Influence of two different representations of the G-matrix to the in-medium nucleon-nucleon cross sections

We calculate the in-medium nucleon-nucleon scattering cross sections from the G-matrix using the Dirac-Brueckner-Hartree-Fock (DBHF) approach. And we investigate the influence of the different representations of the G-matrix to the cross sections, the difference of which is mainly from the different effective masses.

Effects of selection and drift on G matrix evolution in a heterogeneous environment: a multivariate Qst-Fst Test with the freshwater snail Galba truncatula.

Unraveling the effect of selection vs. drift on the evolution of quantitative traits is commonly achieved by one of two methods. Either one contrasts population differentiation estimates for genetic markers and quantitative traits (the Q(st)-F(st) contrast) or multivariate methods are used to study the covariance between sets of traits. In particular, many studies have focused on the genetic variance-covariance matrix (the G matrix). However, both drift and selection can cause changes in G. To understand their joint effects, we recently combined the two methods into a single test (accompanying article by Martin et al.), which we apply here to a network of 16 natural populations of the freshwater snail Galba truncatula. Using this new neutrality test, extended to hierarchical population structures, we studied the multivariate equivalent of the Q(st)-F(st) contrast for several life-history traits of G. truncatula. We found strong evidence of selection acting on multivariate phenotypes. Selection was homogeneous among populations within each habitat and heterogeneous between habitats. We found that the G matrices were relatively stable within each habitat, with proportionality between the among-populations (D) and the within-populations (G) covariance matrices. The effect of habitat heterogeneity is to break this proportionality because of selection for habitat-dependent optima. Individual-based simulations mimicking our empirical system confirmed that these patterns are expected under the selective regime inferred. We show that homogenizing selection can mimic some effect of drift on the G matrix (G and D almost proportional), but that incorporating information from molecular markers (multivariate Q(st)-F(st)) allows disentangling the two effects.

Medium-spin states in Ge-70 and the role of the g(9/2) orbital

Medium-spin states of Ge-70 have been studied via the Ni-60(C-12,2p gamma)Ge-70 reaction at 45 MeV. The ground-state band and the second 0(+) band have been extended to the 12(+) and 8(+) states, respectively. Two negative-parity bands, one of which has a coupled structure and the other has a decoupled structure, have been observed additionally. Although the latter decoupled structure was known up to the (21(-)) state from a previous experiment, the part of the level scheme up to the 15(-) state has been largely modified by the present experiment. Backbendings observed in the positive- and negative-parity yrast bands have been compared with those of the neighboring even Ge isotopes. The experimental level structure has been compared with the shell-model calculations in the model space (2p(3/2), 1f(5/2), 2(p1/2), 1g(9/2)) employing two kinds of effective interactions, one of which is an extended P + QQ interaction with monopole interactions and the other is developed from a renormalized G matrix. Microscopic structures of the observed bands have been discussed with the help of the shell-model calculations.

Bioengineered 3D platform to explore cell-ECM interactions and drug resistance of epithelial ovarian cancer cells

The behaviour of cells cultured within three-dimensional (3D) structures rather than onto two-dimensional (2D) culture plastic more closely reflects their in vivo responses. Consequently, 3D culture systems are becoming crucial scientific tools in cancer cell research. We used a novel 3D culture concept to assess cell-matrix interactions implicated in carcinogenesis: a synthetic hydrogel matrix equipped with key biomimetic features, namely incorporated cell integrin-binding motifs (e.g. RGD peptides) and the ability of being degraded by cell-secreted proteases (e.g. matrix metalloproteases). As a cell model, we chose epithelial ovarian cancer, an aggressive disease typically diagnosed at an advanced stage when chemoresistance occurs. Both cell lines used (OV-MZ-6, SKOV-3) proliferated similarly in 2D, but not in 3D. Spheroid formation was observed exclusively in 3D when cells were embedded within hydrogels. By exploiting the design flexibility of the hydrogel characteristics, we showed that proliferation in 3D was dependent on cell-integrin engagement and the ability of cells to proteolytically remodel their extracellular microenvironment. Higher survival rates after exposure to the anti-cancer drug paclitaxel were observed in cell spheroids grown in hydrogels (40-60%) compared to cell monolayers in 2D (20%). Thus, 2D evaluation of chemosensitivity may not reflect pathophysiological events seen in patients. Because of the design flexibility of their characteristics and their stability in long-term cultures (28 days), these biomimetic hydrogels represent alternative culture systems for the increasing demand in cancer research for more versatile, physiologically relevant and reproducible 3D matrices.

Large body size in an island-dwelling bird : a microevolutionary analysis

Island races of passerine birds display repeated evolution towards larger body size compared with their continental ancestors. The Capricorn silvereye (Zosterops lateralis chlorocephalus) has become up to six phenotypic standard deviations bigger in several morphological measures since colonization of an island approximately 4000 years ago. We estimated the genetic variance-covariance (G) matrix using full-sib and 'animal model' analyses, and selection gradients, for six morphological traits under field conditions in three consecutive cohorts of nestlings. Significant levels of genetic variance were found for all traits. Significant directional selection was detected for wing and tail lengths in one year and quadratic selection on culmen depth in another year. Although selection gradients on many traits were negative, the predicted evolutionary response to selection of these traits for all cohorts was uniformly positive. These results indicate that the G matrix and predicted evolutionary responses are consistent with those of a population evolving in the manner observed in the island passerine trend, that is, towards larger body size.

CSSI-PRO: a method for secondary structure type editing, assignment and estimation in proteins using linear combination of backbone chemical shifts

Estimation of secondary structure in polypeptides is important for studying their structure, folding and dynamics. In NMR spectroscopy, such information is generally obtained after sequence specific resonance assignments are completed. We present here a new methodology for assignment of secondary structure type to spin systems in proteins directly from NMR spectra, without prior knowledge of resonance assignments. The methodology, named Combination of Shifts for Secondary Structure Identification in Proteins (CSSI-PRO), involves detection of specific linear combination of backbone H-1(alpha) and C-13' chemical shifts in a two-dimensional (2D) NMR experiment based on G-matrix Fourier transform (GFT) NMR spectroscopy. Such linear combinations of shifts facilitate editing of residues belonging to alpha-helical/beta-strand regions into distinct spectral regions nearly independent of the amino acid type, thereby allowing the estimation of overall secondary structure content of the protein. Comparison of the predicted secondary structure content with those estimated based on their respective 3D structures and/or the method of Chemical Shift Index for 237 proteins gives a correlation of more than 90% and an overall rmsd of 7.0%, which is comparable to other biophysical techniques used for structural characterization of proteins. Taken together, this methodology has a wide range of applications in NMR spectroscopy such as rapid protein structure determination, monitoring conformational changes in protein-folding/ligand-binding studies and automated resonance assignment.

Urey-Bradley potential function for the in-plane vibrations of boric acid

The Urey-Bradley force constants for the in-plane vibrations of the boric acid molecule are calculated using the Wilson's F-G matrix method. They are as follows: KO-H=5·23, KB-O=4·94, HBOH=0·36, {Mathematical expression}, F00=0·68 and FBH=0·98 in units of 105 dynes/cm. Using the force constants, the frequencies are recalculated and the calculated values agree with the observed values satisfactorily. The in-plane vibrational frequencies of deuterated boric acid are also calculated and again satisfactory agreement with the observed values is found.

High-resolution methyl edited GFT NMR experiments for protein resonance assignments and structure determination

Three-dimensional (3D) structure determination of proteins is benefitted by long-range distance constraints comprising the methyl groups, which constitute the hydrophobic core of proteins. However, in methyl groups (of Ala, Ile, Leu, Met, Thr and Val) there is a significant overlap of C-13 and H-1 chemical shifts. Such overlap can be resolved using the recently proposed (3,2)D HCCH-COSY, a G-matrix Fourier transform (GFT) NMR based experiment, which facilitates editing of methyl groups into distinct spectral regions by combining their C-13 chemical shifts with that of the neighboring, directly attached, C-13 nucleus. Using this principle, we present three GFT experiments: (a) (4,3)D NOESY-HCCH, (b) (4,3)D H-1-TOCSY-HCCH and (c) (4,3)D C-13-TOCSY-HCCH. These experiments provide unique 4D spectral information rapidly with high sensitivity and resolution for side-chain resonance assignments and NOE analysis of methyl groups. This is exemplified by (4,3)D NOESY-HCCH data acquired for 17.9 kDa non-deuterated cytosolic human J-protein co-chaperone, which provided crucial long-range distance constraints for its 3D structure determination.

NMR methods for fast data acquisition

NMR spectroscopy has witnessed tremendous advancements in recent years with the development of new methodologies for structure determination and availability of high-field strength spectrometers equipped with cryogenic probes. Supported by these advancements, a new dimension in NMR research has emerged which aims to increase the speed with data is collected and analyzed. Several novel methodologies have been proposed in this direction. This review focuses on the principles on which these different approaches are based with an emphasis on G-matrix Fourier transform NMR spectroscopy.

GFT projection NMR for efficient H-1/C-13 sugar spin system identification in nucleic acids

A newly implemented G-matrix Fourier transform (GFT) (4,3)D HC(C)CH experiment is presented in conjunction with (4,3)D HCCH to efficiently identify H-1/C-13 sugar spin systems in C-13 labeled nucleic acids. This experiment enables rapid collection of highly resolved relay 4D HC(C)CH spectral information, that is, shift correlations of C-13-H-1 groups separated by two carbon bonds. For RNA, (4,3)D HC(C)CH takes advantage of the comparably favorable 1'- and 3'-CH signal dispersion for complete spin system identification including 5'-CH. The (4,3)D HC(C)CH/HCCH based strategy is exemplified for the 30-nucleotide 3'-untranslated region of the pre-mRNA of human U1A protein.

A fast NMR method for resonance assignments: application to metabolomics

We present a new method for rapid NMR data acquisition and assignments applicable to unlabeled (C-12) or C-13-labeled biomolecules/organic molecules in general and metabolomics in particular. The method involves the acquisition of three two dimensional (2D) NMR spectra simultaneously using a dual receiver system. The three spectra, namely: (1) G-matrix Fourier transform (GFT) (3,2)D C-13, H-1] HSQC-TOCSY, (2) 2D H-1-H-1 TOCSY and (3) 2D C-13-H-1 HETCOR are acquired in a single experiment and provide mutually complementary information to completely assign individual metabolites in a mixture. The GFT (3,2)D C-13, H-1] HSQC-TOCSY provides 3D correlations in a reduced dimensionality manner facilitating high resolution and unambiguous assignments. The experiments were applied for complete H-1 and C-13 assignments of a mixture of 21 unlabeled metabolites corresponding to a medium used in assisted reproductive technology. Taken together, the experiments provide time gain of order of magnitudes compared to the conventional data acquisition methods and can be combined with other fast NMR techniques such as non-uniform sampling and covariance spectroscopy. This provides new avenues for using multiple receivers and projection NMR techniques for high-throughput approaches in metabolomics.

Simultaneous acquisition of three NMR spectra in a single experiment for rapid resonance assignments in metabolomics

NMR-based approach to metabolomics typically involves the collection of two-dimensional (2D) heteronuclear correlation spectra for identification and assignment of metabolites. In case of spectral overlap, a 3D spectrum becomes necessary, which is hampered by slow data acquisition for achieving sufficient resolution. We describe here a method to simultaneously acquire three spectra (one 3D and two 2D) in a single data set, which is based on a combination of different fast data acquisition techniques such as G-matrix Fourier transform (GFT) NMR spectroscopy, parallel data acquisition and non-uniform sampling. The following spectra are acquired simultaneously: (1) C-13 multiplicity edited GFT (3,2)D HSQC-TOCSY, (2) 2D H-1- H-1] TOCSY and (3) 2D C-13- H-1] HETCOR. The spectra are obtained at high resolution and provide high-dimensional spectral information for resolving ambiguities. While the GFT spectrum has been shown previously to provide good resolution, the editing of spin systems based on their CH multiplicities further resolves the ambiguities for resonance assignments. The experiment is demonstrated on a mixture of 21 metabolites commonly observed in metabolomics. The spectra were acquired at natural abundance of C-13. This is the first application of a combination of three fast NMR methods for small molecules and opens up new avenues for high-throughput approaches for NMR-based metabolomics.

两个冠醚分子在简正坐标分析及NRCC程序在微机上的移植

本文用加拿大国立研究院(National Research Council of Canada) Fuhrer等人编制的FORTRAN语言程序（以下简称NRCC程序），对两个冠醚类化合物进行了简正坐标分析，这两个化合物分子是二氧六环(C_4H_8O_2)和12－冠－4(C_8H_(16)O_4)。作者用Synder和Zerbi提出的一般价力场，计算了二氧六环的36个简正振动频率，精化四次后的结果误差为14.04 cm~(-1)，得到了二氧六环的精化力场和势能分析矩阵；做了12－冠－4－的中红外光谱(3200-5000cm~(-1))。远红外光谱(500-70cm~(-1))和拉曼光谱(3200-50 cm~(-1)，从而归属出12－冠－4的78个简正振动频率实验值；利用二氧六环的精化力场作为初始力场，计算了12－冠－4的简正振动频率，对78个简正振动频率进行了精化计算，精化三次后的结果误差为13.99 cm~(-1)，精化后得到12－冠－4的精化力场和势能分布矩阵；将NRCC程序以BASIC语言移至TRS-80微型机上，对二氧六环进行了计算，结果良好，首次给出二氧六环一般价力场的势能分布。一、对二氧六环的处理 二氧六环分子式C_4H_8O_2，合14个原子，有3N－6＝36个简正振动频率。分子结构系由二个乙氧基(-CH_2-CH_2-O-)单元组成的含有四个碳，两个氧的六元环，平衡态分子为椅式构象，属于C_(2h)点群，36个简正振动频率分为四个对称类Ag、Au、Bg和Bu，分布是：Ag 10个，Bg 8个，Au 9个，Bu9个。二氧六环的分子结构及坐标示意图见28而图5，定义了14个伸缩内坐标，26个弯曲内坐标，6个扭曲内坐标，共46个，C－C键长1.54A，C-O键长1.41 A，C－H键长1.096A，键角都用109°28'。用CART程序（NRCC程序之一）计算二氧六环14个原子的笛卡尔坐标，用GMAT程序（NRCC程序之二）计算其B矩阵和G矩阵，用FPERT程序（NRCC程序之三）计算其简正振动频率、精化力场，计算用一般价力场，引入V矩阵对称化，将46个坐标化为46个（内）对称坐标，10个多余坐标在FPERT程序计算中除去。二、对12－冠－4的处理 12－冠－4分子式C_8H_(16)O_4，含28个原子，共3N－6＝78个简正振动频率，分子结构为四个乙氧基(-CH_2-CH_2-O-)单元组成的含八个碳、四个氧的12元环，自由分子的12－冠－4属于C点群。结构数据引自Groth的X光衍射分数和坐标，自己编制了BASIC语言程度将分数坐标化为笛卡尔坐标，用GMAT程序计算B矩阵和G矩阵，FPERT程序计算78个简正振动频率、精化力场、计算势能分布矩阵，引入U矩阵将92个内坐标化为92个对称坐标，14个多余坐标在FPERT程序中自动除去。三、结果 势能分布矩阵给出分子的振动归属，对这两个冠醚类分子的3N－6个简正振动频率，可以划分为五个振动区域。1．C－H伸缩振动区（3000－2800 cm~(-1)） 在该区中，二氧六环有八个值：2974、2966、2854和2867 cm~(-1)各两个，12－冠－4有16个值：2935、2923、2915和2907 cm~(-1)各两个，2860 cm~(-1)8个，高于2900 cm~(-1)者为反对称伸缩振动，低于2900 cm~(-1)者为对称伸缩振动。2．亚甲基弯曲振动之一(1500-1400 cm~(-1)) 该区的主要振动是亚甲基剪式振动(Scissor)，其它振动小于10％二氧六环在该区有四个频率：1443、1461、1451和1457 cm~(-1)，12－冠－4有八个频率：1466、1450、1450和1405 cm~(-1)各两个。3．亚甲基弯曲振动区二(1400-1200 cm~(-1))该区的主要振动模式为亚甲基的颤动(wag)、卷曲(twist)和摆动(rock)振动，其它振动小于13％。二氧六环在该区有八个频率：1334、1303、1396、1216、1367、1264、1377和1296 cm~(-1)，12－冠－4有十六个频率：1388、1363、……1229 cm~(-1)（其中1288、1307cm~(-1)非简并，其余皆两重简并）。4．环的骨架伸缩振动区(1200-600 cm~(-1))该区振动模式复杂，除环的骨架伸缩振动外，还有亚甲基的wag、twist、rock以及环的骨架弯曲振动，而且这些振动的势能分布值都不小。二氧六环在该区有十一个频率，从1127至610 cm~(-1)，12－冠－4有二十个频率，从1135至184 cm~(-1)且大都是二重简并的。5．低频区(600-50cm~(-1))这两个分子在低频区的势能分布略有差别。二氧六环在该区有五个频率：503、486、427、276和224 cm~(-1)，主要振动模式为骨架弯曲振动和扭曲振动，C－O、C－C的扭曲振动在三个最低频率中分布占10－30％。12－冠－4在该区有18个频率，除570和547cm~(-1)处，都是二重简并的，六个最低频率的振动模式完全属于C－O、C－C键的扭曲振动，其它振动小于10％，所以200 cm~(-1)以下可称为12－冠－4的扭曲振动区，在600－200cm~(-1)之间的12个频率主要是骨架的弯曲振动，也有一定量的亚甲基wag、twist、rock振动。12－冠－4的简正坐标分析尚未有人做过。二氧六环的计算结果与Snyder和Zerbi的分析相吻合，12－冠－4和二氧六环两分子势能分布的相对一致性证明了对12－冠－4的简正坐标分析基本是正确的。本文比较了二分子的力常数和振动频率，探讨了环的大小对振动光谱的影响。四、NRCC程序简介 NRCC程序由CART、GMAT和FPERT三个程序组成，即可联一起运用，亦可分开独立进行运算。该程序功能强，所占内存大，适于大、中型计算机使用。CART程序之名字取自Cartisian Co-or-dinates的前四个字母，功能系由分子结构参数（键长、键角）计算分子内各原子的笛卡尔坐标。GMAT程序之名字取自G matrix的前四个字母，功能系由分子内各原子的笛卡尔坐标，原子质量和内坐标定义计算分子内各原子的坐标交换矩阵B和Wilson振动动能矩阵G。FPERT程序之名字取自F Perturbation的前五个字母，功能系由分子振动功能矩阵G、势能常数即力常数矩阵F计算分子的简正振动频率和势能分布矩阵，再通过实验频率精化势能矩阵F。NRCC程序可对含30个原子、60个内坐标的分子进行简正坐标分析，扩充后容量增大一倍。该程序可选用一般价力场(General Valence Force Field, 简称GVFF)和UBS力场(Urey-Bradley-Shimanouchi Force Field)，简称UBSFF或UBFF)。可选用对称化U矩阵，可自行决定力场精化次数和阻尼常数以限制精化结果的收敛性。五、NRCC程序在TRS－80微型机上移植试尝（该部分曾在第三届长春夏季化学讨论会上宣读）针对NRCC程序占内存空间大、难以在微型机上实现的情况，作者将NRCC程序改编为BASIC语言，改变程序的原来结构，形成一组BASIC语言程序：CART／BAS、GMAT／BAS和VIFR／BAS，改编后的BASIC程序在TRS－80微型机调试通过，TRS－80机字长8位，New Dos系统内存32K。改写后的程序只保持了原程序的基本原理，在内存，语句上改动很大，以适于微型机使用。数据在程序中直接嵌入，利于修改替换，且BASIC语言简单易学，便于操作。CART／BAS程序可计算含30个原子以内的分子的笛卡尔坐标，GMAT／BAS程序可计算含20个原子、45个内坐标的分子的G矩阵，VIFR／BAS程序可计算含15个原子的分子的简正振动频率。利用这组程序，作者以二氧六环分子为例做了一些试尝运算，误差14.4 cm~(-1)，相对误差1.8%，结果较理想。