Discovery of selective and orally available spiro-3-piperidyl ATP-competitive MK2 inhibitors

The identification of a potent, selective, and orally available MK2 inhibitor series is described. The initial absence of oral bioavailability was successfully tackled by moving the basic nitrogen of the spiro-4-piperidyl moiety towards the electron-deficient pyrrolepyridinedione core, thereby reducing the pK_a and improving Caco-2 permeability. The resulting racemic spiro-3-piperidyl analogues were separated by chiral preparative HPLC, and the activity towards MK2 inhibition was shown to reside mostly in the first eluting stereoisomer. This led to the identification of new MK2 inhibitors, such as (S)-23, with low nanomolar biochemical inhibition (EC₅₀ 7.4 nM) and submicromolar cellular target engagement activity (EC₅₀ 0.5 μM).     

Draft genome sequences of six Escherichia coli isolates from the stepwise model of emergence of Escherichia coli O157:H7

Enterohemorrhagic Escherichia coli (EHEC) of serotype O157:H7 has been implicated in food-borne illnesses worldwide. An evolutionary model was proposed in which the highly pathogenic EHEC O157:H7 serotype arose from its ancestor, enteropathogenic E. coli (EPEC) O55:H7 (sorbitol fermenting [SOR(+)] and β-glucuronidase positive [GUD(+)]), through sequential gain of virulence, phenotypic traits, and serotype change. Here we report six draft genomes of strains belonging to this evolutionary model: two EPEC O55:H7 (SOR(+) GUD(+)) strains, two nonmotile EHEC O157:H(-) strains (SOR(+) GUD(+)) containing plasmid pSFO157, one EHEC O157:H7 (SOR(-) GUD(+)) strain, and one O157:H7 strain containing plasmid pSFO157 (SOR(+) GUD(+)).     

Chloroplast DNA Diversity in Populations of Wild and Cultivated Barley

Chloroplast DNA (cpDNA) diversity was found within and among populations (245 accessions total) of wild barley, Hordeum vulgare L. ssp. spontaneum Koch from Israel and Iran. Three polymorphic restriction sites (HindIII, EcoRI, BclI) which define three distinct cpDNA lineages were detected. One lineage is common to populations in the Hule Valley and Kinneret of northern Israel, and in Iran. The second lineage is found predominantly in the Lower Jordan Valley and Negev. The distribution of the third lineage is scattered but widespread throughout Israel. Sixty two accessions of cultivated barleys, H. vulgare L., were found, with two exceptions, to belong to just one cpDNA lineage of wild barley, indicating that the cpDNA of cultivated barley is less variable than its wild ancestor. These results demonstrate the need for assessing intraspecific cpDNA variability prior to choosing single accessions for phylogenetic constructions at the species level and higher.     

Knowledge and beliefs of international travellers about the transmission and prevention of HIV infection.

OBJECTIVES: To measure the perceived risk of acquired immunodeficiency syndrome (AIDS) among international travellers, to measure their knowledge of the transmission and prevention of HIV infection abroad and to identify some of the determinants of this knowledge. DESIGN: Survey. SETTING: Travellers'' immunization clinic providing mostly primary preventive care to international travellers. PARTICIPANTS: All clients aged 18 to 50 years seen at the clinic between Oct. 2 and Dec. 21, 1989, before their departure. MAIN OUTCOME MEASURES: Sixteen statements measured knowledge of transmission and prevention of HIV infection. Standardized scales measured health beliefs. RESULTS: The response rate was 81% (331/409). Compared with other diseases AIDS was perceived to be associated with a low risk except by those travelling to countries with a high prevalence of AIDS. Most of the clients were found to have a good knowledge of HIV transmission to travellers, although some myths remained popular and some real routes of transmission, especially blood, remained underrated. In all, 70% of the subjects believed in the efficacy of condoms when used with local people, as compared with 79% when used with other tourists; this difference was greatest among travellers who perceived AIDS as being particularly severe but difficult to prevent. The determinants of the knowledge of HIV transmission and prevention were a high level of education, a mother tongue other than French, unmarried status, a high prevalence of AIDS at the destination, the duration of the trip and a high perceived risk of HIV infection. CONCLUSIONS: Counselling should teach travellers (a) not to underestimate their risk of HIV infection during their trip, (b) to decrease the risk of requiring health care in developing countries and (c) to rely on their own prudent sexual behaviour rather than on their assessment of the level of risk posed by the environment.     

The misleading effects of composite taxa in supermatrices

With the amount of available sequence data rapidly increasing, supermatrices are at the forefront of systematic studies. As an alternative to supertrees, supermatrices utilize a total evidence approach where different genes and other lines of data are merged into a single data matrix, which is then analyzed in an attempt to obtain the phylogeny that best explains the data. However, questions may arise when combining data sets in which one or more taxa do not have sequences available for each individual gene. Two possible solutions to this situation are to either leave all taxa separate and code unavailable sequences as missing, or to combine taxa at a level for which monophyly is assumed a priori. By reanalyzing the previous work of, we show that combining taxa may yield misleading results, i.e., hypotheses of relationships that are not supported by the underlying data.     

The forensic analysis of foodborne bacterial pathogens in the age of whole‐genome sequencing

The forensic evaluation of bacterial pathogens presents new challenges to the forensic science community. This review examines bacterial pathogens as objects of forensic comparison, focusing on their nucleic acid sequences as an important aspect of the comparison process. Because of the clonal propagation of most bacterial pathogens, a phylogenetic approach to understanding the diversity and using this understanding to address common forensic questions is explored. As a general phylogenetic framework is now employed in human mitochondrial DNA analysis, we will use the relevant concepts and approaches common in this area to develop this approach further. We also address the impact of the current ease and prevalence of whole‐genome DNA sequence analysis in the forensic comparison process.     

miR-216 and miR-217 expression is reduced in transgenic mouse models of pancreatic adenocarcinoma,knockout of miR-216/miR-217 host gene is embryonic lethal

Mice harboring a G12D activating Kras mutation are among the most heavily studied models in the field of pancreatic adenocarcinoma (PDAC) research. miRNAs are differentially expressed in PDAC from patients and mouse models of PDAC. To better understand the relationship that Kras activation has on miRNA expression, we profiled the expression of 629 miRNAs in RNA isolated from the pancreas of control, young, and old P48^+/Cre;LSL-KRAS^G12D as well as PDX-1-Cre;LSL-KRAS^G12D mice. One hundred of the differentially expressed miRNAs had increased expression in the advanced disease (old) P48^+/Cre;LSL-KRAS^G12D compared to wild-type mice. Interestingly, the expression of three miRNAs, miR-216a, miR-216b, and miR-217, located within a ～30-kbp region on 11qA3.3, decreased with age (and phenotype severity) in these mice. miR-216/-217 expression was also evaluated in another acinar-specific ELa-Kras^G12D mouse model and was downregulated as well. As miR-216/-217 are acinar enriched, reduced in human PDAC and target KRAS, we hypothesized that they may maintain acinar differentiation or represent tumor suppressive miRNAs. To test this hypothesis, we deleted a 27.9-kbp region of 11qA3.3 containing the miR-216/-217 host gene in the mouse’s germ line. We report that germ line deletion of this cluster is embryonic lethal in the mouse. We estimate that lethality occurs shortly after E9.5. qPCR analysis of the miR-216b and miR-217 expression in the heterozygous animals showed no difference in expression, suggesting haplosufficiency by some type of compensatory mechanism. We present the differential miRNA expression in Kras^G12D transgenic mice and report lethality from deletion of the miR-216/-217 host gene in the mouse’s germ line.