A simple Cα-SC potential with higher accuracy for protein fold recognition

In this paper, an improved C_α-SC energy potential designed for protein fold recognition was reported. It consists of three extremely simple interaction terms which are supposed to be the dominant interactions in protein folding: residue-residue contact, hydrophobicity and pseudodihedral potentials. The potential function only contains 210 contacts, one hydrophobic and one torsion parameters, which have been optimized using an interior point algorithm of linear programming. Tests of the derived potential function on commonly used decoy sets illustrate that it outperforms most of the existing coarse-grained potentials in terms of its capabilities in recognizing native structures and consistency in achieving high Z-scores across decoy sets, and it has almost equivalent performance to the potentials which considered complex intra-molecular interactions. The results show that our scoring function is a generally prospective potential for protein structure prediction and modeling with regard to its recognition and computation efficacy.     

Common basis for the mechanism of metallo and non-metallo KDO8P synthases

The three-dimensional structures of metal and non-metal enzymes that catalyze the same reaction are often quite different, a clear indication of convergent evolution. However, there are interesting cases in which the same scaffold supports both a metal and a non-metal catalyzed reaction. One of these is 3-deoxy-D-manno-octulosonate 8-phosphate (KDO8P) synthase (KDO8PS), a bacterial enzyme that catalyzes the synthesis of KDO8P and inorganic phosphate (P_i) from phosphoenolpyruvate (PEP), arabinose 5-phosphate (A5P), and water. This reaction is one of the key steps in the biosynthesis of bacterial endotoxins. The evolutionary tree of KDO8PS is evenly divided between metal and non-metal forms, both having essentially identical structures. Mutagenesis and crystallographic studies suggest that one or two residues at most determine whether or not KDO8PS requires a metal for function, a clear example of “minimalist evolution”. Quantum mechanical/molecular mechanical (QM/MM) simulations of both the enzymatic and non-enzymatic synthesis of KDO8P have revealed the mechanism underlying the switch between metal and non-metal dependent catalysis. The principle emerging from these studies is that this conversion is possible in KDO8PS because the metal is not involved in an activation process, but primarily contributes to orienting properly the reactants to lower the activation energy, an action easily mimicked by amino acid side-chains.     

Production of hydrogen peroxide and redox cycling can explain how sanguinarine and chelerythrine induce rapid apoptosis

Sanguinarine and chelerythrine are naturally occurring benzophenanthridines with multiple biological activities. Sanguinarine is believed to be a potential anticancer agent but its mechanism of action has not been fully elucidated. We previously found that it causes oxidative DNA damage and very rapid apoptosis that is not mediated by p53-dependent DNA damage signaling. Here we show that sanguinarine and chelerythrine cause the production of large amounts of reactive oxygen species (ROS), in particular hydrogen peroxide, which may deplete cellular antioxidants and provide a signal for rapid execution of apoptosis. Several oxidoreductases contribute to cell death induced by sanguinarine and chelerythrine which appear to be reduced upon entering the cell. We propose a model in which the generation of lethal amounts of hydrogen peroxide is explained by enzyme-catalyzed redox cycling between the reduced and oxidized forms of the phenanthridines and discuss the implications of such a mechanism for potential pharmaceutical applications.     

孕妇孕期营养指导及体质量控制对妊娠结局的影响

目的:对孕妇进行孕期营养指导及体质量控制,探究其对妊娠结局的影响。方法:将2011年2月-2014年2月期间我院收治的孕产妇150例纳入本次研究,所有研究对象随机均衡分为研究组和对照组,每组各75例。对照组孕产妇仅行常规妇科检查,研究组孕产妇在医护人员指导下行孕期营养指导和体质量控制,比较两组分娩方式,妊娠过程状况及围产儿情况。结果:研究组剖宫产率为17.33%低于对照组的57.33%,组间差异存在统计学意义(P0.05)。研究组贫血、羊水过少、产后出血率均低于对照组,差异有统计学意义(P0.05)。研究组胎龄及巨大儿及胎儿窘迫率均低于对照组,差异有统计学意义(P0.05)。结论:孕产妇在孕期进行营养膳食指导,控制体质量在合理范围内,可以改善孕妇妊娠结局,降低妊娠过程中并发症发病率,提高围产儿状况,保证孕妇和婴儿健康。     

Modelling potential habitat of the invasive ctenophore <Emphasis Type="Italic">Mnemiopsis leidyi</Emphasis> in Aegean Sea

The invasive ctenophore Mnemiopsis leidyi was accidentally introduced into the Black Sea in the early 1980s and it was first sighted in the Aegean Sea (Eastern Mediterranean) in the early 1990s. This article presents a first attempt to develop a predictive spatial model based on M. leidyi presence data and satellite environmental data from the Aegean Sea during early summer, in order to identify those areas in the Greek Seas and the entire Mediterranean basin that could serve as potential habitat for the species. Generalized additive models (GAM) were applied. The final GAM model indicated higher probability of finding M. leidyi present in depths of 65–135 m and sea surface temperature values of 21–25°C. Furthermore, the significant interaction between photosynthetically active radiation (PAR) and sea level anomaly (SLA) indicated a higher probability of M. leidyi presence in low values of PAR and SLA. In the next step, the final GAM was applied in a prediction grid of mean monthly satellite values for June 2004–2006 in order to estimate probability of M. leidyi presence in the Hellenic Seas and the whole Mediterranean basin at a GIS resolution of 4 km. In the Aegean Sea, species potential habitat included areas influenced by the Black Sea Water (e.g. Thracian Sea, Limnos-Imvros plateau), gulfs that are affected by river runoffs, such as the Thermaikos, Strymonikos and Patraikos gulfs, or areas with strong anthropogenic influence such as the Saronikos gulf. Areas with the same environmental conditions as those in Aegean Sea have been indicated in certain spots of the Levantine Sea as well as in coastal waters of Egypt and Libya, although their spatial extent varied largely among years examined. However, the occurrence of conditions that are linked to high probability of M. leidyi presence does not necessarily mean that these areas can support successful reproduction, high population or bloom levels, since these depend on a combination of temperature, salinity, food availability and the abundance of predators. Guest editor: V. D. Valavanis Essential Fish Habitat Mapping in the Mediterranean     

Modeling and predicting potential spawning habitat of anchovy (Engraulis encrasicolus) and round sardinella (Sardinella aurita) based on satellite environmental information

Anchovy and round sardinella are two important small pelagic species in the Mediterranean that spawn during the summer period. This is a first attempt to model and predict the two species’ potential spawning habitats in this area. Generalized additive models (GAMs) were constructed based on satellite environmental variables and presence/absence egg data, available from ichthyoplankton surveys conducted in the North Aegean Sea during early summer (June 2003–2006). These models were subsequently used to predict the probability of anchovy and round sardinella spawning in the Greek Seas as well as the entire Mediterranean and Black Sea during the same month of the year. The interaction of bottom depth and chlorophyll explained most of the deviance in the presence/absence GAMs of both species, indicating spawning over continental shelf areas with increased surface chlorophyll values. Round sardinella spawned closer to coast than anchovy. Predicted potential spawning areas for anchovy and round sardinella in unsampled areas of the Greek Seas and the entire Mediterranean and Black Sea were in good agreement with existing information on the distribution and extent of the spawning grounds, especially for anchovy. Modeling the species’ reproductive activity in relation to easily accessible environmental information and applying the models in a predictive way could be an initial, low-cost step to designate potential spawning fish habitats. Guest editor: V. D. Valavanis Essential Fish Habitat Mapping in the Mediterranean     

Forest structure of a subtropical mangrove along a river inferred from potential tree height and biomass

The hypothesis was tested that potential tree height and biomass in mangroves decrease downstream with the tidal gradient along the Okukubi River in Okinawa Island, Japan. The mangrove stands consisted of Bruguiera gymnorrhiza (L.) Lamk. and Kandelia obovata (S., L.) Yong (Rhizophoraceae). Four sites were selected considering the distance from the mouth of the river. Soil salinity increased downstream, while soil total nitrogen content decreased. The soil redox potential did not vary along the river. Maximum gross photosynthesis and tree height for each species decreased downstream. The potential tree height (H_max) inferred from the stem diameter (D_0.1)–tree height (H) relationship ( a, h, coefficient) in each species decreased downstream. The tree density (ρ)–mean tree size () relationships ( K, α, coefficient) determined for four sites revealed that the mean tree size at any given tree density decreased downstream, which indicates the decrease of potential biomass. Furthermore, an index for biomass () was homogeneous within a site regardless of tree density, i.e. the value of α at each site did not differ significantly from 1.0 (p > 0.05). The decreases in potential tree height and biomass may be partially ascribed to the stressful environments at the downstream sites characterized by high salinity (>2.6%) and nitrogen-poor soils (<0.25 ppt) in our study area.     

Transitions of interaction outcomes in a uni-directional consumer-resource system

A uni-directional consumer-resource system of two species is analyzed. Our aim is to understand the mechanisms that determine how the interaction outcomes depend on the context of the interaction; that is, on the model parameters. The dynamic behavior of the model is described and, in particular, it is demonstrated that no periodic orbits exist. Then the parameter (factor) space is shown to be divided into four regions, which correspond to the four forms of interaction outcomes; i.e. mutualism, commensalism, parasitism and amensalism. It is shown that the interaction outcomes of the system transition smoothly among these four forms when the parameters of the system are varied continuously. Varying each parameter individually or varying pairs of parameters can also lead to smooth transitions between the interaction outcomes. The analysis leads to both conditions for which each species achieves its maximal density, and situations in which periodic oscillations of the interaction outcomes emerge.     

A novel mitovirus from Buergenerula spartinae infecting the invasive species Spartina alterniflora

Spartina alterniflora,a coastal saltmarsh plant,has been classified as one of sixteen invasive alien species by the State Environmental Protection Administration of China.Nearly forty years of propagation and intru-sion of this plant has resulted in some harmful effects on the economic development of coastal areas,due to its proliferation.     

Oligomeric State of Purified Transient Receptor Potential Melastatin-1 (TRPM1), a Protein Essential for Dim Light Vision

Transient receptor potential melastatin-1 (TRPM1) is essential for the light-induced depolarization of retinal ON bipolar cells. TRPM1 likely forms a multimeric channel complex, although almost nothing is known about the structure or subunit composition of channels formed by TRPM1 or any of its close relatives. Recombinant TRPM1 was robustly expressed in insect cells, but only a small fraction was localized to the plasma membrane. Similar intracellular localization was observed when TRPM1 was heterologously expressed in mammalian cells. TRPM1 was affinity-purified from Sf9 cells and complexed with amphipol, followed by detergent removal. In blue native gels and size exclusion chromatography, TRPM1 migrated with a mobility consistent with detergent- or amphipol-bound dimers. Cross-linking experiments were also consistent with a dimeric subunit stoichiometry, and cryoelectron microscopy and single particle analysis without symmetry imposition yielded a model with approximate 2-fold symmetrical features. Finally, electron microscopy of TRPM1-antibody complexes revealed a large particle that can accommodate TRPM1 and two antibody molecules. Taken together, these data indicate that purified TRPM1 is mostly dimeric. The three-dimensional structure of TRPM1 dimers is characterized by a small putative transmembrane domain and a larger domain with a hollow cavity. Blue native gels of solubilized mouse retina indicate that TRPM1 is present in two distinct complexes: one similar in size to the recombinant protein and one much larger. Because dimers are likely not functional ion channels, these results suggest that additional partner subunits participate in forming the transduction channel required for dim light vision and the ON pathway.