Variation in human recombination rates and its genetic determinants

BACKGROUND: Despite the fundamental role of crossing-over in the pairing and segregation of chromosomes during human meiosis, the rates and placements of events vary markedly among individuals. Characterizing this variation and identifying its determinants are essential steps in our understanding of the human recombination process and its evolution. STUDY DESIGN/RESULTS: Using three large sets of European-American pedigrees, we examined variation in five recombination phenotypes that capture distinct aspects of crossing-over patterns. We found that the mean recombination rate in males and females and the historical hotspot usage are significantly heritable and are uncorrelated with one another. We then conducted a genome-wide association study in order to identify loci that influence them. We replicated associations of RNF212 with the mean rate in males and in females as well as the association of Inversion 17q21.31 with the female mean rate. We also replicated the association of PRDM9 with historical hotspot usage, finding that it explains most of the genetic variance in this phenotype. In addition, we identified a set of new candidate regions for further validation. SIGNIFICANCE: These findings suggest that variation at broad and fine scales is largely separable and that, beyond three known loci, there is no evidence for common variation with large effects on recombination phenotypes.     

In vivo characterization of the homing endonuclease within the polB gene in the halophilic archaeon Haloferax volcanii

Inteins are parasitic genetic elements, analogous to introns that excise themselves at the protein level by self-splicing, allowing the formation of functional non-disrupted proteins. Many inteins contain a homing endonuclease (HEN) gene, and rely on its activity for horizontal propagation. In the halophilic archaeon, Haloferax volcanii, the gene encoding DNA polymerase B (polB) contains an intein with an annotated but uncharacterized HEN. Here we examine the activity of the polB HEN in vivo, within its natural archaeal host. We show that this HEN is highly active, and able to insert the intein into both a chromosomal target and an extra-chromosomal plasmid target, by gene conversion. We also demonstrate that the frequency of its incorporation depends on the length of the flanking homologous sequences around the target site, reflecting its dependence on the homologous recombination machinery. Although several evolutionary models predict that the presence of an intein involves a change in the fitness of the host organism, our results show that a strain deleted for the intein sequence shows no significant changes in growth rate compared to the wild type.     

Multisensory integration of natural odors and sounds in the auditory cortex

Motherhood is associated with different forms of physiological alterations including transient hormonal changes and brain plasticity. The underlying impact of these changes on the emergence of maternal behaviors and sensory processing within the mother's brain are largely unknown. By using in?vivo cell-attached recordings in the primary auditory cortex of female mice, we discovered that exposure to pups' body odor reshapes neuronal responses to pure tones and natural auditory stimuli. This olfactory-auditory interaction appeared naturally in lactating mothers shortly after parturition and was long lasting. Naive virgins that had experience with the pups also showed an appearance of olfactory-auditory integration in A1, suggesting that multisensory integration may be experience dependent. Neurons from lactating mothers were more sensitive to sounds as compared to those from experienced mice, independent of the odor effects. These uni- and multisensory cortical changes may facilitate the detection and discrimination of pup distress calls and strengthen the bond between mothers and their neonates. VIDEO ABSTRACT:     

Bioremediation of DDT contaminated soil using brown-rot fungi

The ability of brown-rot fungi (BRF) to eliminate DDT in artificially and historically contaminated soil was investigated to determine whether the BRF would be suitable for the bioremediation of DDT in soil. Gloeophyllum trabeum, Fomitopsis pinicola and Daedalea dickinsii showed an ability to eliminate DDT in artificially contaminated sterilized (SL) and un-sterilized (USL) soils. The addition of Fe²⁺ to the soil system enhanced the ability of some BRF to eliminate DDT. In the contaminated SL soil, the DDT was eliminated by approximately 41%, 9% and 15% by G. trabeum, F. pinicola and D. dickinsii, respectively. Compared with the controls, in the USL soil approximately 43%, 29% and 32% of DDT was eliminated and approximately 20%, 9% and 26% of DDD (1,1-dichloro-2,2-bis (4-chlorophenyl) ethane) was detected as a metabolic product with G. trabeum, F. pinicola and D. dickinsii, respectively. Of the BRF, G. trabeum demonstrated the greatest ability to eliminate DDT both in the SL and USL soils. G. trabeum was applied to a historically contaminated soil which had a DDT concentration more than three times the artificially contaminated soil. G. trabeum remediated about 64% of the initial DDT with the addition of Fe²⁺. There were no significant differences in the results with or without the addition of Fe²⁺, indicating that G. trabeum can be used directly for the degradation of DDT in soil without any other additional treatment. This study identified that G. trabeum is the most promising BRF for use in the bioremediation of DDT contaminated soil.     

Anchoring of bacterial effectors to host membranes through host-mediated lipidation by prenylation: a common paradigm

Post-translational lipidation by prenylation of the CaaX-box C-terminal motif in eukaryotic proteins facilitates anchoring of hydrophilic proteins, such as Ras and Rab, to membranes. A large cadre of bacterial effectors injected into host cells is anchored to host membranes by unknown mechanisms. As already documented for Legionella and Salmonella, we propose a common paradigm of microbial exploitation of the host prenylation machinery for anchoring of injected effectors to host membranes. This is supported by numerous potential microbial CaaX-box-containing proteins identified using refined bioinformatic tools. We also propose utilization of the CaaX motif as a membrane-targeting tag for proteins expressed in eukaryotic cells to facilitate deciphering of biological function.     

The role of reduction in iron uptake processes in a unicellular, planktonic cyanobacterium

In many aquatic environments the essential micronutrient iron is predominantly complexed by a heterogeneous pool of strong organic chelators. Research on iron uptake mechanisms of cyanobacteria inhabiting these environments has focused on endogenous siderophore production and internalization. However, as many cyanobacterial species do not produce siderophores, alternative Fe acquisition mechanisms must exist. Here we present a study of the iron uptake pathways in the unicellular, planktonic, non-siderophore producing strain Synechocystis sp. PCC 6803. By applying trace metal clean techniques and a chemically controlled growth medium we obtained reliable and reproducible short-term (radioactive assays) and long-term (growth experiments) iron uptake rates. We found that Synechocystis 6803 is capable of acquiring iron from exogenous ferrisiderophores (Ferrioxamine-B, FeAerobactin) and that unchelated, inorganic Fe is a highly available source of iron. Inhibition of iron uptake by the Fe(II)-specific ligand, ferrozine, indicated that reduction of both inorganic iron and ferrisiderophore complexes occurs before transport through the plasma membrane. Measurements of iron reduction rates and the inhibitory effect of ferrozine on growth supported this conclusion. The reduction-based uptake strategy is well suited for acquiring iron from multiple complexes in dilute aquatic environments and may play an important role in other cyanobacterial strains.     

GTP binding to the ROC domain of DAP-kinase regulates its function through intramolecular signalling

Death-associated protein kinase (DAPk) was recently suggested by sequence homology to be a member of the ROCO family of proteins. Here, we show that DAPk has a functional ROC (Ras of complex proteins) domain that mediates homo-oligomerization and GTP binding through a defined P-loop motif. Upon binding to GTP, the ROC domain negatively regulates the catalytic activity of DAPk and its cellular effects. Mechanistically, GTP binding enhances an inhibitory autophosphorylation at a distal site that suppresses kinase activity. This study presents a new mechanism of intramolecular signal transduction, by which GTP binding operates in cis to affect the catalytic activity of a distal domain in the protein.     

The autophagy protein Atg12 associates with antiapoptotic Bcl-2 family members to promote mitochondrial apoptosis

Autophagy and apoptosis constitute important determinants of cell fate and engage in a complex interplay in both physiological and pathological settings. The molecular basis of this crosstalk is poorly understood and relies, in part, on "dual-function" proteins that operate in both processes. Here, we identify the essential autophagy protein Atg12 as a positive mediator of mitochondrial apoptosis and show that Atg12 directly regulates the apoptotic pathway by binding and inactivating prosurvival Bcl-2 family members, including Bcl-2 and Mcl-1. The binding occurs independently of Atg5 or Atg3 and requires a unique BH3-like motif in Atg12, characterized by interaction studies and computational docking. In apoptotic cells, knockdown of Atg12 inhibited Bax activation and cytochrome c release, while ectopic expression of Atg12 antagonized the antiapoptotic activity of Mcl-1. The interaction between Atg12 and Bcl-2 family members may thus constitute an important point of convergence between autophagy and apoptosis in response to specific signals.