The tail sheath structure of bacteriophage T4: a molecular machine for infecting bacteria

The contractile tail of bacteriophage T4 is a molecular machine that facilitates very high viral infection efficiency. Its major component is a tail sheath, which contracts during infection to less than half of its initial length. The sheath consists of 138 copies of the tail sheath protein, gene product (gp) 18, which surrounds the central non‐contractile tail tube. The contraction of the sheath drives the tail tube through the outer membrane, creating a channel for the viral genome delivery. A crystal structure of about three quarters of gp18 has been determined and was fitted into cryo‐electron microscopy reconstructions of the tail sheath before and after contraction. It was shown that during contraction, gp18 subunits slide over each other with no apparent change in their structure.     

Computational models for mechanics of morphogenesis

In the developing embryo, tissues differentiate, deform, and move in an orchestrated manner to generate various biological shapes driven by the complex interplay between genetic, epigenetic, and environmental factors. Mechanics plays a key role in regulating and controlling morphogenesis, and quantitative models help us understand how various mechanical forces combine to shape the embryo. Models allow for the quantitative, unbiased testing of physical mechanisms, and when used appropriately, can motivate new experimentaldirections. This knowledge benefits biomedical researchers who aim to prevent and treat congenital malformations, as well as engineers working to create replacement tissues in the laboratory. In this review, we first give an overview of fundamental mechanical theories for morphogenesis, and then focus on models for specific processes, including pattern formation, gastrulation, neurulation, organogenesis, and wound healing. The role of mechanical feedback in development is also discussed. Finally, some perspectives aregiven on the emerging challenges in morphomechanics and mechanobiology. Birth Defects Research (Part C) 96:132–152, 2012. © 2012 Wiley Periodicals, Inc.     

Replicating rather than nonreplicating adenovirus-human immunodeficiency virus recombinant vaccines are better at eliciting potent cellular immunity and priming high-titer antibodies

A major challenge in combating the human immunodeficiency virus (HIV) epidemic is the development of vaccines capable of inducing potent, persistent cellular immunity and broadly reactive neutralizing antibody responses to HIV type 1 (HIV-1). We report here the results of a preclinical trial using the chimpanzee model to investigate a combination vaccine strategy involving sequential priming immunizations with different serotypes of adenovirus (Ad)/HIV-1(MN)env/rev recombinants and boosting with an HIV envelope subunit protein, oligomeric HIV(SF162) gp140deltaV2. The immunogenicities of replicating and nonreplicating Ad/HIV-1(MN)env/rev recombinants were compared. Replicating Ad/HIV recombinants were better at eliciting HIV-specific cellular immune responses and better at priming humoral immunity against HIV than nonreplicating Ad-HIV recombinants carrying the same gene insert. Enhanced cellular immunity was manifested by a greater frequency of HIV envelope-specific gamma interferon-secreting peripheral blood lymphocytes and better priming of T-cell proliferative responses. Enhanced humoral immunity was seen in higher anti-envelope binding and neutralizing antibody titers and better induction of antibody-dependent cellular cytotoxicity. More animals primed with replicating Ad recombinants mounted neutralizing antibodies against heterologous R5 viruses after one or two booster immunizations with the mismatched oligomeric HIV-1(SF162) gp140deltaV2 protein. These results support continued development of the replicating Ad-HIV recombinant vaccine approach and suggest that the use of replicating vectors for other vaccines may prove fruitful.     

Implications of goat eradication on the survivorship of the Galapagos hawk

Non-native mammals cause ecological disasters in island ecosystems and their eradication is usually considered beneficial to native biodiversity. Goats (Capra hircus) were introduced to Santiago Island, Galapagos, Ecuador, in the early 1800s, and their numbers increased to about 100,000 by 1970. A goat eradication campaign initiated in 2002 was successful, eliminating the last individuals in 2006. To evaluate the effects of goat eradication, between 1998 and 2010 we studied the Galapagos hawk (Buteo galapagoensis) population on Santiago Island before, during, and after eradication. We used a 12-year data set in a capture–mark–recapture analysis to estimate the apparent survivorship of territorial adults in 33 breeding territories, and a 5-year data set to estimate the population sizes of the floater (non-territorial) fraction of the population. Juvenile floaters showed a drastic decline starting in 2006 and continuing in 2007, 2008, and 2010, which we attribute to the completion of goat eradication in 2006, and subsequent habitat changes. We found a significant decline in adult survivorship after the goat eradication program. Additionally, group size positively affected adult survivorship in this cooperatively polyandrous raptor, presumably reflecting the benefit of shared defense and offspring provisioning during harsher conditions. The changes in the hawk population after goat eradication are an example of unforeseen consequences of a restoration program, and we hypothesize that these changes are adjustments towards a new equilibrium under the current ecosystem characteristics and capacity. © 2012 The Wildlife Society.     

Land-use intensification systematically alters the size structure of aquatic communities in the Neotropics

Land-use and land-cover transitions can affect biodiversity and ecosystem functioning in a myriad of ways, including how energy is transferred within food-webs. Size spectra (i.e. relationships between body size and biomass or abundance) provide a means to assess how food-webs respond to environmental stressors by depicting how energy is transferred from small to larger organisms. Here, we investigated changes in the size spectrum of aquatic macroinvertebrates along a broad land-use intensification gradient (from Atlantic Forest to mechanized agriculture) in 30 Brazilian streams. We expected to find a steeper size spectrum slope and lower total biomass in more disturbed streams due to higher energetic expenditure in physiologically stressful conditions, which has a disproportionate impact on large individuals. As expected, we found that more disturbed streams had fewer small organisms than pristine forest streams, but, surprisingly, they had shallower size spectrum slopes, which indicates that energy might be transferred more efficiently in disturbed streams. Disturbed streams were also less taxonomically diverse, suggesting that the potentially higher energy transfer in these webs might be channelled via a few efficient trophic links. However, because total biomass was higher in pristine streams, these sites still supported a greater number of larger organisms and longer food chains (i.e. larger size range). Our results indicate that land-use intensification decreases ecosystem stability and enhances vulnerability to population extinctions by reducing the possible energetic pathways while enhancing efficiency between the remaining food-web linkages. Our study represents a step forward in understanding how land-use intensification affects trophic interactions and ecosystem functioning in aquatic systems.     

Defective Autophagy and mTORC1 Signaling in Myotubularin Null Mice

Autophagy is a vesicular trafficking pathway that regulates the degradation of aggregated proteins and damaged organelles. Initiation of autophagy requires several multiprotein signaling complexes, such as the ULK1 kinase complex and the Vps34 lipid kinase complex, which generates phosphatidylinositol 3-phosphate [PtdIns(3)P] on the forming autophagosomal membrane. Alterations in autophagy have been reported for various diseases, including myopathies. Here we show that skeletal muscle autophagy is compromised in mice deficient in the X-linked myotubular myopathy (XLMTM)-associated PtdIns(3)P phosphatase myotubularin (MTM1). Mtm1-deficient muscle displays several cellular abnormalities, including a profound increase in ubiquitin aggregates and abnormal mitochondria. Further, we show that Mtm1 deficiency is accompanied by activation of mTORC1 signaling, which persists even following starvation. In vivo pharmacological inhibition of mTOR is sufficient to normalize aberrant autophagy and improve muscle phenotypes in Mtm1 null mice. These results suggest that aberrant mTORC1 signaling and impaired autophagy are consequences of the loss of Mtm1 and may play a primary role in disease pathogenesis.     

Increased risk of lung cancer associated with a functionally impaired polymorphic variant of the human DNA glycosylase NEIL2

Human NEIL2, one of five oxidized base-specific DNA glycosylases, is unique in preferentially repairing oxidative damage in transcribed genes. Here we show that depletion of NEIL2 causes a 6-7-fold increase in spontaneous mutation frequency in the HPRT gene of the V79 Chinese hamster lung cell line. This prompted us to screen for NEIL2 variants in lung cancer patients' genomic DNA. We identified several polymorphic variants, among which R103Q and R257L were frequently observed in lung cancer patients. We then characterized these variants biochemically, and observed a modest decrease in DNA glycosylase activity relative to the wild type (WT) only with the R257L mutant protein. However, in reconstituted repair assays containing WT NEIL2 or its R257L and R103Q variants together with other DNA base excision repair (BER) proteins (PNKP, Polβ, Lig IIIα and XRCC1) or using NEIL2-FLAG immunocomplexes, an ~5-fold decrease in repair was observed with the R257L variant compared to WT or R103Q NEIL2, apparently due to the R257L mutant's lower affinity for other repair proteins, particularly Polβ. Notably, increased endogenous DNA damage was observed in NEIL2 variant (R257L)-expressing cells relative to WT cells. Taken together, our results suggest that the decreased DNA repair capacity of the R257L variant can induce mutations that lead to lung cancer development.