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PubMed2026

Microbial decomposer diversity and metabolic function during the decomposition of brine shrimp carcasses in a saline lake.

BACKGROUND: Decomposition of brine shrimp carcasses has a crucial role in carbon cycling of saline lakes, yet the microbial dynamics remain poorly understood. RESULTS: Here we integrated metagenomics, metatranscriptomics, culturomics, metabolomics, and microcosm experiments to investigate microbial community succession and function during brine shrimp (Artemia sp.) carcass decomposition in Barkol Lake, a hypersaline lake in China. A total of 149 metagenome-assembled genomes (MAGs) and 77 pure culture genomes were recovered across 33 phyla, with 72.12% genomes representing species-level novel lineages. Our results reveal diverse bacterial and archaeal taxa, including novel lineages from CG03, T1Sed10-126 and rare archaeal taxa (Asgardarchaeota, Thermoplasmatota, Nanoarchaeota, and Halobacteriota), involved in degradation of biomacromolecules-proteins, carbohydrates, lipids, and nucleic acids-via extracellular hydrolysis, nutrient transport, and intracellular catabolism. These taxa exhibit substrate preferences, rapidly responding to the breakdown of polysaccharides and proteins, followed by lipids and nucleic acids. Hydrolyzed oligomers are further oxidized by various microbes through fermentation, sulfate reduction, and methanogenesis via metabolic handoffs. Additionally, viral auxiliary metabolic genes (AMGs) further enhance microbial host functions, contributing to key ecological processes such as carbon cycling and stress response. A temporally structured microbial decomposer network (MDN) was observed, driving mineralization cascades from fermentation to sulfate reduction and methanogenesis. CONCLUSIONS: This study reveals microbial metabolic handoffs and virus-mediated modulation as critical mechanisms for organic matter turnover, expanding the known diversity and function of decomposers in saline ecosystems. Our findings offer new insights into biogeochemical processes in saline lakes and highlight a synergistic microbial decomposer network involving bacteria, archaea, and viruses that collectively drive nutrient cycling during brine shrimp carcass decomposition. Video Abstract.

Animals↗
PubMed1990

[The prevalence of bronchial asthma in a selected sample of the adult Prague population].

The authors assessed the prevalence of bronchial asthma in 8458 18-year-old and older inhabitants of an economic area in Prague 8. The population of the area up to December 31, 1987 was 90,458 adults. The health communities were selected in a random way to comprise the central as well as peripheral parts of Prague 8. By means of questionnaires information was assembled from 70.9% of the respondents and after supplementation of data by various doctors the scope of information was 89.9% (7605/8458). For detailed examination 902 subjects were selected with "confirmed" and suspect symptoms of asthma. The anamnestic data were analyzed and pulmonary ventilation was examined (flow-volume), and depending on indication, also the provocation or bronchodilatation inhalation test, skin tests, and total IgE. The cumulative prevalence of bronchial asthma was 2.3% +/- 0.3% (174/7605). The highest prevalence values were in subjects under 20 years--3.5% and under 30 years--3.6%. The contemporary prevalence was 2.0% +/- 0.3% (152/7605). Nonatopic asthma was recorded in 54%, atopic asthma in 46% of the subjects.

Adolescent↗
PubMed1993

The postoperative incidence of small bowel obstruction following standard, open appendectomy and cholecystectomy: a six-year retrospective cohort study at Yale-New Haven Hospital.

The incidence of postoperative small bowel obstruction (SBO) after standard, open appendectomy and cholecystectomy was calculated during a six-year period at a university medical center hospital, which is the larger of two local, community hospitals. A cohort of 567 patients who underwent either a standard, open appendectomy or cholecystectomy from 1 October 1985 through 30 September 1986 was assembled. Of these patients, 182 (32.1%) were readmitted to the hospital prior to 1 October 1991 and thereby received follow-up. The time-related incidence of readmission to the hospital with a specific diagnosis of SBO as estimated by the Kaplan-Meier method was tabulated. This analysis revealed the following incidence rates of postoperative SBO: 10.7% following appendectomy during 64 months of follow-up (n = 41) and 6.4% following cholecystectomy during 67 months (n = 141). The Kaplan-Meier product-limit incidence of postoperative SBO was significantly different for standard appendectomy versus standard cholecystectomy (Breslow-Cox P value < 0.0277). This implies that the anatomical position and/or the likelihood of perioperative infection associated with open, abdominal surgery plays a significant role in subsequent adhesion formation and development of SBO. These data may be compared to laparoscopic techniques in future studies.

Appendectomy↗
PubMed2005

Chromatin and the DNA damage response.

The impact of chromatin structure upon the DNA damage response is becoming increasingly apparent. We can reasonably expect many more papers showing how chromatin and chromatin modifications impact upon aspects of the DNA damage response. Here, we present our perspective on some recent developments in this exciting area of cell biology. We aim that this review will be of interest to those who study the DNA damage response, but not usually in the context of chromatin, and equally to those who study chromatin, but not the DNA damage response. It seems likely that these two communities will increasingly share common questions and interests.

Cell Cycle Proteins↗
PubMed2026

Genome mining of alkaliphilic cyanobacterial consortia: identification of biosynthetic gene clusters in Sodalinema and associated heterotrophs.

Alkaline soda lakes are high-pH environments that host specialized microbial communities with potential for biotechnology and natural product discovery. We characterized three Sodalinema-dominated cyanobacterial consortia enriched from Canadian soda lakes over 510 days. Using hybrid metagenomic sequencing and metatranscriptomics across pH, alkalinity, and temperature gradients, we reconstructed high-quality metagenome-assembled genomes and assessed functional activity. All consortia converged toward cyanobacteria dominance and exhibited temperature optima between 21&#xb0;C and 30&#xb0;C. Phylogenetic analysis placed Sodalinema genomes within a distinct clade affiliated with Candidatus Sodalinema alkaliphilum. Genomic analysis indicated complete biosynthetic pathways for vitamin B5, vitamin B7, and the molybdenum cofactor, but incomplete pathways for vitamins B1, B9, and B12, consistent with patterns observed in Sodalinema yuhuli. Metatranscriptomic profiles showed increased expression of genes involved in phycocyanin and carotenoid biosynthesis at pH 10.2 relative to pH 8.5. Biosynthetic gene cluster analysis revealed that most secondary metabolic potential resided in heterotrophic community members. Roseinatronobacter encoded pathways for N-acyl homoserine lactones, osmoprotectants, betalactones, and prodigiosin, while Alkalimonas, Wenzhouxiangella, and members of the Kiloniellales encoded clusters for lanthipeptides, cyclodipeptides, hydrogen cyanide, and pyrroloquinoline quinone. These findings indicate functional partitioning within the consortia and highlight the contribution of heterotrophs to secondary metabolism.IMPORTANCEAlkaline soda lakes contain microbial communities adapted to high pH that remain underexplored for biotechnology. This study focuses on Sodalinema, a filamentous cyanobacterium that dominates enriched consortia from Canadian soda lakes, and its associated heterotrophic partners. We show that while Sodalinema drives primary productivity, heterotrophic bacteria encode most of the pathways for antimicrobial and signaling compounds. These interactions may support community stability and defense against competing microorganisms. By linking genomic potential with gene expression, this work identifies alkaline cyanobacterial consortia as a source of bioactive compounds and provides a framework for exploring extremophilic microbial communities for natural product discovery.

Sodalinema↗
PubMed2005

Critical factors for assembling a high volume of DNA barcodes.

Large-scale DNA barcoding projects are now moving toward activation while the creation of a comprehensive barcode library for eukaryotes will ultimately require the acquisition of some 100 million barcodes. To satisfy this need, analytical facilities must adopt protocols that can support the rapid, cost-effective assembly of barcodes. In this paper we discuss the prospects for establishing high volume DNA barcoding facilities by evaluating key steps in the analytical chain from specimens to barcodes. Alliances with members of the taxonomic community represent the most effective strategy for provisioning the analytical chain with specimens. The optimal protocols for DNA extraction and subsequent PCR amplification of the barcode region depend strongly on their condition, but production targets of 100K barcode records per year are now feasible for facilities working with compliant specimens. The analysis of museum collections is currently challenging, but PCR cocktails that combine polymerases with repair enzyme(s) promise future success. Barcode analysis is already a cost-effective option for species identification in some situations and this will increasingly be the case as reference libraries are assembled and analytical protocols are simplified.

Biodiversity↗
PubMedDate not supplied

Speech and language therapy services to education in England and Wales.

Services for children with speech and language needs in England and Wales are in a period of change. The context is subject to major systemic pressures deriving from government policies. These include the development of inclusive education and encouragement of multiprofessional collaboration in policy development and practice ('joined up thinking'). In addition, structures at local level are changing with the establishment of unitary authorities and the change from Health Trusts to Primary Care Trusts. Professional practice is also changing with a shift from clinical to community settings for speech and language therapists working with children. The present study reports on a survey sponsored by the Department for Education and Employment, Department of Health and the Welsh Assembly to identify the nature of speech and language therapy (SLT) services provided to education in England and Wales. The sample comprised all SLT service managers (n = 133, response rate 74%). The results indicate that services vary greatly in size and in their SLT: child ratio, with a mean of one SLT to 4257 child population. The caseload was highest for the 5-10 age group, and service delivery was targeted at these children, with low levels of work with secondary aged pupils. Most provision in educational settings was made to mainstream schools, but the provision of SLT time per child was substantially higher in specialist language resources. Apart from the preschool phase, most SLT provision was for children with statements of special educational needs. Prioritization of service delivery was usually by severity of need. The provision of bilingual SLT services was very limited, with only 14.0 full-time equivalents SLTs fluent in a community language, other than Welsh, where proportionately availability was much greater. Most LEAs funded SLT posts, although these were usually employed as part of the SLT service, with only about 10% of LEAs employing SLTs direct. However, 55.5% of SLT managers reported that recruitment and retention were problematic, resulting in gaps in the service. These findings are discussed with respect to changes driven by professional judgements on the nature of optimal service delivery, and government policy, with particular reference to inclusion and equity of service delivery.

Adolescent↗
PubMed2006

Finding novel genes in bacterial communities isolated from the environment.

MOTIVATION: Novel sequencing techniques can give access to organisms that are difficult to cultivate using conventional methods. When applied to environmental samples, the data generated has some drawbacks, e.g. short length of assembled contigs, in-frame stop codons and frame shifts. Unfortunately, current gene finders cannot circumvent these difficulties. At the same time, the automated prediction of genes is a prerequisite for the increasing amount of genomic sequences to ensure progress in metagenomics. RESULTS: We introduce a novel gene finding algorithm that incorporates features overcoming the short length of the assembled contigs from environmental data, in-frame stop codons as well as frame shifts contained in bacterial sequences. The results show that by searching for sequence similarities in an environmental sample our algorithm is capable of detecting a high fraction of its gene content, depending on the species composition and the overall size of the sample. The method is valuable for hunting novel unknown genes that may be specific for the habitat where the sample is taken. Finally, we show that our algorithm can even exploit the limited information contained in the short reads generated by 454 technology for the prediction of protein coding genes. AVAILABILITY: The program is freely available upon request.

Algorithms↗
PubMed1993

An experimentally derived data set constructed for testing large-scale DNA sequence assembly algorithms.

A data set consisting of DNA sequences from a large-scale shotgun DNA cloning and sequencing project has been collected and posted for public release. The purpose is to propose a standard genomic DNA sequencing data set by which various algorithms and implementations can be tested. This set of data is divided into two subsets, one containing raw DNA sequence data (1023 clones) and the other consisting of the corresponding partially refined or edited DNA sequence data (820 clones). Suggested criteria or guidelines for this data refinement are presented so that algorithms for preprocessing and screening raw sequences may be developed. Development of such preprocessing, screening, aligning, and assembling algorithms will expedite large-scale DNA sequencing projects so that the complete unambiguous consensus DNA sequences will be made available to the general research community in a quicker manner. Smaller scale routine DNA sequencing projects will also be greatly aided by such computational efforts.

Algorithms↗
PubMed2001

Chemoselective approaches to glycoprotein assembly.

Oligosaccharides on proteins and lipids play central roles in human health and disease. The molecular analysis of glycoconjugate function has benefited tremendously from new methods for their chemical synthesis, which provides homogeneous material not attainable from biosynthetic systems. Still, glycoconjugate synthesis requires the manipulation of multiple stereocenters and protecting groups and remains the domain of a few expert laboratories around the world. This Account summarizes chemoselective approaches for assembling homogeneous glycoconjugates that attempt to reduce the barriers to their synthesis. The objective of these methods is to make glycoconjugate synthesis accessible to a broader community, thereby accelerating progress in glycobiology.

Carbohydrate Sequence↗
PubMed2006

Gene expression within a dynamic nuclear landscape.

Molecular imaging in living cells or organisms now allows us to observe macromolecular assemblies with a time resolution sufficient to address cause-and-effect relationships on specific molecules. These emerging technologies have gained much interest from the scientific community since they have been able to reveal novel concepts in cell biology, thereby changing our vision of the cell. One main paradigm is that cells stochastically vary, thus implying that population analysis may be misleading. In fact, cells should be analyzed within time-resolved single-cell experiments rather than being compared to other cells within a population. Technological imaging developments as well as the stochastic events present in gene expression have been reviewed. Here, we discuss how the structural organization of the nucleus is revealed using noninvasive single-cell approaches, which ultimately lead to the resolution required for the analysis of highly controlled molecular processes taking place within live cells. We also describe the efforts being made towards physiological approaches within the context of living organisms.

Animals↗
PubMed2006

The cost of uncomplicated childhood fevers to Kenyan households: implications for reaching international access targets.

BACKGROUND: Fever is the clinical hallmark of malaria disease. The Roll Back Malaria (RBM) movement promotes prompt, effective treatment of childhood fevers as a key component to achieving its optimistic mortality reduction goals by 2010. A neglected concern is how communities will access these new medicines promptly and the costs to poor households when they are located in rural areas distant to health services. METHODS: We assemble data developed between 2001 and 2002 in Kenya to describe treatment choices made by rural households to treat a child's fever and the related costs to households. Using a cost-of-illness approach, we estimate the expected cost of a childhood fever to Kenyan households in 2002. We develop two scenarios to explore how expected costs to households would change if more children were treated at a health care facility with an effective antimalarial within 48 hours of fever onset. RESULTS: 30% of uncomplicated fevers were managed at home with modern medicines, 38% were taken to a health care facility (HCF), and 32% were managed at home without the use of modern medicines. Direct household cash expenditures were estimated at $0.44 per fever, while the total expected cost to households (cash and time) of an uncomplicated childhood fever is estimated to be $1.91. An estimated mean of 1.42 days of caretaker time devoted to each fever accounts for the majority of household costs of managing fevers. The aggregate cost to Kenyan households of managing uncomplicated childhood fevers was at least $96 million in 2002, equivalent to 1.00% of the Kenyan GDP. Fewer than 8% of all fevers were treated with an antimalarial drug within 24 hours of fever onset, while 17.5% were treated within 48 hours at a HCF. To achieve an increase from 17.5% to 33% of fevers treated with an antimalarial drug within 48 hours at a HCF (Scenario 1), children already being taken to a HCF would need to be taken earlier. Under this scenario, direct cash expenditures would not change, and total household costs would fall slightly to $1.86 because caretakers also save time with prompt treatment if the child has malaria. CONCLUSION: The management of uncomplicated childhood fevers imposes substantial costs on Kenyan households. Achieving substantial improvements in the numbers of fevers treated within 48 hours at a HCF with an effective antimalarial drug (Scenario 1) will not impose additional costs on households. Achieving additional improvements in fevers treated promptly at a HCF (Scenario 2) will impose additional costs on some households roughly equal to average cash expenses for transportation to a HCF. Additional financing mechanisms that further reduce the costs of accessing care at a HCF and/or that make artemisinin-based combination therapies (ACTs) accessible for home management need to be developed and evaluated as a top priority.

Antimalarials↗
PubMed2000

The metamorphosis of communication, the knowledge revolution, and the maintenance of a contemporary perspective during the 21st century.

OBJECTIVE: To define and discuss elements of the escalation in scientific data availability and their importance to neurosurgery. METHODS: This multifactorial essay describes the evolution of communication methodologies, the information revolution, and the advent and effect of Internet communication with its potential effect on the practice of neurosurgery, professional assemblies, journals, and the infrastructure of the discipline. Practical and philosophical viewpoints are rendered to assess the existing and developing availability of information to the neurosurgical community. CONCLUSION: Knowledge must be discerned from information. The individual does not have the luxury of detachment and must remain consistently, intellectually, and actively involved in the adaptations required to stay truly informed and current.

Communication↗
PubMed2000

Bill would establish pilot project for denturism in Kentucky.

HB 238 has been reported favorably to the floor of the House of Representatives by the Committee on Licensing and Occupations, but has not yet been acted upon by the full House. When asked whether he thought his legislation would be approved, Representative Burch said he thought the bill had a "50-50" chance of passing the Kentucky legislature this year. Sources within the Kentucky dental laboratory and dental communities disagree on the legislation's chances for passage. Some within the industry feel the legislation simply does not have enough votes to pass the General Assembly, primarily because of opposition from the Kentucky Dental Association. Others speculate that the bill has a better opportunity to be approved this year than it did in the previous years when it was introduced. The Kentucky General Assembly adjourns its session for the year 2000 on April 12, so there will be a quick answer to the question of whether HB 238 will be approved. The May issue of this column will provide details.

Dentists↗
PubMed2025

16S rRNA and Metagenomic Datasets of Gastrointestinal Microbiota in Fetal and 7-Day-Old Goat Kids.

The perinatal period (from late gestation to the neonatal stage) in ruminants is a critical phase for fetal organ maturation, where ecological succession of gastrointestinal microbial communities significantly impacts livestock production efficiency. However, research remains insufficient regarding the distribution patterns and functional annotation of microbial communities across different gastrointestinal compartments during this period. This study characterized early microbiota dynamics in Hutianshi Goats using 16S rRNA sequencing (4 fetal goats at 90&#x2009;&#xb1;&#x2009;10 gestational days) and metagenomics (3 7-day-old goat&#xa0;kids). The fetal goat group generated 852,694 valid reads, yielding 688,277 high-quality reads after chimera removal for downstream analysis. The 7-day-old goat kids group produced 1,081,588,182 final valid reads, after data processing and assembly, 8,561,345 contigs were generated. Gene prediction identified 6,095,352 genes. Multi-database annotations (NR, KEGG, CAZy, etc.) revealed functional potential and antimicrobial resistance traits. The public release of this dataset facilitates academic understanding of microbial community dynamics and host-microbe interactions during this developmental stage, providing both theoretical foundations and data resources for ruminant developmental biology and precision breeding regulation.

Animals↗
PubMed2006

An atlas of gene expression from seed to seed through barley development.

Assaying relative and absolute levels of gene expression in a diverse series of tissues is a central step in the process of characterizing gene function and a necessary component of almost all publications describing individual genes or gene family members. However, throughout the literature, such studies lack consistency in genotype, tissues analyzed, and growth conditions applied, and, as a result, the body of information that is currently assembled is fragmented and difficult to compare between different studies. The development of a comprehensive platform for assaying gene expression that is available to the entire research community provides a major opportunity to assess whole biological systems in a single experiment. It also integrates detailed knowledge and information on individual genes into a unified framework that provides both context and resource to explore their contributions in a broader biological system. We have established a data set that describes the expression of 21,439 barley genes in 15 tissues sampled throughout the development of the barley cv. Morex grown under highly controlled conditions. Rather than attempting to address a specific biological question, our experiment was designed to provide a reference gene expression data set for barley researchers; a gene expression atlas and a comparative data set for those investigating genes or regulatory networks in other plant species. In this paper we describe the tissues sampled and their transcriptomes, and provide summary information on genes that are either specifically expressed in certain tissues or show correlated expression patterns across all 15 tissue samples. Using specific examples and an online tutorial, we describe how the data set can be interrogated for patterns and levels of barley gene expression and how the resulting information can be used to generate and/or test specific biological hypotheses.

Databases, Genetic↗
PubMed2006

Lithographic techniques and surface chemistries for the fabrication of PEG-passivated protein microarrays.

This article presents a new technique to fabricate patterns of functional molecules surrounded by a coating of the inert poly(ethylene glycol) (PEG) on glass slides for applications in protein microarray technology. The chief advantages of this technique are that it is based entirely on standard lithography processes, makes use of glass slides employing surface chemistries that are standard in the microarray community, and has the potential to massively scale up the density of microarray spots. It is shown that proteins and antibodies can be made to self-assemble on the functional patterns in a microarray format, with the PEG coating acting as an effective passivating agent to prevent non-specific protein adsorption. Various standard surface chemistries such as aldehyde, epoxy and amine are explored for the functional layer, and it is conclusively demonstrated that only an amine-terminated surface satisfies all the process constraints imposed by the lithography process sequence. The effectiveness of this microarray technology is demonstrated by patterning fluorescent streptavidin and a fluorescent secondary antibody using the well-known and highly specific interaction between biotin and streptavidin.

Adsorption↗