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At least 253 records · Page 14Linked to original sources
PubMed2002

Secular growth and its harmful ramifications.

Secular growth has been occurring in Europe for about 150 years. In the USA, since 1900, each new generation has increased by an average of 1in (2.54cm) in height and about 10lb (4.54kg) in weight. This trend has generally been viewed as favorable and tallness is admired, with the current ideal height for a man in the Western world being 6ft 2in (188cm). The Japanese have increased in height since the end of the Second World War by about 5in (12.7cm) in height and the Chinese have been growing at the rate of 2.54cm/decade since the 1950s. In spite of admiring greater height, a world population of increasing height and body-weight is a major threat to our environment, health and survival. Based on more than two decades of research, quantitative data are given for increased use of resources, and increased pollution, energy and fiscal costs resulting from a population of larger people. The laws of scaling are described to show why the impact of increasing stature has a non-linear impact on consumption, body-weight, strength, pollution and economic costs. Paleontological findings indicating that larger body size increases the risk of extinction are also discussed. Various studies indicate a loss of 0.47 year of longevity for each cm increment of height. Caloric restricted diets are also reviewed for their applicability to humans. Recommendations are made for dietary practices to moderate growth in our youth and to postpone development of chronic or degenerative diseases.

Animals↗
PubMed2026

Phage bioinformatics tools: a review of computational approaches for bacteriophage research.

Rising clinical interest in phage therapy and the exponential growth of metagenomic sequence catalogues have driven a rapid expansion of bacteriophage bioinformatics. More than 80 dedicated tools, mostly published since 2020, now span identification, assembly, annotation, taxonomy, lifestyle prediction, defence-system detection, and host prediction. Aimed at experienced practitioners and developers, this review synthesizes the field through the lens of three successive computational paradigms: sequence homology, bounded by database completeness; machine learning, constrained by labelled training data; and foundation models, which now achieve Matthews correlation coefficients above 0.95 in identification tasks and, through structure-informed prediction, raise functional annotation to over half of phage genes. Furthermore, we map the upstream components, namely, gene callers, homology engines, protein language models, and structural search tools, that underpin most downstream pipelines, exposing shared infrastructure and ecosystem-level fragility when dependencies change. To translate this into practice, we propose web-based and command-line reference workflows calibrated to user expertise and sample types. Finally, we set an agenda for the next wave of tool development. Roughly half of phage genes still resist functional annotation despite structural methods; no broadly generalizable strain-level host predictor exists for phage therapy; varying true-positive rates (0%-97%) underscore the absence of standardized community benchmarks analogous to Critical Assessment of Structure Prediction or Critical Assessment of Metagenome Interpretation. As generative genome models begin designing synthetic phages, progress will depend less on producing standalone tools than on rigorous evaluation, interoperable infrastructure, and clinically meaningful prediction targets.

Computational Biology↗
PubMed1994

Ecosystem theory of evolution and social ethics.

Ecosystem evolution is driven by general laws for open systems aiming at immortality (first genetical then also cultural) of its components. Evolutionary impulses spread downward from ecosystem disturbances to population strategies to genome structures (opposite to the upward causation of traditional theory). Environmental cycles work as winding engine pushing evolution a step further at each round. Natural selection is being slackened with time while memory elaborates to conscious level. General trend is from unsustained growth to stability, individuation, increased diversity, standing biomass to productivity to dead mass ratios. Progressive evolution is interrupted by biospheric crises, or backward developments. Human activities contribute to the latter while for sustainable existence it will be necessary to switch from the crisis to the progress scheme. Human morals are grounded in million years of pre-human and pre-historic human evolution. However to be taught by nature means to comply with its progressive rather than backward tendencies. Human history as a continuation of the animal history is a perpetual struggle against natural selections.

Biological Evolution↗
PubMed2006

Ecological consequences of major hydrodynamic disturbances on coral reefs.

A recent tsunami and an apparent increase in the frequency of severe tropical storms underscore the need to understand and predict the ecological consequences of major hydrodynamic disturbances. Reef corals provide the habitat structure that sustains the high biodiversity of tropical reefs, and thus provide the foundation for the ecosystem goods and services that are critical to many tropical societies. Here we integrate predictions from oceanographic models with engineering theory, to predict the dislodgement of benthic reef corals during hydrodynamic disturbances. This generalizes earlier work, by incorporating colonies of any shape and by explicitly examining the effects of hydrodynamic gradients on coral assemblage structure. A field test shows that this model accurately predicts changes in the mechanical vulnerability of coral colonies, and thus their size and shape, with distance from the reef crest. This work provides a general framework for understanding and predicting the effects of hydrodynamic disturbances on coral reef communities; such disturbances have a major role in determining species zonation and coexistence on coral reefs, and are critical determinants of how coral assemblages will respond to changes in the frequency and intensity of tropical storms associated with a changing climate.

Animals↗
PubMed2004

Waste crankcase oil: an environmental contaminant with potential to modulate estrogenic responses.

Used engine, or crankcase, oil is frequently discarded into the environment resulting in significant pollution of both aquatic and terrestrial ecosystems. The chemical composition of crankcase oils changes with use, and in general, used, or waste, crankcase oil is considered more toxic than the original oil. Polycyclic aromatic hydrocarbons (PAHs) are major constituents of crankcase oil and may exhibit both estrogenic and antiestrogenic activity. In the present study, the estrogenic activity and antiestrogenic activity of both new (unused) and waste crankcase oils were examined in a human breast cancer cell culture assay. Concentrations of 5, 10, 15, 20, or 25 ppm of new oil or waste oil did not alter either the preconfluent or postconfluent cell growth when tested in control medium. In contrast, waste crankcase oil significantly reduced the postconfluent growth of cells grown in medium containing 0.1 nM 17 beta-estradiol. Results from mechanistic assays using [3H]-17 beta-estradiol demonstrated that waste crankcase oil both increased the metabolism of 17 beta-estradiol, and displaced 17 beta-estradiol from the estrogen receptor in MCF-7 cells. The observed antiestrogenic activity of the waste crankcase oil suggests that this pollutant has the potential to alter estrogenic responses, and therefore its presence in the environment may be of concern for reproductive health.

Breast Neoplasms↗
PubMed1999

Psr1, a nuclear localized protein that regulates phosphorus metabolism in Chlamydomonas.

Understanding the ways in which phosphorus metabolism is regulated in photosynthetic eukaryotes is critical for optimizing crop productivity and managing aquatic ecosystems in which phosphorus can be a major source of pollution. Here we describe a gene encoding a regulator of phosphorus metabolism, designated Psr1 (phosphorus starvation response), from a photosynthetic eukaryote. The Psr1 protein is critical for acclimation of the unicellular green alga Chlamydomonas reinhardtii to phosphorus starvation. The N-terminal half of Psr1 contains a region similar to myb DNA-binding domains and the C-terminal half possesses glutamine-rich sequences characteristic of transcriptional activators. The level of Psr1 increases at least 10-fold upon phosphate starvation, and immunocytochemical studies demonstrate that this protein is nuclear-localized under both nutrient-replete and phosphorus-starvation conditions. Finally, Psr1 and angiosperm proteins have domains that are similar, suggesting a possible role for Psr1 homologs in the control of phosphorus metabolism in vascular plants. With the identification of regulators such as Psr1 it may become possible to engineer photosynthetic organisms for more efficient utilization of phosphorus and to establish better practices for the management of agricultural lands and natural ecosystems.

Adaptation, Physiological↗
PubMed1999

Modelling of genetically engineered microorganisms introduction in closed artificial microcosms.

The possibility of introducing genetically engineered microorganisms (GEM) into simple biotic cycles of laboratory water microcosms was investigated. The survival of the recombinant strain Escherichia coli Z905 (Apr, Lux+) in microcosms depends on the type of model ecosystems. During the absence of algae blooming in the model ecosystem, the part of plasmid-containing cells E. coli decreased fast, and the structure of the plasmid was also modified. In conditions of algae blooming (Ankistrodesmus sp.) an almost total maintenance of plasmid-containing cells was observed in E. coli population. A mathematics model of GEM's behavior in water ecosystems with different level of complexity has been formulated. Mechanisms causing the difference in luminescent exhibition of different species are discussed, and attempts are made to forecast the GEM's behavior in water ecosystems.

Animals↗
PubMed2004

Monitoring and modeling horizontal gene transfer.

Monitoring efforts have failed to identify horizontal gene transfer (HGT) events occurring from transgenic plants into bacterial communities in soil or intestinal environments. The lack of such observations is frequently cited in biosafety literature and by regulatory risk assessment. Our analysis of the sensitivity of current monitoring efforts shows that studies to date have examined potential HGT events occurring in less than 2 g of sample material, when combined. Moreover, a population genetic model predicts that rare bacterial transformants acquiring transgenes require years of growth to out-compete wild-type bacteria. Time of sampling is there-fore crucial to the useful implementation of monitoring. A population genetic approach is advocated for elucidating the necessary sample sizes and times of sampling for monitoring HGT into large bacterial populations. Major changes in current monitoring approaches are needed, including explicit consideration of the population size of exposed bacteria, the bacterial generation time, the strength of selection acting on the transgene-carrying bacteria, and the sample size necessary to verify or falsify the HGT hypotheses tested.

Ecosystem↗
PubMed2004

Problems in monitoring horizontal gene transfer in field trials of transgenic plants.

Transgenic crops are approved for release in some countries, while many more countries are wrestling with the issue of how to conduct risk assessments. Controls on field trials often include monitoring of horizontal gene transfer (HGT) from crops to surrounding soil microorganisms. Our analysis of antibiotic-resistant bacteria and of the sensitivity of current techniques for monitoring HGT from transgenic plants to soil microorganisms has two major implications for field trial assessments of transgenic crops: first, HGT from transgenic plants to microbes could still have an environmental impact at a frequency approximately a trillion times lower than the current risk assessment literature estimates the frequency to be; and second, current methods of environmental sampling to capture genes or traits in a recombinant are too insensitive for monitoring evolution by HGT. A model for HGT involving iterative short-patch events explains how HGT can occur at high frequencies but be detected at extremely low frequencies.

Ecosystem↗
PubMed2026

The novel transcriptional activator Bhr1 combining NTPase and Zn(II)2Cys6 DNA-binding domains controls (hemi-)cellulase response to mannose-rich substrates in the white-rot fungus Dichomitus squalens.

The regulatory landscape responsible for lignocellulose degradation in white-rot basidiomycete fungi remains largely unexplored. In this study, we characterize a novel transcriptional activator, Bhr1, in the white-rot fungus Dichomitus squalens. Bhr1 exhibits an unusual domain architecture that combines a septin-like P-loop NTPase fold with Zn(II)2Cys6 DNA-binding domains and plays a critical role in activating (hemi-)cellulase enzyme production when D. squalens is exposed to mannose-rich substrates. Using CRISPR/Cas9-mediated gene editing, we generated a bhr1 disruption mutant that displayed distinct phenotypes and enzyme activity profiles on mannose and guar gum compared to the wild type. RNA sequencing data indicate that Bhr1 induces specific (hemi-)cellulase-encoding genes without altering the expression of genes encoding sugar transporters or sugar metabolic enzymes. Phylogenetic analyses show that Bhr1 is basidiomycete specific and largely restricted to saprotrophic and plant-associated Agaricomycetes fungi. Based on the domain architecture of Bhr1 and the effects of its disruption in D. squalens, our findings reveal a lineage-specific regulatory innovation in basidiomycetes that is distinct from those described in ascomycetes. Elucidating the function and evolutionary conservation of Bhr1 advances our understanding of lignocellulose degradation at the molecular level in basidiomycete fungi and may inform studies of their ecological adaptation and the development of biotechnological applications.IMPORTANCEUnderstanding the transcriptional regulatory mechanisms in white-rot fungi, such as Dichomitus squalens, is crucial for advancing our knowledge of lignocellulose degradation. This study identifies D. squalens Bhr1 as a key regulator of (hemi-)cellulase production on mannose-rich substrates and further distinguishes basidiomycete transcription factors involved in plant biomass degradation from their ascomycete counterparts. Our findings highlight the significance of lineage-specific regulators in facilitating adaptive enzyme production for efficient biomass utilization, which is critical to carbon cycling in terrestrial ecosystems. This work establishes a foundation for exploring novel regulatory strategies among wood-degrading fungi, potentially enabling targeted strain engineering in biotechnological applications.

Mannose↗
PubMed1999

Extent and degree of hybridization between exotic (Spartina alterniflora) and native (S. foliosa) cordgrass (Poaceae) in California, USA determined by random amplified polymorphic DNA (RAPDs).

Spartina alterniflora, smooth cordgrass, native to the eastern USA, was introduced into south San Francisco Bay approximately 25 years ago. It has spread by purposeful introduction of rooted plants and dispersal of seeds on the tides. Previous work suggested that S. alterniflora was competitively superior to the native California cordgrass, S. foliosa, and that the two species hybridized. The present study determined the spread of S. alterniflora and S. foliosa x alterniflora hybrids in California and examined the degree of hybridization. We used nuclear DNA markers diagnostic for each species to detect the parental species and nine categories of hybrids. The California coast outside San Francisco Bay contained only the native species. All hybrid categories exist in the Bay, implying that several generations of crossing have occurred and that hybridization is bidirectional. Hybrids were found principally near sites of deliberate introduction of the exotic species. Where S. alterniflora was deliberately planted, we found approximately equal numbers of S. alterniflora and hybrid individuals; S. foliosa was virtually absent. Marshes colonized by water-dispersed seed contained the full gamut of phenotypes with intermediate-type hybrids predominating. The proliferation of hybrids could result in local extinction of S. foliosa. What is more, S. alterniflora has the ability to greatly modify the estuary ecosystem to the detriment of other native species and human uses of the Bay. To the extent that they share these engineering abilities, the proliferation of cordgrass hybrids could grossly alter the character of the San Francisco Bay.

Journal Article↗
PubMed2002

Stable augmentation of activated sludge with foreign catabolic genes harboured by an indigenous dominant bacterium.

Comamonas sp. rN7 is a phenol-degrading bacterium that represents the dominant catabolic population in activated sludge. The present study examined the utility of this bacterium for establishing foreign catabolic genes in phenol-digesting activated sludge. The phc genes coding for phenol hydroxylase and its transcriptional regulators of C. testosteroni R5 were integrated into the chromosome of strain rN7. The specific phenol-oxygenating activity of a resultant transformant designated rN7(R503) was three times higher than the activity of strain rN7, and the phc genes were stably inherited by rN7(R503) grown in a non-selective laboratory medium. Inoculation of phenol-acclimatized activated sludge with rN7(R503) resulted in a high phenol-oxygenating activity and improved resistance to phenol-shock loading compared to sludge inoculated with either no cells, rN7 or R5. Quantitative competitive polymerase chain reaction (PCR) showed that the phc genes were retained in the rN7(R503)-inoculated sludge at a density of more than 108 copies per ml of mixed liquor for more than 35 days, whereas those in the R5-inoculated sludge disappeared rapidly. No transfer of the phc genes to other indigenous populations was apparent in the rN7(R503)-harbouring sludge. From these results, we concluded that the phenol treatment of the activated sludge was enhanced by the phc genes harboured by the rN7(R503) population. This study suggests a possible bioaugmentation strategy for stably utilizing foreign catabolic genes in natural ecosystems.

Biodegradation, Environmental↗
PubMed2003

Microbially influenced corrosion as a model system for the study of metal microbe interactions: a unifying electron transfer hypothesis.

The general term biomineralisation refers to biologically induced mineralisation in which an organism modifies its local microenvironment creating conditions such that there is chemical precipitation of mineral phases extracellularly. Most usually this results from an oxidation or reduction carried out by some microbial species, with the formation of a recognised biomineralised product. These reactions play a major role in microbial physiology and ecology, and are of central importance to such engineering consequences as microbial mining and microbially influenced corrosion. This paper will examine metal microbe interactions, both in naturally occurring microbial ecosystems and in two particular cases of biocorrosion, with the objective of putting forward a unifying hypothesis relevant to the understanding of each of these apparently disparate processes.

Anaerobiosis↗
PubMed2001

Biogeochemical and ecological considerations in designing wetland treatment systems in post-mining landscapes.

Although wetlands have gained acceptance as important components of ecosystems in post-mining landscapes in the past decade, their roles in contaminant retention/removal have not been well integrated into the designing of restoration programs. This paper describes the integration of sediment microbial activities and natural precipitation processes, along with approaches to defining the contaminant load from the mine wastes. The contaminant removal rates, which can be expected by a wetland sediment, are summarized and how they need to be reflected in the wetland size required, and the carbon supply which is needed. Contaminant loading from mining wastes can be balanced by wetland ecological processes, including wetland primary production and microbial mineralization in the sediment. This ecological engineering approach is demonstrated using case studies on hard-rock mining waste in Canada.

Canada↗
PubMed1997

Engineering of Biosphere 2: closure and energy.

As an experimental apparatus, Biosphere 2 was predicated on material closure to permit investigation of ecological processes without unknown sources or sinks outside the ecosystems under study. The atmospheric leak rate is demonstrated to be less than 10% per year. The enabling technology to achieve the low leak rate is expansion chambers called "lungs." Closure enables use of mass balance equations to track chemical pathways (e.g., of carbon dioxide and oxygen). Energy and information pass across the enclosure without incurring any material transfer. Water is fully recycled.

Air Conditioning↗