Scaling of species diversity and body mass in mammals: Cope’s rule and the evolutionary cost of large size

Abstract

Equations are constructed describing the inverse correlation of species diversity and body mass in extant and Cenozoic mammals. Cope’s rule, the tendency for many mammal clades to increase in body size through time, through phyletic change in single lineages or turnover within species groups, is interpreted as a probability function reducing diversity potential as a tradeoff for ecological/evolutionary gains. The inverse rule predicts that large species in clades will be less diverse than smaller species and, unless origination rates remain high among smaller clade members, clades conforming to Cope’s rule will decline in diversity, moving towards extinction. This proposition is evaluated in the Cenozoic histories of five North American mammal clades; cotton rats, felids, canids, hyaenodontids, and equids. Diversity potential of different size classes within the 3.75 million year phyletic history of the muskrat, Ondatra zibethicus, is also examined. A corollary prediction of the inverse rule, that large species should have longer durations (species lifespans) than small species, is unresolved. Successful clades maintain small size or a significant number of smaller species relative to clade average size. The potential loss of unique extant large mammal species justifies the conservation effort to protect them. The similarity of scaling exponents of species diversity to mass around a slope of -1.0 suggests that species diversity is correlated with home range size, the latter related to the probability of population fragmentation.     

Rutin as promising drug for the treatment of Parkinson’s disease: an assessment of MAO-B inhibitory potential by docking,molecular dynamics and DFT studies

ABSTRACT

Inhibitors of monoamine oxidase (MAO)-B have been used for many years in the therapy of Parkinson’s disease (PD). Owing to the safety concerns of the currently used agents, the discovery of novel scaffolds is of considerable interest. MAO-B inhibitory potential of rutin, a flavonoid derived from natural sources, has been established in experimental findings. Hence, the current study seeks to examine the interactions between rutin and crystal structure of human MAO-B enzyme. Molecular docking calculations, as well as molecular dynamics simulations, were employed to investigate the binding mode and the stability of the rutin/MAO-B complex. Energies of highest occupied/lowest unoccupied molecular orbitals were computed through DFT studies and used to calculate electron affinity, hardness, chemical potential, electronegativity, and electrophilicity index in order to investigate the capability of these parameters to influence the ligand–receptor interactions. It was found that rutin traverses both the entrance cavity and the substrate cavity, forcing the Ile-199 ‘gate’ to rotate into its open conformation. It results in the fusion of the two cavities of the MAO-B binding site and directly leads to better binding interactions. Results of the current study can be used for lead modification and development of novel drugs for the treatment of PD.     

Study of PE and iPP orientations on the surface of carbon nanotubes by using molecular dynamic simulations

In this study, the early stage of interfacial crystallisation behaviour of low molecular weight polyethylene (PE) and isotactic polypropylene (iPP) oligomer on the surface of carbon nanotubes (CNTs) with different diameters, chiralities and topography structures was studied using MD simulations. We started to simulate the effect of CNTs chirality and diameter on PE molecular chain orientation, and then the effect of CNTs topography structure on PE and iPP molecular chain orientation was investigated. Finally, some experiments were carried out to prove the simulated results. Our study shows that for CNTs with a diameter comparable with the radius of gyration (R_g) of a polymer chain, an easy orientation of PE chains along CNTs axis is observed for all the systems of the CNTs with different chiralities due to a geometric confinement effect. For CNTs with a much larger diameter, multiple orientation of PE chains is induced on its surface due to the lattice matching between graphite lattice and PE molecular chains. In this case, the chirality of CNTs dominates the orientation of graphite lattice, which determines the orientation of PE chains arrangement on CNTs surface. More importantly, it was found that the groove structure formed by CNT bundles is very useful for the stabilisation of polymer chain, and thus facilitates the orientation of molecular chain along the long axis of CNTs. As a result, a novel nanohybrid shish–kebab (NHSK) structure with CNTs acting as central shish while polymer lamellae as kebab can be successfully obtained for both PE with zigzag conformation and iPP with helical conformation. This simulation result was well supported by the experimental observation. Our study could provide not only a deep understanding of the origin of the polymer chain orientation on CNTs surface but also the guidance for the preparation of polymer/CNTs nanocomposites with novel NHSK structure.     

Studies On The Cross Strand Hydrogen Bonds In DNA Double Helices

Abstract

A systematic analysis has been carried out to examine all the stereochemically possible bifurcated hydrogen bonds including those of cross strand type between propeller twisted base pairs in DNA double helices by stereochemical considerations involving base pairs alone and by molecular mechanics studies on dimer and trimer duplexes. The results show that there are limited number of combinations of adjacent base pairs that would facilitate bifurcated cross- strand hydrogen bond (CSH). B-type helices concomitant with negative propeller twist seem to be more favored for the occurrence of CSH than canonical A-type helices because of slide in the latter. The results also demonstrate that helices with appropriate sequences may possess continuous run of these propeller twist driven cross strand hydrogen bonds indicating that they may infact be considered as yet another general structural feature of DNA helices.     

Compensatory nature of Chargaff’s second parity rule

The second parity rule of Chargaff (A≈T and G≈C within one strand) holds all over the living world with minor exceptions. It is maintained with higher accuracy for long sequences. The question addressed in the article is how different sequence types, with different biases from the parity, contribute to the general effect. It appears that the sequence segments with biases of opposite sign are intermingled, so that with sufficient sequence lengths the parity is established. The parity rule seems to be a cumulative result of a number of independent processes in the genome evolution, with the parity as their intrinsic property. Symmetrical appearance of simple repeats and of Alu sequences in the human DNA strands, and other contributions to the Chargaff parity II rule are discussed.     

Identification of DNA-binding proteins by incorporating evolutionary information into pseudo amino acid composition via the top-n-gram approach

DNA-binding proteins are crucial for various cellular processes and hence have become an important target for both basic research and drug development. With the avalanche of protein sequences generated in the postgenomic age, it is highly desired to establish an automated method for rapidly and accurately identifying DNA-binding proteins based on their sequence information alone. Owing to the fact that all biological species have developed beginning from a very limited number of ancestral species, it is important to take into account the evolutionary information in developing such a high-throughput tool. In view of this, a new predictor was proposed by incorporating the evolutionary information into the general form of pseudo amino acid composition via the top-n-gram approach. It was observed by comparing the new predictor with the existing methods via both jackknife test and independent data-set test that the new predictor outperformed its counterparts. It is anticipated that the new predictor may become a useful vehicle for identifying DNA-binding proteins. It has not escaped our notice that the novel approach to extract evolutionary information into the formulation of statistical samples can be used to identify many other protein attributes as well.     

Clock gene PERIOD3 polymorphism is associated with susceptibility to Graves’ disease but not to Hashimoto’s thyroiditis

ABSTRACT

Circadian disruption has been linked with immune-related morbidities including autoimmune diseases. PERIOD3 (PER3) clock gene is a key player in the mammalian circadian system. This study evaluated the possible association of PER3 rs2797685 (G/A) polymorphism and susceptibility of autoimmune thyroid diseases (AITD) and assessed if this SNP contributes to disease characteristics and serum levels of interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α). The PER3 rs2797685 (G/A) polymorphism was assessed in 125 patients with AITD [Graves’ disease (GD), 69; Hashimoto’s thyroiditis (HT), 56] and 115 unrelated healthy controls. Subjects carrying at least one variant allele of PER3 rs2797685 (GA+AA) had increased risk for GD (OR 1.9, 95% CI 1–3.61, p= .05). There were no differences in the frequencies of genotypes and alleles of the PER3 rs2797685 polymorphism between HT patients and control subjects. No association was observed between genotypes of the studied SNP and any of the disease characteristics in GD and HT patients. The GA+AA genotype of PER3 rs2797685 was associated with lower levels of IL-6 in patients with Graves’ disease. There were no differences between genotypes of the studied SNP regarding TNF-α levels in GD, HT or control groups. In conclusion, this study provides the first evidence for a genetic association between GD and the PER3 gene, highlighting the possible relevance of polymorphisms in clock genes in the etiopathogenesis of AITD. However, functional studies to identify the underlying molecular mechanisms of this association are needed to translate these findings to clinical applications.     

Sleep/wake patterns and circadian typology in preschool children based on standardized parental self-reports

We studied the sleep/wake patterns and circadian typology of Japanese preschool children living in the Tokyo metropolitan area (193 boys and 190 girls, 4–6 years of age) from June to July 2012 based on a standardized parental self-reporting questionnaire. Our major findings are as follows: (1) sleep/wake timing was delayed, and the duration of nocturnal sleep (sleep period as well as time in bed) increased from that on scheduled days (weekdays) to that on free days (weekends) for all ages. (2) The duration of daily sleep (24?h), including daytime nap, was longer for 4-year-old children compared with that in 5- to 6-year-old children, but not significantly different between scheduled and free days within each age group. (3) The distribution of chronotypes was 36.3% for morning (M)-type, 48.8% for neither (N)-type and 11.2% for evening (E)-type, and this distribution was independent of sex or age. (4) Sleep/wake timing delays were observed from M-type and N-type to E-type during scheduled and free days. (5) The duration of nocturnal sleep decreased but increased for 24-h sleep time from M-type and N-type to E-type on scheduled days. (6) Sleep durations did not differ among chronotypes on free days. (7) Chronotypes were associated with parents’ diurnal preferences, mealtimes and attendance at kindergartens or childcare centers but not with sex, age, season of birth, exposure to multimedia or exposure to morning sunlight in their bedrooms. When these results were compared with those for older children and adolescents, similar sleep/wake patterns and circadian typology were observed, although to a lesser degree, in children as young as 4–6 years of age. Napping may compensate, in part, for an accumulated weekday sleep deficit. The distribution of chronotypes was associated with differences in sleep/wake timing and duration and was influenced by the parents’ diurnal preferences and lifestyles. Further research on preschool children is required to investigate whether circadian typology affects their behavioral, emotional and cognitive development.     

METAMORPHOSIS OF THE LARVA OF THE POLYCHAETE ARENICOLA CRISTATA. MORPHOLOGY OF THE ‘HOUR-GLASS’ STAGE

The constricted ‘waist’ of the metamorphosing larva of the polychaete Arenicola cristata is described, using light and electron microscopy. The constriction is shown to be the consequence of the discharge and collapse of a post-trochal ring of epithelial cells which remain as functional components of the post-metamorphic juvenile. Morphological differentiation of neuro-effector and interneuronal contacts is initiated at this time. Muscular and neural changes are discussed in terms of their role in effecting metamorphosis.     

The ‘other side’ of embedded ness: A case‐study of the interplay of economy and ethnicity

As interest in ethnics and their entrepreneurial activities has grown in recent years, sociologists have come to emphasize the importance of ethnic social structures as the source of actions propelling business growth. In a sign of convergence with the ‘new economic sociology’, recent literature suggests that embeddedness in ethnic networks and communities leads to cooperative, if not conformist, behaviour among ethnic economic actors. This article looks at the ‘other side’ of embeddedness, through a case‐study of African‐American, Caribbean, Korean and white construction contractors in New York City. I argue that, in construction, the embeddedness of economic behaviour in ongoing social relations among a myriad of social actors impedes access to outsiders. Embeddedness contributes to the liabilities of newness that all neophytes encounter, breeding a preference for established players with track records. However, the convergence of economic and ethnic ties has a further baneful effect, since outsiders also fall outside those networks that define the industrial community. While African‐American, Caribbean and Korean outsiders all experience these barriers in similar ways, they differ in the adaptive strategies that they have pursued. African Americans appear to be most disadvantaged, in part because they have been the most exposed to the social closure that results from the mobilization of white ethnics’ social capital. By contrast, Caribbeans and Koreans entered the labour market in societies where racial domination played little or no role in labour market outcomes ‐ a considerable asset since construction skills are transferable from one society to another. The Koreans appear to be the most embedded in ethnic networks, through which they secure jobs and skilled labour, though class factors play a role here as well and even the Koreans must reach out beyond the ethnic community for a clientele. By contrast, ethnic solidarity operates less powerfully among the black contractors, who are tied to a community where intra‐ethnic diversity and internal competition have grown as a result of immigration. In the absence of an ethnic market, black'entrepreneurs turn to the state, whose requirements and dependence on union labour expose black builders to risks from which their Korean counterparts are sheltered.