How does the genetic assassin select its neuronal target?

Through many different routes of analysis, including human familial studies and animal models, we are identifying an increasing number of genes that are causative for human neurodegenerative disease and are now in a position for many such disorders to dissect the molecular pathology that gives rise to neuronal death. Yet a paradox remains: The majority of the genes identified cause neurodegeneration in specific neuronal subtypes, but the genes themselves are ubiquitously expressed. Furthermore, the different mutations in the same gene may cause quite different types of neurodegeneration. Something in our understanding of neurodegenerative disease is clearly missing, and we refer to this as the phenomenon of ??neuronal targeting.?? Here we discuss possible explanations for neuronal targeting, why specific neuronal subtypes are vulnerable to specific mutations in ubiquitously expressed genes.     

Human grief: Is its intensity related to the reproductive value of the deceased?

Thurstone's method of comparative judgement was used to measured the intensity of grief that parents of high-, moderate-, and low-reproductive value were expected to experience at the death of male and female children of different ages. The results were correlated with reproductive values for male and female British Columbians and for !Kung Bushwomen. Grief ratings were more highly correlated with reproductive value than with age and more highly correlated with reproductive values of !King Bushwomen than with those of British Columbians. The correlations were higher for male- than for female-stimulus children. The correlations of female ratings with reproductive value were higher than male ratings with reproductive value, although not as high as expected. However, the correlation between grief ratings and reproductive value did not increase as the reproductive value of the raters declined.     

The circadian cycle: is the whole greater than the sum of its parts?

The term 'circadian rhythm' describes an oscillatory behavior in the absence of exogenous environmental cues, with a period of about a day. As yet, we don't fully understand which biological mechanisms join together to supply a stable and self-sustained oscillation with such a long period. By chipping away at the molecular mechanism with genetic approaches, some common features are emerging. In combining molecular analyses and physiological experiments, those features that are crucial for structuring a circadian day could be uncovered.     

Does the growth temperature of a prokaryote influence the purine content of its mRNAs?

The formation and breaking of hydrogen bonds between nucleic acid bases are dependent on temperature. The high G+C content of organisms was surmised to be an adaptation for high temperature survival because of the thermal stability of G:C pairs. However, a survey of genomic GC% and optimum growth temperature (OGT) of several prokaryotes revoked any direct relation between them. Significantly high purine (R=A or G) content in mRNAs is also seen as a selective response for survival among thermophiles. Nevertheless, the biological relevance of thermophiles loading their unstable mRNAs with excess purines (purine-loading or R-loading) is not persuasive. Here, we analysed the mRNA sequences from the genomes of 168 prokaryotes (as obtained from NCBI Genome database) with their OGTs ranging from -5 °C to 100 °C to verify the relation between R-loading and OGT. Our analysis fails to demonstrate any correlation between R-loading of the mRNA pool and OGT of a prokaryote. The percentage of purine-loaded mRNAs in prokaryotes is found to be in a rough negative correlation with the genomic GC% (r(2)=0.655, slope=-1.478, P<000.1). We conclude that genomic GC% and bias against certain combinations of nucleotides drive the mRNA-synonymous (sense) strands of DNA towards variations in R-loading.     

Leprosy – clues about the biochemistry of Mycobacterium leprae and its host-dependency from the genome

Deletions and the appearance of pseudogenes in pathways of carbon source utilisation and energy metabolism best explain the host-dependency and failure to culture Mycobacterium leprae axenically. From the genome sequence it is possible to predict that acetate and galactose cannot be used as carbon sources, while pyruvate can only be catabolised. Glycerol, glucose, and fatty acids could be used for glycolysis, the pentose cycle and -oxidation which are complete. Retrospective functional genomics – interpreting work before the completion of the genome project – supports the failure of M. leprae to use acetate as well as another prediction that metabolic flux from pyruvate to acetyl-CoA would be very low. However, the loss of a second icd gene (compared with M. tuberculosis), predicted to encode isocitrate dehydrogenase, did not diminish the specific activity of the enzyme. The genes for respiratory pathways are extremely limited, being present for oxidative phosphorylation as a result of electron transport only using FADH as an electron donor. In contrast, all the major biosynthetic pathways are complete except that M. leprae is a natural methionine auxotroph: this is predicted not to be attenuating, or explain host-dependency since methionine would be present in rich culture media.     

Malaria: Could its unusual epigenome be the weak spot?

The epigenetic contribution to the regulation and maintenance of gene expression patterns by histone modifications is well established in eukaryotes. In Plasmodium falciparum, the mechanisms and factors regulating gene expression during progression through its infected red blood cell cycle (iRBC) and underlying mutually exclusive expression of antigenic variation genes involved in immune evasion are far from understood. Recently, the first comprehensive analyses of the P. falciparum chromatin landscape at different iRBC stages have been performed. These studies uncovered the existence of well-defined heterochromatic regions within a generally euchromatic epigenome. Notably, silencing of genes encoding for virulence determinants such as var genes, appears to be orchestrated by the concerted action of the Sir2 and HP1 orthologs and the presence of the histone mark, H3K9me3. Epigenetic speciation could make the parasite exquisitely vulnerable to epigenetic drug treatment, unless this deadly parasite still has a number of tricks up his sleeves.     

Was the Scanner Calibration Slide used for its intended purpose?

In the article, Scanner calibration revisited, BMC Bioinformatics 2010, 11:361, Dr. Pozhitkov used the Scanner Calibration Slide, a key product of Full Moon BioSystems to generate data in his study of microarray scanner PMT response and proposed a mathematic model for PMT response [1]. In the end, the author concluded that "Full Moon BioSystems calibration slides are inadequate for performing calibration," and recommended "against using these slides." We found these conclusions are seriously flawed and misleading, and his recommendation against using the Scanner Calibration Slide was not properly supported.     

pRb or its cousins: Who controls the family business?

Comment on: Bazarov A, et al. Cell Cycle 2012; 11:1008–1013More than 90% of human cancers are of epithelial origin. Cellular senescence of human mammary epithelial cells (HMECs) is an important barrier that protects cells from immortalization; the first step in breast cancer development.¹ Although induction of tumor suppressor p16 is not evident in some types of normal human fibroblasts undergoing senescence,² in cultured HMECs, senescence occurs by a robust p16 induction, and cells that acquire silencing of p16Ink4a locus eventually proliferate and undergo senescence again by telomere shortening in a p53-dependent manner.¹ Therefore, p16 induction is a critical barrier to immortalize HMECs in culture. p16 inhibits kinase activity of Cdk4/6-cyclinD complexes, which inactivate three pRb family proteins: pRb, p107 and p130. However, the relative contribution of these three pRb family proteins to HMEC senescence is not well understood.In a recent issue of Cell Cycle, Bazarov et al. examined the role of each pRb family protein in p16-mediated senescence in breast cancer cell lines and in HMECs (Fig. 1).³ They showed that knockdown of each of the three pRb family proteins individually did not abrogate senescence mediated by ectopically expressed p16 in the breast cancer cell lines MDA-MB-231 and MCF7. However, the senescence induced by ectopic p16 was abrogated if they introduced E7, which inactivates all three pRb family proteins. Their data suggest that two of pRb family proteins can compensate for the loss of each pRb family protein to induce p16-mediated senescence in these cancer cells. The remaining question is whether all three pRb family members play an additive role, and whether the inactivation of at least two members of the pRb family is required to overcome p16-induced senescence in breast cancer cells. On the other hand, they showed that abrogation of pRb, but not of p107 and/ or p130, attenuates senescence in HMECs, suggesting a non-redundant critical role of pRb in HMEC senescence. These data are consistent with a recent report demonstrating that pRb has a non-redundant role in repressing DNA replication during H-ras-induced senescence of human fibroblasts,⁴ and explain why pRb, but not p107 or p130, is frequently mutated in cancer. Interestingly, although abrogation of pRb is critical for HMECs escaping senescence, simultaneous depletion of pRb together with either p107, p130 or both accelerates bypass of senescence. This suggests that p107 and p130 help pRb to trigger/maintain HMEC senescence in culture and possibly in vivo. Although each pRb family protein preferentially binds to different members of the E2F family,⁵ the contribution of each E2F family protein in escaping p16-mediated senescence remains unclear. Therefore, it will be interesting to see whether the critical role of pRb, and a supportive role of p130 and p107, in p16-mediated HMEC senescence depend on how each pRb family protein interacts with an E2F family protein.Open in a separate windowFigure 1. Contribution of pRb family proteins to p16-mediated senescence in breast cancer cells and HMECs. Knockdown of each of the three pRb family proteins in breast cancer cells does not abrogate ectopic p16-induced senescence, suggesting that either two of pRb family proteins can compensate for the loss of each pRb family proteins or all three of pRb family proteins play an additive role in p16-mediated senescence in breast cancer cells. On the other hand, knockdown of pRb, but not of p107 or p130, abrogates HMEC senescence, suggesting a non-redundant critical role for pRb in senescence of HMECs. However, the knockdown of either p107 or p130, in conjunction with pRb depletion, abrogates HMEC senescence more efficiently than pRb knockdown alone. This suggests a supporting role for p107 and p130 in maintaining HMEC senescence.Bazarov et al. also showed that even aggressive p53-negative breast cancer cells undergo cellular senescence upon ectopic p16 expression. These results are quite encouraging from an epigenetic therapy point of view. Silencing of p16 often occurs in breast cancer cells via promoter methylation. During DNA replication, cells require new p16 promoter methylation to keep p16 silenced. The observations of Bazarov et al. suggest that we may be able to stop the growth of even aggressive p53-negative breast cancers in patients by inducing p16 expression in cancer cells using DNA methylation inhibitors. Back to the question of running family business: “it appears that pRb is still the boss, but in some cases, it may get a helping hand from his cousins- p107 and p130.”     

Evolution of the term “cellular senescence” and its impact on the current cytogerontological research

The term “cellular/cell senescence” was first introduced by Leonard Hayflick to describe the “age-related” changes in normal eukaryotic cells during aging in vitro, i.e., over the exhaustion of their mitotic potential. In the “classic” variant, it was assumed that cells “grow old” with the help of some internal mechanism, which leads to accumulation of various macromolecular defects (DNA damage in the first place). Currently, as a rule, “cellular senescence” means accumulation/appearance of particular “biomarkers of aging” in cells (they are most often transformed cells that do not demonstrate any replicative senescence) under the influence of various external factors (oxidative stress, H₂O₂, mitomycin C, ethanol, ionizing radiation, doxorubicin, etc.) that cause DNA damage. This phenomenon has been called DDR (DNA Damage Response). Among the said biomarkers, there are senescence-associated beta-galactosidase activity, expression of p53 and p21 proteins as well as of proteins involved in the regulation of inflammation, such as IL-6 or IL-8, activation of oncogenes, etc. Thus, “aging/senescence” of cells does not occur simply by itself—it takes place because of the influence of DNA-damaging agents. This approach, in my opinion, despite being very important to define a strategy to fight cancer, distracts us, yet again, from the study of the real mechanisms of aging. It should be emphasized that the “stationary phase aging” model developed in my laboratory also allows registering the occurrence of certain biomarkers of aging in cultured cells, but in this case they arise due to the restriction of their proliferation by contact inhibition, i.e., due to a rather physiological impact, which does not cause any damage to cells by itself (the situation is similar to what we observe in a whole multicellular organism).     

How does the brain control its own activity? A new function for the basal ganglia

It has long been a problem in neuroscience to known how the brain controls its own activity, how it is able to control the level of CNS excitability and how it is able to select and act on some information as opposed to some other information. In this paper I propose a new theory in which the basal ganglia play a role in selecting information ("selective attention") and in controlling the general level of excitability of the CNS ("state control"), the two processes being to some extent interdependent. The basal ganglia achieve these functions by actions on the thalamic-frontal cortical axis and on the brainstem mesencephalic reticular formation.     

Quantum-chemical investigation of the structure and the antioxidant properties of α-lipoic acid and its metabolites

Quantum-chemical computations were used to investigate the structure-antioxidant parameter relationships of α-lipoic acid and its natural metabolites bisnorlipoic acid and tetranorlipoic acid in their oxidized and reduced forms. The enantiomers of lipoic and dihydrolipoic acid were optimized using the B3LYP/6-311+G(3df,2p), B3LYP/aug-cc-pVDZ and MP2(full)/6-31+G(d,p) levels of theory as isolated molecules and in the presence of water. The geometries of the metabolites and the values of their antioxidant parameters (proton affinity, bond dissociation enthalpy, adiabatic ionization potential, spin density, and the highest occupied molecular orbital energy) were calculated at the B3LYP/6-311+G(3df,2p) level of theory. The results obtained reveal similarities between these structures: a pentatomic, nonaromatic ring is present in the oxidized forms, while an unbranched aliphatic chain (as found in saturated fatty acids) is present in both the oxidized and the reduced forms. Analysis of the spin density and the highest occupied molecular orbital energy revealed that the SH groups exhibited the greatest electron-donating activities. The values obtained for the proton affinity, bond dissociation enthalpy and adiabatic ionization potential indicate that the preferred antioxidant mechanisms for α-lipoic acid and its metabolites are sequential proton loss electron transfer in polar media and hydrogen atom transfer in vacuum.     

Variation in the reproductive performance of the Trollius–Chiastocheta mutualism at the edge of its range in north-east Germany

Empirical studies into obligate pollination mutualisms which elucidate the variation in reproductive performance of shrinking populations within human-altered environments are rare. This study focuses on the obligate pollination mutualism between Trollius europaeus (Ranunculaceae) and fly species of the genus Chiastocheta which act both as the plant’s main pollinators and as predators in that their larvae eat a fraction of the developing seeds. The study area is situated in the lowlands of north-east Germany. Many populations of T. europaeus have become comparatively small and scattered in this region as a consequence of agricultural land use intensification. We studied the plant’s reproductive fitness in populations ranging in size from 7 to 12,000 flowers. In a field experiment, we applied four pollination treatments and also recorded fly density in 28 natural T. europaeus populations. The fitness of the offspring from 19 populations was studied in a common garden experiment. In both approaches, a reduction in the fitness of small host plant populations could be demonstrated. Fitness loss can be put down to the quantitative and qualitative limitation of pollen caused by inbreeding and the negative feedback on relative seed set caused by the reduced ability of small plant populations to support a sufficiently large fly population. Although increases in fly density are associated with rising predation costs, the plant species’ net benefit is a positive function of its population size. Our study highlights the reproductive variability of the Trollius–Chiastocheta interaction along a population size gradient in a marginal region of its range, thus contributing to the understanding of the overall variability of this mutualism.     

Ammonite evolution and its bearing on the Cenomanian — Turonian boundary problem

Recent records ofVascoceras andNigericeras from the Cenomanian are reviewed and considered to be based upon mis-identification and/or questionable stratigraphic evidence. Phylogenetic relationships suggest that both these genera are wholly Turonian. The new genusProvascoceras is erected for the uppermost CenomanianVascoceras diartianus (d’Oreigny) whilst the Upper CenomanianPseudotissotia inopinata Kennedy & Bayliss is shown to be an homoeomorphous offshoot ofAcompsoceras, unrelated to the Turonian genus, for which the new genusKennediella is proposed. A refined zonal subdivision of the Turonian Stage is proposed.     

Ubiquitin and its kin: how close are the family ties?

Modification of proteins by the covalent attachment of ubiquitin is known to target them for degradation by proteasomes. Several proteins have been discovered recently that are related to ubiquitin or function similarly. Some of these proteins act as modifiers; others bear ubiquitin-like domains embedded in their polypeptide chain but do not form conjugates with cellular proteins. Ubiquitin-like proteins mediate an impressive range of cellular functions, including cell-cycle progression, DNA repair and apoptosis. Recent discoveries endorse the view that, in many cases, the function of the relatives of ubiquitin is linked to the ubiquitin pathway.