Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes

BACKGROUND: Listeria monocytogenes is a food-borne pathogen that causes infections with a high-mortality rate and has served as an invaluable model for intracellular parasitism. Here, we report complete genome sequences for two L. monocytogenes strains belonging to serotype 4a (L99) and 4b (CLIP80459), and transcriptomes of representative strains from lineages I, II, and III, thereby permitting in-depth comparison of genome- and transcriptome -based data from three lineages of L. monocytogenes. Lineage III, represented by the 4a L99 genome is known to contain strains less virulent for humans. RESULTS: The genome analysis of the weakly pathogenic L99 serotype 4a provides extensive evidence of virulence gene decay, including loss of several important surface proteins. The 4b CLIP80459 genome, unlike the previously sequenced 4b F2365 genome harbours an intact inlB invasion gene. These lineage I strains are characterized by the lack of prophage genes, as they share only a single prophage locus with other L. monocytogenes genomes 1/2a EGD-e and 4a L99. Comparative transcriptome analysis during intracellular growth uncovered adaptive expression level differences in lineages I, II and III of Listeria, notable amongst which was a strong intracellular induction of flagellar genes in strain 4a L99 compared to the other lineages. Furthermore, extensive differences between strains are manifest at levels of metabolic flux control and phosphorylated sugar uptake. Intriguingly, prophage gene expression was found to be a hallmark of intracellular gene expression. Deletion mutants in the single shared prophage locus of lineage II strain EGD-e 1/2a, the lma operon, revealed severe attenuation of virulence in a murine infection model. CONCLUSION: Comparative genomics and transcriptome analysis of L. monocytogenes strains from three lineages implicate prophage genes in intracellular adaptation and indicate that gene loss and decay may have led to the emergence of attenuated lineages

Seroepidemiological study on the spread of SARS-CoV-2 in Germany:

The SARS-CoV-2 coronavirus has spread rapidly across Germany. Infections are likely to be under-recorded in the notification data from local health authorities on laboratory-confirmed cases since SARS-CoV-2 infections can proceed with few symptoms and then often remain undetected. Seroepidemiological studies allow the estimation of the proportion in the population that has been infected with SARS-CoV-2 (seroprevalence) as well as the extent of undetected infections. The ‘CORONA-MONITORING bundesweit’ study (RKI-SOEP study) collects biospecimens and interview data in a nationwide population sample drawn from the German Socio-Economic Panel (SOEP). Participants are sent materials to self-collect a dry blood sample of capillary blood from their finger and a swab sample from their mouth and nose, as well as a questionnaire. The samples returned are tested for SARS-CoV-2 IgG antibodies and SARS-CoV-2 RNA to identify past or present infections. The methods applied enable the identification of SARS-CoV-2 infections, including those that previously went undetected. In addition, by linking the data collected with available SOEP data, the study has the potential to investigate social and health-related differences in infection status. Thus, the study contributes to an improved understanding of the extent of the epidemic in Germany, as well as identification of target groups for infection protection

Seroepidemiologische Studie zur bundesweiten Verbreitung von SARS-CoV-2 in Deutschland: Studienprotokoll von CORONA-MONITORING bundesweit (RKI-SOEP-Studie)

Das Coronavirus SARS-CoV-2 hat sich in kurzer Zeit bundesweit ausgebreitet. In den Meldedaten der Gesundheitsämter zu laborbestätigten Infektionsfällen ist von einer Untererfassung des Infektionsgeschehens auszugehen, da Infektionen häufig unentdeckt bleiben, zum Beispiel weil sie symptomarm verlaufen. In seroepidemiologischen Studien kann der Bevölkerungsanteil mit durchgemachter SARS-CoV-2-Infektion (Seroprävalenz) wie auch der Umfang unentdeckter Infektionen abgeschätzt werden. In der Studie CORONA-MONITORING bundesweit (RKI-SOEP-Studie) werden Bioproben und Befragungsdaten in einer deutschlandweiten Bevölkerungsstichprobe des Sozio-oekonomischen Panels (SOEP) erhoben. Den Teilnehmenden werden Materialien zur selbstständigen Gewinnung einer Trockenblutprobe aus Kapillarblut des Fingers und einer Abstrichprobe aus Mund und Nase sowie ein Fragebogen postalisch zugesendet. Die zurückgesendeten Proben werden auf SARS-CoV-2-IgG-Antikörper und SARS-CoV-2-RNA zur Identifikation einer durchgemachten oder aktuellen Infektion untersucht. Die eingesetzten Methoden ermöglichen es, auch solche SARS-CoV-2-Infektionen zu erkennen, die bislang unentdeckt blieben. Durch die Verknüpfung mit bereits vorhandenen SOEP-Daten hat die Studie das Potenzial, auch soziale und gesundheitsbezogene Unterschiede im Infektionsstatus zu untersuchen. So kann die Studie zu einem verbesserten Verständnis des Ausmaßes der Epidemie in Deutschland wie auch zur Identifikation von Zielgruppen für den Infektionsschutz beitragen

Guidelines and Recommendations on Yeast Cell Death Nomenclature

Elucidating the biology of yeast in its full complexity has major implications for science, medicine and industry. One of the most critical processes determining yeast life and physiology is cellular demise. However, the investigation of yeast cell death is a relatively young field, and a widely accepted set of concepts and terms is still missing. Here, we propose unified criteria for the definition of accidental, regulated, and programmed forms of cell death in yeast based on a series of morphological and biochemical criteria. Specifically, we provide consensus guidelines on the differential definition of terms including apoptosis, regulated necrosis, and autophagic cell death, as we refer to additional cell death routines that are relevant for the biology of (at least some species of) yeast. As this area of investigation advances rapidly, changes and extensions to this set of recommendations will be implemented in the years to come. Nonetheless, we strongly encourage the authors, reviewers and editors of scientific articles to adopt these collective standards in order to establish an accurate framework for yeast cell death research and, ultimately, to accelerate the progress of this vibrant field of research

Guidelines and recommendations on yeast cell death nomenclature

Elucidating the biology of yeast in its full complexity has major implications for science, medicine and industry. One of the most critical processes determining yeast life and physiology is cel-lular demise. However, the investigation of yeast cell death is a relatively young field, and a widely accepted set of concepts and terms is still missing. Here, we propose unified criteria for the defi-nition of accidental, regulated, and programmed forms of cell death in yeast based on a series of morphological and biochemical criteria. Specifically, we provide consensus guidelines on the differ-ential definition of terms including apoptosis, regulated necrosis, and autophagic cell death, as we refer to additional cell death rou-tines that are relevant for the biology of (at least some species of) yeast. As this area of investigation advances rapidly, changes and extensions to this set of recommendations will be implemented in the years to come. Nonetheless, we strongly encourage the au-thors, reviewers and editors of scientific articles to adopt these collective standards in order to establish an accurate framework for yeast cell death research and, ultimately, to accelerate the pro-gress of this vibrant field of research

Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes

ABSTRACT: BACKGROUND: Listeria monocytogenes is a food-borne pathogen that causes infections with a high-mortality rate and has served as an invaluable model for intracellular parasitism. Here, we report complete genome sequences for two L. monocytogenes strains belonging to serotype 4a (L99) and 4b (CLIP80459), and transcriptomes of representative strains from lineages I, II, and III, thereby permitting in-depth comparison of genome- and transcriptome -based data from three lineages of L. monocytogenes. Lineage III, represented by the 4a L99 genome is known to contain strains less virulent for humans. RESULTS: The genome analysis of the weakly pathogenic L99 serotype 4a provides extensive evidence of virulence gene decay, including loss of several important surface proteins. The 4b CLIP80459 genome, unlike the previously sequenced 4b F2365 genome harbours an intact inlB invasion gene. These lineage I strains are characterized by the lack of prophage genes, as they share only a single prophage locus with other L. monocytogenes genomes 1/2a EGD-e and 4a L99. Comparative transcriptome analysis during intracellular growth uncovered adaptive expression level differences in lineages I, II and III of Listeria, notable amongst which was a strong intracellular induction of flagellar genes in strain 4a L99 compared to the other lineages. Furthermore, extensive differences between strains are manifest at levels of metabolic flux control and phosphorylated sugar uptake. Intriguingly, prophage gene expression was found to be a hallmark of intracellular gene expression. Deletion mutants in the single shared prophage locus of lineage II strain EGD-e 1/2a, the lma operon, revealed severe attenuation of virulence in a murine infection model. CONCLUSION: Comparative genomics and transcriptome analysis of L. monocytogenes strains from three lineages implicate prophage genes in intracellular adaptation and indicate that gene loss and decay may have led to the emergence of attenuated lineages

Recurrence and prediction of abnormal uterine bleeding and re-intervention after initial hysteroscopic treatment:a retrospective cohort study

Purpose To estimate the incidence of recurrence of complaints and repeated interventions after hysteroscopic treatment for abnormal uterine bleeding in premenopausal women and to determine potential predictors for re-intervention. Methods This is a retrospective cohort study in two secondary care centers in the Netherlands. We included 313 premenopausal women who underwent hysteroscopy for complaints of abnormal uterine bleeding and who had intrauterine pathology visualized at ultrasound. The intrauterine structure was hysteroscopically removed. These women were compared with women who had a hysteroscopy for abnormal uterine bleeding, but in whom hysteroscopy showed no abnormalities. We used Chi-squared test for categorical variables and independent-samples T test for continuous variables. p Values less than 0.05 were considered to indicate statistical significance. Results In total, 262 women had intrauterine pathology removed at hysteroscopy; 136 (52%) women had recurrence of complaints, while 101 women (39%) underwent re-intervention. Heavy menstrual bleeding at baseline and multiparity were predictive factors for recurrence of abnormal uterine bleeding and re-intervention. In the 51 women with abnormal uterine bleeding in whom hysteroscopy showed no intrauterine abnormality, 29 women (60%) had recurrence of complaints and 12 (24%) a re-intervention. Conclusion In premenopausal women with abnormal uterine bleeding, treatment of intrauterine pathology often does not reduce the complaints, thus questioning the effectiveness of hysteroscopic removal of these structures

Seroepidemiological study on the spread of SARS-CoV-2 in populations in especially affected areas in Germany – Study protocol of the CORONA-MONITORING lokal study

At a regional and local level, the COVID-19 pandemic has not spread out uniformly and some German municipalities have been particularly affected. The seroepidemiological data from these areas helps estimate the proportion of the population that has been infected with SARS-CoV-2 (seroprevalence), as well as the number of undetected infections and asymptomatic cases. In four municipalities which were especially affected, 2,000 participants will be tested for an active SARS-CoV-2 infection (oropharyngeal swab) or a past infection (blood specimen IgG antibody test). Participants will also be asked to fill out a short written questionnaire at study centres and complete a follow-up questionnaire either online or by telephone, including information on issues such as possible exposure, susceptability, symptoms and medical history. The CORONA-MONITORING lokal study will allow to determine the proportion of the population with SARS-CoV-2 antibodies in four particularly affected locations. This study will increase the accuracy of estimates regarding the scope of the epidemic, help determine risk and protective factors for an infection and therefore also identify especially exposed groups and, as such, it will be crucial towards planning of prevention measures

Seroepidemiologische Studie zur Verbreitung von SARS-CoV-2 in der Bevölkerung an besonders betroffenen Orten in Deutschland – Studienprotokoll von CORONA-MONITORING lokal

Die COVID-19-Epidemie ist in Deutschland regional und lokal unterschiedlich ausgeprägt und eine Reihe von Gemeinden ist überproportional stark davon betroffen. Seroepidemiologische Informationen aus besonders betroffenen Gebieten können helfen, auch für andere Regionen den Bevölkerungsanteil mit durchgemachter SARS-CoV-2-Infektion (Seroprävalenz) sowie den Dunkelzifferanteil und den Anteil asymptomatischer Verläufe abzuschätzen. In vier besonders betroffenen Gemeinden werden jeweils 2.000 Teilnehmende in einem temporären Studienzentrum mit Untersuchungsbussen oder während eines Hausbesuchs durch einen Rachenabstrich auf eine aktive SARS-CoV-2- Infektion und im Rahmen einer Blutentnahme auf SARS-CoV-2-IgG-Antikörper untersucht. Zudem werden im Rahmen eines schriftlichen Kurzfragebogens im Untersuchungszentrum und einer wahlweise webbasierten oder telefonischen Nachbefragung weitere Informationen zu verschiedenen Themen, wie mögliche Expositionen, Suszeptibilität (Empfänglichkeit), Symptomatik und Krankheitsgeschichte erhoben. Durch die Studie CORONA-MONITORING lokal können Aussagen zum Bevölkerungsanteil mit Antikörpern gegen SARSCoV- 2 an vier besonders betroffenen Orten getroffen werden. So kann das tatsächliche Ausmaß der Epidemie besser abgeschätzt, Risiko- und Schutzfaktoren für eine Infektion ermittelt und somit auch besonders exponierte Gruppen identifiziert werden, was für die Planung von Präventionsmaßnahmen essenziell ist