Three Independent Determinants of Protein Evolutionary Rate

One of the most widely accepted ideas related to the evolutionary rates of proteins is that functionally important residues or regions evolve slower than other regions, a reasonable outcome of which should be a slower evolutionary rate of the proteins with a higher density of functionally important sites. Oddly, the role of functional importance, mainly measured by essentiality, in determining evolutionary rate has been challenged in recent studies. Several variables other than protein essentiality, such as expression level, gene compactness, protein–protein interactions, etc., have been suggested to affect protein evolutionary rate. In the present review, we try to refine the concept of functional importance of a gene, and consider three factors—functional importance, expression level, and gene compactness, as independent determinants of evolutionary rate of a protein, based not only on their known correlation with evolutionary rate but also on a reasonable mechanistic model. We suggest a framework based on these mechanistic models to correctly interpret the correlations between evolutionary rates and the various variables as well as the interrelationships among the variables.     

Spider silk fibres in artificial nerve constructs promote peripheral nerve regeneration

Abstract.  Objective : In our study, we describe the use of spider silk fibres as a new material in nerve tissue engineering, in a 20-mm sciatic nerve defect in rats. Materials and methods : We compared isogenic nerve grafts to vein grafts with spider silk fibres, either alone or supplemented with Schwann cells, or Schwann cells and matrigel. Controls, consisting of veins and matrigel, were transplanted. After 6 months, regeneration was evaluated for clinical outcome, as well as for histological and morphometrical performance. Results : Nerve regeneration was achieved with isogenic nerve grafts as well as with all constructs, but not in the control group. Effective regeneration by isogenic nerve grafts and grafts containing spider silk was corroborated by diminished degeneration of the gastrocnemius muscle and by good histological evaluation results. Nerves stained for S-100 and neurofilament indicated existence of Schwann cells and axonal re-growth. Axons were aligned regularly and had a healthy appearance on ultrastructural examination. Interestingly, in contrast to recently published studies, we found that bridging an extensive gap by cell-free constructs based on vein and spider silk was highly effective in nerve regeneration. Conclusion : We conclude that spider silk is a viable guiding material for Schwann cell migration and proliferation as well as for axonal re-growth in a long-distance model for peripheral nerve regeneration.     

Membrane perturbation by mastoparan 7 elicits a broad alteration in lipid composition of L1210 cells

Mastoparan 7 (Mas-7), an amphiphilic peptide possessing membrane perturbing activity, has been known to selectively stimulate some lipases. To examine changes in the lipid composition induced by Mas-7, we carried out systemic lipid analysis of L1210 cells after Mas-7 treatment. The total lipid was determined by HPLC, gas-liquid chromatography, and electrospray ionization mass spectrometry in conjunction with differential radiolabelling with [(32)P]orthophosphate, [(3)H]myristic acid, and [(3)H]arachidonic acid. The lipid analysis revealed multiple changes in more than 10 lipid classes. Free fatty acids (FFAs) and phosphatidylethanol (PEt), the phospholipase D product in the presence of ethanol, were increased significantly and phosphatidylcholine (PC) was decreased. Digitonin, a membrane permeabilizing reagent, similarly affected the lipid composition of L1210. The FFA released showed a very broad distribution of saturated, monounsaturated, and polyunsaturated fatty acids, implying that phospholipase A(2) alone could not account for all of the FFAs released. By comparing the molecular species of PEt with those of endogenous PC, we showed that phospholipase D in L1210 cells appeared to act selectively on diacyl-PC. The perturbation-induced alterations in the lipid composition brought about by Mas-7 might play a crucial role in the physiology of the affected cells.     

Localization of dopamine D1 and D2 receptor mRNAs in the rat systemic and pulmonary vasculatures.

The present study was designed to evaluate the expression of dopamine D1 and D2 receptor mRNAs in systemic and pulmonary vasculatures. Using specific antisense riboprobes for dopamine D1 and D2 receptor cDNAs, in situ hybridization histochemistry was performed in the aorta, common carotid artery, vertebral artery, pulmonary artery, and superior vena cava of the adult male Sprague Dawley rat. In the case of the aorta, common carotid artery, and vertebral artery, dopamine D1 receptor mRNAs localized mainly in the smooth muscle cells of the tunica media. However, the signals of dopamine D2 receptor mRNAs were found in the endothelium and subendothelial layer of tunica intima, and interstitial cells of tunica adventitia. In the case of the pulmonary artery, signals of dopamine D1 receptor mRNAs were detected within the tunica intima, media, and adventitia. Expression of D2 receptor mRNAs was detected in the walls of small blood vessels within the tunica adventitia of the pulmonary artery. There were no detectable signals of dopamine D1 and D2 receptor mRNAs in the vein. The uneven distribution of dopamine D1 and D2 receptor mRNAs in the rat systemic vasculatures and pulmonary artery suggests that dopamine differentially regulates the vasodilation of the systemic and pulmonary arteries through the differential stimulation of dopamine D1 and D2 receptor.     

Using genetic variation to study human disease.

The generation of a draft sequence of the human genome has spawned a unique opportunity to investigate the role of genetic variation in human diseases. The difference between any two human genomes has been estimated to be less than 0.1% overall, but still, this means that there are at least several million nucleotide differences per individual. The study of single nucleotide polymorphisms (SNPs), the most common type of variant, is likely to contribute substantially to deciphering genetic determinants of common and rare diseases. The effort to identify SNPs has been accelerated by three developments: the availability of sequence data from the genome project, improved informatic tools for searching the former and high-throughput genotype platforms. With these new tools in hand, dissecting the genetics of disease will rapidly move forward, although a number of formidable challenges will have to be met to see its promise realized in clinical medicine.     

High‐Capacity Concentration Gradient Li[Ni0.865Co0.120Al0.015]O2 Cathode for Lithium‐Ion Batteries

A Ni‐rich concentration‐gradient Li[Ni_0.865Co_0.120Al_0.015]O₂ (NCA) cathode is prepared with a Ni‐rich core to maximize the discharge capacity and a Co‐rich particle surface to provide structural and chemical stability. Compared to the conventional NCA cathode with a uniform composition, the gradient NCA cathode exhibits improved capacity retention and better thermal stability. Even more remarkably, the gradient NCA cathode maintains 90% of its initial capacity after 100 cycles when cycled at 60 °C, whereas the conventional cathode exhibits poor capacity retention and suffers severe structural deterioration. The superior cycling stability of the gradient NCA cathode largely stemmed from the gradient structure combines with the Co‐rich surface, which provides chemical stability against electrolyte attack and reduces the inherent internal strain observed in all Ni‐rich layered cathodes in their charged state, thus providing structural stability against the repeated anisotropic volume changes during cycling. The high discharge capacity of the proposed gradient NCA cathode extends the driving range of electric vehicles and reduces battery costs. Furthermore, its excellent capacity retention guarantees a long battery life. Therefore, gradient NCA cathodes represent one of the best classes of cathode materials for electric vehicle applications that should satisfy the demands of future electric vehicles.     

Cloning and characterization of a new broadspecific β-glucosidase from Lactococcus sp. FSJ4

A β-glucosidase gene bglX was cloned from Lactococcus sp. FSJ4 by the method of shotgun. The bglX open reading frame consisted of 1,437 bp, encoding 478 amino acids. SDS-PAGE showed a recombinant bglX monomer of 54 kDa. Substrate specificity study revealed that the enzyme exhibited multifunctional catalysis activity against pNPG, pNPX and pNPGal. This enzyme shows higher activity against aryl glycosides of xylose than those of glucose or galactose. The enzyme exhibited the maximal activity at 40 °C, and the optimal pH was 6.0 with pNPG and 6.5 with pNPX as the substrates. Molecular modeling and substrate docking showed that there should be one active center responsible for the mutifuntional activity in this enzyme, since the active site pocket was substantially wide to allow the entry of pNPG, pNPX and pNPGal, which elucidated the structure–function relationship in substrate specificities. Substrate docking results indicated that Glu180 and Glu377 were the essential catalytic residues of the enzyme. The CDOCKER_ENERGY values obtained by substrate docking indicated that the enzyme has higher activity against pNPX than those of pNPG and pNPGal. These observations are in conformity with the results obtained from experimental investigation. Therefore, such substrate specificity makes this β-glucosidase of great interest for further study on physiological and catalytic reaction processes.