SingmiR: a single-cell miRNA alignment and analysis tool

Single-cell RNA sequencing (RNA-seq) has revolutionized our understanding of cell biology, developmental and pathophysiological molecular processes, paving the way toward novel diagnostic and therapeutic approaches. However, most of the gene regulatory processes on the single-cell level are still unknown, including post-transcriptional control conferred by microRNAs (miRNAs). Like the established single-cell gene expression analysis, advanced computational expertise is required to comprehensively process newly emerging single-cell miRNA-seq datasets. A web server providing a workflow tailored for single-cell miRNA-seq data with a self-explanatory interface is currently not available. Here, we present SingmiR, enabling the rapid (pre-)processing and quantification of human miRNAs from noncoding single-cell samples. It performs read trimming for different library preparation protocols, generates automated quality control reports and provides feature-normalized count files. Numerous standard and advanced analyses such as dimension reduction, clustered feature heatmaps, sample correlation heatmaps and differential expression statistics are implemented. We aim to speed up the prototyping pipeline for biologists developing single-cell miRNA-seq protocols on small to medium-sized datasets. SingmiR is freely available to all users without the need for a login at https://www.ccb.uni-saarland.de/singmir.

Experimental capture of miRNA targetomes: disease-specific 3'UTR library-based miRNA targetomics for Parkinson's disease

The identification of targetomes remains a challenge given the pleiotropic effect of miRNAs, the limited effects of miRNAs on individual targets, and the sheer number of estimated miRNA-target gene interactions (MTIs), which is around 44,571,700. Currently, targetome identification for single miRNAs relies on computational evidence and functional studies covering smaller numbers of targets. To ensure that the targetome analysis could be experimentally verified by functional assays, we employed a systematic approach and explored the targetomes of four miRNAs (miR-129-5p, miR-129-1-3p, miR-133b, and miR-873-5p) by analyzing 410 predicted target genes, both of which were previously associated with Parkinson's disease (PD). After performing 13,536 transfections, we validated 442 of the 705 putative MTIs (62,7%) through dual luciferase reporter assays. These analyses increased the number of validated MTIs by at least 2.1-fold for miR-133b and by a maximum of 24.3-fold for miR-873-5p. Our study contributes to the experimental capture of miRNA targetomes by addressing i) the ratio of experimentally verified MTIs to predicted MTIs, ii) the sizes of disease-related miRNA targetomes, and iii) the density of MTI networks. A web service to support the analyses on the MTI level is available online ( https://ccb-web.cs.uni-saarland.de/utr-seremato ), and all the data have been added to the miRATBase database ( https://ccb-web.cs.uni-saarland.de/miratbase ).

ZEBRA: a hierarchically integrated gene expression atlas of the murine and human brain at single-cell resolution

The molecular causes and mechanisms of neurodegenerative diseases remain poorly understood. A growing number of single-cell studies have implicated various neural, glial, and immune cell subtypes to affect the mammalian central nervous system in many age-related disorders. Integrating this body of transcriptomic evidence into a comprehensive and reproducible framework poses several computational challenges. Here, we introduce ZEBRA, a large single-cell and single-nucleus RNA-seq database. ZEBRA integrates and normalizes gene expression and metadata from 33 studies, encompassing 4.2 million human and mouse brain cells sampled from 39 brain regions. It incorporates samples from patients with neurodegenerative diseases like Alzheimer's disease, Parkinson's disease, and Multiple sclerosis, as well as samples from relevant mouse models. We employed scVI, a deep probabilistic auto-encoder model, to integrate the samples and curated both cell and sample metadata for downstream analysis. ZEBRA allows for cell-type and disease-specific markers to be explored and compared between sample conditions and brain regions, a cell composition analysis, and gene-wise feature mappings. Our comprehensive molecular database facilitates the generation of data-driven hypotheses, enhancing our understanding of mammalian brain function during aging and disease. The data sets, along with an interactive database are freely available at https://www.ccb.uni-saarland.de/zebra.

ABC-HuMi: the Atlas of Biosynthetic Gene Clusters in the Human Microbiome

The human microbiome has emerged as a rich source of diverse and bioactive natural products, harboring immense potential for therapeutic applications. To facilitate systematic exploration and analysis of its biosynthetic landscape, we present ABC-HuMi: the Atlas of Biosynthetic Gene Clusters (BGCs) in the Human Microbiome. ABC-HuMi integrates data from major human microbiome sequence databases and provides an expansive repository of BGCs compared to the limited coverage offered by existing resources. Employing state-of-the-art BGC prediction and analysis tools, our database ensures accurate annotation and enhanced prediction capabilities. ABC-HuMi empowers researchers with advanced browsing, filtering, and search functionality, enabling efficient exploration of the resource. At present, ABC-HuMi boasts a catalog of 19 218 representative BGCs derived from the human gut, oral, skin, respiratory and urogenital systems. By capturing the intricate biosynthetic potential across diverse human body sites, our database fosters profound insights into the molecular repertoire encoded within the human microbiome and offers a comprehensive resource for the discovery and characterization of novel bioactive compounds. The database is freely accessible at https://www.ccb.uni-saarland.de/abc_humi/.

WebQUAST: online evaluation of genome assemblies

Selecting proper genome assembly is key for downstream analysis in genomics studies. However, the availability of many genome assembly tools and the huge variety of their running parameters challenge this task. The existing online evaluation tools are limited to specific taxa or provide just a one-sided view on the assembly quality. We present WebQUAST, a web server for multifaceted quality assessment and comparison of genome assemblies based on the state-of-the-art QUAST tool. The server is freely available at https://www.ccb.uni-saarland.de/quast/. WebQUAST can handle an unlimited number of genome assemblies and evaluate them against a user-provided or pre-loaded reference genome or in a completely reference-free fashion. We demonstrate key WebQUAST features in three common evaluation scenarios: assembly of an unknown species, a model organism, and a close variant of it.

miEAA 2023: updates, new functional microRNA sets and improved enrichment visualizations

MicroRNAs (miRNAs) are small non-coding RNAs that play a critical role in regulating diverse biological processes. Extracting functional insights from a list of miRNAs is challenging, as each miRNA can potentially interact with hundreds of genes. To address this challenge, we developed miEAA, a flexible and comprehensive miRNA enrichment analysis tool based on direct and indirect miRNA annotation. The latest release of miEAA includes a data warehouse of 19 miRNA repositories, covering 10 different organisms and 139 399 functional categories. We have added information on the cellular context of miRNAs, isomiRs, and high-confidence miRNAs to improve the accuracy of the results. We have also improved the representation of aggregated results, including interactive Upset plots to aid users in understanding the interaction among enriched terms or categories. Finally, we demonstrate the functionality of miEAA in the context of ageing and highlight the importance of carefully considering the miRNA input list. MiEAA is free to use and publicly available at https://www.ccb.uni-saarland.de/mieaa/.

isomiRdb: microRNA expression at isoform resolution

A significant fraction of mature miRNA transcripts carries sequence and/or length variations, termed isomiRs. IsomiRs are differentially abundant in cell types, tissues, body fluids or patients' samples. Not surprisingly, multiple studies describe a physiological and pathophysiological role. Despite their importance, systematically collected and annotated isomiR information available in databases remains limited. We thus developed isomiRdb, a comprehensive resource that compiles miRNA expression data at isomiR resolution from various sources. We processed 42 499 human miRNA-seq datasets (5.9 × 1011 sequencing reads) and consistently analyzed them using miRMaster and sRNAbench. Our database provides online access to the 90 483 most abundant isomiRs (>1 RPM in at least 1% of the samples) from 52 tissues and 188 cell types. Additionally, the full set of over 3 million detected isomiRs is available for download. Our resource can be queried at the sample, miRNA or isomiR level so users can quickly answer common questions about the presence/absence of a particular miRNA/isomiR in tissues of interest. Further, the database facilitates to identify whether a potentially interesting new isoform has been detected before and its frequency. In addition to expression tables, isomiRdb can generate multiple interactive visualisations including violin plots and heatmaps. isomiRdb is free to use and publicly available at: https://www.ccb.uni-saarland.de/isomirdb.

AB0044 REDUCED PERIPHERAL BLOOD MYELOID CELLS IN PATIENTS WITH VEXAS SYNDROME

Background

Systemic inflammatory or dysimmune diseases (SIDDs) are encountered in up to a quarter of patients with myelodysplastic syndromes (MDS). Recently identified VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) syndrome, associated with somatic mutations in UBA1, encompasses a range of severe inflammatory conditions along with hematologic abnormalities, including myelodysplasia. Only limited data are available on the pathophysiology of MDS-associated SIDDs, and especially about the role of different myeloid cell subsets.

Objectives

The aim of this study was to describe the phenotype of myeloid immune cells (dendritic cells and monocytes) in MDS patients with associated SIDDs, and to compare their distribution with MDS patients without SIDDs and controls.

Methods

Phenotype analysis by flow cytometry from PBMCs of 14 MDS patients with SIDDs, 23 MDS patients without SIDDs and 7 controls without MDS and SIDDs. Eight of the 14 MDS/SIDDs patients (57%) had a somatic UBA1 mutation.

Results

In this study analyzing peripheral blood myeloid immune cells in MDS patients with and without SIDDs, we observed a quantitative reduction of different DC and monocyte subsets in MDS/SIDDs patients, especially in patients with active SIDDs and above all in patients with newly described VEXAS syndrome.

Conclusion

Further functional studies are warranted to better understand the mechanisms and the consequences of the phenotypic modulations of immune myeloid cells in the pathophysiology of MDS-associated SIDDs, especially in VEXAS syndrome.

Disclosure of Interests

None declared

OUP accepted manuscript

Despite recent methodology and reference database improvements for taxonomic profiling tools, metagenomic assembly and genomic binning remain important pillars of metagenomic analysis workflows. In case reference information is lacking, genomic binning is considered to be a state-of-the-art method in mixed culture metagenomic data analysis. In this light, our previously published tool BusyBee Web implements a composition-based binning method efficient enough to function as a rapid online utility. Handling assembled contigs and long nanopore generated reads alike, the webserver provides a wide range of supplementary annotations and visualizations. Half a decade after the initial publication, we revisited existing functionality, added comprehensive visualizations, and increased the number of data analysis customization options for further experimentation. The webserver now allows for visualization-supported differential analysis of samples, which is computationally expensive and typically only performed in coverage-based binning methods. Further, users may now optionally check their uploaded samples for plasmid sequences using PLSDB as a reference database. Lastly, a new application programming interface with a supporting python package was implemented, to allow power users fully automated access to the resource and integration into existing workflows. The webserver is freely available under: https://www.ccb.uni-saarland.de/busybee.

PLSDB: advancing a comprehensive database of bacterial plasmids

Plasmids are known to contain genes encoding for virulence factors and antibiotic resistance mechanisms. Their relevance in metagenomic data processing is steadily growing. However, with the increasing popularity and scale of metagenomics experiments, the number of reported plasmids is rapidly growing as well, amassing a considerable number of false positives due to undetected misassembles. Here, our previously published database PLSDB provides a reliable resource for researchers to quickly compare their sequences against selected and annotated previous findings. Within two years, the size of this resource has more than doubled from the initial 13,789 to now 34,513 entries over the course of eight regular data updates. For this update, we aggregated community feedback for major changes to the database featuring new analysis functionality as well as performance, quality, and accessibility improvements. New filtering steps, annotations, and preprocessing of existing records improve the quality of the provided data. Additionally, new features implemented in the web-server ease user interaction and allow for a deeper understanding of custom uploaded sequences, by visualizing similarity information. Lastly, an application programming interface was implemented along with a python library, to allow remote database queries in automated workflows. The latest release of PLSDB is freely accessible under https://www.ccb.uni-saarland.de/plsdb.

Further characterization of clinical and laboratory features occurring in VEXAS syndrome in a large-scale analysis of multicenter case-series of 116 French patients

BACKGROUND

A new autoinflammatory syndrome related to somatic mutations of UBA1 was recently described and called VEXAS syndrome.

OBJECTIVE

To describe clinical characteristics, laboratory findings and outcomes of VEXAS syndrome.

DESIGN

Case-series.

SETTING

Patients referred to a French multicenter registry between November 2020 and May 2021.

PATIENTS

116 patients with VEXAS syndrome.

MEASUREMENTS

Frequency and median of parameters and vital status, from diagnosis to the end of the follow-up.

RESULTS

Main clinical features were skin lesions (83.5%), non-infectious fever (63.6%), weight loss (62%), lung involvement (49.6%), ocular symptoms (38.8%), relapsing chondritis (36.4%), venous thrombosis (34.7%), lymph nodes (33.9%), and arthralgia (27.3%). Hematological disease was present in 58 cases (50%), considered as myelodysplastic syndrome (MDS, n= 58) and monoclonal gammapathy of unknown significance (n=12).UBA1 mutations included p.M41T (44.8%), p.M41V (30.2%), p.M41L (18.1%), and splice mutations (6.9%). After a median follow-up of 3.0 years, 18 patients died (15.5%), from infectious origin (n=9) and MDS progression (n=3). Unsupervised analysis identified 3 clusters: cluster 1 (47%) with mild-to-moderate disease; cluster 2 (16%) with underlying MDS and higher mortality rates; cluster 3 (37%) with constitutional manifestations, higher C-reactive protein levels and less frequent chondritis. Five-year probability of survival was 84.2% in cluster 1, 50.5 % in cluster 2, and 89.6% in cluster 3. UBA1 p.Met41Leu mutation was associated with a better prognosis.

CONCLUSION

VEXAS syndrome displays a large spectrum of organ manifestations and shows different clinical and prognostic profiles. It also raises a potential impact of the identified UBA1 mutation.

Aviator: a web service for monitoring the availability of web services

With Aviator, we present a web service and repository that facilitates surveillance of online tools. Aviator consists of a user-friendly website and two modules, a literature-mining based general and a manually curated module. The general module currently checks 9417 websites twice a day with respect to their availability and stores many features (frontend and backend response time, required RAM and size of the web page, security certificates, analytic tools and trackers embedded in the webpage and others) in a data warehouse. Aviator is also equipped with an analysis functionality, for example authors can check and evaluate the availability of their own tools or those of their peers. Likewise, users can check the availability of a certain tool they intend to use in research or teaching to avoid including unstable tools. The curated section of Aviator offers additional services. We provide API snippets for common programming languages (Perl, PHP, Python, JavaScript) as well as an OpenAPI documentation for embedding in the backend of own web services for an automatic test of their function. We query the respective APIs twice a day and send automated notifications in case of an unexpected result. Naturally, the same analysis functionality as for the literature-based module is available for the curated section. Aviator can freely be used at https://www.ccb.uni-saarland.de/aviator.

miRMaster 2.0: multi-species non-coding RNA sequencing analyses at scale

Analyzing all features of small non-coding RNA sequencing data can be demanding and challenging. To facilitate this process, we developed miRMaster. After the analysis of over 125 000 human samples and 1.5 trillion human small RNA reads over 4 years, we present miRMaster 2 with a wide range of updates and new features. We extended our reference data sets so that miRMaster 2 now supports the analysis of eight species (e.g. human, mouse, chicken, dog, cow) and 10 non-coding RNA classes (e.g. microRNAs, piRNAs, tRNAs, rRNAs, circRNAs). We also incorporated new downstream analysis modules such as batch effect analysis or sample embeddings using UMAP, and updated annotation data bases included by default (miRBase, Ensembl, GtRNAdb). To accommodate the increasing popularity of single cell small-RNA sequencing data, we incorporated a module for unique molecular identifier (UMI) processing. Further, the output tables and graphics have been improved based on user feedback and new output formats that emerged in the community are now supported (e.g. miRGFF3). Finally, we integrated differential expression analysis with the miRNA enrichment analysis tool miEAA. miRMaster is freely available at https://www.ccb.uni-saarland.de/mirmaster2.

AB0161 CLONAL HEMATOPOIESIS IS INCREASED AND NOT RELATED TO AGING IN SYSTEMIC SCLEROSIS

Background:

Systemic sclerosis (SSc) is an autoimmune disease characterized by fibrosis, microangiopathy and immune dysfunctions including dysregulation of proinflammatory cytokines. Clonal hematopoiesis of indeterminate potential (CHIP) is defined by the acquisition of somatic mutations in hematopoietic stem cells leading to detectable clones in the blood. Recent data have shown a higher risk of cardiovascular disease in patients with CHIP resulting from increased production of proinflammatory cytokines and accelerated atherosclerosis. Eventual links between CHIP and autoimmune diseases are undetermined.

Objectives:

The aim of our study was to evaluate the prevalence of CHIP in SSc patients and its association with clinical phenotype.

Methods:

Forty-one genes frequently mutated in myeloid malignancies were sequenced in peripheral blood mononuclear cells from 90 SSc patients and from 44 healthy donors.

Results:

A total of 15 somatic variants was detected in 13/90 SSc patients (14%) and 4 somatic variants in 4/44 (9%) HD (p=0.58). The prevalence of CHIP was significantly higher in younger SSc patients than in HD: 25% (6/24) vs 4% (1/26) (p=0.045) under 50 years and 17% (7/42) vs 3% (1/38) (p=0.065) under 60 years. The prevalence of CHIP in patients over 70 years was similar in SSc patients and healthy donors

For SSc patients the most common mutations occurred inDNMT3A(7 variants). Other variants involvedATM,SF3B1, SETBP1, TET2,TP53,NF1orCBL. The distribution of gene mutations was overall comparable in SSc patients and in previously described CHIP series (3)

In most SSc patients, we identified a single CHIP mutation. Several mutations were detected in two SSc patients:SETBP1andNF1in one and,TET2andATMin the other Clonal mutations included missense (n=10), nonsense (n=3), frameshift (n=1) and a single splice site mutation. In all HD we detected a single CHIP mutation which occurred inDNMT3A, TP53 and CSF3R

Variant allele frequencies (VAF) of CHIP mutations ranged from 2 to 18.6% and did not differ between genes (DNMT3Aor others). Mean age was the same in patients withDNMT3Amutations or with other mutations. However, C>T transversions, that have been associated with ageing were more frequent inDNMT3Avariants than in other genes, suggesting distinct mechanisms for mutation acquisition or clonal selection No major differences in clinical and laboratory data were observed between SSc patients with or without CHIP. SSc subtypes, disease duration, different organ involvements and the prevalence of ischemic events were not associated with the presence of CHIP, except less frequent pyrosis in patients with CHIP than those without. SSc patients with CHIP had significantly more anti-RNA polymerase III antibodies than those without CHIP (p=0.045) At the time of analysis, 45 SSc patients had received a treatment for SSc which consisted in low-dose steroids, hydroxychloroquine, mycophenolate mofetil, cyclophosphamide or methotrexate. SSc patients with CHIP were significantly more exposed to cyclophosphamide (3/13 vs. 3/77) (p=0.04) (5, 6.5 and 11 gram respectively between 5 years to 8 years before the NGS sequencing analysis), but among these cyclophosphamide-exposed SSc the age was over 65 in 2/3 of them. When considering all immunosuppressive drugs (cyclophosphamide, methotrexate and mycophenolate mofetil) SSc patients with CHIP were not more exposed than those without CHIP (p=0.75) No patient developed any hematologic malignancy and no cytopenia during the median follow-up of 13 months (0-24 months). One SSc patients with CHIP developed a small lung cancer few months after NGS testing.

Conclusion:

Whether CHIP increases the risk to develop SSc or is a consequence of a SSc-derived modified bone marrow micro-environment remains to be explored.

Acknowledgments:

na

Disclosure of Interests:

None declared

What's the target: understanding two decades of in silico microRNA-target prediction

MOTIVATION

Since the initial discovery of microRNAs as post-transcriptional, regulatory key players in the 1990s, a total number of $2656$ mature microRNAs have been publicly described for Homo sapiens. As discovery of new miRNAs is still on-going, target identification remains to be an essential and challenging step preceding functional annotation analysis. One key challenge for researchers seems to be the selection of the most appropriate tool out of the larger multiverse of published solutions for a given research study set-up.

RESULTS

In this review we collectively describe the field of in silico target prediction in the course of time and point out long withstanding principles as well as recent developments. By compiling a catalog of characteristics about the 98 prediction methods and identifying common and exclusive traits, we signpost a simplified mechanism to address the problem of application selection. Going further we devised interpretation strategies for common types of output as generated by frequently used computational methods. To this end, our work specifically aims to make prospective users aware of common mistakes and practical questions that arise during the application of target prediction tools.

AVAILABILITY

An interactive implementation of our recommendations including materials shown in the manuscript is freely available at https://www.ccb.uni-saarland.de/mtguide.

Low-Cost Electronic Tagging System for Bee Monitoring

This paper introduces both a hardware and a software system designed to allow low-cost electronic monitoring of social insects using RFID tags. Data formats for individual insect identification and their associated experiment are proposed to facilitate data sharing from experiments conducted with this system. The antennas’ configuration and their duty cycle ensure a high degree of detection rates. Other advantages and limitations of this system are discussed in detail in the paper.

A Longitudinal Study of the Factor VII Rise during Pregnancy

A longitudinal study of 21 pregnant women has been undertaken using a variety of factor VII assays, including factor VIIa, to investigate the increase of factor VIIc. All assays demonstrated significant rises (p <0.001), most marked for factor VIIa (82%) and factor VIIc rabbit (81%). Smaller rises were seen for factor VIIc bovine (50%) and VII antigen (40%). Three indirect measures of activity state, factor VIIc rabbit:antigen, bovine:antigen and bovine:rabbit, provided conflicting data. Factor VIIa:antigen showed a significant increase of 36% (p <0.001). Within individual pregnancies the change in factor VIIc rabbit and antigen correlated with maternal weight gain (p <0.05). Two activity state measures, bovine:rabbit and bovine:antigen, showed negative correlation with birthweight. The increases in both zymogen and in activity state appear to contribute to the factor VIIc rise. The extent of this rise appears to be influenced by maternal weight gain. Increased factor VII activation is associated with reduced foetal growth.

Clinical and economic impact of various strategies for varicella immunity screening and vaccination of health care personnel

BACKGROUND

Exposure to patients with varicella or herpes zoster causes considerable disruption to a health care facility's operations and has a significant health and economic impact. However, practices related to screening for immunity and immunization of health care personnel (HCP) for varicella vary widely.

METHODS

A decision tree model was built to evaluate the cost-effectiveness of 8 different strategies of screening and vaccinating HCP for varicella. The outcomes are presented as probability of acquiring varicella, economic impact of varicella per employee per year, and cost to prevent additional cases of varicella. Monte Carlo simulations and 1-way sensitivity analyses were performed to address the uncertainties inherent to the model. Alternative epidemiologic and technologic scenarios were also analyzed.

RESULTS

Performing a clinical screening followed by serologic testing of HCP with negative history diminished the cost impact of varicella by >99% compared with not having a program. Vaccinating HCP with negative screen cost approximately $50,000 per case of varicella prevented at the current level of U.S. population immunity, but was projected to be cost-saving at 92% or lower immunity prevalence. Improving vaccine acceptance rates and using highly sensitive assays also optimize cost-effectiveness.

CONCLUSION

Strategies relying on screening and vaccinating HCP for varicella on employment were shown to be cost-effective for health care facilities and are consistent with current national guidelines for varicella prevention.

Proximal row carpectomy: Is early postoperative mobilisation the right rehabilitation protocol?

PURPOSE OF THE STUDY

To determine the feasibility and interest of an early rehabilitation protocol with no initial immobilisation after proximal row carpectomy.

MATERIAL AND METHODS

Thirteen patients were included in this retrospective study. Range of motion (ROM) and wrist strength (grip strength and grasp strength) were evaluated 3 and 6 weeks after surgery on the both wrists (operated and non-operated). Postoperatively, patients had no immobilisation of the wrist, and began a rehabilitation program immediately after surgery in the department of Physical Therapy and Rehabilitation under multidisciplinary team supervision. The same surgical technique was used for all patients by the same surgeon.

RESULTS

Six weeks after PRC, there was a 25-51% deficit in passive ROM and 54-64% deficit in active ROM compared to the corresponding non-operated wrist. Six weeks after PRC, mean overall grip strength was nearly 55% and Jamar dynamometer grip strength was 51% of the contralateral side.

DISCUSSION

This study shows that immediate immobilisation following PRC is unnecessary, and that early rehabilitation is of the essence. Early rehabilitation could reduce the delay necessary to recover range of motion and strength, and probably the time to return to work.

LEVEL OF EVIDENCE

Level 4, prospective cohort study.

Neutron activation analysis for the demonstration of amphibolite rock-weathering activity of a yeast

Neutron activation analysis was employed in a survey of weathering abilities of rock surface microorganisms. A yeast isolated from an amphibolite of a megalithic grave was found actively to concentrate, in media and in or on cells, iron and other elements when grown in the presence of ground rock. This was demonstrated by comparing a spectrum of neutron-activated amphibolite powder (particle size, 50 to 100 mum) with the spectra of neutron-activated, lyophilized yeast cells which had grown with or without amphibolite powder added to different media. The most active yeast (IFAM 1171) did not only solubilize Fe from the rock powder, but significant amounts of Co, Eu, Yb, Ca, Ba, Sc, Lu, Cr, Th, and U were also mobilized. The latter two elements occurred as natural radioactive isotopes in this amphibolite. When the yeast cells were grown with neutron-activated amphibolite, the cells contained the same elements. Furthermore, the growth medium contained Fe, Co, and Eu which had been solubilized from the amphibolite. This indicates the presence, in this yeast strain, of active rockweathering abilities as well as of uptake mechanisms for solubilized rock components.

Isolation and properties of ferromanganese-depositing budding bacteria from baltic sea ferromanganese concretions

Hyphal budding bacteria were observed by electron microscopy in thin sections of surface material from Baltic Sea ferromanganese concretions. Similar bacteria were also observed in and isolated from enrichment cultures prepared from the same concretion material. Three morphologically similar strains of Mn-Fe-depositing budding bacteria were isolated from the enrichment cultures. Strain B-4 possessed extracellular anionic polymers that accumulated Mn oxides. Mn deposition by B-4 was inhibited by elevated concentrations of Mn, 0.05% glutaraldehyde, 0.1 mM HgCl(2), and heating at 93 degrees C for 15 min, suggesting the participation of an enzyme protein in the Mn-depositing activity.

Diversity and structure of hyphomicrobium populations in a sewage treatment plant and its adjacent receiving lake

Budding methylotrophic bacteria resembling Hyphomicrobium spp. were counted for 12 months in a German sewage treatment plant by most-probable-number (MPN) methods. Influent samples contained up to 2 x 10(sup4) cells ml(sup-1), activated sludge consistently contained 1 x 10(sup5) to 5 x 10(sup5) cells ml(sup-1), and the effluent contained 1 x 10(sup3) to 4 x 10(sup3) cells ml(sup-1). The receiving lake had only 2 to 12 cells ml(sup-1). Six morphological groups with different growth requirements could be observed among 1,199 pure cultures that had been isolated from MPN dilutions. With dot blot DNA hybridizations, 671 isolates were assigned to 30 hybridization groups (HGs) and 84 could not be classified. Only HG 22 hybridized with a known species, Hyphomicrobium facilis IFAM B-522. Fourteen HGs (HGs 8 to 20 and HG 22) were specific for the lake; most others occurred only in the treatment plant. HGs 1, 3, and 26 were found in the activated sludge tank throughout the year, and HGs 27 and 28 were found for most of the year. In summary, it was demonstrated that bacteria with nearly identical and specific morphologies and nutritional types showed a high level of genetic diversity, although they were isolated under the same conditions and from the same treatment plant or its receiving lake. A directional exchange of these genetically different populations was possible but less significant, as was shown by the establishment of distinct populations in specific stations.

Interaction of integrin receptors with extracellular matrix is involved in trophoblast giant cell migration in bovine placentomes

Integrins are heterodimeric glycoproteins involved in cell-cell and cell-extracellular matrix adhesion and signal transduction. We evaluated the distribution and the putative role of integrin receptors and extracellular matrix (ECM) proteins during trophoblast giant cell (TGC) migration and fusion with uterine epithelial cells in the cow. Placentomes from 24 cows, covering day 80 to day 270 of gestation, were used for indirect immunohistochemistry against integrin subunits alpha(1), alpha(2), alpha(3), alpha(4), alpha(5), alpha(6), alpha(v), beta(1), beta(3), beta(4)and ECM proteins collagen type I and IV, fibronectin, laminin. The basement membranes of fetal and maternal epithelia and endothelia were immunoreactive for laminin, fibronectin and collagen IV. Collagens I and IV were found in maternal stroma, while fibronectin was present in fetal and maternal stroma. The integrin subunits alpha(2), alpha(6)and beta(1)were observed in basal aspects of fetal and maternal epithelial and endothelial cells. Additionally, the alpha(6)and beta(1)integrin subunits were colocalized with laminin on TGC. The integrin alpha(2)subunit was also found on TGC, but localized with a strong gradient to the basal side. Cells of the maternal connective tissue, including endothelium, expressed alpha(1), alpha(2), alpha(3), alpha(5), alpha(6), alpha(v), beta(3)and beta(4). The expression of alpha(2), alpha(5), alpha(v), beta(3)and beta(4) occurred mainly in the septal tips. Cells of the fetal mesenchyme were positive for integrin subunits alpha(1), alpha(2), alpha(3), alpha(4), alpha(5), alpha(6), and beta(1). Our results indicate that alpha(2)beta(1)collagen and alpha(6)beta(1)laminin receptors anchor epi- and endothelial cells to basement membranes. We suggest that TGC migrate along a matrix of laminin and maintain cell-cell contact with mononuclear trophoblast cells via alpha(2)beta(1)heterodimers. Integrins in maternal stroma and fetal mesenchyme may be involved in the regulation of proliferation and differentiation of maternal septa and fetal villi.

Characterization of 15 selected coccal bacteria isolated from Antarctic rock and soil samples from the McMurdo-Dry Valleys (South-Victoria Land)

Approximately 1500 cultures of microorganisms were isolated from rocks and soils of the Ross Desert (McMurdo-Dry Valleys). From these, 15 coccoid strains were chosen for more detailed investigation. They were characterized by morphological, physiological and chemotaxonomical properties. All isolates were Gram-positive, catalase-positive and nonmotile. Six strains showed red pigmentation and could be identified as members of the genera Micrococcus (M. roseus, M. agilis) or Deinococcus. In spite of their coccoid morphology, the remaining nine strains had to be associated with coryneform bacteria (Arthrobacter, Brevibacterium), because of their cell wall composition and G+C ratios. Most of the strains were psychrotrophic, but one strain was even obligately psychrophilic, with a temperature maximum below 20 degrees C. Red cocci had in vitro pH optima above 9.0 although they generally originated from acid samples. Most isolates showed a preference for sugar alcohols and organic acids, compounds which are commonly known to be released by lichens, molds and algae, the other components of the cryptoendolithic ecosystem. These properties indicate that our strains are autochthonous members of the natural Antarctic microbial population.

Transfusion transmissible virus TTV and its putative role in the etiology of liver disease

TTV, the transfusion transmissible hepatitis virus infects mainly patients at risk for parenteral exposure and hence, prone to develop chronic liver disease, as well as healthy populations worldwide. Most TTV infections appear to occur parenterally, with viremia detected frequently in blood donors and blood products. The substantial proportion of asymptomatic individuals never exposed to blood-borne agents, and its high prevalence among healthy subjects implicates the fecal-oral route as another potential for transmission. According to the TTV DNA levels detected in liver tissue, it apparently replicates in hepatocytes, and TTV DNA is present in sera of patients with posttransfusion hepatitis of unknown etiology closely correlated with ALT levels. However, TTV initiating the development of chronic liver disease or causing posttransfusion hepatitis could not be confirmed, as most patients positive for TTV DNA remain asymptomatic and those progressing towards chronic liver disease are invariably coinfected with either the hepatitis B or C virus. Also, TTV coinfection does not aggravate the symptoms associated with hepatitis B or C. Similarly, it does not cause posthepatitis aplastic anemia, and high-risk patients can immunologically clear the viral DNA. In conclusion, being widely distributed and apparently nonpathogenic, TTV might represent an opportunistic but innocent virus reminiscent of hepatitis G virus, with a negligible role in the etiology of chronic liver disease.

Core promoter and precore mutants of hepatitis B virus: prevalence and clinical relevance in chronic hepatitis patients

The present study was conducted to determine prevalence and exact type, as well as nucleotide position of the precore/core mutations of hepatitis B virus found in Thai patients diagnosed with chronic hepatitis and/or cirrhosis in relation to the clinical parameters established with the respective patients. To that end, 24 HBeAg-positive and 56 HBeAg-negative individuals were selected at random from a cohort of altogether 256 chronic liver disease patients. DNA was extracted from their blood sera, amplified by polymerase chain reaction using semi-nested primers and subjected to direct sequencing. Clinically, the HBeAg-positive chronic hepatitis patients displayed significantly higher transaminase levels than those negative for HBeAg. Our results showed 2 of the 7 (28.6%) PCR-positive HBeAg-positive sera displaying double mutations in the core promoter region at position 1762/64. The nucleotide sequences obtained from the 24 PCR-positive HBeAg-negative sera revealed 18 (75%) mutations in the core promoter region (1762/64), and/or 7 (29.2%) mutations at position 1753, and/or 6 (25%) mutations of the start codon (1814), and/or 8 of (33.3%) nucleotide 1896 turning codon 28 into a stop codon and one sample (4.2%) displaying a deletion between nucleotides 1758-1772. It is suggested that the mutations observed have an impact on the DNA secondary structure in such a way that successful transcription of the HBeAg gene is rendered impossible. To what extent this mutation influences the severity of chronic liver disease remains to be elucidated.

Increasing susceptibility to HAV among members of the young generation in Thailand

The prevalence of antibodies to hepatitis A virus was studied in 961 children and adolescents, randomly selected from five different provinces in Thailand (Chonburi, Lopburi, Udonthani, Nakhon Si Thammarat and Lopburi). The highest prevalence was found in Nakhon Si Thammarat, with 32.1 percent of those aged 10-14 years and 57.1 percent of those aged 15-18 years showing evidence of protective immunity. However, this high rate could be explained by an outbreak of hepatitis A in 1992. In the remaining four provinces, the pattern was typically age-related in that all individuals showed between zero and 13 percent antibody prevalence until reaching the 15-to-18-year age group where it increased to between 5.6 and 22.7 percent. The overall sero-prevalence among all age groups was 7.9 percent. Thus, the majority of the younger generation is susceptible to hepatitis A virus infection thereby enhancing the impact, should an outbreak occur. Preventive measures that might be taken are education aimed at better hygiene and sanitation, as well as vaccination of susceptible individuals within high-risk populations.

Clinical associations and prognostic significance of serum anti-p53 antibodies in Thai patients with hepatocellular carcinoma

Mutations of the p53 gene have been reported to be of prognostic significance in hepatocellular carcinoma (HCC). However, the clinical associations and prognostic value of anti-p53 antibodies, known to be products of the host immune response to these mutations, have been controversial. Serum anti-p53 antibodies were measured in 121 Thai patients diagnosed with HCC using a specific enzyme-linked immunosorbent assay (ELISA) kit. The clinical/pathological characteristics of the patients were compared with respect to the presence of serum anti-p53 antibodies. Cox regression analysis was performed to assess factor interaction and association with survival. Anti-p53 antibodies were detected in 13.2% (16 of 121) of our patients. There were no differences between groups with regard to age, sex, viral markers (HBsAg or anti-HCV), severity of liver disease and tumor advancement. The median survival rates for patients positive and negative for anti-p53 antibodies were 4.0 and 3.0 months, respectively (p = 0.443, by log-rank test). Multivariate analysis demonstrated that an advanced Okuda stage, lack of therapy and presence of portal vein thrombosis were independent factors related to the prognosis of the patients. Nonetheless, the presence of anti-p53 antibodies did not constitute a predictive variable associated with a poorer prognosis. Serum assay of anti-p53 antibodies, although rapid and easily performed, may not be suitable as an alternative to molecular detection of mutations in assessing tumor advancement and prognosis of patients with HCC.

Impact of hepatitis B immunisation as part of the EPI

Since 1992, hepatitis B vaccine has been an integrated part of Thailand's expanded programme on immunisation (EPI). Based on the data from five representative provinces, we have evaluated its impact on the countrywide prevalence of HBV infection and carrier rate. The population studied comprised 400-488 healthy and immuno-competent, subjects per area. The subjects' ages ranged from 6 months to 18 years. We examined their sera for viral hepatitis markers using commercially available test kits and established the coverage rate of hepatitis B vaccination after its inclusion into the EPI to be 71.2-94.3%. The number of individuals undergoing the complete course of vaccinations had increased four-fold. Consequently, only 0.7% of the children born after the implementation of this the novel EPI strategy were HBV carriers.

Parvovirus B19 antibodies in immunocompromized children in Thailand

Parvovirus B19, a non-enveloped single stranded DNA virus is distributed worldwide. Sero-prevalence in adult populations amounts to approximately 50%. Clinical manifestations vary depending on the Immune status of the infected individuals and may include mild childhood Infection as well as hydrops fetalis due to intrauterine infection. To determine the prevalence of this infection among the immunocompromized individuals in Thailand, we determined, by indirect ELISA, levels of IgM and IgG antibodies to the parvovirus B19 in 106 immunocompromized children. These included 49 children who were on chemotherapy for treatment of malignancies, 18 who were receiving immunosuppressive drugs after organ transplantations, 14 who were under a regimen of corticosteroids and 25 who were positive for antibodies to HIV. The average prevalence of IgG antibodies in 106 children was 16.0%; the prevalence of antibodies was 33.3% in post-transplanted group, 16% in children positive for HIV, 12.2% in the group receiving chemotherapy for malignancies and 7.6% in the group treated with corticosteroids. All children were negative for IgM antibodies to parvovirus B19.

Persistence of antibodies to the surface antigen of the hepatitis B virus (anti-HBs) in children subjected to the Expanded Programme on Immunization (EPI), including hepatitis-B vaccine, in Thailand

Will hepatitis-B vaccine administered at birth, and at 2 and 6 months of age, as an integral part of Thailand's Expanded Programme on Immunization, provide long-term protection? In an attempt to answer this question, residents of five provinces (representing five distinct geographical areas of Thailand) who were aged 1-10 years and had received this course of vaccination were enrolled on a serological study. Each was tested, with ELISA, for the surface antigen of hepatitis B (HBsAg) and for antibodies against this antigen (anti-HBs) or against the core antigen (anti-HBc). Over all age-groups, the prevalences of HBsAg, anti-HBs and anti-HBc were 0.67%, 71.4% and 5.5%, respectively. Although the prevalence of anti-HBs decreased with age, it remained at 56%-65% among those aged 6-10 years. Between 2% and 17% of the subjects aged 1-9 years had high titres of anti-HBs. Based on these results, an additional booster, still a controversial issue, does not appear to be required in order to prevent infection with hepatitis B virus and thus permit the eventual eradication of chronic carriage and its fatal sequelae in Thailand.

Prevalence of antibodies to parvovirus B 19 in Thailand

Infection with human parvovirus B 19, a single-stranded non-enveloped DNA virus of worldwide distribution, is rather common and displays a broad spectrum of clinical manifestations of varying severity, depending on the patient's immune response. As the target of infection are the erythroid precursor cells, patients can experience an aplastic crisis. Usually, at least in immunocompetent individuals, viremia ceases with the appearance of virus-specific antibodies in the patient's serum whereupon the patients retain lifelong immunity to reinfection. Since data as to the prevalence of this agent has not been established for Thailand, the purpose of the present study was to investigate its frequency among 3 distinct groups, comprising 30 healthy children. 64 children with acute unrelated illness, and 35 voluntary blood donors, respectively, by means of enzyme linked immunosorbent assay. Our results have shown that, as reported for other countries, anti-parvovirus IgG increases in an age-dependent manner and is established at an overall prevalence of 20.16%, inviting the conclusion that the local population is infected by this agent as frequently as those of other countries in the Far East. Further studies need to be undertaken in order to elucidate its prevalence among members of high-risk groups.

New LL-diaminopimelic acid-containing actinomycetes from hypersaline, heliothermal and meromictic Antarctic Ekho Lake: Nocardioides aquaticus sp. nov. and Friedmanniella [correction of Friedmannielly] lacustris sp. nov

Two Gram-positive, non-motile and aerobic bacteria were isolated from a water sample of the hypersaline Ekho Lake, Antarctica. The cocci or short rods grew well on oligotrophic PYGV agar of pH 7.5 and at 26 degrees C. Strains EL-17KT and EL-17AT both required thiamine and biotin, strain EL-17AT also required nicotinic acid. Carbon sources utilized by both strains were acetate, pyruvate, alpha-D-glucose, glutamate and (weakly) citrate, but succinate, malate or butyrate were utilized only by EL-17KT. Gelatin, starch and DNA were hydrolyzed, NH, was formed from peptone, and nitrate was reduced aerobically by both strains. The isolates had the same temperature tolerance for growth in the range tested (below 3 to above 33.5 degrees C) and pH range (<5.5 to >9.5) and were sensitive to chloramphenicol and penicillin G. Their cell walls contained LL-diaminopimelic acid and had a single glycine residue as interpeptide bridge. Strain EL-17AT contained glycine at position 1 of the peptide subunit (peptidoglycan type A 3gamma'). Isolates EL-17KT and EL-17AT differed in their maximum NaCl tolerance, which was 15% or 6-8%, respectively. The major fatty acid of EL-17KT was C18:1 and that of EL-17AT was ai-C15:0. The major respiratory quinones of EL-17KT and EL-17AT were MK-8(H4) and MK-9(H4), respectively. The former isolate had 69 mol% G+C, the latter had 73 mol% G+C. Comparative 16S rRNA gene sequencing revealed phylogenetic relationships of isolate EL-17KT with the genus Nocardioides, with N. pyridinolyticus and N. plantarum as the closest relatives. Phenotypic and genotypic characteristics support the description of a new species, Nocardioides aquaticus sp. nov., with EL-17KT as the type strain (= DSM 11439T). Isolate EL-17AT is related to the genus Friedmanniella, with E antarctica and E spumicola as the closest relatives. The differentiating characteristics support the description of a new species, Friedmanniella lacustris sp. nov., with EL-17AT as the type strain (= DSM 11465T).