Flexibility of the alpha-spectrin N-terminus by EPR and fluorescence polarization

The structure and flexibility of the biologically important alpha-spectrin amino terminal region was examined by the use of fluorescence and EPR spectroscopy. The region studied has been previously demonstrated to be essential for the alpha-spectrin:beta-spectrin association of the tetramerization site. Appropriate spectroscopic probe moieties were coupled to this region in a recombinant fragment of human erythroid alpha-spectrin. There was good agreement between the EPR and fluorescence techniques in most of this region. Mobility determinations indicated that a portion of the region was relatively immobilized. This is significant, since although predictive methods have indicated that this region should be alpha-helical, previous experimental evidence obtained on smaller synthetic peptides had indicated that this region was disordered. Observed rigidity appears to be incompatible with such a disordered state, and has important ramifications for the flexibility of this molecule that is so integral to its role in stabilizing erythrocyte membranes.     

中国西南纵向岭谷区外来入侵植物对生物多样性的影响

论述中国西南纵向岭谷区外来入侵植物对生物多样性的影响。中国西南纵向岭谷区是我国生物多样性保护的关键地区。目前,该区域已成为外来植物入侵的重灾区,外来入侵植物种类多达70余种,其中,紫茎泽兰Ageratina adenophora（Eupatoriumadenophorum）、飞机草Chromolaena odorata（Eupatorium odoratum）和肿柄菊Tithonia diversifolia等在该区域危害严重,该区域的生态系统的结构与功能遭受破坏,本地物种面临灭绝,农、林、牧生产乃至区域的生态安全受到威胁。该区域的外来入侵植物的危害居全国之冠。研究该区域的外来入侵植物,揭示其危害规律,遏制其危害速度,最终清除该区域的外来入侵植物,恢复该区域的生态平衡,具有十分重要的现实意义和科学价值。文中详细论述了外来入侵植物对植物物种多样性、植物群落多样性、生态系统多样性、农牧业及林业的影响,最后指出消除和控制外来入侵植物的途径。     

A physical map of the Q region of B10.P

The murine class I MHC Q region is part of a large complex multigene family whose members have various peptide-binding functions. The structure of the Q region is complex, varying extensively in the b, d, k, and q haplotypes so far examined. To better understand the structural heterogeneity, we examined the Q region of B10.P, a strain whose immunological characteristics are distinct from other haplotypes. A total of 89 cosmids were isolated from genomic DNA. The B10.P Q region was found to contain seven genes in a 190-kb cluster linked to D^p and two additional Q genes in a separate 55-kb cluster. The gene arrangement in this haplotype was unique and did not correspond to any other haplotype; this underscores the complexity of chromosomal structure in this region. In addition to the Q region clusters, Tla region was tentatively aligned in five clusters spanning approximately 300 kb. One 37-kb M region cosmid was also identified. Received: 24 February 1995 / Accepted: 10 October 1995     

Effect of the degree of polar mismatching on traffic jam formation in fast axonal transport

This paper simulates an axon with a region of reversed microtubule (MT) polarity, and investigates how the degree of polar mismatching in this region affects the formation of organelle traps in the axon. The model is based on modified Smith–Simmons equations governing molecular-motor-assisted transport in neurons. It is established that the structure that develops as a result of a region with disoriented MTs consists of two organelle traps, the trap to the left of this region accumulates plus-end-oriented organelles and the trap to the right of this region accumulates minus-end-oriented organelles. The presence of such a structure is shown to inhibit the transport of organelles down the axon. The degree by which the transport of organelles is inhibited depends on the degree of polar mismatching of MTs in the region between MT traps. Four cases with a different degree of polar mismatching are investigated.     

Price of disorder in the lac repressor hinge helix

The Lac system of genes has been pivotal in understanding gene regulation. When the lac repressor protein binds to the correct DNA sequence, the hinge region of the protein goes through a disorder to order transition. The structure of this region of the protein is well understood when it is in this bound conformation, but less so when it is not. Structural studies show that this region is flexible. Our simulations show this region is extremely flexible in solution; however, a high concentration of salt can help kinetically trap the hinge helix. Thermodynamically, disorder is more favorable without the DNA present.     

Rat IGF-I cDNA's contain multiple 5'-untranslated regions

DNA sequencing of several independent rat IGF-I cDNA clones has revealed three different 5'-untranslated region sequences which contain multiple, upstream, in-frame initiation codons. Use of these codons could generate N-terminal heterogeneity in IGF-I precursor proteins. One of these 5'-untranslated region sequences contains a 40-bp segment which is an inverted repeat of a region in the common 3'-untranslated region. The ends of the IGF-I mRNA corresponding to this cDNA could form a stable duplex structure. Such a complex could prevent ribosomal access to the AUG codons preceding the coding region for the pre-pro-IGF-I peptide, suggesting the possibility of translational regulation of this form of IGF-I mRNA. The 3'-untranslated region inverted repeat sequence also is present in human and mouse IGF-I cDNA's, and, intriguingly, is more highly conserved than the rest of the 3'-untranslated region.     

Nucleotide sequence of the promoter region of the melibiose operon of Escherichia coli

The nucleotide sequence of the promoter region of the melibiose operon of E. coli was determined. Consensus sequences for the -35 region, the Pribnow box and the binding site for cyclic AMP receptor protein were found in this region. The possible secondary structure of this DNA region was very similar to that of the promoter region of the lactose operon. A possible initiation ATG preceded by a Shine-Dalgarno sequence with proper spacing was present just downstream of the promoter region. The possible sequence of 52 amino acid residues in the NH2 terminus of the alpha-galactosidase were determined.     

A role for the polyproline domain of p53 in its regulation by Mdm2

The p53 protein plays a key role in the cellular response to stress by inducing cell growth arrest or apoptosis. The polyproline region of p53 has been shown to be important for its growth suppression activity. p53 protein lacking the polyproline region has impaired apoptotic activity and altered specificity for certain apoptotic target genes. Here we describe the role of this region in the regulation of p53 by its inhibitor Mdm2. p53 lacking the polyproline region was identified to be more susceptible to inhibition by Mdm2. Furthermore, the absence of this region renders p53 more accessible to ubiquitination, nuclear export, and Mdm2-mediated degradation. This increased sensitivity to Mdm2 results from an enhanced affinity of Mdm2 toward p53 lacking the polyproline region. Our results provide a new explanation for the impaired growth suppression activity of p53 lacking this region. The polyproline region is proposed to be important in the modulation of the inhibitory effects of Mdm2 on p53 activities and stability.     

Aspirin upregulates expression of urokinase type plasminogen activator receptor (uPAR) gene in human colon cancer cells through AP1

In this study, the effects of acetylsalicylic acid (aspirin) on the expression of uPAR and the mechanism by which it regulates expression of uPAR was examined in two different colon cancer cell lines HCT116 and GEO, respectively. The study shows that under physiological concentration, aspirin upregulates steady-state level expression of uPAR mRNA as well as expression of uPAR protein. Using a transient transfection assay, a region corresponding to -1 to -398 region of uPAR promoter has been identified which shows maximum responsiveness to aspirin treatment and found that this region is sufficient for the aspirin-induced up-regulation of uPAR. A stable integration of a single copy of this region coupled to luciferase reporter gene into the HCT116 genome also behaved similarly. Using gel mobility shift assays, it is found that the distal AP1 region between -171 and -186 is responsible for the aspirin-induced up-regulation of uPAR. Mutation of this region reduced up-regulation. Supershift assays identify that the bound proteins at this region are c-Jun and Fra-1. Real-time PCR analysis showed more than 4-fold increase in the binding of c-Jun and a 1.6-fold increase in the binding of Fra-1 in this region and this up-regulation corresponds to an increased binding of acetylated histone H4 in this region. Since an increase in the expression of uPAR corresponds to an increase in the migration of the cell, a migration assay was performed and result showed a 3-fold increased migration of HCT116 cells through the vitronectin-coated layer. Thus, an AP1 mediated pathway for aspirin induced up-regulation of uPAR has been identified.     

A complex rearrangement on chromosome 22 affecting both homologues; haplo-insufficiency of the Cat eye syndrome region may have no clinical relevance

The presence of highly homologous sequences, known as low copy repeats, predisposes for unequal recombination within the 22q11 region. This can lead to genomic imbalances associated with several known genetic disorders. We report here a developmentally delayed patient carrying different rearrangements on both chromosome 22 homologues, including a previously unreported rearrangement within the 22q11 region. One homologue carries a deletion of the proximal part of chromosome band 22q11. To our knowledge, a ‘pure’ deletion of this region has not been described previously. Four copies of this 22q11 region, however, are associated with Cat eye syndrome (CES). While the phenotypic impact of this deletion is unclear, familial investigation revealed five normal relatives carrying this deletion, suggesting that haplo-insufficiency of the CES region has little clinical relevance. The other chromosome 22 homologue carries a duplication of the Velocardiofacial/DiGeorge syndrome (VCFS/DGS) region. In addition, a previously undescribed deletion of 22q12.1, located in a relatively gene-poor region, was identified. As the clinical features of patients suffering from a duplication of the VCFS/DGS region have proven to be extremely variable, it is impossible to postulate as to the contribution of the 22q12.1 deletion to the phenotype of the patient. Additional patients with a deletion within this region are needed to establish the consequences of this copy number alteration. This study highlights the value of using different genomic approaches to unravel chromosomal alterations in order to study their phenotypic impact.     

Mapping of quantitative trait locus related to submergence tolerance in rice with aid of chromosome walking.

The major QTL for submergence tolerance was locate in the 5.9 cM interval between flanking RFLP markers. To narrow down this region, a physical map was constructed using YAC and BAC clones. A 400-kb YAC was identified in this region and later its end fragments were used to screen a rice BAC library. Through chromosome walking, 24 positive BAC clones formed two contigs around linked-RFLP markers, R1164 and RZ698. Using one YAC end, six BAC ends and three RFLP markers, a fine-scale map was constructed of the 6.8-cM interval of S10709-RZ698 on rice chromosome 9. The submergence tolerance and related trait were located in a small, well-defined region around BAC-end marker 180D1R and RFLP marker R1164. The physical-to-map distance ratio in this region is as small as 172.5 kb/cM, showing that this region is a hot spot for recombination in the rice genome.     

The lac repressor hinge helix in context: The effect of the DNA binding domain and symmetry

The Lac system of genes has been an important model system in understanding gene regulation. When the dimer lac repressor protein binds to the correct DNA sequence, the hinge region of the protein goes through a disorder to order transition. The hinge region is disordered when binding to nonoperator sequences. This region of the protein must pay a conformational entropic penalty to order when it is bound to operator DNA. Structural studies show that this region is flexible. Previous simulations showed that this region is disordered when free in solution without the DNA binding domain present. Our simulations corroborate that this region is extremely flexible in solution, but we find that the presence of the DNA binding domain proximal to the hinge helix and salt make the ordered conformation more favorable even without DNA present.     

青海湖地区植被及其分布规律

青海湖地区位于青藏高原东北部。境内复杂的地貌类型及青海湖的存在对植被有重要影响。本区植物种类贫乏,现有种子植物52科、174属、445种。主要植被类型有寒温性针叶林、高原河谷灌丛、高寒灌丛、沙生灌丛、温性草原、高寒草原、高寒草甸、沼泽草甸、高寒流石坡植被等。植被分布表现出明显的规律性变化。草原分布于湖盆及河谷地带,由东而西植被类型有更加适应寒旱趋势。温性草原以青海湖为中心;呈环带状分布,而高寒草原的分布则与生境寒冷干旱相一致。山地垂直带谱表现为草原带、高寒灌丛与高寒草甸带以及高寒流石坡植被带。本区植被水平地带性分异受到青海湖的影响,其植被组合及特征表现出与青藏高原植被的明显相似性。作为祁连山南麓中部地区的一个大型山间盆地,其东西方向界于青海省东部地区和柴达木盆地之间,植被东西方向的水平地带性并未表现出明显的过渡特征。根据植被特点及分布规律分析,本区植被有其自身的特殊性,并与青藏高原隆升之后气候寒冷干旱相一致。因此,青海湖地区就整体而言应属祁连山地区植被一个相对独立的组成部分。     

A general approach to confidence regions for optimal factor levels of response surfaces

For a response surface experiment, an approximate hypothesis test and an associated confidence region is proposed for the minimizing (or maximizing) factor-level configuration. Carter et al. (1982, Cancer Research 42, 2963-2971) show that confidence regions for optimal conditions provide a way to make decisions about therapeutic synergism. The response surface may be constrained to be within a specified, bounded region. These constraint regions can be quite general. This allows for more realistic constraint modeling and a wide degree of applicability, including constraints occurring in mixture experiments. The usual assumption of a quadratic model is also generalized to include any regression model that is linear in the model parameters. An intimate connection is established between this confidence region and the Box-Hunter (1954, Biometrika 41, 190-199) confidence region for a stationary point. As a byproduct, this methodology also provides a way to construct a confidence interval for the difference between the optimal mean response and the mean response at a specified factor-level configuration. The application of this confidence region is illustrated with two examples. Extensive simulations indicate that this confidence region has good coverage properties.     

Identification of mouse adenovirus type 1 early region 1: DNA sequence and a conserved transactivating function.

The left end of the genome of mouse adenovirus type 1 (also known as strain FL) was characterized by determination of the DNA sequence, amino acid similarities with early region proteins of primate adenoviruses, and a functional assay. Several specific DNA sequence features were similar to those found in human adenoviruses, and open reading frames from this region could encode proteins similar to human adenovirus early region 1A and early region 1B proteins. DNAs from this region were tested in transient-expression assays in human and mouse cells were found to transactivate the human adenovirus type 5 early region 3 promoter fused to the chloramphenicol acetyltransferase gene. The data indicate structural and functional homologies between mouse adenovirus type 1 early region 1 and early region 1 of primate adenoviruses.     

Molecular dynamics simulations of a helicase

Helicases are ubiquitous enzymes involved in nucleic acid metabolism. The PcrA DNA helicase is an essential bacterial protein involved in rolling circle plasmid replication and DNA repair. Recent crystal structures of PcrA bound to DNA indicate that a flexible loop mediates a functionally important rigid-body-domain rotation. In this study, we report stochastic boundary molecular dynamics simulations focused on this region for wild-type and mutants designed to increase the rigidity of the region. Residues in the region that were helix-disfavoring, such as glycine, threonine, and others, were mutated to alanine. The simulated dynamics, analyzed with a variety of measures of structure and mobility, indicate that a few point mutations will substantially increase helix formation in this region. Subnanosecond stochastic boundary molecular dynamics simulations at several temperatures offer a rapid protocol for assessing large numbers of mutants and provides a novel strategy for the design of experiments to test the role of this flexible loop region in the function of PcrA.     

DNA sequence comparative analysis of the 3pter-p26 region of human genome

Most proterminal regions of human chromosomes are GC-rich and gene-rich. Chromosome 3p is an exception. Its proterminal region is GC-poor, and likely to lose heterozy-gosity, thus causing a number of fatal diseases. Except one gap left in the telomeric position, the proterminal region of human chromosome 3p has been completely sequenced. The detailed sequence analysis showed: (i) the GC content of this region was 38.5%, being the lowest among all the human proterminal regions; (ii) this region contained 20 known genes and 22 predicted genes, with an average gene size of 97.5 kb. The previously mapped gene Cntn3 was not found in this region, but instead located in the 74 Mb position of human chromosome 3p; (iii) the interspersed repeats of this region were more active than the average level of the whole human genome, especially (TA)n, the content of which was twice the genome average; (iv) this region had a conserved synteny extending from 104.1 Mb to 112.4 Mb on the mouse chromosome 6, which was 8% larger in size, not in accordance with the whole genome comparison, probably because the 3pter-p26 region was more likely to lose neocleitides and its mouse synteny had more active interspersed repeats.