Genomic analysis of Kazachstania aerobia and Kazachstania servazzii reveals duplication of genes related to acetate ester production

Kazachstania aerobia and Kazachstania servazzii can affect wine aroma by increasing acetate ester concentrations, most remarkably phenylethyl acetate and isoamyl acetate. The genetic basis of this is unknown, there being little to no sequence data available on the genome architecture. We report for the first time the near-complete genome sequence of the two species using long-read (PacBio) sequencing (K. aerobia 20 contigs, one scaffold; and K. servazzii 22 contigs, one scaffold). The annotated genomes of K. aerobia (12.5 Mb) and K. servazzii (12.3 Mb) were compared to Saccharomyces cerevisiae genomes (laboratory strain S288C and wine strain EC1118). Whilst a comparison of the two Kazachstania spp. genomes revealed few differences between them, divergence was evident in relation to the genes involved in ester biosynthesis, for which gene duplications or absences were apparent. The annotations of these genomes are valuable resources for future research into the evolutionary biology of Kazachstania and other yeast species (comparative genomics) as well as understanding the metabolic processes associated with alcoholic fermentation and the production of secondary 'aromatic' metabolites (transcriptomics, proteomics and metabolomics).

Modern yeast development: finding the balance between tradition and innovation in contemporary winemaking

A key driver of quality in wines is the microbial population that undertakes fermentation of grape must. Winemakers can utilise both indigenous and purposefully inoculated yeasts to undertake alcoholic fermentation, imparting wines with aromas, flavours and palate structure and in many cases contributing to complexity and uniqueness. Importantly, having a toolbox of microbes helps winemakers make best use of the grapes they are presented with, and tackle fermentation difficulties with flexibility and efficiency. Each year the number of strains available commercially expands and more recently, includes strains of non-Saccharomyces, strains that have been improved using both classical and modern yeast technology and mixed cultures. Here we review what is available commercially, and what may be in the future, by exploring recent advances in fermentation relevant strain improvement technologies. We also report on the current use of microbes in the Australian wine industry, as reported by winemakers, as well as regulations around, and sentiment about the potential use of genetically modified organisms in the future.

OUP accepted manuscript

In winemaking, slow or stuck alcoholic fermentation can impact processing efficiency and wine quality. Residual fructose in the later stages of fermentation can leave the wine ‘out of specification’ unless removed, which requires reinoculation or use of a more fructophilic yeast. As such, robust, fermentation efficient strains are still highly desirable to reduce this risk. We report on a combined EMS mutagenesis and Directed Evolution (DE) approach as a ‘proof of concept’ to improve fructose utilization and decrease fermentation duration. One evolved isolate, Tee 9, was evaluated against the parent, AWRI 796 in defined medium (CDGJM) and Semillon juice. Interestingly, Tee 9 exhibited improved fermentation in CDGJM at several nitrogen contents, but not in juice. Genomic comparison between AWRI 796 and Tee 9 identified 371 mutations, but no chromosomal copy number variation. A total of 95 noncoding and 276 coding mutations were identified in 297 genes (180 of which encode proteins with one or more substitutions). Whilst introduction of two of these, Gid7 (E726K) or Fba1 (G135S), into AWRI 796 did not lead to the fermentation improvement seen in Tee 9, similar allelic swaps with the other mutations are needed to understand Tee 9’s adaption to CDGJM. Furthermore, the 378 isolates, potentially mutagenized but with the same genetic background, are likely a useful resource for future phenotyping and genome-wide association studies.

Influence of Kazachstania spp. on the chemical and sensory profile of red wines

We report the fermentative traits of two Kazachstania species (K. aerobia and K. servazzii) in non-sterile red wine and the resulting chemical and sensory properties. This builds on our previous work which revealed that Kazachstania spp. increased acetate esters in sterilised white wine. In this study Kazachstania spp. were initially evaluated in laboratory-scale fermentations (500 mL) in Merlot must to assess whether similar increases in chemical/volatile compounds would occur. The impact of malolactic fermentation (MLF) by Oenococcus oeni (VP41) on aroma composition was considered and found to reduce ester profiles in Merlot wines. The sensory implications of sequential inoculation with Kazachstania spp., followed by Saccharomyces cerevisiae, were then evaluated in small-lot fermentations (7 kg) of Shiraz must. Fungal diversity was monitored during early fermentation stages and was influenced by the early implantation of Kazachstania spp., followed by the dominance of S. cerevisiae. The effect of MLF in Shiraz wines was inconclusive due to high ethanol levels providing an inhospitable environment for lactic acid bacteria. When compared to S. cerevisiae alone, Kazachstania spp. significantly increased acetate esters, particularly phenylethyl acetate and isoamyl acetate, in both Merlot and Shiraz. The Shiraz wines fermented with Kazachstania spp. had higher jammy and red fruit aroma/flavour compared to S. cerevisiae (monoculture) wines. No influence was observed on colour one-year post-bottling. Results from this study show the contribution of Kazachstania spp. to the aroma profile of red wines and demonstrate their potential as starter cultures for improving the aromatic complexity of wines.

Disruption of ECM33 in diploid wine yeast EC1118: cell morphology and aggregation and their influence on fermentation performance

When investigating yeast gene function in relation to fermentation, many screens rely on haploid yeast derivatives. This, however, is not representative of industrial strains, which are typically diploid. One such example is the disruption of ECM33, which was associated with improved fermentation in the haploid wine yeast C911D, but remains uncharacterised in a diploid industrial strain background. We report on the homozygous disruption of ECM33 in Lalvin EC1118 using CRISPR/Cas9. EC1118 ecm33 resulted in a reduction of fermentation duration in a defined medium with limiting and sufficient nitrogen (-20% and -13%, respectively) when shaken. Increased cell size and aggregation, a phenotype previously unidentified in ecm33∆ as haploid yeast tend to aggregate, was also observed. This phenotype led to premature settling thereby the yeast behaving similarly to EC1118 in wine-like semi-static fermentations in a chemically defined medium. Further assessment in semi-static Riesling and Chardonnay fermentations inoculated based on cell number or biomass resulted in no significant difference or significantly slower fermentation duration in comparison the EC1118, nullifying the benefits of this mutation unless agitation is applied. This study draws attention to phenotypes being condition-dependent, highlighting the need to characterise and verify fermentation efficiency mutations in industrial yeast.

Sulfate transport mutants affect hydrogen sulfide and sulfite production during alcoholic fermentation

Hydrogen sulfide is a common wine fault, with a rotten-egg odour, which is directly related to yeast metabolism in response to nitrogen and sulfur availability. In grape juice, sulfate is the most abundant inorganic sulfur compound, which is taken up by yeast through two high-affinity sulfate transporters, Sul1p and Sul2p, and a low affinity transporter, Soa1p. Sulfate contributes to H₂ S production under nitrogen limitation, by being reduced via the Sulfur Assimilation Pathway (SAP). Therefore, yeast strains with limited H₂ S are highly desirable. We report on the use of toxic analogues of sulfate following ethyl methane sulfate treatment, to isolate six wine yeast mutants that produce no or reduced H₂ S and SO₂ during fermentation in synthetic and natural juice. Four amino acid substitutions (A99V, G380R, N588K and E856K) in Sul1p were found in all strains except D25-1 which had heterozygous alleles. Two changes were also identified in Sul2p (L268S and A470T). The Sul1p (G380R) and Sul2p (A470T) mutations were chosen for further investigation as these residues are conserved amongst SLC26 membrane proteins (including sulfate permeases). The mutations were introduced into EC1118 using Crispr cas9 technology and shown to reduce accumulation of H₂ S and do not result in increased SO₂ production during fermentation of model medium (chemically defined grape juice) or Riesling juice. The Sul1p (G380R) and Sul2p (A470T) mutations are newly reported as causal mutations. Our findings contribute to knowledge of the genetic basis of H₂ S production as well as the potential use of these strains for winemaking and in yeast breeding programmes.

Iterative synthetic strategies and gene deletant experiments enable the first identification of polysulfides in Saccharomyces cerevisiae

Polysulfides, potential signalling molecules, were synthesised and then found and explored for the first time in yeast.

Appropriate vacuolar acidification in Saccharomyces cerevisiae is associated with efficient high sugar fermentation

Vacuolar acidification serves as a homeostatic mechanism to regulate intracellular pH, ion and chemical balance, as well as trafficking and recycling of proteins and nutrients, critical for normal cellular function. This study reports on the importance of vacuole acidification during wine-like fermentation. Ninety-three mutants (homozygous deletions in lab yeast strain, BY4743), which result in protracted fermentation when grown in a chemically defined grape juice with 200 g L^-1 sugar (pH 3.5), were examined to determine whether fermentation protraction was in part due to a dysfunction in vacuolar acidification (VA) during the early stages of fermentation, and whether VA was responsive to the initial sugar concentration in the medium. Cells after 24 h growth were dual-labelled with propidium iodide and vacuolar specific probe 6-carboxyfluorescein diacetate (6-CFDA) and examined with a FACS analyser for viability and impaired VA, respectively. Twenty mutants showed a greater than two-fold increase in fluorescence intensity; the experimental indicator for vacuolar dysfunction; 10 of which have not been previously annotated to this process. With the exception of Δhog1, Δpbs2 and Δvph1 mutants, where dysfunction was directly related to osmolality; the remainder exhibited increased CF-fluorescence, independent of sugar concentration at 20 g L^-1 or 200 g L^-1. These findings offer insight to the importance of VA to cell growth in high sugar media.

Yeast genes involved in regulating cysteine uptake affect production of hydrogen sulfide from cysteine during fermentation

An early burst of hydrogen sulfide (H2S) produced by Saccharomyces cerevisiae during fermentation could increase varietal thiols and therefore enhance desirable tropical aromas in varieties such as Sauvignon Blanc. Here we attempted to identify genes affecting H2S formation from cysteine by screening yeast deletion libraries via a colony colour assay on media resembling grape juice. Both Δlst4 and Δlst7 formed lighter coloured colonies and produced significantly less H2S than the wild type on high concentrations of cysteine, likely because they are unable to take up cysteine efficiently. We then examined the nine known cysteine permeases and found that deletion of AGP1, GNP1 and MUP1 led to reduced production of H2S from cysteine. We further showed that deleting genes involved in the SPS-sensing pathway such as STP1 and DAL81 also reduced H2S from cysteine. Together, this study indirectly confirms that Agp1p, Gnp1p and Mup1p are the major cysteine permeases and that they are regulated by the SPS-sensing and target of rapamycin pathways under the grape juice-like, cysteine-supplemented, fermentation conditions. The findings highlight that cysteine transportation could be a limiting factor for yeast to generate H2S from cysteine, and therefore selecting wine yeasts without defects in cysteine uptake could maximise thiol production potential.

Genome-wide identification of the Fermentome; genes required for successful and timely completion of wine-like fermentation by Saccharomyces cerevisiae

Background

Wine fermentation is a harsh ecological niche to which wine yeast are well adapted. The initial high osmotic pressure and acidity of grape juice is followed by nutrient depletion and increasing concentrations of ethanol as the fermentation progresses. Yeast’s adaptation to these and many other environmental stresses, enables successful completion of high-sugar fermentations. Earlier transcriptomic and growth studies have tentatively identified genes important for high-sugar fermentation. Whilst useful, such studies did not consider extended growth (>5 days) in a temporally dynamic multi-stressor environment such as that found in many industrial fermentation processes. Here, we identify genes whose deletion has minimal or no effect on growth, but results in failure to achieve timely completion of the fermentation of a chemically defined grape juice with 200 g L⁻¹ total sugar.

Results

Micro- and laboratory-scale experimental fermentations were conducted to identify 72 clones from ~5,100 homozygous diploid single-gene yeast deletants, which exhibited protracted fermentation in a high-sugar medium. Another 21 clones (related by gene function, but initially eliminated from the screen because of possible growth defects) were also included. Clustering and numerical enrichment of genes annotated to specific Gene Ontology (GO) terms highlighted the vacuole’s role in ion homeostasis and pH regulation, through vacuole acidification.

Conclusion

We have identified 93 genes whose deletion resulted in the duration of fermentation being at least 20% longer than the wild type. An extreme phenotype, ‘stuck’ fermentation, was also observed when DOA4, NPT1, PLC1, PTK2, SIN3, SSQ1, TPS1, TPS2 or ZAP1 were deleted. These 93 Fermentation Essential Genes (FEG) are required to complete an extended high-sugar (wine-like) fermentation. Their importance is highlighted in our Fermentation Relevant Yeast Genes (FRYG) database, generated from literature and the fermentation-relevant phenotypic characteristics of null mutants described in the Saccharomyces Genome Database. The 93-gene set is collectively referred to as the ‘Fermentome’. The fact that 10 genes highlighted in this study have not previously been linked to fermentation-related stresses, supports our experimental rationale. These findings, together with investigations of the genetic diversity of industrial strains, are crucial for understanding the mechanisms behind yeast’s response and adaptation to stresses imposed during high-sugar fermentations.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-552) contains supplementary material, which is available to authorized users.

Proline transport and stress tolerance of ammonia-insensitive mutants of the PUT4-encoded proline-specific permease in yeast

The imino amino acid, proline, has roles in both cellular nutrition and response to stress. Proline uptake in Saccharomyces cerevisiae is largely mediated by a high affinity, specific permease, Put4p, and a low affinity general amino acid permease, Gap1p. Both are subject to nitrogen catabolite repression (NCR) and nitrogen catabolite inactivation (NCI). In order for proline to be fully exploited, its transport must be derepressed, as occurs upon depletion of preferred nitrogen sources, and molecular oxygen must be present to allow the first step of catabolism via proline oxidase. This study focuses on the isolation of variants of Put4p, which are insensitive to repression by a preferred nitrogen source (ammonia) and their subsequent effect on proline transport and stress tolerance. Specific amino acid residues in the carboxy-terminal region of Put4p were targeted by site-directed mutagenesis. Substitution at Serine(605), a potential phosphorylation target, led to the amelioration of ammonia-induced down-regulation of Put4p. When combined with a promoter mutation (-160), the S(605)A mutation resulted in increased proline uptake and accumulation. This increase in proline accumulation was associated with increased cell viability in conditions of high temperature and osmotic stress raising possible benefits in industrial fermentation applications.

International collaboration between US and Thailand on a clinical trial of treatment for HIV-associated cryptococcal meningitis

BACKGROUND

International clinical trials can provide scientific and logistic benefits in spite of the many challenges. Determining whether a country, especially a developing country, is an appropriate location for the research should include in-country consultation and partnering to assess its social value for the population; that treatments are relevant for the population under study; and that the research infrastructure and ethical oversight are adequate. Collaboration increases the likelihood of study success and helps ensure that benefits accrue to recruited populations and their community.

PURPOSE

This paper describes our experiences on a bi-national study and may provide guidance for those planning to engage in future collaborations.

METHODS

A Thai and United States team collaborated to develop and implement a phase II clinical trial for HIV-associated cryptococcal meningitis to assess safety and tolerability of combination therapy vs. standard treatment. Clinical and cultural differences, regulatory hurdles and operational issues were addressed before and during the study to ensure a successful collaboration between the 2 groups.

RESULTS

The international multicenter study allowed for more rapid enrollment, reduced costs to complete the study, sharing of the benefits of research, greater generalizability of results and capacity building in Thailand; quality metrics in Thailand were equivalent to or better than those in the U.S.

CONCLUSIONS

Conducting successful clinical trials internationally requires early and ongoing collaboration to ensure the study meets sites' requirements and expectations, conforms to varying national regulations, adheres to data quality standards and is responsive to the health needs of studied populations.

Optimisation of industrial strains of Saccharomyces cerevisiae using recombinant and non-recombinant methods

The production of fermented beverages such as beer and wine is typically achieved using strains of Saccharomyces cerevisiae, which have been selected for their reliable fermentative properties and desirable sensory contribution to the end product. Even so, these strains are not without shortcomings and new strains are constantly being sought. In aiming to provide such strains, working with industrial isolates has its own set of challenges. Wine strains of S. cerevisiae are typically of higher ploidy or aneuploid, frequently lack convenient selectable markers and are homothallic. Laboratory strains, along with their comprehensive set of genetic tools, might be a more convenient research vehicle, but the fact remains that such strains fare poorly under the highly stressful conditions of industrial fermentations: sugar contents of over 200 g/L; low nutrient availability and pH; and high final ethanol concentrations. More importantly, the wines produced by laboratory strains of yeast frequently display poor sensory properties. Put simply, laboratory yeast lack the desirable phenotypic characteristics needed to make wine of quality to enable industrially relevant studies.

Application of the reuseable, selectable marker to industrial yeast: construction and evaluation of heterothallic wine strains of , possessing minimal foreign DNA sequences

The characterisation of wine yeasts and the complex metabolic processes influencing wine fermentation and the quality of wine might best be achieved by exploiting the standard classical and recombinant genetic techniques which have been successfully used with laboratory strains. However, application of these techniques to industrial strains has been restricted because such strains are typically prototrophic and often polyploid. To overcome this problem, we have identified commercial wine strains with good mating and sporulation properties from which heterothallic derivatives were constructed by disruption of the HO gene. Consequently, these haploids are amenable to genetic analysis, whilst retaining desirable wine-making properties. The approach used was an adaptation of a previously published gene disruption procedure for laboratory yeast and is based on the acquisition of geneticin resistance from a removable KanMX marker. The present work is the first report of the application of a construct of this type to the disruption of the HO gene in wine yeasts that are in common commercial use. Most of the 4.9-kb disruption construct was successfully removed from the genome of the haploid derivative strains by loop-out of the KanMX marker through meiotic recombination. Sequencing of the HO region confirmed the reduction of foreign sequences to a 582-bp fragment comprised largely of a single direct repeat at the target gene. The removal of the active foreign gene (conferring antibiotic resistance) allows the application of other constructs based on the KanMX module without the need to resort to other selectable marker systems. Laboratory-scale fermentation trials typically showed minimal differences between the HO disruptants and the parental wine strains in terms of fermentation kinetics and formation of key metabolites.

Comparing stimulation-induced pain during percutaneous (intramuscular) and transcutaneous neuromuscular electric stimulation for treating shoulder subluxation in hemiplegia

OBJECTIVE

To determine whether percutaneous (intramuscular) neuromuscular electric stimulation (perc-NMES) is less painful than transcutaneous neuromuscular electric stimulation (trans-NMES) for treating shoulder subluxation in hemiplegia.

DESIGN

Double-blind, crossover trial.

SETTING

University-affiliated tertiary care hospital.

PARTICIPANTS

A convenience sample of 10 hemiplegic subjects with at least 1 fingerbreadth of glenohumeral subluxation.

INTERVENTIONS

All subjects received 3 randomly ordered pairs of perc-NMES and trans-NMES to the supraspinatus and posterior deltoid muscles of the subluxated shoulder. Both types of stimulation were optimized to provide full joint reduction with minimal discomfort.

MAIN OUTCOME MEASURES

Pain was assessed after each stimulation with a 10-cm visual analog scale (VAS) and the McGill Pain Questionnaire, using the Pain Rating Index (PRI) scoring method. Subjects were asked which type of stimulation they would prefer for 6 weeks of treatment. Wilcoxon's signed-rank test was used to compare median differences in VAS and PRI between perc-NMES and trans-NMES.

RESULTS

Median VAS scores for perc-NMES and trans-NMES were 1 and 5.7, respectively (p = .007). Median PRI scores for perc-NMES and trans-NMES were 7 and 19.5, respectively (p = .018). Nine of the 10 subjects preferred perc-NMES to trans-NMES for treatment.

CONCLUSION

Data suggest that perc-NMES is less painful than trans-NMES in the treatment of shoulder subluxation in hemiplegia.

Percutaneous intramuscular neuromuscular electric stimulation for the treatment of shoulder subluxation and pain in patients with chronic hemiplegia: a pilot study

OBJECTIVE

To investigate the feasibility of percutaneous intramuscular neuromuscular electric stimulation (perc-NMES) for treating shoulder subluxation and pain in patients with chronic hemiplegia.

DESIGN

Before-after trial.

SETTING

University-affiliated tertiary care hospital.

PARTICIPANTS

A convenience sample of 8 neurologically stable subjects with chronic hemiplegia and shoulder subluxation.

INTERVENTION

Six weeks of perc-NMES to the subluxated shoulder.

MAIN OUTCOME MEASURES

Shoulder subluxation (radiograph), shoulder pain (Brief Pain Inventory), motor impairment (Fugl-Meyer score), shoulder pain-free external rotation (handheld goniometer), and disability (FIM instrument) were assessed before treatment (T1), after 6 weeks of neuromuscular stimulation (T2), and at 3-month follow-up (T3). A 1-way, repeated-measures analysis of variance using the generalized estimating equation approach was used to evaluate differences from T1 to T2 and from T1 to T3 for all outcome measures.

RESULTS

Subluxation (p =.0117), pain (p =.0115), shoulder pain-free external rotation (p <.0001), and disability (p =.0044) improved significantly from T1 to T2. Subluxation (p =.0066), pain (p =.0136), motor impairment (p <.0001), shoulder pain-free external rotation (p =.0234), and disability (p =.0152) improved significantly from T1 to T3.

CONCLUSIONS

Perc-NMES is feasible for treating shoulder dysfunction in hemiplegia and may reduce shoulder subluxation, reduce pain, improve range of motion, enhance motor recovery, and reduce disability in patients with chronic hemiplegia and shoulder subluxation. Further investigation is warranted.

Functional expression, purification, and characterization of recombinant human pyruvate carboxylase

The cDNA-encoding human pyruvate carboxylase (hPC) has been assembled and cloned into a very high efficiency mammalian expression vector and the construct transfected into 293T kidney cells. Stable clones expressing very high levels of hPC were produced and used as a source of the enzyme. Purification of the recombinant hPC was performed by selective precipitation with 40% ammonium sulfate followed by a single step avidin affinity chromatography, with an overall yield of 20%. Recombinant hPC purified by this method yielded a single band on SDS-PAGE with a specific activity of 20 U/mg. Kinetic analysis demonstrated that the recombinant human PC has the same properties as the native enzyme isolated from liver autopsy. This is the first report of production and purification of recombinant PC.

An assessment of two training interventions designed to increase the knowledge of obstetrical nurses and nurse-midwives about the maternal serum triple screen

The purpose of this study was to assess the effects of two brief training interventions designed to improve nurses' and nurse-midwives' knowledge about the maternal serum triple screen. The low intervention consisted of written information on the triple screen; the high intervention consisted of written information plus a one hour oral presentation. Knowledge was assessed at baseline, immediately following the oral presentation (high intervention only), and one month following the interventions. Forty-seven nurses, nurse-midwives and nursing assistants participated. Sixteen respondents (34 per cent) who routinely talk to patients about the triple screen obtained a score of less than 70 per cent on the knowledge questionnaire at baseline assessment. Respondents' knowledge about the maternal serum triple screen included areas that needed to be improved in order for them to be able to provide patients with accurate and complete information. Both interventions assessed in this study resulted in an increase in participants' knowledge about the maternal serum triple screen, however the high intervention was more effective. This study presents evidence that improvements in health care professionals' knowledge can be made with brief educational interventions.

Prenatal diagnosis of ring chromosome 6 in a fetus with hydrocephalus

A patient with ring chromosome 6/monosomy 6 mosaicism is presented. At 25 weeks' gestation, ultrasound examination demonstrated fetal hydrocephalus. Amniocentesis was performed. The fetal karyotype was 45,XY,-6/ 45,XY,-6,+f/46,XY,r(6)(p25q27). Delivery of this male infant was by Caesarean section at 37 weeks' gestation. The karyotype in peripheral blood lymphocytes was 46,XY,r(6)(p25q27) with no indications of mosaicism. The infant had hydrocephalus which required treatment with a ventriculoperitoneal shunt at 22 days of age. He had no other obvious serious congenital anomalies. By 17 months he had developed microcephaly, seizures, severe bilateral hearing loss, and global development delay. This patient provides information regarding phenotypic variability of ring chromosome 6 and also reinforces the importance of offering amniocentesis if fetal hydrocephalus is detected as an isolated anomaly.

Identification of novel alternatively spliced pyruvate carboxylase mRNAs with divergent 5'-untranslated regions which are expressed in a tissue-specific manner

We have identified and characterized multiple mRNA transcripts of rat and human pyruvate carboxylases [EC 6.4.1.1] using rapid amplification of cDNA 5' ends-polymerase chain reaction (RACE-PCR). Five alternative forms of rat pyruvate carboxylase cDNAs have been identified in liver, kidney, brain, and adipose tissue and these are expressed in a tissue-specific manner. Two alternative forms of human pyruvate carboxylase cDNA have also been identified in liver. These pyruvate carboxylase cDNAs have a common coding region but differ in their 5' untranslated regions (5'UTRs), suggesting that they are generated by alternative splicing of the primary transcript. Southern blot analysis of restriction enzyme digested rat genomic DNA revealed that pyruvate carboxylase is encoded by a single copy gene.

Polymorphism of the yeast pyruvate carboxylase 2 gene and protein: effects on protein biotinylation

In Saccharomyces cerevisiae there are two isoenzymes of pyruvate carboxylase (Pyc) encoded by separate genes designated PYC1 and PYC2. We report the isolation and sequencing of a PYC2 gene, and the localization of both genes on the physical map of S. cerevisiae. Comparison with the previously reported sequence [Stucka, Dequin, Salmon and Gancedo (1991) Mol. Gen. Genet. 229, 307-315] revealed significant differences within the open reading frame. The most notable difference was near the 3' end, where we found a single base deletion reducing the open reading frame by 15 bases. We have confirmed the C-terminus of Pyc2 encoded by the gene isolated here by expressing and purifying an 86-amino-acid biotin-domain peptide. In addition, we investigated the effects of the two changes in the Pyc2 biotin domain (K1155R substitution and Q1178P/five-amino-acid extension) on the extent of biotinylation in vivo by Escherichia coli biotin ligase, and compared the biotinylation of peptides containing these changes with that of two different-length Pyc1 biotin-domain peptides. The K1155R substitution had very little effect on biotinylation, but the five-amino-acid C-terminal extension to Pyc2 and the N-terminal extension to Pycl both improved biotinylation in vivo.

A new hospital library: a marketing opportunity

A new or remodeled library presents a unique marketing opportunity for the hospital librarian. Furthermore, a well-designed library markets itself through its convenience, attractiveness, and ease of use. A marketing approach to library planning takes into account needs of users and of library staff and considers the librarian's relations with the architect as well as with hospital employees. This paper describes ways to combine library planning with marketing techniques and specifies aspects of the library that contribute to its good image.

Assignment of the human pyruvate carboxylase gene (PC) to 11q13.4 by fluorescence in situ hybridisation

The gene for pyruvate carboxylase (PC) has been localised by fluorescence in situ hybridisation to normal and FRA11A human chromosomes. PC maps to 11q13 and distal to FRA11A, localising PC to 11q13.4-->q13.5.

Designing the smaller library: a hospital looks to the future

Like other libraries, hospital libraries are preparing for a future which will include a mix, as yet undetermined, of print and electronic information. This case study relates how the library at St. Jude Children's Research Hospital was designed to meet the needs of users and staff and to balance them with the need for more sophisticated methods of retrieving, storing, and delivering information. Details are provided on planning process and on design features such as lighting and color.

Health and Well-Being of Childbearing Women in Rural and Urban Contexts

As part of the national focus on women's health issues, it is important to identify those health-related characteristics of rural women that distinguish them from women living in urban settings. The aim of this study was to compare rural and urban childbearing women on socioeconomic characteristics, perceived stress, health-related practices, illness symptoms, parenting confidence, and body weight. One hundred sixty-five midwestern women responded to a health survey sent to them six months after childbirth. Rural women were younger and less educationally and economically advantaged compared to urban women. Before adjusting for these differences, rural women were less self-actualized, more interpersonally isolated, and reported less healthy nutrition than urban women. These differences disappeared when socioeconomic differences were adjusted. Rural and urban mothers did not differ in most other areas, including perceived stress, parenting confidence, and body weight. Compared to national norms, the perceived stress levels of both rural and urban mothers were significantly higher than a probability sample of U.S. women. Findings support the role of socioeconomic factors as contributing to risk of poor health promotion among rural childbearing women.

Regulation of pyruvate carboxylase isozyme (PYC1, PYC2) gene expression in Saccharomyces cerevisiae during fermentative and nonfermentative growth

In Saccharomyces cerevisiae there are two isoenzymes of pyruvate carboxylase (Pyc) encoded by separate genes, designated PYC1 and PYC2. In the wild type yeast, the expression of both genes is influenced by both the growth phase and the type of carbon source, indicating discrete regulatory mechanisms and metabolic roles for PYC1 and PYC2. On glucose minimal medium PYC1 and PYC2 are differentially regulated as shown by a constant level of PYC1 expression throughout the main growth phase compared to a high level of PYC2 expression only in the early growth phase. On ethanol minimal medium, the growth-related pattern of PYC1 and PYC2 expression was similar as shown by a 3.6-fold decline from early to mid log phase. PYC1 expression, however, was activated 10-fold above PYC2 mRNA levels during this period of growth. To further investigate the roles of the two PYC genes we determined the growth phenotypes and expression levels of PYC in pyc1 and pyc2 single null mutants. During fermentative growth, the lack of either PYC gene had little effect on the level and pattern of expression of the other PYC gene, indicating further their separate regulation. In comparison to the pyc2 null, the pyc1 null strain showed a 3- to 4-fold lower level of Pyc activity and Pyc protein concentration. Moreover, the pyc1 null showed a strong requirement for L-aspartate for efficient growth, indicating the importance of PYC1 expression for the synthesis of C4 intermediates. DV6.2 (PYC1, pyc2 delta) showed a 3.2-fold higher level of activity on ethanol minimal medium when compared to growth on glucose minimal medium, and supported growth in the absence of L-aspartate. The pyc1 null, MW21.3 (pyc1 delta, PYC2), on the other hand, did not support growth on ethanol in the absence of aspartate. This study represents the first report on the characterisation of expression of the PYC genes in yeast throughout growth. Their metabolic roles for both fermentative and gluconeogenic growth are considered.

Rhinometry and open-mouth posture in young children

A biracial sample of 348 elementary school children who were in the first grade were assessed for open-mouth posture (OMP) in the natural environment. In addition, rhinometry was performed on 296 of the children. Means were computed for percent OMP and cross-sectional nasal airway. Results indicated that, in general, these children exhibited relatively high rates of OMP. Boys displayed significantly greater OMP than girls, and black children showed significantly larger cross-sectional nasal areas than white children. A significant correlation between OMP and nasal area only was evident for children exhibiting OMP during more than 80% of the observation intervals. The implications of the findings were discussed.

Intratracheal aerosolization of endotoxin in the rat: a model of the adult respiratory distress syndrome (ARDS)

A technique is described for the intratracheal aerosolization of endotoxin into the rat. Using a miniaturized nozzle within the tracheal lumen to optimize uniform distribution 0.5 ml of an endotoxin solution (7 mg/kg) was aerosolized and dispersed throughout the lung. Time course studies of pulmonary function and histological changes revealed marked functional and morphological changes by 24 h. Histopathologic changes consisted of widespread pulmonary oedema and a diffuse neutrophilic alveolitis. At the same time, there were significant decreases in tidal volume, minute ventilation and lung compliance. Haematologic changes were also seen, including profound thrombocytopaenia and leukopaenia together with an increased haematocrit, indicating systemic effects in this model. Bronchoalveolar lavage (BAL) at 24 h revealed significant increases in BAL protein, erythrocytes and neutrophils. The functional, cytological and histological changes observed after endotoxin challenge mimic those seen in the Adult Respiratory Distress Syndrome in humans and can thus be used as a model to compare the efficacy of a variety of therapeutic interventions for this syndrome.

Yeast pyruvate carboxylase: identification of two genes encoding isoenzymes

In Saccharomyces cerevisiae, pyruvate carboxylase [EC 6.4.1.1] has an important anaplerotic role in the production of oxaloacetate from pyruvate. We report here the existence of two pyruvate carboxylase isozymes, which are encoded by separate genes within the yeast genome. Null mutants were constructed by one step gene disruption of the characterised PYC gene in the yeast genome. The mutants were found to have 10-20% residual pyruvate carboxylase activity, which was attributable to a protein of identical size and immunogenically related to pyruvate carboxylase. Immunocytochemical labelling studies on ultrathin sections of embedded whole cells from the null mutants showed the isozyme to be located exclusively in the cytoplasm. We have mapped the genes encoding both enzymes and shown the previously characterised gene, designated PYC1, to be on chromosome VII whilst PYC2 is on chromosome II.

Isolation of a yeast mutant deficient in pyruvate carboxylase activity

To improve our understanding of the catalytic mechanism and regulatory properties of pyruvate carboxylase (EC 6.4.1.1), an important biotin-dependent enzyme, we have sought to isolate mutants in Saccharomyces cerevisiae which are defective in pyruvate carboxylase activity. One mutant was isolated which was unable to grow on glucose minimal medium unless supplemented with aspartate. Although the enzyme had only 25% of the wild type pyruvate carboxylase activity, Western analysis and RNase protection analysis demonstrated that the mutant gene was expressed at approximately 70% of the wild type level. On the basis of genetic crosses and complementation tests, we have attributed the defect to mutations in the PYC gene encoding pyruvate carboxylase.

Effects of adrenergic antagonists on cocaine-induced changes in respiratory function

Cocaine-induced changes in respiratory rate (f), tidal volume (VT), total pulmonary ventilation (VE), dynamic lung compliance (Cdyn) and total pulmonary resistance (RL) were measured in anesthetized, spontaneously breathing Sprague-Dawley rats using a whole-body plethysmograph and an esophageal manometer. Carotid arterial pressure and heart rate were simultaneously monitored. An intravenous (i.v.) dose of 10 mg/kg of cocaine was lethal in all rats tested with death resulting from respiratory failure occurring between 0.25 and 1.5 min after dosing. At an i.v. dosage of 5 mg/kg, cocaine was nonlethal, although a reduction in VE was evident during the first minute after dosing. This reduction in VE was due to a decrease in f and the lack of a compensatory increase in VT. A slight decrease in RL also became evident approximately five minutes after dosing. Pretreatment with the nonselective alpha-adrenergic antagonist phentolamine (10 mg/kg) prevented the cocaine-induced depression in VE by reducing the decrease in f and blocking the inhibition of a compensatory increase in VT. In contrast, pretreatment with the nonselective beta-adrenergic antagonist propranolol (1 mg/kg) potentiated the cocaine-induced decrease in VE by enhancing the depression of f. Pretreatment with propranolol also caused a cocaine-dependent decrease in Cdyn. At a dosage of 0.3 mg/kg, labetalol, a compound possessing both nonselective alpha- and beta 1-antagonist activity (1:7) appeared to cause only a minimal potentiation of the cocaine-induced depressions in VE and f. Pretreatment with propranolol or labetalol also resulted in the death of 20% of the rats administered 5 mg/kg of cocaine.(ABSTRACT TRUNCATED AT 250 WORDS)

Transport of the yeast ATP synthase beta-subunit into mitochondria. Effects of amino acid substitutions on targeting

We have isolated the yeast ATP2 gene encoding the beta-subunit of mitochondrial ATP synthase and determined its nucleotide sequence. A fusion between the N-terminal 15 amino acid residues of beta-subunit and the mouse cytosolic protein dihydrofolate reductase (DHFR) was transcribed and translated in vitro and found to be transported into isolated yeast mitochondria. A fusion with the first 35 amino acid residues of beta-subunit attached to DHFR was not only transported but also proteolytically processed by a mitochondrial protease. Amino acid substitutions were introduced into the N-terminal presequence of the beta-subunit by bisulphite mutagenesis of the corresponding DNA. The effects of these mutations on mitochondrial targeting were assessed by transport experiments in vitro using DHFR fusion proteins. All of the mutants, harbourin from one to six amino acid substitutions in the first 14 residues of the presequence, were transported into mitochondria, though at least one of them (I8) was transported and proteolytically processed at a much reduced rate. The I8 mutant beta-subunit also exhibited poor transport and processing in vivo, and expression of this mutant polypeptide failed to complement the glycerol- phenotype of a yeast ATP2 mutant. More remarkably, the expression of I8 beta-subunit induced a more general growth defect in yeast, possibly due to interference with the transport of other, essential, mitochondrial proteins.

An analysis of auditory alphabet confusions

The present study, using the nonhierarchical overlapping clustering algorithm MAPCLUS to fit the Shepard-Arabie (1979) ADCLUS model, attempted to derive a set of features that would accurately describe the auditory alphabet confusions present in the data matrices of Conrad (1964) and Hull (1973). Separate nine-cluster solutions accounted for 80% and 89% of the variance in the matrices, respectively. The clusters revealed that the most frequently confused letter names contained common vowels and phonetically similar consonants. Further analyses using INDCLUS, an individual differences extension of the MAPCLUS algorithm and ADCLUS model, indicated that while the patterns of errors in the two matrices were remarkably similar, some differences were also apparent. These differences reflected the differing amounts of background noise present in the two studies.

Serology for automated cytotoxicity testing. II. Routine reading of HLA-typing using the Contrast Fluorescence Test

We have previously reported on the "Contrast Fluorescence Test" (CFT), a method for the fluorimetric of living vs dead lymphocytes and have proposed its use in automated HLA typing. In this report, we present data obtained with the CFT in the evaluation of an automated system built around the Zonax instrument (Zeiss America, Inc.). 13,664 individual CFT results were read by the machine and compared with manual readings; assignment of HLA specificity was done independently but using the same logic by hand and by machine. Excellent correlation of the instrumented and manual serological readings and identical antigen assignments were observed.

When children die: death in current children's literature and its use in a library

Death and dying are dealt with realistically and sympathetically in current children's literature. Books can play an important role in helping children suffering from catastrophic illness by showing how other children have coped with similar situations; they can also form a basis for bibliotherapy with patients. This paper examines current trends in children's literature and describes how these books have been incorporated into a patient library at St. Jude Children's Research Hospital.

The HLA system in congenital rubella patients with and without diabetes

The HLA antigens of 173 patients with the congenital rubella syndrome (CR) are reported. Twenty-one of these patients are also clinically diabetic, and among them the frequencies of the HLA antigens DR2 and DR3 are significantly lower and higher, respectively, than in CR patients without diabetes or in controls. These data suggest that the genes that control susceptibility to type I or insulin-dependent diabetes mellitus are necessary for the development of glucose intolerance in CR patients.