A 28-Year History of HIV-1 Drug Resistance and Transmission in Washington, DC

Washington, DC consistently has one of the highest annual rates of new HIV-1 diagnoses in the United States over the last 10 years. To guide intervention and prevention strategies to combat DC HIV infection, it is helpful to understand HIV transmission dynamics in a historical context. Toward this aim, we conducted a retrospective study (years 1987–2015) of 3,349 HIV pol sequences (1,026 bp) from 1,995 individuals living in the DC area belonging to three different cohorts. We coupled HIV sequence data with clinical information (sex, risk factor, race/ethnicity, viral load, subtype, anti-retroviral regimen) to identify circulating drug resistant mutations (DRM) and transmission clusters and assess their persistence over time. Of the transmission clusters identified in the DC area, 78.0 and 31.7% involved MSM and heterosexuals, respectively. The longest spread of time for a single cluster was 5 years (2007–2012) using a distance-based network inference approach and 27 years (1987–2014) using a maximum likelihood phylogenetic approach. We found eight subtypes and nine recombinants. Genetic diversity increased steadily over time with a slight peak in 2009 and remained constant thereafter until 2015. Nucleotide diversity also increased over time while relative genetic diversity (BEAST) remained relatively steady over the last 28 years with slight increases since 2000 in subtypes B and C. Sequences from individuals on drug therapy contained the highest total number of DRMs (1,104–1,600) and unique DRMs (63–97) and the highest proportion (>20%) of resistant individuals. Heterosexuals (43.94%), MSM (40.13%), and unknown (44.26%) risk factors showed similar prevalence of DRMs, while injection drug users had a lower prevalence (33.33%). Finally, there was a 60% spike in the number of codons with DRMs between 2007 and 2010. Past patterns of HIV transmission and DRM accumulation over time described here will help to predict future efficacy of ART drugs based on DRMs persisting over time and identify risk groups of interest for prevention and intervention efforts within the DC population. Our results show how longitudinal data can help to understand the temporal dynamics of HIV-1 at the local level

T-pattern detection in the scientific literature of this century: A systematic review

Scientific literature contains mainly systematic reviews focused on substantial aspects, but there are also approaches that have combined both substantial and methodological aspects, which is our preferred option since it undeniably adds value. The aims of this study were: (1) to carry out a systematic review of the literatura on T-Pattern analysis (TPA), and (2) to explore the possible contribution of mixed methods research to the integration of qualitative and quantitative elements on a synthesis level.Methods: Based on PRISMA guidelines, searches were carried out in the Scopus, PsycINFO, and Web of Science databases. The general search syntax was: “THEME” AND (“T-Patterns” OR “T Patterns”) carried out in title, keywords and abstract. In addition, we included empirical articles on THEME and T-Patterns collected in other sources based on citations in several empirical works and consultations with different authors. This selection process resulted in 125 primary documents making up this systematic review. Results: The results showed that the detection of structures in behavior patterns forms a nexus between studies carried out in very diverse fields and contexts. Most studies are observational, whilst the applicability and power of T-Pattern detection are extraordinary. It allows the researcher to go deeper in a robust analysis that responds to the integration of qualitative and quantitative elements which constitutes the leit motive of mixed methods; and also to discover the deep, hidden structure that underlies the respective databases, regardless of the methodology used in each study. The possibilities in assigning parameters notably increase the options for obtaining results and their interpretation. Discussion: It is relevant the extraordinary strength and applicability of T-pattern detection. There is a high presence of T-pattern detection and analysis in studies using observational methodology. It is necessary commit to consolidating the methodological analysis of selected works, as taking individual and collective responsibility for improving methodological quality of TPA studies, taking advantage of the resources provided by the THEME program

Phylogenetic analysis of apicomplexan parasites infecting commercially valuable species from the North-East Atlantic reveals high levels of diversity and insights into the evolution of the group

Background: The Apicomplexa from aquatic environments are understudied relative to their terrestrial counterparts, and the seminal work assessing the phylogenetic relations of fish-infecting lineages is mostly based on freshwater hosts. The taxonomic uncertainty of some apicomplexan groups, such as the coccidia, is high and many genera were recently shown to be paraphyletic, questioning the value of strict morphological and ecological traits for parasite classification. Here, we surveyed the genetic diversity of the Apicomplexa in several commercially valuable vertebrates from the NorthEast Atlantic, including farmed fish. Results: Most of the sequences retrieved were closely related to common fish coccidia of Eimeria, Goussia and Calyptospora. However, some lineages from the shark Scyliorhinus canicula were placed as sister taxa to the Isospora, Caryospora and Schellakia group. Additionally, others from Pagrus caeruleostictus and Solea senegalensis belonged to an unknown apicomplexan group previously found in the Caribbean Sea, where it was sequenced from the water column, corals, and fish. Four distinct parasite lineages were found infecting farmed Dicentrarchus labrax or Sparus aurata. One of the lineages from farmed D. labrax was also found infecting wild counterparts, and another was also recovered from farmed S. aurata and farm-associated Diplodus sargus. Conclusions: Our results show that marine fish apicomplexans are diverse, and we highlight the need for a more extensive assessment of parasite diversity in this phylum. Additionally, parasites recovered from S. canicula were recovered as basal to their piscine counterparts reflecting hosts phylogeny

Tyramine biosynthesis is transcriptionally induced at low pH and improves the fitness of Enterococcus faecalis in acidic environments

© 2014, Springer-Verlag Berlin Heidelberg. Enterococcus faecalis is a commensal bacterium of the human gut that requires the ability to pass through the stomach and therefore cope with low pH. E. faecalis has also been identified as one of the major tyramine producers in fermented food products, where they also encounter acidic environments. In the present work, we have constructed a non-tyramine-producing mutant to study the role of the tyramine biosynthetic pathway, which converts tyrosine to tyramine via amino acid decarboxylation. Wild-type strain showed higher survival in a system that mimics gastrointestinal stress, indicating that the tyramine biosynthetic pathway has a role in acid resistance. Transcriptional analyses of the E. faecalis V583 tyrosine decarboxylase cluster showed that an acidic pH, together with substrate availability, induces its expression and therefore the production of tyramine. The protective role of the tyramine pathway under acidic conditions appears to be exerted through the maintenance of the cytosolic pH. Tyramine production should be considered important in the adaptability of E. faecalis to acidic environments, such as fermented dairy foods, and to survive passage through the human gastrointestinal tract.This work was funded by the Ministry of Economy and Competitiveness, Spain (AGL2013-45431-R) and the Spanish National Research Council (CSIC201270E144). M.P. is beneficiary of an FPU fellowship from the Spanish Ministry of Education.Peer Reviewe

Is256 abolishes gelatinase activity and biofilm formation in a mutant of the nosocomial pathogen enterococcus faecalis v583

Enterococcus faecalis is one of the most controversial species of lactic acid bacteria. Some strains are used as probiotics, while others are associated with severe and life-threatening nosocomial infections. Their pathogenicity depends on the acqui-sition of multidrug resistance and virulence factors. Gelatinase, which is required in the first steps of biofilm formation, is an important virulence determinant involved in E. faecalis pathogenesis, including endocarditis and peritonitis. The gene that codes for gelatinase (gelE) is controlled by the Fsr quorum-sensing system, whose encoding genes (fsrA, fsrB, fsrC, and fsrD) are located immediately upstream of gelE. The integration of a DNA fragment into the fsr locus of a derived mutant of E. faecalis V583 suppressed the gelatinase activity and prevented biofilm formation. Sequence analysis indicated the presence of IS256 integrated into the fsrC gene at nucleotide position 321. Interestingly, IS256 is also associated with biofilm formation in Staphylococcus epidermidis and Staphylococcus aureus. This is the first description of an insertion sequence that prevents biofilm formation in E. faecalis. Copyright de NRC Research PressPeer Reviewe

An Earthworm Riddle: Systematics and Phylogeography of the Spanish Lumbricid Postandrilus

As currently defined, the genus Postandrilus Qui and Bouché, 1998, (Lumbricidae) includes six earthworm species, five occurring in Majorca (Baleares Islands, western Mediterranean) and another in Galicia (NW Spain). This disjunct and restricted distribution raises some interesting phylogeographic questions: (1) Is Postandrilus distribution the result of the separation of the Baleares-Kabylies (BK) microplate from the proto-Iberian Peninsula in the Late Oligocene (30-28 Mya)--vicariant hypothesis? (2) Did Postandrilus diversify in Spain and then colonize the Baleares during the Messinian salinity crisis (MSC) 5.96-5.33 Mya--dispersal hypothesis? (3) Is the distribution the result of a two-step process--vicariance with subsequent dispersal?To answer these questions and assess Postandrilus evolutionary relationships and systematics, we collected all of the six Postandrilus species (46 specimens - 16 locations) and used Aporrectodea morenoe and three Prosellodrilus and two Cataladrilus species as the outgroup. Regions of the nuclear 28S rDNA and mitochondrial 16S rDNA, 12S rDNA, ND1, COII and tRNA genes (4,666 bp) were sequenced and analyzed using maximum likelihood and Bayesian methods of phylogenetic and divergence time estimation. The resulting trees revealed six new Postandrilus species in Majorca that clustered with the other five species already described. This Majorcan clade was sister to an Iberian clade including A. morenoe (outgroup) and Postandrilus bertae. Our phylogeny and divergence time estimates indicated that the split between the Iberian and Majorcan Postandrilus clades took place 30.1 Mya, in concordance with the break of the BK microplate from the proto-Iberian Peninsula, and that the present Majorcan clade diversified 5.7 Mya, during the MSC.Postandrilus is highly diverse including multiple cryptic species in Majorca. The genus is not monophyletic and invalid as currently defined. Postandrilus is of vicariant origin and its radiation began in the Late Oligocene

Genetic and functional analysis of biogenic amine production capacity among starter and non-starter lactic acid bacteria isolated from artisanal cheeses

© 2015, Springer-Verlag Berlin Heidelberg. This work reports the capacity of 137 strains of starter and non-starter LAB belonging to nine species of the genera Lactobacillus, Lactococcus, Streptococcus and Leuconostoc (all isolated from artisanal cheeses) to produce histamine, tyramine, putrescine and β-phenylethylamine, the biogenic amines (BA) most commonly found in dairy products. Production assays were performed in liquid media supplemented with the appropriate precursor amino acid; culture supernatants were then tested for BA by (U)HPLC. In addition, the presence of key genes involved in the biosynthetic pathways of the target BA, including the production of putrescine via the agmatine deiminase pathway, was assessed by PCR. Twenty strains were shown to have genes involved in the synthesis of BA; these belonged to the species Lactobacillus brevis (4), Lactobacillus curvatus (3), Lactococcus lactis (11) and Streptococcus thermophilus (2). With the exception of the two S. thermophilus strains, all those possessing genes involved in BA production synthesized the corresponding compound. Remarkably, all the putrescine-producing strains used the agmatine deiminase pathway. Four L. brevis and two L. curvatus strains were found able to produce both tyramine and putrescine. There is increasing interest in the use of autochthonous LAB strains in starter and adjunct cultures for producing dairy products with ‘particular geographic indication’ status. Such strains should not produce BA; the present results show that BA production capacity should be checked by (U)HPLC and PCR.This work was funded by the Ministry of Economy and Competitiveness, Spain (AGL2013-45431-R), the Fundación para el Fomento en Asturias de la Investigación Científica Aplicada y la Tecnología (FICYT), cofunded by FEDER (GRUPIN14-137) and the INIA (RM2011-00005-00-00).Peer Reviewe

Mastitis modifies the biogenic amines profile in human milk, with significant changes in the presence of histamine, putrescine and spermine

Biogenic amines (BAs) are low molecular weight nitrogenous organic compounds with different biological activities. Putrescine, spermidine and spermine are essential for the development of the gut and immune system of newborns, and are all found in human milk. Little is known, however, about the role of histamine, tyramine or cadaverine in breast milk. Nor is it known whether mastitis alters the BA composition of milk. The BA profile of human milk, and the influence of mastitis on BA concentrations, were therefore investigated. Putrescine, spermidine and spermine were the main BAs detected. In mastitis-affected milk, the concentrations of putrescine, spermine and histamine were higher.This work was performed with the financial support of the Spanish Ministry of Economy and Competitiveness (AGL2013-45431-R and AGL2013-41980P) and the GRUPIN14-137 project (which is co-financed by the Plan for Science, Technology and Innovation of the Principality of Asturias 2014-2017 and the European Regional Development Funds). M.P. was the recipient of an FPU (Programa de Formacion del Profesorado Universitario) fellowship from the Spanish Ministry of Education, Culture and Sport.Peer Reviewe

Evolutionary origins of metabolic reprogramming in cancer

Metabolic changes that facilitate tumor growth are one of the hallmarks of cancer. These changes are not specific to tumors but also take place during the physiological growth of tissues. Indeed, the cellular and tissue mechanisms present in the tumor have their physiological counterpart in the repair of tissue lesions and wound healing. These molecular mechanisms have been acquired during metazoan evolution, first to eliminate the infection of the tissue injury, then to enter an effective regenerative phase. Cancer itself could be considered a phenomenon of antagonistic pleiotropy of the genes involved in effective tissue repair. Cancer and tissue repair are complex traits that share many intermediate phenotypes at the molecular, cellular, and tissue levels, and all of these are integrated within a Systems Biology structure. Complex traits are influenced by a multitude of common genes, each with a weak effect. This polygenic component of complex traits is mainly unknown and so makes up part of the missing heritability. Here, we try to integrate these different perspectives from the point of view of the metabolic changes observed in cancer.This work was supported in JPL’s lab by Grant PID2020-118527RB-I00 funded by MCIN/AEI/10.13039/501100011039; Grant PDC2021-121735-I00 funded by MCIN/AEI/10.13039/501100011039 and by the “European Union Next Generation EU/PRTR.”, the Regional Government of Castile and León (CSI234P18 and CSI144P20). SCLl was the recipient of a Ramón y Cajal research contract from the Spanish Ministry of Economy and Competitiveness and was supported by grant RTI2018-094130-B-100 funded by MCIN/AEI/10.13039/501100011039 and by “ERDF A way of making Europe.” RCC and AJN are funded by fellowships from the Spanish Regional Government of Castile and León. NGS is a recipient of an FPU fellowship (MINECO/FEDER). MJPB is funded by grant PID2020-118527RB-I00 funded by MCIN/AEI/10.13039/501100011039. J.C. is partially supported by grant GRS2139/A/20 (Gerencia Regional de Salud de Castilla y León) and by the Instituto de Salud Carlos III (PI18/00587 and PI21/01207), co-financed by FEDER funds, and by the “Programa de Intensificación” of the ISCIII, grant number INT20/00074. We thank Phil Mason for English language support

Morphology and characterisation of the relict facies on the internal continental shelf in the Gulf of Cadiz, between Ayamonte and Huelva (southern Iberian Peninsula)

The objectives of the present paper are the determination of the morphologic characteristics of the superficial Quaternary relict facies on the internal continental shelf in the Gulf of Cadiz, between Ayamonte and Huelva (southern Spain), their characterisation, and their evolution in the final phases of the last eustatic hemicycle. The study area extends from the mouth of the Guadiana River to the mouth of the Tinto-Odiel River, and from the 6 m isobath to the 56 m isobath. High-resolution seismic profiles (3.5 kHz and Geopulse, 175 J), sonographic profiles (SSS, 100 kHz), and bathymetric profiles (Echotrac sounder) were used in this study. Sediment samples were obtained using Van Veen and Shipek drags. Bathymetric, physiographic, lithologic and morphologic analyses were performed to determine the superficial sediment distribution, relict facies distribution, and thickness of the unconsolidated sediment cover. Analysis of the data obtained indicated that the relict facies beaches and coastal barriers associated with coastal spits located in the ancient outlets of the rivers. Relict facies were grouped into well-differentiated depths, indicating that their position on the continental shelf is influenced by the still-stands and the periods of rapid sea-level changes. The nature of the outcropping relict facies shows that their final configuration can be related to the shelf construction processes, as well as to the most important Holocene transgressive phases.Los objetivos de este trabajo son la determinación de las características morfológicas, la caracterización de las facies relictas cuaternarias superficiales y el estudio de su evolución con relación a las fases finales del último hemiciclo eustático en la plataforma continental interna del golfo de Cádiz, entre Ayamonte y Huelva. El área de estudio abarca desde la desembocadura del río Guadiana hasta la del río Tinto-Odiel y desde los 6 m hasta 56 m de profundidad. Se utilizó gran cantidad de material geofísico, en el que se encuentran perfiles sísmicos de alta resolución (3.5 kHz y Geopulse, 175 J), perfiles sonográficos y perfiles batimétricos, además de muestras de sedimentos obtenidas con dragas Van Veen y Shipek. Con esta información se han realizado análisis batimétricos, fisiográficos, litológicos y morfológicos, además de determinar la distribución de los sedimentos superficiales y de las facies relictas y de cuantificar la potencia de la cobertera sedimentaria. Con todos los datos obtenidos se ha determinado que las facies relictas son interpretadas como playas y cordones litorales asociados a flechas litorales situadas en las antiguas desembocaduras de los ríos. Las formas descritas están agrupadas en zonaciones batimétricas bien diferenciadas, lo que indica que su posición en la plataforma continental está influida por las paradas y etapas de movimiento rápido del nivel del mar. Las características de las facies relictas aflorantes indican que su configuración final puede estar relacionada con los procesos de edificación de la plataforma a partir de las mayores fases transgresivas holocenas.Instituto Español de Oceanografí