Evolutionary genetics of MHC class II beta genes in the brown hare, <Emphasis Type="Italic">Lepus europaeus</Emphasis>

The genes of the major histocompatibility complex (MHC) are attractive candidates for investigating the link between adaptive variation and individual fitness. High levels of diversity at the MHC are thought to be the result of parasite-mediated selection and there is growing evidence to support this theory. Most studies, however, target just a single gene within the MHC and infer any evidence of selection to be representative of the entire gene region. Here we present data from three MHC class II beta genes (DPB, DQB, and DRB) for brown hares in two geographic regions and compare them against previous results from a class II alpha-chain gene (DQA). We report moderate levels of diversity and high levels of population differentiation in the DQB and DRB genes (Na = 11, D _est = 0.071 and Na = 15, D _est = 0.409, respectively), but not for the DPB gene (Na = 4, D _est = 0.00). We also detected evidence of positive selection within the peptide binding region of the DQB and DRB genes (95% CI, ω > 1.0) but found no signature of selection for DPB. Mutation and recombination were both found to be important processes shaping the evolution of the class II genes. Our findings suggest that while diversifying selection is a significant contributor to the generally high levels of MHC diversity, it does not act in a uniform manner across the entire MHC class II region. The beta-chain genes that we have characterized provide a valuable set of MHC class II markers for future studies of the evolution of adaptive variation in Leporids.     

A Cholesterol Recognition Motif in Human Phospholipid Scramblase 1

Human phospholipid scramblase 1 (SCR) catalyzes phospholipid transmembrane (flip-flop) motion. This protein is assumed to bind the membrane hydrophobic core through a transmembrane domain (TMD) as well as via covalently bound palmitoyl residues. Here, we explore the possible interaction of the SCR TMD with cholesterol by using a variety of experimental and computational biophysical approaches. Our findings indicate that SCR contains an amino acid segment at the C-terminal region that shows a remarkable affinity for cholesterol, although it lacks the CRAC sequence. Other 3-OH sterols, but not steroids lacking the 3-OH group, also bind this region of the protein. The newly identified cholesterol-binding region is located partly at the C-terminal portion of the TMD and partly in the first amino acid residues in the SCR C-terminal extracellular coil. This finding could be related to the previously described affinity of SCR for cholesterol-rich domains in membranes.     

Cholera Toxin Production during Anaerobic Trimethylamine N-Oxide Respiration Is Mediated by Stringent Response in Vibrio cholerae

As a facultative anaerobe, Vibrio cholerae can grow by anaerobic respiration. Production of cholera toxin (CT), a major virulence factor of V. cholerae, is highly promoted during anaerobic growth using trimethylamine N-oxide (TMAO) as an alternative electron acceptor. Here, we investigated the molecular mechanisms of TMAO-stimulated CT production and uncovered the crucial involvement of stringent response in this process. V. cholerae 7th pandemic strain N16961 produced a significantly elevated level of ppGpp, the bacterial stringent response alarmone, during anaerobic TMAO respiration. Bacterial viability was impaired, and DNA replication was also affected under the same growth condition, further suggesting that stringent response is induced. A ΔrelA ΔspoT ppGpp overproducer strain produced an enhanced level of CT, whereas anaerobic growth via TMAO respiration was severely inhibited. In contrast, a ppGpp-null strain (ΔrelA ΔspoT ΔrelV) grew substantially better, but produced no CT, suggesting that CT production and bacterial growth are inversely regulated in response to ppGpp accumulation. Bacterial capability to produce CT was completely lost when the dksA gene, which encodes a protein that works cooperatively with ppGpp, was deleted. In the ΔdksA mutant, stringent response growth inhibition was alleviated, further supporting the inverse regulation of CT production and anaerobic growth. In vivo virulence of ΔrelA ΔspoT ΔrelV or ΔdksA mutants was significantly attenuated. The ΔrelA ΔspoT mutant maintained virulence when infected with exogenous TMAO despite its defective growth. Together, our results reveal that stringent response is activated under TMAO-stimulated anaerobic growth, and it regulates CT production in a growth-dependent manner in V. cholerae.     

Automatic construction of an anatomical coordinate system for three-dimensional bone models of the lower extremities – Pelvis,femur, and tibia

Automated methods for constructing patient-specific anatomical coordinate systems (ACSs) for the pelvis, femur and tibia were developed based on the bony geometry of each, derived from computed tomography (CT). The methods used principal axes of inertia, principal component analysis (PCA), cross-sectional area, and spherical and ellipsoidal surface fitting to eliminate the influence of rater's bias on reference landmark selection. Automatic ACSs for the pelvis, femur, and tibia were successfully constructed on each 3D bone model using the developed algorithm. All constructions were performed within 30 s; furthermore, between- and within- rater errors were zero for a given CT-based 3D bone model, owing to the automated nature of the algorithm. ACSs recommended by the International Society of Biomechanics (ISB) were compared with the automatically constructed ACS, to evaluate the potential differences caused by the selection of the coordinate system. The pelvis ACSs constructed using the ISB-recommended system were tilted significantly more anteriorly than those constructed automatically (range, 9.6–18.8°). There were no significant differences between the two methods for the femur. For the tibia, significant differences were found in the direction of the anteroposterior axis; the anteroposterior axes identified by ISB were more external than those in the automatic ACS (range, 17.5–25.0°).     

Spatial Scaling Effects on Soil Bacterial Communities in Malaysian Tropical Forests

Spatial scaling to some extent determines biodiversity patterns in larger organisms, but its role in microbial diversity patterns is much less understood. Some studies have shown that bacterial community similarity decreases with distance, whereas others do not support this. Here, we studied soil bacterial communities of tropical rainforest in Malaysia at two spatial scales: a local scale with samples spaced every 5 m over a 150-m transect, and a regional scale with samples 1 to 1,800 km apart. PCR-amplified soil DNA for the bacterial 16S rRNA gene targeting the V1–V3 region was pyrosequenced using Roche/454 GS FLX Titanium platform. A ranked partial Mantel test showed a weak correlation between spatial distance and whole bacterial community dissimilarity, but only at the local scale. In contrast, environmental distance was highly correlated with community dissimilarity at both spatial scales, stressing the greater role of environmental variables rather than spatial distance in determining bacterial community variation at different spatial scales. Soil pH was the only environmental parameter that significantly explained the variance in bacterial community at the local scale, whereas total nitrogen and elevation were additional important factors at the regional scale. We obtained similar results at both scales when only the most abundant OTUs were analyzed. A variance partitioning analysis showed that environmental variables contributed more to bacterial community variation than spatial distance at both scales. In total, our results support a strong influence of the environment in determining bacterial community composition in the rainforests of Malaysia. However, it is possible that the remaining spatial distance effect is due to some of the myriad of other environmental factors which were not considered here, rather than dispersal limitation.     

Translational Regulation of NeuroD1 Expression by FMRP: Involvement in Glutamatergic Neuronal Differentiation of Cultured Rat Primary Neural Progenitor Cells

Fragile X mental retardation protein (FMRP) is encoded by Fmr1 gene in which mutation is known to cause fragile X syndrome characterized by mental impairment and other psychiatric symptoms similar to autism spectrum disorders. FMRP plays important roles in cellular mRNA biology such as transport, stability, and translation as an RNA-binding protein. In the present study, we identified potential role of FMRP in the neural differentiation, using cortical neural progenitor cells from Sprague–Dawley rat. We newly found NeuroD1, an essential regulator of glutamatergic neuronal differentiation, as a new mRNA target interacting with FMRP in co-immunoprecipitation experiments. We also identified FMRP as a regulator of neuronal differentiation by modulating NeuroD1 expression. Down-regulation of FMRP by siRNA also increased NeuroD1 expression along with increased pre- and post-synaptic development of glutamatergic neuron, as evidenced by Western blot and immunocytochemistry. On the contrary, cells harboring FMRP over-expression construct showed decreased NeuroD1 expression. Treatment of cultured neural precursor cells with a histone deacetylase inhibitor, valproic acid known as an inducer of hyper-glutamatergic neuronal differentiation, down-regulated the expression of FMRP, and induced NeuroD1 expression. Our study suggests that modulation of FMRP expression regulates neuronal differentiation by interaction with its binding target mRNA, and provides an example of the gene and environmental interaction regulating glutamatergic neuronal differentiation.     

Expression machinery of GM4: the excess amounts of GM3/GM4S synthase (ST3GAL5) are necessary for GM4 synthesis in mammalian cells

The ganglioside GM4 is a sialic acid-containing glycosphingolipid mainly expressed in mammalian brain and erythrocytes. GM4 is synthesized by the sialylation of galactosylceramide (GalCer), while the ganglioside GM3 is synthesized by the sialylation of lactosylceramide (LacCer). Recently, the enzyme GM3 synthase was found to be responsible for the synthesis of GM4 in vitro and in vivo, yet the mechanism behind GM4 expression in cells remains unclear. In this study, we attempted to establish GM4-reconstituted cells to reveal the regulation of GM4 synthesis. Interestingly, GM4 was not detected in RPMI 1846 cells expressing LacCer, GalCer, and GM3. Similarly, GM4 was not detected in CHO-K1 cells, even when such cells expressing LacCer and GM3 were stably transfected with the GalCer synthase (GalCerS) gene. GM4 became detectable only when the GM3/GM4 synthase (GM3/GM4S, ST3GAL5) gene was overexpressed in either RPMI 1846 or CHO-K1/GalCerS cells. A mutant of the B16 melanoma cell line, GM-95, lacks GlcCer and LacCer, due to an absence of GlcCer synthase, but carries endogenous LacCer synthase and GM3/GM4S. GalCer became detectable after transfection of GalCerS into GM95 cells, but the GM95/GalCerS reconstituted cells did not express GM4, indicating that competition between the substrates LacCer and GalCer for GM3/GM4S does not cause the failure of GM4 synthesis. These results suggest that the expression machinery of GM4 under physiological conditions is independent from that of GM3.     

π‐Extended Narrow‐Bandgap Diketopyrrolopyrrole‐Based Oligomers for Solution‐Processed Inverted Organic Solar Cells

A series of narrow‐bandgap π‐conjugated oligomers based on diketopyrrolopyrrole chromophoric units coupled with benzodithiophene, indacenodithiophene, thiophene, and isoindigo cores are designed and synthesized for application as donor materials in solution‐processed small‐molecule organic solar cells. The impacts of these different central cores on the optoelectronic and morphological properties, carrier mobility, and photovoltaic performance are investigated. These π‐extended oligomers possess broad and intense optical absorption covering the range from 550 to 750 nm, narrow optical bandgaps of 1.52–1.69 eV, and relatively low‐lying highest occupied molecular orbital (HOMO) energy levels ranging from ?5.24 to ?5.46 eV in their thin films. A high power conversion efficiency of 5.9% under simulated AM 1.5G illumination is achieved for inverted organic solar cells based on a small‐molecule bulk‐heterojunction system consisting of a benzodithiophene‐diketopyrrolopyrrole‐containing oligomer as a donor and [6,6]‐phenyl‐C₇₁‐butyric acid methyl ester (PC₇₁BM) as an acceptor. Transmission electron microscopy and energy‐dispersive X‐ray spectroscopy reveal that interpenetrating and interconnected donor/acceptor domains with pronounced mesoscopic phase segregation are formed within the photoactive binary blends, which is ideal for efficient exciton dissociation and charge transport in the bulk‐heterojunction devices.     

Miscanthus: Genetic Diversity and Genotype Identification Using ISSR and RAPD Markers

Due to the limited number of molecular studies focused on European gene pool investigation, it is necessary to perform plant material recognition. Eighteen accessions of three Miscanthus species, namely, M. × giganteus, M. sinensis, M. sacchariflorus were evaluated with the use of molecular marker systems such as: inter simple sequence repeats (ISSRs), random amplified polymorphic DNA (RAPD), and by estimation of ploidy level based on flow cytometry. As a result, only one ISSR primer (ISSR1) and three RAPD primers (RAPD1, RAPD2, RAPD4) were required to identify all genotypes. Moreover, the use of the above mentioned molecular markers enable the proper species recognition of the interspecific hybrid M. × giganteus “Floridulus,” which has been previously mislabeled as M. floridulus. The highest genetic similarity coefficient (0.94) was observed between M. × giganteus clones, which indicates that the genetic diversity within this species was very low. Whereas M. sinensis genotypes represented a relatively wide diversity with similarity coefficient of 0.58. Cluster analysis using UPGMA grouped the 18 accessions in three clusters according to species affiliation including relabeled M. × giganteus “Floridulus,” which proved to be closely related to M.  × giganteus. Similar groupings were evident in the PCoA analysis.