Generating artificial homologous proteins according to the representative family character in molecular mechanics properties - an attempt in validating an underlying rule of protein evolution

The molecular mechanics property is the foundation of many characters of proteins. Based on intramolecular hydrophobic force network, the representative family character underlying a protein’s mechanics property is described by a simple two-letter scheme. The tendency of a sequence to become a member of a protein family is scored according to this mathematical representation. Remote homologs of the WW-domain family could be easily designed using such a mechanistic signature of protein homology. Experimental validation showed that nearly all artificial homologs have the representative folding and bioactivity of their assigned family. Since the molecular mechanics property is the only consideration in this study, the results indicate its possible role in the generation of new members of a protein family during evolution.

Vibration of an Adhered Microbeam Under a Periodically Shaking Electrical Force

The vibration analysis of an adhered S-shaped microbeam under alternating sinusoidal voltage is presented. The shaking force is the electrical force due to the sinusoidal voltage. During vibration, both the microbeam deflection and the adhesion length keep changing. The microbeam deflection and adhesion length are numerically determined by the iteration method. As the adhesion length keeps changing, the domain of the equation of motion for the microbeam (unadhered part) changes correspondingly, which results in changes of the structure natural frequencies. For this reason, the system can never reach a steady state. The transient behaviors of the microbeam under different shaking frequencies are compared. We deliberately choose the initial conditions to compare our dynamic results with the existing static theory. The paper also analyzes the changing behavior of adhesion length during vibration and an asymmetric pattern of adhesion length change is revealed, which may be used to guide the dynamic de-adhering process. The abnormal behavior of the adhered microbeam vibrating at almost the same frequency under two quite different shaking frequencies is also shown. The Galerkin method is used to discretize the equation of motion and its convergence study is also presented. The model is only applicable in the case that the peel number is equal to 1. Some other model limitations are also discussed.

A scheme for multiple sequences alignment optimization-an improvement based on family representative mechanics features

As a basic tool of modern biology, sequence alignment can provide us useful information in fold, function, and active site of protein. For many cases, the increased quality of sequence alignment means a better performance. The motivation of present work is to increase ability of the existing scoring scheme/algorithm by considering residue–residue correlations better. Based on a coarse-grained approach, the hydrophobic force between each pair of residues is written out from protein sequence. It results in the construction of an intramolecular hydrophobic force network that describes the whole residue–residue interactions of each protein molecule, and characterizes protein's biological properties in the hydrophobic aspect. A former work has suggested that such network can characterize the top weighted feature regarding hydrophobicity. Moreover, for each homologous protein of a family, the corresponding network shares some common and representative family characters that eventually govern the conservation of biological properties during protein evolution. In present work, we score such family representative characters of a protein by the deviation of its intramolecular hydrophobic force network from that of background. Such score can assist the existing scoring schemes/algorithms, and boost up the ability of multiple sequences alignment, e.g. achieving a prominent increase (50%) in searching the structurally alike residue segments at a low identity level. As the theoretical basis is different, the present scheme can assist most existing algorithms, and improve their efficiency remarkably.

Rapid evolution, genetic variations, and functional association of the human spermatogenesis-related gene NYD-SP12

NYD-SP12 is a recently identified spermatogenesis-related gene with a pivotal role in human testis development. In this study, we analyzed between-species divergence and within-species variation of NYD-SP12 in seven representative primate species, four wo

Evolution of the DRD2 gene haplotype and its association with alcoholism in Mexican Americans

The human D2 dopamine receptor gene (DRD2) plays a central role in the neuromodulation of appetitive behaviors and is implicated in having a possible role in susceptibility to alcoholism. We genotyped an SNP in DRD2 Exon 8 in 251 nonalcoholic, unrelated, healthy controls and 200 alcoholic Mexican Americans. The DRD2 haplotypes were analyzed using the Exon 8 genotype in combination with five other SNP genotypes, which were obtained from our previous study. The ancestral origins of the DRD2 polymorphisms have been determined by sequencing the homologous region in other higher primates. Twenty DRD2 haplotypes, defined as H1 to H20 based on their frequency from high to low, were obtained in this major minority population. The ancestral haplotype "I-132-G-C-G-A1" and two one-step mutation haplotypes were absent in our study population. The haplotype H1, "I-B1-T-C-A-A1", with the highest frequency in the population, is a three-step mutation from the ancestral form. The first five or eight major haplotypes make up 87% or 95% of the entire population, respectively. The prevalence of the haplotype H1+ (H1/H1 and H1/Hn genotypes) is significantly higher in alcoholics and alcoholic subgroups, including early onset drinkers and benders, than in their respective control groups. The Promoter -141C allele is in linkage disequilibrium (LD) with five other loci in the nonalcoholic group, but not in the alcoholic group. All of the other five loci are in LD in both the alcoholic and control groups. The DRD2 TaqI B allele is in complete LD with the allele located in intron 6. Five SNPs, Promoter -141C, TaqI B (or Intron 6), Exon 7, Exon 8, and TaqI A, are sufficient to define the DRD2 haplotypes in Mexican Americans. Our data indicate that the DRD2 haplotypes are associated with alcoholism in Mexican Americans. (c) 2005 Elsevier Inc. All rights reserved.

Electromagnetic-field-induced cohesive force enhancement in a metallic nanowire

We theoretically study the conducting electronic contribution to the cohesive force in a metallic nanowire irradiated under a transversely polarized external electromagnetic field at low temperatures and in the ballistic regime. In the framework of the free-electron model, we have obtained a time-dependent two-level electronic wavefunction by means of a unitary transformation. Using a thermodynamic statistical approach with this wavefunction, we have calculated the cohesive force in the nanowire. We show that the cohesive force can be divided into two components, one of which is independent of the electromagnetic field (static component), which is consistent with the existing results in the literature. The magnitude of the other component is proportional to the electromagnetic field strength. This extra component of the cohesive force is originally from the coherent coupling between the two lateral energy levels of the wire and the electromagnetic field.

Flying lemurs – The 'flying tree shrews'? Molecular cytogenetic evidence for a Scandentia-Dermoptera sister clade

Background: Flying lemurs or Colugos (order Dermoptera) represent an ancient mammalian lineage that contains only two extant species. Although molecular evidence strongly supports that the orders Dermoptera, Scandentia, Lagomorpha, Rodentia and Primates form a superordinal clade called Supraprimates (or Euarchontoglires), the phylogenetic placement of Dermoptera within Supraprimates remains ambiguous. Results: To search for cytogenetic signatures that could help to clarify the evolutionary affinities within this superordinal group, we have established a genome-wide comparative map between human and the Malayan flying lemur (Galeopterus variegatus) by reciprocal chromosome painting using both human and G. variegatus chromosome-specific probes. The 22 human autosomal paints and the X chromosome paint defined 44 homologous segments in the G. variegatus genome. A putative inversion on GVA 11 was revealed by the hybridization patterns of human chromosome probes 16 and 19. Fifteen associations of human chromosome segments (HSA) were detected in the G. variegatus genome: HSA1/3, 1/10, 2/21, 3/ 21, 4/8, 4/18, 7/15, 7/16, 7/19, 10/16, 12/22 (twice), 14/15, 16/19 (twice). Reverse painting of G. variegatus chromosome-specific paints onto human chromosomes confirmed the above results, and defined the origin of the homologous human chromosomal segments in these associations. In total, G. variegatus paints revealed 49 homologous chromosomal segments in the HSA genome. Conclusion: Comparative analysis of our map with published maps from representative species of other placental orders, including Scandentia, Primates, Lagomorpha and Rodentia, suggests a signature rearrangement (HSA2q/21 association) that links Scandentia and Dermoptera to one sister clade. Our results thus provide new evidence for the hypothesis that Scandentia and Dermoptera have a closer phylogenetic relationship to each other than either of them has to Primates.

Analysis of the practical force accuracy of electromagnet-based nanoindenters

Two important factors that influence the force accuracy of the electromagnet-based nano-indenters but have not yet attracted much attention are analyzed, and a more reasonable way to estimate the force accuracy is presented in this paper. MTS Nano Indenter (R), with the characteristics of a coil suspended in a uniform magnetic field by two sets of springs acting as an actuator and force measuring unit, is used as an example. One of the two factors is the uniformity of the magnetic field. The other is the stiffness of the supporting spring. Consequently, the practical force accuracy varies considerably from test to test because it firmly depends on the working position of the coil and the displacement stroke. A reasonable estimated accuracy value is of the order of 10 degrees mu N for typical indentation tests with a 10(2) nm indentation depth or a 10 degrees mN test force. (C) 2010 Elsevier Ltd. All rights reserved.

Sensitisation identification of stainless steel to intergranular stress corrosion cracking by atomic force microscopy

A new technique was developed for characterisation of stainless steel to intergramilar stress corrosion cracking by atomic force microscopy. The technique proved to be effective in sensitisation identification of AISI 304 stainless steel and might be promising in sensitisation identification of other stainless steels. (c) 2007 Elsevier B.V. All rights reserved.

急倾斜金属矿体开采岩体移动规律与变形趋势预测研究

Rockmass movement due to mining steep metallic ore body is a considerable question in the surface movement and deformation issue caused by underground mining. Research on coal mining induced rockmass movement and its prediction problem have been performed for a long-term, and have achieved great progress at home and abroad. However, the rockmass movement caused by mining steep metal mine is distinctivly different from coal seam mining.. Existing surface movement laws and deformation prediction methods are not applicable to the rockmass movement caused by mining steep metal mine. So far the home and abroad research to this theory is presently at an early stage, and there isn’t mature theory or practical prediction method, which made a great impact on production. In this paper, the research object—Jinchuan nickel mine, which is typical steep metal mine, characterized by complex geological conditions, developed faults, cracked rockmass, high geostress, and prominent engineering stability problems. In addition, backfill mining method is used in the mine, the features of rockmass movement caused by this mining method are also different from other mining methods. In this paper, the laws of rock mass movement, deformation and destroy mechanism, and its prediction were analyzed based on the collection of data, detailed in-sit engineering geology survey, ground movement monitoring by GPS, theoretical analysis and numerical simulation. According to the GPS monitoring of ground surface movement, ground subsidence basin with apparent asymmetry is developing, the influence scope is larger in the upper faulted block than in the lower faulted block, and the center of ground movement is moving along the upper faulted block direction with increasing depth of mining. During the past half and seven years, the largest settlement has amounted to 1287.5mm, and corresponding horizontal displacement has amounted to 664.6mm. On the ground surface, two fissure belts show a fast-growing trend of closure. To sum up, mining steep metal mine with backfill method also exist the same serious problem of rockmass movement hazards. Fault, as a low intensity zone in rockmass, when it located within the region of mining influence, the change of potential energy mainly consumed in fault deformation associated with rockmass structure surface friction, which is the essence of displacement and stress barrier effects characterized by fault rupture zone. when steep fault located in the tensile deformation region incurred by underground excavation, no matter excavation in hangingwall or in footwall of the fault, there will be additional tensile stress on the vertical fault plane and decrease in the shear strength, and always showing characteristics of normal fault slip, which is the main reason of fault escarpment appeared on the ground surface. The No.14 shaft deformation and failure is triggered by fault activation, which showed with sidewall move, rupture, and break down features as the main form of a concentrated expression of fault effects. The size and orientation of principal stress in surrounding rock changed regularly with mining; therefore, roadway deformation and damage at different stages have different characteristics and distribution models. During the process of mining, low-intensity weak structures surface always showed the most obvious reaction, accompany with surface normal stress decrease and shear strength bring down, to some extent, occurred with relative slide and deformation. Meanwhile, the impact of mining is a relatively long process, making the structure surface effect of roadway deformation and damage more prominent than others under the influence of mining. Roadway surrounding rockmass deformation caused by the change of strain energy density field after excavation mainly belongs to elastic deformation, and the correspondented damage mainly belongs to brittle rupture, in this circumstance, surrounding rockmass will not appear large deformation. The large deformation of surrounding rockmass can only be the deformation associated with structure surface friction or the plastic deformation of itself, which mainly caused by the permanent self-weigh volume force，and long-term effect of mining led to the durability of this deformation Good pitting fill effect and supporting effect of backfill, as well as the friction of rockmass structure surface lead to obvious macro-rockmass movement with long-lag characteristics. In addition, the loss of original intensity and new structure surface arisen increased flexibility in rockmass and fill deformation in structure surface, which made the time required for rockmass potential energy translate into deformation work associated with plastic deformation and structure surface friction consumed much, and to a large extent, eliminated the time needed to do those plastic work during repeated mining, all of which are the fundamental reason of rockmass movement aftereffect more significant than before. Mining steep deposits in high tectonic stress area and in gravity stress area have different movement laws and deformation mechanism. The steep deposit, when the vertical size of the mining areas is smaller than the horizontal size of the orebody, no matter mining in gravity stress area or in high tectonic stress area, they have similar features of ground movement with mining horizontal orebody; contrarily, there will appear double settlement centers on the ground surface under the condition of mining in high tectonic stress area, while there will always be a single center under the other condition. Meanwhile the ground movement lever, scale of mining influence area and macro features of ground movement, deformation and fracture are also different from mining in gravity stress area, and the fundamental reason lies in the impact of orientation of the maximum principal stress on rock movement features in in-site rock stress field. When mining thick and steep deposit, the ground surface movement and deformation characteristic curves are significantly different from excavating the horizontal ore bed and thin steep deposit. According to the features of rockmass movement rate, the development process of mining-induced rockmass movement is divided into three stages: raising stage, steadily stage and gradually decay stage. Considering the actual exploitation situation, GPS monitoring results and macro-characteristics of surface movement, the current subsidence pattern of Jinchuan No.2 mine is in the early stage of development. Based on analysis of surface movement rate, surface subsidence rate increase rapidly when mining in double lever at the same time, and reach its peak until the exploitation model ended. When double lever mining translate into single, production decreased, surface subsidence rate suddenly start to reduce and maintain a relatively low value, and the largest subsidence center will slowly move along with the hangingwall ore body direction with increasing depth of mining, at the same time, the scope and extent of subsidence in footwall ore body will begin magnify, and a sub-settlement center will appear on ground surface, accompanied with the development and closure trend of ground fissure, the surrounding rockmass of shaft and roadway will be confronted to more frequent and severe deformation and failure, and which will have a negative impact on the overall stability of No.2 mine mining. On the premise of continuity of rockmass movement, gray system model can be used in ground rockmass movement prediction for good results. Under the condition of backfill mining step by step, the loose effect of compact status of the hard, broken rockmass led to lower energy release rate, although surrounding rockmass has high elastic energy, loose and damage occurred in the horizontal ore body, which made the mining process safety without any large geological hazards. During the period of mining the horizontal ore body to end, in view of its special “residual support role”, there will be no large scale rockmass movement hazards. Since ground surface movement mainly related to the intensity of mining speed and backfill effect, on the premise of constant mining speed, during the period of mining the horizontal ore body to end, the rate of ground surface rockmass movement and deformation won’t have sudden change.

边坡动力响应分析及应用研究

As a marginal subject, dynamic responses of slopes is not only an important problem of engineering geology (Geotechnical problem), but also of other subjects such as seismology, geophysics, seismic engineering and engineering seismic and so on. Owning to the gulf between different subjects, it is arduous to study dynamic responses of slopes and the study is far from ripeness. Studying on the dynamic responses of slopes is very important in theories as well as practices. Supported by hundreds of bibliographies, this paper systemically details the development process of this subject, introduces main means to analyze this subject, and then gives brief remarks to each means respectively. Engineering geology qualitative analysis is the base of slopes dynamic responses study. Because of complexity of geological conditions, engineering geology qualitative analysis is very important in slopes stability study, especially to rock slopes with complex engineering geology conditions. Based on research fruits of forerunners, this paper summarizes factors influencing slopes dynamic stability into five aspects as geology background, stratums, rock mass structure, and topography as well as hydrogeology condition. Based on rock mass structure controlling theory, engineering geology model of the slope is grouped into two typical classes, one is model with obvious controlling discontinuities, which includes horizontal bedded slope, bedding slope, anti-dip slope, slide as well as slope with base rock and weathered crust; the other is model without obvious controlling discontinuities, which includes homogeneous soil slope, joint rock mass slope. Study on slope failure mechanism under dynamic force, the paper concludes that there are two effects will appear in slope during strong earthquake, one is earthquake inertia force, the other is ultra pore pressure buildup. The two effects lead to failure of the slope. To different types of slope failure, the intensity of two effects acting on the slope is different too. To plastic flow failure, pore pressure buildup is dominant; to falling rock failure and toppling failure, earthquake inertia force is dominant in general. This paper briefly introduces the principle of Lagrangian element method. Through a lot of numerical simulations with FLAC3D, the paper comprehensively studies dynamic responses of slopes, and finds that: if the slope is low, displacement, velocity and acceleration are linear enlarging with elevation increasing in vertical direction; if the slope is high enough, displacement, velocity and acceleration are not linear with elevation any more, on the other hand, they fluctuate with certain rhythm. At the same time, the rhythm appears in the horizontal direction in the certain area near surface of the slope. The distribution form of isoline of displacement, velocity and acceleration in the section of the slope is remarkably affected by the slope angle. In the certain area near the slope surface, isoline of displacement, velocity and acceleration is parallel to the surface of the slope, in the mean time, the strike direction of the extreraum area is parallel to the surface of the slope too. Beyond this area, the isoline direction and the strike direction of the extremum area turn to horizontal with invariable distance. But the rhythm appearing or not has nothing to with the slope angle. The paper defines the high slope effect and the low slope effect of slopes dynamic responses, discusses the threshold height H^t of the dynamic high slope effect, and finds that AW is proportional to square root of the dynamic elastic moduli El P , at the same time, it is proportional to period Tof the dynamic input. Thus, the discriminant of H^t is achieved. The discriminant can tell us that to a slope, if its height is larger than one fifth of the wavelength, its response regular will be the dynamic high slope effect; on the other hand, its response regular will be the dynamic low slope effect. Based on these, the discriminant of different slopes taking on same response under the same dynamic input is put forward in this paper. At the same time, the paper studies distribution law of the rhythm extremum point of displacement, velocity and acceleration, and finds that there exists relationship of N = int among the slope height H, the number of the rhythm extremum VHlhro) point N and ffthre- Furthermore, the paper points out that if N^l, the response of the slope will be dynamic high slope effect; \fNforce model as well as pore pressure model of Martin-Finn-Seed, a method for estimating the permanent displacement of the slide is put forward in this paper, and then put it into dynamic analysis of the left abutment slope of Jinping hydropower station. The forecasting result is almost coincided with numerical simulation result. The Jinping hydropower station, located at the middle stream of Yalongjiang River and the west side of Jinpingdahewan, is the highest double-curvature arch dam planned in building in the world. However, deep fractures are well developed at the left abutment slope, so stability of the slope is a key engineering geological problem. The paper studies the dynamic stability of the slope. In the analysis, considering regional geology and regional seismology of the slope, combining with characteristics of the slope as well as the scale of the project, PGA(peak ground acceleration) of the site is decided (about 197.1cm/s2) by engineering seismology, and then the seismic input used in the slope dynamic analysis is determined. Comprehensive studies are carried out on the slope, especially to its deep fractures, and then the paper concludes that the deep fractures of slope are the result of the combination unloading effect of gravity and tectonic stress. At the same time, the failure model of the slope under dynamic input is attained. Based on these, the stability is comprehensively studied for section IV-IV with numerical simulation method as well as method putting forward in chapter 5. At last, the paper concludes that under dynamic input, the section will slide along fault f9, some deep fractures and fault/5 with certain permanent displacement, and this must be taken into consideration in the engineering.