bluuebunny/crossref_metadata_2025 huggingface dataset:
Sequence of a 9·8 kb segment of yeast chromosome II including the three genes of the MAL3 locus and three unidentified open reading frames
Authors: Feuermann M. , Charbonnel L. , De Montigny J. , Bloch J.‐C. , Potier S. , Souciet J.‐L.
Published: May 2005

We report the DNA sequence of a segment located on the right arm of chromosome II from Saccharomyces cerevisiae S288C near the subtelomeric sequences. The sequence was determined using a random cloning strategy followed by an oligonucleotide‐directed sequencing. The segment contains four non‐overlapping open reading frames (ORFs) YBR297w, YBR298c, YBR299w and YBR301c, and two overlapping ones (YBR300c and YBR300w). Three of them—YBR297w, YBR298c and YBR299w—are the MAL3R (transcriptional regulatory protein), MAL3T (maltose permease) and MAL3S (maltase) genes of the MAL3 locus previously localized. The three other ORFs are unidentified. Another MAL locus (MAL1) has been localized on chromosome VII. The Mal− phenotype of strain S288c cannot be explained by telomeric silencing. The sequences have been submitted to the EMBL data library under Accession Numbers Z36166; Z36167; Z36168; Z36169 and Z36171.
Analysis of a 32·8 kb segment of yeast chromosome IV reveals 21 open reading frames, including TPS2, PPH3, RAD55, SED1, PDC2, AFR1, SSS1, SLU7 and a tRNA for arginine
Authors: Coster Françoise , Jonniaux Jean‐Luc , Goffeau Andre
Published: May 2005

We report the nucleotide sequence of a 32·8 kb DNA segment from the right arm of Saccharomyces cerevisiae chromosome IV. The sequence contains 20 open reading frames (ORFs) longer than 300 bp as well as the 240 bp gene coding for the essential SSS1 secretory protein. Nine ORFs previously totally or partially sequenced (TPS2, PPH3, RAD55, SED1, PDC2, AFR1, SSS1, SLU7 and D4478) are presented, as well as the transmembrane protein D4405, the leucine zipper containing D4495 and a new tRNA for arginine. D4456 and D4461 are separated by a single in‐frame stop codon only. The other five ORFs show no particular features or significant homology. The sequence is recorded in EMBL database under Accession Number X82086.
Localization of the FAR3 gene: Genetic mapping and molecular cloning using a chromosome walk‐‘n’‐roll strategy
Authors: Horecka Joe
Published: May 2005

FAR3 is a newly‐discovered yeast gene required specifically for pheromone‐mediated cell cycle arrest. I have used strains harboring the far3‐1 mutation to map the gene to the right arm of chromosome XIII, establishing the gene order CEN13‐LYS7‐MCM1‐FAR3. I cloned the FAR3 gene based on its genetic map position using a strategy that combined chromosome walking and a related technique termed ‘chromosome rolling’. In addition to the genetic and physical localization of FAR3, I present data that suggest corrections to the tentative map positions of VAN1 and ARG80.
Characteristics of spontaneous revertants in haploid yeast
Authors: Korogodina V. L. , Korogodin V. I. , Maiorova E. S. , Simonyan N. V.
Published: May 2005

The appearance dynamics of spontaneous revertants in adenine‐ or leucine‐auxotrophic haploid Saccharomyces cerevisiae strains has been studied using mathematical simulation methods. In the case of adenine auxotrophs an increase in the number of revertants with decreasing metabolite content is found to result mainly from increasing the rate of intragenic suppressor mutations. In the case of leucine auxotrophs revertants result from increasing the appearance of mutants formed at similar rates under different cultivation conditions. In the latter case the appearance of mutant colonies increases with decreasing size of colonies of the initial auxotrophic cells. The last can simulate so‐called adaptive mutagenesis. The heterogeneity of revertants appearing in different time periods is described.
Characterization of Na+/H+‐antiporter gene closely related to the salt‐tolerance of yeast Zygosaccharomyces rouxii
Authors: Watanabe Yasuo , Miwa Satoko , Tamai Youichi
Published: May 2005

In order to clarify the relationship between salt‐tolerance of Zygosaccharomyces rouxii and the function of Na+/H+‐antiporter, a gene was isolated from Z. rouxii which exhibited homology to the Na+/H+‐antiporter gene (sod2) from Schizosaccharomyces pombe. This newly isolated gene (Z‐SOD2) encoded a product of 791 amino acids, which was larger than the product encoded by its Sz. pombe homologue. The predicted amino‐acid sequence of Z‐Sod2p was highly homologous to that of the Sz. pombe protein, but included an extra‐hydrophilic stretch in the C‐terminal region. The expression of Z‐SOD2 was constitutive and independent of NaCl‐shock. Z‐SOD2‐disruptants of Z. rouxii did not grow in media supplemented with 3 M‐NaCl, but grew well in the presence of 50% sorbitol, indicating that the function of Z‐SOD2 was closely related to the salt‐tolerance of Z. rouxii. Several genes are also compared and discussed in relation to the salt‐tolerance of Z. rouxii. The nucleotide sequence data reported in this paper will appear in the GSDB, DDBJ, EMBL and NCBI nucleotide sequence databases with the following accession number: D43629.
Expression and secretion of antifreeze peptides in the yeast Saccharomyces cerevisiae
Authors: Driedonks R. A. , Toschka H. Y. , van Almkerk J. W. , Schäffers I. M. , Verbakel J. M. A.
Published: May 2005

The antifreeze peptide AFP6 from the polar fish Pseudopleuronectus americanus has been expressed in and secreted by the yeast Saccharomyces cerevisiae as a biologically active molecule. The gene for the 37 amino acid long peptide has been chemically synthesized using yeast preferred codons. Subsequently, the gene has been cloned into an episomal expression vector as well as in a multicopy integration vector, which is mitotically more stable. The expression is under the control of the inducible GAL7 promoter. The enzyme α‐galactosidase has been investigated as a carrier protein to facilitate expression and secretion of AFP. In order to reach increased expression levels, tandem repeats of the AFP gene (up to eight copies) have been cloned. In most cases the genes are efficiently expressed and the products secreted. The expression level amounts to approximately 100 mg/l in the culture medium. In a number of genetic constructs the genes are directly linked and expressed as AFP multimers. In other constructs linker regions have been inserted between the AFP gene copies, that allow the peptide to be processed by specific proteinases, either from the endogenous yeast proteolytic system or from a non‐yeast source. The latter requires a separate processing step after yeast cultivation to obtain mature AFP. In all these cases proteolytic processing is incomplete, generating a heterogeneous mixture of mature AFP, carrier and chimeric protein, and/or a mixture of AFP‐oligomers. The antifreeze activity has been demonstrated for such mixtures as well as for AFP multimers.
Sequence and functional analysis of a 7·2 kb DNA fragment containing four open reading frames located between RPB5 and CDC28 on the right arm of chromosome II
Authors: Rose Matthias , Kiesau Peter , Proft Markus , Entian Karl‐Dieter
Published: May 2005

In a coordinated approach, several laboratories sequenced Saccharomyces cerevisiae chromosome II during the European BRIDGE project. Here we report on the sequence and functional analysis of a 7217 bp fragment located on the right arm of chromosome II between RPB5 and CDC28. The fragment contains four open reading frames probably encoding proteins of 79·2 kDa (corresponding gene YBR156c), 12·1 kDa (YBR157c), 62·7 kDa (YBR158w) and 38·7 kDa (YBR159w). All four open reading frames encode new proteins, as concluded from data base searches. The respective genes were destroyed by gene replacement in one allele of diploid cells. After sporulation and tetrad analysis, the resulting mutant haploid strains were investigated. No phenotype with respect to spore germination, viability, carbohydrate utilization, and growth was found for YBR157c, encoding the smallest open reading frame investigated. Gene replacement within the YBR156c gene encoding a highly basic and possibly nuclear located protein was lethal. Ybr158 revealed similarities to the Grr1 (Cat80) protein with respect to the leucine‐rich region. Cells harboring a mutation in the YBR158w gene showed strongly reduced growth as compared to the wild‐type cells. The protein predicted from YBR159w shared 33% identical amino acid residues with the human estradiol 17‐beta‐hydroxysterol dehydrogenase 3. Haploid ybr159c mutants were only able to grow at reduced temperatures, but even under these conditions the mutants grew slower than wild‐type strains. The DNA sequence was deposited at the EMBL data base with accession numbers Z36025 (YBR156c), Z36026 (YBR157c), Z36027 (YBR158w) and Z36028 (YBR159w).
Transcriptional regulation by an upstream repression sequence from the yeast enolase gene ENO1
Authors: Carmen Andrew A. , Brindle Paul K. , Park Chang Seo , Holland Michael J.
Published: May 2005

The activity of an upstream repression sequence (URS element) that mediates a 20‐fold repression of ENO1 expression in cells grown in a medium containing glucose was characterized. Sequences that are sufficient for orientation‐dependent ENO1 URS element activity were mapped between positions ‐241 and ‐126 relative to the ENO1 transcriptional initiation site. The ENO1 URS element repressed transcription of the yeast CYC1 gene when positioned between the CYC1 upstream activation sequences (UAS elements) and TATAAA boxes. The ENO1 URS element failed to repress transcription of the wild‐type yeast enolase gene ENO2; however, expression of an ENO2 gene lacking one of the ENO2 UAS elements was efficiently repressed by the ENO1 URS element, suggesting that the URS element interferes with the transcriptional activation by some, but not all, UAS elements. In contrast to the ENO1 gene, the ENO1 URS element repressed CYC1 and ENO2 expression in cells grown on glucose or glycerol plus lactate. Evidence is presented that the ENO1 URS element also functions during stationary growth phase.
Identification of peroxisomal membrane ghosts with an epitope‐tagged integral membrane protein in yeast mutants lacking peroxisomes
Authors: Purdue P. Edward , Lazarow Paul B.
Published: May 2005

Many yeast peroxisome biogenesis mutants have been isolate in which peroxisomes appear to be completely absent. Introduction of a wild‐type copy of the defective gene causes the reappearance of peroxisomes, despite the fact that new peroxisomes are thought to form only from pre‐existing peroxisomes. This apparent paradox has been explained for similar human mutant cell lines (from patients with Zellweger syndrome) by the discovery of peroxisomal membrane ghosts in the mutant cells (Santos, M. J., T. Imanaka, H. Shio, G. M. Small and P. B. Lazarow. 1988. Science 239, 1536–1538). Introduction of a wild‐type gene is thought to restore to the ghosts the ability to import matrix proteins, and thus lead to the refilling of the peroxisomes. It is vitally important to our understanding of peroxisome biogenesis to determine whether the yeast mutants contain ghosts. We have solved this problem by introducing an epitope‐tagged version of Pas3p, a peroxisome integral membrane protein (that is essential for peroxisome biogenesis). Nucleotides encoding a nine amino acid HA epitope were added to the PAS3 gene immediately before the stop codon. The tagged gene (PAS3HA) was inserted in the genome, replacing the wild‐type gene at its normal locus. It was fully functional (the cells assembled peroxisomes normally and grew on oleic acid) but the expression level was too low to detect the protein with monoclonal antibody 12CA5. PAS3HA was expressed in greater quantity from an episomal plasmid with the CUP1 promoter. The gene product, Pas3pHA, was detected by immunogold labelling on the membranes of individual and clustered peroxisomes; the clusters appeared as large spots in immunofluorescence. PAS3HA was similarly expressed in peroxisome biogenesis mutants peb2 and peb4, which lack morphologically recognizable peroxisomes. Gold‐labelled membranes were clearly visible in both mutants: in peb2 the labelled membrane vesicles were generally much smaller than those in peb4, which resembled normal peroxisomes in size.
VIV. Yeast sequencing reports. Sequencing analysis of a 24·7 kb fragment of yeast chromosome XIV identifies six known genes, a new member of the hexose transporter family and ten new open reading frames
Authors: Maftahi M. , Nicaud J.‐M. , Levesque H. , Gaillardin C.
Published: May 2005

The DNA sequence of a 24·7 kb region covering the left arm of chromosome XIV from Saccharomyces cerevisiae was determined. This region contains 17 open reading frames (ORFs) which code for proteins of more than 100 amino acids. Five ORFs correspond to the KRE1, ATP11, DAL82, RFA2 and MCK1 loci, described previously. Two ORFs present high similarity to known proteins: NO345 with the hexose transporter family, and NO351 with the yeast chorismate mutase/prephenate dehydratase enzyme encoded by PHA2. Six ORFs show limited similarity with known proteins or some specific features: NO339 presents 11 potential transmembrane domains. NO343, which is internal to NO345, presents a putative signal sequence and a potential transmembrane domain. NO348 shows similarity with YCW2, TUP1 and SEC13. NO364 reveals a signature for a pyridoxal‐phosphate attachment site. Finally, NO384 and NO388 present a biased amino acid composition, being rich in Asn or Glu/Lys/Arg, respectively. Four other ORFs (NO342, NO376, NO381 and NO397) show no similarity to proteins within the databases screened. The sequence has been entered in the EMBL data library under Accession Number Z46259.
UVS112—A gene involved in excision repair of yeast
Authors: Kozhina Tatiana , Kozhin Sergey , Stepanova Vera , Yarovoy Boris , Donich Vladimir , Fedorova Irina , Korolev Vladimir
Published: May 2005

In this study we show that the previously described uvs112 (uvs12) mutation blocks one of the steps of the excision repair pathway. The properties of this mutation permit the assignment of the UVS112 gene to the RAD3 epistasis group. It was established that the uvs112 mutation caused a 2·5‐fold reduction in the number of recombinants produced by conversion and also significantly increased the frequency of mitotic crossing‐over in interplasmid recombination. Tetrad analysis placed the UVS112 gene on the left arm of chromosome IX, approximately 20 cM from HIS5. The analysis of mitotic recombination revealed that UVS112 lies between HIS6 and HIS5, and is an allele of the RAD25 gene.
Restoration of peroxisome formation in two conditional peroxisome‐deficient mutants of Hansenula polymorpha during growth of cells on specific organic nitrogen sources
Authors: Titorenko Vladimir I. , Evers Melchior E. , Van Der Klei Ida J. , Harder Wim , Veenhuis Marten
Published: May 2005

Expression of the peroxisome‐deficient (Per−) phenotype by per mutants of Hansenula polymorpha is shown to be dependent on specific environmental conditions. Analysis of our collection of constitutive and conditional per mutants showed that, irrespective of the carbon source used, the mutants invariably lacked functional peroxisomes when ammonium sulphate was used as a nitrogen source. However, in two temperature‐sensitive (ts) mutants, per13‐6ts and per14‐11ts, peroxisomes were present at the restrictive temperature when cells were grown on organic nitrogen sources which are known to induce peroxisomes in wild‐type cells, namely D‐alanine (for both mutants) or methylamine (for per14‐11ts). These organelles displayed normal wild‐type properties with respect to morphology, mode of development and protein composition.

However, under these conditions not all the peroxisomal matrix proteins synthesized were correctly located inside peroxisomes. Detailed biochemical and (immuno) cytochemical analyses indicated that during growth of cells on methanol in the presence of either D‐alanine or methylamine, a minor portion of these proteins (predominantly alcohol oxidase, dihydroxyacetone synthase and catalase) still resided in the cytosol. This residual cytosolic activity may explain the observation that the functional restoration of the two ts mutants is not complete under these conditions, as is reflected by the retarded growth of the cells in batch cultures on methanol.
X. Yeast sequencing reports. The sequence of 24·3 kb from chromosome X reveals five complete open reading frames, all of which correspond to new genes, and a tandem insertion of a ty1 transposon
Authors: Zagulski M. , Babinska B. , Gromadka R. , Migdalski A. , Rytka J. , Sulicka J. , Herbert C. J.
Published: May 2005

We have determined the complete nucleotide sequence of a 24·3 kb segment from chromosome X carried by the cosmid pEJ103. The sequence encodes five complete open reading frames (ORFs), none of which correspond to previously described genes; however, four of these ORFs display interesting similarities with sequences present in the databanks. The sequence also contains a tandem insertion of a Ty1 element. An investigation of the Ty1 polymorphism in other strains has revealed that the original insertion occurred within an ORF. Finally, the structure of the Ty1 repeat suggests a mechanism by which it may have been generated. The sequence has been deposited in the EMBL data library under the Accession Number X87297 for the complete sequence and X87298 for the δty1 version.
XIV. Yeast sequencing reports. A 43·5 kb segment of yeast chromosome XIV, which contains MFA2, MEP2, CAP/SRV2, NAM9, FKB1/FPR1/RBP1, MOM22 and CPT1, predicts an adenosine deaminase gene and 14 new open reading frames
Authors: Mallet Laurent , Bussereau Françoise , Jacquet Michel
Published: May 2005

A 43,481 bp fragment from the left arm of chromosome XIV of Saccharomyces cerevisiae was sequenced. A gene for tRNAphe and 23 non‐overlapping open reading frames (ORFs) were identified, seven of which correspond to known yeast genes: MFA2, MEP2, CAP/SRV2, NAM9, FKB1/FPR1/RBP1, MOM22 and CPT1. One ORF may correspond to the yet unindentified yeast adenosine deaminase gene. Among the 15 other ORFs, four exhibit known signatures, which include a protein tyrosine phosphatase, a cytoskeleton‐associated protein and two ATP‐binding proteins, four have similarities with putative proteins of yeast or proteins from other organisms and seven exibit no significant similarity with amino acid sequences described in data banks. One ORF is identical to yeast expressed sequence tags (EST) and therefore corresponds to an expressed gene. Six ORFs present similarities to human dbESTs, thus identifying motifs conserved during evolution. Nine ORFs are putative transmembrane proteins. In addition, one overlapping and three antisense ORFs, which are not likely to be functional, were detected. The sequence has been deposited in the EMBL data bank under Accession Number Z46843.
Molecular characterization of the PEL1 gene encoding a putative phosphatidylserine synthase
Authors: Janitor Martin , Jarosch Ernst , Schweyen Rudolf J. , S̈bík Július
Published: May 2005

In the yeast Saccharomyces cerevisiae the PEL1 gene is essential for the viability of rho−/rhoo petite mutants, and its mutation in respiring cells results in a pleiotropic phenotype. Results of complementation analysis with different subclones of chromosomal DNA and re‐sequencing of the YCL4w‐YCL3w segment of chromosome III demonstrate that the coding region of the PEL1 gene corresponds to 1467 bp. The size of the PEL1 transcript in Northern blot analysis was estimated to be approximately 1·5 kb. Transcription initiation in wild‐type cells was found to occur at the position −9 relative to the ATG. The PEL1 gene was moderately expressed irrespective of the state of the mitochondrial genome and the nature of the carbon sources. Disruption of the PEL1 gene was not lethal and resulted in the same phenotype as observed with the pel1 mutant, i.e. the cells were not able to survive ethidium bromide mutagenesis, were thermosensitive for growth on glucose at 37°C and failed to grow on minimal glycerol medium. Although the Pel1 protein exhibits significant similarity to a family of phosphatidylserine synthases, the disrupted PEL1 gene was not complemented by the multicopy plasmid‐borne CHO1 gene encoding an essential yeast phosphatidylserine synthase. The Accession Number of the PEL1 gene in the EMBL data library is Z48162.
DOGR1 and DOGR2: Two genes from Saccharomyces cerevisiae that confer 2‐deoxyglucose resistance when overexpressed
Authors: Randez‐Gil Francisca , Blasco Amalia , Prieto Jose Antonio , Sanz Pascual
Published: May 2005

Saccharomyces cerevisiae contains two genes (DOGR1 and DOGR2) that are able to confer 2‐deoxyglucose resistance when they are overexpressed. These genes are very similar, sharing 92% identity at the protein level. They code for two isoenzymes with 2‐deoxyglucose‐6 phosphate (2‐DOG‐6P) phosphatase activity. These enzymes have been purified and characterized. DogR1p shows an optimum pH of 6, an optimum temperature of 30°C and a KM on 2‐DOG‐6P of 17 mM. DogR2p shows a similar optimum pH, but the optimum temperature is 40°C and it exhibits a KM on 2‐DOG‐6P of 41 mM. Both enzymes require 10 mM‐MgCl2 for maximal activity and they are inhibited by inorganic phosphate.
Schizosaccharomyces pombe RNase MRP RNA is homologous to metazoan RNase MRP RNAs and may provide clues to interrelationships between RNase MRP and RNase P
Authors: Paluh Janet L. , Clayton David A.
Published: May 2005

RNase MRP and RNase P ribonucleoproteins are structurally and functionally similar across a large evolutionary distance. To better characterize possible complex interrelationships between these two enzymes, we have employed the fission yeast Schizosaccharomyces pombe. Unlike Saccharomyces cerevisiae, S. pombe is believed to harbour only one genetic locus for the RNA component of RNase P and does not contain a known mitochondrially encoded RNase P RNA. We have identified the single nuclear gene for the RNA component of RNase MRP in S. pombe, mrp‐1, by homology to vertebrate RNase MRP RNAs. The mrp‐1 gene encodes an RNA of maximum mature length 400 nucleotides that shares a high degree of identity, in evolutionarily conserved regions, to both vertebrate RNase MRP RNAs and S. pombe RNase P RNA. Disruption of mrp‐1 in the diploid strain SP826 and sporulation of tetrads resulted in a 2 dead:2 viable segregation, consistent with the gene being essential. Lethality is rescued by a plasmid‐borne copy of mrp‐1. Partially purified ribonucleoprotein RNase MRP activity correctly and efficiently processed all previously characterized heterologous mitochondrial RNA substrates. The compact mitochondrial genome of S. pombe contains sequence elements with >50% identity to mammalian D‐loop CSBI and CSBII elements. The identification of mrp‐1 in S. pombe should facilitate not only comparisons between the related ribonucleoproteins RNase MRP and RNase P, but should also provide an opportunity for genetic elucidation of RNase MRP function in a situation reflective of the animal kingdom.
Functional analysis reports. Precise gene disruption in Saccharomyces cerevisiae by double fusion polymerase chain reaction
Authors: Amberg David C. , Botstein David , Beasley Ellen M.
Published: May 2005

We adapted a fusion polymerase chain reaction (PCR) strategy to synthesize gene disruption alleles of any sequenced yeast gene of interest. The first step of the construction is to amplify sequences flanking the reading frame we want to disrupt and to amplify the selectable marker sequence. Then we fuse the upstream fragment to the marker sequence by fusion PCR, isolate this product and fuse it to the downstream sequence in a second fusion PCR reaction. The final PCR product can then be transformed directly into yeast. This method is rapid, relatively inexpensive, offers the freedom to choose from among a variety of selectable markers and allows one to construct precise disruptions of any sequenced open reading frame in Saccharomyces cerevisiae.
IV. Yeast sequencing reports. GUF1, a gene encoding a novel evolutionarily conserved gtpase in budding yeast
Authors: Kiser Gretchen L. , Weinert Ted A.
Published: May 2005

While sequencing a region of chromosome IV adjacent to the checkpoint gene MEC3, we identified a gene we call GUF1 (GTPase of Unknown Function), which predicts a 586 amino acid GTPase of the elongation factor‐type class. The predicted Guf1p protein bears striking sequence similarity to both LepA from Escherichia coli (43% identical) and LK1236·1 from Caenorhabditis elegans (42% identical). Analysis of both a guf1δ deletion and a putative constitutive‐activating mutant (GUF1HG) revealed that GUF1 is not essential nor did mutant cells reveal any marked phenotype. The GenBank Accession Number for the GUF1 sequence is U22360.
Proton production and consumption pathways in yeast metabolism. A chemostat culture analysis
Authors: Castrillo J. I. , De Miguel I. , Ugalde U. O.
Published: May 2005

In this investigation, a method for the accurate quantitative determination of net proton production or consumption in biological cultures has been devised. Cells are cultured under constant pH conditions. The specific rate of proton production or consumption by the culture (qH+, mmol h−1 per g biomass) is proportional to the mmol of base or acid required to maintain constant pH per unit time, and this equivalence is independent of the buffering capacity of the culture medium.

The above method has been applied to chemostat cultures of Candida utilis growing on glucose or glycerol as carbon source, and different nitrogen sources. The results indicate that the nitrogen assimilation pathway alone determines the value of qH+, and a fixed stoichiometric relationship between nitrogen uptake rate qN (meq h−1 per g biomass) and qH+ has been found for each nitrogen source employed. Thus, qH+/qN values of +1, 0 and − 1 were found for ammonium ions, urea and nitrate respectively. Under oxidative metabolism, the contribution of carbon catabolism to the value of qH+ was undetectable.

Since qN may be related to growth and production of type 1 compounds in fermentation processes, the parameter qH+ was incorporated into a model of growth and energy metabolism in chemostat culture (Castrillo and Ugalde, Yeast 10, 185–197, 1994), resulting in adequate simulations of experimentally observed culture performance. Thus, it is suggested that qH+ may be employed as a simple and effective control parameter for biotechnological processes involving biomass‐related products.
VII. Yeast sequencing reports. DNA sequence analysis of a 35 kb segment from Saccharomyces cerevisiae chromosome VII reveals 19 open reading frames including RAD54, ACE1/CUP2, PMR1, RCK1, AMS1 and CAL1/CDC43
Authors: James C. M. , Indge K. J. , Oliver S. G.
Published: May 2005

We present DNA sequence data from a 35 364 bp region on the left arm of chromosome VII of Saccharomyces cerevisiae. This region contains 19 open reading frames (ORFs). ORF G1821 corresponds to the RAD54 gene involved in repair and recombination (Emery et al., 1991). G1810 is identical to the ACE1 gene sequenced by Szczypka and Thiele (1989), required for copper‐inducible transcription of the CUP1 gene. The first 693 bp on the minus strand represent part of the 3′ non‐coding region from the P‐type ATPase gene PMR1, previously sequenced by Rudolph et al. (1989), which is identical to the SSC1 gene (Smith et al., 1988). G1845 corresponds to the RCK1 protein kinase gene from S. cerevisiae (Dahlkvist and Sunnerhagen, 1994). G1861 is almost identical to the α‐mannosidase gene AMS1 reported by Yoshihisa and Anraku (1989) and G1864 has 100% identity with the yeast CAL1 gene (Ohya et al., 1989)/CDC43 gene (Johnson et al., 1990) which is involved in control of cell polarity. This region also contains a gene specifying a Leu‐tRNA precursor and a remnant of a tau element. ORF G1880 shows some similarity to the S. cerevisiae SNF2, STH1 and NPS1 genes and to the human ERCC1 gene. A 93 bp region shows similarity to yeast EST sequenced by Burns et al. (1994). None of the remaining ORFs has similarity to any sequence within the databases screened. The sequence described in this paper has been deposited in the EMBL Data Library under the Accession Number Z48618.
The chromosome ends of Saccharomyces cerevisiae
Authors: Louis Edward J.
Published: May 2005

Yeast chromosome ends are similar in structure and function to chromosome ends in most, if not all, eukaryotic organisms. There is a G‐rich terminal repeat at the ends which is maintained by telomerase. In addition to the classical functions of protecting the end from degradation and end‐to‐end fusions, and completing replication, yeast telomeres have several interesting properties including: non‐nucleosomal chromatin structure; transcriptional position effect variegation for genes with adjacent telomeres; nuclear peripheral localization; apparent physical clustering; non‐random recombinational interactions. A number of genes have been identified that are involved in modifying one or more of these properties. These include genes involved in general DNA metabolism, chromatin structure and telomere maintenance. Adjacent to the terminal repeat is a mosaic of middle repetitive elements that exhibit a great deal of polymorphism both between individual strains and among different chromosome ends. Much of the sequence redundancy in the yeast genome is found in the sub‐telomeric regions (within the last 25 kb of each end). The sub‐telomeric regions are generally low in gene density, low in transcription, low in recombination, and they are late replicating. The only element which appears to be shared by all chromosome ends is part of the previously defined X element containing an ARS consensus. Most of the ‘core’ X elements also contain an Abf1p binding site and a URS1‐like element, which may have consequences for the chromatin structure, nuclear architecture and transcription of native telomeres. Possible functions of sub‐telomeric repeats include: fillers for increasing chromosome size to some minimum threshold level necessary for chromosome stability; barrier against transcriptional silencing; a suitable region for adaptive amplification of genes; secondary mechanism of telomere maintenance via recombination when telomerase activity is absent.
Pre‐discharge B‐type natriuretic peptide predicts early recurrence of decompensated heart failure in patients admitted to a general medical unit
Authors: Verdiani Valerio , Nozzoli Carlo , Bacci Francesca , Cecchin Adriana , Rutili Maria Serena , Paladini Sergio , Olivotto Iacopo
Published: May 2005

Background

B‐type natriuretic peptide (BNP) represents a promising predictor of early (30 days) re‐admission in patients with heart failure (HF) admitted to cardiology units. Whether BNP retains its predictive value in unselected patients admitted to general medical wards is unknown.

Methods

We determined BNP levels on admission and pre‐discharge in 100 consecutive patients (71 male, mean age 78±10 years) admitted to a general medical unit due to decompensated HF. Follow‐up after discharge was 30 days.

Results

Of the 100 patients, 86 had ≥1 comorbid conditions. Median BNP was 739 pg/ml on admission (25th–75th percentile 355–1333 pg/ml, respectively), and 414 pg/ml pre‐discharge (25th–75th percentile 220–696 pg/ml). Seventeen patients were re‐admitted or died within 30 days. Patients with pre‐discharge BNP values >75th percentile (696 pg/ml) had greater risk of re‐hospitalisation, as compared to values ≤696 pg/ml (56% vs. 4%, respectively; p<0.001). Negative predictive value for this cut‐off was 96%. BNP values >75th percentile were associated with a 15.0 independent relative hazard (RH) of early re‐admission or death (95% CI 4.2–53.8; p<0.0001). The other independent predictor was a NYHA class ≥III at discharge (RH 2.9; 95% CI 1.1–9.3; p<0.05).

Conclusion

In a general medical unit, pre‐discharge BNP levels were a strong independent predictor of early re‐admission or death due to HF, irrespective of substantial comorbidity and advanced age.
Comparison of Palmar Tilt, Radial Inclination and Ulnar Variance in Left and Right Wrists
Authors: HOLLEVOET N. , VAN MAELE G. , SEYMORTIER P. VAN. , VERDONK R.
Published: May 2005

Standard radiographs of both wrists of 50 healthy volunteers were taken. The mean differences between the right and left wrists were 1.5° for radial inclination, 0.5 mm for ulnar variance and 2.5 ° for palmar tilt. The variability of the left-right differences were compared with the variability of the whole group and were significantly less for radial inclination, ulnar variance and palmar tilt. We conclude that both wrists of one individual can be considered as symmetrical for the tested parameters and that the contralateral wrist provides a better reference than population data.
Corrective Osteotomy of Malunited Fractures of Phalanges and Metacarpals
Authors: GOLLAMUDI S. , JONES W.A.
Published: May 2005

We have retrospectively reviewed our experience of corrective osteotomies for phalangeal and metacarpal malunions in eleven patients over a 5-year period. Rotational metacarpal malunion treated by metacarpal osteotomy and AO plate fixation can be performed with confidence of achieving a good or excellent result. Phalangeal osteotomy remains a daunting undertaking for most hand surgeons. Our indifferent results are probably due to the inclusion of three intraarticular malunions treated by extraarticular osteotomy. An alternative approach to these malunions may be appropriate.
Endoscopic Carpal Tunnel Release in Selected Rheumatoid Patients
Authors: BELCHER H. J. C. R. , VARMA S. , SCHONAUER F.
Published: May 2005

Twenty endoscopic carpal tunnel releases were performed in 15 patients with quiescent seropositive rheumatoid arthritis using the Agee technique. Patients were not considered for endoscopic carpal tunnel release if there was florid synovitis with crepitus or loss of active finger flexion, if there was evidence of flexor tendon rupture or if they had previously undergone surgery in the region. Access to the tunnel was significantly easier than normal and visualization of the flexor retinaculum was satisfactory in all cases. There were no complications. We conclude that endoscopic carpal tunnel release can he safely performed in selected patients with rheumatoid arthritis. The absence of a palmar scar can be a great advantage to these disabled patients.
Brachial Plexus Neuropathy
Authors: GEERTZEN J. H. B. , GROOTHOFF J. W. , NICOLAI J.-P. , RIETMAN J. S.
Published: May 2005

This retrospective study assessed the long-term outcome of brachial plexus neuropathy in 16 patients. The mean follow up was 8 years. Nine patients complained of persistent pain and muscle weakness, four had continuing problems with various activities of daily living and 11 had trouble with some housekeeping activities. Furthermore, eight of the patients had to change their occupation.
A Novel Use for Lead Shields in Theatre: The Hartshill Window
Authors: ROBERTS P. J. , WADE R. H. , THOMAS O. L. , PORTER N.
Published: May 2005

The problem of radiation exposure to surgeons during radiographic screening has been previously highlighted. We describe a simple, cheap and reusable device for reducing exposure time and improving image quality during the treatment of wrist and hand fractures.
Coccidioidomycosis Fungal Infection in the Hand Mimicking a Metacarpal Enchondroma
Authors: HUANG J. I. , SEEGER L. L. , JONES N. F.
Published: May 2005

Coccidioidomycosis, an infection caused by the fungus Coccidioides immitis, rarely affects the hand, but we report an unusual case which mimicked the radiological appearance of an enchondroma in the metacarpal. Curettage and bone grafting in combination with long-term antifungal therapy are necessary for successful treatment of coccidioidomycosis of the hand.
The Development of Hand Surgery in Japan and the Japanese Society for Surgery of the Hand
Authors: TAMAI S.
Published: May 2005

Japanese hand surgeons have contributed articles to our journal for many years. This article describes advances in Hand Surgery in Japan and introduces a section of this issue which is devoted to articles from Japan. (The Editor)
The Proximal Ligamentous Component of the Triangular Fibrocartilage Complex
Authors: NAKAMURA T. , MAKITA A.
Published: May 2005

The proximal ligamentous component of the triangular fibrocartilage complex (TFCC) was studied anatomically using 15 fresh-frozen cadaver hand forearm specimens. Changes in the length of either side of this component were analysed during forearm rotation with the complete three-dimensional structure of the TFCC preserved. The proximal ligamentous component consists of three portions: dorsal, central and palmar. The dorsal and palmar portions connect the radius and ulna directly. These were recognized in all specimens whereas the central portion was not constant. The morphology of the proximal component was categorized into three types: fan-shaped, V-shaped, and funnel-shaped in five wrists each. Changes in ligament length during forearm rotation were measured using fine wires under slight tension that paralleled the ligaments from origin to insertion. The dorsal and palmar portions demonstrated three trends: the dorsal portion increased in length from supination to pronation whereas the palmar portion increased in length from pronation to supination; the length of the dorsal portion remained almost constant as the palmar portion increased in length from pronation to supination; the length of the palmar portion remained almost constant while the dorsal portion lengthened from supination to pronation. These variations appear to be related to which portion of the ligament was attached nearest to the centre of the ulnar fovea, where the rotational axis of the forearm passes. The portion attaching nearest to the fovea demonstrated a nearly isometric length pattern, whereas the portion which attached at a distance showed greater extensibility. These findings suggest that the proximal component of the TFCC corresponds to a true radioulnar ligament, and the isometric and eccentric fibres act mutually during forearm rotation.
Heptameric (L12)6/L10 rather than canonical pentameric complexes are found by tandem MS of intact ribosomes from thermophilic bacteria
Authors: Ilag Leopold L. , Videler Hortense , McKay Adam R. , Sobott Frank , Fucini Paola , Nierhaus Knud H. , Robinson Carol V.
Published: May 2005

Ribosomes are universal translators of the genetic code into protein and represent macromolecular structures that are asymmetric, often heterogeneous, and contain dynamic regions. These properties pose considerable challenges for modern-day structural biology. Despite these obstacles, high-resolution x-ray structures of the 30S and 50S subunits have revealed the RNA architecture and its interactions with proteins for ribosomes fromThermus thermophilus, Deinococcus radiodurans, andHaloarcula marismortui. Some regions, however, remain inaccessible to these high-resolution approaches because of their high conformational dynamics and potential heterogeneity, specifically the so-called L7/L12 stalk complex. This region plays a vital role in protein synthesis by interacting with GTPase factors in translation. Here, we apply tandem MS, an approach widely applied to peptide sequencing for proteomic applications but not previously applied to MDa complexes. Isolation and activation of ions assigned to intact 30S and 50S subunits releases proteins S6 and L12, respectively. Importantly, this process reveals, exclusively while attached to ribosomes, a phosphorylation of L12, the protein located in multiple copies at the tip of the stalk complex. Moreover, through tandem MS we discovered a stoichiometry for the stalk protuberance onThermus thermophilusand other thermophiles and contrast this assembly with the analogous one on ribosomes from mesophiles. Together with evidence for a potential interaction with the degradosome, these results show that important findings on ribosome structure, interactions, and modifications can be discovered by tandem MS, even on well studied ribosomes fromThermus thermophilus.
Nutritional study of the Islanders on Tristan da Cunha, 1966
Authors: Chambers Margaret A. , Southgate D. A. T.
Published: May 2005

1. A description of the population resident on Tristan da Cunha during the winter of 1966 is given.

2. Sources of food supplies are discussed.

3. A brief description of island meal patterns is given and methods of food preparation are discussed.

4. Samples of unusual foods and unique dishes consumed on Tristan da Cunha were collected and analysed for moisture, total nitrogen, fat, calcium, iron and ascorbic acid.

5. The dietary patterns and way of life of the Islanders resident on Tristan da Cunha have changed owing to contact with the outside world and to the development of a monetary economy. These changes were accelerated by the enforced period of 2 years spent in England. The Islanders are now very dependent upon a cash economy and subsistence agriculture provides only a relatively small part of the present diet.
The effects of vitamin E deficiency on the total fatty acids and the phospholipid fatty acids of rat tissues
Authors: Lee D. J. W. , Barnes M. McC.
Published: May 2005

1. A vitamin E-low diet containing 7% stripped lard was given to hooded rats for periods up to 14 months. Control rats were given the same diet with a vitamin E supplement (I i.u./rat per day).

2. No consistent pattern of changes was found in the total fatty acids of testis, lung, spleen, pancreas, heart, kidney, liver, brain, skeletal muscle and small intestine from rats given the deficient diet for 5, 6 or 7 months when compared with control rats.

3. The fatty acids of the total phospholipid from the same tissues were examined after 4, 5, 8 or 14 months. In the rats deficient in vitamin E the polyunsaturated fatty acids of the linoleic series (ω6) decreased, except for 20:4ω6, which in some tissues tended to increase. After 14 months there were considerable decreases in the percentages of all theω6 series including 20:4ω6 with increases in the percentages of 18:1ω9 and 20:3ω9 the pattern was similar to that found in essential fatty acid deficiency.
Mammary metabolism in lactating sows: arteriovenous differences of milk precursors and the mammary metabolism of [14C]glucose and [14C]acetate
Authors: Linzell J. L. , Mepham T. B. , Annison E. F. , West C. E.
Published: May 2005

1. The following techniques, which have been applied successfully to goats, were used to study mammary metabolism in lactating sows:(I) measurements of mammary arteriovenous (A-V) differences in milk precursors in the conscious undisturbed animal (five sows); (2) continuous intravenous infusion of [U-14C]glucose with concomitant arterial and mammary venous blood sampling for measurement of mammary blood flow and specific radioactivity of glucose and CO, (one sow); (3) perfusion of the isolated gland in vitro (eight glands from four sows), with the inclusion of [U-14C]glucose (two glands) and [U-14C]acetate(two glands) in the substrate mixture.

2. Sow mammary tissue was similar to that goats in its milk yield, blood flow, and glucose uptake per unit weight of tissue. As in goats, mammary uptake of glucose was many times that of the rest of the body and the total mammary tissue was utilizing about half of the total glucose entering the circulation. Glucose was a major source of milk lactose and glycerol and of mammary CO2.

3. Of the plasma lipid components, only the triglyceride fraction was consistently and significantly removed by the gland. In contrast to the results obtained for the goat, both [U-14C[acetate and [U-14C]glucose carbon were used for milk fatty acid synthesis, and although the pattern of labelling of fatty acid from each precursor was similar, the formation of fatty acids from glucose was at least five times greater than that from acetate. Quantitative evaluation of the contribution of these precursors was not possible, but the RQ (1.09–1.63) suggest that in some instances it may have been considerable.

4. The substantial A-V differences of most plasma essential amino acids suggest that these are the sole precursors of the corresponding residues in the mammary synthesized protein. The low A-V differences for several non-essential amino acids suggest that these are synthe- sized in the gland; this suggestion is supported by the incorporation of glucose carbon into non-essential amino acid residues of casein observed in one experiment. However, in contrast to results with the goat, mammary absorption of serine was consistently large.
Dietary depletion of vitamin B12and the excretion of methylmalonic acid in the rat
Authors: Williams D. L. , Spray G. H. , Newman G. E. , O'brien J. R. P.
Published: May 2005

1. A semi-synthetic vitamin B12-deficient diet, based on soya flour, is described. When supplemented with cydnocobalamin the diet appeared to be adequate for growth and reproduction in the rat.

2. Compared with their litter-mates on the supplemented diet, rats fed on the deficient diet from weaning showed reduced levels of vitamin B12activity in the plasma and tissues, but their growth rates were unaffected unless they were bred from mothers that had been given the deficient diet since mating.

3. When they were reared on the deficient diet, rats bred from mothers on the deficient diet since mating excreted much more methylmalonic acid in the urine than their litter-mates on the supplemented diet. There was wide variation in the level of excretion, both between different animals and from day to day in the same animal.

4. Starvation for more than 16 h caused a marked depression in the amount of methylmalonic acid excreted by rats on the deficient diet.

5. Intraperitoneal injection of sodium propionate into deficient animals after starvation for 24 h caused increased excretion of methylmalonic acid during the following 16 h of continued starvation. Isoleucine had a similar but smaller effect.

6. Tested in the starved animal, sodium propionate and valine given either by intra- peritoneal injection or by mouth, and isoleucine given intraperitoneally, caused increases in the excretion of methylmalonic acid. In contrast, methionine had no effect and threonine only a slight effect.
Production, absorption, distribution and excretion of vitamin B12in sheep
Authors: Smith R. M. , Marston Late H. R.
Published: May 2005

1. The efficiency of production and utilization of vitamin B12was studied with sheep given a cobalt-deficient diet with and without supplementary Co (1 mg/d). Vitamin B12to lignin ratios in rumen contents were used to estimate minimum rates of production and these were related to faecal and urinary excretion. Tissue distribution and excretion of vitamin B12were studied with [58Co]cyanocobalamin and 5′-deoxyadenosyl[60Co]cobalamin.

2. Labelled Co was rapidly sequestered by particulate material in the rumen and was largely excreted in the faeces. Most of the vitamin B12in whole rumen contents was contained in micro-organisms, but was released on incubation at pH 2. Added cyanocobalamin was partly degraded in the rumen.

3. The vitamin B12to lignin ratio in rumen contents began to decline 1–3 d after cessation of a daily Co drench. Estimated ruminal production of vitamin B12on full feed was not less than 400–700 μg/d with supplementary Co and 50–110 μg/d from the Co (0.01–0.05 μg/g dry weight) in the basal diet. Production of vitamin B12appeared to be limited by food intake with or without additional Co.

4. At full feed the efficiency of production of vitamin B12from Co in the basal diet was about 13% while that from added Co was about 3%. Part of the vitamin B12produced in the rumen was degraded before reaching the faeces and about 5% was absorbed. The minimum total requirements of sheep for vitamin B12are assessed at about 11 μg/d.

5. Injected 5′-deoxyadenosylcobalamin was better retained than injected cyanocobalamin, faecal excretion exceeded urinary excretion with both. Labelled cobalamin was selectively retained by liver (particularly by the mitochondria), kidneys and the walls of parts of the alimentary tract. Vitamin B12was secreted into the duodenum and reabsorbed in the ileum, but little secretion occurred above the duodenum and little absorption below the small intestine.