Biological ageing with birth rate controlled by mutations in the Penna model

Summary Within the Penna model, we assume a modification with a reproduction rate B that depends on the health state of the individual defined by the number of bad mutations. The idea is that biologically weaker individuals has got less chance to produce offsprings. The results obtained from simulations and for typical set of model parameters show that then the mortality rate q(a) is increasing faster with age a. The maximum age is also limited from about 50 percent of the biological maximum life-span for the standard Penna model, to about 40 percent. We also conclude that bad mutation distribution r(a) is altered so that younger individuals may accommodate significantly more bad mutations, up to 25 percent, as compared with the standard model (5 percent). In summary, it makes sense to force less productivity for older and weaker individuals.     

Prediction of the human life expectancy

We have simulated demographic changes in the human population using the Penna microscopic model, based on the simple Monte Carlo method. The results of simulations have shown that during a few generations changes in the genetic pool of a population are negligible, while improving the methods of compensation of genetic defects or genetically determined proneness to many disorders drastically affects the average life span of organisms. Age distribution and mortality of the simulated populations correspond very well to real demographic data available from different countries. Basing on the comparison of structures of real human populations and the results of simulations it is possible to predict changes in the age structure of populations in the future.     

Catastrophic senescence and semelparity in the Penna aging model

The catastrophic senescence of the Pacific salmon is among the initial tests used to validate the Penna aging model. Based on the mutation accumulation theory, the sudden decrease in fitness following reproduction may be solely attributed to the semelparity of the species. In this work, we report other consequences of mutation accumulation. Contrary to earlier findings, such dramatic manifestation of aging depends not only on the choice of breeding strategy but also on the value of the reproduction age, R, and the mutation threshold, T. Senescence is catastrophic when T ￡ R.T \le R. As the organism’s tolerance for harmful genetic mutations increases, the aging process becomes more gradual. We observe senescence that is threshold dependent whenever T > R. That is, the sudden drop in survival rate occurs at age equal to the mutation threshold value.     

The Sensitivity of the Stationary Age Class Distribution o Changes in the Life History Components

The influence of the various components of the life history on the stationary age class distribution of a population was studied by applying the Leslie matrix model and then considering the single age class frequencies as well as the average age and the cumulative age class distribution in the stationary state. Since, for fixed survival probabilities, the effects of the (age specific) fecundities were shown to be already expressed by the (ultimate) growth rate, this investigation was concentrated on the influence of the survival probabilities and the growth rate. After having supplemented some useful details concerning the dependence of the growth rate on the life history and introduction of the shift concept as an interpretation of cumulative distributions, the mathematical results could be given a biologically intelligible meaning: An increase in the growth rate for fixed survival probabilities is followed by a shift of all age class frequencies to earlier ages. Whereas age specific changes in fecundity do not result in age specific changes in the stationary age class distribution, increases in survival up to and including age k, say, do exhibit such changes in that they cause a shift of age class frequencies at least from those ages exceeding k to earlier ages.     

Diploidization and chromosomal pairing affinities in the tetraploid wheats and their putative amphiploid progenitor

Summary The genomes of the diploid wheats Triticum boeoticum and T. urartu are closely related, giving 7II in the f₁ hybrid (T^bT^u) and 8.4 (0–14) II + 2.5 (0–7) IV in the derived amphiploid (T^bT^bT^uT^u). The genomes of the tetraploid wheats are also closely related, giving up to 7II at the polyhaploid level (AB) in the absence of the gene Ph but 14II at the tetraploid level (AABB) in the normal presence of Ph. If the amphiploid is the progenitor of the tetraploids, one or the other homoeologue (T^b or T^u) in each of the 7 homoeologous groups (the 7 potential IV) must have differentiated with respect to pairing affinity in order to account for 14II in the tetraploid. Consequently, in tetraploid X amphiploid hybrids (T^bT^uAB) carrying the Ph gene from the tetraploid, the seven differentiated chromosomes (B) would be expected to give 7I while, on the basis of their observed chiasma frequency, T^b, T^u and the less differentiated A would be expected to give 4.17I + 3.57II + 3.23III), assuming homoeologous pairing. The expected chromosomal configuration freqencies at MI (11.17I + 3.57II + 3.23III) closely fit the observed values (11.22I + 3.45II + 3.19III + 0.071IV) for such hybrids (X² = 0.0046; P>0.99). Thus diploidization of the boeoticum-urartu amphiploid clearly could account for the origin of the tetraploid wheats. Furthermore, T. aestivum X amphiploid hybrids (T^bT^uABD) with and without Ph indicated that B as well as A chomosomes tended to pair with their presumed T^bT^u homologues in the absence of Ph. Other tests showed that the tetraploid wheats could not plausibly have originated from any postulated Triticum-Sitopsis (TTSS) parental combinations with or without such chromosomal differentiation.     

Life‐history traits and population decline of the Atlantic mackerel Scomber scombrusin the Adriatic Sea

This study investigated demographic structure and reproductive characteristics of the Atlantic mackerel Scomber scombrus, in relation to landing trends in the northern‐central Adriatic Sea. Results highlighted the occurrence of only small‐sized and young‐age individuals, and a marked decline from the 1990s to the present in maximum age (from 8 to 3 years) and total length (L_T; from 420 to 360 mm). Fecundity ranged between 40 000 and 190 000 eggs, and was related to female L_T. High levels of atresia implied lower values of actual fecundity. Sexual maturity was attained by 72·8% of individuals in their first year of life at 200 mm. The reduction in maximum L_T resulted in a marked decline in the population egg production, while the reduction in maximum age implied that females participated in fewer spawning events.     

Cytogenetic studies in Cochlearia L. (Cruciferae). The chromosomal constitution of C. danica L.

Genome analysis has been used to investigate the relationship of C. danica L. to the diploid and tetraploid species in the genus. The results of this analysis suggest that C. danica has the genomic constitution A¹ ₇ A¹ ₇ A² ₇ A² ₇ T₇ T₇. Both A₇ genomes in C. danica are segmentally differentiated from the A₇ genome in C. groenlandica L. and from the similar A₆ genomes in C. pyrenaica DC. and C. officinalis L. but, in hybrids, are capable of some pairing with these genomes. A² ₇ is more distantly related to A₇ and A₆ than is A¹ ₇ and in A₇ some of the differentiation has taken place by reciprocal translocations. A¹ ₇ and A² ₇ still retain enough homology for pairing between them. The T₇ genome has no homology with any of the A genomes but may be derived from an ancestral T₆ genome.     

Obesity among People with and without Mental Retardation across Adulthood

Objective: This study was designed to explore obesity during adulthood and the likelihood of moving out of obesity among 1809 adults without disability and 680 adults with mental retardation who received care at the same primary care practices during the period of 1990 to 2003. Research Method and Procedures: A retrospective observational design using medical records first identified patients with mental retardation (MR) and age‐matched controls without disabilities. Data on BMI collected during each primary care visit allowed exploration of obesity at three levels. Moving out of obesity was defined as having a BMI <25 kg/m². We also abstracted data on age, sex, race, and other medical conditions. Results: For adults 20 to 29 years of age, 33.1% of patients without disability and 21% of patients with MR had a BMI >30 kg/m². Between the ages of 50 and 59 years, 40.5% of the patients without disability and 35.2% of the patients with MR had a BMI >30 kg/m². Patients with mild MR had similar prevalence rates of obesity and patients with severe MR had significantly lower prevalence of obesity compared with the patients without disability through 50 years of age. Throughout the period from 20 to 60 years of age, between 15% and 40% of individuals with and without MR, who were previously obese, were not currently obese. Discussion: Throughout the adult years, an increasing proportion of individuals with and without MR are obese. However, obesity is not a chronic state; many people transition back to a normal body weight.     

Planctomycetes attached to algal surfaces: Insight into their genomes

Planctomycetes are bacteria with complex molecular and cellular biology. They have large genomes, some over 7 Mb, and complex life cycles that include motile cells and sessile cells. Some live on the complex biofilm of macroalgae. Factors governing their life in this environment were investigated at the genomic level. We analyzed the genomes of three planctomycetes isolated from algal surfaces. The genomes were 6.6 Mbp to 8.1 Mbp large. Genes for outer-membrane proteins, peptidoglycan and lipopolysaccharide biosynthesis were present. Rubripirellula obstinata LF1^T, Roseimaritima ulvae UC8^T and Mariniblastus fucicola FC18^T shared with Rhodopirellula baltica and R. rubra SWK7 unique proteins related to metal binding systems, phosphate metabolism, chemotaxis, and stress response. These functions may contribute to their ecological success in such a complex environment. Exceptionally huge proteins (6000 to 10,000 amino-acids) with extracellular, periplasmic or membrane-associated locations were found which may be involved in biofilm formation or cell adhesion.     

Innovative molecular diagnosis of Trichinella species based on β‐carbonic anhydrase genomic sequence

Trichinellosis is a helminthic infection where different species of Trichinella nematodes are the causative agents. Several molecular assays have been designed to aid diagnostics of trichinellosis. These assays are mostly complex and expensive. The genomes of Trichinella species contain certain parasite‐specific genes, which can be detected by polymerase chain reaction (PCR) methods. We selected β‐carbonic anhydrase (β‐CA) gene as a target, because it is present in many parasites genomes but absent in vertebrates. We developed a novel β‐CA gene‐based method for detection of Trichinella larvae in biological samples. We first identified a β‐CA protein sequence from Trichinella spiralis by bioinformatic tools using β‐CAs from Caenorhabditis elegans and Drosophila melanogaster. Thereafter, 16 sets of designed primers were tested to detect β‐CA genomic sequences from three species of Trichinella, including T. spiralis, Trichinella pseudospiralis and Trichinella nativa. Among all 16 sets of designed primers, the primer set No. 2 efficiently amplified β‐CA genomic sequences from T. spiralis, T. pseudospiralis and T. nativa without any false‐positive amplicons from other parasite samples including Toxoplasma gondii, Toxocara cati and Parascaris equorum. This robust and straightforward method could be useful for meat inspection in slaughterhouses, quality control by food authorities and medical laboratories.     

Determinants of growth of the flammable grass,Triodia scariosa: Consequences for fuel dynamics under climate change in the Mediterranean region of South Eastern Australia

Environmental conditions may influence the presence and strength of competitive interactions between different life forms, thereby shaping community composition and structure, and corresponding fuel dynamics. Woodland and shrubland communities of the Mediterranean climate region of South Eastern Australia contain a varied mixture of herbaceous and woody plants. The ratio of herbaceous to woody plants changes along gradients of temperature, moisture and soil fertility. This study aimed to experimentally examine the relative importance of, and interactions between environmental controls (moisture and soil fertility) on the balance of dominant herbaceous (Triodia scariosa) and woody plants (e.g. Acacia ligulata and Leptospermum coriaceum) and their ultimate effects on fuel and fire regimes. The results suggest that environmental determinants of the growth of T. scariosa are likely to be more important than interactions with shrubs in controlling the distribution of T. scariosa. The growth of T. scariosa was consistently higher under hot temperatures and on the less fertile yellow sands, which dominate the south of the region. The results suggest that there is strong potential for the distribution and abundance of T. scariosa to be altered in the future with changes in temperature associated with climate change. The distribution of soil types across the Mediterranean climate region of South Eastern Australia may be predisposed to favour the southerly expansion of T. scariosa‐dominated communities in the future under a warmer climate.     

A hydrothermal time model explains the cardinal temperatures for seed germination

Temperature (T) and water potential (y) are two primary environmental regulators of seed germination. Seeds exhibit a base or minimum T for germination (T_b), an optimum T at which germination is most rapid (T_o), and a maximum or ceiling T at which germination is prevented (T_c). Germination at suboptimal T can be characterized on the basis of thermal time, or the T in excess of T_b multiplied by the time to a given germination percentage (t_g). Similarly, germination at reduced y can be characterized on a hydrotime basis, or t_g multiplied by the y in excess of a base or threshold y that just prevents germination (y_b). Within a seed population, the variation in thermal times to germination among different seed fractions (g) is based on a normal distribution of y_b values among seeds (y_b(g)). Germination responses across a range of suboptimal T and y can be described by a general hydrothermal time model that combines the T and y components, but this model does not account for the decrease in germination rates and percentages when T exceeds T_o. We report here that supra‐optimal temperatures shift the ψ_b(g) distribution of a potato (Solanum tuberosum L.) seed population to more positive values, explaining why both germination rates and percentages are reduced as T increases above T_o. A modified hydrothermal time model incorporating changes in ψ_b(g) at T > T_o describes germination timing and percentage across all T and ψ at which germination can occur and provides physiologically relevant indices of seed behaviour.     

Electron spin resonance study of the isolated lipid components from Blastocladiella emersonii zoospores

The physical properties of the plasma membrane of the aquatic phycomycete Blastocladiella emersonii were investigated, in particular the effects of cations on membrane structure. Intact zoospores and lipid extracts were labelled with the spin-labels 5-nitroxystearate (5-NS), 12-nitroxystearate (12-NS), and 2,2,6,6-tetramethylpiperidine-1-oxyl (Tempo). Electron spin resonance spectroscopy indicated a total of three breaks in plots of the hyperfine splitting parameter, 2T_|, order parameter, S, and the partition coefficient, f, vs. temperature. The first and third break points (T_L and T_H) were found to be independent of the external K⁺, Ca²⁺, or Mg²⁺ concentrations. They were similar to the break points found in aqueous dispersions of lipid extracts and correlate well with the temperature limits for zoospore viability. In contrast, the middle break point (T_M) was markedly influenced by the external Ca²⁺ concentration. Ca²⁺ increased T_M from 12°C (no Ca²⁺ added) to 22°C (10 mM Ca²⁺), i.e., growth temperature. K⁺ reversed this Ca²⁺ effect, downshifting T_M from 22°C to 10°C. A comparison of the physico-chemical effects of these ions on the membrane, as revealed by the cation-induced shift in T_M, is closely correlated with the temperature dependence and physiological effects of cations on zoospore differentiation. This suggests that cations may modify the physical state of the plasma membrane and be involved in regulating the initial changes during zoospore encystment.     

Life‐history traits of the common snook Centropomus undecimalis in a Caribbean estuary and large‐scale biogeographic patterns relevant to management

The ecology of common snook Centropomus undecimalis in Amatique Bay, a tropical estuary in eastern Guatemala, was investigated and life‐history traits were used to conduct a meta‐analysis of the species from Florida to Brazil. The reproduction cycle of C. undecimalis in Amatique was strongly related to the precipitation cycle, with a lag of 2 months. Spawning occurred from April to November with a peak spawning after the onset of the summer rains. Protandric sex reversal occurred early in the dry season (December) before somatic recovery from spawning. The growth cycle preceded that of body condition by c. 1 month, and was out of phase with the reproductive cycle. Growth was fast, as many individuals reached >70% of the maximum observed total length (L_T, 102 cm) after 3 years. Sex transition occurred within a relatively narrow L_T range (70–79 cm), but over a wide range of ages, indicating plasticity in this respect. The meta‐analysis indicated a latitudinal‐temperature gradient in life‐history traits, as well as different seasonal patterns relative to temperature and hydrographical cycles. Centropomus undecimalis from cooler winter waters (e.g. Florida) reach larger maximum L_T and L_T at sex change, as well as greater gonado‐somatic indices and longer life spans. Further, increased fishing mortality results in younger age at sex reversal and male predominance in the populations compared. Recognition of large‐scale biogeographic patterns in this important, but little studied, fish species helps in the formulation of management advice in other areas of its occurrence.     

Comparative genomics analysis of Nitriliruptoria reveals the genomic differences and salt adaptation strategies

The group Nitriliruptoria, recently classified as a separate class of phylum Actinobacteria, has five members at present, which belong to halophilic or halotolerant Actinobacteria. Here, we sequenced the genomes of Egicoccus halophilus EGI 80432^T and Egibacter rhizosphaerae EGI 80759^T, and performed a comparative genomics approach to analyze the genomic differences and salt adaptation mechanisms in Nitriliruptoria. Phylogenetic analysis suggested that Euzebya tangerina F10^T has a closer phylogenetic relationship to Euzebya rosea DSW09^T, while genomic analysis revealed highest genomic similarity with Nitriliruptor alkaliphilus ANL-iso2^T and E. halophilus EGI 80432^T. Genomic differences of Nitriliruptoria were mainly observed in genome size, gene contents, and the amounts of gene in per functional categories. Furthermore, our analysis also revealed that Nitriliruptoria possess similar synthesis systems of solutes, such as trehalose, glutamine, glutamate, and proline. On the other hand, each member of Nitriliruptoria species possesses specific mechanisms, K⁺ influx and efflux, betaine and ectoine synthesis, and compatible solutes transport to survive in various high-salt environments.

     

Ontogenetic diet changes in bottlenose dolphins (Tursiops truncatus) reflected through stable isotopes

The ability of stable isotope analysis to provide insight into ontogenetic dietary changes was examined using bottlenose dolphin tooth and skin samples. Teeth were subsampled to compare tissue produced early in life (outer tooth) to that produced later in life (inner tooth). Outer tooth had significantly higher δ¹⁵N values than the corresponding inner sample from the same tooth (n= 60, P= 0.0041), indicating that there was a temporal shift to a lower δ¹⁵N diet. There were no significant δ¹³C differences. Higher δ¹⁵N values in young have previously been attributed to the period of suckling. Analysis of skin tissue from stranded animals of different developmental stages similarly indicated that the δ¹⁵N values were significantly higher in young animals. Further comparisons indicated that the primary influence for this difference was animals with lengths less than or equal to the largest neonatal dolphin. This difference likely reflects an ontogenetic dietary shift from a sole reliance on milk to a combination of milk and prey species during the first year of life.     

Declining expression of a single epithelial cell‐autonomous gene accelerates age‐related thymic involution

Age‐related thymic involution may be triggered by gene expression changes in lymphohematopoietic and/or nonhematopoietic thymic epithelial cells (TECs). The role of epithelial cell‐autonomous gene FoxN1 may be involved in the process, but it is still a puzzle because of the shortage of evidence from gradual loss‐of‐function and exogenous gain‐of‐function studies. Using our recently generated loxP‐floxed‐FoxN1(fx) mouse carrying the ubiquitous CreER^T (uCreER^T) transgene with a low dose of spontaneous activation, which causes gradual FoxN1 deletion with age, we found that the uCreER^T‐fx/fx mice showed an accelerated age‐related thymic involution owing to progressive loss of FoxN1⁺ TECs. The thymic aging phenotypes were clearly observable as early as at 3–6 months of age, resembling the naturally aged (18–22‐month‐old) murine thymus. By intrathymically supplying aged wild‐type mice with exogenous FoxN1‐cDNA, thymic involution and defective peripheral CD4⁺ T‐cell function could be partially rescued. The results support the notion that decline of a single epithelial cell‐autonomous gene FoxN1 levels with age causes primary deterioration in TECs followed by impairment of the total postnatal thymic microenvironment, and potentially triggers age‐related thymic involution in mice.     

Oryzicola mucosus gen. nov., sp. nov., a novel slime producing bacterium belonging to the family Phyllobacteriaceae isolated from the rhizosphere of rice plants

A novel Gram-stain negative, asporogenous, slimy, rod-shaped, non-motile bacterium ROOL2^T was isolated from the root samples collected from a rice field located in Ilsan, South Korea. Phylogenetic analysis of the 16S rRNA sequence showed 96.5% similarity to Tianweitania sediminis Z8^T followed by species of genera Mesorhizobium (96.4–95.6%), Aquabacterium (95.9–95.7%), Rhizobium (95.8%) and Ochrobactrum (95.6%). Strain ROOL2^T grew optimally at 30 °C in the presence of 1–6% (w/v) NaCl and at pH 7.5. The major respiratory quinone was ubiquinone-10 and the major cellular fatty acids were C_18:1ω7c, summed feature 4 (comprising iso-C_17:1 I and/or anteiso-C_17:1 B) and summed feature 8 (comprising C_18:1ω6c and/or C_18:1ω7c). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylmethylethanolamine, phosphatidylglycerol, one unidentified aminolipid and two unidentified lipids. The assembled draft genome of strain ROOL2^T had 28 contigs with N50 value of 656,326 nt, total length of 4,894,583 bp and a DNA G?+?C content of 61.5%. The average amino acid identity (AAI) values of strain ROOL2^T against the genomes of related members belonging to the same family were below 68% and the ANI and dDDH values between the strain ROOL2^T and the type strains of phylogenetically related species were 61.8–76.3% and 19.4–21.1%, respectively. Strain ROOL2^T only produces carotenoid-type pigment when grown on LB agar and slime on R2A agar. In the presence of tryptophan, strain ROOL2^T produced indole acetic acid (IAA), a phytohormone in plant growth and development. Gene clusters for indole-3-glycerol phosphatase and tryptophan synthase were found in the genome of strain ROOL2^T. The genotypic and phenotypic characteristics indicated that strain ROOL2^T represents a novel genus belonging the family Phyllobacteriaceae, for which the name Oryzicola mucosus gen. nov., sp. nov. is proposed. The type strain is ROOL2^T (KCTC 82711 ^T?=?NBRC 114717 ^T).

     

Seasonal changes in temperature response of photosynthesis and its contribution to annual carbon gain in Daphniphyllum humile,an evergreen understorey shrub

We evaluated seasonal variation in photosynthetic temperature dependence and its contribution to annual carbon gain in an evergreen understorey shrub, Daphniphyllum humile Maxim, growing at the forest border and in the understorey of a deciduous forest. Plants at both sites exhibited similar optimal temperatures for photosynthesis (T_opt). The activation energy for ribulose‐1,5‐bisphosphate (RuBP) carboxylation (H_aV) at both sites tended to be higher in summer than in spring or autumn, suggesting that H_aV may be the controlling factor in the T_opt shift in D. humile. In contrast to the seasonal changes in T_opt, the maximum photosynthetic rate at the optimal temperature (P_opt) differed between the two sites: it was lower in autumn than in summer at the forest border, but was the same in summer and autumn in the understorey. In the understorey plants, nitrogen content (N_area) increased in autumn, but this was not the case for forest border plants. In addition, Rubisco content increased significantly in autumn in the understorey leaves but decreased distinctly in forest border leaves. Increased N_area and Rubisco in understorey leaves resulted in increased in photosynthesis in autumn. Annual carbon gain was 30.8 mol·m^?2 in forest border leaves and 5.8 mol·m^?2 in understorey leaves. Carbon gain in understorey leaves during the short period after overstorey leaf fall and before snow accumulation was approximately 49% of annual carbon gain. Furthermore, autumn carbon gain calculated using activation energy of summer with autumn photosynthetic parameters underestimated the autumn carbon gain by as much as 31%. In conclusion, photosynthetic temperature acclimation may be a key factor in increasing annual carbon gain in understorey D. humile.