Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici

The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic or genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) in diverse isolates. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30% of the genome. LOH altered genotypes for more than 11,000 single-nucleotide variant sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici.     

The Prion Protein Preference of Sporadic Creutzfeldt-Jakob Disease Subtypes

Sporadic Creutzfeldt-Jakob disease (CJD) is the most prevalent manifestation of the transmissible spongiform encephalopathies or prion diseases affecting humans. The disease encompasses a spectrum of clinical phenotypes that have been correlated with molecular subtypes that are characterized by the molecular mass of the protease-resistant fragment of the disease-related conformation of the prion protein and a polymorphism at codon 129 of the gene encoding the prion protein. A cell-free assay of prion protein misfolding was used to investigate the ability of these sporadic CJD molecular subtypes to propagate using brain-derived sources of the cellular prion protein (PrP^C). This study confirmed the presence of three distinct sporadic CJD molecular subtypes with PrP^C substrate requirements that reflected their codon 129 associations in vivo. However, the ability of a sporadic CJD molecular subtype to use a specific PrP^C substrate was not determined solely by codon 129 as the efficiency of prion propagation was also influenced by the composition of the brain tissue from which the PrP^C substrate was sourced, thus indicating that nuances in PrP^C or additional factors may determine sporadic CJD subtype. The results of this study will aid in the design of diagnostic assays that can detect prion disease across the diversity of sporadic CJD subtypes.     

Ecology of Borrelia burgdorferi sensu lato in Europe: transmission dynamics in multi-host systems, influence of molecular processes and effects of climate change

The analysis of different multi-host systems suggests that even hosts that are not capable of transmitting Borrelia burgdorferi sensu lato (s.l.) to the tick vector, Ixodes ricinus, or that are secondary reservoirs for these agents contribute to the intensity of transmission and to the overall risk of Lyme borreliosis, through the process of vector augmentation and pathogen amplification. On the other hand, above certain threshold densities, or in the presence of competition with primary reservoir hosts or low attachment rate of ticks to reservoir hosts, incompetent or less competent hosts may reduce transmission through dilution. The transmission of B. burgdorferi s.l. is affected by molecular processes at the tick-host interface including mechanisms for the protection of spirochaetes against the host's immune response. Molecular biology also increasingly provides important identification tools for the study of tick-borne disease agents. Ixodes ricinus and B. burgdorferi s.l. are expanding their geographical range to northern latitudes and to higher altitudes through the effects of climate change on host populations and on tick development, survival and seasonal activity. The integration of quantitative ecology with molecular methodology is central to a better understanding of the factors that determine the main components of Lyme borreliosis eco-epidemiology and should result in more accurate predictions of the effects of climate change on the circulation of pathogens in nature.     

Protein dynamics and enzyme catalysis: the ghost in the machine?

One of the most controversial questions in enzymology today is whether protein dynamics are significant in enzyme catalysis. A particular issue in these debates is the unusual temperature-dependence of some kinetic isotope effects for enzyme-catalysed reactions. In the present paper, we review our recent model [Glowacki, Harvey and Mulholland (2012) Nat. Chem. 4, 169-176] that is capable of reproducing intriguing temperature-dependences of enzyme reactions involving significant quantum tunnelling. This model relies on treating multiple conformations of the enzyme-substrate complex. The results show that direct 'driving' motions of proteins are not necessary to explain experimental observations, and show that enzyme reactivity can be understood and accounted for in the framework of transition state theory.     

Is footprint shape a good predictor of arboreality in sigmondontine rodents from a neotropical savanna?

We investigated the relation between the footprint shape of the fore and hind feet of sigmodontine rodents and their levels of arboreal activity. Footprint shape was obtained by analyzing the impressions left by identified animals captured in the field after being forced to pass through ink-tracking tunnels or by pressing their previously inked feet on a paper sheet. We used geometric morphometric techniques that use superimposition of landmarks (centers of the pads) to obtain footprint shape variables, which were reduced using multivariate analysis (principal component analysis). Arboreal activity was inferred on the basis of the proportions of individuals captured in arboreal traps (1.5–2.5 m height). Regression analysis of body size and the variable that best represented the footprint shapes (first principal component—PC1) did not indicate significant allometric effects on such shapes. We did not detect any significant phylogenetic effects on the arboreal activity of the rodents, either. The results indicated that the PC1 concerning footprint shapes of ten sigmodontine rodents efficiently reflects the degree of use of arboreal strata by these animals. The species studied showed different levels of arboreal activity and their hind footprints (r ² = 0.94) were better indicators of arboreality than the fore footprints (r ² = 0.53). These findings suggest a likely trade off for the fore feet functions. Such functions are probably not strictly related to locomotion. Other biomechanical functions (e.g., shock absorption) and/or manipulation (e.g., food manipulation and grooming) may exert relatively greater influence on the shape of fore feet.     

Haploinsufficiency of a spliceosomal GTPase encoded by EFTUD2 causes mandibulofacial dysostosis with microcephaly

Mandibulofacial dysostosis with microcephaly (MFDM) is a rare sporadic syndrome comprising craniofacial malformations, microcephaly, developmental delay, and a recognizable dysmorphic appearance. Major sequelae, including choanal atresia, sensorineural hearing loss, and cleft palate, each occur in a significant proportion of affected individuals. We present detailed clinical findings in 12 unrelated individuals with MFDM; these 12 individuals compose the largest reported cohort to date. To define the etiology of MFDM, we employed whole-exome sequencing of four unrelated affected individuals and identified heterozygous mutations or deletions of EFTUD2 in all four. Validation studies of eight additional individuals with MFDM demonstrated causative EFTUD2 mutations in all affected individuals tested. A range of EFTUD2-mutation types, including null alleles and frameshifts, is seen in MFDM, consistent with haploinsufficiency; segregation is de novo in all cases assessed to date. U5-116kD, the protein encoded by EFTUD2, is a highly conserved spliceosomal GTPase with a central regulatory role in catalytic splicing and post-splicing-complex disassembly. MFDM is the first multiple-malformation syndrome attributed to a defect of the major spliceosome. Our findings significantly extend the range of reported spliceosomal phenotypes in humans and pave the way for further investigation in related conditions such as Treacher Collins syndrome.     

The structure and functioning of the couplon in the mammalian cardiomyocyte

The couplons of the cardiomyocyte form nanospaces within the cell that place the L-type calcium channel (Ca_v1.2), situated on the plasmalemma, in opposition to the type 2 ryanodine receptor (RyR2), situated on the sarcoplasmic reticulum. These two molecules, which form the basis of excitation–contraction coupling, are separated by a very limited space, which allows a few Ca²⁺ ions passing through Ca_v1.2 to activate the RyR2 at concentration levels that would be deleterious to the whole cell. The limited space also allows Ca²⁺ inactivation of Ca_v1.2. We have found that not all couplons are the same and that their properties are likely determined by their molecular partners which, in turn, determine their excitability. In particular, there are a class of couplons that lie outside the RyR2-Ca_v1.2 dyad; in this case, the RyR2 is close to caveolin-3 rather than Ca_v1.2. These extra-dyadic couplons are probably controlled by the multitude of molecules associated with caveolin-3 and may modulate contractile force under situations such as stress. It has long been assumed that like the skeletal muscle, the RyR2 in the couplon are arranged in a structured array with the RyR2 interacting with each other via domain 6 of the RyR2 molecule. This arrangement was thought to provide local control of RyR2 excitability. Using 3D electron tomography of the couplon, we show that the RyR2 in the couplon do not form an ordered pattern, but are scattered throughout it. Relatively few are in a checkerboard pattern—many RyR2 sit edge-to-edge, a configuration which might preclude their controlling each other's excitability. The discovery of this structure makes many models of cardiac couplon function moot and is a current avenue of further research     

Sex-biased dispersal, haplodiploidy and the evolution of helping in social insects

In his famous haplodiploidy hypothesis, W. D. Hamilton proposed that high sister-sister relatedness facilitates the evolution of kin-selected reproductive altruism among Hymenopteran females. Subsequent analyses, however, suggested that haplodiploidy cannot promote altruism unless altruists capitalize on relatedness asymmetries by helping to raise offspring whose sex ratio is more female-biased than the population at large. Here, we show that haplodiploidy is in fact more favourable than is diploidy to the evolution of reproductive altruism on the part of females, provided only that dispersal is male-biased (no sex-ratio bias or active kin discrimination is required). The effect is strong, and applies to the evolution both of sterile female helpers and of helping among breeding females. Moreover, a review of existing data suggests that female philopatry and non-local mating are widespread among nest-building Hymenoptera. We thus conclude that Hamilton was correct in his claim that 'family relationships in the Hymenoptera are potentially very favourable to the evolution of reproductive altruism'.