Predictors of incubation costs in seabirds: an evolutionary perspective

Energy costs during breeding play an important role in the evolution of life history traits. Seabirds show substantial variation in both incubation shift length (ISL) and metabolic rates. However, it is still unclear how variation in life history traits relates to incubation metabolic rates (IMR). Here, we examine the relationship between IMR and life history traits, including ISL, fledging strategy (precocial to altricial), incubation period, nest location (surface vs. underground) and clutch mass relative to adult body mass for 30 species of seabirds collated from the literature. Using both conventional non‐phylogenetic and phylogenetic generalized least‐squares approaches, we show that IMR is negatively associated with ISL, relative clutch mass and with underground nesting, while fledging strategy and incubation period have no impact on IMR once phylogeny is accounted for. Maximum likelihood reconstructions further suggest than ancestral seabirds had average ISL and relative clutch mass, and were surface nesters. We conclude that lower metabolic rates during incubation are associated with both an increased incubation shift length that allows animals to travel farther, as well as the evolutionary emergence of underground nesting that requires less social interaction.     

Redesigning metabolic networks using mathematical programming

The design of new generation bioprocessing plants is increasingly dependent on the design of process-compatible microorganisms. The latter, whether through genetic or physiological manipulations, can be greatly assisted by metabolic engineering. An emerging powerful tool in metabolic engineering research is computer-assisted cell design using mathematical programming. In this work, the problem of optimizing cellular metabolic networks has been formulated as a Mixed Integer Nonlinear Programming (MINLP) model. The model can assist genetic engineers to identify which cellular enzymes should be modified, and the new levels of activity required to produce an optimal network. Results are presented from the tricarboxylic acid cycle in Dictyostelium discoideum. Copyright 1998 John Wiley & Sons, Inc.     

Underground Metameric Complex in the Source-Sink System of Rhizome-Forming Perennial Cereals <Emphasis Type="Italic">Bromopsis inermis</Emphasis> and <Emphasis Type="Italic">Phalaroides arundinacea</Emphasis>

Morphophysiological characteristics of rhizomes and growth relationships between underground shoots and aboveground orthotropic shoots were studied in two species of perennial monocotyledonous plants—Hungarian brome (Bromopsis inermis (Leyss.) Holub.) and reed canary-grass (Phalaroides arundinacea (L.) Rauschert.). The underground metameric complex was shown to be comparable with the aerial shoots in terms of the number, biomass, and metabolic activity of the shoots. The role of the underground metameric complex in the source-sink system of perennial rhizome-forming cereals is determined by a significant proportion of rhizomes in plant biomass (30–50%), formation of a large amount of meristems in the underground stock of vegetative reproduction (more than 1000 per plant), a comparatively high respiration rate (1.5 mg CO₂/(g dry wt h)), and a high nitrogen content (3.5%). No pronounced growth response was found in the rhizome upon plant treatment with growth regulators (GA and chlorocholine chloride) and upon decapitation of plant shoots. It is concluded that the underground metameric complex of the perennial monocotyledonous herbaceous plants is relatively autonomous from the orthotropic shoots.     

The anaerobic degradation of l-serine and l-threonine in enterobacteria: networks of pathways and regulatory signals

The mechanisms controlling the biosynthesis and degradation of l-serine and l-threonine are remarkably complex. Their metabolism forms a network of pathways linking several amino acids, central primary metabolites such as pyruvate, oxaloacetate and 3-phosphoglycerate, and C₁ metabolism. Studies on the degradation of these amino acids in Escherichia coli have revealed the involvement of fascinating enzymes that utilise quite diverse catalytic mechanisms. Moreover, it is emerging that both environmental and metabolic signals have a major impact in controlling enzyme synthesis. This is exemplified by the anaerobically regulated tdc operon, which encodes a metabolic pathway for the degradation of serine and threonine. Studies on this pathway are beginning to provide insights into how an organism adapts its genetic makeup to meet the physiological demands of the cell. Received: 30 August 1998 / Accepted: 9 October 1998     

Life in the slow lane: molecular mechanisms of estivation

Estivation is a state of aerobic hypometabolism used by organisms to endure seasonally arid conditions, often in desert environments. Estivating species are often active for only a few weeks each year to feed and breed and then retreat to estivate in sheltered sites, often underground. In general, estivation includes a strong reduction in metabolic rate, a primary reliance on lipid oxidation to fuel metabolism, and methods of water retention, both physical (e.g. cocoons) and metabolic (e.g. urea accumulation). The present review focuses on several aspects of metabolic adaptation during estivation including changes in the activities of enzymes of intermediary metabolism and antioxidant defenses, the effects of urea on estivator enzymes, enzyme regulation by reversible protein phosphorylation, protein kinases and phosphatases involved in signal transduction mechanisms, and the role of gene expression in estivation. The focus is on two species: the spadefoot toad, Scaphiopus couchii, from the Arizona desert; and the land snail, Otala lactea, a native of the Mediterranean region. The mechanisms of metabolic depression in estivators are similar to those seen in hibernation and anaerobiosis, and contribute to the development of a unified set of biochemical principles for the control of metabolic arrest in nature.     

Increasing the flux in metabolic pathways: A metabolic control analysis perspective

The problems of engineering increased flux in metabolic pathways are analyzed in terms of the understanding provided by metabolic control analysis. Over-expression of a single enzyme is unlikely to be effective unless it is known to have a high flux control coefficient, which can be used as an approximate predictive tool. This is likely to rule out enzymes subject to feedback inhibition, because it transfers control downstream from the inhibited enzyme to the enzymes utilizing the feedback metabolite. Although abolishing feedback inhibition can restore flux control to an enzyme, it is also likely to cause large increases in the concentrations of metabolic intermediates. Simultaneous and coordinated over-expression of most of the enzymes in a pathway can, in principle, produce substantial flux increases without changes in metabolite levels, though technically it may be difficult to achieve. It is, however, closer to the method used by cells to change flux levels, where coordinated changes in the level of activity of pathway enzymes are the norm. Another option is to increase the demand for the pathway product, perhaps by increasing its rate of excretion or removal. Copyright 1998 John Wiley & Sons, Inc.     

Bacterial dehalogenation

Halogenated organic compounds are produced industrially in large quantities and represent an important class of environmental pollutants. However, an abundance of haloorganic compounds is also produced naturally. Bacteria have evolved several strategies for the enzyme-catalyzed dehalogenation and degradation of both haloaliphatic and haloaromatic compounds: (i) Oxidative dehalogenation is the result of mono- or dioxygenase-catalyzed, co-metabolic or metabolic reactions. (ii) In dehydrohalogenase-catalyzed dehalogenation, halide elimination leads to the formation of a double bond. (iii) Substitutive dehalogenation in most cases is a hydrolytic process, catalyzed by halidohydrolases, but there also is a “thiolytic” mechanism with glutathione as cosubstrate. Dehalogenation by halohydrin hydrogen-halide lyases is the result of an intramolecular substitution reaction. (iv) A distinct dechlorination mechanism involves methyl transfer from chloromethane onto tetrahydrofolate. (v) Reductive dehalogenations are co-metabolic processes, or they are specific reactions involved in substrate utilization (carbon metabolism), or reductive dehalogenation is coupled to energy conservation: some anaerobic bacteria use a specific haloorganic compound as electron acceptor of a respiratory process. This review discusses the mechanisms of enzyme-catalyzed dehalogenation reactions, describes some pathways of the bacterial degradation of haloorganic compounds, and indicates some trends in the biological treatment of organohalogen-polluted air, groundwater, soil, and sediments. Received: 24 June 1998 / Received revision: 1 September 1998 / Accepted: 3 September 1998     

Curating a comprehensive set of enzymatic reaction rules for efficient novel biosynthetic pathway design

Enzyme substrate promiscuity has significant implications for metabolic engineering. The ability to predict the space of possible enzymatic side reactions is crucial for elucidating underground metabolic networks in microorganisms, as well as harnessing novel biosynthetic capabilities of enzymes to produce desired chemicals. Reaction rule-based cheminformatics platforms have been implemented to computationally enumerate possible promiscuous reactions, relying on existing knowledge of enzymatic transformations to inform novel reactions. However, past versions of curated reaction rules have been limited by a lack of comprehensiveness in representing all possible transformations, as well as the need to prune rules to enhance computational efficiency in pathway expansion. To this end, we curated a set of 1224 most generalized reaction rules, automatically abstracted from atom-mapped MetaCyc reactions and verified to uniquely cover all common enzymatic transformations. We developed a framework to systematically identify and correct redundancies and errors in the curation process, resulting in a minimal, yet comprehensive, rule set. These reaction rules were capable of reproducing more than 85% of all reactions in the KEGG and BRENDA databases, for which a large fraction of reactions is not present in MetaCyc. Our rules exceed all previously published rule sets for which reproduction was possible in this coverage analysis, which allows for the exploration of a larger space of known enzymatic transformations. By leveraging the entire knowledge of possible metabolic reactions through generalized enzymatic reaction rules, we are able to better utilize underground metabolic pathways and accelerate novel biosynthetic pathway design to enable bioproduction towards a wider range of new molecules.     

Biogeochemical characterization of four depleted gas reservoirs for conversion into underground hydrogen storage

Depleted gas reservoirs are a valuable option for underground hydrogen storage (UHS). However, different classes of microorganisms, which are capable of using free H₂ as a reducing agent for their metabolism, inhabit deep underground formations and can potentially affect the storage. This study integrates metagenomics based on Illumina-NGS sequencing of bacterial and archaeal 16S rRNA and dsrB and mcrA functional genes to unveil the composition and the variability of indigenous microbial populations of four Italian depleted reservoirs. The obtained mcrA sequences allow us to implement the existing taxonomic database for mcrA gene sequences with newly classified sequences obtained from the Italian gas reservoirs. Moreover, the KEGG and COG predictive functional annotation was used to highlight the metabolic pathways potentially associated with hydrogenotrophic metabolisms. The analyses revealed the specificity of each reservoir microbial community, and taxonomic and functional data highlighted the presence of an enriched number of taxa, whose activity depends on both reservoir hydrochemical composition and nutrient availability, of potential relevance in the context of UHS. This study is the very first to address the profiling of the microbial population and allowed us to perform a preliminary assessment of UHS feasibility in Italy.     

Characterization of 14 different putative protein kinase cDNA clones of the C4 plantSorghum bicolor

C₄ photosynthesis is functionally dependent on metabolic interactions between mesophyll- and bundle-sheath cells. Although the C₄ cycle is biochemically well understood, many aspects of the regulation of enzyme activities, gene expression and cell differentiation are elusive. Protein kinases are likely involved in these regulatory processes, providing links to hormonal, metabolic and developmental signal-transduction pathways. Here we describe the cloning and characterization of 14 different putative protein kinase leaf cDNA clones from the C₄ plant Sorghum bicolor. These genes belong to three different protein kinase subfamilies: ribosomal protein S6 kinases, SNF1-like protein kinases, and receptor-like protein kinases. We report the partial cDNA sequences, mesophyll/bundle-sheath steady-state mRNA ratios, mesophyll/etiolated leaf steady-state mRNA ratios, and the positions of 14 protein kinase genes on the genetic map of S. bicolor. Only three of the protein kinase genes described here are expressed preferentially in mesophyll cells as compared with the bundle-sheath. Received: 16 January 1998 / Accepted: 3 April 1998     

Effect of Crude Oil and Chemical Additives on Metabolic Activity of Mixed Microbial Populations in Fresh Marsh Soils

Abstract Hydrocarbons increase abundance of hydrocarbon-degrading microorganisms, but also decrease microbial diversity. This could disrupt ecosystem dynamics by altering soil organic matter mineralization and resultant nutrient remineralization rates. Crude oil, which is known to contain toxins and reduce microbial diversity, was hypothesized to reduce gross metabolic activity of mixed microbial populations in wetland soils. Soil respiration and Eh were compared, for 6 months, among microcosms containing marsh soils that differed in soil organic matter (Panicum hemitomon Shult. or Sagittaria lancifolia L. dominated marshes), crude oil (Arabian crude, Louisiana crude, or no oil), and additives (a cleaner, a dispersant, fertilizer, or no additive). No treatment slowed activity; instead, Louisiana plus fertilizer and all Arabian treatments temporarily accelerated activity. Additional C respired from oiled microcosms exceeded C added as crude oil by 1.4 to 3.5 times. Thus, much additional C originated from soil organic matter rather than crude oil. Crude oils temporarily lowered soil Eh, which is consistent with accelerated metabolism and demand for electron acceptors. The lack of inhibition observed at the community level does not necessarily indicate an absence of toxicity. Instead, tolerant species with metabolic versatility probably maintained activity. Stimulation probably resulted from removal of micronutrient limitation, rather than removal of grazing pressure or macronutrient limitation. Regardless, accelerated soil organic matter mineralization surely accelerated nutrient remineralization. This might explain some reports of crude oil stimulating plant growth. These results are not inconsistent with theoretical and experimental conclusions regarding effects of biodiversity on ecosystem stability and productivity, nor are they inconsistent with conclusions that crude oils contain components that are toxic to microbes, vegetation, and fauna. However, these data do indicate that crude oils also contain components that temporarily stimulate metabolic activity of surviving microbes. Received: 27 April 1998; Accepted: 15 July 1998     

Impact assessment of risk parameters of underground coal mining on the environment

Coal is an important energy source but it has a significant negative impact on the environmental processes. This paper analyses the impact, measurement, and input of parameters representing potential environmental polluters in the information system (IS).

The methodology of recording and systematization includes the following parameters: coal deposits; climate parameters; roads; rivers; land and surrounding objects; air polluters; water polluters; and soil polluters. Methods for calculating land deformation, air polluter emissions, and noise impact are also presented.

Based on the number and specificity of analyzed data, the paper provides a concept of the IS and an overview of environmental impact of underground coal mine technological units. The concept was used to present the results of a research conducted at the underground coal mine “Soko” in Serbia.

The results of this research can help many potential users realize their goals. Those goals are preventive by nature, since negative environmental impact can be predicted, which enables the environmental protection experts to take appropriate measures.     

Derivatization and separation of 2,4,6-trinitrotoluene metabolic products

2,4,6-Triaminotoluene (TAT), an oxygen sensitive metabolic product of 2,4,6-trinitrotoluene (TNT) reduction, was derivatized yielding oxygen stable products using a procedure previously employed for the stabilization of other O2sensitive TNT metabolic products. A HPLC method is presented that allows for the separation of diverse intermediates and products of TNT metabolism following the derivatization procedure. © Rapid Science Ltd. 1998     

Sperm cells and foreign DNA: a controversial relation

Sperm cells from a variety of species share the spontaneous ability to take up foreign DNA. That feature has been exploited to generate genetically modified animals with variable efficiency in different species. An unexpectedly large set of factors appears to modulate the interaction of sperm cells with exogenous DNA. The binding is mediated by specific DNA-binding proteins and is antagonized by an inhibitory factor in the seminal fluid. A portion of sperm-bound DNA is internalized in nuclei, a process mediated by CD4 molecules. Sperm interaction with foreign DNA triggers endogenous nuclease(s) that cleaves both the exogenous and the genomic DNA, eventually leading to a cell death process which resembles apoptosis. Internalized foreign DNA sequences reach the nuclear matrix and undergo recombination with chromosomal DNA. From these studies, a surprising network of metabolic functions is beginning to emerge in mature spermatozoa, which are normally repressed and are specifically activated upon exposure to appropriate stimuli. BioEssays 20:955–964, 1998. © 1998 John Wiley & Sons, Inc.     

Seasonal changes in anatomical and morphological structure and the content of phytohormones and sugars in underground shoots of a long-rhizome perennial grass <Emphasis Type="Italic">Phalaroides arundinacea</Emphasis>

Seasonal changes in the anatomical and morphological structure and metabolic activity of rhizomes were studied in a perennial grass reed canary-grass (Phalaroides arundinacea (L.) Rauschert). An active formation of the underground stock of meristems and a rhizome weight accumulation were shown in the later half of a growth period, after a decline in the growth of aboveground shoots. A reduction in the cross-section area and the relative contribution of the central cylinder together with of an increase in the volume of a cortex parenchyma were found in the rhizomes at the end of the growth period. In autumn, the rhizomes were characterized by the high content of cytokinins and oligosaccharides; which reserves determines the resistance of underground shoots to low temperatures and prevents the frost damage to underground meristems, whereas the levels of other phytohormones (IAA, ABA, and GA) significantly decreased at this period. In the autumn, the optimum temperatures for the rhizome growth shifted to low above-zero temperatures, reflecting the adaptation of morphogenetic processes related to the bud formation. The authors conclude that the temperature depression rather than the accumulation of growth inhibitors is the basic factor determining rhizome exogenous dormancy.     

Protein targeting to subnuclear higher order structures: A new level of regulation and coordination of nuclear processes

Though there are no separating membranes within the nucleus, different factors are often concentrated at sites where their respective function is required, a phenomenum referred to as functional organization of the nucleus. How is then this organization achieved and how are the different metabolic processes integrated in the nucleus? One emerging principle was revealed by the identification of protein domains that, though not involved in catalysis, regulate enzyme activity at a higher order level by targeting enzymes to the right place at the right time. These targeting sequences constitute an assembly code for nuclear ‘protein factories,’ which ensure the extremely high efficiency and accuracy needed in a complex and competitive environment as the living mammalian cell. J. Cell. Biochem. 70:222– 230, 1998. © 1998 Wiley-Liss, Inc.     

Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations

As in many deep underground environments, the microbial communities in subsurface high‐CO₂ ecosystems remain relatively unexplored. Recent investigations based on single‐gene assays revealed a remarkable variety of organisms from little studied phyla in Crystal Geyser (Utah, USA), a site where deeply sourced CO₂‐saturated fluids are erupted at the surface. To provide genomic resolution of the metabolisms of these organisms, we used a novel metagenomic approach to recover 227 high‐quality genomes from 150 microbial species affiliated with 46 different phylum‐level lineages. Bacteria from two novel phylum‐level lineages have the capacity for CO₂ fixation. Analyses of carbon fixation pathways in all studied organisms revealed that the Wood‐Ljungdahl pathway and the Calvin‐Benson‐Bassham Cycle occurred with the highest frequency, whereas the reverse TCA cycle was little used. We infer that this, and selection for form II RuBisCOs, are adaptions to high CO₂‐concentrations. However, many autotrophs can also grow mixotrophically, a strategy that confers metabolic versatility. The assignment of 156 hydrogenases to 90 different organisms suggests that H₂ is an important inter‐species energy currency even under gaseous CO₂‐saturation. Overall, metabolic analyses at the organism level provided insight into the biochemical cycles that support subsurface life under the extreme condition of CO₂ saturation.     

The cost of living slowly: metabolism,Q10 and repeatability in a South American harvestman

Abstract Resources are usually considered to be limited in caves and underground habitats. Therefore, lower metabolic rates of ectotherms in these environments should be advantageous. The standard metabolic rate (SMR) of the common harvestman Pachylus paessleri Roewer, 1913 (Arachnida, Opiliones) is determined at two ambient temperatures. Repeatability of SMR is estimated by two methods: (i) product–moment correlation on residuals of body mass and (ii) variance components. Estimations of the thermal sensitivity of metabolic rate (individual Q₁₀). SMR of P. paessleri at 20 °C show a mean of 19.01 ± 6.04 and 14.99 ± 3.64 μL CO₂ h^?1 for males and females, respectively. Thermal sensitivity of SMR is 2.11 ± 0.23 with a substantial coefficient of variation of 26.7%. In males, residuals of CO₂ release are significantly repeatable (r_p = 0.61) between measurements realized 5 months apart, which reflects the consistency of this trait over time. As typical soil inhabitants, the harvestman P. paessleri present a lower metabolic rate in comparison with arthropods of similar body mass (e.g. arachnids). Although the coefficient of thermal sensitivity is within of the range reported for arthropods inhabiting Mediterranean zones, it is lower than expected for an organism with such a low SMR. This appears to be the first report of repeatability of metabolic rate in a harvestman species.     

Effects of seasonal snow on the growing season of temperate vegetation in China

Variations in seasonal snowfall regulate regional and global climatic systems and vegetation growth by changing energy budgets of the lower atmosphere and land surface. We investigated the effects of snow on the start of growing season (SGS) of temperate vegetation in China. Across the entire temperate region in China, the winter snow depth increased at a rate of 0.15 cm yr^?1 (P = 0.07) during the period 1982–1998, and decreased at a rate of 0.36 cm yr^?1 (P = 0.09) during the period 1998–2005. Correspondingly, the SGS advanced at a rate of 0.68 day yr^?1 (P < 0.01) during 1982–1998, and delayed at a rate of 2.13 day yr^?1 (P = 0.07) during 1998–2005, against a warming trend throughout the entire study period of 1982–2005. Spring air temperature strongly regulated the SGS of both deciduous broad‐leaf and coniferous forests, whereas the winter snow had a greater impact on the SGS of grassland and shrubs. Snow depth variation combined with air temperature contributed to the variability in the SGS of grassland and shrubs, as snow acted as an insulator and modulated the underground thermal conditions. In addition, differences were seen between the impacts of winter snow depth and spring snow depth on the SGS; as snow depths increased, the effect associated went from delaying SGS to advancing SGS. The observed thresholds for these effects were snow depths of 6.8 cm (winter) and 4.0 cm (spring). The results of this study suggest that the response of the vegetation's SGS to seasonal snow change may be attributed to the coupling effects of air temperature and snow depth associated with the underground thermal conditions.