bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of the U1C L13 mutation and temperature regulation of yeast commitment complex formation
Authors: Du Hansen , Tardiff Daniel F. , Moore Melissa J. , Rosbash Michael
Published: October 2004

The U1 small nuclear ribonucleoprotein particle U1C protein has a zinc finger-like structure (C2H2 motif) at its N terminus, which is conserved from yeast to humans. Mutations of amino acid L13 within this domain rescue the essential function of the helicase protein Prp28p. Prp28p has been implicated in unwinding the 5′ splice site (5′ss)–U1 small nuclear RNA (snRNA) base-pairing, to allow replacement of U1 snRNA with U6 snRNA during spliceosome assembly. The L13 phenotype has therefore been interpreted to indicate that WT U1C contributes to 5′ss–U1 snRNA stabilization by binding to the RNA duplex. We show here that an L13 mutant extract cannot form stable base-pairing at room temperature but is permissive for U1–5′ss base-pairing at low temperature. This phenotype is similar to that of a U1C-depleted extract, indicating that the U1C L13 mutation is a strong loss-of-function mutation. The two mutant extracts are unlike a WT extract, which undergoes stable pairing at room temperature but little or no pairing at low temperature. Taken together with previous results and the failure to observe a direct interaction of U1C with the U1–5′ss duplex, the data suggest that U1C contributes indirectly to stable U1–5′ss base-pairing under permissive conditions. A model is proposed to account for the L13 results.
Ion motions in molecular dynamics simulations on DNA
Authors: Ponomarev Sergei Y. , Thayer Kelly M. , Beveridge David L.
Published: October 2004

Counterions play a significant role in DNA structure and function, and molecular dynamics (MD) simulations offer the prospect of detailed description of the dynamical structure of ions at the molecular level. However, the motions of mobile counterions are notably slow to converge in MD on DNA. Obtaining accurate and reliable MD simulations requires knowing just how much sampling is required for convergence of each of the properties of interest. To address this issue, MD on a d(CGCGAATTCGCG) duplex in a dilute aqueous solution of water and 22 Na
+
counterions was performed until convergence was achieved. The calculated first shell ion occupancies and DNA–Na
+
radial distribution functions were computed as a function of time to assess convergence, and compared with relaxation times of the DNA internal parameters shift, slide, rise, tilt, roll, and twist. The sequence dependence of fractional occupancies of ions in the major and minor grooves of the DNA is examined, and the possibility of correlation between ion proximity and DNA minor groove widths is investigated.
Cup is a nucleocytoplasmic shuttling protein that interacts with the eukaryotic translation initiation factor 4E to modulate
Drosophila
ovary development
Authors: Zappavigna Vincenzo , Piccioni Federica , Villaescusa J. Carlos , Verrotti Arturo C.
Published: October 2004

In
Drosophila
, the product of the
fs (2)cup
gene (Cup) is known to be crucial for diverse aspects of female germ-line development. Its functions at the molecular level, however, have remained mainly unexplored. Cup was found to directly associate with eukaryotic translation initiation factor 4E (eIF4E). In this report, we show that Cup is a nucleocytoplasmic shuttling protein and that the interaction with eIF4E promotes retention of the Cup protein in the cytoplasm. Cup is required for the correct accumulation and localization of eIF4E within the posterior cytoplasm of developing oocytes. We furthermore show that
cup
and
eIF4E
interact genetically, because a reduction in the level of
eIF4E
activity deteriorates the development and growth of ovaries bearing homozygous
cup
mutant alleles. Our results reveal a crucial role for the Cup–eIF4E complex in ovary-specific developmental programs.
Delayed gadolinium‐enhanced MRI of cartilage (dGEMRIC): intra‐ and interobserver variability in standardized drawing of regions of interest
Authors: Tiderius C. J. , Tjörnstrand J. , Åkeson P. , Södersten K. , Dahlberg L. , Leander P.
Published: October 2004

Purpose: To establish the reproducibility of a standardized region of interest (ROI) drawing procedure in delayed gadolinium‐enhanced magnetic resonance imaging (MRI) of cartilage (dGEMRIC).

Material and Methods: A large ROI in lateral and medial femoral weight‐bearing cartilage was drawn in images of 12 healthy male volunteers by 6 investigators with different skills in MRI. The procedure was done twice, with a 1‐week interval. Calculated T1‐values were evaluated for intra‐ and interobserver variability.

Results: The mean interobserver variability for both compartments ranged between 1.3% and 2.3% for the 6 different investigators without correlation to their experience in MRI. Post‐contrast intra‐observer variability was low in both the lateral and the medial femoral cartilage, 2.6% and 1.5%, respectively. The larger variability in lateral than in medial cartilage was related to slightly longer and thinner ROIs.

Conclusion: Intra‐observer variability and interobserver variability are both low when a large standardized ROI is used in dGEMRIC. The experience of the investigator does not affect the variability, which further supports a clinical applicability of the method.
Mortality from external causes in Lithuania: looking for critical points in time and place
Authors: Kalediene Ramune , Starkuviene Skirmante , Petrauskiene Jadvyga
Published: October 2004

Aim: A study was undertaken to analyse trends in mortality from major external causes of death, and to detect urban/rural differences by cut points over the period of socioeconomic transition. Methods: Information on deaths from major external causes (traffic accidents, suicides, and homicides) for the 1990 - 2000 period was obtained from Lithuanian Department of Statistics. Mortality rates were age standardized, using the European standard, and analysed, according to (urban/rural) residence and sex. The Jointpoint analysis was used to identify the best-fitting points, wherever a statistically significant change in mortality occurred. Results: The most critical point for external causes of mortality during the period of transition was the year 1994, when an increasing mortality trend reversed to a decreasing one. Mortality from suicides primarily caused these positive changes. Changes in mortality from traffic accidents were not significantly associated with the period under analysis. Numerous less favourable trends in rural areas, including suicide rates, traffic accidents, and homicides, are likely to stratify urban/rural health outcomes in the future. Conclusion: Despite a recent decline, mortality from external causes remains at an extremely high level in Lithuania. Future progress requires sustained improvements in prevention, and serious attention to external causes of death in health policy development.
Is calcaneal stiffness more sensitive to physical activity than forearm bone mineral density? A population-based study of persons aged 20 - 79 years
Authors: Grahn Kronhed Ann-Charlotte , Knutsson Inger , Löfman Owe , Timpka Toomas , Toss Göran , Möller Margareta
Published: October 2004

Aims: The aim of this study was to investigate the associations between forearm bone mineral density (BMD), calcaneal stiffness, and physical activity levels in a normal population using different non-invasive methods. Methods: The participants were invited to undergo bone measurements using single photon absorptiometry of the forearm and quantitative ultrasound (QUS) of the calcaneal bone, and also to complete a questionnaire. Physical activity levels were designated low, moderate, and high in the question on leisure-time activity. Results: There were 956 participants included in the present study. Forearm BMD in the eighth age decade was 0.40 g/cm2 (95% CI 0.33 - 0.46 g/cm2) lower than in the third decade among women and 0.28 g/cm2 (95% CI 0.18 - 0.37 g/cm2) lower among men. The differences in calcaneal stiffness between the same age decades were 22.4 (95% CI 17.5 - 27.4) among women and 15.8 (95% CI 8.0 - 23.5) among men. The correlation between forearm BMD and calcaneal stiffness was 0.58 (95% CI 0.52 - 0.64) in women and 0.34 (95% CI 0.25 - 0.42) in men. Reported moderate and high leisure-time activity levels in both genders were associated with higher calcaneal stiffness but not with forearm BMD. Conclusions: The QUS may be used to measure the effect of present physical activity levels on calcaneal bone at the population level. Further longitudinal studies are warranted in order to determine the most appropriate non-invasive method in population-based studies.
Adolescent alcohol use, psychological health, and social integration
Authors: Hoel Sindre , Magne Eriksen Bjørn , Breidablik Hans-Johan , Meland Eivind
Published: October 2004

Aim: Alcohol use and intoxication are highly prevalent among adolescents and may be an important element of the socialization process in the teenage years. Significant short- and long-term health consequences seem evident. The aim of this study was to investigate the relationship between alcohol consumption and several aspects of psychological health and social integration in adolescents. Methods: The study is based on data from a 1997 cross-sectional survey of 828 Norwegian tertiary school students in Førde (91% of all students). Three hundred and eighty (46%) were female. The majority of students were aged 20 or younger, with 64% aged 15 - 17. Four groups were defined according to frequency of alcohol intoxication. Emotional health and social integration in the four groups are reported as means and the differences from the reference groups (with 95% confidence limits) were estimated. Control of confounding and interaction was performed. Results: The study reveals that alcohol intoxication is an established element of mid-teenage behaviour for both sexes. It was found that depressive complaints and psychosomatic problems increased with increasing frequency of intoxication. Alcohol use is not only associated with improving friendship quantity but also with an improved quality of friendships. Heavy consumers report greater problems with relations with school and with their parents, especially in early adolescence. Conclusions: Though adolescents with moderate and heavy alcohol consumption are more sociable with friends, abstainers and light drinkers appear emotionally healthier. They succeed to a greater extent in a wide variety of social arenas, particularly in comparison with heavy consumers.
Bridges, pathways and valleys: labour market position and risk of hospitalization in a Swedish sample aged 55 - 63
Authors: Hyde Martin , Hagberg Jan , Oxenstierna Gabriel , Theorell Töres , Westerlund Hugo
Published: October 2004

Background: The combination of population ageing and increasingly early labour market exit (LME) throughout Europe has made older age a key issue in social policy and research. There is increasing awareness that older people are a heterogeneous group in which health inequalities persist. However, the effects of different types of LME on health have received relatively little attention. Existing studies reach different conclusions. This might be due to several reasons: different types of LME are rarely explored in conjuncture; studies often lack objective assessments of health and frequently rely on small populations. This paper aims to test the relative effects of different LME on the risk of hospitalization compared with those who remained in paid employment. Methods: Using Government register data on pooled cross-section samples of Swedish workers aged 55 - 63 years (n=7,024) the authors have compared the likelihood of hospitalization for three types of LME - disability pension (förtidpension), unemployment, and early retirement - with those who continue working. Results: Controlling for previous hospitalization, sex, age, social class, and health at work a significant increased risk of hospitalization was found following LME for the unemployed (OR=1.98). Conclusion: Early LME is a varied process with mixed effects on health, and hence is of possible importance for policy, which, therefore, requires more attention. Programmes to help older unemployed workers back into work will have positive health effects for individuals and reduce welfare costs of hospitalization.
Review Article: Indigenous health in the Arctic: an overview of the circumpolar Inuit population
Authors: Bjerregaard Peter , Kue Young T. , Dewailly Eric , Ebbesson Sven O.E.
Published: October 2004

The health of the Inuit has undergone substantial changes over the past five centuries, as a result of social, cultural, and economic changes brought about by interactions with Europeans. This process was accelerated considerably in the second half of the twentieth century. The incidence of infectious diseases has declined considerably but is still high compared with Western societies. Chronic diseases such as diabetes and cardiovascular disease are on the increase, while accidents, suicides, violence, and substance abuse are of major importance for the pattern of ill health in most Inuit communities. Lifestyle changes, social change, and changes in society and the environment are major determinants of health among the Inuit.
Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs
Authors: Zheng Xiangqun H. , Lu Fu , Wang Zhen-Yuan , Zhong Fei , Hoover Jeffrey , Mural Richard
Published: October 2004

Motivation: The identification of orthologous gene pairs is generally based on sequence similarity. Gene pairs that are mutually ‘best hits’ between the genomes being compared are asserted to be orthologs. Although this method identifies most orthologous gene pairs with high confidence, it will miss a fraction of them, especially genes in duplicated gene families. In addition, the approach depends heavily on the completeness and quality of gene annotation. When the gene sequences are not correctly represented the approach is unlikely to find the correct ortholog. To overcome these limitations, we have developed an approach to identify orthologous gene pairs using shared chromosomal synteny and the annotation of protein function.

Results: Assembled mouse and human genomes were used to identify the regions of conserved synteny between these genomes. ‘Syntenic anchors’ are conserved non-repetitive locations between mouse and human genomes. Using these anchors, we identified blocks of sequences that contain consistently ordered anchors between the two genomes (syntenic blocks). The synteny information has been used to help us identify orthologous gene pairs between mouse and human genomes. The approach combines the mutual selection of the best tBlastX hits between human and mouse transcripts, and inferring gene orthologous relationships based on sharing syntenic anchors, collocating in the same syntenic blocks and sharing the same annotated protein function. Using this approach, we were able to find 19 357 orthologous gene pairs between human and mouse genomes, a 20% increase in the number of orthologs identified by conventional approaches.

Contact:  richard.mural@celera.com
Biological sequence analysis through the one-dimensional percolation transform and its enhanced version
Authors: da Fontoura Costa Luciano
Published: October 2004

Motivation: The necessity to characterize the spatial uniformity (or lack of it) of symbols in biological sequences, given its implications for identification of the properties of the structures associated with the sequences.

Methods: A one-dimensional version of a recently introduced percolation-based approach is presented, which allows the accurate quantification of symbol distributions even in the presence of co-existing densities. An enhanced version of this methodology, which uses an agglomerative process to organize hierarchically the sequence into subsequences, is also proposed and illustrated.

3. Results: The potential of the proposed methodology is illustrated with respect to synthetic and real data (1881 zebrafish and 1200 Xenopus proteins) and compared to two alternative multiscale methodologies, with encouraging results including the possibility to identify particularly remarkable amino acid arrangements in proteins.

4. Contact:  luciano@if.sc.usp.br
III. CERTAIN CRIMINAL PROCEEDINGS IN FRANCE REPUBLIC OF THE CONGO v FRANCE), PROVISIONAL MEASURES, ORDER OF 17 JUNE 20031
Authors: David Turns
Published: October 2004

In its decision in the Arrest Warrant case,2 the International Court of Justice studiedly refused to address systematically the legality and ambit of a purported exercise in absentia of universal criminal jurisdiction by one State over a government minister of another State. This, coupled with the dicta of certain judges with reservations as to the scope of universal jurisdiction3 and the (at best) lukewarm support for such jurisdiction displayed by certain other judges,4 might be taken as a discouragement to States to engage in similar exercises of jurisdiction. However, the contemporary trend in many developed States in favour of taking measures of extraterritorial enforcement jurisdiction to apprehend and punish the alleged perpetrators of serious international law crimes, coupled with the entry into force of the Statute of the International Criminal Court, indicates that more such attempts are quite likely to be made. Within a year of its decision in the Arrest Warrant case, the ICJ again found itself the forum for a similar dispute. On 9 December 2002 the Republic of the Congo (‘the Congo’) filed an Application instituting proceedings against France5 in circumstances notably resembling those that had prompted the Democratic Republic of the Congo (‘the DRC’) to act against Belgium. Again, the Applicant was an African State protesting against an alleged abuse of universal jurisdiction and failure to respect immunities on the part of its European former colonial ruler. Despite the prima facie similarity between the two cases, however, the chances that the eventual decision in the Certain Criminal Proceedings case will go beyond the Arrest Warrant case to elucidate the doctrine of universal jurisdiction are very slight. This note is confined to considering the circumstances behind the Congolese Application and Request for the Indication of a Provisional Measure, and the Court's response thereto in its Order of 17 June 2003.
A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size
Authors: Jorgensen Paul , Rupeš Ivan , Sharom Jeffrey R. , Schneper Lisa , Broach James R. , Tyers Mike
Published: October 2004

Cell-size homeostasis entails a fundamental balance between growth and division. The budding yeast Saccharomyces cerevisiae establishes this balance by enforcing growth to a critical cell size prior to cell cycle commitment (Start) in late G1 phase. Nutrients modulate the critical size threshold, such that cells are large in rich medium and small in poor medium. Here, we show that two potent negative regulators of Start, Sfp1 and Sch9, are activators of the ribosomal protein (RP) and ribosome biogenesis (Ribi) regulons, the transcriptional programs that dictate ribosome synthesis rate in accord with environmental and intracellular conditions. Sfp1 and Sch9 are required for carbon-source modulation of cell size and are regulated at the level of nuclear localization and abundance, respectively. Sfp1 nuclear concentration responds rapidly to nutrient and stress conditions and is regulated by the Ras/PKA and TOR signaling pathways. In turn, Sfp1 influences the nuclear localization of Fhl1 and Ifh1, which bind to RP gene promoters. Starvation or the absence of Sfp1 causes Fhl1 and Ifh1 to localize to nucleolar regions, concomitant with reduced RP gene transcription. These findings suggest that nutrient signals set the critical cell-size threshold via Sfp1 and Sch9-mediated control of ribosome biosynthetic rates.
Dosage-sensitive requirement for mouse Dll4 in artery development
Authors: Duarte António , Hirashima Masanori , Benedito Rui , Trindade Alexandre , Diniz Patrícia , Bekman Evguenia , Costa Luís , Henrique Domingos , Rossant Janet
Published: October 2004

Involvement of the Notch signaling pathway in vascular development has been demonstrated by both gain- and loss-of-function mutations in humans, mice, and zebrafish. In zebrafish, Notch signaling is required for arterial identity by suppressing the venous fate in developing artery cells. In mice, the Notch4 receptor and the Delta-like 4 (Dll4) ligand are specifically expressed in arterial endothelial cells, suggesting a similar role. Here we show that the Dll4 ligand alone is required in a dosage-sensitive manner for normal arterial patterning in development. This implicates Dll4 as the specific mammalian endothelial ligand for autocrine endothelial Notch signaling, and suggests that Dll4 may be a suitable target for intervention in arterial angiogenesis.
Haploinsufficient lethality and formation of arteriovenous malformations in Notch pathway mutants
Authors: Krebs Luke T. , Shutter John R. , Tanigaki Kenji , Honjo Tasuku , Stark Kevin L. , Gridley Thomas
Published: October 2004

The Notch signaling pathway is essential for embryonic vascular development in vertebrates. Here we show that mouse embryos heterozygous for a targeted mutation in the gene encoding the DLL4 ligand exhibit haploinsufficient lethality because of defects in vascular remodeling. We also describe vascular defects in embryos homozygous for a mutation in the Rbpsuh gene, which encodes the primary transcriptional mediator of Notch signaling. Conditional inactivation of Rpbsuh function demonstrates that Notch activation is essential in the endothelial cell lineage. Notch pathway mutant embryos exhibit defects in arterial specification of nascent blood vessels and develop arteriovenous malformations. These results demonstrate that vascular remodeling in the mouse embryo is sensitive to Dll4 gene dosage and that Notch activation in endothelial cells is essential for embryonic vascular remodeling.
Tsc2 is not a critical target of Akt during normal Drosophila development
Authors: Dong Jixin , Pan Duojia
Published: October 2004

Signaling by insulin and target of rapamycin are both required for cell growth, but their interrelationships remain poorly defined. It was reported that Akt, an essential component of the insulin pathway, stimulates growth by phosphorylating and inhibiting tuberous sclerosis complex 2 (TSC2). Here we evaluate this model genetically in Drosophila by engineering Tsc2 mutants in which the Akt phosphorylation sites are changed to nonphosphorylatable or phospho-mimicking residues. Strikingly, such mutants completely rescue the lethality and cell growth defects of Tsc2-null mutants. Taken together, our data suggest that Tsc2 is not a critical substrate of Akt in normal Drosophila development.
Mitochondrial Genome Variation in Eastern Asia and the Peopling of Japan
Authors: Tanaka Masashi , Cabrera Vicente M. , González Ana M. , Larruga José M. , Takeyasu Takeshi , Fuku Noriyuki , Guo Li-Jun , Hirose Raita , Fujita Yasunori , Kurata Miyuki , Shinoda Ken-ichi , Umetsu Kazuo , Yamada Yoshiji , Oshida Yoshiharu , Sato Yuzo , Hattori Nobutaka , Mizuno Yoshikuni , Arai Yasumichi , Hirose Nobuyoshi , Ohta Shigeo , Ogawa Osamu , Tanaka Yasushi , Kawamori Ryuzo , Shamoto-Nagai Masayo , Maruyama Wakako , Shimokata Hiroshi , Suzuki Ryota , Shimodaira Hidetoshi
Published: October 2004

To construct an East Asia mitochondrial DNA (mtDNA) phylogeny, we sequenced the complete mitochondrial genomes of 672 Japanese individuals (http://www.giib.or.jp/mtsnp/index_e.html). This allowed us to perform a phylogenetic analysis with a pool of 942 Asiatic sequences. New clades and subclades emerged from the Japanese data. On the basis of this unequivocal phylogeny, we classified 4713 Asian partial mitochondrial sequences, with <10% ambiguity. Applying population and phylogeographic methods, we used these sequences to shed light on the controversial issue of the peopling of Japan. Population-based comparisons confirmed that present-day Japanese have their closest genetic affinity to northern Asian populations, especially to Koreans, which finding is congruent with the proposed Continental gene flow to Japan after the Yayoi period. This phylogeographic approach unraveled a high degree of differentiation in Paleolithic Japanese. Ancient southern and northern migrations were detected based on the existence of basic M and N lineages in Ryukyuans and Ainu. Direct connections with Tibet, parallel to those found for the Y-chromosome, were also apparent. Furthermore, the highest diversity found in Japan for some derived clades suggests that Japan could be included in an area of migratory expansion to Continental Asia. All the theories that have been proposed up to now to explain the peopling of Japan seem insufficient to accommodate fully this complex picture.
Close Split of Sorghum and Maize Genome Progenitors
Authors: Swigoňová Zuzana , Lai Jinsheng , Ma Jianxin , Ramakrishna Wusirika , Llaca Victor , Bennetzen Jeffrey L. , Messing Joachim
Published: October 2004

It is generally believed that maize (Zea maysL. ssp.mays) arose as a tetraploid; however, the two progenitor genomes cannot be unequivocally traced within the genome of modern maize. We have taken a new approach to investigate the origin of the maize genome. We isolated and sequenced large genomic fragments from the regions surrounding five duplicated loci from the maize genome and their orthologous loci in sorghum, and then we compared these sequences with the orthologous regions in the rice genome. Within the studied segments, we identified 11 genes that were conserved in location, order, and orientation. We performed phylogenetic and distance analyses and examined the patterns of estimated times of divergence for sorghum and maize gene orthologs and also the time of divergence for maize orthologs. Our results support a tetraploid origin of maize. This analysis also indicates contemporaneous divergence of the ancestral sorghum genome and the two maize progenitor genomes about 11.9 million years ago (Mya). On the basis of a putative conversion event detected for one of the genes, tetraploidization must have occurred before 4.8 Mya, and therefore, preceded the major maize genome expansion by gene amplification and retrotransposition.
Genetic and Haplotype Diversity Among Wild-Derived Mouse Inbred Strains
Authors: Ideraabdullah Folami Y. , de la Casa-Esperón Elena , Bell Timothy A. , Detwiler David A. , Magnuson Terry , Sapienza Carmen , de Villena Fernando Pardo-Manuel
Published: October 2004

With the completion of the mouse genome sequence, it is possible to define the amount, type, and organization of the genetic variation in this species. Recent reports have provided an overview of the structure of genetic variation among classical laboratory mice. On the other hand, little is known about the structure of genetic variation among wild-derived strains with the exception of the presence of higher levels of diversity. We have estimated the sequence diversity due to substitutions and insertions/deletions among 20 inbred strains of Mus musculus, chosen to enable interpretation of the molecular variation within a clear evolutionary framework. Here, we show that the level of sequence diversity present among these strains is one to two orders of magnitude higher than the level of sequence diversity observed in the human population, and only a minor fraction of the sequence differences observed is found among classical laboratory strains. Our analyses also demonstrate that deletions are significantly more frequent than insertions. We estimate that 50% of the total variation identified in M. musculus may be recovered in intrasubspecific crosses. Alleles at variants positions can be classified into 164 strain distribution patterns, a number exceeding those reported and predicted in panels of classical inbred strains. The number of strains, the analysis of multiple loci scattered across the genome, and the mosaic nature of the genome in hybrid and classical strains contribute to the observed diversity of strain distribution patterns. However, phylogenetic analyses demonstrate that ancient polymorphisms that segregate across species and subspecies play a major role in the generation of strain distribution patterns.
Inverted Repeat Structure of the Human Genome: The X-Chromosome Contains a Preponderance of Large, Highly Homologous Inverted Repeats That Contain Testes Genes
Authors: Warburton Peter E. , Giordano Joti , Cheung Fanny , Gelfand Yefgeniy , Benson Gary
Published: October 2004

We have performed the first genome-wide analysis of the Inverted Repeat (IR) structure in the human genome, using a novel and efficient software package called Inverted Repeats Finder (IRF). After masking of known repetitive elements, IRF detected 22,624 human IRs characterized by arm size from 25 bp to >100 kb with at least 75% identity, and spacer length up to 100 kb. This analysis required 6 h on a desktop PC. In all, 166 IRs had arm lengths >8 kb. From this set, IRs were excluded if they were in unfinished/unassembled regions of the genome, or clustered with other closely related IRs, yielding a set of 96 large IRs. Of these, 24 (25%) occurred on the X-chromosome, although it represents only ∼5% of the genome. Of the X-chromosome IRs, 83.3% were ≥99% identical, compared with 28.8% of autosomal IRs. Eleven IRs from Chromosome X, one from Chromosome 11, and seven already described from Chromosome Y contain genes predominantly expressed in testis. PCR analysis of eight of these IRs correctly amplified the corresponding region in the human genome, and six were also confirmed in gorilla or chimpanzee genomes. Similarity dot-plots revealed that 22 IRs contained further secondary homologous structures partially categorized into three distinct patterns. The prevalence of large highly homologous IRs containing testes genes on the X- and Y-chromosomes suggests a possible role in male germ-line gene expression and/or maintaining sequence integrity by gene conversion.
Decoding Human Regulatory Circuits
Authors: Thompson William , Palumbo Michael J. , Wasserman Wyeth W. , Liu Jun S. , Lawrence Charles E.
Published: October 2004

Clusters of transcription factor binding sites (TFBSs) which direct gene expression constitutecis-regulatory modules (CRMs). We present a novel algorithm, based on Gibbs sampling, which locates, de novo, thecisfeatures of these CRMs, their component TFBSs, and the properties of their spatial distribution. The algorithm finds 69% of experimentally reported TFBSs and 85% of the CRMs in a reference data set of regions upstream of genes differentially expressed in skeletal muscle cells. A discriminant procedure based on the output of the model specifically discriminated regulatory sequences in muscle-specific genes in an independent test set. Application of the method to the analysis of 2710 10-kb fragments upstream of annotated human genes identified 17 novel candidate modules with a false discovery rate ≤0.05, demonstrating the applicability of the method to genome-scale data.
Predicting Subcellular Localization via Protein Motif Co-Occurrence
Authors: Scott Michelle S. , Thomas David Y. , Hallett Michael T.
Published: October 2004

The prediction of subcellular localization of proteins from their primary sequence is a challenging problem in bioinformatics. We have created a Bayesian network localization predictor called PSLT that is based on the combinatorial presence of InterPro motifs and specific membrane domains in human proteins. This probabilistic framework generates a likelihood of localization to all organelles and allows to predict multicompartmental proteins. When used to predict on nine compartments, PSLT achieves an accuracy of 78% as estimated by using a 10-fold cross-validation test and a coverage of 74%. When used to predict the localization of proteins from other closely related species, it achieves a prediction accuracy and a coverage >80%. We compared the localization predictions of PSLT to those determined through GFP-tagging and microscopy for a group of human proteins. We found two general classes of proteins that are mislocalized by the GFP-tagging strategy but are correctly localized by PSLT. This suggests that PSLT can be used in combination with experimental approaches for localization to identify proteins for which additional experimental validation is required. We used our predictor to annotate all 9793 human proteins from SWISS-PROT release 41.25, 16% of which are predicted by PSLT to be present in more than one compartment.
High-Content Screening Microscopy Identifies Novel Proteins With a Putative Role in Secretory Membrane Traffic
Authors: Starkuviene Vytaute , Liebel Urban , Simpson Jeremy C. , Erfle Holger , Poustka Annemarie , Wiemann Stefan , Pepperkok Rainer
Published: October 2004

Here we describe the establishment of microscope-based functional screening assays in intact cells that allow us to systematically identify new proteins involved in secretory membrane traffic, and proteins that can influence the integrity of the Golgi complex. We were able to identify 20 new proteins that affected either secretory transport, Golgi morphology, or both, when overexpressed in cells. Control experiments with human orthologs to yeast proteins with a role in membrane traffic, or already well characterized mammalian regulators of the secretory pathway, confirmed the specificity and significance of our results. Proteins localized to the Golgi complex or endoplasmic reticulum (ER) showed preferential interference in our assays. Bioinformatic analysis of the new proteins interfering with membrane traffic and/or Golgi integrity revealed broad functional variety, but demonstrated a bias towards proteins with predicted coiled-coil domains and repeat structures. Extending our approach to a much larger set of novel proteins in the future will be an important step toward a more comprehensive understanding of the molecular basis of the secretory pathway. It will also serve as an example for similar microscope-based screens addressing different biological questions.
Gene Loss and Movement in the Maize Genome
Authors: Lai Jinsheng , Ma Jianxin , Swigoňová Zuzana , Ramakrishna Wusirika , Linton Eric , Llaca Victor , Tanyolac Bahattin , Park Yong-Jin , Jeong O-Young , Bennetzen Jeffrey L. , Messing Joachim
Published: October 2004

Maize (Zea mays L. ssp. mays), one of the most important agricultural crops in the world, originated by hybridization of two closely related progenitors. To investigate the fate of its genes after tetraploidization, we analyzed the sequence of five duplicated regions from different chromosomal locations. We also compared corresponding regions from sorghum and rice, two important crops that have largely collinear maps with maize. The split of sorghum and maize progenitors was recently estimated to be 11.9 Mya, whereas rice diverged from the common ancestor of maize and sorghum ∼50 Mya. A data set of roughly 4 Mb yielded 206 predicted genes from the three species, excluding any transposon-related genes, but including eight gene remnants. On average, 14% of the genes within the aligned regions are noncollinear between any two species. However, scoring each maize region separately, the set of noncollinear genes between all four regions jumps to 68%. This is largely because at least 50% of the duplicated genes from the two progenitors of maize have been lost over a very short period of time, possibly as short as 5 million years. Using the nearly completed rice sequence, we found noncollinear genes in other chromosomal positions, frequently in more than one. This demonstrates that many genes in these species have moved to new chromosomal locations in the last 50 million years or less, most as single gene events that did not dramatically alter gene structure.
Divergence of Spatial Gene Expression Profiles Following Species-Specific Gene Duplications in Human and Mouse
Authors: Huminiecki Lukasz , Wolfe Kenneth H.
Published: October 2004

To examine the process by which duplicated genes diverge in function, we studied how the gene expression profiles of orthologous gene sets in human and mouse are affected by the presence of additional recent species-specific paralogs. Gene expression profiles were compared across 16 homologous tissues in human and mouse using microarray data from the Gene Expression Atlas for 1575 sets of orthologs including 250 with species-specific paralogs. We find that orthologs that have undergone recent duplication are less likely to have strongly correlated expression profiles than those that remain in a one-to-one relationship between human and mouse. There is a general trend for paralogous genes to become more specialized in their expression patterns, with decreased breadth and increased specificity of expression as gene family size increases. Despite this trend, detailed examination of some particular gene families where species-specific duplications have occurred indicated several examples of apparent neofunctionalization of duplicated genes, but only one case of subfunctionalization. Often, the expression of both copies of a duplicated gene appears to have changed relative to the ancestral state. Our results suggest that gene expression profiles are surprisingly labile and that expression in a particular tissue may be gained or lost repeatedly during the evolution of even small gene families. We conclude that gene duplication is a major driving force behind the emergence of divergent gene expression patterns.
A Comprehensive Genetic Map of the Cattle Genome Based on 3802 Microsatellites
Authors: Ihara Naoya , Takasuga Akiko , Mizoshita Kazunori , Takeda Haruko , Sugimoto Mayumi , Mizoguchi Yasushi , Hirano Takashi , Itoh Tomohito , Watanabe Toshio , Reed Kent M. , Snelling Warren M. , Kappes Steven M. , Beattie Craig W. , Bennett Gary L. , Sugimoto Yoshikazu
Published: October 2004

A microsatellite-based high-density genetic map facilitates for fine mapping of hereditary traits of interest, characterization of meiosis, and providing a foundation for physical map construction. Here, we developed a comprehensive genetic map on the basis of >880,000 genotypes across the USDA MARC cattle reference families with a potential genetic resolution of 0.8 cM at the 95% confidence level (∼800 kb in the bovine genome). We incorporated 2325 microsatellites into the second-generation genetic map by linkage analysis based on sex-averaged two-point LOD scores (>3.0), of which 2293 were fine-mapped by multipoint linkage analysis. The new 3160-cM map comprised of 29 sex-averaged autosomal linkage groups and a sex-specific X-chromosome linkage group includes 3960 markers with 2389 positions, resulting in an average interval size of 1.4 cM. More than half (51%) of the total length of the map is covered with intervals of 2.0 cM or less, and the largest gap is a 10.2-cM interval on the X-linkage group. The new map should accelerate fine mapping and positional cloning of genes for genetic diseases and economically important traits in cattle, as well as related livestock species, such as sheep and goat.
Characterization of the Maize Endosperm Transcriptome and Its Comparison to the Rice Genome
Authors: Lai Jinsheng , Dey Nrisingha , Kim Cheol-Soo , Bharti Arvind K. , Rudd Stephen , Mayer Klaus F.X. , Larkins Brian A. , Becraft Philip , Messing Joachim
Published: October 2004

The cereal endosperm is a major organ of the seed and an important component of the world's food supply. To understand the development and physiology of the endosperm of cereal seeds, we focused on the identification of genes expressed at various times during maize endosperm development. We constructed several cDNA libraries to identify full-length clones and subjected them to a twofold enrichment. A total of 23,348 high-quality sequence-reads from 5′- and 3′-ends of cDNAs were generated and assembled into a unigene set representing 5326 genes with paired sequence-reads. Additional sequencing yielded a total of 3160 (59%) completely sequenced, full-length cDNAs. From 5326 unigenes, 4139 (78%) can be aligned with 5367 predicted rice genes and by taking only the “best hit” be mapped to 3108 positions on the rice genome. The 22% unigenes not present in rice indicate a rapid change of gene content between rice and maize in only 50 million years. Differences in rice and maize gene numbers also suggest that maize has lost a large number of duplicated genes following tetraploidization. The larger number of gene copies in rice suggests that as many as 30% of its genes arose from gene amplification, which would extrapolate to a significant proportion of the estimated 44,027 candidate genes of its entire genome. Functional classification of the maize endosperm unigene set indicated that more than a fourth of the novel functionally assignable genes found in this study are involved in carbohydrate metabolism, consistent with its role as a storage organ.
Large-Scale Mutagenesis of the Yeast Genome Using a Tn7-Derived Multipurpose Transposon
Authors: Kumar Anuj , Seringhaus Michael , Biery Matthew C. , Sarnovsky Robert J. , Umansky Lara , Piccirillo Stacy , Heidtman Matthew , Cheung Kei-Hoi , Dobry Craig J. , Gerstein Mark B. , Craig Nancy L. , Snyder Michael
Published: October 2004

We present here an unbiased and extremely versatile insertional library of yeast genomic DNA generated by in vitro mutagenesis with a multipurpose element derived from the bacterial transposon Tn7. This mini-Tn7 element has been engineered such that a single insertion can be used to generate a lacZ fusion, gene disruption, and epitope-tagged gene product. Using this transposon, we generated a plasmid-based library of ∼300,000 mutant alleles; by high-throughput screening in yeast, we identified and sequenced 9032 insertions affecting 2613 genes (45% of the genome). From analysis of 7176 insertions, we found little bias in Tn7 target-site selection in vitro. In contrast, we also sequenced 10,174 Tn3 insertions and found a markedly stronger preference for an AT-rich 5-base pair target sequence. We further screened 1327 insertion alleles in yeast for hypersensitivity to the chemotherapeutic cisplatin. Fifty-one genes were identified, including four functionally uncharacterized genes and 25 genes involved in DNA repair, replication, transcription, and chromatin structure. In total, the collection reported here constitutes the largest plasmid-based set of sequenced yeast mutant alleles to date and, as such, should be singularly useful for gene and genome-wide functional analysis.
Quantification of Multiple Gene Expression in Individual Cells
Authors: Peixoto António , Monteiro Marta , Rocha Benedita , Veiga-Fernandes Henrique
Published: October 2004

Quantitative gene expression analysis aims to define the gene expression patterns determining cell behavior. So far, these assessments can only be performed at the population level. Therefore, they determine the average gene expression within a population, overlooking possible cell-to-cell heterogeneity that could lead to different cell behaviors/cell fates. Understanding individual cell behavior requires multiple gene expression analyses of single cells, and may be fundamental for the understanding of all types of biological events and/or differentiation processes. We here describe a new reverse transcription-polymerase chain reaction (RT-PCR) approach allowing the simultaneous quantification of the expression of 20 genes in the same single cell. This method has broad application, in different species and any type of gene combination. RT efficiency is evaluated. Uniform and maximized amplification conditions for all genes are provided. Abundance relationships are maintained, allowing the precise quantification of the absolute number of mRNA molecules per cell, ranging from 2 to 1.28×109 for each individual gene. We evaluated the impact of this approach on functional genetic read-outs by studying an apparently homogeneous population (monoclonal T cells recovered 4 d after antigen stimulation), using either this method or conventional real-time RT-PCR. Single-cell studies revealed considerable cell-to-cell variation: All T cells did not express all individual genes. Gene coexpression patterns were very heterogeneous. mRNA copy numbers varied between different transcripts and in different cells. As a consequence, this single-cell assay introduces new and fundamental information regarding functional genomic read-outs. By comparison, we also show that conventional quantitative assays determining population averages supply insufficient information, and may even be highly misleading.
Repeated Evolution of the Pyrrolizidine Alkaloid–Mediated Defense System in Separate Angiosperm Lineages w⃞
Authors: Reimann Andreas , Nurhayati Niknik , Backenköhler Anita , Ober Dietrich
Published: October 2004

Species of several unrelated families within the angiosperms are able to constitutively produce pyrrolizidine alkaloids as a defense against herbivores. In pyrrolizidine alkaloid (PA) biosynthesis, homospermidine synthase (HSS) catalyzes the first specific step. HSS was recruited during angiosperm evolution from deoxyhypusine synthase (DHS), an enzyme involved in the posttranslational activation of eukaryotic initiation factor 5A. Phylogenetic analysis of 23 cDNA sequences coding for HSS and DHS of various angiosperm species revealed at least four independent recruitments of HSS from DHS: one within the Boraginaceae, one within the monocots, and two within the Asteraceae family. Furthermore, sequence analyses indicated elevated substitution rates within HSS-coding sequences after each gene duplication, with an increased level of nonsynonymous mutations. However, the contradiction between the polyphyletic origin of the first enzyme in PA biosynthesis and the structural identity of the final biosynthetic PA products needs clarification.
Phytochrome Phosphorylation Modulates Light Signaling by Influencing the Protein–Protein Interaction[W]
Authors: Kim Jeong-Il , Shen Yu , Han Yun-Jeong , Park Joung-Eun , Kirchenbauer Daniel , Soh Moon-Soo , Nagy Ferenc , Schäfer Eberhard , Song Pill-Soon
Published: October 2004

Plant photoreceptor phytochromes are phosphoproteins, but the question as to the functional role of phytochrome phosphorylation has remained to be elucidated. We investigated the functional role of phytochrome phosphorylation in plant light signaling using a Pfr-specific phosphorylation site mutant, Ser598Ala of oat (Avena sativa) phytochrome A (phyA). The transgenic Arabidopsis thaliana (phyA-201 background) plants with this mutant phyA showed hypersensitivity to light, suggesting that phytochrome phosphorylation at Serine-598 (Ser598) in the hinge region is involved in an inhibitory mechanism. The phosphorylation at Ser598 prevented its interaction with putative signal transducers, Nucleoside Diphosphate Kinase-2 and Phytochrome-Interacting Factor-3. These results suggest that phosphorylation in the hinge region of phytochromes serves as a signal-modulating site through the protein–protein interaction between phytochrome and its putative signal transducer proteins.