Improved strategy for large-scale DNA sequencing using DNaseI cleavage for generating random subclones

Large-scale DNA sequencing projects require the use of specific and reliable strategies. Here, we describe an improved strategy using DNaseI cleavage and sequencing strategy using DNaseI cleavage and sequencing from both ends of the plasmid inserts. This strategy yields better results than those obtained using partial digestion with restriction enzymes and cloning in single-stranded vectors.

Complete DNA sequence of yeast chromosome II

In the framework of the EU genome-sequencing programmes, the complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome II (807 188 bp) has been determined. At present, this is the largest eukaryotic chromosome entirely sequenced. A total of 410 open reading frames (ORFs) were identified, covering 72% of the sequence. Similarity searches revealed that 124 ORFs (30%) correspond to genes of known function, 51 ORFs (12.5%) appear to be homologues of genes whose functions are known, 52 others (12.5%) have homologues the functions of which are not well defined and another 33 of the novel putative genes (8%) exhibit a degree of similarity which is insufficient to confidently assign function. Of the genes on chromosome II, 37-45% are thus of unpredicted function. Among the novel putative genes, we found several that are related to genes that perform differentiated functions in multicellular organisms of are involved in malignancy. In addition to a compact arrangement of potential protein coding sequences, the analysis of this chromosome confirmed general chromosome patterns but also revealed particular novel features of chromosomal organization. Alternating regional variations in average base composition correlate with variations in local gene density along chromosome II, as observed in chromosomes XI and III. We propose that functional ARS elements are preferably located in the AT-rich regions that have a spacing of approximately 110 kb. Similarly, the 13 tRNA genes and the three Ty elements of chromosome II are found in AT-rich regions. In chromosome II, the distribution of coding sequences between the two strands is biased, with a ratio of 1.3:1. An interesting aspect regarding the evolution of the eukaryotic genome is the finding that chromosome II has a high degree of internal genetic redundancy, amounting to 16% of the coding capacity.

A 12.5 kb fragment of the yeast chromosome II contains two adjacent genes encoding ribosomal proteins and six putative new genes, one of which encodes a putative transcriptional factor

The nucleotide sequence of a 12.5 kb fragment localized to the right arm of chromosome II of Saccharomyces cerevisiae has been determined. The sequence contains eight putative genes. Two of them are contiguous and represent two ribosomal protein genes: SUP46 and URP1. SUP46 is implicated in translation fidelity and encodes the ribosomal protein S13. URP1 is homologous to the rat ribosomal protein gene L21. The open reading frame (ORF) YBR1245 is similar in its N-terminal part to transcription factors like SRF and MCM1. The ORF YBR1308 shows homology with proteins of the AAA-family (ATPases Associated with diverse cellular Activities). Two genes are predicted to encode putative membrane proteins.

Ticlopidine and fatal aplastic anemia in an elderly woman

OBJECTIVE

To report a case of aplastic anemia that developed during ticlopidine treatment.

CASE SUMMARY

An 84-year-old woman was started on ticlopidine for secondary stroke prevention. Within six weeks of initiating ticlopidine therapy she developed aplastic anemia. She was hospitalized and received empiric antibiotics, antifungal agents, blood transfusions, platelets, and granulocyte colony-stimulating factor. The patient died on day 76 after beginning ticlopidine.

DISCUSSION

Hematologic effects such as neutropenia, thrombocytopenia, agranulocytosis, thrombotic thrombocytopenic purpura, and pancytopenia have been described with the use of ticlopidine. Previous case reports have associated ticlopidine with the development of aplastic anemia.

CONCLUSIONS

Ticlopidine can produce fatal hematologic adverse effects, and its use should be reserved as second-line therapy.

Immunization requirements for pharmacy students

OBJECTIVE

To identify current immunization requirements for pharmacy students throughout the US.

DESIGN

Self-administered questionnaire.

SETTING

Seventy-five colleges and schools of pharmacy in the US.

MAIN OUTCOME MEASURES

Immunization policies, immunologic requirements, timing of vaccination in relation to the beginning of clerkship experience, payment, mechanism to revise policies.

DATA ANALYSIS

Descriptive statistics.

RESULTS

Overall, 57 programs (81 percent) have an immunization program in place, but 13 programs (19 percent) have no immunization program. More than 50 percent of the colleges or schools reported requiring that pharmacy students have measles, mumps, rubella, tetanus, and purified protein derivative of tuberculin (PPD) vaccinations upon entry of clerkship. Only 25 college or schools of pharmacy (44 percent) required students to have the hepatitis B vaccine and 8 (14 percent) to have a PPD evaluation upon completion of clerkship experience. Responsibility for the immunization program was shared evenly between the clerkship coordinator and the student health clinic. Approximately 65 percent of programs maintain an immunization record on file for each student. Completion of immunizations was required in 36 schools (64 percent) before entering clerkship activities, 15 (26 percent) before entrance to the professional program, and 3 (5 percent) in the first year of the program. Six schools (11 percent) had a program in place for less than one year, 27 (47 percent) between one and five years, and 24 (42 percent) for more than five years. At the majority of schools, students are responsible for the cost of immunization.

CONCLUSIONS

Most schools of pharmacy do not adhere to the specific immunization recommendations described by the Centers for Disease Control and Prevention for healthcare workers. Pharmacy schools need to reexamine their immunization policies and update them to reflect the most current standards. We suggest a policy for immunization of pharmacy students.

Nucleotide sequence analysis of an 11.7 kb fragment of yeast chromosome II including BEM1, a new gene of the WD-40 repeat family and a new member of the KRE2/MNT1 family

This paper reports the DNA sequence and analysis of an 11.7 kb segment localized on the right arm of Saccharomyces cerevisiae chromosome II. This fragment contains one incomplete and five long and non-overlapping open reading frames (ORFs) designated from centromere to telomere-proximal side as: YBR1406, 1409, 1410, 1411, 1412 and 1413. YBR1406 corresponds to the 5' end to PG11 encoding phosphoglucoisomerase. YBR1410 encodes a polypeptide of 798 amino acids whose C terminus contains five repeats (WD-40 repeat) similar to those found in the beta-subunits of G proteins and different yeast proteins such as Tup1, Prp4 and Cdc4. The higher similarity score is obtained with dTAFII80, a component of the RNA polymerase II transcriptional complex TFIID. YBR1411 encodes a polypeptide of 464 amino acids which belongs to the family of alpha-mannosyltransferases: KRE2/MNT1, KTR1, KTR2, YUR1 and the product of previously sequenced ORF YBR1445. YBR1412 corresponds to BEM1. The two ORFs, YBR1409 and YBR1413, which do not exhibit significant similarity with any known coding sequences, define new genes.

A 12.8 kb segment, on the right arm of chromosome II from Saccharomyces cerevisiae including part of the DUR1,2 gene, contains five putative new genes

A 12,820 bp fragment from the right arm of chromosome II of Saccharomyces cerevisiae was sequenced and analysed. This fragment contains six non-overlapping long open reading frames (ORFs) designated from the centromere- to the telomere-proximal ends as: YBR1441, 1443, 1444, 1445, 1446 and 1448. YBR1441 encodes a polypeptide of 845 amino acids which shares a long consensus domain with products of S. cerevisiae MCM2, MCM3, CDC46 and Schizosaccharomyces pombe cdc21+ genes. These genes are involved in DNA replication. YBR1445 encodes a polypeptide of 404 amino acids which has strong similarity with the S. cerevisiae KRE2/MNT1, YUR1, KTR1 gene products. The KRE2/MNT1 protein is an alpha-1,2- mannosyltransferase. The product of YBR1444, which encodes a protein of 375 amino acids, presents a lipase signature sequence and a peroxisomal targeting signal. YBR1448, whose sequence extends further on the telomere-proximal end of the fragment, is identical to the 3' end of the DUR1,2 gene encoding urea amidolyase. The two ORFs, YBR1443 and YBR1446, exhibit no significant similarity with any known gene.

RIM2, MSI1 and PGI1 are located within an 8 kb segment of Saccharomyces cerevisiae chromosome II, which also contains the putative ribosomal gene L21 and a new putative essential gene with a leucine zipper motif

We report the DNA sequence of an 8 kb segment localized on the right arm of chromosome II from Saccharomyces cerevisiae. The sequence reveals the presence of eight open reading frames (ORFs). Three of them, YBR1402, YBR1405 and YBR1406 are previously sequenced genes, respectively the RIM2 (replication in mitochondria), MSI1 (multicopy suppressor of IRA1 gene) and PGI1 (phosphoglucoisomerase) genes. The predicted product of the ORF YBR1401 could be the putative yeast ribosomal protein L21. A new essential gene, YBR1403, has been identified by disruption; it possesses a leucine zipper motif.

Counseling in special populations: the elderly patient

This seventh installment in the series on value-added services provides pharmacists with a systematic approach to identifying and meeting the special counseling-related needs of the ambulatory elderly patient. The article describes the physical, mental, and social changes that characteristically accompany the aging process and that create special problems for pharmacists and their elderly patients during the delivery of pharmaceutical care. It also describes a systematic approach that pharmacists can use to evaluate whether their elderly patients need special counseling. Finally, it illustrates how the principles that are discussed can be applied in the practice setting.

Histone H1a subtype presents structural differences compared to other histone H1 subtypes. Evidence for a specific motif in the C-terminal domain

Following a previous isolation by reverse-phase HPLC of five histone H1 subtypes from adult rat liver, purity of three of them, H1a, H1b and H1d (according to Lennox's nomenclature), was achieved. Structural features of these three subtypes were investigated. Partial cleavage of these subtypes by endoproteinase Glu-C showed a different behavior of the H1a subtype when compared to the H1b and H1d subtypes. Under the conditions used in this work, the H1b and H1d subtypes present three major sites accessible to the endoproteinase Glu-C, while the H1a subtype presents only one major site accessible to the proteinase. Partial N-terminal sequence of the different fragments obtained after proteolysis indicated that the two H1b and H1d subtypes were cleaved inside the globular domain (Glu-54,-75) and between the globular domain and the C-terminal one (Glu-116). The H1a subtype was only cleaved between the globular domain and the C-terminal tail (Glu-116), though Glu-54 and Glu-75 sites were present. These results would suggest some differences in the conformation of these proteins. Furthermore, the partial determined sequences of H1b and H1d showed 85% similarity to each other (the main differences were threonine residues instead of alanine residues in the C-terminal domain) while H1a was only 60% similar to H1b and H1d, for the sequences which aligned. The strongest differences between the H1a subtype and the two other subtypes were observed in the first amino acid residues of the C-terminal domain. The 117-126 amino acid residues (SKASTTKVTV) of H1a were quite different from those of H1b and H1d. This sequence, which showed a number of serine and threonine residues, was not found in any other histone sequence, after consultation with data bases. This H1a subtype was a minor component in adult liver (2.4%). As it was described in testis as a major component, testis histone H1 proteins were fractionated onto reverse-phase HPLC under the same conditions as those used for histone H1 proteins from liver. The pure testis H1a fraction was submitted to the endoproteinase Glu-C digestion. The pattern digestion was the same as that observed for liver H1a. The two 44-76 and 117-126 determined amino acid residues of H1a from testis were strictly identical to those of liver H1a. We demonstrate that H1a is the same protein in liver and testis and we give evidence for a specific motif SKASTTKVTV (117-126 residues) in the sequence of the C-terminal domain.(ABSTRACT TRUNCATED AT 400 WORDS)

["Spontaneous" ischemic colitis: infectious or medicamentous colitis? 25 cases]

The diagnosis of non-gangrenous ischaemic colitis is difficult to assert when histological findings are not specific and when no precipitating cardiovascular event can be found. The constant absence of relapse after the initial episode suggests that an extraneous triggering event is involved. We have studied retrospectively 25 cases of spontaneous ischaemic colitis, looking for a non-haemodynamic triggering event. At the onset of colitis 9 patients had been taking non-steroidal anti-inflammatory drugs or antibiotics for 2 weeks or less. In 3 other patients colitis was associated with Escherichia coli O157:H7 infection. Striking clinical, endoscopic and histological similarities exist between ischaemic colitis on the one hand and colitis caused by absorption of non-steroidal anti-inflammatory drugs or ampicillin and the colitis reported in E. coli O157:H7 infection on the other hand. Non-steroidal anti-inflammatory drugs and E. coli O157:H7 intestinal infection, possibly facilitated by an antibiotic treatment with e.g. ampicillin, could be either non-haemodynamic triggering factors for ischaemic colitis, or responsible per se for a transient acute colitis with the same characteristics as ischaemic colitis.

The CCS1 gene from Saccharomyces cerevisiae which is involved in mitochondrial functions is identified as IRA2 an attenuator of RAS1 and RAS2 gene products

The ccs1-1 mutation of Saccharomyces cerevisiae, which has been previously described, is associated with an increase in cytochrome content, in respiration, and in ATP synthesis. In addition, this mutation leads to the same phenotype as cells de-regulated in the cAMP pathway. From a yeast genomic library, we have isolated a DNA fragment in a recombinant plasmid pCD1 which complements the ccs1-1 mutation. Homologous integration of this DNA in the genome occurs at the CCS1 locus. An 11 kb of the DNA insert is necessary for complementation. Sequencing part of the fragment identifies CCS1 as the IRA2 gene. The IRA2 gene is known to encode an attenuator of RAS gene product activity which stimulates the GTPase activity of the RAS proteins. This result underlines the involvement of cAMP-dependent phosphorylation in mitochondrial function. We present the sequence of 1 kb DNA upstream of the putative ATG of the IRA2/CCS1 gene product which is devoid of an ORF and could contain several regulatory sites.

Brachial plexus palsy with the use of haloperidol and a geriatric chair

An 81-year-old white man was admitted to an intermediate care facility because of increased wandering and confusion secondary to dementia. On the first day after admission, the patient tried to leave the facility and was hitting and kicking the employees. Haloperidol 0.5 mg tid was prescribed to help control his behavior. He became more agitated and confused; haloperidol was then increased to 1 mg qid and the patient was confined to a geriatric chair to prevent injuries. Cogwheel movements, rigidity, and marked sedation were documented. A right brachial plexus palsy was diagnosed. This case demonstrated the hazards of two commonly used interventions in a nursing home: antipsychotic agents and the geriatric chair.

Tuberculosis in the elderly: incidence, manifestations, PPD skin tests, and preventive therapy

Tuberculosis is a chronic infection caused by Mycobacterium tuberculosis. The incidence of tuberculosis has declined dramatically over the past decades, but it is still highly prevalent in the geriatric population. This report describes the etiology, clinical manifestations, and immunologic changes of tuberculosis in the elderly. The basis for tuberculin skin testing and its interpretation in patients over 65 years of age are discussed, as well as the controversies regarding preventive therapy with isoniazid in the elderly. Guidelines for tuberculosis screening in long-term care facilities are proposed.

[Endoscopic treatments of digestive hemorrhages of ulcerative origin]

Recently introduced techniques of endoscopic haemostasis for bleeding ulcers offer hopes of improvement in their prognosis. Injections of such haemostatic products as absolute alcohol, adrenaline or polidocanol seem to possess the maximum advantages, including low cost, universal use, technical simplicity and easy application at the patient's bedside. The development for other techniques, such as laser photocoagulation, electrocoagulation and thermocoagulation appear to be limited by their high cost and by the difficulties encountered in their application.

Bullous pemphigoid associated with captopril

Captopril is commonly prescribed to patients with hypertension and congestive heart failure. Adverse dermatological reactions have been reported in about ten percent of patients receiving captopril. This case report describes a 77-year-old white woman who developed bullous pemphigoid associated with the use of captopril. The patient presented with bullous eruptions localized on the palms of both hands about 50 days after captopril 25 mg bid was started. Biopsy report was consistent with bullous pemphigoid. Captopril therapy was discontinued and the lesions healed after oral corticosteroid therapy was initiated.

Inhibition of liver glutathione S-transferase activity in rats by hypolipidemic drugs related or unrelated to clofibrate

The effects of in vivo administration of six hypolipidemic drugs on rat liver glutathione S-transferase activity were compared. This activity was measured with sulfobromophthalein (BSP), 1,2-dichloro-4-nitrobenzene (DCNB) or 1-chloro-2,4-dinitrobenzene (CDNB) as substrate. Except for the nicotinic acid derivative ethanolamine oxiniacate, all the compounds tested significantly reduced it, whether or not they were related to clofibrate. The hepatic glutathione concentration either remained unchanged or only increased slightly after treatment with the various drugs. When measured, the maximal excretion rate of bile BSP dropped significantly, but not that of phenol-3,6-dibromophthalein (DBSP). Hepatic dye uptake and storage were not impaired. These results show that hypolipidemic drugs of the peroxisome proliferator type inhibit rat liver glutathione S-transferase activity and may reduce transport of anions conjugated with glutathione before excretion.