Methodological considerations for ghrelin isoforms assay in clinical evaluation in anorexia nervosa

The growing interest concerning the role of metabolic sensors in various eating disorders requires the implementation of a strict methodology to collect, store and process blood samples in clinical studies. In particular, measurement of isoforms of the appetite-stimulating hormone, ghrelin, has been challenging in clinical settings. Indeed the acyl ghrelin (AG) isoform is rapidly degraded into desacyl ghrelin (DAG) by blood esterases, thus optimal conditions for the conservation of AG and accurate determination of AG/DAG ratio should be used. Here, we compared different protease inhibitors (Aprotinin, PHMB, AEBSF) during blood collection, increasing delays (0–180 min) before centrifugation, plasma supplementation with various HCl concentrations, storage durations of frozen plasma (8 and 447 days) and immunoenzyme-assay procedures (one-step versus sequential) in healthy subjects. Optimal conditions were obtained by collecting blood with aprotinin and supplementation of plasma with 0.1 N HCl with subsequent freezing for at least 8 days and using one-step assay. Under such conditions, different patterns of secretion of ghrelin isoforms were characterized in patients with restrictive-type anorexia nervosa (AN-R) before and after nutritional recovery. We illustrate the pulsatile variations of ghrelin isoforms according to the time around a meal and hunger rates in 3 patients with AN-R. This study offers a comprehensive comparison of various conditions using selective and specific immunoassays for both ghrelin isoforms in order to optimize assay sensitivity and consistency among procedures. These assay conditions could therefore be widely used to elucidate precisely the role of ghrelin isoforms on eating behavior in physiological and pathological situations.

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Treatment conditions and assay procedures are critical for ghrelin isoforms level determination in plasma.

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Specific treatment conditions allow long term stability of ghrelin isoforms.

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HCl supplementation of plasma before freezing improves AG/DAG ratio on the short and long term.

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Variations of ghrelin isoforms occur with meal timing and chronic nutritional status in patients with anorexia nervosa.

Saccharomyces cerevisiae como alternativa de reemplazo a los antibióticos promotores de crecimiento en alimentación animal

El presente trabajo de revisión bibliográfica, exhibe el mecanismo de acción, modo de empleo, dosis utilizadas y beneficios demostrados por Saccharomyces cerevisiae en animales de producción comercial. Varios estudios demuestran que la levadura se utiliza en diferentes dosis y concentraciones como cultivo (probiótico) o sus paredes celulares (prebiótico), atribuyendo impacto positivo de S. cerevisiae sobre los parámetros productivos y reproductivos de los animales, incremento en la digestibilidad de nutrientes, mejoras sobre las variables de morfometria intestinal, regulación del pH ruminal, modulación de la población microbiana, beneficios en el sistema inmunológico, disminución en la concentración de amoniaco, entre otros; no obstante, se debe considerar que la acción benéfica de la levadura difiere por el pH, temperatura de extracción, composición nutricional, cepa utilizada, dosis, concentración, modo de empleo y por la diversidad de dietas ofrecidas a los animales. Los resultados obtenidos en investigaciones recientes conllevan a concluir que, el uso de Saccharomyces cerevisiae como aditivo en la alimentación animal puede sustituir a los antibióticos promotores de crecimiento, logrando similares resultados a los APC, sin dejar residuos en los productos y subproductos de los animales que resulten perjudiciales al consumidor.

High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains

BACKGROUND

Temperate phages influence the density, diversity and function of bacterial populations. Historically, they have been described as carriers of toxins. More recently, they have also been recognised as direct modulators of the gut microbiome, and indirectly of host health and disease. Despite recent advances in studying prophages using non-targeted sequencing approaches, methodological challenges in identifying inducible prophages in bacterial genomes and quantifying their activity have limited our understanding of prophage-host interactions.

RESULTS

We present methods for using high-throughput sequencing data to locate inducible prophages, including those previously undiscovered, to quantify prophage activity and to investigate their replication. We first used the well-established Salmonella enterica serovar Typhimurium/p22 system to validate our methods for (i) quantifying phage-to-host ratios and (ii) accurately locating inducible prophages in the reference genome based on phage-to-host ratio differences and read alignment alterations between induced and non-induced prophages. Investigating prophages in bacterial strains from a murine gut model microbiota known as Oligo-MM¹² or sDMDMm2, we located five novel inducible prophages in three strains, quantified their activity and showed signatures of lateral transduction potential for two of them. Furthermore, we show that the methods were also applicable to metagenomes of induced faecal samples from Oligo-MM¹² mice, including for strains with a relative abundance below 1%, illustrating its potential for the discovery of inducible prophages also in more complex metagenomes. Finally, we show that predictions of prophage locations in reference genomes of the strains we studied were variable and inconsistent for four bioinformatic tools we tested, which highlights the importance of their experimental validation.

CONCLUSIONS

This study demonstrates that the integration of experimental induction and bioinformatic analysis presented here is a powerful approach to accurately locate inducible prophages using high-throughput sequencing data and to quantify their activity. The ability to generate such quantitative information will be critical in helping us to gain better insights into the factors that determine phage activity and how prophage-bacteria interactions influence our microbiome and impact human health. Video abstract.

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms.

Video Abstract

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A catalog of 47 million genes was generated from 370 globally distributed metagenomes

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Meta-omics data integration disentangled the mechanisms of changes in transcript pools

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Transcript pool changes of metabolic marker genes show distinct mechanistic patterns

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Community turnover as a response to ocean warming may be strongest in polar regions

The Ocean Gene Atlas: exploring the biogeography of plankton genes online

The Ocean Gene Atlas is a web service to explore the biogeography of genes from marine planktonic organisms. It allows users to query protein or nucleotide sequences against global ocean reference gene catalogs. With just one click, the abundance and location of target sequences are visualized on world maps as well as their taxonomic distribution. Interactive results panels allow for adjusting cutoffs for alignment quality and displaying the abundances of genes in the context of environmental features (temperature, nutrients, etc.) measured at the time of sampling. The ease of use enables non-bioinformaticians to explore quantitative and contextualized information on genes of interest in the global ocean ecosystem. Currently the Ocean Gene Atlas is deployed with (i) the Ocean Microbial Reference Gene Catalog (OM-RGC) comprising 40 million non-redundant mostly prokaryotic gene sequences associated with both Tara Oceans and Global Ocean Sampling (GOS) gene abundances and (ii) the Marine Atlas of Tara Ocean Unigenes (MATOU) composed of >116 million eukaryote unigenes. Additional datasets will be added upon availability of further marine environmental datasets that provide the required complement of sequence assemblies, raw reads and contextual environmental parameters. Ocean Gene Atlas is a freely-available web service at: http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/.

Microbial abundance, activity and population genomic profiling with mOTUs2

Metagenomic sequencing has greatly improved our ability to profile the composition of environmental and host-associated microbial communities. However, the dependency of most methods on reference genomes, which are currently unavailable for a substantial fraction of microbial species, introduces estimation biases. We present an updated and functionally extended tool based on universal (i.e., reference-independent), phylogenetic marker gene (MG)-based operational taxonomic units (mOTUs) enabling the profiling of >7700 microbial species. As more than 30% of them could not previously be quantified at this taxonomic resolution, relative abundance estimates based on mOTUs are more accurate compared to other methods. As a new feature, we show that mOTUs, which are based on essential housekeeping genes, are demonstrably well-suited for quantification of basal transcriptional activity of community members. Furthermore, single nucleotide variation profiles estimated using mOTUs reflect those from whole genomes, which allows for comparing microbial strain populations (e.g., across different human body sites).

Innate immunity restricts Citrobacter rodentium A/E pathogenesis initiation to an early window of opportunity

Citrobacter rodentium infection is a mouse model for the important human diarrheal infection caused by enteropathogenic E. coli (EPEC). The pathogenesis of both species is very similar and depends on their unique ability to form intimately epithelium-adherent microcolonies, also known as "attachment/effacement" (A/E) lesions. These microcolonies must be dynamic and able to self-renew by continuous re-infection of the rapidly regenerating epithelium. It is unknown whether sustained epithelial A/E lesion pathogenesis is achieved through re-infection by planktonic bacteria from the luminal compartment or local spread of sessile bacteria without a planktonic phase. Focusing on the earliest events as C. rodentium becomes established, we show here that all colonic epithelial A/E microcolonies are clonal bacterial populations, and thus depend on local clonal growth to persist. In wild-type mice, microcolonies are established exclusively within the first 18 hours of infection. These early events shape the ongoing intestinal geography and severity of infection despite the continuous presence of phenotypically virulent luminal bacteria. Mechanistically, induced resistance to A/E lesion de-novo formation is mediated by TLR-MyD88/Trif-dependent signaling and is induced specifically by virulent C. rodentium in a virulence gene-dependent manner. Our data demonstrate that the establishment phase of C. rodentium pathogenesis in vivo is restricted to a very short window of opportunity that determines both disease geography and severity.

D-Alanine-Controlled Transient Intestinal Mono-Colonization with Non-Laboratory-Adapted Commensal E. coli Strain HS

Soon after birth the mammalian gut microbiota forms a permanent and collectively highly resilient consortium. There is currently no robust method for re-deriving an already microbially colonized individual again-germ-free. We previously developed the in vivo growth-incompetent E. coli K-12 strain HA107 that is auxotrophic for the peptidoglycan components D-alanine (D-Ala) and meso-diaminopimelic acid (Dap) and can be used to transiently associate germ-free animals with live bacteria, without permanent loss of germ-free status. Here we describe the translation of this experimental model from the laboratory-adapted E. coli K-12 prototype to the better gut-adapted commensal strain E. coli HS. In this genetic background it was necessary to complete the D-Ala auxotrophy phenotype by additional knockout of the hypothetical third alanine racemase metC. Cells of the resulting fully auxotrophic strain assembled a peptidoglycan cell wall of normal composition, as long as provided with D-Ala and Dap in the medium, but could not proliferate a single time after D-Ala/Dap removal. Yet, unsupplemented bacteria remained active and were able to complete their cell cycle with fully sustained motility until immediately before autolytic death. Also in vivo, the transiently colonizing bacteria retained their ability to stimulate a live-bacteria-specific intestinal Immunoglobulin (Ig)A response. Full D-Ala auxotrophy enabled rapid recovery to again-germ-free status. E. coli HS has emerged from human studies and genomic analyses as a paradigm of benign intestinal commensal E. coli strains. Its reversibly colonizing derivative may provide a versatile research tool for mucosal bacterial conditioning or compound delivery without permanent colonization.

Three axis vector magnet set-up for cryogenic scanning probe microscopy

We describe a three axis vector magnet system for cryogenic scanning probe microscopy measurements. We discuss the magnet support system and the power supply, consisting of a compact three way 100 A current source. We obtain tilted magnetic fields in all directions with maximum value of 5T along z-axis and of 1.2T for XY-plane magnetic fields. We describe a scanning tunneling microscopy-spectroscopy (STM-STS) set-up, operating in a dilution refrigerator, which includes a new high voltage ultralow noise piezodrive electronics and discuss the noise level due to vibrations. STM images and STS maps show atomic resolution and the tilted vortex lattice at 150 mK in the superconductor β-Bi2Pd. We observe a strongly elongated hexagonal lattice, which corresponds to the projection of the tilted hexagonal vortex lattice on the surface. We also discuss Magnetic Force Microscopy images in a variable temperature insert.

Microbiota-derived compounds drive steady-state granulopoiesis via MyD88/TICAM signaling

Neutropenia is probably the strongest known predisposition to infection with otherwise harmless environmental or microbiota-derived species. Because initial swarming of neutrophils at the site of infection occurs within minutes, rather than the hours required to induce "emergency granulopoiesis," the relevance of having high numbers of these cells available at any one time is obvious. We observed that germ-free (GF) animals show delayed clearance of an apathogenic bacterium after systemic challenge. In this article, we show that the size of the bone marrow myeloid cell pool correlates strongly with the complexity of the intestinal microbiota. The effect of colonization can be recapitulated by transferring sterile heat-treated serum from colonized mice into GF wild-type mice. TLR signaling was essential for microbiota-driven myelopoiesis, as microbiota colonization or transferring serum from colonized animals had no effect in GF MyD88(-/-)TICAM1(-/-) mice. Amplification of myelopoiesis occurred in the absence of microbiota-specific IgG production. Thus, very low concentrations of microbial Ags and TLR ligands, well below the threshold required for induction of adaptive immunity, sets the bone marrow myeloid cell pool size. Coevolution of mammals with their microbiota has probably led to a reliance on microbiota-derived signals to provide tonic stimulation to the systemic innate immune system and to maintain vigilance to infection. This suggests that microbiota changes observed in dysbiosis, obesity, or antibiotic therapy may affect the cross talk between hematopoiesis and the microbiota, potentially exacerbating inflammatory or infectious states in the host.

[Endotrachael aspiration protocol in patients with serious cranial trauma. study of neurophysiological variables]

Aspiration of tracheobronchial secretions can cause noxious effects on neurophysiological variables. Different studies that refer to aspiration of secretions in Serious Cranial Trauma use hyperinsuflation and hyperoxygenation to minimize its repercussion on Intracranial Pressure and thus try to not contribute to the secondary lesion. After reviewing these studies, a protocol of tracheobronchial secretion aspiration was performed in our ICU in patients with serious cranial trauma subjected to mechanical ventilation in order to assess the effect of the aspiration of secretions in the neurophysiological variables following homogeneous and standardized guidelines. Neurological, hemodynamic, oxygenation and ventilation variables were analyzed before, during and after aspiration of secretions. When the results were compared before and during this, we observed a decrease in the Intracranial Pressure with increase of Cerebral Perfusion Pressure (due to increase of Mean Blood Pressure), maintaining the levels of PaCO2 and jugular saturation of O2, with an increase in the airway pressures. After finishing the aspiration process, all the affected values recovered. It is concluded that the aspiration of tracheobronchial secretions in patients with Severe Cranial Trauma, after standardized hyperinsuflation and hyperoxygenation, does not alter the hydrodynamics or brain use of O2.

[Program for nursing certification in critical care]

This article presents the Nursing Certification Program in Critical Care through which the Spanish Society of Intensive Nursing and Coronary Units (SEEIUC) accredits, by means of a diploma, the professional competence of graduate nurses in the care of critically ill patients. The program describes the system of certification and focuses on the study material for the examination, which is grouped into eleven thematic units. The first exam will be held 10 June 1999 in Palma de Mallorca, coinciding with the XXV National Congress of the SEEIUC.

[Certification of professional competence in critical care. Opinion survey]

This article gathers the results and conclusions derived from a survey performed by the Work Group of the SEEIUC dedicated to the development of the Professional Certificate in Intensive Care. The survey was carried out with the aim of obtaining the opinion of nursing professionals who work in Intensive Care Units, about the training and requirements which are necessary to work in these units. The questionnaires were sent to all the members of the SEEIUC and to a great number of mixed, surgical, trauma and coronary ICUs all over the country. Among the opinions which were collected, the following ones must be pointed out: specific nursing knowledgement is necessary to work in Intensive Care; experience is essential to acquire confidence and good command of the job; nursing professionals need mechanisms which help their professional development; and the Certificate Programme is accepted as a valid system which certificates professional competence.

Focal infections due to non-typhi Salmonella in patients with AIDS: report of 10 cases and review

Bacteremia due to non-typhi Salmonella is frequent in human immunodeficiency virus (HIV)-infected patients; however, focal complications rarely have been reported. Ten of 38 HIV-infected patients (26.3%) with salmonellosis documented over a period of 9 years had focal suppurative complications; only 19 (3.9%) of 490 adults without HIV infection who were seen during the same period had focal complications (P = .001). Infections of the urinary tract, lungs, and soft tissue, followed by arthritis, endocarditis, and meningitis were most frequently seen. Although salmonellosis occasionally heralded HIV infection, most patients were severely immunocompromised and had CD4 cell counts of <100/mm3. The mortality rate was 50%, equivalent to that observed among patients with other immunosuppressive disorders (52.6%). Major emphasis must be put on intensive therapy for salmonella bacteremia and prevention of its complications.

[Spontaneous meningitis caused by gram-negative bacilli]

OBJECTIVE

To analyze the causative factors, clinical and microbiological characteristics, and prognosis in spontaneous meningitis caused by Gram-negative rods in adult patients.

METHODS

Descriptive and retrospective study of all clinical records and microbiological findings in patients diagnosed of meningitis by Gram-negative bacilli, from 1973 to 1995, at Fundación Jiménez Díaz.

RESULTS

Twenty patients had spontaneous meningitis caused by Gram-negative bacilli (2.1% of all diagnosed meningitis during this period). Fourteen patients were older than 65 years (range: 36-81; p < 0.05). Ninety-five percent of cases had an extranosocomial origin (p < 0.001). Ninety percent of patients had some underlying disease (p < 0.001). Twelve patients were immunosuppressed. Seven patients had changes in the urinary tract or repeated UTI infections. The most common clinical symptoms were a decrease in consciousness level, fever, and neck stiffness. Cerebrospinal fluid (CSF) in 18 patients showed cellular and biochemical changes. The CSF smear revealed the presence of Gram-negative bacilli in 15 patients. E. coli was the microorganism recovered most frequently. Immunosuppression (p < 0.05), septic shock (p < 0.001) and antimicrobial therapy not including a third generation cephalosporin (p < 0.01) were independently associated with mortality.

CONCLUSIONS

Spontaneous meningitis by Gram-negative bacilli is an uncommon infection. It occurs mainly in immunosuppressed patients older than 65 years or with changes in the urinary tract. It usually has an extranosocomial origin. The investigation of CSF is a highly effective for diagnosis. Therapy with third generation cephalosporins has notably improved its prognosis.

Effect of pH and buffer system on the in-vitro activity of five antifungals against yeasts

We have compared the effect of various media on the in-vitro activity of amphotericin B, flucytosine, fluconazole, itraconazole and ketoconazole against 93 clinical yeast isolates by a micro-broth dilution technique. The media used were: RPMI 1640 with 2% glucose, buffered with 0.165 M MOPS at pH 7.0; the same medium, but buffered at pH 7.4; and the same medium, but buffered at pH 7.4 with 0.15% sodium bicarbonate. The three media gave similar results with azole antifungals and flucytosine, but the medium buffered at pH 7.0 failed to detect different populations of yeasts with respect to amphotericin B susceptibility. In the case of the media buffered at pH 7.4, Candida krusei was significantly less susceptible to amphotericin B than Candida albicans or Torulopsis glabrata. We could not evaluate the results obtained with Candida parapsilosis and Cryptococcus neoformans since these species did not grow adequately in all three media.

Bronchoalveolar lavage for the diagnosis of disseminated toxoplasmosis in AIDS patients

The usefulness of cell culture of bronchoalveolar lavage fluid for the diagnosis of toxoplasmosis in immunocompromised hosts has not been stressed previously. We report an acquired immunodeficiency syndrome patient with disseminated toxoplasmosis who was diagnosed by isolation of Toxoplasma gondii in cell cultures from bronchoalveolar lavage fluid.

[Analysis of the situation of intensive care units]

Since 1990, the Sociedad Española de Enfermería Intensiva y Unidades Coronarias has carried out initiatives aiming to collect data which allows us to make an analysis of the status of the ICU nurses and the characteristics of the Units where these professionals develop their activity. This project was performed during 1992 and 1993, with a survey in 132 sanitary centres of the public network in the national territory, in which information about the number of ICUs and their number of beds, number of nurses and assistants in the institution and those ones specifically assigned to ICU, number of admissions, average stay, occupation percentage, admission causes, use of systems of valuation of the seriousness index, staff seniority, shift systems, staff stability, etc; all this data and others referring to 1991. From 53 hospitalary centres that answered the questionnaire, we obtained information of 94 ICUs in which there was an average of 10.4 beds, with 550 admissions per unit (average/year) and an index of occupation of 78%. The average number of nurses who work in each ICU was 22.7, with a nurse/bed ratio in the global calculation of staff of 2.18. In the analysis of shifts, the nurse/bed ratio was one nurse to every 2.08 patients (1:2.08) when there is a maximum of staff during the morning shift. This index is lower in the other shifts. The average of assistants is 12.1 with an assistant/bed ratio of 1.17. When studying the shifts systems, the rotatory shift outstands in 53.19% of ICUs and the existence of rotation systems of staff in other units is 8.5%. With reference to the characteristics of the staff, the average seniority of Nurses was 6.7 years, 76.4% have own their post and the percentage of new intake in 1991 was 22.5%. The lack of incentives to work in ICU is notable, the most problematic aspects being the insufficient economic remuneration, lack of motivation, scarce human resources and insufficient training, among others. Finally, according to the teaching and research activity performed in the units, 5.4% of ICUs have a nurse in the unit with exclusive dedication to teaching, in 20.4% there are nurses who keep a contractual relationship with University Nursing Schools, in 42.6% of the units there are training programs for the new staff and 67% perform some sort of research activity although in most of the cases it is only sporadic.