Intercontinental disjunctions between eastern Asia and western North America in vascular plants highlight the biogeographic importance of the Bering land bridge from late Cretaceous to Neogene

This review shows a close biogeographic connection between eastern Asia and western North America from the late Cretaceous to the late Neogene in major lineages of vascular plants (flowering plants, gymnosperms, ferns and lycophytes). Of the eastern Asian–North American disjuncts, conifers exhibit a high proportion of disjuncts between eastern Asia and western North America. Several lineages of ferns also show a recent disjunct pattern in the two areas. In flowering plants, the pattern is commonly shown in temperate elements between northeastern Asia and northwestern North America, as well as elements of the relict boreotropical and Neogene mesophytic and coniferous floras. The many cases of intercontinental biogeographic disjunctions between eastern Asia and western North America in plants supported by recent phylogenetic analyses highlight the importance of the Bering land bridge and/or the plant migrations across the Beringian region from the late Cretaceous to the late Neogene, especially during the Miocene. The Beringian region has permitted the filtering and migration of certain plant taxa since the Pliocene after the opening of the Bering Strait, as many conspecific taxa or closely related species occur on both sides of Beringia.     

Electron tomographic analysis of cytoskeletal cross-bridges in the paranodal region of the node of Ranvier in peripheral nerves

The node of Ranvier is a site for ionic conductances along myelinated nerves and governs the saltatory transmission of action potentials. Defects in the cross-bridging and spacing of the cytoskeleton are a prominent pathological feature in diseases of the peripheral nerve. Electron tomography was used to examine cytoskeletal–cytoskeletal, membrane–cytoskeletal, and heterologous cell connections in the paranodal region of the node of Ranvier in peripheral nerves. Focal attachment of cytoskeletal filaments to each other and to the axolemma and paranodal membranes of the Schwann cell via narrow cross-bridges was visualized in both neuronal and glial cytoplasm. A subset of intermediate filaments associates with the cytoplasmic surfaces of supramolecular complexes of transmembrane structures that are presumed to include known and unknown junctional proteins. Mitochondria were linked to both microtubules and neurofilaments in the axoplasm and to neighboring smooth endoplasmic reticulum by narrow cross-bridges. Tubular cisternae in the glial cytoplasm were also linked to the paranodal glial cytoplasmic loop juxtanodal membrane by short cross-bridges. In the extracellular matrix between axon and Schwann cell, junctional bridges formed long cylinders linking the two membranes. Interactions between cytoskeleton, membranes, and extracellular matrix associations in the paranodal region are likely critical not only for scaffolding, but also for intracellular and extracellular communication.     

Region-specific role of water in collagen unwinding and assembly

Conformational stability of the collagen triple helix affects its turnover and determines tissue homeostasis. Although it is known that the presence of imino acids (prolines or hydroxyprolines) confer stability to the molecule, little is known regarding the stability of the imino-poor region lacking imino acids, which plays a key role in collagen cleavage. In particular, there have been continuing debates about the role of water in collagen stability. We addressed these issues using molecular dynamics simulations on 30-residue long collagen triple helices, including a structure that has a biologically relevant 9-residue imino-poor region from type III collagen (PDB ID: 1BKV). A torsional map approach was used to characterize the conformational motion of the molecule that differ between imino-rich and imino-poor regions. At temperatures 300 K and above, unwinding initiates at a common cleavage site, the glycine-isoleucine bond in the imino-poor region. This provides a linkage between previous observations that unwinding of the imino-poor region is a requirement for collagenase cleavage, and that isolated collagen molecules are unstable at body temperature. We found that unwinding of the imino-poor region is controlled by dynamic water bridges between backbone atoms with average lifetimes on the order of a few picoseconds, as the degree of unwinding strongly correlated with the loss of water bridges, and unwinding could be either prevented or enhanced, respectively by enforcing or forbidding water bridge formation. While individual water bridges were short-lived in the imino-poor region, the hydration shell surrounding the entire molecule was stable even at 330 K. The diameter of the hydrated collagen including the first hydration shell was about 14 A, in good agreement with the experimentally measured inter-collagen distances. These results elucidate the general role of water in collagen turnover: water not only affects collagen cleavage by controlling its torsional motion, but it also forms a larger-scale lubrication layer mediating collagen self-assembly.     

Electrostatic contribution to the thermodynamic and kinetic stability of the homotrimeric coiled coil Lpp-56: A computational study

The protein moiety of the Braun's E. coli outer membrane lipoprotein (Lpp-56) is an attractive object of biophysical investigation in several aspects. It is a homotrimeric, parallel coiled coil, a class of coiled coils whose stability and folding have been studied only occasionally. Lpp-56 possesses unique structural properties and exhibits extremely low rates of folding and unfolding. It is natural to ask how the specificity of the structure determines the extraordinary physical chemical properties of this protein. Recently, a seemingly controversial data on the stability and unfolding rate of Lpp-56 have been published (Dragan et al., Biochemistry 2004;43: 14891-14900; Bjelic et al., Biochemistry 2006;45:8931-8939). The unfolding rate constant measured using GdmCl as the denaturing agent, though extremely low, was substantially higher than that obtained on the basis of thermal unfolding. If this large difference arises from the effect of screening of electrostatic interactions induced by GdmCl, electrostatic interactions would appear to be an important factor determining the unusual properties of Lpp-56. We present here a computational analysis of the electrostatic properties of Lpp-56 combining molecular dynamics simulations and continuum pK calculations. The pH-dependence of the unfolding free energy is predicted in good agreement with the experimental data: the change in DeltaG between pH 3 and pH 7 is approximately 60 kJ mol(-1). The results suggest that the difference in the stability of the protein observed using different experimental methods is mainly because of the effect of the reduction of electrostatic interactions when the salt (GdmCl) concentration increases. We also find that the occupancy of the interhelical salt bridges is unusually high. We hypothesize that electrostatic interactions, and the interhelical salt bridges in particular, are an important factor determining the low unfolding rate of Lpp-56.     

Structural and magnetic behavior of mono- and dinuclear nickel (II) complexes of N,N′-bis-(3,5-dipiperidin-1-yl-[2,4,6]triazin-1-yl)-pyridin-2-ylmethyl-ethane-1,2-diamine

Reaction of nickel (II) perchlorate with the ligand N,N′-bis-(3,5-dipiperidin-1-yl-[2,4,6]triazin-1-yl)-pyridin-2-ylmethyl-ethane-1,2-diamine yields an octahedral Ni(II) high-spin complex 1 ([C₄₀H₅₆N₁₄Ni(H₂O)(CH₃OH)](ClO₄)₂(CH₃OH)₂) with moderate zero-field splitting (ZFS) axial distortion parameter D/k_B = 5.37 K. The ligand contributes a N4 donor set; the remaining two coordinating positions are occupied by coordinating solvents molecules. Exchange of the coordinating solvents molecules in complex 1 to thiocyanate moieties leads to formation of complex 2 ([C₄₀H₅₆N₁₄Ni(NCS)₂](CHCl)₃) with an extended parameter D/k_B = 8.80 K. The analysis of the structural and magnetic properties of complexes 1 and 2 led to the design of dinuclear complex 3 ([C₄₀H₅₆N₁₄NiN₃]₂(ClO₄)₂(CH₃OH)₂), where two azido groups were utilized as bridging ligands. The double azido bridges in complex 3 cross each other to form a rarely observed non-coplanar (N₃)₂ structure. The magnetic behavior of complex 3 reveals ferromagnetic coupling interactions characterized by J/k_B = 23.25 K, D₁/k_B = 7.90 K, D₂/k_B = 0.54 K.     

红豆杉高产细胞系快速建立和更新的新方法

目的：通过优化培养基和培养条件,建立太行红豆杉速生细胞系,为红豆杉细胞工厂化生产提供原种细胞系和繁殖技术。方法：以太行红豆杉为材料,筛选B5、WPS、MS等3种培养基和6-卞基嘌呤（6-BA）、萘乙酸（NAA）、2,4-二氯苯氧乙酸（2,4-D）等3种激素组合,采用液体、半固体、纸桥共3种培养方法继代培养并筛选高产细胞系。结果：B5＋NAA（1.0mg/L）＋6-BA（0.5mg/L）＋2,4-D（1.0mg/L）为最适愈伤组织诱导培养基,诱导率达100%;B5＋NAA（1.0～1.5mg/L）＋2,4-D（1.5～2.0mg/L）＋6-BA（0.5mg/L）为最佳继代培养基,生长量最高可达0.30g/（g·d）（鲜重）。结论：初步建立了红豆杉细胞系快速建立和繁殖新方法,用半固体培养产生初代细胞系、液体培养将细胞系同步化、纸桥培养快速繁殖细胞系,并通过检测紫杉醇含量不断更新细胞系。该细胞系体系建立方法简单,纯化速度快,易更新,产物细胞系可作为工厂化生产的原种细胞系。     

Calculation of Proteins’ Total Side-Chain Torsional Entropy and Its Influence on Protein-Ligand Interactions

Despite the high density within a typical protein fold, the ensemble of sterically permissible side-chain repackings is vast. Here, we examine the extent of this variability that survives energetic biases due to van der Waals interactions, hydrogen bonding, salt bridges, and solvation. Monte Carlo simulations of an atomistic model exhibit thermal fluctuations among a diverse set of side-chain arrangements, even with the peptide backbone fixed in its crystallographic conformation. We have quantified the torsional entropy of this native-state ensemble, relative to that of a noninteracting reference system, for 12 small proteins. The reduction in entropy per rotatable bond due to each kind of interaction is remarkably consistent across this set of molecules. To assess the biophysical importance of these fluctuations, we have estimated side-chain entropy contributions to the binding affinity of several peptide ligands with calmodulin. Calculations for our fixed-backbone model correlate very well with experimentally determined binding entropies over a range spanning more than 80 kJ/(mol·308 K).     

The permeability of highway in Gorski kotar (Croatia) for large mammals

The highway from Zagreb to Rijeka stretches 68.5 km through a wildlife core area in Gorski kotar (Croatia). It has 43 viaducts and tunnels, and one specifically constructed (100 m wide) green bridge (Dedin). One quarter of the total highway length consists of possible crossing structures. At Dedin green bridge, a total of 12,519 crossings have been recorded during 793 different days of active infrared monitors being in operation, or 15.8 crossings per day. Two monitored tunnel overpasses had 11.2 and 37.0 crossings per day, respectively, whilst 4.3 crossings occurred per day under one monitored viaduct. Of those crossings, 83.2% were by ungulates and 14.6% by large carnivores. Radio-tracked large carnivores, brown bear (Ursus arctos), grey wolf (Canis lupus) and Eurasian lynx (Lynx lynx), expressed strong positive selection for tunnels and viaducts, whilst avoiding small underpasses or bridges. Selection for the use of Dedin green bridge was equal to its availability. We conclude that this green bridge, constructed as a measure to mitigate the negative effects of the studied highway, served its purpose acceptably. Territorial and dispersing radio-tracked large carnivores crossed the highway 41 times, using both sides of the highway as parts of their home ranges. Overall, the highway in Gorski kotar does not seem to be a barrier. This demonstrates that it is possible to maintain habitat connectivity during the process of planning the highway route.     

Cyanato bridged binuclear nickel(II) and copper(II) complexes with pyridylpyrazole ligand: Synthesis, structure and magnetic properties

Binuclear cyanate bridged nickel(II) complex [Ni(L)(NCO)]₂(PF₆)₂ (1) and copper(II) complex [Cu(L)(NCO)]₂(PF₆)₂ (2), where L is N,N-bis(3,5-dimethylpyrazol-1-ylmethyl)aminomethylpyridine, a tetradentate N₄-coordinated ligand have been synthesized and characterized by physicochemical method. The structures of complexes 1 and 2 have been studied by single crystal X-ray diffraction analysis. The structure analysis reveals that both nickel(II) and copper(II) center are coordinated in distorted octahedral fashion and coordination mode of cyanate ligand is end-to-end (μ-1,3) for complex 1 but it is double end-on (μ-1,1) mode for complex 2. The variable temperature magnetic susceptibility data, measured from 2 to 300 K, show weak antiferromagnetic interaction with J value −6.2(1) cm⁻¹ for complex 1, whereas complex 2 has very weak ferromagnetic interaction with J value +0.5(1) cm⁻¹.     

An analysis of temperature adaptation in cold active, mesophilic and thermophilic Bacillus α-amylases

A comparative biochemical and structural study was performed on a cold active α-amylase from Bacillus cereus (BCA) and two well-known homologous mesophilic and thermophilic α-amylases from Bacillus amyloliquefaciens (BAA) and Bacillus licheniformis (BLA). In spite of a high degree of sequence and structural similarity, drastic variations were found for T_opt as 50, 70 and 90 °C for BCA, BAA and BLA, respectively. The half-lives of thermoinactivation were 1 and 9 min for BCA and BAA at 80 °C respectively, whilst there was no inactivation for BLA at this temperature. Thermodynamic studies on inactivation process suggested that lower thermostability of BCA is due to lower inactivation slope of the Arrhenius plots and subsequently, lower E_a and ΔH^#. Increased K_m and accessible surface area for catalytic residues along with a decreased number of internal interactions in this region in BCA compared to BLA suggest that BCA substrate-binding site might be temperature sensitive and is probably more flexible. On the other hand, fewer ion pairs, destructive substitutions and disruption of aromatic interaction networks in structurally critical regions of Bacillus α-amylases result in a severe decrease in BCA thermostability compared to its mesophilic and thermophilic homologues.