Aging in bacteria

Targeted Hypermutation as a Survival Strategy: A Theoretical Approach

Targeted hypermutation has proven to be a useful survival strategy for bacteria under severe stress and is also used by multicellular organisms in specific instances such as the mammalian immune system. This might appear surprising, given the generally observed deleterious effects of poor replication fidelity/high mutation rate. A previous theoretical model designed to explore the role of replication fidelity in the origin of life was applied to a simulated hypermutation scenario. The results confirmed that the same model is useful for analyzing hypermutation and can predict the effects of the same parameters (survival probability, replication fidelity, mutation effect, and others) on the survival of cellular populations undergoing hypermutation as a result of severe stress.

Our current understanding of the toxicity of altered mito-ribosomal fidelity during mitochondrial protein synthesis: What can it tell us about human disease?

Altered mito-ribosomal fidelity is an important and insufficiently understood causative agent of mitochondrial dysfunction. Its pathogenic effects are particularly well-known in the case of mitochondrially induced deafness, due to the existence of the, so called, ototoxic variants at positions 847C (m.1494C) and 908A (m.1555A) of 12S mitochondrial (mt-) rRNA. It was shown long ago that the deleterious effects of these variants could remain dormant until an external stimulus triggered their pathogenicity. Yet, the link from the fidelity defect at the mito-ribosomal level to its phenotypic manifestation remained obscure. Recent work with fidelity-impaired mito-ribosomes, carrying error-prone and hyper-accurate mutations in mito-ribosomal proteins, have started to reveal the complexities of the phenotypic manifestation of mito-ribosomal fidelity defects, leading to a new understanding of mtDNA disease. While much needs to be done to arrive to a clear picture of how defects at the level of mito-ribosomal translation eventually result in the complex patterns of disease observed in patients, the current evidence indicates that altered mito-ribosome function, even at very low levels, may become highly pathogenic. The aims of this review are three-fold. First, we compare the molecular details associated with mito-ribosomal fidelity to those of general ribosomal fidelity. Second, we gather information on the cellular and organismal phenotypes associated with defective translational fidelity in order to provide the necessary grounds for an understanding of the phenotypic manifestation of defective mito-ribosomal fidelity. Finally, the results of recent experiments directly tackling mito-ribosomal fidelity are reviewed and future paths of investigation are discussed.

Interspecific interactions that affect ageing: Age-distorters manipulate host ageing to their own evolutionary benefits

Genetic causes for ageing are traditionally investigated within a species. Yet, the lifecycles of many organisms intersect. Additional evolutionary and genetic causes of ageing, external to a focal species/organism, may thus be overlooked. Here, we introduce the phrase and concept of age-distorters and its evidence. Age-distorters carry ageing interfering genes, used to manipulate the biological age of other entities upon which the reproduction of age-distorters relies, e.g. age-distorters bias the reproduction/maintenance trade-offs of cells/organisms for their own evolutionary interests. Candidate age-distorters include viruses, parasites and symbionts, operating through specific, genetically encoded interferences resulting from co-evolution and arms race between manipulative non-kins and manipulable species. This interference results in organismal ageing when age-distorters prompt manipulated organisms to favor their reproduction at the expense of their maintenance, turning these hosts into expanded disposable soma. By relying on reproduction/maintenance trade-offs affecting disposable entities, which are left ageing to the reproductive benefit of other physically connected lineages with conflicting evolutionary interests, the concept of age-distorters expands the logic of the Disposable Soma theory beyond species with fixed germen/soma distinctions. Moreover, acknowledging age-distorters as external sources of mutation accumulation and antagonistic pleiotropic genes expands the scope of the mutation accumulation and of the antagonistic pleiotropy theories.

Antibiotic resistance related to biofilm formation in Streptococcus suis

Streptococcus suis (S. suis) is an important zoonotic agent, which seriously impacts the pig industry and human health in various countries. Biofilm formation is likely contributing to the virulence and drug resistance in S. suis. A better knowledge of biofilm formation as well as to biofilm-dependent drug resistance mechanisms in S. suis can be of great significance for the prevention and treatment of S. suis infections. This literature review updates the latest scientific data related to biofilm formation in S. suis and its impact on drug tolerance and resistance.Key points• Biofilm formation is the important reasons for drug resistance of SS infections.• The review includes the regulatory mechanism of SS biofilm formation.• The review includes the drug resistance mechanisms of SS biofilm.

Ancestral germen/soma distinction in microbes: Expanding the disposable soma theory of aging to all unicellular lineages

Life has persisted for about 3.5 billion years (Gy) despite fluctuating environmental pressures and the aging and mortality of individuals. The disposable soma theory (DST) notoriously contributes to explain this persistence for lineages with a clear soma/germen distinction. Beyond such lineages however, the phylogenetic scope of application of the DST is less obvious. Typically, the DST is not expected to explain the survival of microbial species that comprise single-celled organisms apparently lacking a germen/soma distinction. Here, we present an evolutionary argument that generalizes the explanatory scope of DST to the entire microbial world and provides a novel characterization of the deep molecular and evolutionary roots supporting this expanded disposable soma theory of aging. Specifically, we argue that the germen/soma distinction arose early in evolution and identify DNA semi-conservative replication as a critical process through which two forms of rejuvenation could have evolved in the first microbes. Our hypothesis has fundamental and practical implications. First, whereas unicellular organisms were long thought of as potentially immortal, we suggest instead that all unicellular individuals (prokaryotes or protists alike) are very likely to age, either replicatively or physiologically, or both. Second, our theory introduces a profound reconsideration of microbial individuality, whereby, all microbial individuals, as seen by natural selection, present an obligate transient germen/soma distinction during their life cycles. Third, our work promotes the study of cellular division in prokaryotes and in protist mitosis to illuminate the evolutionary origin of the soma and germen division, traditionally studied in animals. These ideas set the stage for progress in the evolutionary theory of aging from a heretofore overlooked microbial perspective.

Screening for a suitable cell membrane anchoring tag for Pseudomonas aeruginosa and applying it in cell membrane real-time tracking to investigate membrane aging

Membrane proteins that have been widely used in drug delivery and cell labeling can localize onto the cell membrane by interacting with lipid bilayers. A membrane-binding tag fused with a fluorescent protein can enable tracking of the cell outline. However, numerous known membrane proteins have species preferences, and thus, a suitable membrane-binding tag for Pseudomonas aeruginosa has not been reported. In this study, we examined the membrane-binding effects of a series of endogenous and exogenous proteins (peptides) in P. aeruginosa; the proteins included LacY, WspA, tsr and its truncated mutant (tsrMut), exotoxin A signal peptide (ESP), and TAT. Among them, tsrMut exhibited a faster and steadier membrane positioning ability than others, and it also did not interfere with bacteria growth. In addition, tsrMut could be further applied for identifying and tracking cell membrane aging areas in real-time. By linking it with a tandem fluorescent timer (EGFP-Tdimer2), the aging areas of the cell membrane could easily be displayed and observed under the microscope. These findings suggest that tsrMut is a highly favorable binding tag for P. aeruginosa and integrating the tag with an aging timer may be a promising approach for studying bacterial membrane senescence at the single-cell level.

Stress hypothesis overload: 131 hypotheses exploring the role of stress in tradeoffs, transitions, and health

Stress is ubiquitous and thus, not surprisingly, many hypotheses and models have been created to better study the role stress plays in life. Stress spans fields and is found in the literature of biology, psychology, psychophysiology, sociology, economics, and medicine, just to name a few. Stress, and the hypothalamic-pituitaryadrenal/interrenal (HPA/I) axis and sympathetic nervous system (SNS), are involved in a multitude of behaviors and physiological processes, including life-history and ecological tradeoffs, developmental transitions, health, and survival. The goal of this review is to highlight and summarize the large number of available hypotheses and models, to aid in comparative and interdisciplinary thinking, and to increase reproducibility by a) discouraging hypothesizing after results are known (HARKing) and b) encouraging a priori hypothesis testing. For this review I collected 214 published hypotheses or models dealing broadly with stress. In the main paper, I summarized and categorized 131 of those hypotheses and models which made direct connections among stress and/or HPA/I and SNS, tradeoffs, transitions, and health. Of those 131, the majority made predictions about reproduction (n = 43), the transition from health to disease (n = 38), development (n = 23), and stress coping (n = 18). Additional hypotheses were classified as stage-spanning or models (n = 37). The additional 83 hypotheses found during searches were tangentially related, or pertained to immune function or oxidative stress, and these are listed separately. Many of the hypotheses share underlying rationale and suggest similar, if not identical, predictions, and are thus not mutually exclusive; some hypotheses spanned classification categories. Some of the hypotheses have been tested multiple times, whereas others have only been examined a few times. It is the hope that multi-disciplinary stress researchers will begin to harmonize their naming of hypotheses in the literature so as to build a clearer picture of how stress impacts various outcomes across fields. The paper concludes with some considerations and recommendations for robust testing of stress hypotheses.

Comparative stress response to food preservation conditions of ST19 and ST213 genotypes of Salmonella enterica serotype Typhimurium

The replacement of the most prevalent Salmonella enterica genotypes has been documented worldwide. Here we tested the hypothesis that the current prevalent sequence type ST213 of serotype Typhimurium in Mexico has a higher resistance to stressful food preservation conditions than the displaced sequence ST19. ST19 showed higher cell viability percentages than ST213 in osmotic (685 mM NaCl) and acidic (pH 3.5) stress conditions and in combination with refrigeration (4 °C) and ambient (≈22 °C) temperatures. Both genotypes showed the same poststress recovery growth. ST213 formed biofilm and filamentous cells (FCs) under stress, whereas ST19 did not. ST213 cells also showed higher motility. The capacity of ST213 to form FCs may explain its lower viability percentages when compared with ST19, i.e., ST213 cells divided less under stress conditions, but FCs had the same recovery capacity of ST19 cells. ST213 presented a higher unsaturated/saturated fatty acids ratio (0.5-0.6) than ST19 (0.2-0.5), which indicates higher membrane fluidity. The transcript levels of the rpoS gene were similar between genotypes under the experimental conditions employed. Biofilm formation, the generation of FCs, cell motility and membrane modification seem to make ST213 more resistant than ST19 to food preservation environments.

Bacterial biofilm formation on implantable devices and approaches to its treatment and prevention

In living organisms, biofilms are defined as complex communities of bacteria residing within an exopolysaccharide matrix that adheres to a surface. In the clinic, they are typically the cause of chronic, nosocomial, and medical device-related infections. Due to the antibiotic-resistant nature of biofilms, the use of antibiotics alone is ineffective for treating biofilm-related infections. In this review, we present a brief overview of concepts of bacterial biofilm formation, and current state-of-the-art therapeutic approaches for preventing and treating biofilms. Also, we have reviewed the prevalence of such infections on medical devices and discussed the future challenges that need to be overcome in order to successfully treat biofilms using the novel technologies being developed.

Aging and immortality in unicellular species

It has been historically thought that in conditions that permit growth, most unicellular species do not to age. This was particularly thought to be the case for symmetrically dividing species, as such species lack a clear distinction between the soma and the germline. Despite this, studies of the symmetrically dividing species Escherichia coli and Schizosaccharomyces pombe have recently started to challenge this notion. They indicate that E. coli and S. pombe do age, but only when subjected to environmental stress. If true, this suggests that aging may be widespread among microbial species in general, and that studying aging in microbes may inform other long-standing questions in aging. This review examines the recent evidence for and against replicative aging in symmetrically dividing unicellular organisms, the mechanisms that underlie aging, why aging evolved in these species, and how microbial aging fits into the context of other questions in aging.

In silico analysis of division times of Escherichia coli populations as a function of the partitioning scheme of non-functional proteins

Recent evidence suggests that cells employ functionally asymmetric partitioning schemes in division to cope with aging. We explore various schemes in silico, with a stochastic model of Escherichia coli that includes gene expression, non-functional proteins generation, aggregation and polar retention, and molecule partitioning in division. The model is implemented in SGNS2, which allows stochastic, multi-delayed reactions within hierarchical, transient, interlinked compartments. After setting parameter values of non-functional proteins’ generation and effects that reproduce realistic intracellular and population dynamics, we investigate how the spatial organization of non-functional proteins affects mean division times of cell populations in lineages and, thus, mean cell numbers over time. We find that division times decrease for increasingly asymmetric partitioning. Also, increasing the clustering of non-functional proteins decreases division times. Increasing the bias in polar segregation further decreases division times, particularly if the bias favors the older pole and aggregates’ polar retention is robust. Finally, we show that the non-energy consuming retention of inherited non-functional proteins at the older pole via nucleoid occlusion is a source of functional asymmetries and, thus, is advantageous. Our results suggest that the mechanisms of intracellular organization of non-functional proteins, including clustering and polar retention, affect the vitality of E. coli populations.

The O-antigen mediates differential survival of Salmonella against communities of natural predators

Antigenically distinct members of bacterial species can be differentially distributed in the environment. Predators known to consume antigenically distinct prey with different efficiencies are also differentially distributed. Here we show that antigenically distinct, but otherwise isogenic and physiologically indistinct, strains of Salmonella enterica show differential survival in natural soil, sediment and intestinal environments, where they would face a community of predators. Decline in overall cell numbers is attenuated by factors that inhibit the action of predators, including heat and antiprotozoal and antihelminthic drugs. Moreover, the fitness of strains facing these predators - calculated by comparing survival with and without treatments attenuating predator activity - varies between environments. These results suggest that relative survival in natural environments is arbitrated by communities of natural predators whose feeding preferences, if not species composition, vary between environments. These data support the hypothesis that survival against natural predators may drive the differential distribution of bacteria among microenvironments.

Priming and memory of stress responses in organisms lacking a nervous system

Experience and memory of environmental stimuli that indicate future stress can prepare (prime) organismic stress responses even in species lacking a nervous system. The process through which such organisms prepare their phenotype for an improved response to future stress has been termed 'priming'. However, other terms are also used for this phenomenon, especially when considering priming in different types of organisms and when referring to different stressors. Here we propose a conceptual framework for priming of stress responses in bacteria, fungi and plants which allows comparison of priming with other terms, e.g. adaptation, acclimation, induction, acquired resistance and cross protection. We address spatial and temporal aspects of priming and highlight current knowledge about the mechanisms necessary for information storage which range from epigenetic marks to the accumulation of (dormant) signalling molecules. Furthermore, we outline possible patterns of primed stress responses. Finally, we link the ability of organisms to become primed for stress responses (their 'primability') with evolutionary ecology aspects and discuss which properties of an organism and its environment may favour the evolution of priming of stress responses.

The development of a malignant tumor is due to a desperate asexual self-cloning process in which cancer stem cells develop the ability to mimic the genetic program of germline cells

To date there is no explanation why the development of almost all types of solid tumors occurs sharing a similar scenario: (1) creation of a cancer stem cell (CSC), (2) CSC multiplication and formation of a multicellular tumor spheroid (TS), (3) vascularization of the TS and its transformation into a vascularized primary tumor, (4) metastatic spreading of CSCs, (5) formation of a metastatic TSs and its transformation into metastatic tumors, and (6) potentially endless repetition of this cycle of events. The above gaps in our knowledge are related to the biology of cancer and specifically to tumorigenesis, which covers the process from the creation of a CSC to the formation of a malignant tumor and the development of metastases. My Oncogerminative Theory of Tumorigenesis considers tumor formation as a dynamic self-organizing process that mimics a self-organizing process of early embryo development. In the initial step in that process, gene mutations combined with epigenetic dysregulation cause somatic cells to be reprogrammed into CSCs, which are immortal pseudo-germline cells. Mimicking the behavior of fertilized germline cells, the CSC achieves immortality by passing through the stages of its life-cycle and developing into a pseudo-blastula-stage embryo, which manifests in the body as a malignant tumor. In this view, the development of a malignant tumor from a CSC is a phenomenon of developmental biology, which we named a desperate asexual self-cloning event. The theory explains seven core characteristics of malignant tumors: (1) CSC immortality, (2) multistep development of a malignant tumor from a single CSC, (3) heterogeneity of malignant tumor cell populations, (4) metastatic spread of CSCs, (5) invasive growth, (6) malignant progression, and (7) selective immune tolerance toward cancer cells. The Oncogerminative Theory of Tumorigenesis suggests new avenues for discovery of revolutionary therapies to treat, prevent, and eradicate cancer.

Bacterial biofilms: a diagnostic and therapeutic challenge

Bacteria have traditionally been regarded as individual organisms growing in homogeneous planktonic populations. However, bacteria in natural environments usually form communities of surface-adherent organisms embedded in an extracellular matrix, called biofilms. Current antimicrobial strategies often fail to control bacteria in the biofilm mode of growth. Treatment failure is particularly frequent in association with intracorporeal or transcutaneous medical devices and compromised host immunity. The rising prevalence of these risk factors over the last decades has paralleled the increase in biofilm infections. This review discusses the shortcomings of current therapies against biofilms both in theory and with clinical examples. Biofilm characteristics are described with a focus on new diagnostic and therapeutic targets.

Protein carbonylation: proteomics, specificity and relevance to aging

Detection and quantification of protein carbonyls present in biological samples has become a popular, albeit indirect, method to determine the existence of oxidative stress. Moreover, the rise of proteomics has allowed the identification of the specific proteins targeted by protein carbonylation. This review discusses these methodologies and proteomic strategies and then focuses on the relationship between protein carbonylation and aging and the parameters that may explain the increased sensitivity of certain proteins to protein carbonylation.

Protein quality control in time and space - links to cellular aging

The evolutionary theory of aging regards aging as an evolved characteristic of the soma, and proponents of the theory state that selection does not allow the evolution of aging in unicellular species lacking a soma-germ demarcation. However, the life history of some microorganisms, reproducing vegetatively by either budding or binary fission, has been demonstrated to encompass an ordered, polar-dependent, segregation of damage leading to an aging cell lineage within the clonal population. In the yeast Saccharomyces cerevisiae and the bacterium Escherichia coli, such segregation is under genetic control and includes an asymmetrical inheritance of protein aggregates and inclusions. Herein, the ultimate and proximate causation for such an asymmetrical inheritance, with special emphasis on damaged/aggregated proteins in budding yeast, is reviewed.

Ageing of trees: application of general ageing theories

The main questions posed in ageing theories are how ageing evolved and whether or not it is programmed. While these questions have not yet been clearly resolved, several groups of possible theories have been published on this topic. However, most of these theories do not consider plants, and the specific traits involved in their ageing mechanisms. The first trait covers clonality and sectoriality and the second concerns the lack of a differentiated germ line. The lack of a germ line prevents telomere shortening which can lead to the transfer of somatic mutations into sexual offspring, while sectoriality in trees causes isolation of potentially catastrophic events in one tree part, thus creating a population of more or less independent modules within one axis. The processes of population dynamics, including ageing, can act within the framework of an individual tree as well as in that of the population as a whole, although the processes involved differ and consequently result in different effects.

Ageing in Escherichia coli requires damage by an extrinsic agent

Evidence for ageing in symmetrically dividing bacteria such as Escherichia coli has historically been conflicting. Early work found weak or no evidence. More recent studies found convincing evidence, but negative results are still encountered. Because bacterial ageing is believed to result from non-genetic (e.g. oxidative) damage, we tested the possibility that the negative outcomes resulted from the lack of an extrinsic damage agent. We found that streptomycin, which produces mistranslated proteins that are more vulnerable to oxidation, was able to induce both damage and ageing in bacterial populations. A dosage effect relating the level of damage to the concentration of streptomycin was observed. Our results explain the previous inconsistencies, because all studies that failed to find evidence for bacterial ageing did not use a damage agent. However, all studies that succeeded in finding evidence utilized fluorescent proteins as a visual marker. We suggest that ageing in those studies was induced by the harmful effects of an extrinsic factor, such as the proteins themselves or the excitation light. Thus, all of the earlier studies can be reconciled and bacterial ageing is a real phenomenon. However, the study and observation of bacterial ageing require the addition of an extrinsic damage agent.

Factors affecting the growth rates of ammonium and nitrite oxidizing bacteria

The maximum specific growth rates of both ammonium oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) were investigated under varying aerobic solids retention time (SRT(a)) and in the presence/absence of anoxic (alternating) conditions. Two bench SBRs, reactor R1 and R2, were run in parallel for 150d. Reactor R1 was operated in aerobic conditions while R2 operated in alternating anoxic/aerobic conditions. The feed (synthetic wastewater), temperature, hydraulic retention time and mixing were identical in both reactors. The SRT(a) in both reactors was, sequentially, set at four values: 5, 4, 3 and 2d. Kinetic tests with the biomasses from both reactors were carried out to estimate the maximum specific growth rates (μ(max)) at each tested SRT(a) and decay rates, in both aerobic and anoxic conditions. The kinetic parameters of nitrifier were estimated through the calibration of a two step nitrification-denitrification activated sludge model. The results point to a slightly higher μ(max,AOB) and μ(max,NOB) in alternating conditions, while both μ(max,AOB) and μ(max,NOB) were shown not to vary in the tested range of SRT(a) (from 2 to 5d) at 20°C. They were relatively high when compared to literature data: 1.05d(-1)<μ(max,AOB)<1.4d(-1) and 0.91d(-1)<μ(max,NOB)<1.31d(-1). The decay coefficients of both AOB and NOB were much higher in aerobic (from 0.22d(-1) to 0.28d(-1)) than in anoxic (0.04d(-1) to 0.16d(-1)) conditions both in R1 and R2, which explained the higher nitrification rates observed in the alternating reactor.

A model for damage load and its implications for the evolution of bacterial aging

Deleterious mutations appearing in a population increase in frequency until stopped by natural selection. The ensuing equilibrium creates a stable frequency of deleterious mutations or the mutational load. Here I develop the comparable concept of a damage load, which is caused by harmful non-heritable changes to the phenotype. A damage load also ensues when the increase of damage is opposed by selection. The presence of a damage load favors the evolution of asymmetrical transmission of damage by a mother to her daughters. The asymmetry is beneficial because it increases fitness variance, but it also leads to aging or senescence. A mathematical model based on microbes reveals that a cell lineage dividing symmetrically is immortal if lifetime damage rates do not exceed a threshold. The evolution of asymmetry allows the lineage to persist above the threshold, but the lineage becomes mortal. In microbes with low genomic mutation rates, it is likely that the damage load is much greater than the mutational load. In metazoans with higher genomic mutation rates, the damage and the mutational load could be of the same magnitude. A fit of the model to experimental data shows that Escherichia coli cells experience a damage rate that is below the threshold and are immortal under the conditions examined. The model estimates the asymmetry level of E. coli to be low but sufficient for persisting at higher damage rates. The model also predicts that increasing asymmetry results in diminishing fitness returns, which may explain why the bacterium has not evolved higher asymmetry.

Almost all living organisms deteriorate with time through the process of aging or senescence. Because most studies on senescence examined organisms possessing a juvenile state, it was thought that bacteria, which reproduce by producing two apparently identical daughter cells, were immortal and not senescent. Recent studies have demonstrated that bacteria senesce because one daughter is allocated a larger share of the mother's load of non-genetic damage. Nonetheless, it is still equivocal whether bacterial senescence renders them mortal. I have developed a model that demonstrates that bacteria can be immortal if they experience damage below a threshold rate. A fit of the model to data shows that bacteria grown under standard laboratory conditions are immortal because they encounter a rate below the threshold. Because bacteria often experience higher damage rates in nature, it is likely that bacteria are generally mortal. The allocation of more damage to one daughter and the resulting mortality is the price bacteria pay to survive higher damage rates. These results suggest that senescence originated with the evolution of the first single-celled organisms and that it is ancestral in all multicellular organisms.

Protein expression is altered during spontaneous sleep in aged Sprague Dawley rats

Age-related changes in brain function include those affecting learning, memory, and sleep-wakefulness. Sleep-wakefulness is an essential behavior that results from the interaction of multiple brain regions, peptides, and neurotransmitters. The biological function(s) of sleep, however, remains unknown due to a paucity of information available at the cellular level. Aged rats exhibit alterations in the circadian and homeostatic influences associated with sleep-wake regulation. We recently showed that alterations in cortical profiles occur after timed bouts of spontaneous sleep in young rats. Examination of the cellular response to sleep-wake in old rats may thus provide insight(s) into the biological function(s) of sleep. To test this hypothesis, we monitored cortical profiles in the frontal cortex of young and old Sprague-Dawley rats after timed bouts of spontaneous sleep-wake behavior. Proteins were separated by two-dimensional electrophoresis (2-DE), visualized by fluorescent staining, imaged, and analyzed as a function of behavioral state and age. Old rats showed a 6-fold increase in total protein expression, independent of the behavioral state at sacrifice. When analyzed according to age and behavioral state, there was a decrease (approximately 46%) in the number of phospho-spots present during SWS in aged animals. SWS-associated spots present only in old animals were associated with multiple functions including vesicular transport, cell signaling, oxidation state, cytoskeletal support, and energy metabolism. These data suggest that the intracellular response to the signaling associated with spontaneous sleep is affected by age and is consistent with the idea that the ability of sleep to fulfill its function(s) may become diminished with age.

Using ratchets and sorters to fractionate motile cells of Escherichia coli by length

This paper describes the fabrication of a composite agar/PDMS device for enriching short cells in a population of motile Escherichia coli. The device incorporated ratcheting microchannels, which directed the motion of swimming cells of E. coli through the device, and three sorting junctions, which isolated successively shorter populations of bacteria. The ratcheting microchannels guided cells through the device with an average rate of displacement of (32 +/- 9) microm s(-1). Within the device, the average length of the cells decreased from 3.8 microm (Coefficient of Variation, CV: 21%) at the entrance, to 3.4 microm (CV: 16%) after the first sorting junction, to 3.2 mum (CV: 19%) after the second sorting junction, to 3.0 mum (CV: 19%) after the third sorting junction.

Stress and How Bacteria Cope with Death and Survival

Bacterial populations that are exposed to rapidly changing and sometimes hostile environments constantly switch between growth, survival, and death. Understanding bacterial survival and death are therefore cornerstones in a full comprehension of microbial life. During the last few years, new insights have emerged regarding the mechanisms of bacterial inactivation under stressful conditions. Particularly under mildly lethal stress, the ultimate cause of inactivation often seems mediated by the cell itself and is subject to additional regulation that integrates information about the global state of the cell and its environmental and social surrounding. This article explores the thin line between bacterial growth and inactivation and focuses on some emerging bacterial survival strategies, both from an individual cell and from a population perspective.

Increased molecular damage and heterogeneity as the basis of aging

Aging at the molecular level is characterized by the progressive accumulation of molecular damage. The sources of damage act randomly through environmental and metabolically generated free radicals, through spontaneous errors in biochemical reactions, and through nutritional components. However, damage to a macromolecule may depend on its structure, localization and interactions with other macromolecules. Damage to the maintenance and repair pathways comprising homeodynamic machinery leads to age-related failure of homeodynamics, increased molecular heterogeneity, altered cellular functioning, reduced stress tolerance, diseases and ultimate death. Novel approaches for testing and developing effective means of intervention, prevention and modulation of aging involve means to minimize the occurrence and accumulation of molecular damage. Mild stress-induced hormesis by physical, biological and nutritional methods, including hormetins, represents a promising strategy for achieving healthy aging and for preventing age-related diseases.

Microbial diversity of culturable heterotrophs in the rhizosphere of salt marsh grass, Porteresia coarctata (Tateoka) in a mangrove ecosystem

A study was conducted to understand the complexity of bacterial diversity of rhizosphere of Porteresia coarctata based on culture dependent method. A large number of bacteria were isolated on nutrient agar medium supplemented with 1% NaCl and the dominant ones were further analyzed with PCR-RFLP method. The sequence analyses of the dominant strains revealed that most of the sequences belonged to members of gamma proteobacteria, firmicutes, bacteroidetes and uncultured bacteria. The phylogenetic analysis of 16S rRNA gene sequences revealed close relationships to a wide range of clones or bacterial species of various divisions. These results afford an understanding of the role of rhizobacteria in alleviating salt stress in Porteresia coarctata expected to contribute towards long-term goal of improving plant-microbe interactions for salinity affected fields.

Spontaneous DNA breakage in single living Escherichia coli cells

Spontaneous DNA breakage is predicted to be a frequent, inevitable consequence of DNA replication and is thought to underlie much of the genomic change that fuels cancer and evolution. Despite its importance, there has been little direct measurement of the amounts, types, sources and fates of spontaneous DNA lesions in living cells. We present a direct, sensitive flow cytometric assay in single living Escherichia coli cells for DNA lesions capable of inducing the SOS DNA damage response, and we report its use in quantification of spontaneous DNA double-strand breaks (DSBs). We report efficient detection of single chromosomal DSBs and rates of spontaneous breakage approximately 20- to 100-fold lower than predicted. In addition, we implicate DNA replication in the origin of spontaneous DSBs with the finding of fewer spontaneous DSBs in a mutant with altered DNA polymerase III. The data imply that spontaneous DSBs induce genomic changes and instability 20-100 times more potently than previously appreciated. Finally, FACS demonstrated two main cell fates after spontaneous DNA damage: viability with or without resumption of proliferation.

Synchronization of cell death in a dinoflagellate population is mediated by an excreted thiol protease

Regulated programmed cell death (PCD) processes have been documented in several phytoplankton species and are hypothesized to play a role in population dynamics. However, the mechanisms leading to the coordinated collapse of phytoplankton blooms are poorly understood. We showed that the collapse of the annual bloom of Peridinium gatunense, an abundant dinoflagellate in Lake Kinneret, Israel, is initiated by CO2 limitation followed by oxidative stress that triggers a PCD-like cascade. We provide evidences that a protease excreted by senescing P. gatunense cells sensitizes younger cells to oxidative stress and may consequently trigger synchronized cell death of the population. Ageing of the P. gatunense cultures was characterized by a remarkable rise in DNA fragmentation and enhanced sensitivity to H2O2. Exposure of logarithmic phase (young) cultures to conditioning media from stationary phase (old) cells sensitized them to H2O2 and led to premature massive cell death. We detected the induction of specific extracellular protease activity, leupeptin-sensitive, in ageing cultures and in lake waters during the succession of the P. gatunense bloom. Partial purification of the conditioned media revealed that this protease activity is responsible for the higher susceptibility of young cells to oxidative stress. Inhibition of the protease activity lowered the sensitivity to oxidative stress, whereas application of papain to logarithmic phase P. gatunense cultures mimicked the effect of the spent media and enhanced cell death. We propose a novel mechanistic framework by which a population of unicellular phytoplankton orchestrates a coordinated response to stress, thereby determine the fate of its individuals.

Proteomic analysis of protein nitration in rat cerebellum: effect of biological aging

3-Nitrotyrosine (3-NT) is a useful biomarker of increasing oxidative stress and protein nitration during biological aging. The proteomic analysis of cerebellar homogenate from Fisher 344/Brown Norway (BN/F1) rats shows an age-dependent increase in protein nitration, monitored by western-blot analysis after two-dimensional gel electrophoresis (2DE), mainly in the acidic region. Analysis of in-gel digests by nanoelectrospray (NSI)-MS/MS resulted in the identification of 16 putatively nitrated proteins. The selective isolation of nitrated proteins using immunoprecipitation, followed by SDS-PAGE and in-gel digest/NSI-MS/MS analysis led to the identification of 22 putatively nitrated proteins, of which 7 were identical to those detected after 2DE. When proteins were separated by solution isoelectrofocusing and analyzed by NSI MS/MS, we obtained MS/MS spectra of 3-NT containing peptides of four proteins - similar to ryanodine receptor 3, low density lipoprotein related receptor 2, similar to nebulin-related anchoring protein isoform C and 2,3 cyclic nucleotide 3-phosphodiesterase. Although the functional consequences of protein nitration for these targets are not yet known, our proteomic experiments serve as a first screen for the more targeted analysis of nitrated proteins from aging cerebellum for functional characterization.

Theories of biological aging: genes, proteins, and free radicals

Traditional categorization of theories of aging into programmed and stochastic ones is outdated and obsolete. Biological aging is considered to occur mainly during the period of survival beyond the natural or essential lifespan (ELS) in Darwinian terms. Organisms survive to achieve ELS by virtue of genetically determined longevity assuring maintenance and repair systems (MRS). Aging at the molecular level is characterized by the progressive accumulation of molecular damage caused by environmental and metabolically generated free radicals, by spontaneous errors in biochemical reactions, and by nutritional components. Damages in the MRS and other pathways lead to age-related failure of MRS, molecular heterogeneity, cellular dysfunctioning, reduced stress tolerance, diseases and ultimate death. A unified theory of biological aging in terms of failure of homeodynamics comprising of MRS, and involving genes, milieu and chance, is acquiring a definitive shape and wider acceptance. Such a theory also establishes the basis for testing and developing effective means of intervention, prevention and modulation of aging.

Symmetrically Dividing Cells of the Fission Yeast Schizosaccharomyces Pombe Do Age

Theories of the evolution of senescence state that symmetrically dividing organisms do not senesce. However, this view is challenged by experimental evidence. We measured by immunofluorescence the occurrence and intensity of protein carbonylation in single and symmetrically dividing cells of Schizosaccharomyces pombe. Cells of S. pombe show different levels of carbonylated proteins. Most cells have little damage, a few show a lot, an observation consistent with the gradual accumulation of carbonylation over time. At reproduction, oxidized proteins are shared between the two resulting cells. These results indicate that S. pombe does age, but does so in a different way from other studied species. Damaged cells give rise to damaged cells. The fact that cells with no or few carbonylated proteins constitute the main part of the population can explain why, although age is not reset to zero in one of the cells during division, the pool of young cells remains large enough to prevent the rapid extinction of the population.

The Thermotoga maritima phenotype is impacted by syntrophic interaction with Methanococcus jannaschii in hyperthermophilic coculture

Significant growth phase-dependent differences were noted in the transcriptome of the hyperthermophilic bacterium Thermotoga maritima when it was cocultured with the hyperthermophilic archaeon Methanococcus jannaschii. For the mid-log-to-early-stationary-phase transition of a T. maritima monoculture, 24 genes (1.3% of the genome) were differentially expressed twofold or more. In contrast, methanogenic coculture gave rise to 292 genes differentially expressed in T. maritima at this level (15.5% of the genome) for the same growth phase transition. Interspecies H2 transfer resulted in three- to fivefold-higher T. maritima cell densities than in the monoculture, with concomitant formation of exopolysaccharide (EPS)-based cell aggregates. Differential expression of specific sigma factors and genes related to the ppGpp-dependent stringent response suggests involvement in the transition into stationary phase and aggregate formation. Cell aggregation was growth phase dependent, such that it was most prominent during mid-log phase and decayed as cells entered stationary phase. The reduction in cell aggregation was coincidental with down-regulation of genes encoding EPS-forming glycosyltranferases and up-regulation of genes encoding beta-specific glycosyl hydrolases; the latter were presumably involved in hydrolysis of beta-linked EPS to release cells from aggregates. Detachment of aggregates may facilitate colonization of new locations in natural environments where T. maritima coexists with other organisms. Taken together, these results demonstrate that syntrophic interactions can impact the transcriptome of heterotrophs in methanogenic coculture, and this factor should be considered in examining the microbial ecology in anaerobic environments.

Microbial diversity in coastal subsurface sediments: a cultivation approach using various electron acceptors and substrate gradients

Microbial communities in coastal subsurface sediments are scarcely investigated and have escaped attention so far. But since they are likely to play an important role in biogeochemical cycles, knowledge of their composition and ecological adaptations is important. Microbial communities in tidal sediments were investigated along the geochemical gradients from the surface down to a depth of 5.5 m. Most-probable-number (MPN) series were prepared with a variety of different carbon substrates, each at a low concentration, in combination with different electron acceptors such as iron and manganese oxides. These achieved remarkably high cultivation efficiencies (up to 23% of the total cell counts) along the upper 200 cm. In the deeper sediment layers, MPN counts dropped significantly. Parallel to the liquid enrichment cultures in the MPN series, gradient cultures with embedded sediment subcores were prepared as an additional enrichment approach. In total, 112 pure cultures were isolated; they could be grouped into 53 different operational taxonomic units (OTU). The isolates belonged to the Proteobacteria, "Bacteroidetes," "Fusobacteria," Actinobacteria, and "Firmicutes." Each cultivation approach yielded a specific set of isolates that in general were restricted to this single isolation procedure. Analysis of the enrichment cultures by PCR and denaturing gradient gel electrophoresis revealed an even higher diversity in the primary enrichments that was only partially reflected by the culture collection. The majority of the isolates grew well under anoxic conditions, by fermentation, or by anaerobic respiration with nitrate, sulfate, ferrihydrite, or manganese oxides as electron acceptors.

Is Escherichia coli getting old?

Whether or not bacteria divide symmetrically, the inheritance of cell poles is always asymmetrical. Because each cell carries an old and a new pole, its daughters will not be the same. Tracking poles of cells and measuring their lengths and doubling times in micro-colonies, Stewart et al.1 observed that growth rate diminished in cells inheriting old poles and concluded that these cells are susceptible to aging. Here, their results are compared with studies on the variabilities of length and age at division. It is argued that the decreased growth rate in old pole cells falls within the expected variation and may therefore be sufficiently far from a catastrophe-like cell death through aging.

Bacterial immobilization and remineralization of N at different growth rates and N concentrations

An experiment was designed to resolve two largely unaddressed questions about the turnover of N in soils. One is the influence of microbial growth rate on mobilization and remineralization of cellular N. The other is to what extent heterotrophic immobilization of NO(3)(-) is controlled by the soil concentration of NH(4)(+). Bacteria were extracted from a deciduous forest soil and inoculated into an aqueous medium. Various N pool dilution/enrichment experiments were carried out to: (1) calculate the gross N immobilization and remineralization rates; (2) investigate their dependence on NH(4)(+)and NO(3)(-) concentrations; (3) establish the microbial preference for NH(4)(+)and NO(3)(-) depending on the NH(4)(+)/NO(3)(-) concentration ratio. Remineralization of microbial N occurred mainly at high growth rates and NH(4)(+) concentrations. There was a positive correlation between NH(4)(+) immobilization and remineralization rates, and intracellular recycling of N seemed to be an efficient way for bacteria to withstand low inorganic N concentrations. Thus, extensive remineralization of microbial N is likely to occur only when environmental conditions promote high growth rates. The results support previous observations of high NO(3)(-) immobilization rates, especially at low NH(4)(+) concentrations, but NO(3)(-) was also immobilized at high NH(4) concentrations. The latter can be understood if part of the microbial community has a preference for NO(3)(-) over NH(4)(+).

Aging and death in an organism that reproduces by morphologically symmetric division

In macroscopic organisms, aging is often obvious; in single-celled organisms, where there is the greatest potential to identify the molecular mechanisms involved, identifying and quantifying aging is harder. The primary results in this area have come from organisms that share the traits of a visibly asymmetric division and an identifiable juvenile phase. As reproductive aging must require a differential distribution of aged and young components between parent and offspring, it has been postulated that organisms without these traits do not age, thus exhibiting functional immortality. Through automated time-lapse microscopy, we followed repeated cycles of reproduction by individual cells of the model organism Escherichia coli, which reproduces without a juvenile phase and with an apparently symmetric division. We show that the cell that inherits the old pole exhibits a diminished growth rate, decreased offspring production, and an increased incidence of death. We conclude that the two supposedly identical cells produced during cell division are functionally asymmetric; the old pole cell should be considered an aging parent repeatedly producing rejuvenated offspring. These results suggest that no life strategy is immune to the effects of aging, and therefore immortality may be either too costly or mechanistically impossible in natural organisms.

Detailed time lapse photography reveals that organisms that divide symmetrically, such as the bacterium E. coli, can indeed age and consequently that no organism is immune to mortality

Survival strategies of infectious biofilms

Modern medicine is facing the spread of biofilm-related infections. Bacterial biofilms are difficult to detect in routine diagnostics and are inherently tolerant to host defenses and antibiotic therapies. In addition, biofilms facilitate the spread of antibiotic resistance by promoting horizontal gene transfer. We review current concepts of biofilm tolerance with special emphasis on the role of the biofilm matrix and the physiology of biofilm-embedded cells. The heterogeneity in metabolic and reproductive activity within a biofilm correlates with a non-uniform susceptibility of enclosed bacteria. Recent studies have documented similar heterogeneity in planktonic cultures. Nutritional starvation and high cell density, two key characteristics of biofilm physiology, also mediate antimicrobial tolerance in stationary-phase planktonic cultures. Advances in characterizing the role of stress response genes, quorum sensing and phase variation in stationary-phase planktonic cultures have shed new light on tolerance mechanisms within biofilm communities.

Achieving immortality in the C. elegans germline

Germline immortality is a topic that has intrigued theoretical biologists interested in aging for over a century. The germ cell lineage can be passed from one generation to the next, indefinitely. In contrast, somatic cells are typically only needed for a single generation and are then discarded. Germ cells may, therefore, harbor rejuvenation mechanisms that enable them to proliferate for eons. Such processes are thought to be either absent from or down-regulated in somatic cells, although cell non-autonomous forms of rejuvenation are formally possible. A thorough description of mechanisms that foster eternal youth in germ cells is lacking. The mysteries of germline immortality are being addressed in the nematode Caenorhabditis elegans by studying mutants that reproduce normally for several generations but eventually become sterile. The mortal germline mutants probably become sterile as a consequence of accumulating various forms of heritable cellular damage. Such mutants are abundant, indicating that several different biochemical pathways are required to rejuvenate the germline. Thus, forward genetics should help to define mechanisms that enable the germline to achieve immortality.