mtDNA diversity in rhesus monkeys reveals overestimates of divergence time and paraphyly with neighboring species

Reconstructions of the human-African great ape phylogeny by using mitochondrial DNA (mtDNA) have been subject to considerable debate. One confounding factor may be the lack of data on intraspecific variation. To test this hypothesis, we examined the effect of intraspecific mtDNA diversity on the phylogenetic reconstruction of another Plio- Pleistocene radiation of higher primates, the fascicularis group of macaque (Macaca) monkey species. Fifteen endonucleases were used to identify 10 haplotypes of 40-47 restriction sites in M. mulatta, which were compared with similar data for the other members of this species group. Interpopulational, intraspecific mtDNA diversity was large (0.5%- 4.5%), and estimates of divergence time and branching order incorporating this variation were substantially different from those based on single representatives of each species. We conclude that intraspecific mtDNA diversity is substantial in at least some primate species. Consequently, without prior information on the extent of genetic diversity within a particular species, intraspecific variation must be assessed and accounted for when reconstructing primate phylogenies. Further, we question the reliability of hominoid mtDNA phylogenies, based as they are on one or a few representatives of each species, in an already depauperate superfamily of primates.      

The in vitro effects of opines and other compounds on DNAs originating from bacteria, and from healthy and tumorous plant tissues

Purified total DNAs were isolated from oncogenic or nononcogenic Agrobacterium tumefaciens cells as well as from normal and crown gall tissues. Opines (octopine, nopaline, lysopine), plant hormone (auxin IAA) and some carcinogenic compounds were used in order to correlate their effects on in vitro strand separation and synthesis of DNAs with in vivo tumorous cell multiplication. Octopine (or nopaline) induced chain opening of DNAs originating from octopine (or nopaline)-metabolizing bacteria and from same bacteria strain-induced tumorous cells. This phenomenon was measured by the increase in DNA hyperchromicity which is concentration dependent. The tested compounds stimulated the in vitro synthesis of the same DNAs. Under the same conditions, in vitro strand separation and synthesis of healthy plant DNA was not (or only slightly) enhanced, except in the case of particular hormone-connected healthy cell DNA. IAA and carcinogens stimulated in vitro synthesis and induced in vitro strand separation (dose-dependent effect) of DNAs isolated from crown gall cells and inducing bacteria. Compared to healthy cell DNAs, these DNAs were thus susceptible to structurally very diversified molecules and in this way behave as do mammalian tissue DNAs. The opine and IAA actions observed here were specific for plant tissue DNA; cancerous human or animal tissue DNAs were insensitive. By their presence in the crown gall cells, opines possibly maintain destabilized areas (required for rapid growth and division) on tumor cell DNA. The cooperative actions of IAA and opines as well as small RNA and RNA fragments on gene activation, might explain the autonomy of plant tumor cells.     

Isolation and characterization of highly liganded protein from brewer's barley grain

Two basic proteins, HLP-1 and HLP-2, were isolated from brewer's barley grain (Hordeum vulgare L.) and characterized as glycoproteins with molecular masses of 16 and 13 kDa and pI values of 7.4 and 8.8, respectively. They could bind sugars, metal ions, and both hydrophobic and hydrophylic molecules of low molecular mass. These characteristics may be related to their potential plant-protecting role.     

"Skittish" Abca2 knockout mice display tremor, hyperactivity, and abnormal myelin ultrastructure in the central nervous system

The ATP-binding cassette transporter 2 (ABCA2) is an endolysosomal protein most highly expressed in the central and peripheral nervous system tissues and macrophages. Previous studies indicated its role in cholesterol/steroid (estramustine, estradiol, and progesterone) trafficking/sequestration, oxidative stress response, and Alzheimer's disease. Developmental studies have shown its expression during macrophage and oligodendrocyte differentiation, processes requiring membrane growth. To determine the in vivo function(s) of this transporter, we generated a knockout mouse from a gene-targeted disruption of the murine ABCA2 gene. Knockout males and females are viable and fertile. However, a non-Mendelian inheritance pattern was shown among male progeny of heterozygous crosses. Compared to wild-type and heterozygous littermates, knockout mice displayed a tremor without ataxia, hyperactivity, and reduced body weight; the latter two phenotypes were more marked in females than in males. This sexual disparity suggests a role for ABCA2 in hormone-dependent neurological and/or developmental pathways. Myelin sheath thickness in the spinal cords of knockout mice was greatly increased compared to that in wild-type mice, while a significant reduction in myelin membrane periodicity (compaction) was observed in both spinal cords and cerebra of knockout mice. Loss of ABCA2 function in vivo resulted in abnormal myelin compaction in spinal cord and cerebrum, an ultrastructural defect that we propose to be the cause of the phenotypic tremor.     

Particular RNA fragments as promoters of leukocyte and platelet formation in rabbits.

Under well-defined conditions, ribosomal RNA from Escherichia coli is fragmented by pancreatic ribonuclease, leading to the appearance of particular RNA fragments. Some of these fragments act as primers for in vitro replication of DNA extracted from blood-cell and platelet-forming tissues. In experimental rabbits they restore in a rapid and harmless way normal circulating leukocyte and platelet levels when these have been drastically decreased by various chemotherapeutic agents mainly used in anticancer therapy. Imbalance between polynuclear and lymphocyte count provoked in rabbits by cyclophosphamide can be rapidly corrected by treating the animal with active RNA fragments.     

Particular small size RNA and RNA fragments from different origins as tumor inducing agents in Datura stramonium

Particular RNA fragments obtained by action of pancreatic ribonuclease on purified RNAs originating from species totally unrelated to Agrobacterium tumefaciens (Escherichia coli, rabbit, monkey) are capable of inducing the formation of transplantable tumorous tissue when introduced at wounded sites in inverted stems of Datura stramonium maintained under axenic conditions on a medium containing auxin and kinetin. Reovirus RNA and a small size RNA (5–6 S) isolated from RNA bound RNA directed DNA polymerase from Escherichia coli also induced the appearance of tumorous tissues which grow on solid synthetic medium in the absence of auxin and kinetin.     

A Reexamination of Correlations of Amino Acids with Particular Secondary Structures

Using the data from Protein Data Bank the correlations of primary and secondary structures of proteins were analyzed. The correlation values of the amino acids and the eight secondary structure types were calculated, where the position of the amino acid and the position in sequence with the particular secondary structure differ at most 25. The diagrams describing these results indicate that correlations are significant at distances between −9 and 10. The results show that the substituents on Cβ or Cγ atoms of amino acid play major role in their preference for particular secondary structure at the same position in the sequence, while the polarity of amino acid has significant influence on α-helices and strands at some distance in the sequence. The diagrams corresponding to polar amino acids are noticeably asymmetric. The diagrams point out the exchangeability of residues in the proteins; the amino acids with similar diagrams have similar local folding requirements. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.