Extracellular DNA secreted in yeast cultures is metabolism-specific and inhibits cell proliferation

Extracellular DNA (exDNA) can be actively released by living cells and different putative functions have been attributed to it. Further, homologous exDNA has been reported to exert species-specific inhibitory effects on several organisms. Here, we demonstrate by different experimental evidence, including 1H-NMR metabolomic fingerprint, that the growth rate decline in Saccharomyces cerevisiae fed-batch cultures is determined by the accumulation of exDNA in the medium. Sequencing of such secreted exDNA represents a portion of the entire genome, showing a great similarity with extrachromosomal circular DNA (eccDNA) already reported inside yeast cells. The recovered DNA molecules were mostly single strands and specifically associated to the yeast metabolism displayed during cell growth. Flow cytometric analysis showed that the observed growth inhibition by exDNA corresponded to an arrest in the S phase of the cell cycle. These unprecedented findings open a new scenario on the functional role of exDNA produced by living cells.

Comparison of multiple definitions for ventilator-associated pneumonia in patients requiring mechanical ventilation for non-pulmonary conditions: preliminary data from PULMIVAP, an Italian multi-centre cohort study

OBJECTIVES

To compare intensivist-diagnosed ventilator-associated pneumonia (iVAP) with four established definitions, assessing their agreement in detecting new episodes.

METHODS

A multi-centric prospective study on pulmonary microbiota was carried out in patients requiring mechanical ventilation (MV). Data collected were used to compare hypothetical VAP onset according to iVAP with the study consensus criteria, the European Centre for Disease Control and Prevention definition, and two versions of the latter adjusted for leukocyte count and fever.

RESULTS

In our cohort of 186 adult patients, iVAPs were 36.6% (68/186, 95% confidence interval 30.0-44.0%), with an incidence rate of 4.64/100 patient-MV-days, and median MV-day at diagnosis of 6. Forty-seven percent of patients (87/186) were identified as VAP by at least one criterion, with a median MV-day at diagnosis of 5. Agreement between intensivist judgement (iVAP/no-iVAP) and the criteria was highest for the study consensus criteria (50/87, 57.4%), but still one-third of iVAP were not identified and 9% of patients were identified as VAP contrary to intensivist diagnosis. VAP proportion differed between criteria (25.2-30.1%).

CONCLUSIONS

Caution is needed when evaluating studies describing VAP incidence. Pre-agreed criteria and definitions that capture VAP's evolving nature provide greater consistency, but new clinically driven definitions are needed to align surveillance and diagnostic criteria with clinical practice.

Critical Aspects of Material Selection in the Packaging and Transporting of Returned Extraterrestrial Samples

In the framework of the EU-funded EURO-CARES project, aimed at determining the actions to develop a European facility for curation of extraterrestrial samples returned by space missions, we identified the requirements (mainly in terms of materials selection) of the transportation containment facility which should contain the Sample Return Capsule (SRC), which in turn contains the extraterrestrial material returned to Earth. Transportation box design for restricted (i.e., possibly related to biological life) and unrestricted samples is different. Packaging and transport of restricted samples must guarantee the samples' preservation from the terrestrial environment and the safety of people performing these operations and, hence, must be done according to World Health Organization (WHO) rules. In the case of unrestricted samples, the only requirement is sample preservation. We propose a triple packaging as follows: (1) primary receptacle; (2) secondary package (plastic material), optional for unrestricted samples; (3) rigid, cushioned outer layer. Only for restricted samples, an additional layer is proposed, that is, the overpack. The primary receptacle coincides with the SRC. The plastic material of the secondary package must have a low outgassing rate (i.e., <10-7 torr/s) and preferably low permeability and cost. Teflon and Neoflon would be the best choices. The outer package must be rigid and resistant to breakage, and our trade-off analysis identified stainless steel and aluminum alloys as best options. The outer should be filled with an inert atmosphere to inhibit oxidation within the sample in case of leak: argon is more inert than nitrogen, but the latter is easily available. The overpack allows the box environment control (e.g., real-time contamination monitoring); ISO containers could be used to this end. Contamination of the environment inside the box can be monitored by different instruments, which should be selected on the basis of mission requirements. There are no mass limitations for box transport by ground or ship, but these solutions imply a long journey duration. Any aircraft might be used for transporting unrestricted samples. Only cargo aircraft may be used for transporting restricted samples, unless the total sample mass is lower than 50 g (WHO guidelines).

Formation and evolution of carbonaceous asteroid Ryugu: Direct evidence from returned samples

Samples of the carbonaceous asteroid Ryugu were brought to Earth by the Hayabusa2 spacecraft. We analyzed 17 Ryugu samples measuring 1 to 8 millimeters. Carbon dioxide-bearing water inclusions are present within a pyrrhotite crystal, indicating that Ryugu's parent asteroid formed in the outer Solar System. The samples contain low abundances of materials that formed at high temperatures, such as chondrules and calcium- and aluminum-rich inclusions. The samples are rich in phyllosilicates and carbonates, which formed through aqueous alteration reactions at low temperature, high pH, and water/rock ratios of <1 (by mass). Less altered fragments contain olivine, pyroxene, amorphous silicates, calcite, and phosphide. Numerical simulations, based on the mineralogical and physical properties of the samples, indicate that Ryugu's parent body formed ~2 million years after the beginning of Solar System formation.

Metabolomics and molecular networking analyses in Arabidopsis thaliana show that extracellular self-DNA affects nucleoside/nucleotide cycles with accumulation of cAMP, cGMP and N6-methyl-AMP

Extracellular DNA (exDNA) widely occurs in the environment due to release by either cell lysis or active secretion. The role of exDNA in plant-soil interactions has been investigated and inhibitory effects on the growth of conspecific individuals by their self-DNA have been reported. Transcriptome analysis in the model plant Arabidopsis thaliana showed a clear recognition by the plant roots of self- and nonself-exDNA, with inhibition occurring only after exposure to the former. In this study, an untargeted metabolomics approach was used to assess at molecular level the plant reactions to exDNA exposure. Thus, the effects on the metabolites profile of A. thaliana after exposure to self- and nonself-exDNA from plants and fish, were studied by NMR, LC-MS, chemometrics and molecular networking analyses. Results show that self-DNA significantly induces the accumulation of RNA constituents (nucleobases, ribonucleosides, dinucleotide and trinucleotide oligomers). Interestingly, AMP and GMP are found along with their cyclic analogues cAMP and cGMP, and in form of cyclic dimers (c-di-AMP and c-di-GMP). Also methylated adenosine monophosphate (m6AMP) and the dimeric dinucleotide N-methyladenylyl-(3'→5') cytidine (m6ApC) increased only in the self-DNA treatment. Such striking evidence of self-DNA effects highlights a major role of exDNA in plant sensing of its environment.

NMR Metabolomics and Chemometrics of Lettuce, Lactuca sativa L., under Different Foliar Organic Fertilization Treatments

Lettuce plants were grown in a greenhouse affected by the fungal pathogen Fusarium oxysporum to test the effects on plant metabolomics by different organic treatments. Three foliar application treatments were applied: a commercial compost tea made of aerobically fermented plant organic matter, a pure lyophilized microalga Artrospira platensis, commonly named spirulina, and the same microalga previously exposed during its culture to a natural uptake from medium enriched with F. oxysporum fragmented DNA (NAT). The experiment is the first attempt to observe in field conditions, the use and effects of a natural microbial library as a carrier of pathogenic fungal DNA for disease control. Untargeted NMR metabolomics and chemometrics showed that foliar organic application significantly reduced fumaric and formic acids, aromatic amino acids, and nucleosides, while increasing ethanolamine. A strong decrease in phenolic acids and an increase in citric acid and glutamine were specifically observed in the NAT treatment. It is noteworthy that the exposure of a known biostimulant microalga to fungal DNA in its culture medium was sufficient to induce detectable changes in the metabolomic profiles of the fertilized plants. These findings deserve further investigation to assess the potential relevance of the presented approach in the field of crop biostimulation and biocontrol of plant pathogens.

Effects of Extracellular Self- and Nonself-DNA on the Freshwater Microalga Chlamydomonas reinhardtii and on the Marine Microalga Nannochloropsis gaditana

The role of extracellular DNA (exDNA) in soil and aquatic environments was mainly discussed in terms of source of mineral nutrients and of genetic material for horizontal gene transfer. Recently, the self-exDNA (conspecific) has been shown to have an inhibitory effect on the growth of that organism, while the same was not evident for nonself-exDNA (non conspecific). The inhibitory effect of self-exDNA was proposed as a universal phenomenon, although evidence is mainly reported for terrestrial species. The current study showed the inhibitory effect of self-exDNA also on photosynthetic aquatic microorganisms. We showed that self-exDNA inhibits the growth of the microalgae Chlamydomonas reinhardtii and Nannochloropsis gaditana, a freshwater and a marine species, respectively. In addition, the study also revealed the phenotypic effects post self-exDNA treatments. Indeed, Chlamydomonas showed the formation of peculiar heteromorphic aggregates of palmelloid cells embedded in an extracellular matrix, favored by the presence of DNA in the environment, that is not revealed after exposure to nonself-exDNA. The differential effect of self and nonself-exDNA on both microalgae, accompanied by the inhibitory growth effect of self-exDNA are the first pieces of evidence provided for species from aquatic environments.

Arabidopsis thaliana Response to Extracellular DNA: Self Versus Nonself Exposure

The inhibitory effect of extracellular DNA (exDNA) on the growth of conspecific individuals was demonstrated in different kingdoms. In plants, the inhibition has been observed on root growth and seed germination, demonstrating its role in plant-soil negative feedback. Several hypotheses have been proposed to explain the early response to exDNA and the inhibitory effect of conspecific exDNA. We here contribute with a whole-plant transcriptome profiling in the model species Arabidopsis thaliana exposed to extracellular self- (conspecific) and nonself- (heterologous) DNA. The results highlight that cells distinguish self- from nonself-DNA. Moreover, confocal microscopy analyses reveal that nonself-DNA enters root tissues and cells, while self-DNA remains outside. Specifically, exposure to self-DNA limits cell permeability, affecting chloroplast functioning and reactive oxygen species (ROS) production, eventually causing cell cycle arrest, consistently with macroscopic observations of root apex necrosis, increased root hair density and leaf chlorosis. In contrast, nonself-DNA enters the cells triggering the activation of a hypersensitive response and evolving into systemic acquired resistance. Complex and different cascades of events emerge from exposure to extracellular self- or nonself-DNA and are discussed in the context of Damage- and Pathogen-Associated Molecular Patterns (DAMP and PAMP, respectively) responses.

A cytofluorimetric analysis of a Saccharomyces cerevisiae population cultured in a fed-batch bioreactor

The yeast Saccharomyces cerevisiae is a reference model system and one of the widely used microorganisms in many biotechnological processes. In industrial yeast applications, combined strategies aim to maximize biomass/product yield, with the fed-batch culture being one of the most frequently used. Flow cytometry (FCM) is widely applied in biotechnological processes and represents a key methodology to monitor cell population dynamics. We propose here an application of FCM in the analysis of yeast cell cycle along the time course of a typical S. cerevisiae fed-batch culture. We used two different dyes, SYTOX Green and SYBR Green, with the aim to better define each stage of cell cycle during S. cerevisiae fed-batch culture. The results provide novel insights in the use of FCM cell cycle analysis for the real-time monitoring of S. cerevisiae bioprocesses.

Translation machinery reprogramming in programmed cell death in Saccharomyces cerevisiae

Programmed cell death involves complex molecular pathways in both eukaryotes and prokaryotes. In Escherichia coli, the toxin-antitoxin system (TA-system) has been described as a programmed cell death pathway in which mRNA and ribosome organizations are modified, favoring the production of specific death-related proteins, but also of a minor portion of survival proteins, determining the destiny of the cell population. In the eukaryote Saccharomyces cerevisiae, the ribosome was shown to change its stoichiometry in terms of ribosomal protein content during stress response, affecting the relative proportion between ohnologs, i.e., the couple of paralogs derived by a whole genome duplication event. Here, we confirm the differential expression of ribosomal proteins in yeast also during programmed cell death induced by acetic acid, and we highlight that also in this case pairs of ohnologs are involved. We also show that there are different trends in cytosolic and mitochondrial ribosomal proteins gene expression during the process. Moreover, we show that the exposure to acetic acid induces the differential expression of further genes coding for products related to translation processes and to rRNA post-transcriptional maturation, involving mRNA decapping, affecting translation accuracy, and snoRNA synthesis. Our results suggest that the reprogramming of the overall translation apparatus, including the cytosolic ribosome reorganization, are relevant events in yeast programmed cell death induced by acetic acid.

Identification of Novel Potential Genes Involved in Cancer by Integrated Comparative Analyses

The main hallmarks of cancer diseases are the evasion of programmed cell death, uncontrolled cell division, and the ability to invade adjacent tissues. The explosion of omics technologies offers challenging opportunities to identify molecular agents and processes that may play relevant roles in cancer. They can support comparative investigations, in one or multiple experiments, exploiting evidence from one or multiple species. Here, we analyzed gene expression data from induction of programmed cell death and stress response in Homo sapiens and compared the results with Saccharomyces cerevisiae gene expression during the response to cell death. The aim was to identify conserved candidate genes associated with Homo sapiens cell death, favored by crosslinks based on orthology relationships between the two species. We identified differentially-expressed genes, pathways that are significantly dysregulated across treatments, and characterized genes among those involved in induced cell death. We investigated on co-expression patterns and identified novel genes that were not expected to be associated with death pathways, that have a conserved pattern of expression between the two species. Finally, we analyzed the resulting list by HumanNet and identified new genes predicted to be involved in cancer. The data integration and the comparative approach between distantly-related reference species that were here exploited pave the way to novel discoveries in cancer therapy and also contribute to detect conserved genes potentially involved in programmed cell death.

anti-HCoV: A web resource to collect natural compounds against human coronaviruses

BACKGROUND

A novel coronavirus, the SARS-CoV2, was revealed to be the cause of COVID19, the pandemic disease that already provoked more than 555.324 deaths in the world (July 10, 2020). No vaccine treatment has been defined against SARS-CoV2 or other human coronaviruses (HCoVs), including those causing epidemic infections, neither appropriate strategies for prevention and care are yet officially suggested.

SCOPE AND APPROACH

We reviewed scientific literature on natural compounds that were defined as potentially effective against human coronaviruses. Our desk research identified non-chemically modified natural compounds that were shown (in vitro) and/or predicted (in silico) to act against one or more phases of human coronaviruses cell cycle.We selected all available information, merged and annotated the data to define a comprehensive list of natural compounds, describing their chemical classification, the source, the action, the specific target in the viral infection. Our aim was to collect possible compounds for prevention and care against human coronaviruses.

KEY FINDINGS AND CONCLUSIONS

The definition of appropriate interventions against viral diseases need a comprehensive view on the infection dynamics and on necessary treatments. Viral targeting compounds to be exploited in food sciences could be of relevant interest to this aim.We collected 174 natural compounds showing effects against human infecting coronaviruses, providing a curated annotation on actions and targets.The data are available in anti-HCoV, a web accessible resource to be exploited for testing and in vivo trials. The website is here launched to favour a community based cooperative effort to call for contribution and expand the collection. To be ready to fight.

A General Process-Based Model for Describing the Metabolic Shift in Microbial Cell Cultures

The metabolic shift between respiration and fermentation at high glucose concentration is a widespread phenomenon in microbial world, and it is relevant for the biotechnological exploitation of microbial cell factories, affecting the achievement of high-cell-densities in bioreactors. Starting from a model already developed for the yeast Saccharomyces cerevisiae, based on the System Dynamics approach, a general process-based model for two prokaryotic species of biotechnological interest, such as Escherichia coli and Bacillus subtilis, is proposed. The model is based on the main assumption that glycolytic intermediates act as central catabolic hub regulating the shift between respiratory and fermentative pathways. Furthermore, the description of a mixed fermentation with secondary by-products, characteristic of bacterial metabolism, is explicitly considered. The model also represents the inhibitory effect on growth and metabolism of self-produced toxic compounds relevant in assessing the late phases of high-cell density culture. Model simulations reproduced data from experiments reported in the literature with different strains of non-recombinant and recombinant E. coli and B. subtilis cultured in both batch and fed-batch reactors. The proposed model, based on simple biological assumptions, is able to describe the main dynamics of two microbial species of relevant biotechnological interest. It demonstrates that a reductionist System Dynamics approach to formulate simplified macro-kinetic models can provide a robust representation of cell growth and accumulation in the medium of fermentation by-products.

Characteristics of 1573 healthcare workers who underwent nasopharyngeal swab testing for SARS-CoV-2 in Milan, Lombardy, Italy

OBJECTIVES

The management of healthcare workers (HCWs) exposed to confirmed cases of coronavirus disease 2019 (COVID-19) is still a matter of debate. We aimed to assess in this group the attack rate of asymptomatic carriers and the symptoms most frequently associated with infection.

METHODS

Occupational and clinical characteristics of HCWs who underwent nasopharyngeal swab testing for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a university hospital from 24 February 2020 to 31 March 2020 were collected. For those who tested positive and for those who tested positive but who were asymptomatic, we checked the laboratory and clinical data as of 22 May to calculate the time necessary for HCWs to then test negative and to verify whether symptoms developed thereafter. Frequencies of positive tests were compared according to selected variables using multivariable logistic regression models.

RESULTS

There were 139 positive tests (8.8%) among 1573 HCWs (95% confidence interval, 7.5-10.3), with a marked difference between symptomatic (122/503, 24.2%) and asymptomatic (17/1070, 1.6%) workers (p < 0.001). Physicians were the group with the highest frequency of positive tests (61/582, 10.5%), whereas clerical workers and technicians had the lowest frequency (5/137, 3.6%). The likelihood of testing positive for COVID-19 increased with the number of reported symptoms; the strongest predictors of test positivity were taste and smell alterations (odds ratio = 76.9) and fever (odds ratio = 9.12). The median time from first positive test to a negative test was 27 days (95% confidence interval, 24-30).

CONCLUSIONS

HCWs can be infected with SARS-CoV-2 without displaying any symptoms. Among symptomatic HCWs, the key symptoms to guide diagnosis are taste and smell alterations and fever. A median of almost 4 weeks is necessary before nasopharyngeal swab test results are negative.

The Role of DNA in the Extracellular Environment: A Focus on NETs, RETs and Biofilms

The capacity to actively release genetic material into the extracellular environment has been reported for bacteria, archaea, fungi, and in general, for microbial communities, but it is also described in the context of multicellular organisms, animals and plants. This material is often present in matrices that locate outside the cells. Extracellular matrices have important roles in defense response and disease in microbes, animal and plants cells, appearing as barrier against pathogen invasion or for their recognition. Specifically, neutrophils extracellular traps (NETs) in animals and root extracellular traps (RETs) in plants, are recognized to be important players in immunity. A growing amount of evidence revealed that the extracellular DNA, in these contexts, plays an active role in the defense action. Moreover, the protective role of extracellular DNA against antimicrobials and mechanical stress also appears to be confirmed in bacterial biofilms. In parallel, recent efforts highlighted different roles of self (homologous) and non-self (heterologous) extracellular DNA, paving the way to discussions on its role as a "Damage-associated molecular pattern" (DAMP). We here provide an evolutionary overview on extracellular DNA in extracellular matrices like RETs, NETs, and microbial biofilms, discussing on its roles and inferring on possible novel functionalities.

The surface composition of asteroid 162173 Ryugu from Hayabusa2 near-infrared spectroscopy

The near-Earth asteroid 162173 Ryugu, the target of the Hayabusa2 sample-return mission, is thought to be a primitive carbonaceous object. We report reflectance spectra of Ryugu's surface acquired with the Near-Infrared Spectrometer (NIRS3) on Hayabusa2, to provide direct measurements of the surface composition and geological context for the returned samples. A weak, narrow absorption feature centered at 2.72 micrometers was detected across the entire observed surface, indicating that hydroxyl (OH)-bearing minerals are ubiquitous there. The intensity of the OH feature and low albedo are similar to thermally and/or shock-metamorphosed carbonaceous chondrite meteorites. There are few variations in the OH-band position, which is consistent with Ryugu being a compositionally homogeneous rubble-pile object generated from impact fragments of an undifferentiated aqueously altered parent body.

Localized aliphatic organic material on the surface of Ceres

Organic compounds occur in some chondritic meteorites, and their signatures on solar system bodies have been sought for decades. Spectral signatures of organics have not been unambiguously identified on the surfaces of asteroids, whereas they have been detected on cometary nuclei. Data returned by the Visible and InfraRed Mapping Spectrometer on board the Dawn spacecraft show a clear detection of an organic absorption feature at 3.4 micrometers on dwarf planet Ceres. This signature is characteristic of aliphatic organic matter and is mainly localized on a broad region of ~1000 square kilometers close to the ~50-kilometer Ernutet crater. The combined presence on Ceres of ammonia-bearing hydrated minerals, water ice, carbonates, salts, and organic material indicates a very complex chemical environment, suggesting favorable environments to prebiotic chemistry.

Distribution of phyllosilicates on the surface of Ceres

The dwarf planet Ceres is known to host phyllosilicate minerals at its surface, but their distribution and origin have not previously been determined. We used the spectrometer onboard the Dawn spacecraft to map their spatial distribution on the basis of diagnostic absorption features in the visible and near-infrared spectral range (0.25 to 5.0 micrometers). We found that magnesium- and ammonium-bearing minerals are ubiquitous across the surface. Variations in the strength of the absorption features are spatially correlated and indicate considerable variability in the relative abundance of the phyllosilicates, although their composition is fairly uniform. These data, along with the distinctive spectral properties of Ceres relative to other asteroids and carbonaceous meteorites, indicate that the phyllosilicates were formed endogenously by a globally widespread and extensive alteration process.

The diurnal cycle of water ice on comet 67P/Churyumov-Gerasimenko

Observations of cometary nuclei have revealed a very limited amount of surface water ice, which is insufficient to explain the observed water outgassing. This was clearly demonstrated on comet 9P/Tempel 1, where the dust jets (driven by volatiles) were only partially correlated with the exposed ice regions. The observations of 67P/Churyumov-Gerasimenko have revealed that activity has a diurnal variation in intensity arising from changing insolation conditions. It was previously concluded that water vapour was generated in ice-rich subsurface layers with a transport mechanism linked to solar illumination, but that has not hitherto been observed. Periodic condensations of water vapour very close to, or on, the surface were suggested to explain short-lived outbursts seen near sunrise on comet 9P/Tempel 1. Here we report observations of water ice on the surface of comet 67P/Churyumov-Gerasimenko, appearing and disappearing in a cyclic pattern that follows local illumination conditions, providing a source of localized activity. This water cycle appears to be an important process in the evolution of the comet, leading to cyclical modification of the relative abundance of water ice on its surface.

Cometary science. The organic-rich surface of comet 67P/Churyumov-Gerasimenko as seen by VIRTIS/Rosetta

The VIRTIS (Visible, Infrared and Thermal Imaging Spectrometer) instrument on board the Rosetta spacecraft has provided evidence of carbon-bearing compounds on the nucleus of the comet 67P/Churyumov-Gerasimenko. The very low reflectance of the nucleus (normal albedo of 0.060 ± 0.003 at 0.55 micrometers), the spectral slopes in visible and infrared ranges (5 to 25 and 1.5 to 5% kÅ(-1)), and the broad absorption feature in the 2.9-to-3.6-micrometer range present across the entire illuminated surface are compatible with opaque minerals associated with nonvolatile organic macromolecular materials: a complex mixture of various types of carbon-hydrogen and/or oxygen-hydrogen chemical groups, with little contribution of nitrogen-hydrogen groups. In active areas, the changes in spectral slope and absorption feature width may suggest small amounts of water-ice. However, no ice-rich patches are observed, indicating a generally dehydrated nature for the surface currently illuminated by the Sun.

Spectroscopic characterization of mineralogy and its diversity across Vesta

The mineralogy of Vesta, based on data obtained by the Dawn spacecraft's visible and infrared spectrometer, is consistent with howardite-eucrite-diogenite meteorites. There are considerable regional and local variations across the asteroid: Spectrally distinct regions include the south-polar Rheasilvia basin, which displays a higher diogenitic component, and equatorial regions, which show a higher eucritic component. The lithologic distribution indicates a deeper diogenitic crust, exposed after excavation by the impact that formed Rheasilvia, and an upper eucritic crust. Evidence for mineralogical stratigraphic layering is observed on crater walls and in ejecta. This is broadly consistent with magma-ocean models, but spectral variability highlights local variations, which suggests that the crust can be a complex assemblage of eucritic basalts and pyroxene cumulates. Overall, Vesta mineralogy indicates a complex magmatic evolution that led to a differentiated crust and mantle.

Polymorphisms in the MBL2 promoter correlated with risk of HIV-1 vertical transmission and AIDS progression

We investigated the polymorphisms of the promoter region of the MBL2 gene, which codifies for the Mannose-binding protein (MBP). The study population included 90 children with vertically acquired HIV-infection, further divided on the basis of the disease rate, 27 HIV exposed-uninfected children, and 74 healthy control subjects matched for ethnic origin to evaluate the MBP involvement in the risk of HIV-1 infection and to assess the role of the MBP promoter in AIDS progression. A region of 380 bp in the promoter of the MBL2 gene was analysed by PCR and direct sequencing of both DNA strands. We found that the polymorphism at position -550 influences the risk of HIV-infection and AIDS progression. Also a 6 bp deletion at position -328 was correlated with HIV-1 infection. This study indicates that the promoter of the MBL2 gene influences vertical transmission of HIV and the course of perinatal infection.

Role of Pasteurella multocida, Pasteurella haemolytica and Salmonella typhimurium porins on inducible nitric oxide release by murine macrophages

The aim of this study was to verify whether Pasteurella haemolytica, P. multocida and Salmonella typhimurium porins could affect the inducible nitric oxide synthase (iNOS) expression and nitric oxide (NO) release by murine resident peritoneal macrophages in vitro. We also compared their effect with that elicited by P. haemolytica, P. multocida and S. typhimurium lipopolysaccharide (LPS) whose biological activity is well known. Variations in NO release and iNOS mRNA expression due to variable concentrations of porins were recorded and compared. We also investigated the synergism between bacterial products and interferon gamma (IFN-gamma). With this aim cells were incubated with porins together with murine rIFN-gamma prior to assessing the presence of NO in the supernatant and mRNA analysis. Porins in themselves were not able to induce NO release by resident peritoneal macrophages. Incubation of macrophages with IFN-gamma in the presence of porins increased NO release, whereas incubation in the presence of the arginine analog N(G)-monomethyl-L-arginine (NMA) inhibited NO release. The greatest NO release was obtained using porins at a concentration of 5 microg/mL. Porins, together with IFN-gamma, were also able to upregulate the mRNA expression of iNOS. Our findings suggest that gram-negative porins are able to modulate inflammatory and immunological responses by affecting the release of NO and the expression of iNOS gene in activated macrophages.

Prognostic value of a CCR5 defective allele in pediatric HIV-1 infection

BACKGROUND

A deletion of 32 base pairs in the CCR5 gene (delta32 CCR5) has been linked to resistance to HIV-1 infection in exposed adults and to the delay of disease progression in infected adults.

MATERIALS AND METHODS

To determine the role of delta32 CCR5 in disease progression of HIV-1 infected children born to seropositive mothers, we studied a polymerase chain reaction in 301 HIV-1 infected, 262 HIV-1 exposed-uninfected and 47 HIV-1 unexposed-uninfected children of Spanish and Italian origin. Infected children were further divided into two groups according to their rate of HIV-1 disease progression: rapid progressors who developed severe clinical and/or immunological conditions within the second year of life, and delayed progressors with any other evolution of disease. Among the latter were the long-term, non-progressors (LTNP) who presented with mild or no symptoms of HIV-1 infection above 8 years of age. Viral phenotype was studied for 45 delayed progressors.

RESULTS

No correlation was found between delta32 CCR5 and mother-to-child transmission of HIV-1. However, the frequency of the deletion was substantially higher in LTNP, compared with delayed (p = 0.019) and rapid progressors (p = 0.0003). In children carrying the delta32 CCRS mutation, the presence of MT-2 tropic virus isolate was associated with a severe immune suppression (p = 0.028); whereas, the presence of MT-2 negative viruses correlated with LTNP (p = 0.010).

CONCLUSIONS

Given the rapidity and simplicity of the assay, the delta32 CCR5 mutation may be a useful predictive marker to identify children with delayed disease progression who, consequently, may not require immediate antiretroviral treatment.

High rate of maternal-infant transmission of hepatitis G virus in HIV-1 and hepatitis C virus-infected women

The prevalence of hepatitis G virus (HGV) infection was investigated in 56 mothers with both human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) infection. Thirty-three (58.8%) women had markers of HGV infection, including 7/15 (46.6%) with no history of parenteral exposure to blood. Sixteen (48%) had HGV RNA in serum by a polymerase chain reaction assay, and 17 (52%) had antibody to E2 viral protein. No woman was positive for both markers. Of 20 infants born to the 16 mothers with HGV viremia, 9 (45%, 95% CI 34-56%) acquired the infection. No infected child seroconverted to HGV during the first year of life. At the latest visit (mean: 37.1 mo, range: 9-89 mo) 7 children were still seronegative HGV RNA carriers, 1 was both RNA- and antibody-negative, while 1 RNA-negative child had developed the E2 antibody. Of the 20 HGV-exposed infants, 2 contracted HCV and 1 HIV-1 (all 3 with HGV coinfection). No abnormalities in clinical findings and ALT levels were observed throughout the follow-up period in the six children with HGV infection alone. Our findings show that HGV infection is widespread among HIV-1- and HCV-infected women. Maternal-infant transmission of HGV is common and occurs independently from that of HIV-1 and HCV in women with triple infection. Most perinatally HGV-infected children develop persistent infection with no clinical or biological signs of liver damage, at least in the first years of life.

Carbonaceous grain processing in space and in the laboratory

Laboratory simulations of carbonaceous grain processing which occurs in space are fundamental to outline an evolutionary pathway for these particles. We consider the UV spectral changes induced in hydrogenated carbon grains by thermal annealing, UV irradiation and ion bombardment. The results give the opportunity to interpret observations in different space environments. In particular, modelling of the optical properties, based on a description of the electronic structure of carbons, indicates small hydrogenated amorphous carbon grains, with different degrees of UV irradiation, as the carrier of the ubiquitous UV interstellar extinction bump.

Effects of the major Pasteurella multocida porin on bovine neutrophils

OBJECTIVE

To evaluate in vitro effect of the major fraction of outer membrane proteins of Pasteurella multocida with porin-like activities on some biological functions of bovine neutrophils.

ANIMALS

Neutrophils from 5 adult cattle.

PROCEDURE

Variations in such biological processes as actin polymerization and chemotaxis and evaluation of hydrogen peroxide attributable to variable concentrations of P multocida were recorded and compared. Data were obtained, using the porin and lipopolysaccharide (LPS) isolated from a strain of P multocida cultivated in brain-heart infusion (BHI) broth. Various concentrations of porin and LPS were analyzed to evaluate changes in functional activation and microbicidal activity of bovine neutrophils.

RESULTS

The 37.5-kd major polypeptide of the outer membrane of P multocida was isolated. Presence of this porin was significantly correlated with variations of some biological functions of bovine neutrophils. These immunocompetent cells had a concentration-dependent increase in actin polymerization and chemotactic activity. A concentration-dependent variation in the oxidative burst also was observed.

CONCLUSIONS

The porins of gram-negative bacteria affect several biological functions of cells involved in the immune response as well as in inflammation. Significant correlation of results of in vitro experiments also was identified between porin and LPS effect. Pretreatment of bovine neutrophils with various concentrations of porin always caused a concentration-dependent increase in examined biological activities.

Long-term resistance to HIV infection in vertical HIV infection: cytokine production, HIV isolation, and HIV phenotype define long-term resistant hosts

We analyzed immunologic (CD4 and CD8 slopes; interferon-gamma, interleukin-2, interleukin-10, and chemokines production; concentration of IgE; beta 2-microglobulin) and virologic (p24; HIV isolability and phenotype; plasma viremia) parameters in HIV vertically infected children > or = 8 years of age without disease progression or mild symptoms and an absolute CD4+ count > or = 500/microliter with CD4+ percentage > or = 25%. The results were compared to those of two control groups: (1) slow progressors, children > or = 8 years of age with moderate symptomatology and/or moderate CD4 depletion, and (2) progressors, children > or = 8 years of age with severe clinical disease and/or severe CD4 depletion. Pediatric long-term resistant hosts were characterized by higher production of interleukin-2 and interferon-gamma and lower production of interleukin-10, normal concentration of IgE, HIV isolates with a non-syncytium-inducing phenotype, and lower plasma viremia. This condition was not associated with the concentration of beta 2-microglobulin, p24, and chemokines, or with HIV isolability. The IL-10/IL-2 ratio best correlated with both CD4 counts and disease progression. Thus, vertically infected children showing resistance to disease progression are immunologically and virologically distinct from those in whom progressive HIV infection is observed.

Increased risk of maternal-infant hepatitis C virus transmission for women coinfected with human immunodeficiency virus type 1. Italian Study Group for HCV Infection in Children

To estimate the risk of mother-to-child transmission of hepatitis C virus (HCV) and identify correlates of transmission, 245 perinatally exposed singleton children followed prospectively beyond 18 months of age were studied. Overall, 28 (11.4%) of the 245 children acquired HCV infection. Transmission occurred in 3 of 80 children (3.7%) whose mothers had HCV infection alone and in 25 of 165 (15.1%; P < .01) whose mothers had concurrent infection with human immunodeficiency virus type 1 (HIV-1). The percentage of HIV-1-infected children was similar (22 of 165, 13.3%), but each virus was transmitted independently; only six infants (3.6%) were coinfected with HCV and HIV-1. The risk of HCV transmission was not associated with maternal HIV-1-related symptoms, intravenous drug use, prematurity, low birth weight, or breast-feeding, whereas it was lower with cesarean section than with vaginal delivery (5.6% vs. 13.9%, P = .06). This suggests that transmission occurs mainly around the time of delivery.

ACTH and cortisol secretions in children with perinatal HIV-1 infection

Serum cortisol and adrenocorticotropic hormone (ACTH) values and CD4 cell count were evaluated in 25 perinatally HIV-1-infected children. The children were divided into three groups: group 1 included eight asymptomatic or paucisymptomatic children, group 2 nine moderately symptomatic children, and group 3 eight children with severe clinical manifestations. Group 1 children were without antiretroviral therapy; the remaining children received zidovudine (AZT) treatment. Only one group 3 patient had primary adrenal insufficiency. No significant differences in cortisol and ACTH secretion were found either between all HIV-1-infected and 126 age- and sex-matched normal children or among the three groups of patients. Mean CD4 cell count of each group declined in parallel to disease progression. No correlations were found between cortisol or ACTH values and CD4 cell count. Adrenal failure may be a late complication of HIV-1 infection and should be searched for in severely ill patients. Our data argue against the hypothesis of a cortisol-induced shift from T-helper-1 (Th1) to Th2 cytokine production profile as the pathogenetic mechanism of progression to AIDS.

Natural history of perinatal hepatitis C virus infection

In order to outline the natural course of perinatal hepatitis C virus (HCV) infection, we prospectively followed seven HCV-positive children for a mean period of 65.1 months (range, 26-90 months). Physical examination findings, growth, and bilirubin and immunoglobulin levels were constantly normal. All children were still viremic at last analysis. HCV-RNA was almost constantly detected throughout follow-up, with the exception of the first days of life. All children had initial increases (of variable duration) in alanine aminotransferase values: four children subsequently had normal or borderline values for years, with exacerbation of inflammatory activity in two cases. IgM antibodies to HCV were found in three of the seven patients. Autoantibodies developed in two children. Liver biopsy, performed on five patients, documented different degrees of chronic persistent hepatitis. Thus, recovery from perinatal HCV infection seems unlikely, and chronic hepatitis develops in most infected children, including those with prolonged intervals of remission of inflammatory activity.

Iron deficiency and intestinal malabsorption in HIV disease

Children with human immunodeficiency virus (HIV) infection have a higher prevalence of intestinal malabsorption. Anemia is also a common feature in these children. The aims of this work were (a) to establish the prevalence of iron deficiency in HIV-infected children, (b) to test the hypothesis that iron deficiency is related to intestinal malabsorption, (c) to see whether it may contribute to anemia, and (d) to evaluate the sensitivity of oral iron load in the investigation of intestinal function. To accomplish these goals, 71 HIV-infected symptomatic children were enrolled. Iron serum values were determined before and after oral load with ferrous sulfate. The correlation between basal and post-load iron levels was evaluated by linear regression. Xylose level after oral load, fecal fat, and fecal alpha 1-antitrypsin concentration were also determined. Iron deficiency was detected in 48% of patients, and it was significantly associated with intestinal iron malabsorption. Sugar malabsorption, steatorrhea, and fecal protein loss were detected in 26, 36, and 17% of patients, respectively. Low hemoglobin levels were detected in 66% of patients. The majority of children with iron deficiency also had anemia. Preliminary data showed that oral iron administration was sufficient for raising hemoglobin in children with normal iron absorption, whereas parenteral administration was required in those with iron malabsorption. We conclude that (a) iron deficiency is a major feature of pediatric HIV infection, (b) it is related to intestinal malabsorption, and (c) it contributes to anemia. Finally, oral iron load is a sensitive test for investigating intestinal function.

Anti-HIV-1 antibody avidity is correlated with clinical status in infected children

Avidity of antibodies to gp41 and p24, CD4 cell count, and free and dissociated p24 antigen were assessed in 37 HIV-1-infected children, in order to evaluate whether the avidity of anti-HIV-1 antibodies is related to the disease status in perinatally infected children. The HIV-infected children were divided into two groups. Group 1 included 25 children: 2 not symptomatic (CDC category N), 12 mildly (A) and 11 moderately (B) symptomatic; group 2 included 12 children with severe clinical manifestations (C). The same parameters were assayed longitudinally in four children: two with long-term nonprogressive disease and two with fatal outcome. Antibody avidity was significantly higher in group 1 than in group 2 children (7272 +/- 4788 vs. 2624 +/- 1344 D50, p < 0.01), as was the CD4 cell count (1295 +/- 1122 vs. 348 +/- 488 cells/mm3, p < 0.01). No differences between the two groups were observed in either free or dissociated p24 antigen. Combined measures of antibody avidity and CD4 cell count showed the best correlation with the clinical status (r = 0.57, p = 0.001). In the two children with nonprogressive disease the antibody avidity remained high throughout the follow-up, whereas in those with clinical deterioration its decline preceded, by at least 8 months, the drop in CD4 cells and, by at least 23 months, the appearance of AIDS. In conclusion the avidity of anti-HIV-1 antibodies is reduced in HIV-infected children with advanced disease state and seems an earlier predictor of disease progression than CD4 cell count.

Human immunodeficiency virus infection as risk factor for mother-to-child hepatitis C virus transmission; persistence of anti-hepatitis C virus in children is associated with the mother's anti-hepatitis C virus immunoblotting pattern

To determine the rate of vertical transmission of hepatitis C virus (HCV), we prospectively studied 45 babies born to anti-HCV-positive women with or without concomitant infection with the human immunodeficiency virus (HIV). We performed a second-generation recombinant immunoblotting assay, alanine transaminase (ALT) evaluation, and HCV-RNA testing on sera from 27 infants of HCV+, HIV- mothers and 18 babies of HCV+, HIV+ women, at birth and thereafter. After birth, HCV antibodies progressively disappeared within 12 months in all children but one, whose mother was HCV+, HIV+; this child was the only one who showed detectable levels of HCV-RNA and abnormal ALT values throughout the follow-up (range, 12 to 27 months). Viremia was persistently negative, and ALT levels were continuously normal in the remaining infants, showing that "seronegative" infection with HCV was absent in both groups. Clearance of passively acquired anti-HCV antibodies was found to be slower among babies born to HIV+ mothers (22.3% vs. 3.8% at 12 months, P = .03) and children whose mothers showed three or four anti-HCV reactivities by immunoblotting maintained anti-HCV for longer periods compared with babies born to mothers with one or two anti-HCV reactivities (P = .0001). Seventeen of 27 babies born to HCV+, HIV- mothers were breast-fed, and none of them was infected, confirming the apparent safety for HCV of breast milk. In summary, according to our study, vertical transmission of HCV is an infrequent event, and the presence of HIV in the mother is not an important co-factor for transmission of HCV infection.

Reduced immunoglobulin kappa/lambda light chain ratio in perinatally HIV-1-infected children

In 27 perinatally human immunodeficiency virus type 1 (HIV-1)-infected children, we measured, by immunonephelometry, the kappa/lambda light chain ratio (KLR) of serum immunoglobulins. The latter is a recently available laboratory index reflecting the balance between the synthesis of K isotypes and L isotypes. KLR was consistent over time in each subject, and was significantly lower than that of an age-matched normal population, independently of disease status and therapy. These data indicate a bias, in these subjects, to produce preferentially lambda rather than kappa light chains, contributing to the multiple B-cell abnormalities in HIV-1-infected children.

Growth impairment, IGF I hyposecretion and thyroid dysfunction in children with perinatal HIV-1 infection

We evaluated the growth pattern, bone age, insulin-like growth factor I (IGF I) secretion and thyroid function in 24 perinatally infected children: 9 asymptomatic or paucisymptomatic (group 1) and 15 with a more advanced disease state and treated with zidovudine (group 2). Statural and ponderal growth were compared with those of 37 at-risk children who seroreverted. During the two-year follow-up, 22% of children in group 1 had impaired growth, 33% bone age delay, 45% reduced IGF I levels but none had thyroid dysfunction. In group 2, 53% had growth failure, 53% bone age delay, 86% reduced IGF I levels and 40% thyroid dysfunction. Among seroreverters, none showed growth impairment; statistically significant differences were found for height, weight and height velocity between perinatally infected children and seroreverters. Since auxological and hormonal evaluations run parallel to the clinical course of infection, these indices may be useful in monitoring disease progression.

Asymptomatic women at high risk of vertical HIV-1 transmission to their fetuses

OBJECTIVE

To identify how reliably CD4+ (helper) lymphocyte count and p24 antigenaemia can predict mother-to-infant transmission of human immunodeficiency virus type 1 (HIV-1).

DESIGN

Prospective study.

SETTING

University of Turin Center for Intravenous Drug Users (IVDU) and/or HIV-1 seropositive pregnant women.

SUBJECTS

Twenty-nine infants born to asymptomatic seropositive women from November 1985 to June 1991.

RESULTS

Seven children (24%) developed symptomatic infection, while 22 healthy seronegative children at the age of 18 months were considered uninfected. A CD4+ lymphocyte count persistently < 500/mm3 during pregnancy was associated significantly with the child's infection status with a relative risk (RR) of 11.4. (CI 1.58-82.05). A marked association (RR 13.6) (CI 1.93-95.72) was similarly detected between maternal antigenaemia and the risk of the child being infected. In a multivariate logistic analysis, crude and adjusted odds ratios (OR) of transmission were 27.0 (95% CI 2.5-291.2) and 35.6 (1.1-1159) for low CD4+ counts; 64 (3.2-1261) and 51.6 (2.5-1058) for p24 antigenaemia.

CONCLUSIONS

Asymptomatic HIV positive women with a CD4+ count below 500/mm3 or p24 antigenaemia are about ten times as likely to transmit the virus to their children. CD4+ lymphocytes decrease during pregnancy and a low CD4+ cell count early in pregnancy remains low up to delivery. Therefore knowledge that they have a low CD4+ lymphocyte count early in pregnancy may help women to decide whether or not to continue their pregnancy.

Oral lesions in children born to HIV-1 positive women

A cohort of 69 children born to HIV-1 positive women was studied to evaluate types, prevalences and relationships to clinical stages of HIV-1-related oral lesions. In addition, relationships among C. albicans biotypes, clinical features of oral candidiasis and HIV-1 disease were investigated. C. albicans biotypes did not correlate with clinical features of oral lesions, disease stages and CD4+ lymphocyte count. Of 8 patients with recurrent oral candidiasis, 4 changed clinical features and 5 changed biotype. Our study pointed out the high frequency (28.9%) of oral lesions, especially caused by fungi and the importance of the examination of the oral cavity in children born to HIV-1 positive women.