Genome-Wide Functional Divergence after the Symbiosis of Proteobacteria with Insects Unraveled through a Novel Computational Approach

Symbiosis has been among the most important evolutionary steps to generate biological complexity. The establishment of symbiosis required an intimate metabolic link between biological systems with different complexity levels. The strict endo-cellular symbiotic bacteria of insects are beautiful examples of the metabolic coupling between organisms belonging to different kingdoms, a eukaryote and a prokaryote. The host (eukaryote) provides the endosymbiont (prokaryote) with a stable cellular environment while the endosymbiont supplements the host's diet with essential metabolites. For such communication to take place, endosymbionts' genomes have suffered dramatic modifications and reconfigurations of proteins' functions. Two of the main modifications, loss of genes redundant for endosymbiotic bacteria or the host and bacterial genome streamlining, have been extensively studied. However, no studies have accounted for possible functional shifts in the endosymbiotic proteomes. Here, we develop a simple method to screen genomes for evidence of functional divergence between two species clusters, and we apply it to identify functional shifts in the endosymbiotic proteomes. Despite the strong effects of genetic drift in the endosymbiotic systems, we unexpectedly identified genes to be under stronger selective constraints in endosymbionts of aphids and ants than in their free-living bacterial relatives. These genes are directly involved in supplementing the host's diet with essential metabolites. A test of functional divergence supports a strong relationship between the endosymbiosis and the functional shifts of proteins involved in the metabolic communication with the insect host. The correlation between functional divergence in the endosymbiotic bacterium and the ecological requirements of the host uncovers their intimate biochemical and metabolic communication and provides insights on the role of symbiosis in generating species diversity.     

"Ring pledget": a new concept for secure apex closure during transapical aortic valve implantation

Transapical aortic valve implantation requires puncture of the left ventricle apex and insertion of a 32-French delivery sheath. A critical step in the procedure consists of secure closure of the ventricular apex. We describe 2 cases of apical rupture of 42 transapical aortic valve implantations. Furthermore, we describe the use of a newly designed single circular Teflon pledget that can help to avoid this complication. This pledget provides a more secure and uniform shrinkage of the entire apex to close the defect left by the delivery sheath.     

A putative Alzheimer's disease risk allele in PCK1 influences brain atrophy in multiple sclerosis

Background

Brain atrophy and cognitive dysfunction are neurodegenerative features of Multiple Sclerosis (MS). We used a candidate gene approach to address whether genetic variants implicated in susceptibility to late onset Alzheimer''s Disease (AD) influence brain volume and cognition in MS patients.

Methods/Principal Findings

MS subjects were genotyped for five single nucleotide polymorphisms (SNPs) associated with susceptibility to AD: PICALM, CR1, CLU, PCK1, and ZNF224. We assessed brain volume using Brain Parenchymal Fraction (BPF) measurements obtained from Magnetic Resonance Imaging (MRI) data and cognitive function using the Symbol Digit Modalities Test (SDMT). Genotypes were correlated with cross-sectional BPF and SDMT scores using linear regression after adjusting for sex, age at symptom onset, and disease duration. 722 MS patients with a mean (±SD) age at enrollment of 41 (±10) years were followed for 44 (±28) months. The AD risk-associated allele of a non-synonymous SNP in the PCK1 locus (rs8192708^G) is associated with a smaller average brain volume (P = 0.0047) at the baseline MRI, but it does not impact our baseline estimate of cognition. PCK1 is additionally associated with higher baseline T2-hyperintense lesion volume (P = 0.0088). Finally, we provide technical validation of our observation in a subset of 641 subjects that have more than one MRI study, demonstrating the same association between PCK1 and smaller average brain volume (P = 0.0089) at the last MRI visit.

Conclusion/Significance

Our study provides suggestive evidence for greater brain atrophy in MS patients bearing the PCK1 allele associated with AD-susceptibility, yielding new insights into potentially shared neurodegenerative process between MS and late onset AD.     

A comparative study on intra-articular versus systemic gene electrotransfer in experimental arthritis

BACKGROUND: Electric pulse mediated gene transfer has been applied successfully in vivo for increasing naked DNA administration in various tissues. To achieve non-viral gene transfer into arthritic joint tissue, we investigated the use of electrotransfer (ET). Because anti-inflammatory cytokine strategies have proven efficient in experimental models of arthritis, we compared the therapeutic efficiency of local versus systemic delivery of the interleukin-10 (IL-10) using in vivo ET. METHODS: A plasmid vector expressing IL-10 was transferred into DBA/1 mouse knee joints by ET with 12 pulses of variable duration and voltage. The kinetics of transgene expression were analyzed by specific enzyme-linked immunosorbent assay (ELISA) in sera and knees. Optimal conditions were then used to deliver increasing amounts of IL-10 plasmid intra-articularly (i.a.) in the collagen-induced arthritis (CIA) mouse model. The therapeutic efficiency was compared with the potency of intra-muscular (i.m.) ET. RESULTS: Following i.a. ET, local IL-10 secretion peaked on day 7 and dropped 2 weeks after. A second ET produced the same kinetics without enhancing gene transfer efficiency, while transgene was still detected in injected muscles 4 weeks after ET. Only the i.m. ET of 25 microg of IL-10 significantly inhibited all the clinical and biological features of arthritis. The i.a. ET only showed mild improvement of arthritis when 100 microg of IL-10 plasmid were electrotransfered weekly from day 18 following arthritis induction. CONCLUSIONS: The present results suggest that gene transfer into arthritic joints by ET is an effective means to deliver anti-inflammatory cytokines. However, short duration of transgene expression impedes a significant effect for the treatment of arthritis, making i.m. ET more potent than i.a. ET for clinical benefit in CIA.     

GRAST: a new way of genome reduction analysis using comparative genomics

MOTIVATION: Establishment of intra-cellular life involved a profound re-configuration of the genetic characteristics of bacteria, including genome reduction and rearrangements. Understanding the mechanisms underlying these phenomena will shed light on the genome rearrangements essential for the development of an intra-cellular lifestyle. Comparison of genomes with differences in their sizes poses statistical as well as computational problems. Little efforts have been made to develop flexible computational tools with which to analyse genome reduction and rearrangements. RESULTS: Investigation of genome reduction and rearrangements in endosymbionts using a novel computational tool (GRAST) identified gathering of genes with similar functions. Conserved clusters of functionally related genes (CGSCs) were detected. Heterogeneous gene and gene cluster non-functionalization/loss are identified between genome regions, functional gene categories and during evolution. Results show that gene non-functionalisation has accelerated during the last 50 MY of Buchnera's evolution while CGSCs have been static.     

The Lichfield bone study: the skeletal response to exercise in healthy young men

The skeletal response to short-term exercise training remains poorly described. We thus studied the lower limb skeletal response of 723 Caucasian male army recruits to a 12-wk training regime. Femoral bone volume was assessed using magnetic resonance imaging, bone ultrastructure by quantitative ultrasound (QUS), and bone mineral density (BMD) using dual-energy X-ray absorptiometry (DXA) of the hip. Left hip BMD increased with training (mean ± SD: 0.85 ± 3.24, 2.93 ± 4.85, and 1.89 ± 2.85% for femoral neck, Ward's area, and total hip, respectively; all P < 0.001). Left calcaneal broadband ultrasound attenuation rose 3.57 ± 0.5% (P < 0.001), and left and right femoral cortical volume by 1.09 ± 4.05 and 0.71 ± 4.05%, respectively (P = 0.0001 and 0.003), largely through the rise in periosteal volume (0.78 ± 3.14 and 0.59 ± 2.58% for right and left, respectively, P < 0.001) with endosteal volumes unchanged. Before training, DXA and QUS measures were independent of limb dominance. However, the dominant femur had higher periosteal (25,991.49 vs. 2,5572 mm(3), P < 0.001), endosteal (6,063.33 vs. 5,983.12 mm(3), P = 0.001), and cortical volumes (19,928 vs. 19,589.56 mm(3), P = 0.001). Changes in DXA, QUS, and magnetic resonance imaging measures were independent of limb dominance. We show, for the first time, that short-term exercise training in young men is associated not only with a rise in human femoral BMD, but also in femoral bone volume, the latter largely through a periosteal response.     

<Superscript>1</Superscript>H, <Superscript>15</Superscript>N and <Superscript>13</Superscript>C resonance assignments and secondary structure of PulG,the major pseudopilin from <Emphasis Type="Italic">Klebsiella oxytoca</Emphasis> type 2 secretion system

Bacteria use complex transporters to secrete functionally relevant proteins to the extracellular medium. The type 2 secretion system (T2SS) translocates folded proteins involved in bacterial nutrient acquisition, virulence and adaptation. The T2SS pseudopilus is a periplasmic filament, assembled by the polymerization of PulG subunits, the major pseudopilin. Pseudopilin proteins have a conserved N-terminal hydrophobic segment followed by a more variable C-terminal periplasmic and globular domain. To better understand the mechanism of assembly and function of the T2SS, we have been studying the structure and dynamics of PulG by NMR, as well as its interaction with other components of the secretion machinery. As a first step on this study, here we reported the chemical shift assignments of PulG C-terminal domain and its secondary structure prediction based on NMR data.     

Derlin-dependent retrograde transport from endosomes to the Golgi apparatus

Cells have to maintain stable plasma membrane protein and lipid compositions under normal conditions and to remodel their plasma membranes in response to stimuli. This maintenance and remodeling require that integral membrane proteins at the plasma membrane that become misfolded, because of the relatively harsher extracellular milieu or carbohydrate and amino acid sequence changes, are degraded. We had previously shown that Derlin proteins, required for quality control mechanisms in the endoplasmic reticulum, also localize to endosomes and function in the degradation of misfolded integral membrane proteins at the plasma membrane. In this study, we show that Derlin proteins physically associate with sorting nexins that function in retrograde membrane transport from endosomes to the Golgi apparatus. Using genetic studies in Caenorhabditis elegans and ricin pulse-chase analyses in murine RAW264.7 macrophages, we show that the Derlin-sorting nexin interaction is physiologically relevant. Our studies suggest that at least some integral membrane proteins that are misfolded at the plasma membrane are retrogradely transported to the Golgi apparatus and ultimately to the endoplasmic reticulum for degradation via resident quality control mechanisms.     

Effect of maturation conditions on light and temperature requirements during seed germination of Citrullus colocynthis from the Arabian Desert

• Seed germination of Citrullus colocynthis, as in many other species of Cucurbitaceae, is inhibited by light, particularly at low temperatures. Germination response to light and temperature has been attributed to day length and temperature during seed maturation. This study assessed the effects of these factors on the germination response of C. colocynthis to temperature and light quality.
• Ripe fruits were collected from natural habitats during December and February and germinated at three temperatures (15/25, 20/30 and 25/35 °C) in five light treatments (dark, white light and Red:Far Red (R:FR) ratios of 0.30, 0.87 and 1.19). Additionally, unripe fruits were also collected from natural habitats and completed their maturation in growth chambers under different day lengths (6, 16 and 24 h of darkness) at 10/20 °C, and in darkness at both 10/20 °C and 25/35 °C. Mature seeds of the different treatments were germinated in the same five light treatments at 15/25 °C.
• Germination was significantly higher in the dark than that in any light treatment. Seeds matured at higher temperatures (i.e. seeds from the December collection and those matured at 25/35 °C) had significantly higher germination than those matured at lower temperatures (i.e. seeds from the February collection and those matured at 10/20 °C). Dark germination was significantly higher for the December collection than for the February collection. Seeds of the two collections germinated in the dark only at 15/25 °C. However, seeds matured in a growth chamber at 10/20 °C in darkness germinated at 15/25 °C in all light treatments, except for the R:FR ratio 0.30. Seeds of the different treatments failed to germinate in FR‐rich light.
• This study demonstrates that both temperature and day length during seed maturation play significant roles in the germination response of C. colocynthis. Additionally, the dark requirement for germination is likely beneficial for species with the larger seeds, such as C. colocynthis, which produce bigger seedlings that are able to emerge from deep soils and are competitively superior under dense vegetation and resource‐limited conditions.