bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differences in p53 and cadherin–catenin complex expression between histological subtypes in diffusely infiltrating gastric carcinoma
Authors: Kozuki T , Yao T , Nakamura S , Matsumoto T , Tsuneyoshi M 
Published: September 2002

Aims:  The aim of this study was to elucidate possible clinicopathological differences between diffusely infiltrating gastric carcinoma of ‘pure type’ (poorly differentiated carcinoma without any glandular component) and ‘mixed type’ (coexistence of poorly differentiated carcinoma and intramucosal glandular component).Methods and results:  The clinicopathological features and immunohistochemical expression of p53 and intercellular adhesion molecules (E‐cadherin and α‐, β‐ and γ‐catenins) were compared between the patients with pure (n=59) and mixed (n=56) types of diffusely infiltrating gastric carcinoma. Intestinal metaplasia (P < 0.01), prominent lymphatic permeation (P < 0.001) and lymph node metastasis (P < 0.05) were more frequently observed in mixed type than in pure type, while survival probability did not differ between the two groups. The frequency of p53 over‐expression was higher in mixed type (56%) than in pure‐type (19%) (P < 0.001). In mixed type, p53 expression was not different between glandular and poorly differentiated components. By contrast, the expression of adhesion molecules was more frequently preserved in glandular components than in poorly differentiated components.Conclusions:  These two subtypes seem to be different in nature and biological behaviour. The preservation of adhesion molecules in mixed type may be associated with higher incidence of lymphatic permeation and lymph node metastasis.
Centro-Central Union for the Prevention of Neuroma Formation after Finger Amputation
Authors: BELCHER H. J. C. R. , PANDYA A. N. 
Published: September 2002

Sixty digits undergoing terminalization were randomized to undergo either simple transection of the digital nerves (control) or direct suture of the nerves to each other (centro-central union, CCU). Thirty-one digits were available for review with a minimum follow-up of one year following the surgery. Assessment was by visual analogue scales (VAS) and clinical examination. Measurements included static two-point discrimination (S2PD) for sensation, dolorimetry for stump tenderness and grip-strength. Resting pain, cold intolerance and perceived tenderness were comparable in the two groups. Perceived and observed touch sensitivity were better in the control group but the stumps in this group were more tender than those in the CCU group. We conclude that CCU results in more comfortable stumps but causes greater loss of sensitivity. It is a simple and worthwhile adjunct to digital amputation.
Origin and geologic features of Taal Lake, Philippines
Authors: Ramos Emmanuel G. 
Published: September 2002

Taal Lake was formed by a series of catastrophic volcanic eruptions and other geologic processes whose character slowly evolved as the large basinal depression and the lake took form. During the early stage of Taal's life, large scale magmatic activity was very common in this part of Luzon including the caldera-forming eruptions that created parts of Laguna de Bai and the smaller scale eruptions that formed the cones and volcanic peaks in the area. Around Taal, large eruptions were carving large bowl-shaped depressions on one part while depositing thick pyroclastic rocks on more distant sites. During the last stages of the large scale magmatic eruptions, a lake must have been already present, leading to the phreatic eruptions that created the crossbedded, base-surge pyroclastics found on the upper layers of the terrain around the lake. These phreatic eruptions created smaller circular depressions that later coalesced to form the present caldera. With much of the magma exhausted after periods of protracted eruptions, the scale of volcanism was reduced and mostly centered in the region where Volcano Island is now located. Combined with the hills near Balite and Bilibinwang, development of Volcano Island formed an east-west trending ridge that divided the lake in two. Tectonic uplift and erosion on the northern shores of the young lake and the presence of deeper craters on the south led to contrasts in the depths of the depressions. Smaller scale geologic processes marked the last stage in the development of the lake. Landslides modified the steep slopes, and large blocks of land were shifted vertically and horizontally along faults by slow tectonic movements. More sediments shed from the small region drained by the lake were being deposited and volcanism continued mostly on Volcano Island.
Numerous large circular craters on the shores of the lake suggest the explosive origin of the whole Taal Lake depression. The flat-bottomed lake is shallower by about 100 m on the north. Faults are found mostly on the northern slopes, where large-scale landslide blocks are also common. Landslide features are also found underwater particularly near the steep shores. Most of the historic volcanism had been centered on Taal Volcano Island, and these are often of the explosive phreatic type reflecting the influence of the lake on magmatic activity. The resources and the people residing near the lake are still under the threat of the same active geologic processes that created Taal Lake.
Zinc‐substituted Desulfovibrio gigas desulforedoxins: Resolving subunit degeneracy with nonsymmetric pseudocontact shifts
Authors: Goodfellow Brian J. , Nunes Sofia G. , Rusnak Frank , Moura Isabel , Ascenso Carla , Moura José J.G. , Volkman Brian F. , Markley John L. 
Published: September 2002

AbstractDesulfovibrio gigas desulforedoxin (Dx) consists of two identical peptides, each containing one [Fe‐4S] center per monomer. Variants with different iron and zinc metal compositions arise when desulforedoxin is produced recombinantly from Escherichia coli. The three forms of the protein, the two homodimers [Fe(III)/Fe(III)]Dx and [Zn(II)/Zn(II)]Dx, and the heterodimer [Fe(III)/Zn(II)]Dx, can be separated by ion exchange chromatography on the basis of their charge differences. Once separated, the desulforedoxins containing iron can be reduced with added dithionite. For NMR studies, different protein samples were prepared labeled with 15N or 15N + 13C. Spectral assignments were determined for [Fe(II)/Fe(II)]Dx and [Fe(II)/Zn(II)]Dx from 3D 15N TOCSY‐HSQC and NOESY‐HSQC data, and compared with those reported previously for [Zn(II)/Zn(II)]Dx. Assignments for the 13Cα shifts were obtained from an HNCA experiment. Comparison of 1H–15N HSQC spectra of [Zn(II)/Zn(II)]Dx, [Fe(II)/Fe(II)]Dx and [Fe(II)/Zn(II)]Dx revealed that the pseudocontact shifts in [Fe(II)/Zn(II)]Dx can be decomposed into inter‐ and intramonomer components, which, when summed, accurately predict the observed pseudocontact shifts observed for [Fe(II)/Fe(II)]Dx. The degree of linearity observed in the pseudocontact shifts for residues ≥8.5 Å from the metal center indicates that the replacement of Fe(II) by Zn(II) produces little or no change in the structure of Dx. The results suggest a general strategy for the analysis of NMR spectra of homo‐oligomeric proteins in which a paramagnetic center introduced into a single subunit is used to break the magnetic symmetry and make it possible to obtain distance constraints (both pseudocontact and NOE) between subunits.
How do two unrelated antibodies, HyHEL‐10 and F9.13.7, recognize the same epitope of hen egg‐white lysozyme?
Authors: Pons Jaume , Stratton Jennifer R. , Kirsch Jack F. 
Published: September 2002

AbstractThe anti‐hen egg‐white lysozyme (HEWL) antibodies HyHEL‐10 and F9.13.7 recognize a common epitope. The structures of the complexes differ, however, in the numbers of electrostatic and hydrogen‐bond interactions and in the distributions of contacts between the light and heavy chains. The equilibria and kinetics characterizing the F9.13.7 complex formation were evaluated for both wild‐type and mutant derivatives of HEWL to help to understand how the different contacts are effectively used in the complexes with the two antibodies. Three epitope hot spots, Y20, K96, and R73 (destabilization > 4 kcal/mole), were found by alanine scanning mutagenesis. The first two constitute two of the three hot spots in the HyHEL‐10 complex. The hot spots of the HyHEL‐10 paratope are centered on the HEWL epitope; whereas R73 (HEWL), the only important light‐chain‐contacting residue, is clearly separated from the other hot spots of the F9.13.7 complex. The larger number of epitope warm plus hot spots found in the F9.13.7 complex compared with that of HyHEL‐10 shows that the specificity of the former is greater even though the KD value is 20‐fold larger. Conservative mutations showed that the specificity enhancement is related to the greater number of functional polar and hydrogen bond interactions in the F9.13.7 complex. Alanine scanning mutagenesis would not have illuminated these distinctions. It is shown that the concept of antigen specificity, as defined by cross‐reactivity with natural variant antigens, is flawed by phylogenetic bias, and that specificity can only be defined by the use of unbiased epitopes, which are conveniently accessed by site‐directed mutagenesis.
PrfA protein of Bacillus species: Prediction and demonstration of endonuclease activity on DNA
Authors: Rigden Daniel J. , Setlow Peter , Setlow Barbara , Bagyan Irina , Stein Richard A. , Jedrzejas Mark J. 
Published: September 2002

AbstractThe prfA gene product of Gram‐positive bacteria is unusual in being implicated in several cellular processes; cell wall synthesis, chromosome segregation, and DNA recombination and repair. However, no homology of PrfA with other proteins has been evident. Here we report a structural relationship between PrfA and the restriction enzyme PvuII, and thereby produce models that predict that PrfA binds DNA. Indeed, wild‐type Bacillus stearothermophilus PrfA, but not a catalytic site mutant, nicked one strand of supercoiled plasmid templates leaving 5′‐phosphate and 3′‐hydroxyl termini. This activity, much lower on linear or relaxed circular double‐stranded DNA or on single‐stranded DNA, is consistent with a role for this protein in chromosome segregation, DNA recombination, or DNA repair.
A simple model for polyproline II structure in unfolded states of alanine‐based peptides
Authors: Pappu Rohit V. , Rose George D. 
Published: September 2002

AbstractThe striking similarity between observed circular dichroism spectra of nonprolyl homopolymers and that of regular left‐handed polyproline II (PII) helices prompted Tiffany and Krimm to propose in 1968 that unordered peptides and unfolded proteins are built of PII segments linked by sharp bends. A large body of experimental evidence, accumulated over the past three decades, provides compelling evidence in support of the original hypothesis of Tiffany and Krimm. Of particular interest are the recent experiments of Shi et al. who find significant PII structure in a short unfolded alanine‐based peptide. What is the physical basis for PII helices in peptide and protein unfolded states? The widely accepted view is that favorable chain‐solvent hydrogen bonds lead to a preference for dynamical fluctuations about noncooperative PII helices in water. Is this preference simply a consequence of hydrogen bonding or is it a manifestation of a more general trend for unfolded states which are appropriately viewed as chains in a good solvent? The prevalence of closely packed interiors in folded proteins suggests that under conditions that favor folding, water—which is a better solvent for itself than for any polypeptide chain—expels the chain from its midst, thereby maximizing chain packing. Implicit in this view is a complementary idea: under conditions that favor unfolding, chain‐solvent interactions are preferred and in a so‐called good solvent, chain packing density is minimized. In this work we show that minimization of chain packing density leads to preferred fluctuations for short polyalanyl chains around canonical, noncooperative PII‐like conformations. Minimization of chain packing is modeled using a purely repulsive soft‐core potential between polypeptide atoms. Details of chain‐solvent interactions are ignored. Remarkably, the simple model captures the essential physics behind the preference of short unfolded alanine‐based peptides for PII helices. Our results are based on a detailed analysis of the potential energy landscape which determines the system's structural and thermodynamic preferences. We use the inherent structure formalism of Stillinger and Weber, according to which the energy landscape is partitioned into basins of attraction around local minima. We find that the landscape for the experimentally studied seven‐residue alanine‐based peptide is dominated by fluctuations about two noncooperative structures: the left‐handed polyproline II helix and its symmetry mate.
A CH domain‐containing N terminus in NuMA?
Authors: Novatchkova Maria , Eisenhaber Frank 
Published: September 2002

AbstractNuclear mitotic apparatus protein (NuMA) is an essential vertebrate component in organizing microtubule ends at spindle poles. The NuMA‐dynactin/dynein motor multiprotein complex not only explains the transport of NuMA along spindle fibers but also is linked to the process of microtubule focusing. The interaction sites of NuMA to dynein/dynactin have not been mapped. In the yet functionally uncharacterized N terminus of NuMA, we predict a calponin‐homology (CH) domain, a motif with binding activity for actin‐like molecules. We substantiate the primary sequence analysis‐based prediction with secondary structure and fold recognition analysis, and we propose the N‐terminal CH domain of NuMA as a likely interaction site for actin‐related protein 1 (Arp1) protein of the dynactin/dynein complex.
Adaptation of Alphaviruses to Heparan Sulfate: Interaction of Sindbis and Semliki Forest Viruses with Liposomes Containing Lipid-Conjugated Heparin
Authors: Smit Jolanda M. , Waarts Barry-Lee , Kimata Koji , Klimstra William B. , Bittman Robert , Wilschut Jan 
Published: September 2002

ABSTRACT
Passage of Sindbis virus (SIN) in BHK-21 cells has been shown to select for virus mutants with high affinity for the glycosaminoglycan heparan sulfate (HS). Three loci in the viral spike protein E2 (E2:1, E2:70, and E2:114) have been identified that mutate during adaptation and independently confer on the virus the ability to bind to cell surface HS (W. B. Klimstra, K. D. Ryman, and R. E. Johnston, J. Virol. 72:7357-7366, 1998). In this study, we used HS-adapted SIN mutants to evaluate a new model system involving target liposomes containing lipid-conjugated heparin (HepPE) as an HS receptor analog for the virus. HS-adapted SIN, but not nonadapted wild-type SIN TR339, interacted efficiently with HepPE-containing liposomes at neutral pH. Binding was competitively inhibited by soluble heparin. Despite the efficient binding of HS-adapted SIN to HepPE-containing liposomes at neutral pH, there was no fusion under these conditions. Fusion did occur, however, at low pH, consistent with cellular entry of the virus via acidic endosomes. At low pH, wild-type or HS-adapted SIN underwent fusion with liposomes with or without HepPE with similar kinetics, suggesting that interaction with the HS receptor analog at neutral pH has little influence on subsequent fusion of SIN at low pH. Finally, Semliki Forest virus (SFV), passaged frequently on BHK-21 cells, also interacted efficiently with HepPE-containing liposomes, indicating that SFV, like other alphaviruses, readily adapts to cell surface HS. In conclusion, the liposomal model system presented in this paper may serve as a novel tool for the study of receptor interactions and membrane fusion properties of HS-interacting enveloped viruses.
Magnitude and Frequency of Cytotoxic T-Lymphocyte Responses: Identification of Immunodominant Regions of Human Immunodeficiency Virus Type 1 Subtype C
Authors: Novitsky V. , Cao H. , Rybak N. , Gilbert P. , McLane M. F. , Gaolekwe S. , Peter T. , Thior I. , Ndung'u T. , Marlink R. , Lee T. H. , Essex M. 
Published: September 2002

ABSTRACTA systematic analysis of immune responses on a population level is critical for a human immunodeficiency virus type 1 (HIV-1) vaccine design. Our studies in Botswana on (i) molecular analysis of the HIV-1 subtype C (HIV-1C) epidemic, (ii) frequencies of major histocompatibility complex class I HLA types, and (iii) cytotoxic T-lymphocyte (CTL) responses in the course of natural infection allowed us to address HIV-1C-specific immune responses on a population level. We analyzed the magnitude and frequency of the gamma interferon ELISPOT-based CTL responses and translated them into normalized cumulative CTL responses. The introduction of population-based cumulative CTL responses reflected both (i) essentials of the predominant virus circulating locally in Botswana and (ii) specificities of the genetic background of the Botswana population, and it allowed the identification of immunodominant regions across the entire HIV-1C. The most robust and vigorous immune responses were found within the HIV-1C proteins Gag p24, Vpr, Tat, and Nef. In addition, moderately strong responses were scattered across Gag p24, Pol reverse transcriptase and integrase, Vif, Tat, Env gp120 and gp41, and Nef. Assuming that at least some of the immune responses are protective, these identified immunodominant regions could be utilized in designing an HIV vaccine candidate for the population of southern Africa. Targeting multiple immunodominant regions should improve the overall vaccine immunogenicity in the local population and minimize viral escape from immune recognition. Furthermore, the analysis of HIV-1C-specific immune responses on a population level represents a comprehensive systematic approach in HIV vaccine design and should be considered for other HIV-1 subtypes and/or different geographic areas.
RU5 of Mason-Pfizer Monkey Virus 5′ Long Terminal Repeat Enhances Cytoplasmic Expression of Human Immunodeficiency Virus Type 1
gag-pol
and Nonviral Reporter RNA
Authors: Hull Stacey , Boris-Lawrie Kathleen 
Published: September 2002

ABSTRACT

Retroviruses utilize an unspliced version of their primary transcription product as an RNA template for synthesis of viral Gag and Pol structural and enzymatic proteins. Cytoplasmic expression of the
gag-pol
RNA is achieved despite the lack of intron removal and the presence of a long and highly structured 5′ untranslated region that inhibits efficient ribosome scanning. In this study, we have identified for the first time that the 5′ long terminal repeat (LTR) of Mason-Pfizer monkey virus (MPMV) facilitates Rev/Rev-responsive element-independent expression of HIV-1
gag-pol
reporter RNA. The MPMV RU5 region of the LTR is necessary and directs functional interaction with cellular posttranscriptional modulators present in human 293 and monkey COS cells but not in quail QT-6 cells and does not require any viral protein. Deletion of MPMV RU5 decreases the abundance of spliced mRNA but has little effect on cytoplasmic accumulation of unspliced
gag-pol
RNA despite complete elimination of detectable Gag protein production. MPMV RU5 also exerts a positive effect on the cytoplasmic expression of intronless
luc
RNA, and ribosomal profile analysis demonstrates that MPMV RU5 directs subcellular localization of the
luc
transcript to polyribosomes. Our findings have a number of similarities with those of reports on 5′ terminal posttranscriptional control elements in spleen necrosis virus and human foamy virus RNA and support the model that divergent retroviruses share 5′ terminal RNA elements that interact with host proteins to program retroviral RNA for productive cytoplasmic expression.
Selective Translation of Eukaryotic mRNAs: Functional Molecular Analysis of GRSF-1, a Positive Regulator of Influenza Virus Protein Synthesis
Authors: Kash John C. , Cunningham Dawn M. , Smit Maria W. , Park Youngwoo , Fritz David , Wilusz Jeffrey , Katze Michael G. 
Published: September 2002

ABSTRACT

To understand the regulation of cap-dependent translation initiation mediated by specific 5′ untranslated region (UTR) RNA-protein interactions in mammalian cells, we have studied the selective translation of influenza virus mRNAs. Previous work has shown that the host cell mRNA binding protein guanine-rich sequence factor 1 (GRSF-1) bound specifically to conserved viral 5′ UTR sequences and stimulated translation of viral 5′ UTR-driven mRNAs in vitro. In the present study, we have characterized the functional domains of GRSF-1 and mapped the RNA binding activity of GRSF-1 to RRM 2 (amino acids 194 to 275) with amino-terminal deletion glutathione
S
-transferase (GST)-GRSF-1 proteins. When these mutants were assayed for functional activity in vitro, deletion of an Ala-rich region (Δ[2-94]) appeared to diminish translational stimulation, while deletion of the Ala-rich region in addition to RRM 1 (Δ[2-194]) resulted in a 4-fold increase in translational activation over wild-type GRSF-1 (an overall 20-fold increase in activity). We have also mapped the GRSF-1 RNA binding site on influenza virus NP and NS1 5′ UTRs, which was determined to be the sequence AGGGU. With polysome fractionation and cDNA microarray analysis, we have identified cellular and viral mRNAs containing putative GRSF-1 binding sites that were transcriptionally up-regulated and selectively recruited to polyribosomes following influenza virus infection. Taken together, these studies demonstrate that RRM 2 is critical for GRSF-1 RNA binding and translational activity. Further, our data suggest GRSF-1 functions by selectively recruiting cellular and viral mRNAs containing 5′ UTR GRSF-1 binding sites to polyribosomes, which is mediated through interactions with cellular proteins.
Influenza Virus Can Enter and Infect Cells in the Absence of Clathrin-Mediated Endocytosis
Authors: Sieczkarski Sara B. , Whittaker Gary R. 
Published: September 2002

ABSTRACT
Influenza virus has been described to enter host cells via clathrin-mediated endocytosis. However, it has also been suggested that other endocytic routes may provide additional entry pathways. Here we show that influenza virus may enter and infect HeLa cells that are unable to take up ligands by clathrin-mediated endocytosis. By overexpressing a dominant-negative form of the Eps15 protein to inhibit clathrin-mediated endocytosis, we demonstrate that while transferrin uptake and Semliki Forest virus infection were prevented, influenza virus could enter and infect cells expressing Eps15Δ95/295. This finding is supported by the successful infection of cells with influenza virus in the presence of chemical treatments that block endocytosis, namely, chlorpromazine and potassium depletion. We show also that influenza virus may infect cells incapable of uptake by caveolae. Treatment with the inhibitors nystatin, methyl-β-cyclodextrin, and genistein, as well as transfection of cells with dominant-negative caveolin-1, had no effect on influenza virus infection. By combining inhibitory methods to block both clathrin-mediated endocytosis and uptake by caveolae in the same cell, we demonstrate that influenza virus may infect cells by an additional non-clathrin-dependent, non-caveola-dependent endocytic pathway. We believe this to be the first conclusive analysis of virus entry via such a non-clathrin-dependent pathway, in addition to the traditional clathrin-dependent route.