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1.
Arch Microbiol ; 206(6): 281, 2024 May 28.
Article in English | MEDLINE | ID: mdl-38805057

ABSTRACT

As a legume crop widely cultured in the world, faba bean (Vicia faba L.) forms root nodules with diverse Rhizobium species in different regions. However, the symbionts associated with this plant in Mexico have not been studied. To investigate the diversity and species/symbiovar affiliations of rhizobia associated with faba bean in Mexico, rhizobia were isolated from this plant grown in two Mexican sites in the present study. Based upon the analysis of recA gene phylogeny, two genotypes were distinguished among a total of 35 isolates, and they were identified as Rhizobium hidalgonense and Rhizobium redzepovicii, respectively, by the whole genomic sequence analysis. Both the species harbored identical nod gene cluster and the same phylogenetic positions of nodC and nifH. So, all of them were identified into the symbiovar viciae. As a minor group, R. hidalgonense was only isolated from slightly acid soil and R. redzepovicii was the dominant group in both the acid and neutral soils. In addition, several genes related to resistance to metals (zinc, copper etc.) and metalloids (arsenic) were detected in genomes of the reference isolates, which might offer them some adaptation benefits. As conclusion, the community composition of faba bean rhizobia in Mexico was different from those reported in other regions. Furthermore, our study identified sv. viciae as the second symbiovar in the species R. redzepovicii. These results added novel evidence about the co-evolution, diversification and biogeographic patterns of rhizobia in association with their host legumes in distinct geographic regions.


Subject(s)
Phylogeny , Rhizobium , Soil Microbiology , Symbiosis , Vicia faba , Vicia faba/microbiology , Rhizobium/genetics , Rhizobium/isolation & purification , Rhizobium/classification , Mexico , Bacterial Proteins/genetics , Root Nodules, Plant/microbiology , Soil/chemistry , N-Acetylglucosaminyltransferases/genetics , Oxidoreductases/genetics , Rec A Recombinases/genetics , Multigene Family
2.
Mol Ecol ; 33(8): e17321, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38529721

ABSTRACT

Fundamental to holobiont biology is recognising how variation in microbial composition and function relates to host phenotypic variation. Sponges often exhibit considerable phenotypic plasticity and also harbour dense microbial communities that function to protect and nourish hosts. One of the most prominent sponge genera on Caribbean coral reefs is Agelas. Using a comprehensive set of morphological (growth form, spicule), chemical and molecular data on 13 recognised species of Agelas in the Caribbean basin, we were able to define only five species (=clades) and found that many morphospecies designations were incongruent with phylogenomic and population genetic analyses. Microbial communities were also strongly differentiated between phylogenetic species, showing little evidence of cryptic divergence and relatively low correlation with morphospecies assignment. Metagenomic analyses also showed strong correspondence to phylogenetic species, and to a lesser extent, geographical and morphological characters. Surprisingly, the variation in secondary metabolites produced by sponge holobionts was explained by geography and morphospecies assignment, in addition to phylogenetic species, and covaried significantly with a subset of microbial symbionts. Spicule characteristics were highly plastic, under greater impact from geographical location than phylogeny. Our results suggest that while phenotypic plasticity is rampant in Agelas, morphological differences within phylogenetic species affect functionally important ecological traits, including the composition of the symbiotic microbial communities and metabolomic profiles.


Subject(s)
Agelas , Porifera , Animals , Phylogeny , Caribbean Region , West Indies , Coral Reefs , Porifera/genetics
3.
Infect Genet Evol ; 118: 105554, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38246398

ABSTRACT

Malaria parasites are known to infect a variety of vertebrate hosts, including ungulates. However, ungulates of Amazonia have not been investigated. We report for the first time, the presence of parasite lineages closely related to Plasmodium odocoilei clade 1 and clade 2 in free-ranging South American red-brocket deer (Mazama americana; 44.4%, 4/9) and gray-brocket deer (Mazama nemorivaga; 50.0%, 1/2). We performed PCR-based analysis of blood samples from 47 ungulates of five different species collected during subsistence hunting by an indigenous community in the Peruvian Amazon. We detected Plasmodium malariae/brasilianum lineage in a sample from red-brocket deer. However, no parasite DNA was detected in collared peccary (Pecari tajacu; 0.0%, 0/10), white-lipped peccary (Tayassu pecari; 0.0%, 0/15), and tapir (Tapirus terrestris; 0.0%, 0/11). Concordant phylogenetic analyses suggested a possible co-evolutionary relationship between the Plasmodium lineages found in American deer and their hosts.


Subject(s)
Deer , Plasmodium , Animals , Phylogeny , Peru/epidemiology , Plasmodium/genetics , Perissodactyla
4.
Entropy (Basel) ; 25(7)2023 Jul 07.
Article in English | MEDLINE | ID: mdl-37509976

ABSTRACT

This paper starts by presenting an empirical finding in the U.S. stock market: Between 2001 and 2021, high productivity was achieved when the Shannon evenness-measuring the inverse of concentration-dropped. Conversely, when the Shannon evenness soared, productivity plunged. The same inverse relationship between evenness and productivity has been observed in several ecosystems. This suggests explaining this result by adopting the business ecosystem perspective, i.e., regarding the tangle of interactions between companies as an ecological network, in which companies play the role of species. A useful strategy to model such ecological communities is through ensembles of synthetic communities of pairwise interacting species, whose dynamics is described by the Lotka-Volterra generalized equations. Each community is specified by a random interaction matrix whose elements are drawn from a uniform distribution centered around 0. It is shown that the inverse relationship between productivity and evenness can be generated by varying the strength of the interaction between companies. When the strength increases, productivity increases and simultaneously the market evenness decreases. Conversely, when the strength decreases, productivity decreases and evenness increases. This strength can be interpreted as reflecting the looseness of monetary policy, thus providing a link between interest rates and market structure.

5.
Proc Natl Acad Sci U S A ; 119(31): e2204131119, 2022 08 02.
Article in English | MEDLINE | ID: mdl-35905321

ABSTRACT

Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. These proteins constitute excellent model systems to investigate how evolution relates to structure, folding, and function. Here, we propose a scheme to map evolutionary information at the sequence level to a coarse-grained model for repeat-protein folding and use it to investigate the folding of thousands of repeat proteins. We model the energetics by a combination of an inverse Potts-model scheme with an explicit mechanistic model of duplications and deletions of repeats to calculate the evolutionary parameters of the system at the single-residue level. These parameters are used to inform an Ising-like model that allows for the generation of folding curves, apparent domain emergence, and occupation of intermediate states that are highly compatible with experimental data in specific case studies. We analyzed the folding of thousands of natural Ankyrin repeat proteins and found that a multiplicity of folding mechanisms are possible. Fully cooperative all-or-none transitions are obtained for arrays with enough sequence-similar elements and strong interactions between them, while noncooperative element-by-element intermittent folding arose if the elements are dissimilar and the interactions between them are energetically weak. Additionally, we characterized nucleation-propagation and multidomain folding mechanisms. We show that the global stability and cooperativity of the repeating arrays can be predicted from simple sequence scores.


Subject(s)
Ankyrin Repeat , Protein Folding , Models, Chemical
6.
Front Microbiol ; 12: 674004, 2021.
Article in English | MEDLINE | ID: mdl-34168631

ABSTRACT

Marine sponges are known to harbor a diverse and complex microbiota; however, a vast majority of surveys have been investigating the prokaryotic communities in the north hemisphere and Australia. In addition, the mechanisms of microbial community assembly are poorly understood in this pivotal player of the ecosystem. Thus, this survey addressed the holobiome of the sponge species in the São Paulo region (Brazil) for the first time and investigated the contribution of neutral and niche processes of prokaryotic, fungal, and unicellular eukaryotic assemblage in three sympatric species Aplysina caissara, Aplysina fulva, and Tedania ignis along with environmental samples. The compositions of the holobiome associated with the sponges and detected in environmental samples were strikingly different. Remarkably, between 47 and 88% of the assigned operational taxonomic units (OTUs) were specifically associated with sponge species. Moreover, around 77, 69, and 53% of the unclassified OTUs from prokaryotic, fungal, and unicellular eukaryotic communities, respectively, showed less than 97% similarity with well-known databases, suggesting that sponges from the southwestern Atlantic coast are an important source of microbial novelty. These values are even higher, around 80 and 61% of the unclassified OTUs, when excluding low abundance samples from fungal and unicellular eukaryotic datasets, respectively. Host species were the major driver shaping the sponge-associated microbial community. Deterministic processes were primarily responsible for the assembly of microbial communities in all sponge species, while neutral processes of prokaryotic and fungal community assembly were also detected in the sympatric A. caissara and T. ignis replicates, respectively. Most of the species-rich sponge-associated lineages from this region are also found in the Northern seas and many of them might play essential roles in the symbioses, such as biosynthesis of secondary metabolites that exhibit antimicrobial and antiviral activities, as well as provide protection against host predation. Overall, in this study the microbiota was assembled by interactions with the host sponge in a deterministic-based manner; closely related sponge species shared a strong phylogenetic signal in their associated prokaryotic and fungal community traits and Brazilian sponges were a reservoir of novel microbial species.

7.
Ticks Tick Borne Dis ; 12(5): 101754, 2021 09.
Article in English | MEDLINE | ID: mdl-34126403

ABSTRACT

This study addresses a meta-analysis of the distribution of Rickettsia spp. in the Neotropical region, as well as their associations with ticks and vertebrates. A total of 219 published reports on Rickettsia in ticks in the target region were compiled, providing 599 records of 31 species of Rickettsia recorded in 50 species of Ixodidae. The aim is to capture the phylogenetic relationships between rickettsiae and the ticks carrying them in the target region, with a focus on the co-speciation ticks-rickettsiae. We compared the phylogeny of ticks, the records of rickettsiae, the environmental gradients colonized by ticks and the effect of the phylogenetic composition of vertebrates feeding ticks on the detection of Rickettsia in ticks. Results show that differences in rickettsial composition in ticks do not depend on the vertebrate's blood-source. This is the first time this result is demonstrated. This study pinpoints that some Neotropical rickettsial organisms are associated with well-defined phylogenetical clusters of ticks. Secondarily, and probably only in a few cases, rickettsiae share species of phylogenetically distant ticks distributed along a gradient of environmental traits in which the ticks overlap (i.e., the different strains of Rickettsia parkeri sensu lato). We outline the importance of some ticks that share hosts and habitat: these ticks may act as "bridges" for the circulation of rickettsial species. There are also many species of Rickettsia that have been detected so far in only one tick species, pointing to a tight relationship or to the lack of data preventing conclusions about the detection of these bacteria in other ticks. Two species, namely Rickettsia amblyommatis and Rickettsia bellii have been recorded in the majority of ticks in the region (mainly Amblyomma spp.) and seem to be not associated with definite tick species because they may be an essential symbiont of the ticks. We conclude that an adequate analysis of rickettsiae-ticks-habitat is necessary to address the human health issues derived from the infections by rickettsiae.


Subject(s)
Host-Parasite Interactions , Ixodidae/microbiology , Rickettsia , Amblyomma/classification , Animals , Biological Evolution , Ecosystem , Evolution, Molecular , Nymph/microbiology , Phylogeny , Rickettsia/classification , Rickettsia/genetics , Rickettsia/isolation & purification , South America , Tick Infestations
8.
Am J Med Genet C Semin Med Genet ; 184(4): 1060-1077, 2020 12.
Article in English | MEDLINE | ID: mdl-33325159

ABSTRACT

We carried out an exhaustive review regarding human skin color variation and how much it may be related to vitamin D metabolism and other photosensitive molecules. We discuss evolutionary contexts that modulate this variability and hypotheses postulated to explain them; for example, a small amount of melanin in the skin facilitates vitamin D production, making it advantageous to have fair skin in an environment with little radiation incidence. In contrast, more melanin protects folate from degradation in an environment with a high incidence of radiation. Some Native American populations have a skin color at odds with what would be expected for the amount of radiation in the environment in which they live, a finding challenging the so-called "vitamin D-folate hypothesis." Since food is also a source of vitamin D, dietary habits should also be considered. Here we argue that a gene network approach provides tools to explain this phenomenon since it indicates potential alleles co-evolving in a compensatory way. We identified alleles of the vitamin D metabolism and pigmentation pathways segregated together, but in different proportions, in agriculturalists and hunter-gatherers. Finally, we highlight how an evolutionary approach can be useful to understand current topics of medical interest.


Subject(s)
Skin Pigmentation , Vitamin D , Adaptation, Physiological/genetics , Biological Evolution , Humans , Skin , Skin Pigmentation/genetics , American Indian or Alaska Native
9.
Front Microbiol ; 11: 961, 2020.
Article in English | MEDLINE | ID: mdl-32508782

ABSTRACT

Over the years, many researchers have reported a great diversity of bacteriophages infecting members of the Ralstonia solanacearum species complex (RSSC). This diversity has driven bacterial evolution by leading the emergence and maintenance of bacterial defense systems to combat phage infection. In this work, we present an in silico study of the arsenal of defense systems that RSSC harbors and their evolutionary history. For this purpose, we used a combination of genomic, phylogenetic and associative methods. We found that in addition to the CRISPR-Cas system already reported, there are eight other antiphage defense systems including the well-known Restriction-Modification and Toxin-Antitoxin systems. Furthermore, we found a tenth defense system, which is dedicated to reducing the incidence of plasmid transformation in bacteria. We undertook an analysis of the gene gain and loss patterns of the defense systems in 15 genomes of RSSC. Results indicate that the dynamics are inclined toward the gain of defense genes as opposed to the rest of the genes that were preferably lost throughout evolution. This was confirmed by evidence on independent gene acquisition that has occurred by profuse horizontal transfer. The mutation and recombination rates were calculated as a proxy of evolutionary rates. Again, genes encoding the defense systems follow different rates of evolution respect to the rest of the genes. These results lead us to conclude that the evolution of RSSC defense systems is highly dynamic and responds to a different evolutionary regime than the rest of the genes in the genomes of RSSC.

10.
Acta Trop ; 208: 105515, 2020 May 12.
Article in English | MEDLINE | ID: mdl-32407792

ABSTRACT

This study focuses on the parasitic associations of mites and ticks infesting reptiles and amphibians through a multifocal approach. Herein, reptiles (n= 3,596) and amphibians (n= 919) were examined to ensure representativeness of the Brazilian herpetofauna megadiversity. The overall prevalence was calculated to better understand which were the preferred hosts for each order of Acari (Trombidiformes, Mesostigmata and Ixodida), as well as to determine which orders frequently parasitize reptiles and amphibians in Brazil, and their host specificity. Infestation rates were calculated [prevalence, mean intensity (MI) and mean abundance (MA)] for each order and species, determining which mites and ticks are more likely to be found parasitizing the ectothermic tetrapod fauna. Parasitic niches and preferred locations were recorded to help identify specific places exploited by different Acari, and to determine the host-parasite adaptations, specificity, and relationships in terms of co-evolution. In total 4,515 reptiles and amphibians were examined, of which 170 specimens were infested by mites and ticks (overall prevalence of 3.8%). Trombidiformes mites were prevalent in lizards (55.3%), followed by Ixodida on snakes (24.7%). Mesostigmata mites were the less prevalent, being identified only on Squamata reptiles (4.3% on snakes, 2.4% on lizards). In amphibians, Ixodida ticks were the most prevalent (63.2%), followed by Trombidiformes (34.6%), and lastly Oribatida (2%). From the 13 species of Trombidiformes identified, Eutrombicula alfreddugesi (19.9%) was the most abundant in terms of number of host species and infested individuals. Specimens of Ixodida, yet more common, showed low preferred locations and different values of infestation rates. Co-infestations were recorded only on snakes. Lizard mites generally adhered to the ventral celomatic area (Pterygosomatidae), and some species to the pocket-like structures (Trombiculidae). Lizards, at variance from snakes, have adapted to endure high parasitic loads with minimum effects on their health. The high number of mites recorded in the digits of toads (Cycloramphus boraceiensis, Corythomantis greening, Cycloramphus dubius, Leptodactylus latrans, Melanophryniscus admirabilis) could lead to avascular necrosis. Frogs were often infested by Hannemania larvae, while Rhinella toads were likely to be infested by Amblyomma ticks. Of note, Rhinella major toad was found infested by an oribatid mite, implying first a new parasitic relationship. The effect of high parasitic loads on critically endangered species of anurans deserves further investigation. Our results add basic knowledge to host association of mites and ticks to Brazilian reptiles and amphibians, highlighting that routine ectoparasite examination is needed in cases of quarantine as well as when for managing reptiles and amphibians in captivity given the wide diversity of Acari on the Brazilian ectothermic tetrapod fauna.

11.
Toxins (Basel) ; 12(1)2020 01 02.
Article in English | MEDLINE | ID: mdl-31906535

ABSTRACT

Toxin-antitoxin systems (TASs) are widely distributed in prokaryotes and encode pairs of genes involved in many bacterial biological processes and mechanisms, including pathogenesis. The TASs have not been extensively studied in Listeria monocytogenes (Lm), a pathogenic bacterium of the Firmicutes phylum causing infections in animals and humans. Using our recently published TASmania database, we focused on the known and new putative TASs in 352 Listeria monocytogenes genomes and identified the putative core gene TASs (cgTASs) with the Pasteur BIGSdb-Lm database and, by complementarity, the putative accessory gene TAS (acTASs). We combined the cgTASs with those of an additional 227 L. monocytogenes isolates from our previous studies containing metadata information. We discovered that the differences in 14 cgTAS alleles are sufficient to separate the four main lineages of Listeria monocytogenes. Analyzing these differences in more details, we uncovered potentially co-evolving residues in some pairs of proteins in cgTASs, probably essential for protein-protein interactions within the TAS complex.


Subject(s)
Bacterial Toxins/metabolism , Listeria monocytogenes/physiology , Toxin-Antitoxin Systems , Animals , Antitoxins , Bacterial Proteins/genetics , Genome , Genome, Bacterial , Genomics , Humans , Toxins, Biological , Virulence
12.
Acta Trop, v. 208, 105515, mai. 2020
Article in English | Sec. Est. Saúde SP, SESSP-IBPROD, Sec. Est. Saúde SP | ID: bud-3042

ABSTRACT

This study focuses on the parasitic associations of mites and ticks infesting reptiles and amphibians through a multifocal approach. Herein, reptiles (n= 3,596) and amphibians (n= 919) were examined to ensure representativeness of the Brazilian herpetofauna megadiversity. The overall prevalence was calculated to better understand which were the preferred hosts for each order of Acari (Trombidiformes, Mesostigmata and Ixodida), as well as to determine which orders frequently parasitize reptiles and amphibians in Brazil, and their host specificity. Infestation rates were calculated [prevalence, mean intensity (MI) and mean abundance (MA)] for each order and species, determining which mites and ticks are more likely to be found parasitizing the ectothermic tetrapod fauna. Parasitic niches and preferred locations were recorded to help identify specific places exploited by different Acari, and to determine the host-parasite adaptations, specificity, and relationships in terms of co-evolution. In total 4,515 reptiles and amphibians were examined, of which 170 specimens were infested by mites and ticks (overall prevalence of 3.8%). Trombidiformes mites were prevalent in lizards (55.3%), followed by Ixodida on snakes (24.7%). Mesostigmata mites were the less prevalent, being identified only on Squamata reptiles (4.3% on snakes, 2.4% on lizards). In amphibians, Ixodida ticks were the most prevalent (63.2%), followed by Trombidiformes (34.6%), and lastly Oribatida (2%). From the 13 species of Trombidiformes identified, Eutrombicula alfreddugesi (19.9 %) was the most abundant in terms of number of host species and infested individuals. Specimens of Ixodida, yet more common, showed low preferred locations and different values of infestation rates. Co-infestations were recorded only on snakes. Lizard mites generally adhered to the ventral celomatic area (Pterygosomatidae), and some species to the pocket-like structures (Trombiculidae). Lizards, at variance from snakes, have adapted to endure high parasitic loads with minimum effects on their health. The high number of mites recorded in the digits of toads (Cycloramphus boraceiensis, Corythomantis greening, Cycloramphus dubius, Leptodactylus latrans, Melanophryniscus admirabilis) could lead to avascular necrosis. Frogs were often infested by Hannemania larvae, while Rhinella toads were likely to be infested by Amblyomma ticks. Of note, Rhinella major toad was found infested by an oribatid mite, implying first a new parasitic relationship. The effect of high parasitic loads on critically endangered species of anurans deserves further investigation. Our results add basic knowledge to host association of mites and ticks to Brazilian reptiles and amphibians, highlighting that routine ectoparasite examination is needed in cases of quarantine as well as when for managing reptiles and amphibians in captivity given the wide diversity of Acari on the Brazilian ectothermic tetrapod fauna.

13.
Parasit Vectors ; 12(1): 240, 2019 May 16.
Article in English | MEDLINE | ID: mdl-31097007

ABSTRACT

BACKGROUND: Theory predicts that parasites can affect and thus drive their hosts' niche. Testing this prediction is key, especially for vector-borne diseases including Chagas disease. Here, we examined the niche use of seven triatomine species that occur in Mexico, based on whether they are infected or not with Trypanosoma cruzi, the vectors and causative parasites of Chagas disease, respectively. Presence data for seven species of triatomines (Triatoma barberi, T. dimidiata, T. longipennis, T. mazzottii, T. pallidipennis, T. phyllosoma and T. picturata) were used and divided into populations infected and not infected by T. cruzi. Species distribution models were generated with Maxent 3.3.3k. Using distribution models, niche analysis tests of amplitude and distance to centroids were carried out for infected vs non-infected populations within species. RESULTS: Infected populations of bugs of six out of the seven triatomine species showed a reduced ecological space compared to non-infected populations. In all but one case (T. pallidipennis), the niche used by infected populations was close to the niche centroid of its insect host. CONCLUSIONS: Trypanosoma cruzi may have selected for a restricted niche amplitude in triatomines, although we are unaware of the underlying reasons. Possibly the fact that T. cruzi infection bears a fitness cost for triatomines is what narrows the niche breadth of the insects. Our results imply that Chagas control programmes should consider whether bugs are infected in models of triatomine distribution.


Subject(s)
Ecosystem , Triatoma/physiology , Triatoma/parasitology , Trypanosoma cruzi/physiology , Animals , Insect Vectors/parasitology , Insect Vectors/physiology , Mexico
14.
Parasitology ; 146(3): 356-362, 2019 03.
Article in English | MEDLINE | ID: mdl-30324904

ABSTRACT

Patterns of genetic variation among populations can reveal the evolutionary history of species. Pinworm parasites are highly host specific and form strong co-evolutionary associations with their primate hosts. Here, we describe the genetic variation observed in four Trypanoxyuris species infecting different howler and spider monkey subspecies in Central America to determine if historical dispersal processes and speciation in the host could explain the genetic patterns observed in the parasites. Mitochondrial (cox1) and ribosomal (28S) DNA were analysed to assess genetic divergence and phylogenetic history of these parasites. Sequences of the 28S gene were identical within pinworms species regardless of host subspecies. However, phylogenetic analyses, haplotype relationships and genetic divergence with cox1 showed differentiation between pinworm populations according to host subspecies in three of the four Trypanoxyuris species analysed. Haplotype separation between host subspecies was not observed in Trypanoxyuris minutus, nor in Trypanoxyuris atelis from Ateles geoffoyi vellerosus and Ateles geoffoyi yucatanensis. Levels of genetic diversity and divergence in these parasites relate with such estimates reported for their hosts. This study shows how genetic patterns uncovered in parasitic organisms can reflect the host phylogenetic and biogeographic histories.


Subject(s)
Alouatta/parasitology , Ateles geoffroyi/parasitology , Biological Evolution , Genetic Variation , Host-Parasite Interactions , Oxyuroidea/genetics , Animals , Costa Rica , Female , Male , Mexico , Monkey Diseases/parasitology , Nicaragua , Oxyuriasis/parasitology , Oxyuriasis/veterinary , Phylogeography
15.
Gene ; 686: 125-140, 2019 Feb 20.
Article in English | MEDLINE | ID: mdl-30423385

ABSTRACT

The WFDC1 gene is frequently down-regulated or lost in prostate cancer, and the encoded protein, ps20, has been implicated in epithelial cell behaviour and angiogenesis. However, ps20 remains largely uncharacterised with respect to its structure and interacting partners. This study characterised the evolution, functionality and structural characteristics of WFDC1/ps20 using phylogenetic reconstruction and other computational approaches. Bayesian phylogenetic analyses suggested that ps20 appeared in a common ancestor of deuterostomes-protostomes. The rate of evolutionary change within the coding regions of vertebrate WFDC1 genes and the synteny conservation in mammals differed from that of other vertebrate clades, indicating a possible functional diversity of ps20 homologues. A gene set enrichment analysis of the genes around WFDC1 (conserved synteny) showed functional relationships between the WFDC1, CDH13, CRISPLD2, IRF8 and TFPI2 genes. The molecular evolution of ps20 has been driven by purifying selection, particularly in the segments corresponding to exons 3 and 4, which encode the most conserved regions of the protein. A co-evolution analysis showed that residues within these regions co-vary with each other during the evolution of ps20. These results show that the regions corresponding to exons 3 and 4 are ps20-specific structure-function modules. Homology modelling of the exon 2-encoded polypeptide and subsequent dynamics calculus using a Gaussian network model showed that residues with high conformational flexibility are part of a loop region involved in protein-protein recognition, given the similarity with other serine protease inhibitors. Residues C96, R94, L105, and C66 are critical for the integrity and functionality of this ps20 region.


Subject(s)
Evolution, Molecular , Models, Molecular , Phylogeny , Proteins , Humans , Protein Domains , Proteins/chemistry , Proteins/genetics , Structural Homology, Protein
16.
Virology ; 525: 117-131, 2018 12.
Article in English | MEDLINE | ID: mdl-30265888

ABSTRACT

E1A is the main transforming protein in mastadenoviruses. This work uses bioinformatics to extrapolate experimental knowledge from Human adenovirus serotype 5 and 12 E1A proteins to all known serotypes. A conserved domain architecture with a high degree of intrinsic disorder acts as a scaffold for multiple linear motifs with variable occurrence mediating the interaction with over fifty host proteins. While linear motifs contribute strongly to sequence conservation within intrinsically disordered E1A regions, motif repertoires can deviate significantly from those found in prototypical serotypes. Close to one hundred predicted residue-residue contacts suggest the presence of stable structure in the CR3 domain and of specific conformational ensembles involving both short- and long-range intramolecular interactions. Our computational results suggest that E1A sequence conservation and co-evolution reflect the evolutionary pressure to maintain a mainly disordered, yet non-random conformation harboring a high number of binding motifs that mediate viral hijacking of the cell machinery.


Subject(s)
Adenovirus E1A Proteins/metabolism , Adenoviruses, Human/metabolism , Adenovirus E1A Proteins/chemistry , Adenovirus E1A Proteins/genetics , Amino Acid Motifs , Amino Acid Sequence , Humans , Protein Conformation , Protein Domains , Protein Modification, Translational
17.
World J Gastroenterol ; 24(28): 3071-3089, 2018 Jul 28.
Article in English | MEDLINE | ID: mdl-30065554

ABSTRACT

Helicobacter pylori (H. pylori) is present in roughly 50% of the human population worldwide and infection levels reach over 70% in developing countries. The infection has classically been associated with different gastro-intestinal diseases, but also with extra gastric diseases. Despite such associations, the bacterium frequently persists in the human host without inducing disease, and it has been suggested that H. pylori may also play a beneficial role in health. To understand how H. pylori can produce such diverse effects in the human host, several studies have focused on understanding the local and systemic effects triggered by this bacterium. One of the main mechanisms by which H. pylori is thought to damage the host is by inducing local and systemic inflammation. However, more recently, studies are beginning to focus on the effects of H. pylori and its metabolism on the gastric and intestinal microbiome. The objective of this review is to discuss how H. pylori has co-evolved with humans, how H. pylori presence is associated with positive and negative effects in human health and how inflammation and/or changes in the microbiome are associated with the observed outcomes.


Subject(s)
Gastrointestinal Microbiome/physiology , Helicobacter Infections/physiopathology , Helicobacter pylori/physiology , Host-Pathogen Interactions/physiology , Inflammation/physiopathology , Biological Coevolution/physiology , Gastric Mucosa/microbiology , Gastric Mucosa/physiopathology , Helicobacter Infections/epidemiology , Helicobacter Infections/microbiology , Helicobacter pylori/pathogenicity , Humans , Inflammation/microbiology
18.
Acta amaz. ; 48(2): 146-150, Apr-June 2018. ilus, tab
Article in English | VETINDEX | ID: vti-734654

ABSTRACT

Informo sobre el comportamiento de robo de néctar del colibrí pico cuña, Schistes geoffroyi (Trochilidae) en la flor campanulada neotropical, Centropogon granulosus (Campanulaceae). Muchas especies de Centropogon se caracterizan por tener una flor tubular curvada de distintas formas y probablemente especializadas para ser polinizadas por los colibríes de pico curvo (Eutoxeres), como es evidente a partir de la curvatura tanto de la flor como del pico. Debido a la exclusividad de este mutualismo, el robo de néctar ha sido ocasionalmente documentado en Centropogon. Aquí amplío el estudio de robo de néctar de Centropogon incluyendo a Schistes geoffroyi. Esta expansión puede ser un indicador de la alta especialización entre el mutualismo de Centropogon y el colibrí de pico curvo, siendo esta más susceptible al robo de néctar de lo que pensaba previamente. Esto genera preguntas acerca de la evolución de la especialización y parasitismo en este grupo tropical, tanto de las campanuladas como de los colibríes.(AU)


I report on nectar robbing behavior of the wedge-billed hummingbird, Schistes geoffroyi (Trochilidae) on the Andean bellflower, Centropogon granulosus (Campanulaceae). Many species of Centropogon are characterized by an abruptly curved corolla tube which is likely specialized for pollination by sicklebill hummingbirds (Eutoxeres), as evident from the matching curvature of flower and bill. Nectar robbing has been documented for some Centropogon spp., but not for sicklebill pollinated C. granulosus. Given recent developments and interest in the Centropogon-sicklebill mutualism, it is pertinent to document any natural history observations that may underlie the ecology and evolution of this pollination system. The establishment of wedge-billed hummingbird as a nectar robber of C. granulosus calls for a new assessment of the ecology and evolution of the highly specialized Centropogon-sicklebill mutualism.(AU)


Subject(s)
Animals , Birds , Pollination , Campanulaceae , Flowers , Plant Nectar
19.
Acta amaz ; Acta amaz;48(2): 146-150, Apr.-June 2018. ilus, tab
Article in English | LILACS, VETINDEX | ID: biblio-1455355

ABSTRACT

Informo sobre el comportamiento de robo de néctar del colibrí pico cuña, Schistes geoffroyi (Trochilidae) en la flor campanulada neotropical, Centropogon granulosus (Campanulaceae). Muchas especies de Centropogon se caracterizan por tener una flor tubular curvada de distintas formas y probablemente especializadas para ser polinizadas por los colibríes de pico curvo (Eutoxeres), como es evidente a partir de la curvatura tanto de la flor como del pico. Debido a la exclusividad de este mutualismo, el robo de néctar ha sido ocasionalmente documentado en Centropogon. Aquí amplío el estudio de robo de néctar de Centropogon incluyendo a Schistes geoffroyi. Esta expansión puede ser un indicador de la alta especialización entre el mutualismo de Centropogon y el colibrí de pico curvo, siendo esta más susceptible al robo de néctar de lo que pensaba previamente. Esto genera preguntas acerca de la evolución de la especialización y parasitismo en este grupo tropical, tanto de las campanuladas como de los colibríes.


I report on nectar robbing behavior of the wedge-billed hummingbird, Schistes geoffroyi (Trochilidae) on the Andean bellflower, Centropogon granulosus (Campanulaceae). Many species of Centropogon are characterized by an abruptly curved corolla tube which is likely specialized for pollination by sicklebill hummingbirds (Eutoxeres), as evident from the matching curvature of flower and bill. Nectar robbing has been documented for some Centropogon spp., but not for sicklebill pollinated C. granulosus. Given recent developments and interest in the Centropogon-sicklebill mutualism, it is pertinent to document any natural history observations that may underlie the ecology and evolution of this pollination system. The establishment of wedge-billed hummingbird as a nectar robber of C. granulosus calls for a new assessment of the ecology and evolution of the highly specialized Centropogon-sicklebill mutualism.


Subject(s)
Animals , Birds , Campanulaceae , Pollination , Flowers , Plant Nectar
20.
Front Microbiol ; 9: 131, 2018.
Article in English | MEDLINE | ID: mdl-29467742

ABSTRACT

This study is about the inter- and intra-specific genetic diversity of trypanosomatids of the genus Angomonas, and their association with Calliphoridae (blowflies) in Neotropical and Afrotropical regions. Microscopic examination of 3,900 flies of various families, mostly Calliphoridae, revealed that 31% of them harbored trypanosomatids. Small subunit rRNA (SSU rRNA) barcoding showed that Angomonas predominated (46%) over the other common trypanosomatids of blowflies of genera Herpetomonas and Wallacemonas. Among Angomonas spp., A. deanei was much more common than the two-other species, A. desouzai and A. ambiguus. Phylogenetic analyses based on SSU rRNA, glycosomal glyceraldehyde-3-phosphate dehydrogenase (gGAPDH) and internal transcribed spacer rDNA (ITS rDNA) sequences revealed a marked genetic diversity within A. deanei, which comprised four infraspecific genotypes (Dea1-Dea4), and four corresponding symbiont genotypes (Kcr1-Kcr4). Host and symbiont phylogenies were highly congruent corroborating their co-divergence, consistent with host-symbiont interdependent metabolism and symbiont reduced genomes shaped by a long coevolutionary history. We compared the diversity of Angomonas/symbionts from three genera of blowflies, Lucilia, Chrysomya and Cochliomyia. A. deanei, A. desouzai, and A. ambiguus were found in the three genera of blowflies in South America. In Africa, A. deanei and A. ambiguus were identified in Chrysomya. The absence of A. desouzai in Africa and its presence in Neotropical Cochliomyia and Lucilia suggests parasite spillback of A. desouzai into Chrysomya, which was most likely introduced four decades ago from Africa into the Neotropic. The absence of correlation between parasite diversity and geographic and genetic distances, with identical genotypes of A. deanei found in the Neotropic and Afrotropic, is consistent with disjunct distribution due to the recent human-mediated transoceanic dispersal of Angomonas by Chrysomya. This study provides the most comprehensive data gathered so far on the genetic repertoires of a genus of trypanosomatids found in flies from a wide geographical range.

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