Puzzling functions of HSV-1 miRNAs in productive and latent infection

Herpes simplex virus (HSV) is a widespread human pathogen able to cause a broad spectrum of diseases of varying severity. HSV-1, and closely related virus HSV-2, employ a number of functions to evade host defense mechanisms and tailor the cellular environment during their complex life cycle comprised of productive and life-long latent infection. Once the latency is established, the virus can periodically reactivate in response to different stimuli and cause recurrent disease. Despite being one of the most intensively studied viruses, many biological aspects involved in the control of the lytic-latent switch and regulation of viral and host gene expression remained unclear. Discovery of the HSV-encoded miRNAs, a class of small regulatory RNAs, led to the hypothesis that they could have a central role in the establishment and maintenance of latency. HSV-1 and HSV-2 encode many miRNAs, differentially expressed during both phases of infection. The functions of HSV-encoded miRNAs have been experimentally addressed by several laboratories; however, the exact roles remain inconclusive. In this review, we will discuss the function of HSV-encoded miRNAs described to date, in terms of their viral and host targets, and the potential significance of such regulation for viral infection.</p

The Effect of Scaling and Root Planing on the Clinical and Microbiological Parameters of Periodontal Diseases

Postojanje parodontnih patogena u subgingivnoj flori parodontitisa rizik je za napredovanje parodontne bolesti. Zato mikrobiološka dijagnostika ima opravdanu indikaciju u otkrivanju patogena, praćenju uspjeha terapije i ishoda bolesti. Svrha ovoga rada bila je prikazati učinak struganja i poliranja korijena (SRP) na kliničke i mikrobiološke čimbenike u 28 pacijenata s kroničnim i agresivnim parodontitisom. Klinička procjena i mikrobiološko testiranje provedeni su prije mehaničke terapije (SRP) i tri mjeseca nakon terapije. Klinički je utvrđeno postojanje ili nepostojanje bakterijskoga plaka i gingivnoga krvarenja, te je određena dubina sondiranja i gubitak pričvrstka prije struganja i poliranja korijena te tri mjeseca nankon toga.Uzorci subgingivnoga plaka uzeti iz parodontnih džepova analizirani su tehnikom lančane reakcije polimeraze (PCR) na nazočnost sedam bakterijskih patogena. Rezultati kliničkih pokazatelja i čestoća bakterijskih vrsta analizirani su prije i poslije terapije Wilcoxson- testom rangova. Srednja vrijednost dubine sondiranja izrazito se je smanjila, od 3,9 na 3 mm. Gubitak pričvrstka smanjio se je umjereno, i to od 4,1 na 3,8 mm. Srednja vrijednost plaka i gingivnoga krvarenja također su smanjeni nakon terapije. Čestoća subgingivnih patogena u ispitanika bila je sljedeća: samo jedna patogena vrsta nađena je u 28,6% ispitanika, dvije vrste u 46,4% i tri u 14,3% ispitanika. Najčešće zastupljeni ispitivani patogeni bili su: Bacteroides forsythus u 85,7%, Porphyromonas gingivalis, Actinobacillus actinomycetemcomitans (A.a.) i Fusobacterium nucleatum u 32,1% ispitanika. Nakon terapije čestoća patogena umjereno se je smanjila. Ukupni broj ispitivanih patogena smanjio se je u 12 ispitanika i taj nalaz bio je statistički znatan (p=0,001). U 16 ispitanika broj patogena ostao je isti, a nije se povećao ni u jednog ispitanika. Nalazi pokazuju da se struganjem i poliranjem korijena u liječenju parodontitisa djelotvorno postiže kliničko i mikrobioloπko poboljšanje smanjenjem čestoće patogena odgovornih za napredovanje bolesti.The occurence of periodontal pathogens in subgingival flora in periodontitis is a risk for periodontal disease progression. Therefore microbiologic diagnostic procedures are justifiably indicated in the detection of pathogens, monitoring of therapy success and outcome of the disease. The aim of this study was to show the effect of scaling and root planing on clinical and microbiological factors in 28 patients with chronic and aggressive periodontitis. Clinical assessment and microbiological testing were performed prior to, and three months after mechanical therapy. The presence or absence of bacterial plaque, gingival bleeding, pocket depth and attachment loss were assessed before and three months after scaling and root planing. Samples of subgingival plaque taken from periodontal pockets, were analysed by polymerase chain reaction technique for the presence of seven bacterial pathogens. Results of clinical parameters and bacterial prevalence were analysed before and after therapy by Wilcoxon Rank test. The mean pocket depth significantly decreased from 3.9 to 3.0 mm. Clinical attachment level decreased moderately from 4.1 to 3.8 mm. Mean plaque and gingival bleeding values also decreased after therapy. The prevalence of subgingival pathogens in relation to subjects was as follows: only one pathogenic species was found in 28.6%, two were found in 46.4% and three in 14.3% of subjects. The most prevalent pathogens were bacteroides forsythus in 85.7%, Porphyromonas gingivalis in 32.1%, Actinobacillus actinomycetemcomitans and Fusobacterium in 32.1% of subjects. After therapy the prevalence of pathogens decreased moderately. The total number of tested pathogens decreased in 12 subjects and this result was statistically significant. (p=0.001). In 16 subjects the number of pathogens was the same, and did not increase in any of the subjects. The results indicate that the effect of scaling and root planing in the treatment of periodontitis was effective in achieving clinical and microbiological improvement by decreasing the prevalence of pathogens responsible for disease progression

sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression

Since the original publication of sRNAtoolbox in 2015, small RNA research experienced notable advances in different directions. New protocols for small RNA sequencing have become available to address important issues such as adapter ligation bias, PCR amplification artefacts or to include internal controls such as spike-in sequences. New microRNA reference databases were developed with different foci, either prioritizing accuracy (low number of false positives) or completeness (low number of false negatives). Additionally, other small RNA molecules as well asmicroRNA sequence and length variants (isomiRs) have continued to gain importance. Finally, the number of microRNA sequencing studies deposited in GEO nearly triplicated from 2014 (280) to 2018 (764). These developments imply that fast and easy-to-use tools for expression profiling and subsequent downstream analysis of miRNAseq data are essential to many researchers. Key features in this sRNAtoolbox release include addition of all major RNA library preparation protocols to sRNAbench and improvements in sRNAde, a tool that summarizes several aspects of small RNA sequencing studies including the detection of consensus differential expression. A special emphasis was put on the user-friendliness of the tools, for instance sRNAbench now supports parallel launching of several jobs to improve reproducibility and user time efficiency.European Union [765492 to M.H.]; Spanish Government [AGL2017-88702-C2-2-R to M.H., J.L.O.]; Instituto de Salud Carlos III, FEDER funds [PIE16/00045 to J.A.M.]; Chair ‘Doctors Galera-Requena in cancer stem cell research’ to JMA and by the Ministry of Education of Spain [FPU13/05662 to R.L., IFI16/00041 to E.A.]; Strategic Research Area (SFO) program of the Swedish Research Council (to V.R.) through Stockholm University (to B.F.). Funding for open access charge: SpanishGovernment [AGL2017-88702-C2-2-R]

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2

Height and body-mass index trajectories of school-aged children and adolescents from 1985 to 2019 in 200 countries and territories: a pooled analysis of 2181 population-based studies with 65 million participants

Summary Background Comparable global data on health and nutrition of school-aged children and adolescents are scarce. We aimed to estimate age trajectories and time trends in mean height and mean body-mass index (BMI), which measures weight gain beyond what is expected from height gain, for school-aged children and adolescents. Methods For this pooled analysis, we used a database of cardiometabolic risk factors collated by the Non-Communicable Disease Risk Factor Collaboration. We applied a Bayesian hierarchical model to estimate trends from 1985 to 2019 in mean height and mean BMI in 1-year age groups for ages 5–19 years. The model allowed for non-linear changes over time in mean height and mean BMI and for non-linear changes with age of children and adolescents, including periods of rapid growth during adolescence. Findings We pooled data from 2181 population-based studies, with measurements of height and weight in 65 million participants in 200 countries and territories. In 2019, we estimated a difference of 20 cm or higher in mean height of 19-year-old adolescents between countries with the tallest populations (the Netherlands, Montenegro, Estonia, and Bosnia and Herzegovina for boys; and the Netherlands, Montenegro, Denmark, and Iceland for girls) and those with the shortest populations (Timor-Leste, Laos, Solomon Islands, and Papua New Guinea for boys; and Guatemala, Bangladesh, Nepal, and Timor-Leste for girls). In the same year, the difference between the highest mean BMI (in Pacific island countries, Kuwait, Bahrain, The Bahamas, Chile, the USA, and New Zealand for both boys and girls and in South Africa for girls) and lowest mean BMI (in India, Bangladesh, Timor-Leste, Ethiopia, and Chad for boys and girls; and in Japan and Romania for girls) was approximately 9–10 kg/m2. In some countries, children aged 5 years started with healthier height or BMI than the global median and, in some cases, as healthy as the best performing countries, but they became progressively less healthy compared with their comparators as they grew older by not growing as tall (eg, boys in Austria and Barbados, and girls in Belgium and Puerto Rico) or gaining too much weight for their height (eg, girls and boys in Kuwait, Bahrain, Fiji, Jamaica, and Mexico; and girls in South Africa and New Zealand). In other countries, growing children overtook the height of their comparators (eg, Latvia, Czech Republic, Morocco, and Iran) or curbed their weight gain (eg, Italy, France, and Croatia) in late childhood and adolescence. When changes in both height and BMI were considered, girls in South Korea, Vietnam, Saudi Arabia, Turkey, and some central Asian countries (eg, Armenia and Azerbaijan), and boys in central and western Europe (eg, Portugal, Denmark, Poland, and Montenegro) had the healthiest changes in anthropometric status over the past 3·5 decades because, compared with children and adolescents in other countries, they had a much larger gain in height than they did in BMI. The unhealthiest changes—gaining too little height, too much weight for their height compared with children in other countries, or both—occurred in many countries in sub-Saharan Africa, New Zealand, and the USA for boys and girls; in Malaysia and some Pacific island nations for boys; and in Mexico for girls. Interpretation The height and BMI trajectories over age and time of school-aged children and adolescents are highly variable across countries, which indicates heterogeneous nutritional quality and lifelong health advantages and risks

Rising rural body-mass index is the main driver of the global obesity epidemic in adults

Body-mass index (BMI) has increased steadily in most countries in parallel with a rise in the proportion of the population who live in cities(.)(1,2) This has led to a widely reported view that urbanization is one of the most important drivers of the global rise in obesity(3-6). Here we use 2,009 population-based studies, with measurements of height and weight in more than 112 million adults, to report national, regional and global trends in mean BMI segregated by place of residence (a rural or urban area) from 1985 to 2017. We show that, contrary to the dominant paradigm, more than 55% of the global rise in mean BMI from 1985 to 2017-and more than 80% in some low- and middle-income regions-was due to increases in BMI in rural areas. This large contribution stems from the fact that, with the exception of women in sub-Saharan Africa, BMI is increasing at the same rate or faster in rural areas than in cities in low- and middle-income regions. These trends have in turn resulted in a closing-and in some countries reversal-of the gap in BMI between urban and rural areas in low- and middle-income countries, especially for women. In high-income and industrialized countries, we noted a persistently higher rural BMI, especially for women. There is an urgent need for an integrated approach to rural nutrition that enhances financial and physical access to healthy foods, to avoid replacing the rural undernutrition disadvantage in poor countries with a more general malnutrition disadvantage that entails excessive consumption of low-quality calories.Peer reviewe

Heterogeneous contributions of change in population distribution of body mass index to change in obesity and underweight NCD Risk Factor Collaboration (NCD-RisC)

From 1985 to 2016, the prevalence of underweight decreased, and that of obesity and severe obesity increased, in most regions, with significant variation in the magnitude of these changes across regions. We investigated how much change in mean body mass index (BMI) explains changes in the prevalence of underweight, obesity, and severe obesity in different regions using data from 2896 population-based studies with 187 million participants. Changes in the prevalence of underweight and total obesity, and to a lesser extent severe obesity, are largely driven by shifts in the distribution of BMI, with smaller contributions from changes in the shape of the distribution. In East and Southeast Asia and sub-Saharan Africa, the underweight tail of the BMI distribution was left behind as the distribution shifted. There is a need for policies that address all forms of malnutrition by making healthy foods accessible and affordable, while restricting unhealthy foods through fiscal and regulatory restrictions

Plan upravljanja istraživačkim podacima - IP-2020-02-2287

Plan upravljanja istraživačkim podacim

Molekulare Mechanismen der Cytomegaloviren Arten Spezifizierung

Viruses have undergone a coevolution with their hosts, resulting in a specific adaptation to them. Consequently, many viruses have a limited host range. Occasionally, viruses acquire an adaptive mutation, which allows infection and replication in a different species as shown recently for the human immunodeficiency virus and influenza virus. Cross-species infections are responsible for the majority of emerging and re-emerging viral diseases. However, little is known about the mechanisms that restrict viruses to a certain host species, and the factors viruses need to cross the species barrier and replicate in a different host. Cytomegaloviruses are prototypes of the beta-herpesvirus subfamily and are highly species specific. They replicate only in cells of their own or a closely related species. The molecular mechanism underlying their species specificity is poorly understood and was investigated in this study. An initial observation showed that murine cytomegalovirus (MCMV) can replicate in human 293 and 911 cells, but not in any other human cells tested. Both cell lines are transformed with adenoviral E1 genes that encode a transcriptional transactivator (E1A) and two suppressors of apoptosis (E1B-55k and E1B-19k). This has led to the hypothesis that these functions are required for MCMV replication in human cells. Further analysis revealed that normal human cells died rapidly after infection of caspase-9-mediated apoptosis. Apoptosis induced by MCMV can be suppressed by broad-spectrum caspase inhibitors, and virus replication can be rescued, indicating a major role of caspases in this process. Furthermore, over-expression of a mitochondria-localized inhibitor of apoptosis, a Bcl-2-like protein, prevented apoptosis induced by this virus. Human cells resistant to apoptosis allowed also an efficient MCMV replication. The important role of Bcl-2-like proteins for cytomegalovirus cross-species infections was subsequently confirmed by inserting the corresponding genes, and other inhibitors of apoptosis and control genes into the MCMV genome. Only recombinant viruses expressing a Bcl-2-like protein were able to replicate in human cells. A single gene of human cytomegalovirus encoding a mitochondrial inhibitor of apoptosis was sufficient to allow MCMV replication in human cells. Moreover, the same principle facilitated replication of the rat cytomegalovirus in human cells. Thus, induction of apoptosis limits rodent cytomegalovirus cross-species infection.Viren durchliefen eine gemeinsame Evolution mit ihren Wirtsorganismen, die zu einer spezifischen Anpassung der Viren an ihren jeweiligen Wirt führte. Als Folge dessen verfügen viele Viren über ein eng begrenztes Wirtsspektrum. Gelegentlich machen Viren Veränderungen durch, die es ihnen erlauben, einen neuen Wirt zu infizieren und in ihm zu replizieren, wie dies in jüngster Vergangenheit beim humanen Immundefizienz-Virus oder beim Grippevirus geschehen ist. Spezies-übergreifende Infektionen sind für die meisten neuen und wiederauftauchenden Viruserkrankungen verantwortlich. Allerdings ist bisher wenig über die Mechanismen bekannt, die Viren auf einen bestimmten Wirt beschränken, und welche Faktoren Viren zur Überwindung der Spezies-Barriere und zur Vermehrung in einer neuen Wirtsspezies benötigen. Cytomegaloviren sind Prototypen der beta-Herpesvirus Unterfamilie und verfügen über eine ausgeprägte Spezies-Spezifität. Sie vermehren sich nur in Zellen der eigenen oder einer eng verwandten Wirtsspezies. Der molekulare Mechanismus, der dieser Spezies-Spezifität zugrunde liegt, ist noch weitgehend unbekannt und stellt deshalb das Thema dieser Arbeit dar. Initiale Beobachtungen zeigten, dass sich das Maus-Cytomegalovirus (MCMV) ausschließlich in menschlichen 293 und 911 Zellen, aber keiner anderen getesteten menschlichen Zelle vermehren ließ. Diese beiden Zelllinien sind mit Adenovirus E1-Genen transformiert, die den Transkriptions-Transaktivator E1A sowie zwei Apoptose-Inhibitoren (E1B-55k und E1B-19k) kodieren. Daher lag die Hypothese nahe, dass diese Funktionen benötigt werden, um eine MCMV-Replikation in menschlichen Zellen zu ermöglichen. Außerdem konnte gezeigt werden, dass normale menschliche Zellen nach Infektion rapide absterben, und zwar durch eine Caspase-9-vermittelte Apoptose. Die Induktion der Apoptose durch MCMV lässt sich durch Caspase-Inhibitoren unterdrücken, wodurch die virale Replikation wiederhergestellt wird. Dies deutet auf eine Schlüsselfunktion der Caspasen für diesen Prozess hin. Durch Überexpression eines mitochondrialen Apoptose-Inhibitors, d.h. eines Bcl-2-ähnlichen Proteins, in menschlichen Zellen ließ sich die Virus-induzierte Apoptose verhindern. Diese Zellen erlaubten ebenfalls eine effiziente MCMV-Replikation. Die Bedeutung Bcl-2-ähnlicher Proteine für die Spezies-übergreifende Cytomegalovirus-Infektion wurde sowohl durch die Integration korrespondierender Gene, alsauch durch die Integration anderer Inhibitioren der Apoptose oder von Kontroll-Genen in das MCMV Genom bestätigt. Nur rekombinante Viren, die ein Bcl-2-ähnliches Protein kodieren, konnten in menschlichen Zellen vermehrt werden. Ein einziges Gen des humanen Cytomegalovirus, das einen mitochondrialen Apoptose-Inhibitor kodiert, reichte aus, um eine MCMV-Replikation in menschlichen Zellen zu ermöglichen. Zusätzlich konnte gezeigt werden, dass dieselben Prinzipien für eine Replikation des Ratten-Cytomegalovirus in menschlichen Zellen gelten. Zusammenfassend kann festgestellt werden, dass die Induktion der Apoptose eine Spezies-übergreifende Infektion bei den Nagetier-Cytomegaloviren einschränkt