clade, which contains the rest of the species. In agreement with this result, E. alvarezi is the most distinct taxa in morphological characters among the continental Epicrates, showing several exclusive features E. crassus appears as the sister taxon of E. assisi and E. cenchria as the sister taxon of E. maurus.The four phylogenetic trees (MP and BI) here presented clearly support the monophyly of the continental Epicrates, there is a non-consistent pattern in niche evolution, as indicated by the lack of correlation between niche similarity and genetic distance. The reconstruction of ancestral characters on the phylogenetic tree shows important variations in environmental variables like elevation, temperature seasonality and minimum temperature of the coldest month. From a hypothetical subtropical ancestor, two different pathways diverge: on one hand, a lineage inhabiting tropical non seasonal areas, represented by E. cenchria and E. maurus; on the other hand, the branch comprising E. alvarezi, a species distributed in template, highly seasonal areas. However, our present data are not enough to assess a possible role of the ecological divergence in the speciation process in the group.Within the continental Epicrates and the phylogenetic analyses here performed support the elevation of E. cenchria, E. crassus, E. maurus, E. assisi, and E. alvarezi to the rank of species suggested by morphological data Epicrates.To sum up, the degree of genetic and ecological divergence among continental Epicrates. The database used includes a total of 105 points of presence of Epicrates alvarezi, 98 of E. crassus, 43 of E. assisi, 56 of E. cenchria and 69 of E. maurus that were gathered from the authors' field data, museum records obtained from http://splink.cria.org.br/ and http://www.herpnet.org/ and literature records We obtained presence data from the five recognized continental species of the genus http://www.ittvis.com/).Two types of variables were used as predictors: topographic  derived from a digital elevation model, and bioclimatic, both obtained from WorldClim To avoid over-parameterize the analyses we extracted the environmental information from each species presence data and performed Pearson correlation tests. For pairs of variables that were highly correlated (coefficient ≥0.8), the variable considered easier to interpret biologically was chosen Several methods are used to estimate the probability area of occurrence of a species from presence-only data; these methods can result overly permissive or overly restrictive GARP uses the values of environmental variables of known occurrences and pseudo-absence data to create a model of the specific requirements of the taxon. We used the “best subsets” procedure http://www.infostat.com.ar/).A principal component analysis (PCA) was made using values of the environmental variables of each pixel with an observed presence record to examine the overall level of divergence in environmental space among the five species studied and to assess which environmental gradients separate the species. To determine whether separation in environmental space was statistically significant, a multivariate analysis of variance (MANOVA) was performed. The species were the fixed factor and PC scores were the dependent variables. A significant MANOVA score indicates potential non-overlap of ecological niche Epicrates, eight of the Caribbean species of Epicrates and two species of the sister genus Eunectes (E. notaeus and E. murinus). Corallus hortulanus and Boa constrictor occidentalis were used as outgroups for phylogenetic reconstructions.We studied specimens of the five continental b (Cyt-b) gene and three nuclear genes, neurotrophin-3 (NT-3), recombination-activating protein 1 (RAG-1) and oocyte maturation factor (c-mos). Primer sequences for these loci are obtained from the literature http://www.macrogenusa.com) in an ABI PRISM 3730x1 DNA automatic analyzer . Sequences obtained in the present study have been deposited in GenBank  and combined mitochondrial and nuclear DNA. For MP analysis, the TNT program Multiple-sequence alignments were done with MUSCLE For BI, the most appropriate model of sequence evolution was selected using JModeltest b gene. The nuclear genes were not used to calculate genetic distances due to their low level of variability, and the absence of data for some species.The Kimura 2 parameter genetic distance (K2P) was calculated using the Cyt-http://www.marksgeneticsoftware.net/tfpga.htm) and 10000 permutations were used in significance testing.To assess whether genetic variation across species is associated with divergence in the ecological niche, a Mantel test http://compare.bio.indiana.edu) was used To estimate overall trends in evolution of niche traits, the Phylogenetic Generalized Least Squares method (PGLS) implemented in COMPARE 4.6b Click here for additional data file.Appendix S2List of the presence data use for the environmental niche model in the continental Epicrates.(DOC)Click here for additional data file.


The sequences of the 16S rRNA genes extracted from fecal samples provide insights into the dynamics of fecal microflora. This potentially gives valuable etiological information for patients whose conditions have been ascribed to unknown pathogens, which cannot be accomplished using routine culture methods. We studied 33 children with diarrhea who were admitted to the Children’s Hospital in Shanxi Province during 2006.Streptococcus as the most dominant fecal bacterial genus at admission. Eight of nine children whom three consecutive fecal samples were collected had Streptococcus as the dominant fecal bacterial genus, including three in the Streptococcus bovis group and three Streptococcus sp., which was reduced during and after recovery. We isolated strains that were possibly from the S. bovis group from feces sampled at admission, which were then identified as Streptococcus lutetiensis from one child and Streptococcus gallolyticus subsp. pasteurianus from two children. We sequenced the genome of S. lutetiensis and identified five antibiotic islands, two pathogenicity islands, and five unique genomic islands. The identified virulence genes included hemolytic toxin cylZ of Streptococcus agalactiae and sortase associated with colonization of pathogenic streptococci.Nineteen of 33 children with diarrhea could not be etiologically diagnosed by routine culture and polymerase chain reaction methods. Eleven of 19 children with diarrhea of unknown etiology had S. lutetiensis and S. gallolyticus subsp. pasteurianus from children with diarrhea of unknown etiology, and found pathogenic islands and virulence genes in the genome of S. lutetiensis.We identified  Escherichia coli, Campylobacter jejuni, Shigella spp., non-typhoidal Salmonella, Giardia lamblia, Cryptosporidium spp. and Entamoeba histolytica-21S. lutgalactiae. The genptococci -25 , and four segment 16S rRNA genes  in the S. bovis group were selected for an evolutionary study. The reference strain of S. lutetiensis (accession number: EU163503) was found to be the nearest strain to the S. lutetiensis genome sequence in our study, showing the same 16S rRNA gene sequences. Compared with the nearest species S. infantarius subsp. infantarius BAA-102 and EU163504, strain 033 had two and three nucleotide differences in the 16S rRNA genes, respectively.Together with the biochemical tests, the results of 16S rRNA gene sequencing with 48 complete genomes for streptococci, two draft genomes  who provided all three specimens with unknown etiology at admission had as the dominant diarrhea . Streptodiarrhea . So, theStreptococcus as the dominant genus, and all showed a reduced the percentage of Streptococcus sp. in fecal microflora of during and after recovery. Two patients had S. salivarius as the dominant species with one showing a reduced the percentage of Streptococcus sp. in fecal microflora during and after recovery. The other patient showed an increase. Three patients had the S. bovis group as the dominant species, and all showed a reduced the percentage of S. bovis group in fecal microflora during and after recovery. This observation suggests that the association of the S. bovis group with diarrhea is worthy of further investigation.Three patients from Group C2 had S. bovis is divided into three biotypes, I , II/1 (S. lutetiensis and S. infantarius), and II/2 , based upon mannitol fermentation and β-glucuronidase activities. S. gallolyticus subsp. gallolyticus is known to be associated with endocarditis and colon carcinoma. S. infantarius, S. lutetiensis and S. gallolyticus subsp. pasteurianus are associated with non-colonic cancer and meningitis. Children with signs of gastrointestinal disturbance at presentation associated with S. bovis were also reported [reported .S. bovis group were isolated from three patients, and PFGE analysis showed that they had their own unique restriction pattern, indicating that the strains within individual patients were identical. The isolates were identified as S. lutetiensis and S. gallolyticus subsp. pasteurianus.The dominant species from the nine patients of group C were cultured and four showed that they were negative. Thirty-six strains of the S. lutetiensis strain isolated from a child with diarrhea. Two previously recognized pathogenicity islands were identified in the genome. GI-6 was found to encode a CPS gene cluster involved in the pathogenicity of S. suis[S. pneumoniae[S. bovis group. These included the putative hemolytic toxin cylZ and the sortase gene associated with adhesion and colonization [We determined and analyzed the full genome sequence of the f S. suis. GI-7 waneumoniae. Eight anization ,24,25.S. bovis group were among the predominant bacteria in some of the patients at admission, and showed a reduction in numbers during treatment and recovery. In addition, we report the first genome sequence of a S. lutetiensis isolate, identifying putative pathogenic islands and virulence genes. However, it was hard to detect all the infectious agents and there were many non-infectious factors that may cause diarrhea; therefore, additional studies are needed to clarify the potential contribution of these bacteria to diarrhea in children.We studied the dynamics of the fecal microbial community in children with diarrhea of unknown etiology and found for the first time that strains of the The authors declare that they have no competing interests.DJ, LL, ZL, HJ, CY and JX conceived and designed the experiments.DJ, SL,YXu and XB performed the experiments.CC, ZZ, PD, HW, YXiong, HZ and LW carried out the molecular genetic studies and participated in the sequence alignment.HS contributed reagents and materials. DJ, MG and JX wrote the manuscript. All authors read and approved the final manuscript.This work was supported by grants  from the Ministry of Science and Technology, the National Key Programs for Infectious Diseases of China; and by grants from the State Key Laboratory for Infectious Disease Prevention and Control, People’s Republic of China.Characteristics of patients and clinical presentation of diarrhea among children included in this study.Click here for fileDominant bacterial species in the feces of the control group.Click here for file


Solanum lycopersicum, is divided into two widely distributed varieties: the cultivated S. lycopersicum var. lycopersicum, and the weedy S. lycopersicum var. cerasiforme. Solanum pimpinellifolium is the most closely related wild species of tomato.Tomato, S. pimpinellifolium and S. l. cerasiforme during the domestication of tomato are still under debate. Some authors consider S. l. cerasiforme to be the ancestor, whereas others think that S. l. cerasiforme is an admixture of S. pimpinellifolium and the cultivated S. l. lycopersicum. It is also not clear whether the domestication occurred in the Andean region or in Mesoamerica. We characterized 272 accessions  were morphologically and genetically using the SolCap platform . The two species were distinguished in a PCA analysis and displayed a rich geographic structure. Solanum lycopersicum var. cerasiforme and S. l. lycopersicum were also differentiated in the PCA and Structure analyses, which supports maintaining them as different varieties. Solanum pimpinellifolium and the Andean S. l. cerasiforme were more diverse than the non-Andean S. lycopersicum. Solanum lycopersicum var. cerasiforme was morphologically and molecularly intermediate between S. pimpinellifolium and tomato. Solanum lycopersicum var. cerasiforme, with the exception of several Ecuadorian and Mexican accessions, is composed of the products of admixture processes according to the Structure analysis. The non-admixtured S. l. cerasiforme might be similar to the ancestral cultivars from which the cultivated tomato originated, and presents remarkable morphological diversity, including fruits of up to 6 cm in diameter. The data obtained would fit a model in which a pre-domestication took place in the Andean region, with the domestication being completed in Mesoamerica. Subsequently, the Spaniards took plants from Mesoamerica to Spain and from there they were exported to the rest of the world.The roles of  Solanum lycopersicum L., formerly Lycopersicon esculentum Mill.), with a yield of 146 million tons in 2010, is the vegetable with the highest worldwide production . Despite its economic importance, some aspects of its origin remain unclear. Most authors agree that Solanum pimpinellifolium L. is the closest wild species to the cultivated tomato, S. lycopersicum var. lycopersicum (S. l. lycopersicum), and that S. lycopersicum var. cerasiforme (S. l cerasiforme), a variety that usually grows in disturbed lands, is the ancestor of the cultivated variety. However, important aspects of the relationships between these species and varieties have yet to be completely clarified.Tomato   and their respective geographical subgroups was carried out using the Arlequin software A principal component analysis (PCA) was carried out with the smart-PCA S. pimpinellifolium group showed a clear substructure in which the coastal and montane accessions were clearly segregated. From here on we will refer to these two clusters as Peruvian and Montane S. pimpinellifolium, respectively. The groups included in the Montane region were Machala, Catamayo and Jaen and were all located in the western and central Andean valleys. These groups showed a clear latitudinal cline that separated the accessions along a geographical north-to-south axis that was clearly seen in the PCA representation.The main S. lycopersicum PCA group, the S. l. cerasiforme and cultivated tomato subgroups were almost completely segregated. The bulk of the Andean S. l. cerasiforme was distributed in a latitudinal cline that comprised the Ecuadorian and northern Peruvian accessions. The S. l. cerasiforme accessions in the Cusco region (southern Peru), which was somewhat closer to S. pimpinellifolium, represent the only exception to this cline. By contrast, the non-Andean S. l. cerasiforme occupied an intermediate position between the San Martín and Zamora S. l. cerasiforme groups and the traditional tomato varieties and heirlooms. The relationship between these S. l. cerasiforme clusters was best appreciated when all three of the first PCA components were taken into account. Whereas in the representation of the first and second components the tomato and northern Peruvian S. l. cerasiforme distributions were close and parallel .S. pimpinellifolium, S. l. cerasiforme and the cultivated tomato  and higher than that of the cultivated tomato (0.35). The polymorphism found in the different groups within these taxa also showed marked differences. For instance, in S. pimpinellifolium, the geographical groups close to the Piura region showed the highest polymorphism (Piura 0.32 and Sullana 0.34), whereas the variability in this species was reduced in the northern  and southern latitudes (e.g. Nazca 0.10).Several indexes related to diversity and heterozygosity were calculated for the different species, varieties and geographical groups . The polS. l. cerasiforme. While the polymorphism found in S. l. cerasiforme from different Andean regions  was similar to that found in S. pimpinellifolium, the genetic polymorphism in Mesoamerica was much lower (0.26). A similar degree of polymorphism (0.24) was found in the traditional cultivated varieties from the same region as well as in the heirlooms from the rest of the world (0.20). In contrast to this low polymorphism a higher level of polymorphism was detected in the modern, improved materials (0.39).Prominent differences in variability were also found within S. pimpinellifolium (13.7%) than in S. l. cerasiforme (9.7%) and S. l. lycopersicum (11.9%), but marked differences between regions were found for this parameter. In S. pimpinellifolium, the maximum heterozygosity was associated with the regions with the highest polymorphism, Piura and Sullana (57.3%), whereas heterozygosity was much lower in the north  and Pedernales (9.3%)) and in the south (Nazca (13.7%)).The ratio of observed to expected heterozygosity (expressed as a percentage) was only slightly higher in S. l. cerasiforme, regional variation in heterozygosity was also found with values as high as 40% in Sucúa and Yucatán and as low as 3% in Pasco and the Canary Islands. In the cultivated tomato, all regions had low heterozygosity, ranging from 1 to 4% for all traditional varieties, while the modern, improved varieties, which included some commercial hybrids, had higher heterozygosity (16.6%).In S. pimpinellifolium, although important differences in frequency were observed when compared to S. lycopersicum. For instance, both the standard ‘tomato’ and ‘pimpinellifolium’ types of leaf  was carried out with the quantitative and ordinal characters to assess which characters were the most discriminant between the three taxa  could be considered moderate. This result is to be expected because, while there is a marked differentiation between the three main groups, within those groups the correlation between the morphological and genetic distance should not be too high. For instance, within S. l. lycopersicum to S. l. cerasiforme as well as the transition from traditional cultivars to modern materials have deprived the Andean region of traditional tomato varieties, as all of the corresponding accessions have ended up as modern or as S. l. cerasiforme.Another potential classification pitfall occurs when distinguishing between traditional varieties and modern improved materials. It is not possible to do this classification based only on the passport data recorded at the collection site. For instance, some accessions collected in traditional markets or in small gardens could include materials derived from modern improved cultivars. Differentiating between traditional and modern varieties can be improved by employing a morphological classification that takes into account characters such as fruit size uniformity, set sequence uniformity, core size and the presence of scars on the fruit. In fact, in this study, once the morphological characterization was completed, several accessions that had been previously considered to be traditional varieties due to their passport data were classified as modern improved materials. These reclassified accessions included, among others, all of the traditional tomato varieties from Ecuador. The invasion of the traditional markets by improved foreign materials was already recorded as early as the 1950s S. pimpinellifolium, the geographic structure of the genetic variability was quite evident, and was tightly correlated with the climate characteristics of each region: the Peruvian coastal desert, the humid and temperate northern Ecuadorian forests and the montane regions of the Andes. These geographically related differences on the level of diversity already described when S. pimpinellifolium was studied with allozymes Genetic variability was not uniform among the different populations of the different taxa. In S. l. lycopersicum, the polymorphism was lower than in the other groups, especially in the non-American cultivars. This result is compatible with previous studies, for instance a recent study by Mazzucato et al. that also found low diversity in the traditional old-world tomato varieties In S. l. cerasiforme, the polymorphism found in different geographical regions was also very different: 0.48 in Ecuador, 0.49 in northern Peru, 0.27 in Mesoamerica and 0.20 in the non-American samples. Rick and Fobes S. l. cerasiforme between S. pimpinellifolium and S. l. lycopersicumIn S. l. cerasiforme was also high. The Andean S. l. cerasiforme had a morphology that was very different from the typical small, uniform fruits of S. l. cerasiforme. In this region, a high morphological variation was found which encompasses that found in S. pimpinellifolium as well as a significant part of the variation typical of the traditional tomato varieties. Especially striking is the variation found in fruit shape and size, which includes very small fruits, almost indistinguishable from those of S. pimpinellifolium, and large fruits that could easily be classified as small tomatoes. In fact, as has already been noted, in 1958 Rick S. l. cerasiforme presented in this study.The morphological diversity of S. l. cerasiforme appears as a coherent group in the PCA when compared to S. pimpinellifolium and S. l. lycopersicum, it also shows a marked substructure, especially in the Andean region. In the PCA carried out without S. pimpinellifolium, three different Andean groups could be defined in S. l. cerasiforme: Ecuador, northern Peru and southern Peru. Moreover, a marked geographical substructure is evident even within these broad regions. For instance, a clear latitudinal cline is observed in Ecuador, both in the PCA and in the Structure analyses  Dunal as the tomato ancestor. According to Brücher, L. humboldtii would have been a wild species, different from S. l. cerasiforme, with fruits between 4 and 6 cm, and with leaves similar in shape to those of S. pimpinellifolium. This species was originally collected by Humboldt and later by Brücher in the Department of Aragua, Venezuela, a region of high rainfall. The classification of the Brücher collections as L. humboldtii was questioned by Teppner S. l. cerasiforme. We consider that both the large- and small-fruited plants could both in fact be classified as S. l. cerasiforme. We have observed accessions of this variety with both large and small fruits and with different leaf types despite being genetically homogeneous and belonging to the same population  The PCA clearly showed that S. l. cerasiforme occupies an intermediate position between S. pimpinellifolium and S. l. lycopersicum, although it is closer to the latter. B) S. l. cerasiforme showed intermediate morphological characteristics in the characters that differentiate S. pimpinellifolium and S. l. lycopersicum. Especially notable in this regard are the characters related to fruit size and style position. On the other hand, there are results that reinforce the role of S. l. cerasiforme as the ancestor of tomato: A) Not all the S. l. cerasiforme accessions seemed to be admixtures according to the Structure analysis; this is the case for accessions collected in Ecuador and northern Peru. B) Most of the genome of the admixtures found in the Ecuadorian S. l. cerasiforme was similar to that of the non-admixtured S. l. cerasiforme from the Sucúa geographical group, so the Ecuadorian admixtures would always include the genome of an ancient non-admixtured S. l. cerasiforme. C) The Ecuadorian accessions, including those that are not admixtures, include plants that could easily be considered traditional small-fruited tomatoes. Moreover, the hybrid-S. l. cerasiforme hypothesis would imply that the ancestral transitional types of intermediate fruit size, created during the domestication process of S. pimpinellifolium, would have disappeared from the present variation observed in the Andean and Mesoamerican regions.Alternatively, Nesbitt and Tanksley proposed that S. l. cerasiforme inhabited a large geographical region in pre-Columbian times, ranging from the Andes to Mesoamerica, and thus the domestication of tomato could have happened in any of these locations. No clear data exists in previous studies that definitively resolves the Andean and Mesoamerican domestication hypotheses S. l. cerasiforme and S. l. lycopersicum. However, Jenkins also admitted that he did not have enough samples from the Andean regions to compare to those from Mesoamerica. This comparison was carried out by Rick and Fobes with isozymes S. l. cerasiforme. Despite this evidence, they preferred the Mesoamerican hypothesis because they also found evidence of hybridizations between S. pimpinellifolium and S. l. cerasiforme in the Andean region that may have confounded the variability measurements.S. l. cerasiforme, we propose that a pre-domestication process took place in the Andean region that created small-fruited tomato varieties adapted to high rainfall climates. These varieties were very similar to the Ecuadorian S. l. cerasiforme accessions with bigger fruits that were included in this study and to those collected by Brücher in Venezuela, which he regarded as the ancestors of the cultivated tomato. However, given the complexity of the genetic variation detected in the Andean region, we cannot completely rule out the alternative possibility that the characters typical of the cultivated tomatoes found in Andean S. l. cerasiforme could have been introduced in more recent times from foreign materials.Taking into account the aforementioned morphological and molecular data regarding Ecuadorian S. l. cerasiforme and those with larger fruits seem to be derived from modern tomato breeds. The modern cultivars are eroding the traditional varieties, as was also noted by Rick S. l. cerasiforme.This question could be better addressed if we had samples of ancient Mesoamerican and Andean tomato varieties, but this is not a trivial task. The Andean accessions collected as traditional tomato varieties in this study were later classified into two groups: those with smaller fruits were reclassified as To settle this conjecture, it would be ideal to have archaeological evidence regarding tomato fruits in pre-Inca Andean cultures, but these remains have not been found in the Andean nor in the Mesoamerican regions S. pimpinellifolium, the Mesoamerican S. l. cerasiforme is closest to the traditional Mesoamerican varieties. As has already been described, the polymorphism and heterozygosity of Mesoamerican S. l. cerasiforme is quite low, and thus the genetic diversity of the traditional varieties that descended from it is also quite low. One trait associated with the decrease in heterozygosity which occurred on the way from Andean S. pimpinellifolium to the worldwide spread of the cultivated tomato, passing through the Andean and Mesoamerican S. l. cerasiforme, is the style position, which has gradually become more inserted  developed by the SolCAP project Prior to any molecular-based analysis, the set of markers to be considered was filtered, with markers with more than 10% missing genotypes or monomorphic (with 95% criteria) being removed. Additionally, when several markers were within 10 Kilobases of one another, all but one were removed.Genetix version 4.05 software The Principal Component Analyses (PCAs) conducted to study the pattern of genetic variation among the accessions were carried out with the filtered markers by using the smartPCA application included in the Eigensoft 3.0 package The standard Köppen-Geiger climate classification displayed in the geographical maps was taken from Peel et al. candisc R library. Both the quantitative and the ordinal characters were used, whereas the nominal and binary ones were discarded for this analysis. The species classification was chosen as the classification variable.The canonical discriminant analysis conducted on the morphological data was carried out using the populations software (http://www.bioinformatics.org/project/?group_id=84). A Mantel correlation test between the genetic and morphological distances was carried out with the mantel.rtest function of the ade4 R package using 1000 permutations to assess the significance.The morphological distances were calculated using R and combining two distance matrixes All charts were prepared by coding custom scripts, available upon request, that used the matplotlib Python library.Figure S1Structure-Estimated Ln Prob of Data for different numbers of populations (K).(TIFF)Click here for additional data file.Figure S2Canonical discriminant analysis. CDA analysis of the quantitative and ordinal morphological data. The projections of the accessions on the first two canonical variables are plotted. The colors used show the different genetic groups and match those in S. pimpinellifolium (triangle), S. l. cerasiforme (square) and S. l. lycopersicum (circle).(TIFF)Click here for additional data file.Table S1Sample list and passport data.(XLS)Click here for additional data file.Table S2Genotypes determined with the SolCap array for all accessions.(CSV)Click here for additional data file.Table S3Morphological characterization data.(XLS)Click here for additional data file.


Since the introduction of continuous ambulatory peritoneal dialysis by Moncrief and Popovich in 1976, the number of patients treated with peritoneal dialysis has continuously increased. Today, approximately 200 000 patients are treated with peritoneal dialysis (PD), and the growth is particularly rapid in many Asian countries.Compared to hemodialysis, PD has been reported to be associated with similar patient survival (or even better during the first months) as well as better quality of life. Therefore, the PD first concept has been adopted in Hong Kong and Thailand. In this special issue about PD, K. Chaudhary et al. discuss the evidence for use of this concept. Then, the benefits and problems with use of PD in the rapidly growing diabetic population are discussed by A. Rocha and coworkers. Quality of life in PD patients is reported by M. Moreiras-Plaza et al., whereas P. Theofilou discusses socioeconomic factors and psychological problems such as depression and anxiety in patients with CKD.Three further articles discuss different complications in PD patients: peritonitis , calcific uremic arteriolopathy (by N. New and coworkers), and C. Kennedy et al. report a case series of patients with pleuroperitoneal leak, a rare but troublesome complication. Other four papers deal with the function of the peritoneal membrane as a dialyzing membrane. L. Oliveira and A. Rodrigues report on the impact of previous renal replacement therapy on the membrane function, whereas S. Mizuiri et al. report on the importance of peritoneal effluent markers and their relation to epithelial to mesenchymal transition, which is thought to be an important part of pathogenetic process causing long-term changes in the peritoneum. Finally, N. Jiang et al. report on the impact of a supplemented low-protein diet on peritoneal membrane transport characteristics, whereas A. W. D. Stavenuiter et al. report on the effect of different peritoneal fluid components on the membrane in a rat model.The guest editors wish to thank all authors for their valuable contributions. Without their efforts, this special issue would not have been possible.Hulya TaskapanHulya TaskapanOlof HeimburgerOlof HeimburgerCengiz UtasCengiz UtasPaul TamPaul Tam


Sequencing of the human genome has greatly impacted the proteomics-based analysis of disease by providing a framework for understanding the proteome of diseased cells, tissues, and biological fluids. Consequently, there is a growing interest in applying proteomics technologies to define protein pathways involved in various diseases, to identify new biomarkers that correlate with diseases, ideally in their early stages, and to accelerate the development of new therapeutic targets. However, disease-related proteomics applications require that we improve our ability to separate and characterize the components of complex protein mixtures in such a way as to boost both throughput and sensitivity. In response to these demands, the proteomics technologies have been improved markedly over recent years. Today, proteomics, in all its various forms, is proving to be invaluable to our understanding of the biochemistry of health and disease and will likely play a central role in the evolution of personalized medicine. In this special issue, we include reports of novel research findings together with several reviews that highlight advances in key areas. The first two papers of this special issue focus on lung cancer. The first paper, by H. C. Gong et al., addresses the profiling of receptor tyrosine kinase pathway activation and the role of key genetic mutations in human lung tumor cell lines and human lung tumors. The authors defined molecular pathways which may assist in development of targeted lung tumor therapies. Within the second paper, Q. Zhang et al. used proteomic profiling to delineate expression and subcellular localization of multiple forms of aldehyde dehydrogenase in lung adenocarcinoma cell lines. The next two papers focus on pancreatic cancer. The third paper, by R. S. Kwon and D. M. Simeone, reviews the use of protein-based biomarkers for the diagnosis of cystic tumors of the pancreas. The fourth paper, by M. Abulaizi et al., utilizes a three-step proteomic protocol  to discover candidate early detection biomarkers of pancreatic cancer.The next two papers focus on breast cancer, with the fifth paper, by D. E. Misek and E. H. Kim, reviewing the development of protein biomarkers for the early detection of breast cancer. The sixth paper, by J. He et al., addresses LC-MS/MS identification of protein biosignatures in breast tumors, as protein-based markers that correctly classify tumor subtypes and predict therapeutic response would be of great clinical utility in guiding patient treatment. The next two papers are both by M. S. Sabel et al., and focus on melanoma. The seventh paper reviews the use of proteomics for the discovery of new prognostic and predictive biomarkers. The eighth paper explores the clinical utility of serum autoantibodies that were detected in melanoma patients. The investigators profiled serum antibodies against melanoma-associated antigens to identify those that may predict nodal positivity, a widely accepted index of metastatic disease. The ninth paper, by E. H. Kim and D. E. Misek, reviews the use of glycoproteomics to identify cancer biomarkers. The tenth paper, by A. Vivekanandan-Giri et al., utilized glycoproteomics to identify novel urinary glycoprotein biomarkers of chronic kidney disease. The issue concludes with two papers that report on novel approaches and related considerations. The eleventh paper, by I. Kiyokawa et al., describes the development of a new surface coating for urinary collection tubes that minimizes the amount of urine protein adsorption onto the walls of the collection tube. Within the final paper of this special issue, T. Hagiwara et al. examine the utility of a solid-phase hexapeptide ligand library in combination with conventional plasma proteomics modalities for comprehensive profiling of intact plasma proteins. David E. MisekDavid E. MisekTadashi KondoTadashi KondoMark W. DuncanMark W. Duncan