bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural Requirements for Recognition of the Human Immunodeficiency Virus Type 1 Core during Host Restriction in Owl Monkey Cells
Authors: Forshey Brett M. , Shi Jiong , Aiken Christopher
Published: December 2004

Human immunodeficiency virus type 1 (HIV-1) infection of simian cells is restricted at an early postentry step by host factors whose mechanism of action is unclear. These factors target the viral capsid protein (CA) and attenuate reverse transcription, suggesting that they bind to the HIV-1 core and interfere with its uncoating. To identify the relevant binding determinants in the capsid, we tested the capacity of viruses containing Gag cleavage site mutations and amino acid substitutions in CA to inhibit restriction of a wild type HIV-1 reporter virus in owl monkey cells. The results demonstrated that a stable, polymeric capsid and a correctly folded amino-terminal CA subunit interface are essential for saturation of host restriction in target cells by HIV-1 cores. We conclude that the owl monkey cellular restriction machinery recognizes a polymeric array of CA molecules, most likely via direct engagement of the HIV-1 capsid in target cells prior to uncoating.
CpG Methylation Directly Regulates Transcriptional Activity of the Human Endogenous Retrovirus Family HERV-K(HML-2)
Authors: Lavie Laurence , Kitova Milena , Maldener Esther , Meese Eckart , Mayer Jens
Published: December 2004

A significant proportion of the human genome consists of stably inherited retroviral sequences. Most human endogenous retroviruses (HERVs) became defective over time. The HERV-K(HML-2) family is exceptional because of its coding capacity and the possible involvement in germ cell tumor (GCT) development. HERV-K(HML-2) transcription is strongly upregulated in GCTs. However, regulation of HERV-K(HML-2) transcription remains poorly understood. We investigated in detail the role of CpG methylation on the transcriptional activity of HERV-K(HML-2) long terminal repeats (LTRs). We find that CpG sites in various HERV-K(HML-2) proviral 5′ LTRs are methylated at different levels in the cell line Tera-1. Methylation levels correlate with previously observed transcriptional activities of these proviruses. CpG-mediated silencing of HERV-K(HML-2) LTRs is further corroborated by transcriptional inactivity of in vitro-methylated 5′ LTR reporter plasmids. However, CpG methylation levels do not solely regulate HERV-K(HML-2) 5′ LTR activity, as evidenced by different LTR activities in the cell line T47D. A significant number of mutated CpG sites in evolutionary old HERV-K(HML-2) 5′ LTRs suggests that CpG methylation had already silenced HERV-K(HML-2) proviruses millions of years ago. Direct silencing of HERV-K(HML-2) expression by CpG methylation enlightens upregulated HERV-K(HML-2) expression in usually hypomethylated GCT tissue.
Characterization and Complete Genome Sequence of a Novel Coronavirus, Coronavirus HKU1, from Patients with Pneumonia
Authors: Woo Patrick C. Y. , Lau Susanna K. P. , Chu Chung-ming , Chan Kwok-hung , Tsoi Hoi-wah , Huang Yi , Wong Beatrice H. L. , Poon Rosana W. S. , Cai James J. , Luk Wei-kwang , Poon Leo L. M. , Wong Samson S. Y. , Guan Yi , Peiris J. S. Malik , Yuen Kwok-yung
Published: December 2004

Despite extensive laboratory investigations in patients with respiratory tract infections, no microbiological cause can be identified in a significant proportion of patients. In the past 3 years, several novel respiratory viruses, including human metapneumovirus, severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV), and human coronavirus NL63, were discovered. Here we report the discovery of another novel coronavirus, coronavirus HKU1 (CoV-HKU1), from a 71-year-old man with pneumonia who had just returned from Shenzhen, China. Quantitative reverse transcription-PCR showed that the amount of CoV-HKU1 RNA was 8.5 to 9.6 × 10
6
copies per ml in his nasopharyngeal aspirates (NPAs) during the first week of the illness and dropped progressively to undetectable levels in subsequent weeks. He developed increasing serum levels of specific antibodies against the recombinant nucleocapsid protein of CoV-HKU1, with immunoglobulin M (IgM) titers of 1:20, 1:40, and 1:80 and IgG titers of <1:1,000, 1:2,000, and 1:8,000 in the first, second and fourth weeks of the illness, respectively. Isolation of the virus by using various cell lines, mixed neuron-glia culture, and intracerebral inoculation of suckling mice was unsuccessful. The complete genome sequence of CoV-HKU1 is a 29,926-nucleotide, polyadenylated RNA, with G+C content of 32%, the lowest among all known coronaviruses with available genome sequence. Phylogenetic analysis reveals that CoV-HKU1 is a new group 2 coronavirus. Screening of 400 NPAs, negative for SARS-CoV, from patients with respiratory illness during the SARS period identified the presence of CoV-HKU1 RNA in an additional specimen, with a viral load of 1.13 × 10
6
copies per ml, from a 35-year-old woman with pneumonia. Our data support the existence of a novel group 2 coronavirus associated with pneumonia in humans.
Efficient Rescue of Hepatitis C Virus RNA Replication bytrans-Complementation with Nonstructural Protein 5A
Authors: Appel Nicole , Herian Ulrike , Bartenschlager Ralf
Published: December 2004

Studies ofHepatitis C virus(HCV) RNA replication have become possible with the development of subgenomic replicons. This system allows the functional analysis of the essential components of the viral replication complex, which so far are poorly defined. In the present study we wanted to investigate whether lethal mutations in HCV nonstructural genes can be rescued bytrans-complementation. Therefore, a series of replicon RNAs carrying mutations in NS3, NS4B, NS5A, and NS5B that abolish replication were transfected into Huh-7 hepatoma cells harboring autonomously replicating helper RNAs. Similar to data described for theBovine viral diarrhea virus(C. W. Grassmann, O. Isken, N. Tautz, and S. E. Behrens, J. Virol. 75:7791-7802, 2001), we found that only NS5A mutants could be efficiently rescued. There was no evidence for RNA recombination between helper and mutant RNAs, and we did not observe reversions in the transfected mutants. Furthermore, we established a transient complementation assay based on the cotransfection of helper and mutant RNAs. Using this assay, we extended our results and demonstrated that (i) inactivating NS5A mutations affecting the amino-terminal amphipathic helix cannot be complemented intrans; (ii) replication of the helper RNA is not necessary to allow efficienttrans-complementation; and (iii) the minimal sequence required fortrans-complementation of lethal NS5A mutations is NS3 to -5A, whereas NS5A expressed alone does not restore RNA replication. In summary, our results provide the first insight into the functional organization of the HCV replication complex.
Covalent Modification of Human Immunodeficiency Virus Type 1 p6 by SUMO-1
Authors: Gurer Cagan , Berthoux Lionel , Luban Jeremy
Published: December 2004

The p6 domain of the human immunodeficiency virus type 1 (HIV-1) Gag polyprotein mediates virion budding from infected cells via protein-protein contacts with the class E vacuolar protein sorting factors, Tsg101 and AIP1/ALIX. Interaction with Tsg101 is strengthened by covalent attachment of monovalent ubiquitin to HIV-1 p6. To identify additional host factors that bind to HIV-1 p6, a human cDNA library was screened in the yeast two-hybrid system. HIV-1 p6 was found to interact with small ubiquitin-like modifier 1 (SUMO-1) as well as the E2 SUMO-1 transfer enzyme, Ubc9. Interaction with p6 was also detected with Daxx, a cellular protein to which SUMO-1 is sometimes covalently attached. SUMO-1 was incorporated into HIV-1 virions where it was protected within the virion membrane from digestion by exogenous protease. Of the two lysine residues in p6, lysine 27 uniquely served as a site of covalent SUMO-1 attachment. As previously reported, though, HIV-1 bearing the p6-K27R mutation replicated just like the wild type. Overproduction of SUMO-1 in HIV-1 producer cells had no apparent effect on virion release or on virion protein or RNA content. Infectivity of the resulting virions, though, was decreased, with the defect occurring after membrane fusion, at the time of viral cDNA synthesis. HIV-1 bearing the p6-K27R mutation was insensitive to SUMO-1 overexpression, suggesting that covalent attachment of SUMO-1 to p6 is detrimental to HIV-1 replication.
Genome of Deerpox Virus
Authors: Afonso C. L. , Delhon G. , Tulman E. R. , Lu Z. , Zsak A. , Becerra V. M. , Zsak L. , Kutish G. F. , Rock D. L.
Published: December 2004

Deerpox virus(DPV), an uncharacterized and unclassified member of thePoxviridae, has been isolated from North American free-ranging mule deer (Odocoileus hemionus) exhibiting mucocutaneous disease. Here we report the genomic sequence and comparative analysis of two pathogenic DPV isolates, W-848-83 (W83) and W-1170-84 (W84). The W83 and W84 genomes are 166 and 170 kbp, containing 169 and 170 putative genes, respectively. Nucleotide identity between DPVs is 95% over the central 157 kbp. W83 and W84 share similar gene orders and code for similar replicative, structural, virulence, and host range functions. DPV open reading frames (ORFs) with putative virulence and host range functions include those similar to cytokine receptors (R), including gamma interferon receptor (IFN-γR), interleukin 1 receptor (IL-1R), and type 8 CC-chemokine receptors; cytokine binding proteins (BP), including IL-18BP, IFN-α/βBP, and tumor necrosis factor binding protein (TNFBP); serpins; and homologues of vaccinia virus (VACV) E3L, K3L, and A52R proteins. DPVs also encode distinct forms of major histocompatibility complex class I, C-type lectin-like protein, and transforming growth factor β1 (TGF-β1), a protein not previously described in a mammalian chordopoxvirus. Notably, DPV encodes homologues of cellular endothelin 2 and IL-1R antagonist, novel poxviral genes also likely involved in the manipulation of host responses. W83 and W84 differ from each other by the presence or absence of five ORFs. Specifically, homologues of a CD30 TNFR family protein, swinepox virus SPV019, and VACV E11L core protein are absent in W83, and homologues of TGF-β1 and lumpy skin disease virus LSDV023 are absent in W84. Phylogenetic analysis indicates that DPVs are genetically distinct from viruses of other characterized poxviral genera and that they likely comprise a new genus within the subfamilyChordopoxvirinae.
Analysis of Translational Initiation in Coxsackievirus B3 Suggests an Alternative Explanation for the High Frequency of R
+4
in the Eukaryotic Consensus Motif
Authors: Harkins Stephanie , Cornell Christopher T. , Whitton J. Lindsay
Published: December 2004

Translational initiation of most eukaryotic mRNAs occurs when a preinitiation complex binds to the 5′ cap, scans the mRNA, and selects a particular AUG codon as the initiation site. Selection of the correct initiation codon relies, in part, on its flanking residues; in mammalian cells, the core of the “Kozak” consensus is R
−3
CCAUGG
+4
(R = purine; the A residue is designated position +1). The R
−3
is considered the most important flanking residue, followed by G
+4
. Picornaviral mRNAs differ from most cellular mRNAs in several ways; they are uncapped, and they contain an internal ribosome entry site that allows the ribosome to bind near the initiation codon. The initiation codon of coxsackievirus B3 (CVB3) is flanked by both R
−3
and G
+4
(AAAATGG). Here, we report the construction of full-length CVB3 genomes that vary at these two positions, and we evaluate the effects of these variant sequences in vitro, in tissue culture cells, and in vivo. A virus with an A→C transversion at position −3 replicates as well as wild-type CVB3, both in tissue culture and in vivo. This virus is highly pathogenic, and its sequence is stable throughout the course of an in vivo infection. Furthermore, the in vitro translation products from this RNA are very similar to the wild type. Thus, R
−3
—thought to be the most functionally important component of the Kozak consensus—appears to be dispensable in CVB3. In contrast, a G-to-C transversion at G
+4
is lethal; RNAs carrying this mutation fail to generate infectious virus either in tissue culture or in vivo. However, in vitro analysis indicates that G
+4
has only a marginal effect on translational initiation, especially if R
−3
is present; instead, the G
+4
is required mainly because the second triplet of the polyprotein open reading frame must encode glycine, without which infectious virus production cannot proceed. In summary, our data indicate that CVB3 remains viable, even in vivo, in the absence of R
−3
, and we propose that the most important factor contributing to the high frequency of G
+4
—not only in CVB but also in other eukaryotic mRNAs, and thus in the consensus motif itself—may be the constraint upon the second amino acid rather than the requirements for translational initiation.
Intensive education combined with low tech ergonomic intervention does not prevent low back pain in nurses
Authors: Hartvigsen J , Lauritzen S , Lings S , Lauritzen T
Published: December 2004

Aims:To evaluate the effectiveness of an intensive educational and low-tech ergonomic intervention programme aimed at reducing low back pain (LBP) among home care nurses and nurses’ aids.

Methods:In 1999, 345 home care nurses and nurses’ aids in four Danish municipalities were studied. Participants in two municipalities constituted the intervention group and participants in the other two served as the control group. In the intervention group, participants were divided into small groups, each of which was assigned one specially trained instructor. During weekly meetings participants were educated in body mechanics, patient transfer, and lifting techniques, and use of low-tech ergonomic aids. In the control group, participants attended a one time only three hour instructional meeting. Information on LBP was collected using the Standardised Nordic Questionnaire supplemented with information on number of episodes of LBP and care seeking due to LBP during the past year.

Results:A total of 309 nurses and nurses’ aids returned the questionnaire at baseline and 255 at follow up in August 2001. At follow up, no significant differences were found between the two groups for any of the LBP variables, and both groups thought that education in patient transfer techniques had been helpful. Within group changes in LBP status was not related to the intervention or to satisfaction with participating in the project.

Conclusions:Intensive weekly education in body mechanics, patient transfer techniques, and use of low-tech ergonomic equipment was not superior to a one time only three hour instructional meeting for home care nurses and nurses’ aids.
Employment characteristics and job loss in patients awaiting surgery on the hip or knee
Authors: Palmer K T , Milne P , Poole J , Cooper C , Coggon D
Published: December 2004

Aims:To investigate the factors, including size of organisation, associated with job loss in patients awaiting surgery to the hip or knee joint.

Methods:A questionnaire was mailed to 498 consecutive patients of working age listed at a district general hospital for major joint replacement, knee arthroscopy, or periacetabular osteotomy. Questions were asked about level of physical disability, duration of symptoms, employment circumstances at the time the joint problem began, and job changes since the onset of symptoms with their reasons. Analysis focused on those in work when their health problem began. Cox regression was used to examine risk factors for job loss related and unrelated to the joint problem, and results were summarised as adjusted hazard ratios (HRs) with 95% confidence intervals (95% CI).

Results:Responses came from 370 (74%) of those mailed, including 278 who were in work when their joint problem began. Of these, 82 (30%) had left their original job mainly or partly because of their joint disorder. Such job loss was more common in those employed in small businesses (HR for <10v⩾10 employees: 1.9, 95% CI 1.2–3.0) and those whose work involved standing for >2 hours per day (HR 2.7, 95% CI 1.2–6.1) No similar associations were found when jobs were left for other reasons. After adjustment for non-sedentary work the association with small business employment remained but was weaker (HR 1.5, 95% CI 0.9–2.5). Modifications to work and access to occupational health advice were not associated with better job retention.

Conclusions:In subjects with disabling hip or knee disease, job retention is poorer in those from small companies—a matter of concern given the rising prevalence of serious joint disease in the British workforce and the tendency of businesses to downsize and subcontract services to smaller enterprises.
Ocular morbidity and fuel use: an experience from India
Authors: Saha A , Kulkarni P K , Shah A , Patel M , Saiyed H N
Published: December 2004

The association of fuel use and ocular morbidity in a village in western India was investigated in a cross sectional prevalence survey involving 469 randomly selected subjects. All subjects were interviewed and underwent medical and ophthalmological examination. Wood use was found to be an important factor in the aetiology of age dependent cataract (OR 2.12, 95% CI 1.03–4.34). When comparing wood only and LPG only users, the odds ratio was 3.47 (95% CI 1.05–11.50). In cases of eye irritation, coal use (OR 2.04, 95% CI 1.13–3.68) and cattle dung use (OR 1.83, 95% CI 1.35–2.47) were shown to be important factors, while male sex posed a lesser risk.
Task based exposure assessment in ergonomic epidemiology: a study of upper arm elevation in the jobs of machinists, car mechanics, and house painters
Authors: Svendsen S W , Mathiassen S E , Bonde J P
Published: December 2004

Aims:To explore the precision of task based estimates of upper arm elevation in three occupational groups, compared to direct measurements of job exposure.

Methods:Male machinists (n = 26), car mechanics (n = 23), and house painters (n = 23) were studied. Whole day recordings of upper arm elevation were obtained for four consecutive working days, and associated task information was collected in diaries. For each individual, task based estimates of job exposure were calculated by weighting task exposures from a collective database by task proportions according to the diaries. These estimates were validated against directly measured job exposures using linear regression. The performance of the task based approach was expressed through the gain in precision of occupational group mean exposures that could be obtained by adding subjects with task based estimates to a group of subjects with measured job exposures in a “validation” design.

Results:In all three occupations, tasks differed in mean exposure, and task proportions varied between individuals. Task based estimation proved inefficient, with squared correlation coefficients only occasionally exceeding 0.2 for the relation between task based and measured job exposures. Consequently, it was not possible to substantially improve the precision of an estimated group mean by including subjects whose job exposures were based on task information.

Conclusions:Task based estimates of mechanical job exposure can be very imprecise, and only marginally better than estimates based on occupation. It is recommended that investigators in ergonomic epidemiology consider the prospects of task based exposure assessment carefully before placing resources at obtaining task information. Strategies disregarding tasks may be preferable in many cases.
Eye complaints in the office environment: precorneal tear film integrity influenced by eye blinking efficiency
Authors: Wolkoff P , Nøjgaard J K , Troiano P , Piccoli B
Published: December 2004

To achieve a common base for understanding work related eye complaints in the office environment, it is necessary to merge approaches from indoor air science, occupational health, and ophthalmology. Based on database searches, it is concluded that precorneal tear film (PTF) alteration leads to eye complaints that may be caused by: (1) thermal factors (low relative humidity; high room temperature); (2) demanding task content (attention decreases blinking and widens the exposed ocular surface area); and (3) individual characteristics (for example, tear film alterations, blinking anomalies, gland dysfunctions, and use of contact lenses). These factors and conditions are able to progressively increase water evaporation and faster thinning of the PTF, which causes dryness and dry spot formation on the cornea, possibly followed by corneal and conjunctiva epithelial alterations and eye complaints. Another possible cause of eye complaints is certain irritating chemical compounds, in addition to oxidation mixtures that are formed in reactions between ozone and unsaturated organic compounds (alkenes). The effect may be exacerbated by low relative humidity.
Variation of DNA amount in 47 populations of the subtribe Artemisiinae and related taxa (Asteraceae, Anthemideae): karyological, ecological, and systematic implications
Authors: Garcia Sònia , Sanz María , Garnatje Teresa , Kreitschitz Agnieszka , McArthur E Durant , Vallès Joan
Published: December 2004

Genome size has been estimated by flow cytometry in 47 populations of 40 species of the tribe Anthemideae (Asteraceae), mainly from Artemisia and other genera of the subtribe Artemisiinae and related taxa. A range of 2C values from 3.54 to 21.22 pg was found. DNA amount per basic chromosome set ranged from 1.77 to 7.70 pg. First genome size estimates are provided for one subtribe, 10 genera, 32 species, and two subspecies. Nuclear DNA amount correlated well with some karyological, physiological and environmental characters, and has been demonstrated as a useful tool in the interpretation of evolutionary relationships within Artemisia and its close relatives.Key words: Artemisia, C value, ecology, evolution, flow cytometry, genome size, nuclear DNA amount variation, phylogeny, polyploidy, systematics.
SSR cross-amplification and variation within coffee trees (Coffeaspp.)
Authors: Poncet V , Hamon P , Minier J , Carasco C , Hamon S , Noirot M
Published: December 2004

Primer sets were developed from 85 Coffea arabica sequences in addition to 25 already published primer sets. They were subsequently used for amplification in six African Coffea species: Coffea canephora (CAN), Coffea eugenioides (EUG), Coffea heterocalyx (HET), Coffea liberica (LIB), Coffea sp. Moloundou (MOL) and Coffea pseudozanguebariae (PSE). The amplification percentages for these 110 primer pairs ranged from 72.7% for LIB to 86.4% for PSE. Good transferability was thus obtained within the Coffea genus. When focusing on the two species CAN and PSE, high genetic diversity, high polymorphic locus rates (above 80%) and a mean allele number per polymorphic locus of more than 3 were noted. The estimated null allele percentage was –11% for PSE and –9% for CAN. Sixty three percent (CAN) and 79.5% (PSE) of the fixation index (Fis) values were positive. The within-species polymorphism information content (PIC) distribution showed two modes for both species. Although the two species shared 30 polymorphic loci, no correlation between CAN and PSE PIC values was obtained. All of these data are discussed in relation to the polymorphism level and the potential use of these SSRs for subsequent analysis of genetic diversity or genetic mapping.Key words: microsatellite, Coffea, transferability, genetic diversity.
Insertional polymorphism of a non-LTR mobile element (NLRCth1) in European populations ofChironomus riparius(Diptera, Chironomidae) as detected by transposon insertion display
Authors: Zampicinini G , Blinov A , Cervella P , Guryev V , Sella G
Published: December 2004

The midge Chironomus riparius is distributed all over the Palearctic region and is well characterized both at the morphological and cytogenetic levels. Here we describe a population study based on the insertional polymorphism of the retroposon NLRCth1, by means of a S-SAP (sequence-specific amplification polymorphism) derived technique (transposon insertion display; TID). While a previous study of allozyme polymorphism in Russian samples showed little variability, all the amplicons we identified are polymorphic. Genetic distances between 6 natural populations were calculated according to Nei and did not show a positive correlation with geographic distances. The genetic diversity detected among individuals of a given population was one order of magnitude higher than that among populations. However, the value of ΦSTwas significant (p < 0.001) and indicates that natural populations are more genetically differentiated than random samples of individuals.Key words: retrotransposable elements, genetic differentiation, Chironomus riparius, sequence-specific amplification polymorphism.
Molecular characterization ofVulmar1, a completemarinertransposon of sugar beet and diversity ofmariner- andEn/Spm-like sequences in the genusBeta
Authors: Jacobs Gunnar , Dechyeva Daryna , Menzel Gerhard , Dombrowski Cora , Schmidt Thomas
Published: December 2004

Transposons of the Tc1-mariner superfamily are widespread in eukaryotic genomes. We have isolated the mariner element Vulmar1 from Beta vulgaris L., which is 3909 bp long and bordered by perfect terminal inverted repeats of 32 bp with homology to terminal inverted repeats of transposons from soybean and rice. According to a characteristic amino acid signature, Vulmar1 can be assigned to the DD39D group of mariner transposons. Vulmar1 is flanked by a 5'-TA-3' target site duplication that is typical for mariner transposons. Southern hybridization revealed that mariner-like copies are highly abundant in Beta species, and sequence analysis of 10 transposase fragments from representative species of the four Beta sections revealed an identity between 34% and 100% after conceptual translation. By fluorescent in situ hybridization, Vulmar1 was detected in distal euchromatin as well as in some intercalary and pericentromeric regions of all B. vulgaris chromosomes. In addition, using PCR, we were able to amplify fragments of the transposase gene of En/Spm-like transposons in the genus Beta. En/Spm-like transposase sequences are highly amplified in four Beta sections and showed a considerable degree of conservation (88.5–100%) at the protein level, while the homology to corresponding regions of En/Spm transposons of other plant species ranges from 49.5% to 62.5%. By fluorescent in situ hybridization, En/Spm-like transposon signals of strong intensity were detected on all chromosomes of B. vulgaris.Key words: Beta vulgaris, mariner transposons, En/Spm transposons, FISH, Vulmar1.
Screening and analysis of differentially expressed genes from an alien addition line of wheatThinopyrum intermediuminduced bybarley yellow dwarf virusinfection
Authors: Jiang Shu-Mei , Zhang Long , Hu Jun , Shi Rui , Zhou Guang-He , Chen Yu-Hong , Yin Wei-Bo , Wang Richard R.-C , Hu Zan-Min
Published: December 2004

The alien addition line TAI-27 contains a pair of chromosomes of Thinopyrum intermedium that carry resistance against barley yellow dwarf virus (BYDV). A subtractive library was constructed using the leaves of TAI-27, which were infected by Schizaphis graminum carrying the GAV strain of BYDV, and the control at the three-leaf stage. Nine differentially expressed genes were identified from 100 randomly picked clones and sequenced. Two of the nine clones were highly homologous with known genes. Of the remaining seven cDNA clones, five clones matched with known expressed sequence tag (EST) sequences from wheat and (or) barley whereas the other two clones were unknown. Five of the nine differentially expressed sequences (WTJ9, WTJ11, WTJ15, WTJ19, and WTJ32) were highly homologous (identities >94%) with ESTs from wheat or barley challenged with pathogens. These five sequences and another one (WTJ18) were also highly homologous (identities >86%) with abiotic stress induced ESTs in wheat or barley. Reverse Northern hybridization showed that seven of the nine differentially expressed cDNA sequences hybridized with cDNA of T. intermedium infected by BYDV. Three of these also hybridized with cDNA of line 3B-2 (a parent of TAI-27) infected by BYDV. The alien chromosome in TAI-27 was microdissected. The second round linker adaptor mediated PCR products of the alien chromosomal DNA were labeled with digoxygenin and used as the probe to hybridize with the nine differentially expressed genes. The analysis showed that seven differentially expressed genes were homologous with the alien chromosome of TAI-27. These seven differentially expressed sequences could be used as ESTs of the alien chromosome of TAI-27. This research laid the foundation for screening and cloning of new specific functional genes conferring resistance to BYDV and probably other pathogens.Key words: suppression subtractive hybridization (SSH), expressed sequence tag (EST), linker adaptor mediated polymerase chain reaction (LA-PCR), chromosome microdissection.
Evolution of cow nonstomach lysozyme genes
Authors: Irwin David M
Published: December 2004

Expansion of the lysozyme gene family is associated with the evolution of the ruminant lifestyle in ruminant artiodactyls such as the cow. Gene duplications allowed recombination between stomach lysozyme genes that may have assisted in the evolution of an enzyme adapted to survive and function in the stomach environment. Despite amplification of lysozyme genes, cow tears, milk, and blood are considered to be lysozyme deficient. Here we have identified 2 new cow lysozyme cDNA sequences and show that at least 4 different lysozymes are expressed in cows in nonstomach tissues and probably function as antibacterial defence enzymes. These 4 lysozyme genes are in addition to the 4 digestive lysozyme genes expressed in the stomach, yielding a number of expressed lysozyme genes in the cow larger than that found in most nonlysozyme-deficient mammals. In contrast to expectations, evidence for recombination between stomach and nonstomach lysozyme genes was found. Recombination, through concerted evolution, may have allowed some lysozymes to acquire the ability to survive in occasional acidic environments.Key words: molecular evolution, adaptive evolution, lysozyme, ruminants, gene duplication, gene evolution.
Inversion frequencies inDrosophila serrataalong an eastern Australian transect
Authors: Stocker Ann Jacob , Foley Brad , Hoffmann Ary
Published: December 2004

Clinal patterns over broad geographic regions provide a way of identifying characteristics of species under selection and are increasingly being used in quantitative trait locus mapping of adaptive genetic variation in Drosophila. However, interpretations of clinal patterns can be complicated by inversions that also vary clinally and reduce recombination in some parts of the genome. Drosophila serrata (Malloch) is an Australian endemic species being used to investigate the genetic basis of geographic variation in climatic adaptation and mate recognition. Here we describe inversions in D. serrata populations from the east coast of Australia, covering tropical and temperate regions. Seven autosomal paracentric inversions and 1 apparently complex X chromosome arrangement were identified from these populations. All inverted arrangements were relatively more common in tropical populations; 2 common inversions showed clinal patterns over part of the range of D. serrata. Inversion polymorphism was relatively higher in tropical populations and almost absent in populations near the cooler southern border, in agreement with findings on other Drosophila species. While these patterns will complicate mapping of adaptive variation in D. serrata, they suggest that this species will be useful in investigatingthe dynamics of inversion-trait associations in natural populations.Key words: inversion polymorphism, geographic variation, latitudinal clines, Drosophila serrata.
Synthesis and cytological characterization of trigeneric hybrids of durum wheat with and withoutPh1
Authors: Jauhar Prem P , Doğramaci M , Peterson T S
Published: December 2004

Wild grasses in the tribe Triticeae, some in the primary or secondary gene pool of wheat, are excellent reservoirs of genes for superior agronomic traits, including resistance to various diseases. Thus, the diploid wheatgrasses Thinopyrum bessarabicum (Savul. and Rayss) Á. Löve (2n = 2x = 14; JJ genome) and Lophopyrum elongatum (Host) Á. Löve (2n = 2x = 14; EE genome) are important sources of genes for disease resistance, e.g., Fusarium head blight resistance that may be transferred to wheat. By crossing fertile amphidiploids (2n = 4x = 28; JJEE) developed from F1hybrids of the 2 diploid species with appropriate genetic stocks of durum wheat, we synthesized trigeneric hybrids (2n = 4x = 28; ABJE) incorporating both the J and E genomes of the grass species with the durum genomes A and B. Trigeneric hybrids with and without the homoeologous-pairing suppressor gene, Ph1, were produced. In the absence of Ph1, the chances of genetic recombination between chromosomes of the 2 useful grass genomes (JE) and those of the durum genomes (AB) would be enhanced. Meiotic chromosome pairing was studied using both conventional staining and fluorescent genomic in situ hybridization (fl-GISH). As expected, the Ph1-intergeneric hybrids showed low chromosome pairing (23.86% of the complement), whereas the trigenerics with ph1b (49.49%) and those with their chromosome 5B replaced by 5D (49.09%) showed much higher pairing. The absence of Ph1 allowed pairing and, hence, genetic recombination between homoeologous chromosomes. Fl-GISH analysis afforded an excellent tool for studying the specificity of chromosome pairing: wheat with grass, wheat with wheat, or grass with grass. In the trigeneric hybrids that lacked chromosome 5B, and hence lacked the Ph1 gene, the wheat–grass pairing was elevated, i.e., 2.6 chiasmata per cell, a welcome feature from the breeding standpoint. Using Langdon 5D(5B) disomic substitution for making trigeneric hybrids should promote homoeologous pairing between durum and grass chromosomes and hence accelerate alien gene transfer into the durum genomes.Key words: alien gene transfer, chiasma (xma) frequency, chromosome pairing, fluorescent genomic in situ hybridization (fl-GISH), homoeologous-pairing regulator, specificity of chromosome pairing, wheatgrass.
Comparative gene-based in silico analysis of transcriptomes in different bovine tissues and (or) organs
Authors: Jiang Zhihua , Wu Xiao-Lin , Garcia Matthew D , Griffin Kirsten B , Michal Jennifer J , Ott Troy L , Gaskins Charles T , Wright Jr. Raymond W
Published: December 2004

A gene-based approach was used to annotate 322 168 cattle expressed sequence tags (ESTs) based on human genes in order to census the transcriptomes, analyze their expression similarities, and identify genes preferentially expressed in different bovine tissues and (or) organs. Of the 34 157 human coding genes used in a standalone BLAST search, 14 928 could be matched with provisional orthologous sequences in a total of 230 135 bovine ESTs. The remaining 92 033 bovine ESTs were estimated to represent an additional 5970 genes in cattle. On average, ~8600 genes were estimated to be expressed in a single tissue and (or) organ and 13 000 in a pooled tissue library. On the basis of the estimated numbers of genes, no more than 3% of genes would be missed when ~34 000 ESTs were sequenced from a single tissue and (or) organ library and ~40 000 ESTs from a pooled source, respectively. Cluster analyses of the gene expression patterns among 12 single tissues and (or) organs in cattle revealed that their expression similarities would depend on physiological functions. In addition, a total of 1502 genes were identified as preferentially expressed genes in these 12 single tissues and (or) organs with LOD (logarithm of the odds, base 10) ≥ 3.0. Therefore, our study provides some insights for further investigating the developmental and functional relations of various tissues and organs in mammals.Key words: cattle, expressed sequence tags (ESTs), orthologous genes, comparative gene-based approach, in silico census, tissue/organs, transcriptomes.
LINKING MANUFACTURING SYSTEMS TO MANUFACTURING STRATEGY IN A CHANGING ENVIRONMENT
Authors: WANG JIAN , TSAO DE-BI , MA SHI-HUA
Published: December 2004

Dealing with change is an essential capability for manufacturing systems. In this paper, we reviewed 30 different kinds of manufacturing systems and identified four common approaches in how they deal with change, i.e. modularity, autonomy, distribution, and integration. We conducted a survey of Chinese manufacturing firms and used regression analysis to find relationships between their competitive priorities and the four approaches. The results provide some useful explanations regarding how a firm's emphases on the approaches in its manufacturing systems are influenced by its competitive priorities. Utilizing linkages between the approaches and competitive priorities, we developed a framework for matching manufacturing systems with manufacturing strategy in an environment filled with change and uncertainty.
GROWTH INHIBITORS OF ENTREPRENEURIAL ACADEMIC SPIN-OFFS: THE CASE OF FINNISH BIOTECHNOLOGY
Authors: TAHVANAINEN ANTTI-JUSSI
Published: December 2004

This study compares Finnish biotechnology SMEs founded by the academic originators of the underlying basic research projects with biotechnology companies of other origins. The comparison facilitates the identification of factors affecting the prosperity of these "academic spin-offs" as a business. Results indicate several inhibitors of growth: Academic spin-offs lack market-orientation and commercial skills, the traditional perception of the academia's detached role within society aggravates the recruitment of skilled labour, and Finland's equity markets are underdeveloped with new seed capital being next to unavailable, as private and foreign venture capitalists invest primarily in companies being already very close to the markets.
CDC/AHA Workshop on Markers of Inflammation and Cardiovascular Disease
Authors: Roberts William L.
Published: December 2004

Inflammation plays a key role in atherosclerosis. A number of different biomarkers of inflammation are measurable in blood. These include cytokines, chemokines, soluble adhesion molecules, and acute-phase reactants. The first 3 groups of molecules are not routinely measured in clinical laboratories. The acute-phase reactants include C-reactive protein (CRP). This analyte is stable and is readily measured by several commercial high-sensitivity (hs) assays, and numerous clinical studies have demonstrated its usefulness as an atherosclerotic risk marker. For these reasons, CRP is currently the inflammatory marker of choice. Comparison of commercial hsCRP assays has demonstrated that many are capable of imprecision of <7% at a CRP concentration of <1 mg/L. Method comparability studies have shown good agreement among some commercial hsCRP assays in terms of quartile assignments, whereas additional standardization efforts are necessary for others. The first goal of standardization is to develop a secondary reference material with a CRP of ≈4 mg/L. This material can be used to assist diagnostic vendors in calibrator value assignment and assay harmonization. Another project is to define clearly what performance characteristics are necessary for hsCRP assays. Preliminary estimates based on the biological variability of CRP indicate that the total allowable analytical error is between 15% and 32%. The former requirement can be met with accuracy and imprecision of <5% and the latter requirement with accuracy and imprecision of <11%. If 2 hsCRP results are averaged, then the imprecision requirements are relaxed slightly. Clinical validation of these performance requirements is also required.
Quantitative Assessment of Angiographic Restenosis After Sirolimus-Eluting Stent Implantation in Native Coronary Arteries
Authors: Popma Jeffrey J. , Leon Martin B. , Moses Jeffrey W. , Holmes David R. , Cox Nicholas , Fitzpatrick Michelle , Douglas John , Lambert Charles , Mooney Michael , Yakubov Steven , Kuntz Richard E.
Published: December 2004

Background—

Sirolimus-eluting stents (SESs) reduce angiographic restenosis in patients with focal, native coronary artery stenoses. This study evaluated the usefulness of SESs in complex native-vessel lesions at high risk for restenosis.

Methods and Results—

Angiographic follow-up at 240 days was obtained in 701 patients with long (15- to 25-mm) lesions in small-diameter (2.5- to 3.5-mm) native vessels who were randomly assigned to treatment with SESs or bare-metal stents (BMSs) in the SIRIUS trial. Quantitative angiographic measurements of minimal lumen diameter and percent diameter stenosis were obtained within the treated segment, within the stent, and within its 5-mm proximal and distal edges. Patients treated with SESs had lower rates of binary (>50% diameter stenosis) angiographic restenosis within the segment (8.9% versus 36.3% with the BMS;
P
<0.001) and within the stent (3.2% versus 35.4% with the BMS;
P
<0.001). SESs were associated with significantly less late lumen loss within the treated segment, within the stent, and within its 5-mm proximal and distal edges (all
P
<0.001). The reduction of restenosis with the SES was consistent in patients at risk for restenosis, including those with small vessels, long lesions, and diabetes mellitus. The frequency of late aneurysms was similar in the 2 groups.

Conclusions—

Compared with BMSs, SESs reduced angiographic late lumen loss within the stent and its adjacent 5-mm margins in patients with complex native-vessel lesions.
Multiple Abnormalities in Glucose and Energy Metabolism and Coordinated Changes in Levels of Adiponectin, Cytokines, and Adhesion Molecules in Subjects With Metabolic Syndrome
Authors: Salmenniemi Urpu , Ruotsalainen Eija , Pihlajamäki Jussi , Vauhkonen Ilkka , Kainulainen Sakari , Punnonen Kari , Vanninen Esko , Laakso Markku
Published: December 2004

Background—

Detailed metabolic defects in glucose and energy metabolism and abnormalities in a variety of cardiovascular risk factors are largely unknown in subjects with the metabolic syndrome.

Methods and Results—

We characterized the metabolic syndrome in 119 nondiabetic offspring of diabetic probands. Cardiovascular risk factors, including cytokines and adhesion molecules, were measured. Insulin sensitivity was assessed by the euglycemic hyperinsulinemic clamp and indirect calorimetry; intra-abdominal fat and subcutaneous fat were assessed by CT; and maximal oxygen consumption was measured with a bicycle ergometer test. By applying factor analysis, we identified a single factor, the metabolic syndrome factor, from the following variables: 2-hour glucose, fasting insulin, body mass index, waist, HDL cholesterol, triglycerides, and mean blood pressure. Subjects with the highest factor score were defined as having the metabolic syndrome. During hyperinsulinemia, the highest factor score was associated with decreased rates of glucose oxidation and nonoxidative glucose disposal, high rates of lipid oxidation, low energy expenditure, and impaired suppression of free fatty acids during hyperinsulinemia. Furthermore, the metabolic syndrome was associated with a high amount of visceral fat, hypoadiponectinemia, a low maximum oxygen uptake, and high levels of C-reactive protein, proinflammatory cytokines, and adhesion molecules.

Conclusions—

The metabolic syndrome is characterized by an excess of intra-abdominal fat, hypoadiponectinemia, insulin resistance in skeletal muscle and adipose tissue, multiple defects in glucose and energy metabolism, and elevated levels of cytokines and adhesion molecules.
Hypercholesterolemia Stimulates Angiotensin Peptide Synthesis and Contributes to Atherosclerosis Through the AT
1A
Receptor
Authors: Daugherty Alan , Rateri Debra L. , Lu Hong , Inagami Tadashi , Cassis Lisa A.
Published: December 2004

Background—

Hypercholesterolemia-induced atherosclerosis is attenuated by either pharmacological antagonism of AT
1
receptors or AT
1A
receptor deficiency. However, the mechanism underlying the pronounced responses to angiotensin II (Ang II) antagonism has not been determined. We hypothesized that hypercholesterolemia stimulates the production of angiotensin peptides to provide a rationale for the profound effect of AT
1A
receptor deficiency on atherogenesis.

Methods and Results—

Atherosclerotic lesions were analyzed in LDL receptor–deficient mice. Immunocytochemical analysis demonstrated that atherosclerotic lesions contained all the components of the conventional pathway for Ang II synthesis. AT
1A
receptor deficiency caused a marked decrease in atherosclerotic lesion size in both the aortic root and arch of male and female mice, without a discernible effect on composition. AT
1A
receptor deficiency–induced reductions in atherosclerosis were independent of systolic blood pressure and measurements of oxidation and chemoattractants. Aortic AT
2
receptor mRNA expression was not altered in AT
1A
receptor–deficient mice, and AT
2
receptor deficiency had no effect on lesion area or cellular composition. Hypercholesterolemia greatly augmented the systemic renin-angiotensin system, as demonstrated by large increases in plasma concentrations of angiotensinogen and angiotensin peptides (Ang II, III, IV, and 4–8). These increases were ablated in hypercholesterolemic AT
1A
receptor–deficient mice.

Conclusions—

AT
1A
receptor deficiency had a striking effect in reducing hypercholesterolemia-induced atherosclerosis in LDL receptor–negative mice. Hypercholesterolemia was associated with increased systemic angiotensinogen and angiotensin peptides, which were reduced in AT
1A
receptor–deficient mice. These results demonstrate that hypercholesterolemia-induced stimulation of angiotensin peptide production provides a basis for the marked effect of AT
1A
receptor deficiency in reducing atherosclerosis.
Patient-Specific Dose and Radiation Risk Estimation in Pediatric Cardiac Catheterization
Authors: Bacher Klaus , Bogaert Evelien , Lapere Régine , De Wolf Daniël , Thierens Hubert
Published: December 2004

Background—

Because of the higher radiosensitivity of infants and children compared with adults, there is a need to evaluate the doses delivered to pediatric patients who undergo interventional cardiac procedures. However, knowledge of the effective dose in pediatric interventional cardiology is very limited.

Methods and Results—

For an accurate risk estimation, a patient-specific Monte Carlo simulation of the effective dose was set up in 60 patients with congenital heart disease who underwent diagnostic (n=28) or therapeutic (n=32) cardiac catheterization procedures. The dose-saving effect of using extra copper filtration in the x-ray beam was also investigated. For diagnostic cardiac catheterizations, a median effective dose of 4.6 mSv was found. Therapeutic procedures resulted in a higher median effective dose of 6.0 mSv because of the prolonged use of fluoroscopy. The overall effect of inserting extra copper filtration into the x-ray beam was a total effective dose reduction of 18% with no detrimental effect on image quality. An excellent correlation between the dose-area product and effective patient dose was found (
r
=0.95). Hence, dose-area product is suitable for online estimation of the effective dose with good accuracy. With all procedures included, the resulting median lifetime risk for stochastic effects was 0.08%.

Conclusions—

Because of the high radiation exposure, it is important to monitor patient dose by dose-area product instrumentation and to use additional beam filtration to keep the effective dose as low as possible in view of the sensitivity of the pediatric patients.