Group additive modeling of substituent effects in monocyclic aromatic hydrocarbon radicals

The thermodynamic properties of the unsubstituted and substituted phenyl, phenoxy, anisyl, benzoyl, styryl and benzyl radicals with six substituents (hydroxy, methoxy, formyl, vinyl, methyl, and ethyl) are calculated with the bond additivity corrected (BAC) post-Hartree-Fock G4 method. Bond dissociation energies of monocyclic aromatic hydrocarbons are calculated and used to identify substituent interactions in these radicals. Benson's Group Additivity (GA) scheme is extended to aromatic radicals by defining 6 GAV and 29 NNI parameters through least squares regression to a database of thermodynamic properties of 369 radicals. Comparison between G4/BAC and GA calculated thermodynamic values shows that the standard enthalpies of formation generally agree within 4 kJ mol−1, whereas the entropies and the heat capacities deviate less than 4 J mol−1 K−1

Repression of Mitochondrial Translation, Respiration and a Metabolic Cycle-Regulated Gene, SLF1, by the Yeast Pumilio-Family Protein Puf3p

Synthesis and assembly of the mitochondrial oxidative phosphorylation (OXPHOS) system requires genes located both in the nuclear and mitochondrial genomes, but how gene expression is coordinated between these two compartments is not fully understood. One level of control is through regulated expression mitochondrial ribosomal proteins and other factors required for mitochondrial translation and OXPHOS assembly, which are all products of nuclear genes that are subsequently imported into mitochondria. Interestingly, this cadre of genes in budding yeast has in common a 3′-UTR element that is bound by the Pumilio family protein, Puf3p, and is coordinately regulated under many conditions, including during the yeast metabolic cycle. Multiple functions have been assigned to Puf3p, including promoting mRNA degradation, localizing nucleus-encoded mitochondrial transcripts to the outer mitochondrial membrane, and facilitating mitochondria-cytoskeletal interactions and motility. Here we show that Puf3p has a general repressive effect on mitochondrial OXPHOS abundance, translation, and respiration that does not involve changes in overall mitochondrial biogenesis and largely independent of TORC1-mitochondrial signaling. We also identified the cytoplasmic translation factor Slf1p as yeast metabolic cycle-regulated gene that is repressed by Puf3p at the post-transcriptional level and promotes respiration and extension of yeast chronological life span when over-expressed. Altogether, these results should facilitate future studies on which of the many functions of Puf3p is most relevant for regulating mitochondrial gene expression and the role of nuclear-mitochondrial communication in aging and longevity

Ancient mtDNA Genetic Variants Modulate mtDNA Transcription and Replication

Although the functional consequences of mitochondrial DNA (mtDNA) genetic backgrounds (haplotypes, haplogroups) have been demonstrated by both disease association studies and cell culture experiments, it is not clear which of the mutations within the haplogroup carry functional implications and which are “evolutionary silent hitchhikers”. We set forth to study the functionality of haplogroup-defining mutations within the mtDNA transcription/replication regulatory region by in vitro transcription, hypothesizing that haplogroup-defining mutations occurring within regulatory motifs of mtDNA could affect these processes. We thus screened >2500 complete human mtDNAs representing all major populations worldwide for natural variation in experimentally established protein binding sites and regulatory regions comprising a total of 241 bp in each mtDNA. Our screen revealed 77/241 sites showing point mutations that could be divided into non-fixed (57/77, 74%) and haplogroup/sub-haplogroup-defining changes (i.e., population fixed changes, 20/77, 26%). The variant defining Caucasian haplogroup J (C295T) increased the binding of TFAM (Electro Mobility Shift Assay) and the capacity of in vitro L-strand transcription, especially of a shorter transcript that maps immediately upstream of conserved sequence block 1 (CSB1), a region associated with RNA priming of mtDNA replication. Consistent with this finding, cybrids (i.e., cells sharing the same nuclear genetic background but differing in their mtDNA backgrounds) harboring haplogroup J mtDNA had a >2 fold increase in mtDNA copy number, as compared to cybrids containing haplogroup H, with no apparent differences in steady state levels of mtDNA-encoded transcripts. Hence, a haplogroup J regulatory region mutation affects mtDNA replication or stability, which may partially account for the phenotypic impact of this haplogroup. Our analysis thus demonstrates, for the first time, the functional impact of particular mtDNA haplogroup-defining control region mutations, paving the path towards assessing the functionality of both fixed and un-fixed genetic variants in the mitochondrial genome

Bacteriophage-Resistant Mutants in Yersinia pestis: Identification of Phage Receptors and Attenuation for Mice

Background: Bacteriophages specific for Yersinia pestis are routinely used for plague diagnostics and could be an alternative to antibiotics in case of drug-resistant plague. A major concern of bacteriophage therapy is the emergence of phageresistant mutants. The use of phage cocktails can overcome this problem but only if the phages exploit different receptors. Some phage-resistant mutants lose virulence and therefore should not complicate bacteriophage therapy. Methodology/Principal Findings: The purpose of this work was to identify Y. pestis phage receptors using site-directed mutagenesis and trans-complementation and to determine potential attenuation of phage-resistant mutants for mice. Six receptors for eight phages were found in different parts of the lipopolysaccharide (LPS) inner and outer core. The receptor for R phage was localized beyond the LPS core. Most spontaneous and defined phage-resistant mutants of Y. pestis were attenuated, showing increase in LD 50 and time to death. The loss of different LPS core biosynthesis enzymes resulted in the reduction of Y. pestis virulence and there was a correlation between the degree of core truncation and the impact on virulence. The yrbH and waaA mutants completely lost their virulence. Conclusions/Significance: We identified Y. pestis receptors for eight bacteriophages. Nine phages together use at least seven different Y. pestis receptors that makes some of them promising for formulation of plague therapeutic cocktails. Most phage-resistant Y. pestis mutants become attenuated and thus should not pose a serious problem for bacteriophag

Chronology of holocene climate and vegetation changes and their connection to cultural dynamics in Southern Siberia

Two sediment sequences from Big Kyzykul Lake and the Shushenskoe paleolake in the Minusinsk depression, Southern Siberia, were studied by pollen, microfossil, and geochemical analyses, as well as radiocarbon dating. The records indicate the persistence of an arid period between ~11.7–7.6 cal kyr BP, increased effective moisture since ~7.6 cal kyr BP, 2 humid impulses at ~5.1 and 2.8 cal kyr BP separated by a dry interval, and the return to generally drier conditions after ~1.5 cal kyr BP. This is contrary to the findings noted for the Eurasian temperate zone, but agrees with proxy data reported for arid and semi-arid zones of Central Asia. Reconstructed changes in climate and environment are in good agreement with archaeological data. Almost no evidence of the Mesolithic-Neolithic cultures has been reported for the depression, which is consistent with a dry early and mid-Holocene. Effective moisture started to rise from ~7.6 cal kyr BP, followed by the beginning of human occupation at ~6 cal kyr BP. Two maxima of humidity are recorded in the late Holocene, corresponding to the arrival of trees in the depression. No gap was to be found from the Early Bronze to the Iron ages cultures at this time, with the exception of a dry interval at ~3.6–3.3 cal kyr BP, when the Minusinsk depression was sparsely occupied. The data obtained suggest a close relationship between climate change and cultural dynamics in the steppe zone of Southern Siberia.