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At least 163 records · Page 9Linked to original sources
PubMed2006

Targets of the master regulator of biofilm formation in Bacillus subtilis.

Wild strains of the spore-forming bacterium Bacillus subtilis are capable of forming architecturally complex communities of cells. The formation of these biofilms is mediated in part by the 15-gene exopolysaccharide operon, epsA-O, which is under the direct negative control of the SinR repressor. We report the identification of an additional operon, yqxM-sipW-tasA, that is required for biofilm formation and is under the direct negative control of SinR. We now show that all three members of the operon are required for the formation of robust biofilms and that SinR is a potent repressor of the operon that acts by binding to multiple sites in the promoter region. Genome-wide analysis of SinR-controlled transcription indicates that the epsA-O and yqxM-sipW-tasA operons constitute many of the most strongly controlled genes in the SinR regulon. These findings reinforce the view that SinR is a master regulator for biofilm formation and further suggest that a principal biological function of SinR is to govern the assembly of complex multicellular communities.

Bacillus subtilis↗
PubMed2000

Is it feasible to construct a community profile of exposure to industrial air pollution?

OBJECTIVE: An epidemiological investigation to assess the validity of residential proximity to industry as a measure of community exposure. METHODS: 19 Housing estates in Teesside (population 1991: 77 330) in north east England were grouped into zones: A=near; B=intermediate; C=further from industry. With residential proximity of socioeconomically matched populations as a starting point a historical land use survey, historical air quality reports, air quality monitoring, dispersion modelling data, and questionnaire data, were examined. RESULTS: The populations in zones A, B, and C were similar for socioeconomic indicators and smoking history. Areas currently closest to industry had also been closest for most of the 20th century. Historical reports highlighted the influence of industrial emissions to local air quality, but it was difficult to follow spatial pollution patterns over time. Whereas contemporary NO(x) and benzene concentrations showed no geographical variation, dispersion modelling of emissions (116 industrial stacks, traffic, and domestic sources) showed a gradient associated with industry. The presumed exposure gradient of areas by proximity to industry (A>B>C) was evident for all of zone A and most of zones B and C. CONCLUSIONS: It was feasible to assemble a picture of community exposure by integration of measurements from different sources. Proximity of residence was a reasonable surrogate for complex community exposure.

Air Pollutants↗
PubMed2001

Impact of atrial fibrillation on the clinical course of hypertrophic cardiomyopathy.

BACKGROUND: Clinical impact of atrial fibrillation (AF) in hypertrophic cardiomyopathy (HCM) is largely unresolved. Thus, we analyzed the prognostic implications of AF in a large, community-based HCM population assembled from Italian and US cohorts. METHODS AND RESULTS: Occurrence of AF and outcome were assessed in 480 consecutive HCM patients (age at diagnosis, 45+/-20 years; 61% male) who were followed up for 9.1+/-6.4 years. AF occurred in 107 patients (22%; incidence, 2%/y) and was independently predicted by advancing age, congestive symptoms, and increased LA size at diagnosis. Patients with AF had increased risk for HCM-related death (OR, 3.7; P<0.002) because of excess heart failure-related mortality but not sudden, unexpected death. This risk associated with AF was substantially greater in patients with outflow obstruction or with earlier development of AF (</=50 years of age). AF patients were also at increased risk for stroke (OR, 17.7; P=0.0001) and severe functional limitation (OR for NYHA class III or IV, 2.8; P<0.0001). Compared with those with exclusively paroxysmal AF, patients developing chronic AF showed higher combined probability of HCM-related death, functional impairment, and stroke (P<0.0001). In a subgroup of 37 patients with AF (35%), the clinical course was largely benign in the absence of stroke and severe symptoms. CONCLUSIONS: In a community-based HCM population, AF (1) was common, with 22% prevalence over 9 years; (2) was associated with substantial risk for heart failure-related mortality, stroke, and severe functional disability, particularly in patients with outflow obstruction, those </=50 years of age, or those developing chronic AF; and (3) was nevertheless compatible with benign outcome in 35% of patients.

Adult↗
PubMed2026

Two worlds beneath: Distinct microbial strategies of the rock-attached and planktonic subsurface biosphere.

BACKGROUND: Microorganisms in groundwater ecosystems exist either as planktonic cells or as attached communities on aquifer rock surfaces. Attached cells outnumber planktonic ones by at least three orders of magnitude, suggesting a critical role in aquifer ecosystem function. However, particularly in consolidated carbonate aquifers, where research has predominantly focused on planktonic microbes, the metabolic potential and ecological roles of attached communities remain poorly understood. RESULTS: To investigate the differences between attached and planktonic communities, we sampled the attached microbiome from passive samplers filled with crushed carbonate rock exposed to oxic and anoxic groundwater in the Hainich Critical Zone Exploratory and compared it to a previously published, extensive dataset of planktonic communities from the same aquifer ecosystem. Microbial lifestyle (attached vs. planktonic) explained more variance in community composition than redox conditions, prompting us to further investigate its role in shaping functional and activity profiles. Metagenomic analysis revealed a striking taxonomic and functional segregation: the 605 metagenome-assembled genomes (MAGs) from attached communities were dominated by Proteobacteria (358 MAGs) and were enriched in genes for biofilm formation, chemolithoautotrophy, and redox cycling (e.g., iron and sulfur metabolism). In contrast, the 891 MAGs from planktonic communities were dominated by Cand. Patescibacteria (464 MAGs) and Nitrospirota (60 MAGs) and showed lower functional versatility. Only a few genera were shared, and even closely related MAGs (>&#x2009;90% average nucleotide identity) differed in assembly size and metabolic traits, demonstrating lifestyle-specific functional adaptation. Analysis of active replication indicated that the active fraction of the attached community was primarily represented by the most abundant MAGs. Planktonic communities featured a higher fraction of active MAGs compared to attached communities, but overall with lower relative abundances. CONCLUSIONS: The high abundance, metabolic specialization, and carbon fixation potential of attached microbes suggest that they are key drivers of subsurface biogeochemical processes. Carbonate aquifers may act as much larger inorganic carbon sinks than previously estimated based on CO2 fixation rates of the planktonic communities alone. Our findings underscore the need to incorporate attached microbial communities into models of subsurface ecosystem function. Video Abstract.

Plankton↗
PubMed2002

[Ecological restoration of Castanopsis carlesii forest in Wupin, Fujian].

Analyses on the effects of the different scales of human disturbance on restoration of Castanopsis carelesii forest in Wupin, Fujian indicated that with increasing degrees of the scales of human disturbance (A class, regeneration by selected cutting; B class, natural regeneration; C class, natural regeneration promoted by artificial tending; D class, Chinese fir forest), the important value of Castanopsis carlesii and the similar index between the communities decreased, and the assembling and abundance degrees of species increased under disturbance of B or C class, and decreased under D class. It could be concluded that the disturbance of A class was light, that of B class was medium and could be restored rapidly, disturbance of C class was also medium but would be restored in a longer period, and that of D class was difficult to be restored due to the intense disturbance.

Animals↗
PubMed1997

Essential criteria for quality systems in medical laboratories.

The introduction of total quality systems in medical and clinical laboratories and accreditation of these laboratories is gaining more and more interest. In several countries laboratories have set up quality systems, and accrediation schemes are also operating. The standards of these schemes have much in common although several differences exist. There exists uncertainty in several countries on the choice of a system. Laboratory specialists are confronted with a new way of thinking concerning the management and daily practice of their laboratories. It is not clear, which standards should be used as a basis, and certainly not how to interpret such standards. Particulary in the European Union, harmonisation of criteria for quality systems is desirable. In the present paper, the document entitled "Essential Criteria for Quality Systems in Medical Laboratories" is presented. The document has been accepted in the general Assembly of the European Communities Confederation of Clinical Chemistry (EC4) and by the working group on Good Laboratory Services of the European Council on Laboratory Medicine (ECLM). The criteria in the document are focussed on the particular situation of medical laboratories, including pre- and post-analytical aspects. Reference is made, where applicable, to EN 45001, ISO 9001 and ISO guide 25 draft 3.

Chemistry, Clinical↗
PubMed2026

Characteristics and assembly mechanisms of tobacco-associated bacteria in typical tobacco-planting regions across China.

INTRODUCTION: Plant-associated microbiota critically modulates host growth and environmental adaptation, yet assembly mechanisms, niche differentiation, and ecological strategies of bacterial communities inhabiting tobacco microhabitats remain poorly elucidated across geographical gradients. METHODS: Here, we systematically characterized bacterial microbiome assembly across five tobacco-associated niches (bulk soil, rhizosphere soil, root, stem, and leaf) from seven typical tobacco-planting regions using 16S rRNA amplicon sequencing, genome annotation, and niche breadth analysis. The independent and interactive effects of geographical location and host compartment on community structure, and further compared genomic traits, functional profiles, and life-history strategies between specialist and generalist bacterial populations were quantified. RESULTS: The results revealed a deterministic soil-plant continuum stratification of bacterial communities and diversity, with progressively simplified communities and decreasing alpha diversity from bulk soil to above-ground tissues, accompanied by progressive dominance of Proteobacteria. Geographical factors predominantly structured soil microbial communities via divergent edaphic properties, while host filtering acted as a universal dominant driver shaping endophytic microbiome assembly. Niche differentiation analysis demonstrated that niche-specialized bacterial ASVs overwhelmingly dominated all microhabitats and geographical sites, whereas generalist taxa only constituted auxiliary populations. Although specialist and generalist microbes exhibited highly conserved core genomic architectures and overall functional repertoires, they displayed distinct niche-specific functional divergence in metabolic pathways, stress resistance, and secondary metabolism across host compartments. Life-history strategy analysis further revealed that Y-strategist represented the core adaptive bacterial population, especially enriched in above-ground tobacco tissues. DISCUSSION: Our study establishes a hierarchical dual-filtering assembly model for tobacco microbiota, clarifies the ecological differentiation and functional adaptation of specialist and generalist bacteria, and provides fundamental insights into the assembly rules and adaptive mechanisms of crop-associated microbiomes for future microbial resource utilization and agricultural microbiome regulation.

biogeography↗
PubMed2007

Soil nutrients influence spatial distributions of tropical tree species.

The importance of niche vs. neutral assembly mechanisms in structuring tropical tree communities remains an important unsettled question in community ecology [Bell G (2005) Ecology 86:1757-1770]. There is ample evidence that species distributions are determined by soils and habitat factors at landscape (<10(4) km(2)) and regional scales. At local scales (<1 km(2)), however, habitat factors and species distributions show comparable spatial aggregation, making it difficult to disentangle the importance of niche and dispersal processes. In this article, we test soil resource-based niche assembly at a local scale, using species and soil nutrient distributions obtained at high spatial resolution in three diverse neotropical forest plots in Colombia (La Planada), Ecuador (Yasuni), and Panama (Barro Colorado Island). Using spatial distribution maps of >0.5 million individual trees of 1,400 species and 10 essential plant nutrients, we used Monte Carlo simulations of species distributions to test plant-soil associations against null expectations based on dispersal assembly. We found that the spatial distributions of 36-51% of tree species at these sites show strong associations to soil nutrient distributions. Neutral dispersal assembly cannot account for these plant-soil associations or the observed niche breadths of these species. These results indicate that belowground resource availability plays an important role in the assembly of tropical tree communities at local scales and provide the basis for future investigations on the mechanisms of resource competition among tropical tree species.

Ecosystem↗
PubMed2000

Nestedness, anti-nestedness, and the relationship between prevalence and intensity in ectoparasite assemblages of marine fish: a spatial model of species coexistence.

Nested species subset patterns consist in a hierarchical structure of species composition in related assemblages, with the species found in depauperate assemblages representing non-random subsets of progressively richer ones. This pattern has been found at the infracommunity level in about a third of the fish ectoparasite assemblages studied to date. Here we present evidence for another non-random structural pattern in assemblages of fish ectoparasites, anti-nestedness, which corresponds to situations in which parasite species are always absent from infracommunities richer than the most depauperate one in which they occur. We show that this pattern is exactly as common as nestedness, and that anti-nested assemblages are characterised by significantly lower prevalence and mean intensities of parasites than nested assemblages. In addition, we found a positive relationship between the prevalence and the mean intensity of parasites across the different assemblages. We propose a link between the nestedness/anti-nestedness continuum and the prevalence-intensity relationship that may involve colonisation-extinction processes. The results presented here suggest that, although nestedness may not be common in parasite communities, other departures from random species assembly are possible, and that some form of structure may be present in many communities. The continuum between nestedness and anti-nestedness also has implications for recent models of species coexistence in communities.

Animals↗
PubMed2025

Diploid genome assembly of human fibroblast cell lines enables clone specific variant calling, improved read mapping and accurate phasing.

Human cell lines are fundamental tools in biomedical research and are widely used in disease modeling, drug development, and many other domains. Here, we present chromosome-level, phased diploid genome assemblies of two popular human cell lines: the BJ foreskin fibroblast line and the IMR-90 fetal lung fibroblast line. Our high-quality assemblies, generated using long-read and Hi-C sequencing data, reveal substantial structural variation, including more than 50,000 insertions, deletions, duplications, and inversions compared to the recent T2T-CHM13v2.0 reference. Our assemblies provide detailed maps of genetic variation, enabling more accurate variant calling and the ability to phase reads when using newly generated or historical sequencing data on these cell lines or their derivatives. All assemblies and associated data have been made available as a resource for the research community. We envision that diploid genome assembly will become a cornerstone approach for personalized medicine in the near future.

Journal Article↗
PubMed2005

PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information.

BACKGROUND: Phages, viruses that infect prokaryotes, are the most abundant microbes in the world. A major limitation to studying these viruses is the difficulty of cultivating the appropriate prokaryotic hosts. One way around this limitation is to directly clone and sequence shotgun libraries of uncultured viral communities (i.e., metagenomic analyses). PHACCS http://phage.sdsu.edu/phaccs, Phage Communities from Contig Spectrum, is an online bioinformatic tool to assess the biodiversity of uncultured viral communities. PHACCS uses the contig spectrum from shotgun DNA sequence assemblies to mathematically model the structure of viral communities and make predictions about diversity. RESULTS: PHACCS builds models of possible community structure using a modified Lander-Waterman algorithm to predict the underlying contig spectrum. PHACCS finds the most appropriate structure model by optimizing the model parameters until the predicted contig spectrum is as close as possible to the experimental one. This model is the basis for making estimates of uncultured viral community richness, evenness, diversity index and abundance of the most abundant genotype. CONCLUSION: PHACCS analysis of four different environmental phage communities suggests that the power law is an important rank-abundance form to describe uncultured viral community structure. The estimates support the fact that the four phage communities were extremely diverse and that phage community biodiversity and structure may be correlated with that of their hosts.

Algorithms↗
PubMed2006

Evolutionary responses of natives to introduced species: what do introductions tell us about natural communities?

Biological invasions dramatically affect the distribution, abundance and reproduction of many native species. Because of these ecological effects, exotic species can also influence the evolution of natives exposed to novel interactions with invaders. Evolutionary changes in natives in response to selection from exotics are usually overlooked, yet common responses include altered anti-predator defenses, changes in the spectrum of resources and habitats used, and other adaptations that allow native populations to persist in invaded areas. Whether a native population is capable of responding evolutionarily to selection from invaders will depend on the demographic impact of the invader, the genetic architecture and genetic variability of the native population and potentially the history of previous invasions. In some cases, natives will fail to evolve or otherwise adapt, and local or global extinction will result. In other cases, adaptive change in natives may diminish impacts of invaders and potentially promote coexistence between invaders and natives. Here, we review the evidence for evolutionary responses of native species to novel community members. We also discuss how the effects of introduced species may differ from those caused by natural range expansions of native species. Notably, introduced species may come from remote biotas with no previous evolutionary history with the native community. In addition, the rate of addition of introduced species into communities is much greater than all but the most extreme cases of historical biotic exchange. Understanding the evolutionary component of exotic/native species interactions is critical to recognizing the long-term impacts of biological invasions, and to understanding the role of evolutionary processes in the assembly and dynamics of natural communities.

Animals↗
PubMed1993

Analysis of the six additional chemicals for in vitro assays of the European Economic Communities' EEC aneuploidy programme using Saccharomyces cerevisiae D61.M and the in vitro porcine brain tubulin assembly assay.

We tested six additional chemicals (acetaldehyde, benomyl, diethylstilboestrol, diethylstilboestrol dipropionate, griseofulvin, and mercaptoethanol) for in vitro systems of the coordinated programme to study aneuploidy induction sponsored by the Commission of the European Communities in two in vitro test systems. Using Saccharomyces cerevisiae D61.M (mitotic chromosomal malsegregation assay), benomyl showed a dose-dependent increase in the frequency of chromosomal malsegregation with a lowest effective dose tested (LEDT) of 30 micrograms/ml (0.1 mM). Diethylstilboestrol (DES) showed solvent-dependent effects. DES dissolved in ethanol induced an increase in chromosomal malsegregation as well as in the frequency of total resistant colonies (mutations and recombinations) with a LEDT around 13 micrograms/ml (0.048 mM). Using dimethylsulfoxide as the solvent, no increases were observed with DES up to 333 micrograms/ml (1.24 mM). Acetaldehyde induced an increase in chromosomal malsegregation with the cold treatment protocol (LEDT: 1.25 microliters/ml (21 mM) and 0.75 microliters/ml (13 mM), respectively) but no increase with the overnight protocol (highest dose tested (HDT): 1.75 microliters/ml; 30 mM). Concerning the frequency of total cycloheximide-resistant colonies (mutations and recombinations) increases were obtained with both protocols. The other three compounds were negative when tested up to toxic doses (survival below 10%), up to the maximum solubility in the solvent used or up to heavy precipitation in the incubation mix. The HDT were 333 micrograms/ml (0.88 mM) for diethylstilboestrol dipropionate, 1,600 micrograms/ml (4.5 mM) for griseofulvin and 0.5 microliters/ml (7 mM) for mercaptoethanol. Concerning effects on porcine brain tubulin assembly in vitro, diethylstilboestrol and griseofulvin inhibited the assembly process. The IC30% (30% inhibition concentration) values were 12.5 microM and 100 microM for DES and griseofulvin, respectively. Mercaptoethanol showed no effects up to 50 mM.

Acetaldehyde↗
PubMed1989

Experience with a non-hospital based technician training program.

A community based technician training program can effectively provide well trained competent technicians with a scope of experience broad enough to meet job responsibilities of diverse health care institutions within the community. The college contacted to assist in developing a technician training program should be well established in the community and accredited by an appropriate national accrediting body. In addition, the college should have existing facilities and services to support the program. Upon determining technician need in the community, an advisory group should be assembled to provide professional input into program direction, curriculum design, training site selection, and other matters of concern to the hospitals and college. With community input, cooperation, and professional direction, a community based technician program can serve its home community with technicians uniformly functional and adaptable to most pharmacy environments and situations.

Community-Institutional Relations↗
PubMed1999

National probability samples in studies of low-prevalence diseases. Part I: Perspectives and lessons from the HIV cost and services utilization study.

OBJECTIVE: To examine the trade-offs inherent in selecting a sample design for a national study of care for an uncommon disease, and the adaptations, opportunities and costs associated with the choice of national probability sampling in a study of HIV/AIDS. SETTING: A consortium of public and private funders, research organizations, community advocates, and local providers assembled to design and execute the study. DESIGN: Data collected by providers or collected for administrative purposes are limited by selectivity and concerns about validity. In studies based on convenience sampling, generalizability is uncertain. Multistage probability sampling through households may not produce sufficient cases of diseases that are not highly prevalent. In such cases, an attractive alternative design is multistage probability sampling through sites of care, in which all persons in the reference population have some chance of random selection through their medical providers, and in which included subjects are selected with known probability. DATA COLLECTION AND PRINCIPAL FINDINGS: Multistage national probability sampling through providers supplies uniquely valuable information, but will not represent populations not receiving medical care and may not provide sufficient cases in subpopulations of interest. Factors contributing to the substantial cost of such a design include the need to develop a sampling frame, the problems associated with recruitment of providers and subjects through medical providers, the need for buy-in from persons affected by the disease and their medical practitioners, as well as the need for a high participation rate. Broad representation from the national community of scholars with relevant expertise is desirable. Special problems are associated with organization of the research effort, with instrument development, and with data analysis and dissemination in such a consortium. CONCLUSIONS: Multistage probability sampling through providers can provide unbiased, nationally representative data on persons receiving regular medical care for uncommon diseases and can improve our ability to accurately study care and its outcomes for diseases such as HIV/AIDS. However, substantial costs and special circumstances are associated with the implementation of such efforts.

Data Collection↗
PubMed2026

Perseus: Lineage-Aware Refinement of Kraken2 Taxonomic Classification for Long Read Metagenomes.

MOTIVATION: Long-read metagenomic sequencing improves assembly contiguity and enables genome-resolved analysis of complex microbial communities, but accurate taxonomic classification of long reads and assembled contigs remains challenging. Highly scalable k-mer-based classifiers such as Kraken2 frequently over-assign fine-rank taxonomic labels when applied to long-read data, producing high false positive classification rates driven by sparse or localized k-mer matches, particularly in microbiomes with extensive taxonomic novelty. RESULTS: We present Perseus, a lineage-aware confidence estimation framework for taxonomic classification that models the spatial distribution and hierarchical consistency of k-mer evidence along sequences. This formulation reframes taxonomic classification as a hierarchical confidence estimation problem rather than a single-rank prediction task. Perseus refines k-mer-level taxonomic signals from Kraken2 using a multi-headed convolutional neural network that estimates calibrated confidence scores for taxonomic correctness at each canonical rank. Using these estimates, Perseus confirms assignments, backs off to higher taxonomic ranks, or abstains when evidence is insufficient, prioritizing correctness and lineage consistency over overly specific assignments. Across simulations of taxonomic novelty and real-world metagenomic datasets, Perseus consistently and substantially reduces the false assignment rate while improving precision and lineage-consistent accuracy. These improvements are most pronounced for long reads and assembled contigs, where spatial context enables reliable discrimination between consistent taxonomic signal and spurious matches. AVAILABILITY AND IMPLEMENTATION: Perseus integrates with existing Kraken2 workflows and is available at https://github.com/matnguyen/perseus.

Journal Article↗