Transporter Proteins as Ecological Assets and Features of Microbial Eukaryotic Pangenomes.

Here we review two connected themes in evolutionary microbiology: (a) the nature of gene repertoire variation within species groups (pangenomes) and (b) the concept of metabolite transporters as accessory proteins capable of providing niche-defining "bolt-on" phenotypes. We discuss the need for improved sampling and understanding of pangenome variation in eukaryotic microbes. We then review the factors that shape the repertoire of accessory genes within pangenomes. As part of this discussion, we outline how gene duplication is a key factor in both eukaryotic pangenome variation and transporter gene family evolution. We go on to outline how, through functional characterization of transporter-encoding genes, in combination with analyses of how transporter genes are gained and lost from accessory genomes, we can reveal much about the niche range, the ecology, and the evolution of virulence of microbes. We advocate for the coordinated systematic study of eukaryotic pangenomes through genome sequencing and the functional analysis of genes found within the accessory gene repertoire.

Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies.

The supergroup Holomycota, composed of Fungi and several related lineages of unicellular organisms (Nucleariida, Rozellida, Microsporidia, and Aphelida), represents one of the major branches in the phylogeny of eukaryotes. Nevertheless, except for the well-established position of Nucleariida as the first holomycotan branch to diverge, the relationships among the other lineages have so far remained unresolved largely owing to the lack of molecular data for some groups. This was notably the case aphelids, a poorly known group of endobiotic phagotrophic protists that feed on algae with cellulose walls. The first molecular phylogenies including aphelids supported their sister relationship with Rozellida and Microsporidia which, collectively, formed a new group called Opisthosporidia (the "Opisthosporidia hypothesis"). However, recent phylogenomic analyses including massive sequence data from two aphelid genera, Paraphelidium and Amoeboaphelidium, suggested that the aphelids are sister to fungi (the "Aphelida $+$ Fungi hypothesis"). Should this position be confirmed, aphelids would be key to understanding the early evolution of Holomycota and the origin of Fungi. Here, we carry out phylogenomic analyses with an expanded taxonomic sampling for aphelids after sequencing the transcriptomes of two species of the genus Aphelidium (Aphelidium insulamus and Aphelidium tribonematis) in order to test these competing hypotheses. Our new phylogenomic analyses including species from the three known aphelid genera strongly rejected the Opisthosporidia hypothesis. Furthermore, comparative genomic analyses further supported the Aphelida $+$ Fungi hypothesis via the identification of 19 orthologous genes exclusively shared by these two lineages. Seven of them originated from ancient horizontal gene transfer events predating the aphelid-fungal split and the remaining 12 likely evolved de novo, constituting additional molecular synapomorphies for this clade. Ancestral trait reconstruction based on our well-resolved phylogeny of Holomycota suggests that the progenitor of both fungi and rozellids, was aphelid-like, having an amoeboflagellate state and likely preying endobiotically on cellulose-containing, cell-walled organisms. Two lineages, which we propose to call Phytophagea and Opisthophagea, evolved from this ancestor. Phytophagea, grouping aphelids and classical fungi, mainly specialized in endobiotic predation of algal cells. Fungi emerged from this lineage after losing phagotrophy in favor of osmotrophy. Opisthophagea, grouping rozellids and Microsporidia, became parasites, mostly of chitin-containing hosts. This lineage entered a progressive reductive process that resulted in a unique lifestyle, especially in the highly derived Microsporidia. [Aphelida, fungi, Holomycota, horizontal gene transfer, phylogenomics, synapomorphy.].

Mortality in patients with unresectable gastric cancer complicated with tumor bleeding.

BACKGROUND: gastric cancer (GC) is a gastrointestinal (GI) neoplasia which often complicates with GI bleeding. It is uncertain if bleeding worsens mortality in this group of patients. AIMS: to compare 30- and 90-day mortality in patients with unresectable GC (uGC) and tumor bleeding versus patients with the same neoplasia without bleeding. METHODS: a retrospective analysis of patients with uGC, with and without tumor bleeding was performed. Survival analysis for 30- and 90-days mortality was performed using Cox regression. Logistic regression was used to identify risk factors associated with mortality and first bleeding episode. RESULTS: 202 patients were included in the analysis (105 cases). Mortality at 90 days was 37.14 % for cases and 20.62 % for controls (p = 0.04). There was a significant difference in hazard ratio (HR) at 90 days for cases compared to controls (HR 1.95, 95 % CI 1.14-3.34, p = 0.02). Cases without palliative chemotherapy had the highest 90-days mortality (HR 5.43, 95 % CI 2.12-13.87, p < 0.01), compared to controls treated with chemotherapy. Predictors for first tumor bleeding were clinical stage IV (OR 2.93, 95 % CI 1.04-8.26, p = 0.04), Helicobacter pylori infection (OR 2.80, 95 % CI 1.35-5.80, p < 0.01) and histologic intestinal-subtype (OR 2.14, 95 % CI 1.07-4.30, p = 0.03). CONCLUSIONS: tumor bleeding increases 90-days mortality in patients with uGC. Prevention of the first bleeding episode might improve outcome in these patients and the recognition of high-risk patients might help decision-making.

Mortality and hospitalization trends for aortic aneurysms and dissections in Mexico.

BACKGROUND: In Mexico, there is a paucity of evidence on mortality and hospitalization patterns associated with aortic aneurysms and dissections. OBJECTIVE: To analyze national databases and describe the epidemiological characteristics of different aortic pathologies. MATERIAL AND METHODS: Retrospective, cross-sectional, observational study, in which mortality and hospitalization attributed to aortic aneurysms and dissections were analyzed. Statistical analysis was performed on Stata 16. RESULTS: A total of 6,049 deaths were documented in the general population, which included 2,367 hospitalizations and 476 (20.1%) in-hospital deaths. In addition, a statistically significant age difference was found between mean age at death in the general population (69.5 years) and the in-hospital death group (64.1 years, p < 0.001). As for hospitalizations secondary to ruptured abdominal aortic aneurysms, 149 cases were identified, with a mean age of 65.6 years, out of whom 53 (35.5%) were under 65 years of age, with a mean age of 47.8 years. CONCLUSIONS: Epidemiological reports of aortic pathology in Mexico are scarce; therefore, implementation of screening and detection programs for aortic pathologies is necessary in order to address the disparities identified in this analysis.

ANTECEDENTES: Existe evidencia escasa en México respecto a la mortalidad y patrones del ingreso hospitalario asociados a aneurismas y disecciones aórticos. OBJETIVO: Analizar las bases de datos nacionales y describir las características epidemiológicas de diferentes patologías aórticas agudas. MATERIAL Y MÉTODOS: Estudio transversal y observacional de una base de datos retrospectiva, en el que se analizó la mortalidad y hospitalización atribuidas a aneurismas y disecciones aórticos. El análisis estadístico se realizó en Stata 16. RESULTADOS: Se documentaron 6049 muertes en la población general, 2367 hospitalizaciones y 476 muertes intrahospitalarias. Adicionalmente, se encontró una diferencia estadísticamente significativa entre las medias de edad de fallecimiento de la población general (65.5 años) y de los pacientes que murieron en el hospital (64.1 años), p < 0.001. En cuanto a las hospitalizaciones secundarias a aneurisma de aorta abdominal roto, 149 casos fueron evidenciados con una media de edad de 65.6 años; 53 (35.5 %) de estos tenía menos de 65 años, con una media de edad de 47.8 años. CONCLUSIONES: Los reportes epidemiológicos de patología aórtica en México son escasos, por ello la implementación de programas de tamizaje y la detección de patologías aórticas son necesarias para mejorar las disparidades encontradas en este análisis.

Expanding the molecular and morphological diversity of Apusomonadida, a deep-branching group of gliding bacterivorous protists.

Apusomonads are cosmopolitan bacterivorous biflagellate protists usually gliding on freshwater and marine sediment or wet soils. These nanoflagellates form a sister lineage to opisthokonts and may have retained ancestral features helpful to understanding the early evolution of this large supergroup. Although molecular environmental analyses indicate that apusomonads are genetically diverse, few species have been described. Here, we morphologically characterize 11 new apusomonad strains. Based on molecular phylogenetic analyses of the rRNA gene operon, we describe four new strains of the known species Multimonas media, Podomonas capensis, Apusomonas proboscidea, and Apusomonas australiensis, and rename Thecamonas oxoniensis as Mylnikovia oxoniensis n. gen., n. comb. Additionally, we describe four new genera and six new species: Catacumbia lutetiensis n. gen. n. sp., Cavaliersmithia chaoae n. gen. n. sp., Singekia montserratensis n. gen. n. sp., Singekia franciliensis n. gen. n. sp., Karpovia croatica n. gen. n. sp., and Chelonemonas dolani n. sp. Our comparative analysis suggests that apusomonad ancestor was a fusiform biflagellate with a dorsal pellicle, a plastic ventral surface, and a sleeve covering the anterior flagellum, that thrived in marine, possibly oxygen-poor, environments. It likely had a complex cell cycle with dormant and multiple fission stages, and sex. Our results extend known apusomonad diversity, allow updating their taxonomy, and provide elements to understand early eukaryotic evolution.

Molecular and morphological characterization of four new ancyromonad genera and proposal for an updated taxonomy of the Ancyromonadida.

Ancyromonads are small biflagellated protists with a bean-shaped morphology. They are cosmopolitan in marine, freshwater, and soil environments, where they attach to surfaces while feeding on bacteria. These poorly known grazers stand out by their uncertain phylogenetic position in the tree of eukaryotes, forming a deep-branching "orphan" lineage that is considered key to a better understanding of the early evolution of eukaryotes. Despite their ecological and evolutionary interest, only limited knowledge exists about their true diversity. Here, we aimed to characterize ancyromonads better by integrating environmental surveys with behavioral observation and description of cell morphology, for which sample isolation and culturing are indispensable. We studied 18 ancyromonad strains, including 14 new isolates and seven new species. We described three new and genetically divergent genera: Caraotamonas, Nyramonas, and Olneymonas, together encompassing four species. The remaining three new species belong to the already-known genera Fabomonas and Ancyromonas. We also raised Striomonas, formerly a subgenus of Nutomonas, to full genus status, on morphological and phylogenetic grounds. We studied the morphology of diverse ancyromonads under light and electron microscopy and carried out molecular phylogenetic analyses, also including 18S rRNA gene sequences from several environmental surveys. Based on these analyses, we have updated the taxonomy of Ancyromonadida.

Risk factors associated to argon plasma coagulation treatment failure in patients with chronic radiation proctopathy.

BACKGROUND: argon plasma coagulation (APC) is the current endoscopic treatment of choice for patients who develop chronic radiation proctopathy. The aim of this study was to identify risk factors associated with treatment failure. METHODS: one hundred and ninety-nine patients treated with argon plasma coagulation in a single center were retrospectively analyzed. RESULTS: twenty-four (12.06 %) patients were classified as APC treatment failures. Requirement of red blood cells transfusion and/or hemoglobin < 7 g/dl (OR 12.19, 95 % CI: 2.78-53.45, p < 0.001) and severe bleeding frequency (OR 2.76, 95 % CI: 1.13-6.72, p = 0.03) at diagnosis and prior to endoscopic therapy were associated with argon plasma coagulation treatment failure. Nineteen patients of the successful therapy group developed bleeding recurrence; no risk factors were associated with a shorter recurrence-free time. More than four APC sessions were associated to a higher risk of surgical intervention for bleeding control (OR 87.00, 95 % CI: 10.23-740.18, p < 0.001). CONCLUSION: requirement of red blood cells transfusion and/or hemoglobin < 7 g/dl and a severe bleeding frequency (more than five days per week) were identified as the most important risk factors for treatment failure in patients with chronic radiation proctopathy.

Ancient Adaptive Lateral Gene Transfers in the Symbiotic Opalina-Blastocystis Stramenopile Lineage.

Lateral gene transfer is a very common process in bacterial and archaeal evolution, playing an important role in the adaptation to new environments. In eukaryotes, its role and frequency remain highly debated, although recent research supports that gene transfer from bacteria to diverse eukaryotes may be much more common than previously appreciated. However, most of this research focused on animals and the true phylogenetic and functional impact of bacterial genes in less-studied microbial eukaryotic groups remains largely unknown. Here, we have analyzed transcriptome data from the deep-branching stramenopile Opalinidae, common members of frog gut microbiomes, and distantly related to the well-known genus Blastocystis. Phylogenetic analyses suggest the early acquisition of several bacterial genes in a common ancestor of both lineages. Those lateral gene transfers most likely facilitated the adaptation of the free-living ancestor of the Opalinidae-Blastocystis symbiotic group to new niches in the oxygen-depleted animal gut environment.

Environmental drivers of plankton protist communities along latitudinal and vertical gradients in the oldest and deepest freshwater lake.

Identifying which abiotic and biotic factors determine microbial community assembly is crucial to understand ecological processes and predict how communities will respond to environmental change. While global surveys aim at addressing this question in the world's oceans, equivalent studies in large freshwater systems are virtually lacking. Being the oldest, deepest and most voluminous freshwater lake on Earth, Lake Baikal offers a unique opportunity to test the effect of horizontal versus vertical gradients in community structure. Here, we characterized the structure of planktonic microbial eukaryotic communities (0.2-30 µm cell size) along a North-South latitudinal gradient (~600 km) from samples collected in coastal and pelagic waters and from surface to the deepest zones (5-1400 m) using an 18S rRNA gene metabarcoding approach. Our results show complex and diverse protist communities dominated by alveolates (ciliates and dinoflagellates), ochrophytes and holomycotan lineages, with cryptophytes, haptophytes, katablepharids and telonemids in moderate abundance and many low-frequency lineages, including several typical marine members, such as diplonemids, syndinians and radiolarians. Depth had a strong significant effect on protist community stratification. By contrast, the effect of the latitudinal gradient was marginal and no significant difference was observed between coastal and surface open water communities. Co-occurrence network analyses showed that epipelagic communities were significantly more interconnected than communities from the dark water column and suggest specific biotic interactions between autotrophic, heterotrophic and parasitic lineages that influence protist community structure. Since climate change is rapidly affecting Siberia and Lake Baikal, our comprehensive protist survey constitutes a useful reference to monitor ongoing community shifts.

Analysis of subcutaneous swine fat via deep Raman spectroscopy using a fiber-optic probe.

Since the fat content of pork is a deciding factor in meat quality grading, the use of a noninvasive subcutaneous probe for real-time in situ monitoring of the fat components is of importance to vendors and other interested parties. In this work, we developed a spectroscopic method using a fiber-optic probe for subcutaneous fat analysis that utilizes spatially offset Raman spectroscopy (SORS). Here, normalized Raman spectra were acquired as a function of spatial offset, and the relative composition of fat-to-skin was determined. We found that the Raman intensity ratio varied disproportionately depending on the fat content and that the variations of the slope were correlated to the thickness of the fat layer. Furthermore, ordinary least square (OLS) regression using two components indicated that the depth-resolved SORS spectra reflected the relative thickness of the fat layer. We concluded that the local distribution of subcutaneous fat could be measured noninvasively using a pair of fiber-optic probes.

Correction to: Evaluation of accuracy dependence of Raman spectroscopic models on the ratio of calibration and validation points for non-invasive glucose sensing.

The authors would like to bring to the reader's attention that the Clarke error grid plot presented in Fig. 3 was generated using codes adapted from following reference.

Revisión sistemática de procedimientos quirúrgicos usados para tratar patología aórtica en México.

INTRODUCTION: In Mexico, there are no appropriate statistical data on aortic disease, which can be treated with medical management or open or endovascular surgical approach. OBJECTIVE: To carry out a systematic search and review of the literature in electronic databases with regard to invasive management of aortic pathology in Mexico. METHOD: A systematic search and narrative review of available literature was carried out using different electronic databases: PubMed, Imbiomed, Clinical Key, Bibliat, Scielo, Sage Journals and Sciencedirect, as well as with the Google Scholar search engine. RESULTS: Ninety articles were found, out of which only 53 met the inclusion criteria. Observational studies and case reports were selected, emphasizing on patient demographics, clinical results, and 30-day postoperative survival. CONCLUSION: An elevated rate of complications is reported for aortic pathologies due to underdiagnosis, which results in management being more complicated and prognosis unfavorable. The creation of a national aortic disease registry is crucial to standardization in the approach and optimization of results.

INTRODUCCIÓN: En México no se cuentan con estadísticas adecuadas acerca de la enfermedad aórtica, que puede ser tratada mediante manejo médico o cirugía abierta o endovascular. OBJETIVO: Identificar la literatura en bases de datos electrónicas relativa al manejo invasivo de la patología aórtica en México. MÉTODO: Se realizó búsqueda sistemática y revisión narrativa de la literatura disponible en diferentes bases de datos electrónicas: PubMed, Imbiomed, Clinical Key, Bibliat, Scielo, Sage Journals, Sciencedirect y con el motor de búsqueda de Google Académico. RESULTADOS: Se encontraron 90 artículos, de los cuales 50 reunían los criterios de inclusión. Fueron seleccionados estudios observacionales y reportes de casos, con énfasis en los datos demográficos de los pacientes, resultados clínicos y la supervivencia posoperatoria a 30 días. CONCLUSIÓN: Se reporta elevada tasa de complicaciones de las enfermedades aórticas debido al infradiagnóstico de estas, que deriva en manejo más complejo y pronóstico desfavorable. La creación de un registro nacional de patología aórtica es crucial para la estandarización en el abordaje y la optimación de los resultados.

HMGA2 and MED12 alterations frequently co-occur in uterine leiomyomas.

OBJECTIVE: Around 70% of uterine leiomyomas show MED12 mutations while overexpression of HMGA2 mRNA is also highly frequent in fibroids. However, previous studies suggested that alterations in both genes are mutually exclusive. In the present study, we searched for mutation in MED12 and analyzed the expression of HMGA2 in 20 uterine leiomyomas and their matched myometrium. METHODS: Normal and tumor tissue obtained from premenopausal women who underwent hysterectomy were collected after surgery and DNA, RNA and proteins were isolated and analyzed for MED12 mutations using Sanger sequencing, HMGA2 mRNA expression by quantitative PCR and HMGA2 protein detection by western blot and immunohistochemistry. RESULTS: 75% of the tumors displayed MED12 mutation while 65% of them showed overexpression of HMGA2 mRNA in leiomyomata compared to myometrial tissues (p = 0,0008). Interestingly, 50% of the tumors showed mutations in MED12 and overexpression of HMGA2 mRNA simultaneously, suggesting that alterations in both genes are relatively frequent in uterine leiomyomas. CONCLUSIONS: Contrary to the present findings, former studies showed that mutations in MED12 and overexpression of HMGA2 are mutually exclusive. Here, we observed that overexpression of HMGA2 mRNA in tumors measured by quantitative PCR and compared to myometrium is a common phenomenon in fibroids and is frequently associated with MED12 mutations. In addition, the common clonal origin of tumors overexpressing HMGA2 mRNA and its expression in few myometrial tissue points to HMGA2 up-regulation as an early event in leiomyoma tumorigenesis.

Evaluation of accuracy dependence of Raman spectroscopic models on the ratio of calibration and validation points for non-invasive glucose sensing.

Optical monitoring of blood glucose levels for non-invasive diagnosis is a growing area of research. Recent efforts in this direction have been inclined towards reducing the requirement of calibration framework. Here, we are presenting a systematic investigation on the influence of variation in the ratio of calibration and validation points on the prospective predictive accuracy of spectral models. A fiber-optic probe coupled Raman system has been employed for transcutaneous measurements. Limit of agreement analysis between serum and partial least square regression predicted spectroscopic glucose values has been performed for accurate comparison. Findings are suggestive of strong predictive accuracy of spectroscopic models without requiring substantive calibration measurements. Graphical abstract.

Impact of Chronic Glucocorticoid Treatment on Cardiovascular Risk Profile in Patients with Systemic Lupus Erythematosus.

BACKGROUND: Systemic lupus erythematosus is highly associated with premature atherosclerosis and cardiovascular events. The origin of this subclinical atherosclerosis has been attributed mainly to the inflammatory nature of the disease. OBJECTIVE: To assess the effect of long-term use of glucocorticoids on cardiovascular risk in patients with systemic lupus erythematosus. MATERIAL AND METHODS: We conducted a registry-based retrospective cohort study. We determined 2 periods: (1) Time 0, that is, time of diagnosis and (2) time 1, that is, when the study was finalized. At both times, the cardiovascular risk was evaluated using the Framingham scale and their scores were compared. Afterward, the change magnitude between the 2 times was evaluated and associated with the cumulative glucocorticoids dose. RESULTS: One hundred one patients were included. The mean ± SD age was 26.5 ± 5 years. Length of disease evolution was of 7.8 ± 4.9 years. There was an 8-point increase in the Framingham score, from -8.1 ± 4 to 0.8 ± 7; P < 0.0001. The correlation between the magnitude of the increase in Framingham score and their corresponding cumulative dose showed a coefficient of 0.88; P < 0.001. CONCLUSIONS: The glucocorticoids are a primary factor that influences cardiovascular risk. There is a directly proportional relationship between the cumulative glucocorticoid dose and the increase in cardiovascular risk.

Automating the Horae: Boundary-work in the age of computers.

This article describes the intense software filtering that has allowed the arXiv e-print repository to sort and process large numbers of submissions with minimal human intervention, making it one of the most important and influential cases of open access repositories to date. This article narrates arXiv's transformation, using sophisticated sorting/filtering algorithms to decrease human workload, from a small mailing list used by a few hundred researchers to a site that processes thousands of papers per month. However, there are significant negative consequences for authors who have been filtered out of arXiv's main categories. There is thus a continued need to check and balance arXiv's boundaries, based on the essential tension between stability and innovation.

Delayed diagnosis of late-onset Pompe disease in patients with myopathies of unknown origin and/or hyperCKemia.

Pompe disease is a rare metabolic myopathy whose diagnosis is sometimes delayed despite being essential for improving clinical outcomes. We aimed to investigate the prevalence of late-onset Pompe disease among patients with a myopathy of unknown etiology, including polymyositis, or with idiopathic rise of creatine kinase (CK) levels, in a department of internal medicine. A cohort study was conducted in 241 subjects: 140 patients with myopathies of unknown origin or increased CK levels, 30 with polymyositis and 71 who constituted the control group of other myopathies. Acid α-glucosidase (GAA) activity was tested in dried blood spots. If a positive result was obtained, GAA activity in isolated lymphocytes and/or genetic testing was performed as a confirmatory diagnosis. Out of the 140 investigated patients, 2 patients with myopathies of unknown origin were confirmed to be positive for Pompe disease. Thus, late-onset Pompe disease should be considered among adult patients with myopathy of unknown origin.

Synthesis of novel bis-1,5-disubstituted-1H-tetrazoles by an efficient catalyst-free Ugi-azide repetitive process.

A series of five novel bis-1,5-disubstituted-1H-tetrazoles (bis-1,5-DS-1H-T) were quickly prepared by a catalyst-free Ugi-azide repetitive process from easily accessible starting materials in excellent yields, either at room temperature (88%-95%) or using mild MW-heating conditions (80%-91%). These molecules may have a wide range of applications, such as chelating agents, organocatalysts and luminescent materials, and mainly as bioactive compounds.

Bringing tacit knowledge back to contributory and interactional expertise: A reply to Goddiksen.

We analyse a recent paper by Goddiksen (2014) where the author raises questions about the relationship between authorship, attribution and Collins & Evans' concept of contributory and interactional expertise. We then highlight recent empirical work in the sociology of climate change science that has made similar points in order to clarify how authorship, division of labour and contribution are handled in real scientific settings. Despite this, Goddiksen's critique of both contributory and interactional expertise is ultimately ineffective because it rests on a misguided attempt to de-socialise these concepts. We conclude by stressing the importance of collective tacit knowledge acquisition through immersion as a critical step in becoming a full-blown contributory or interactional expert.