Observation of the therapeutic effect of Tongyuan needling combined with jingyu herb-separated moxibustion on recurrent implantation failure of kidney deficiency and blood stasis

OBJECTIVES

To observe the therapeutic effect of Tongyuan needling combined with jingyu herb-separated moxibustion on the patients with recurrent implantation failure (RIF) of kidney deficiency and blood stasis undergoing frozen embryo transfer of the conventional hormone replacement therapy cycle.

METHODS

Sixty RIF of kidney deficiency and blood stasis patients who planned for frozen embryo transfer were randomly divided into a combined treatment group (30 cases) and a western medication group (30 cases). In the western medication group, the conventional hormone replacement therapy was performed for endometrial preparation during transfer cycle. On the basis of treatment as the western medication group, in the combined treatment group, Tongyuan needling combined with jingyu herb-separated moxibustion was adopted. Regarding tongyuan needling, the acupoint prescription for Tongdu Tiaoshen (promoting the governor vessel and regulating the spirit, e.g. Dazhui [GV 14], Ganshu [BL 18], Shenshu [BL 23] and back-shu points) and that for Yinqi Guiguan (conducting qi back to the primary, e.g. Zhongwan [CV 12], Qihai [CV 6], Guanyuan [CV 4] and front-mu points) were selected. Acupuncture was delivered at these two prescriptions alternatively each time. After acupuncture, the herb-separated moxibustion (in which, the herbal powder was prepared with the modified Yangjing Zhongyu decoction for cultivating the kidney essence and promoting pregnancy) was operated at Shenque (CV 8). This combined therapy was delivered once every two days, 3 sessions a week till the day of embryo transfer. The pregnancy outcomes (positive rate of human chorionic gonadotropin [β-HCG] and clinical pregnancy rate) were compared between the two groups, as well as the TCM syndrome score, serum estradiol (E2) and progesterone (P) levels, endometrial thickness and type, endometrial blood flow index (pulsatility index [PI], resistance index [RI]) before and after treatment.

RESULTS

After treatment, the clinical pregnancy rate of the combined treatment group was 40.0% (12/30), higher than that of the western medication group (16.7%, 5/30, P<0.05); and the difference in the positive rate of β-HCG was not significant statistically between the two groups (P>0.05). After treatment, the serum levels of E2 and P were elevated (P<0.05), the endometrial thickness was thickened (P<0.05); the scores of TCM syndrome, and the levels of PI and RI were reduced (P<0.05) when compared with those before treatment in the two groups. The proportion of type A endometrium increased compared with that before treatment in the combined treatment group (P<0.05). Except the levels of E2 and P, the above indexes in the combined treatment group were superior to the western medication group (P<0.05).

CONCLUSIONS

On the basis of frozen embryo transfer of conventional hormone replacement cycle, the intervention of Tongyuan needling combined with jingyu herb-separated moxibustion can effectively relieve the clinical symptoms, increase the endometrial blood flow and its thickness, and improve the endometrial receptivity, thereby ameliorate pregnancy outcomes in RIF patients of kidney deficiency and blood stasis.

Oral giant cell tumor or giant cell granuloma: How to know?

Introduction

The distinction between giant cell tumors and giant cell granulomas is challenging, as both entities have overlapping diagnostic criteria, especially in oral locations. The two entities have similar clinical and radiological presentations, but they differ in their prognoses.

Objective

The main objective of this study was to list the clinical, radiological, histological, and prognostic features of maxillomandibular giant cell tumors and giant cell granulomas cases n order to assess their value as a diagnostic referral factor that may allow the distinction between maxillo-mandibular giant cell granuloma and giant cell tumor.

Study design

Data of maxillomandibular giant cell granulomas and giant cell tumors were assessed through a scoping review and a pre-existing systematic review of literature. We have also realized a bicentric retrospective study.

Results

Various criteria facilitate the differential diagnosis like age, size, locularity and presence of necrosis zone but not the gender. The most discriminating factors was symptomatology (reported in 72% of GCTs while only 15% of GCGs) and the distribution pattern of giant cells in the stroma (homogeneously dispersed in 80% of GCTs versus grouped in clusters in 86.7% of GCGs). Recurrences were most described for giant cell tumors than giant cell granulomas. Malignant transformation and pulmonary metastasis were exclusively reported for giant cell tumors.

Conclusion

As clinical and radiological elements are not sufficient to distinguish between these two entities, immunohistochemistry and molecular genetics can be represent diagnostic biomarkers to distinguish giant cell granulomas and giant cell tumors in oral cavity. We have attempted to define the main criteria for the differentiation of giant cell tumor and giant cell granuloma and propose a decision tree for the management of single maxillomandibular giant cell lesions.

Implant Therapy in the Rehabilitation of Treated Mandibular Arteriovenous Malformations

Mandibular arteriovenous malformations are rare congenital malformations that require multidisciplinary care. Implant-supported rehabilitation of significant bone defect after embolization and resection is poorly described in the literature. We present the case of a 24-year-old patient with a right-sided mandibular arteriovenous malformation diagnosed after massive hemorrhage and treated by embolization and resection surgery. Implant rehabilitation was carried out 9 years later with a prior bone graft through iliac extraction and 3 short implants. Implant survival rate and patient satisfaction were evaluated at 3 years postplacement. Arteriovenous malformations treatments frequently result in bone defects that are difficult to reconstruct because of probable unstable vascularization due to embolization. The presence of osteosynthesis material and artifacts at the radiological level complicates implant planning due to the lack of visualization of the inferior alveolar nerve or artery and necessitates the placement of low-height implants. Osteointegration in contact with embolization products should be monitored. The creation of a case series could be of interest in order to better understand implant treatment for patients with a history of arteriovenous malformations.

French guidelines for the management of oral lichen planus (excluding pharmacological therapy)

INTRODUCTION

Oral lichen is a chronic inflammatory disease for which diagnostic management and follow-up are heterogeneous given the absence of specific guidelines in France. Our objective was to develop French multidisciplinary guidelines for the management of oral lichen.

MATERIALS AND METHODS

Working groups from the Groupe d'Etude de la Muqueuse Buccale (GEMUB) formulated a list of research questions and the corresponding recommendations according to the "formal consensus" method for developing practice guidelines. These recommendations were submitted to a group of experts and the degree of agreement for each recommendation was assessed by a scoring group.

RESULTS

Twenty-two research questions, divided into 3 themes (nosological classification and initial assessment, induced oral lichenoid lesions, and follow-up) resulted in 22 recommendations. Initial biopsy for histology is recommended in the absence of reticulated lesions. Biopsy for direct immunofluorescence is recommended for ulcerated, erosive, bullous types and for diffuse erythematous gingivitis. Management should include a periodontal and dental check-up, and investigation for extra-oral lesions. Hepatitis C testing is recommended only if risk factors are present. Definitions, triggering factors and the management of "induced oral lichenoid lesions" were clarified. Oral lichen must be monitored by a practitioner familiar with the disease at least once a year, using objective tools.

CONCLUSION

This formalised consensus of multidisciplinary experts provides clinical practice guidelines on the management and monitoring of oral lichen.

Genomic epidemiology of Corynebacterium striatum from three regions of China: an emerging national nosocomial epidemic

BACKGROUND

Corynebacteritum straitum has been considered as an emerging multi-drug-resistant (MDR) pathogen. Isolation of MDR C. striatum as the only organism from respiratory samples from hospitalized patients is increasing in China.

AIM

To elucidate the genomic epidemiology and evolution of C. striatum in China.

METHODS

A total of 260 isolates from 2016 to 2018 were collected from three hospitals in three regions of China. Antibiotic sensitivity testing was performed on all isolates. Whole-genome sequencing was applied to all isolates to assess their genomic diversity and relationships and detect the presence of antimicrobial resistance genes (ARG) and ARG cassettes.

FINDINGS

Almost all isolates (96.2%, 250/260) showed multi-drug-resistance. Genome sequencing revealed four major lineages with lineage IV emerging as the epidemic lineage. Most of the diversity was developed in the last 6 years. Each hospital has its own predominant clones with potential spread between Hebei and Guangdong hospitals. Genomic analysis further revealed multiple antimicrobial resistance genes.

CONCLUSIONS

Our results suggested that four lineages of C. striatum have spread in parallel across China, causing persistent and extensive transmissions within hospitals. MDR C. striatum infection has become a national epidemic. Antibiotic-driven selection pressure may have played significant roles in forming persistent and predominant clones. Our data provide the basis for surveillance and prevention strategies to control the epidemic caused by MDR C. striatum.

Combined approaches to reveal genes associated with litter size in Yunshang black goats

Intensive artificial selection has been imposed in Yunshang black goats, the first black specialist mutton goat breed in China, with a breeding object of improving reproductive performance, which has contributed to reshaping of the genome including the characterization of SNP, ROH and haplotype. However, variation in reproductive ability exists in the present population. A WGS was implemented in two subpopulations (polytocous group, PG, and monotocous group, MG) with evident differences of litter size. Following the mapping to reference genome, and SNP calling and pruning, three approaches - GWAS, ROH analysis and detection of signatures of selection - were employed to unveil candidate genes responsible for litter size. Consequently, 12 candidate genes containing OSBPL8 with the minimum P-value were uncovered by GWAS. Differences were observed in the pattern of ROH between two subpopulations that shared similar low inbreeding coefficients. Two ROH hotspots and 12 corresponding genes emerged from ROH pool association analysis. Based on the nS_L statistic, 15 and 61 promising genes were disclosed under selection for MG and PG respectively. Of them, some promising genes participate in ovarian function (PPP2R5C, CDC25A, ESR1, RPS26 and SERPINBs), seasonal reproduction (DIO3, BTG1 and CRYM) and metabolism (OSBPL8, SLC39A5 and SERPINBs). Our study pinpointed some novel promising genes influencing litter size, provided a comprehensive insight into genetic makeup of litter size and might facilitate selective breeding in goats.

Angina bullosa haemorrhagica: a systematic review and proposal for diagnostic criteria

The aim of this study was to perform a critical review of published data on the epidemiological, aetiological, clinical, histological, biological, and therapeutic characteristics of patients with angina bullosa haemorrhagica (ABH). A literature search was conducted in the PubMed, Science Direct, Web of Science, and Cochrane Library databases. All publications fulfilling the selection criteria were included in the eligibility assessment according to the PRISMA statement. The full texts of 54 retrieved articles were screened. Forty articles published between 1985 and 2016 describing 225 cases of ABH were finally selected. The mean age of the patients was 55.4 years; the male to female ratio was 0.7. The predominant localization was the palate (66%). A third of patients had no medical history. When specified, a triggering event or promoting factor was frequently found (82%). Biological tests were normal. A biopsy was performed on 35% of the patients. Treatment was symptomatic with a favourable outcome. Recurrences were frequent (62%). In conclusion, ABH is poorly documented and only by studies of low-level evidence. This review did not allow any aetiopathogenic association to be made with a general pathology or treatment. On the basis of this systematic review of the literature, diagnostic criteria aiming to improve the care of patients presenting with ABH are proposed.

WITHDROWN: Osteonecrosis of the jaw in patients traited by denosumab for malignant bone disease: Descriptive study on 9 cases

Ahead of Print article withdrawn by publisher

A rare case of oral metastasis of colon adenocarcinoma

INTRODUCTION

Metastatic carcinoma of the colon is frequently encountered. In the literature, metastasis of malignant tumors in the buccal cavity are rare. They represent less than 1% of oral malignant lesions.

OBSERVATION

We present a case of oral metastasis of colon adenocarcinoma in the mandible of a 62-year-old patient. The physical examination revealed a swelling in the mandibular symphysis associated with dental displacement. The panoramic X-ray showed significant bone lysis of the symphysis. The neoplastic tissue showed marked positivity for Cytokeratin 20 and CDX2, confirming the diagnosis of metastasis of the oral cavity from colorectal adenocarcinoma.

DISCUSSION

Metastatic adenocarcinoma from the colon to the oral cavity are rare but should be included in the differential diagnosis of tumors in the oral cavity.

[Mandibular ameloblastic fibro-odontoma in 3-year-old patient]

INTRODUCTION

The ameloblastic fibro-odontoma (FOA) is a rare benign tumor representing 1-3% of odontogenic tumors. The FOA affects young patients before the age of 20. Surgical treatment allows usually for recovery. Recurrence and malignant transformation are possible.

OBSERVATION

A 3-year-old patient, with no medical and surgical history, was referred for a painless swelling of the right cheek progressing for several months. Radiographic examination showed a large mixed lesion. Buccal and lingual cortices were blown out. Surgical resection was performed under general anesthesia. Microscopically, the lesion consisted of dental tissue composed of mature dentin and enamel and of an epithelial component. These elements allowed for the diagnosis of ameloblastic fibro-odontoma. The postoperative course was uneventful.

DISCUSSION

The management of this 3-year-old patient was delayed due to late consultation. The size of the lesion, that included all dental structures of sector 4, was big considering the very young age of the patient. The primary conservative surgical treatment allowed for preservation of teeth and of the inferior alveolar nerve, the only sequelae being the removal of the germ of the tooth n^o 44 directly involved in the tumor.

Passive Q-switching of microchip lasers based on Ho:YAG ceramics

A Ho:YAG ceramic microchip laser pumped by a Tm fiber laser at 1910 nm is passively Q-switched by single- and multi-layer graphene, single-walled carbon nanotubes (SWCNTs), and Cr²⁺:ZnSe saturable absorbers (SAs). Employing SWCNTs, this laser generated an average power of 810 mW at 2090 nm with a slope efficiency of 68% and continuous wave to Q-switching conversion efficiency of 70%. The shortest pulse duration was 85 ns at a repetition rate of 165 kHz, and the pulse energy reached 4.9 μJ. The laser performance and pulse stability were superior compared to graphene SAs even for a different number of graphene layers (n=1 to 4). A model for the description of the Ho:YAG laser Q-switched by carbon nanostructures is presented. This modeling allowed us to estimate the saturation intensity for multi-layered graphene and SWCNT SAs to be 1.2±0.2 and 7±1  MW/cm², respectively. When using Cr²⁺:ZnSe, the Ho:YAG microchip laser generated 11 ns/25 μJ pulses at a repetition rate of 14.8 kHz.

[Study of remains and dental wastes of a First World War German rest camp]

INTRODUCTION

This article presents the analysis of dental remains and waste from the dental office of a German rest camp of the First World War in order to study the living conditions of the soldiers, the care policy and the prosthetic rehabilitation techniques used in this context.

MATERIALS AND METHODS

The study included both dental and prosthetic remains, revealed during the excavation. The criteria to determine dental and periodontal health were the presence or absence of caries, wear, tartar and periodontal lesion. Location, severity and frequency of each of these parameters were examined. Regarding the prosthetic remains, the type of prosthesis and the materials used were determined.

RESULTS

Three hundred and twenty seven (327) dental remains were analyzed. A high prevalence of large caries, especially in the molar areas, was highlighted. The incisal areas had however more wear and tartar. 183 casts of plaster dental arcade allowed to highlight a significant proportion of posterior edentulous. Prosthetic remains and laboratory waste revealed the use of vulcanite and porcelain for making dentures.

Mycobacterium tuberculosis and non-tuberculous mycobacteria isolates from HIV-infected patients in Guangxi, China

BACKGROUND

Tuberculosis (TB) remains the leading cause of death among human immunodeficiency virus (HIV) infected persons. The prevalence of infection with Mycobacterium tuberculosis and non-tuberculous mycobacteria (NTM) in HIV-infected patients in China is unknown.

OBJECTIVE

To estimate the prevalence of M. tuberculosis and NTM in HIV-infected patients in Guangxi Province, determine their drug resistance profiles, and evaluate the genotype patterns of M. tuberculosis strains.

DESIGN

Samples were collected from two HIV designated hospitals in Guangxi Province between 2005 and 2008. HIV-infected patients who were culture-positive for mycobacteria were included. Drug susceptibility testing was performed for mycobacterial isolates. NTM species was identified by sequencing, and M. tuberculosis isolates were genotyped using the variable number of tandem repeats method.

RESULTS

M. tuberculosis and NTM were identified in respectively 117 (53%) and 102 (47%) HIV-infected patients. Drug resistance was found in 27% and multi-drug-resistant TB (MDR-TB) in 11% of the patients with TB. Previous treatment for TB was significantly associated with MDR-TB. Twenty (17%) TB patients belonged to eight VNTR-defined clusters.

CONCLUSION

The high frequency of NTM among HIV-infected patients raises concerns about accurate species identification before the determination of appropriate treatment. The potential for TB transmission exists among HIV-infected patients. Intensified screening and effective treatment of TB-HIV co-infected patients is urgently needed.

Abstract B57: UBE3A (E6AP) auto antibodies in hepatocellular carcinoma

B57

UBE3A (E6AP) auto antibodies in hepatocellular carcinoma

1Gebreselassie, D., 1Lan, R., 1Loffredo, C.A., 2Abdel-Hamid, M., 1Goldman, R.

1Lombardi Comprehensive Cancer Center Georgetown University Washington, D.C. & 2National Hepatology and Tropical Medicine Research Institute, Cairo, Egypt

Patients with cancer produce auto antibodies that could serve as biomarkers for detection and classification of the disease. To identify auto antibodies associated with hepatocellular carcinoma (HCC), we used a protein array of 5,000 human proteins (Invitrogen) to compare sera of ten cancer free controls and ten patients with HCC matched on age, gender, and viral infection. Thirty six proteins significantly associated with HCC (p&lt;0.05) were spotted on a custom array. The array experiments confirmed increased auto antibodies in HCC for 20 of the 36 candidates. The frequency of increase was as high as 45% for some of the auto antibodies in a comparison of 20 HCC cases and 10 matched controls. To further validate the observed auto antibody response to Ubiquitin protein ligase E3A (UBE3A), we fused cDNA for the protein, with an N-terminal FLAG tag and an enzyme reporter gene, humanized Renilla luciferase (hRluc). The construct was expressed in the Cos-1 mammalian cell line and crude cell lysates were used for quantification of auto antibodies in serum of the same individuals used in the protein array experiment. The assay is based on immunoprecipitation (IP) of the antigenic protein-construct on protein G beads followed by the quantification of hRluc chemiluminescence. Antibodies to the FLAG tag and the antigen of interest were used to optimize the assay. We found that HCC patient sera contain significantly elevated auto antibodies to UBE3A (t-test P&lt;0.01). The autoantibody response to UBE3A was observed in approximately 20% of the HCC patients and correlates with the results of the protein array experiment.

Citation Information: Cancer Prev Res 2008;1(7 Suppl):B57.

Generation of functionally distinct B lymphocytes from common myeloid progenitors

Current models of adult haematopoiesis propose that haematopoietic stem cells (HSCs) differentiate into common lymphoid (CLP) and common myeloid (CMP) progenitors and establish an early separation between myeloid and lymphoid lineages. Nevertheless, the developmental potential of CMP-associated B cells suggests the existence of alternate pathways for B lymphopoesis. The aim of this study was to compare the developmental and functional properties of CMP- and CLP-derived B cells. While both populations matured through pro-B cell and transitional B cell intermediates in the bone marrow and spleen, respectively, following transfer into irradiated mice, mature CMP- and CLP-derived B cells exhibit distinct functional responses. Specifically, CMP-derived B cells did not respond to mitogenic stimulation to the same degree as their CLP-derived counterparts and secrete lower levels of IgM and the inflammatory cytokines such as interleukin (IL)-6 and IL-10. Together, these data suggest the existence of multiple pathways for generating functionally distinct B cells from bone marrow precursors.

Molecular evolution of large virulence plasmid in Shigella clones and enteroinvasive Escherichia coli

Three genes, ipgD, mxiC, and mxiA, all in the invasion region of the Shigella virulence plasmid, were sequenced from strains representing a range of Shigella serotypes and from two enteroinvasive Escherichia coli (EIEC) isolates. The plasmids can be classified into two relatively homogeneous sequence forms which are quite distinct. pINV A plasmids are found in Shigella flexneri strains F6 and F6A, S. boydii strains B1, B4, B9, B10, B14, and B15, S. dysenteriae strains D3, D4, D6, D8, D9, D10, and D13, and the two EIEC strains (M519 and M520). pINV B plasmids are present in S. flexneri strains F1A, F2A, F3A, F3C, F4A, and FY, two S. boydii strains (B11 and B12), and S. sonnei. The D1 pINV plasmid is a recombinant with ipgD gene more closely related to those of pINV A but with mxiA and mxiC genes more closely related to those of pINV B. The phylogenetic relationships of the plasmid and those of the chromosomal genes of Shigella strains are largely consistent. The cluster 1 and cluster 3 strains tested (G.M. Pupo, R. Lan, and P. R. Reeves, Proc. Natl. Acad. Sci. USA 97:10567-10572, 2000) have pINV A and pINV B plasmids, respectively. However, of the three cluster 2 strains (B9, B11, and B15), B9 and B15 have pINV A while B11 has a pINV B plasmid. Those Shigella (D8 and D10 and S. sonnei) and EIEC strains which do not group with the main body of Shigella strains based on chromosomal genes were found to have plasmids belonging to one or the other of the two types and must have acquired these by lateral transfer.

When does a clone deserve a name? A perspective on bacterial species based on population genetics

Molecular population-genetic analysis has revealed that for several human diseases, including tuberculosis, plague and shigellosis, the generally accepted taxonomic status of the organisms involved does not fit the usually accepted genus or species criteria. This raises the question of what species concept to apply to bacteria. We suggest that the species definition in bacteria should be based on analysis of sequence variation in housekeeping genes, and also that the "clone" be given official status in bacterial nomenclature. This will allow demotion of the species or genus status of several traditionally recognized human pathogens, but retention of current names of anomalous species and genera as clone names.

Comparison of Vibrio cholerae pathogenicity islands in sixth and seventh pandemic strains

Epidemic Vibrio cholerae strains possess a large cluster of essential virulence genes on the chromosome called the Vibrio pathogenicity island (VPI). The VPI contains the tcp gene cluster encoding the type IV pilus toxin-coregulated pilus colonization factor which can act as the cholera toxin bacteriophage (CTXPhi) receptor. The VPI also contains genes that regulate virulence factor expression. We have fully sequenced and compared the VPI of the seventh-pandemic (El Tor biotype) strain N16961 and the sixth-pandemic (classical biotype) strain 395 and found that the N16961 VPI is 41,272 bp and encodes 29 predicted proteins, whereas the 395 VPI is 41,290 bp. In addition to various nucleotide and amino acid polymorphisms, there were several proteins whose predicted size differed greatly between the strains as a result of frameshift mutations. We hypothesize that these VPI sequence differences provide preliminary evidence to help explain the differences in virulence factor expression between epidemic strains (i.e., the biotypes) of V. cholerae.

Population genetics of Escherichia coli in a natural population of native Australian rats

Escherichia coli, a normal inhabitant of the intestinal tract of mammals and birds, is a diverse species. Most studies on E. coli populations involve organisms from humans or human-associated animals. In this study, we undertook a survey of E. coli from native Australian mammals, predominantly Rattus tunneyi, living in a relatively pristine environment in the Bundjalung National Park. The genetic diversity was assessed and compared by multilocus enzyme electrophoresis (MLEE), sequence analysis of the mdh (malate dehydrogenase) gene and biotyping using seven sugars. Ninety-nine electrophoretic types were identified from the 242 isolates analysed by MLEE and 15 sequences from the mdh genes sequenced from 21 representative strains. The Bundjalung isolates extend the diversity represented by the E. coli reference (ECOR) set, with new MLEE alleles found in six out of 10 loci. Many of the Bundjalung isolates fell into a discrete group in MLEE. Other Bundjalung strains fell into the recognized E. coli ECOR set groups, but tended to be at the base of both the MLEE and mdh gene trees, implying that these strains are derived independently from ancestral forms of the ECOR groups and that ECOR strains represent only a subset of E. coli adapted to humans and human-associated animals. Linkage disequilibrium analysis showed that the Bundjalung population has an 'epidemic' population structure. The Bundjalung isolates were able to utilize more sugars than the ECOR strains, suggesting that diet plays a prominent role in adaptation of E. coli.

The colanic acid gene cluster of Salmonella enterica has a complex history

The colanic acid gene cluster of Salmonella enterica LT2 was sequenced and compared with that of Escherichia coli K-12. The two clusters are similar with divergence slightly higher than average for genes of the two species. The cluster was divided into four blocks by GC content and seems likely to have transferred from a higher GC content species to the ancestor of E. coli and S. enterica. All 19 genes of K-12 and 13 genes of LT2 appear to have undergone random genetic drift with amelioration of the GC content. However, in the case of S. enterica, we believe that the six genes of the GDP-fucose pathway group were replaced relatively recently by genes closely related to those of the original donor species. Two repetitive elements were observed: a bacterial interspersed mosaic element in the intergenic region between wzx and wcaK in K-12 only and a RSA (repetitive sequence element) sequence between wcaJ and wzx in LT2 only.

Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics

The evolutionary relationships of 46 Shigella strains representing each of the serotypes belonging to the four traditional Shigella species (subgroups), Dysenteriae, Flexneri, Boydii, and Sonnei, were determined by sequencing of eight housekeeping genes in four regions of the chromosome. Analysis revealed a very similar evolutionary pattern for each region. Three clusters of strains were identified, each including strains from different subgroups. Cluster 1 contains the majority of Boydii and Dysenteriae strains (B1-4, B6, B8, B10, B14, and B18; and D3-7, D9, and D11-13) plus Flexneri 6 and 6A. Cluster 2 contains seven Boydii strains (B5, B7, B9, B11, B15, B16, and B17) and Dysenteriae 2. Cluster 3 contains one Boydii strain (B12) and the Flexneri serotypes 1-5 strains. Sonnei and three Dysenteriae strains (D1, D8, and D10) are outside of the three main clusters but, nonetheless, are clearly within Escherichia coli. Boydii 13 was found to be distantly related to E. coli. Shigella strains, like the other pathogenic forms of E. coli, do not have a single evolutionary origin, indicating convergent evolution of Shigella phenotypic properties. We estimate the three main Shigella clusters to have evolved within the last 35,000 to 270,000 years, suggesting that shigellosis was one of the early infectious diseases of humans.

Intraspecies variation in bacterial genomes: the need for a species genome concept

Bacterial populations are clonal. Their evolution involves not only divergence between orthologous genes but also gain of genes from other clones or species, which has only recently been widely appreciated through macrorestriction mapping, genomic subtraction and complete genome sequencing. Genes can also be lost in response to selection or by random mutation after becoming redundant. The bacterial genome is a dynamic structure and intraspecies variation needs to be included in genome analysis if we are to gain insight into the full species genome.

Azido- and isothiocyanato-substituted aryl pyrazoles bind covalently to the CB1 cannabinoid receptor and impair signal transduction

3-Azidophenyl- and 3-isothiocyanatophenyl-and 2-(5'-azidopentyl)- and 2-(5'-isothiocyanatopentyl)pyrazoles were synthesized to determine whether these compounds could behave as covalently binding ligands for the CB1 cannabinoid receptor in rat brain membranes. Heterologous displacement of [3H]CP55940 indicated that the apparent affinity of these compounds for the CB1 receptor was similar to that of the parent compound, SR141716A, with the exception of the 3-isothiocyanato derivatives, which showed a 10-fold loss of affinity. The 3-azidophenyl and 3-isothiocyanatophenyl compounds behaved as antagonists against the cannabinoid agonist desacetyllevonantradol in activation of G proteins [guanosine 5'-O-(y-[35S]thio)triphosphate ([35S]GTPgammaS) binding] and regulation of adenylyl cyclase. The 2-(5'-azidopentyl)- and 2-(5'-isothiocyanatopentyl)pyrazoles were poor antagonists for [35S]GTPgammaS binding, and both compounds failed to antagonize the cannabinoid regulation of adenylyl cyclase. After incubation with the isothiocyanato analogues or UV irradiation of the azido analogues, the 3-substituted aryl pyrazoles formed covalent bonds with the CB1 receptor as evidenced by the loss of specific binding of [3H]CP55940. In the case of the isothiocyanato analogues, the log concentration-response curve for cannabinoid-stimulated [35S]GTPgammaS binding was shifted to the right, indicating that loss of receptors compromised signal transduction capability. These irreversibly binding antagonists might be useful tools for the investigation of tolerance and receptor down-regulation in both in vitro and in vivo studies.

Evolutionary relationships of pathogenic clones of Vibrio cholerae by sequence analysis of four housekeeping genes

Studies of the Vibrio cholerae population, using molecular typing techniques, have shown the existence of several pathogenic clones, mainly sixth-pandemic, seventh-pandemic, and U.S. Gulf Coast clones. However, the relationship of the pathogenic clones to environmental V. cholerae isolates remains unclear. A previous study to determine the phylogeny of V. cholerae by sequencing the asd (aspartate semialdehyde dehydrogenase) gene of V. cholerae showed that the sixth-pandemic, seventh-pandemic, and U.S. Gulf Coast clones had very different asd sequences which fell into separate lineages in the V. cholerae population. As gene trees drawn from a single gene may not reflect the true topology of the population, we sequenced the mdh (malate dehydrogenase) and hlyA (hemolysin A) genes from representatives of environmental and clinical isolates of V. cholerae and found that the mdh and hlyA sequences from the three pathogenic clones were identical, except for the previously reported 11-bp deletion in hlyA in the sixth-pandemic clone. Identical sequences were obtained, despite average nucleotide differences in the mdh and hlyA genes of 1.52 and 3.25%, respectively, among all the isolates, suggesting that the three pathogenic clones are closely related. To extend these observations, segments of the recA and dnaE genes were sequenced from a selection of the pathogenic isolates, where the sequences were either identical or substantially different between the clones. The results show that the three pathogenic clones are very closely related and that there has been a high level of recombination in their evolution.

Structure-activity relationships of pyrazole derivatives as cannabinoid receptor antagonists

As a potent, specific antagonist for the brain cannabinoid receptor (CB1), the biarylpyrazole N-(piperidin-1-yl)-5-(4-chlorophenyl)-1-(2, 4-dichlorophenyl)-4-methyl-1H-pyrazole-3-carboxamide (SR141716A; 1) was the lead compound for initiating studies designed to examine the structure-activity relationships of related compounds and to search for more selective and potent cannabimimetic ligands. A series of pyrazole derivatives was designed and synthesized to aid in the characterization of the cannabinoid receptor binding sites and also to serve as potentially useful pharmacological probes. Therapeutically, such compounds may have the ability to antagonize harmful side effects of cannabinoids and cannabimimetic agents. Structural requirements for potent and selective brain cannabinoid CB1 receptor antagonistic activity included (a) a para-substituted phenyl ring at the 5-position, (b) a carboxamido group at the 3-position, and (c) a 2,4-dichlorophenyl substituent at the 1-position of the pyrazole ring. The most potent compound of this series contained a p-iodophenyl group at the 5-position, a piperidinyl carboxamide at the 3-position, and a 2,4-dichlorophenyl group at the 1-position of the pyrazole ring. The iodinated nature of this compound offers additional utility as a gamma-enriching SPECT (single photon emission computed tomography) ligand that may be useful in characterizing brain CB1 receptor binding in vivo.

Large receptor reserve for cannabinoid actions in the central nervous system

The receptor occupancy required to produce cannabinoid effects in the central nervous system was determined in both a neurochemical and a behavioral assay for cannabinoid actions. In the neurochemical experiments, performed on superfused rat hippocampal slices, electrically evoked [3H]acetylcholine release was inhibited by the cannabinoid agonist, WIN 55212 to 2 with an EC50 of 0.005 microM and maximum effect of 79%. In parallel experiments examining binding of the radiolabeled CB1 antagonist [131I]AM 281 (N-(morpholin-4-yl)-5-(4-[131I]iodophenyl)-1-(2, 4-dichlorophenyl)-4-methyl-1H-pyrazole-3-carboxamide) to living hippocampal slices, WIN 55212 to 2 inhibited [131I]AM 281 binding with an EC50 of 1.3 microM. From these two sets of data it was determined that 50% of maximal inhibition of [3H]acetylcholine release in hippocampal slices occurs at a receptor occupancy of only 0.13% and 95% of maximal inhibition at a receptor occupancy of 7.5%, suggesting the presence of a receptor reserve that is large compared with other G protein-coupled receptor systems in the central nervous system. In behavioral experiments, WIN 55212 to 2 inhibited spontaneous locomotor activity in mice with an ED50 of 0.3 mg/kg, i. v. In in vivo binding experiments using [131I]AM 281, WIN 55212 to 2 failed to produce significant inhibition of radiotracer binding in the mouse brains, except at very high doses (10 mg/kg or greater, i. v.). By contrast, the CB1 antagonist SR 141716A (10 mg/kg, i.p.), completely abolished specific [131I]AM 281 binding. These experiments suggest that behavioral effects of cannabinoids, like neurochemical effects, are produced at very low receptor occupancy.

Mass spectral fragmentation patterns of 1a,3-diaryl-1,1,4, 4-tetrachloro-1a,2,3,4-tetrahydro-1H-azirino

The mass spectrometric behaviour of three 1a,3-diaryl-1,1,4, 4-tetrachloro-1a,2,3,4-tetrahydro-1H-azirino-[2,1-e][1, 6]benzothiazocines has been studied with the aid of mass-analyzed ion kinetic energy spectro--metry and exact mass measurements under electron impact ionization. All compounds show a tendency-to eliminate a neutral substituted/unsubstituted 1,1-dichlorostyrene from the eight-membered thiazocine ring to yield azirino[2,1-c][1, 4]benzothiazine ions, which can then lose a chlorine radical and a sulfur-atom to form azirino[2,1-c][1,4]benzothiazine ions and dihydroquinoline ions. All compounds could also eliminate a chlorine radical plus hydrogen chloride, stepwise or consecutively, to undergo a ring enlargement rearrangement to produce nine-membered 1, 7-benzothiazonine ions. The [M(+) - Cl] ions could undergo a four-membered ring rearrangement to yield 1,5-benzothiazepine ions by loss of 1,1-dichlorostyrene or styrene ions and HCl, and undergo alpha, alpha-cleavage to form benzothiazine ions by loss of arylchlorocyclopropane. The [M(+) - Cl - HCl] ions could further eliminate some atoms, small molecules or molecular fragments to form some abundant fragment ions. Copyright 1999 John Wiley & Sons, Ltd.

Electron impact mass spectra of 1a,3-disubstituted 1,1-dichloro-1,1a, 2,3-tetrahydroazirino [2,1-d][1,5]benzothiazepines

The mass spectrometric behaviour of eight 1a,3-disubstituted 1, 1-dichloro-1,1a,2,3-tetrahydroazirino[2,1-d][1,5]benzothiazepines has been studied with the aid of mass-analyzed ion kinetic energy spectrometry and exact mass measurements under electron impact ionization. All compounds show a tendency to eliminate a chlorine radical from the aziridine ring and then eliminate a neutral propene or substituted/unsubstituted styrene from the thiazepine ring to yield 1,4-benzothiazine ions. They can also lose hydrogen chloride and a chlorine radical, or lose two chlorine atoms, to undergo a ring enlargement rearrangement to produce 1,6-benzothiazocine ions, which can further eliminate propyne or phenylacetylene, or small molecular fragments, to yield some abundant fragment ions.

Molecular basis of ribotype variation in the seventh pandemic clone and its O139 variant of Vibrio cholerae

Ribotyping has been widely used to characterise the seventh pandemic clone including South American and O139 variants which appeared in 1991 and 1992 respectively. To reveal the molecular basis of ribotype variation we analysed the rrn operons and their flanking regions. All but one variation detected by BglI, the most discriminatory enzyme, was found to be due to changes within the rrn operons, resulting from recombination between operons. The recombinants are detected because of the presence of a BglI site in the 16S gene in three of the nine rrn operons and/or changes of intergenic spacer types of which four variants were identified. As the frequency of rrn recombination is high, ribotyping becomes a less useful tool for evolutionary studies and long term monitoring of the pathogenic clones of Vibrio cholerae as variation could undergo precise reversion by the same recombination event.

Variation of the ribosomal operon 16S-23S gene spacer region in representatives of Salmonella enterica subspecies

The 16S-23S spacer regions of two ribosomal operons (rrnA and rrnE) have been sequenced in seven representatives of the Salmonella enterica subspecies. Isolated nucleotide substitutions were found at the same sites as in Escherichia coli but the number of polymorphic sites was much larger, as could be expected for a more heterogeneous species. Still, as in E. coli, most of the variation found was due to insertions and/or deletions affecting blocks of nucleotides generally located at equivalent regions of the putative secondary structure for both species. Isolated polymorphic sites generated phylogenetic trees generally consistent with the subspecies structure and the accepted relationships among the subspecies. However, the sequences of rrnE put subspecies I closer to E. coli K-12 than to the other S. enterica subspecies. The distribution of polymorphisms affecting blocks of nucleotides was much more random, and the presence of equivalent sequences in distantly related subspecies, and even in E. coli, could reflect relatively frequent horizontal transfer. The smallest 16S-23S spacers in other genera of the family Enterobacteriaceae were also sequenced. As expected, the level of variation was much larger. Still, the phylogenetic tree inferred is consistent with those of 16S rRNA or housekeeping genes.

Cholera in the 1990s

Two strains of Vibrio cholerae are currently significant in cholera: a remnant from the sixth pandemic (1899-1923) still present in South Asia and the seventh pandemic strain which emerged in 1961. The 1990s were marked by spread of the seventh pandemic to South America in 1991 and appearance of an O139 form of the seventh pandemic strain in 1992 (or possibly 1991), which in 1993 predominated in some areas but then declined. Molecular analysis showed that the sixth and the seventh pandemic clones are related, but have a different TCP pathogenicity island and possibly different CTX phages, suggesting independent derivation from related environmental strains. Upsurges of the seventh pandemic were accompanied by increased genetic variation enabling the relationships between strains to be studied, but the basis for variation in pathogenicity is not known. There is clearly a risk of new forms arising and a strategy for speedy development of vaccines needs to be established.

Imaging the brain marijuana receptor: development of a radioligand that binds to cannabinoid CB1 receptors in vivo

The major active ingredient of marijuana, (-)-delta9-tetrahydrocannabinol, exerts its psychoactive effects via binding to cannabinoid CB1 receptors, which are widely distributed in the brain. Radionuclide imaging of CB1 receptors in living human subjects would help explore the presently unknown physiological roles of this receptor system, as well as the neurochemical consequences of marijuana dependence. Currently available cannabinoid receptor radioligands are exceedingly lipophilic and unsuitable for in vivo use. We report the development of a novel radioligand, [123I]AM281[N-(morpholin-4-yl)-5-(4-[123I]iodophenyl)-1-(2,4 -dichlorophenyl)-4-methyl-1H-pyrazole-3-carboxamide], that is structurally related to the CB1-selective antagonist SR141716A [N-(piperidin-1-yl)-5-(4-chlorophenyl)-1-(2,4-dichlorophenyl)-4-me thyl-1H-pyrazole-3-carboxamide]. Baboon single photon emission computed tomography studies, mouse brain dissection studies, and ex vivo autoradiography in rat brain demonstrated rapid passage of [123I]AM281 into the brain after intravenous injection, appropriate regional brain specificity of binding, and reduction of binding after treatment with SR141716A. AM281 has an affinity in the low nanomolar range for cerebellar binding sites labeled with [3H]SR141716A in vitro, and binding of [123I]AM281 is inhibited by several structurally distinct cannabinoid receptor ligands. We conclude that [123I]AM281 has appropriate properties for in vivo studies of cannabinoid CB1 receptors and is suitable for imaging these receptors in the living human brain.

Effect of the cannabinoid receptor SPECT agent, AM 281, on hippocampal acetylcholine release from rat brain slices

The SPECT ligand AM 281, a less lipophilic analog of the cannabinoid receptor antagonist SR 141716A, robustly potentiated electrically-evoked release of acetylcholine from superfused hippocampal slices and prevented the inhibition of acetylcholine release by the cannabimimetic drug WIN 55212-2. These results, similar to earlier observations with SR 141716A, indicate that AM 281 is either a cannabinoid receptor antagonist or inverse agonist. Despite showing lower affinity than SR 141716A in hippocampal membrane binding experiments, AM 281 had slightly greater potency than SR 141716A in the hippocampal slice experiments, perhaps because of reduced drug absorption to slice membranes and to the apparatus.

Binding of the non-classical cannabinoid CP 55,940, and the diarylpyrazole AM251 to rodent brain cannabinoid receptors

The binding of [123I]AM251 (a radioiodinated analog of the cannabinoid CB1 receptor antagonist SR141716A) was compared to that of [3H]CP 55,940 in mouse and rat brain preparations. Scatchard analysis of the binding of [123I]AM251 and [3H]CP 55,940 to membranes prepared from mouse cerebellum, striatum and hippocampus yielded similar Bmax values (15-41 pmol/g wet wt tissue). Kd values were lower for [123I]AM251 (0.23-0.62 nM) than for [3H]CP 55,940 (1.3-4 nM). CP 55,940 and SR141716A increased dissociation of [123I]AM251 from binding sites in mouse cerebellar homogenates to a similar extent. The structurally dissimilar cannabinoid receptor ligands THC, methanandamide, WIN 55, 212-2, CP 55,940 and SR141716A were each able to fully compete with binding of both [123I]AM251 and [3H]CP 55,940 in mouse cerebellum. In vitro autoradiography demonstrated that the distribution of binding sites for [123I]AM251 in rat brain was very similar to published distributions of binding sites for [3H]CP 55,940. Together, these observations suggest that AM251 binds to the same site (the cannabinoid CB1 receptor) in rodent brains as CP 55,940. However, the binding site domains which interact with AM251 and CP 55,940 may not be identical, since IC50 values for cannabinoid receptor ligands depended on whether [123I]AM251 or [3H]CP 55,940 was used as radioligand.

Evolutionary relationships among pathogenic and nonpathogenic Escherichia coli strains inferred from multilocus enzyme electrophoresis and mdh sequence studies

Within the species Escherichia coli, there are commensal strains and a variety of pathogenic strains, including enteropathogenic E. coli (EPEC), enterohemorrhagic E. coli (EHEC), enterotoxigenic E. coli (ETEC), enteroinvasive E. coli (EIEC), and urinary tract infection (UTI) strains. The pathogenic strains are identified by serotype and by possession of specific virulence determinants (toxins and adhesions, etc.) encoded by either monocistronic genes, plasmids, or pathogenicity islands. Although there are studies on the relationships between selected pathogenic strains, the relatedness among the majority of the pathogenic forms to each other, to commensal E. coli, and to the genus Shigella (which has often been suggested to be part of E. coli) has not been determined. We used multilocus enzyme electrophoresis (MLEE) at 10 enzyme loci and the sequence of the mdh housekeeping gene to study the genetic relationships of pathogenic E. coli strains (including Shigella clones), namely, 5 EPEC strains (serotypes O111 and O55), 3 EHEC strains (serotype O157), 6 ETEC strains (serotypes O78, O159, and O148), 5 EIEC strains (serotypes O124, O28, and O112), and 13 Shigella strains representing clones Flexneri, Dysenteriae, Boydii, and Sonnei, to commensal E. coli strains. Both the MLEE and mdh sequence trees reveal that EPEC, EHEC, ETEC, EIEC, and UTI strains are distributed among the ECOR set groups, with no overall clustering of EPEC, ETEC, EIEC, or UTI strains. The genus Shigella is shown to comprise a group of closely related pathogenic E. coli strains. Six pathogenic strains, i.e., M502 (EIEC; O112ac:NM), M503 (EPEC; O111:H12), M526 (ETEC; O159:H4), M522 (EPEC; O111ac:H12), M524 (ETEC; O78:H11), and M506 (ETEC; O78:H11), were found to have mdh sequences identical to those of five ECOR group A strains (ECOR5, ECOR10, ECOR14, ECOR6, and K-12). All 11 strains are closely related by MLEE. The results indicate that pathogenic strains of E. coli do not have a single evolutionary origin within E. coli but have arisen many times. The results also suggest the possibility that any E. coli strain acquiring the appropriate virulence factors may give rise to a pathogenic form.

123I-labeled AM251: a radioiodinated ligand which binds in vivo to mouse brain cannabinoid CB1 receptors

We have investigated the binding of 123I-labeled N-(piperidin-1-yl)-5-(4-iodophenyl)-1-(2,4-dichlorophenyl)-4-methy l-1 H-pyrazole-3-carboxamide (AM251), an analog of the cannabinoid receptor antagonist SR141716A [N-(piperidin-1-yl)-5-(4-chlorophenyl)-1-(2,4-dichlorophenyl)-4-me thyl-1 H-pyrazole-3-carboxamide] in the mouse brain. Following intravenous injection, the peak whole-brain uptake of about 1% of the administered activity occurred at about 2 h. By 8 h radioactivity in brain had declined to about half its peak value. High-performance liquid chromatographic analysis showed that > 70% of radioactivity extracted from brain at 2 h was still present as [123I]AM251. Co-injection of SR141716A inhibited the in vivo brain binding of [123I]AM251 dose dependently. At 2 mg/kg, the highest dose that could be tested, inhibition was 50% at 2 h post-administration. The ED50 value calculated assuming that 2 mg/kg gave near-maximal inhibition was about 0.1 mg/kg. In contrast to the brain, radioactivity in other major organs (blood, liver, kidney, heart and lung) was little affected by SR141716A. The regional binding of [123I]AM251 in the brain was consistent with the published distribution of cannabinoid receptors in rat brain, in that the order was hippocampus, striatum > cerebellum > brain stem. delta 9-Tetrahydrocannabinol co-administered intravenously at 10 mg/kg, a dose which induced catalepsy and decreased locomotor activity, decreased the 2 h brain uptake of [123I]AM251 by 10%, but this was not significant (P = 0.08). In in vitro binding assays with mouse hippocampal membranes, tetrahydrocannabinol inhibited binding of [123I]AM251 with an IC50 value of about 700 nM, compared with about 0.2 nM for SR141716A.

Gene transfer is a major factor in bacterial evolution

Lateral gene transfer in four strains of Salmonella enterica has been assessed using genomic subtraction. Strain LT2 (subspecies I serovar Typhimurium) chromosomal DNA was used as target and subtracted by three subspecies I strains of serovars Typhimurium (S21), Muenchen (S71), Typhi (M229), and a subspecies V strain (M321). Data from probing random cosmids of LT2 DNA with preparations of the residual LT2 DNA after subtraction were used to estimate the amounts of LT2 DNA not able to hybridize to strains S21, S71, M229, and M321 to be in the range of 84-106, 191-355, 305-629, and 778-1,286 kb, respectively. Several lines of evidence indicate that most of this DNA is from genes not present in strain M321 and not from genes that have diverged in sequence. The amounts correlate with the divergence of the four strains as revealed by multilocus enzyme electrophoresis and sequence variation of housekeeping genes. Sequence of 39 of the fragments from the M321 subtracted residual LT2 DNA revealed only six inserts of known gene function with evidence of both gain and loss of genes during the development of S. enterica clones. Sixteen of the 39 segments have 45% or lower G+C content, below the species average, but over half are within the normal range for the species. We conclude that even within a species, clones may differ by up to 20% of chromosomal DNA, indicating a major role for lateral transfer, and that on the basis of G+C content, a significant proportion of the DNA is from distantly related species.

The sixth and seventh cholera pandemics are due to independent clones separately derived from environmental, nontoxigenic, non-O1 Vibrio cholerae

The DNA sequences of the asd genes from 45 isolates of Vibrio cholerae (19 clinical O1 isolates, 2 environmental nontoxigenic O1 isolates, and 24 isolates with different non-O1 antigens) were determined. No differences were found within either sixth- or seventh-pandemic isolates; however, variation was found between the two forms and among the non-O1 isolates. O139 isolates had sequences identical to those of seventh-pandemic isolates. Phylogenetic trees with Vibrio mimicus as the outgroup suggest that the sixth-pandemic, seventh-pandemic, and U.S. Gulf isolates are three clones that have evolved independently from different lineages of environmental, nontoxigenic, non-O1 V. cholerae isolates. There is evidence for horizontal transfer of O antigen, since isolates with nearly identical asd sequences had different O antigens, and isolates with the O1 antigen did not cluster together but were found in different lineages. We also found evidence for recombination events within the asd gene of V. cholerae. V. cholerae may have a higher level of genetic exchange and a lower level of clonality than species such as Salmonella enterica and Escherichia coli.

Molecular evolution in the gnd locus of Salmonella enterica

The gnd gene, the structural gene for 6-phosphogluconate dehydrogenase, was sequenced and analyzed in 34 isolates from different serovars of the seven subspecies of Salmonella enterica to provide comparative information on the evolution in this gene, which has been studied extensively in Escherichia coli. The gene tree obtained by the neighbor-joining method in general gave separate branches for each subspecies, with the few exceptions readily explained by recombination. There is evidence of recombination involving transfer of long (more than 400 bp) and short (30-150 bp) segments of DNA. Four of the six long-segment transfers detected are at the 5' end of the gene, and in all four cases a variant of the chi sequence is located close to the recombination junction and appears to have mediated the recombination events. We suggest that in these four cases and in a fifth case with intersubspecies transfer of the whole gnd gene, the adjacent rfb (O antigen) locus may have been transferred in the same event. The estimates of the number of synonymous substitutions per synonymous site, KS, and the number of nonsynonymous substitutions per nonsynonymous site, KA, within the E. coli and S. enterica gnd genes, and also between the two species show an interesting distribution, with KS being lower toward the ends of the gene and KA in particular being lower in the first than in the second domain. In S. enterica, synonymous sites also seem to be subjected to negative selection. The ratio of KA to KS was higher within S. enterica and E. coli than between them, which may indicate that intraspecies variation is essentially between clones and that mildly deleterious mutations can be fixed within clones, which would thus raise KA within species.

Molecular evolution of the seventh-pandemic clone of Vibrio cholerae and its relationship to other pandemic and epidemic V. cholerae isolates

Genetic variation and molecular evolution within the seventh-pandemic clone of Vibrio cholerae O1 and its relationship to other V. cholerae isolates were examined by studying 58 clinical isolates that were epidemiologically unassociated and isolated from patients in different countries over 62 years (1931 to 1993). The sample consisted of 45 isolates from the seventh cholera pandemic (1961 to the present), 3 from the sixth pandemic, 3 from sporadic El Tor outbreaks prior to the seventh pandemic, 2 from the U.S. Gulf Coast, and 5 O139 Bengal isolates. Ribotyping detected 11 polymorphic restriction sites within the seventh-pandemic isolates and showed major differences in ribotypes in comparison with sixth- and pre-seventh-pandemic isolates. O139 isolates were very similar to isolates from the start of the seventh pandemic, differing at only two sites. The majority of seventh-pandemic isolates fall into two groups, the first present from 1961 to the present and found only in Asia and the second arising in 1966 and spreading worldwide. Both groups underwent change over time, allowing a provisional estimate for the nucleotide substitution rate within the seventh pandemic clone.

MULTICOMP: a program for preparing sequence data for phylogenetic analysis

MULTICOMP is a program that assists in the phylogenetic analysis of DNA sequences. It streamlines sequence handling and analysis. Input is from either individual sequence files or a file of aligned sequences. It produces data on variation at DNA and amino acid sequence level and can also convert sequences to data formats suitable for PHYLIP, PAUP and MacClade phylogenetic inference programs. Further, two tree-building programs, NEIGHBOR and DNAPARS, of PHYLIP can be directly run from within it. MULTICOMP performs Sawyer's algorithm for detection of gene conversion. The program facilitates analysis using only part of the data of a data set or using two or more combined data sets.