Horizontal DNA transfer mechanisms of bacteria as weapons of intragenomic conflict

Horizontal DNA transfer (HDT) is a pervasive mechanism of diversification in many microbial species, but its primary evolutionary role remains controversial. Much recent research has emphasised the adaptive benefit of acquiring novel DNA, but here we argue instead that intragenomic conflict provides a coherent framework for understanding the evolutionary origins of HDT. To test this hypothesis, we developed a mathematical model of a clonally descended bacterial population undergoing HDT through transmission of mobile genetic elements (MGEs) and genetic transformation. Including the known bias of transformation toward the acquisition of shorter alleles into the model suggested it could be an effective means of counteracting the spread of MGEs. Both constitutive and transient competence for transformation were found to provide an effective defence against parasitic MGEs; transient competence could also be effective at permitting the selective spread of MGEs conferring a benefit on their host bacterium. The coordination of transient competence with cell-cell killing, observed in multiple species, was found to result in synergistic blocking of MGE transmission through releasing genomic DNA for homologous recombination while simultaneously reducing horizontal MGE spread by lowering the local cell density. To evaluate the feasibility of the functions suggested by the modelling analysis, we analysed genomic data from longitudinal sampling of individuals carrying Streptococcus pneumoniae. This revealed the frequent within-host coexistence of clonally descended cells that differed in their MGE infection status, a necessary condition for the proposed mechanism to operate. Additionally, we found multiple examples of MGEs inhibiting transformation through integrative disruption of genes encoding the competence machinery across many species, providing evidence of an ongoing "arms race." Reduced rates of transformation have also been observed in cells infected by MGEs that reduce the concentration of extracellular DNA through secretion of DNases. Simulations predicted that either mechanism of limiting transformation would benefit individual MGEs, but also that this tactic's effectiveness was limited by competition with other MGEs coinfecting the same cell. A further observed behaviour we hypothesised to reduce elimination by transformation was MGE activation when cells become competent. Our model predicted that this response was effective at counteracting transformation independently of competing MGEs. Therefore, this framework is able to explain both common properties of MGEs, and the seemingly paradoxical bacterial behaviours of transformation and cell-cell killing within clonally related populations, as the consequences of intragenomic conflict between self-replicating chromosomes and parasitic MGEs. The antagonistic nature of the different mechanisms of HDT over short timescales means their contribution to bacterial evolution is likely to be substantially greater than previously appreciated

Évaluation des concentrations des sédiments en suspension en aval de deux bassins de sédimentation situés dans deux tourbières exploitées au Nouveau-Brunswick.

La récolte de la tourbe est une industrie en pleine croissance au Canada. Elle est également pratiquée dans plusieurs pays nordiques entre autre pour répondre à la demande dans le domaine de l’horticulture. Toutefois, la récolte de tourbe peut avoir des effets négatifs sur le milieu environnant tels qu’une charge sédimentaire accrue associée à l'eau de drainage provenant des tourbières exploitées qui se déverse dans les cours d’eau et les rivières en aval de la zone récoltée. L'objectif du présent projet est de mener une étude comparative sur l'efficacité des différentes méthodes d'atténuation de la charge sédimentaire produite par les tourbières exploitées et de tester une approche visant à améliorer l'efficacité des bassins de sédimentation. Deux différentes tourbières (Hardwood et Rogersville) au Nouveau-Brunswick, Canada, ont été étudiées, toutes deux exploitées par Premier Horticulture. Un premier objectif spécifique du présent projet était de déterminer si une corrélation existait entre le débit et la concentration de sédiments en suspension (CSS) et entre les précipitations et les CSS pour les deux tourbières. Les autres objectifs consistaient à déterminer si la charge sédimentaire et l'efficacité du bassin de sédimentation était influencée par les activités d'exploitation ou d’entretien. En outre, un bassin de sédimentation a été modifié durant la présente étude et des épis ont été installés afin de vérifier si l’ajout d’une telle structure pouvait améliorer l'efficacité du bassin de sédimentation. Enfin, les données sur les types et la taille des sédiments déposés dans la rivière en aval des bassins de sédimentation ainsi que la teneur en matière organique de ces sédiments ont été recueillies et analysées. La tourbière Hardwood a un bassin de sédimentation dont la dimension est en accord avec les lignes directrices du Nouveau-Brunswick. Trois stations de suivi ont été installées dans la rivière Portage, qui reçoit les eaux de drainage, pendant la période sans glace en 2007 et 2008. La station 1 était située à 2km en aval de la tourbière exploitée, tandis que la station 2 était située à 10 m en aval de la confluence de la rivière East Branch Portage et d’un chenal (dépression) formé par les eaux de drainage de la tourbière exploitée. La station C3 est située à environ 600 m en amont de la station C2 et de toutes les activités opérationnelles durant cette présente étude. Les données ont été recueillies sur ces sites du 11 mai au 9 novembre 2007 et du 28 mai au 1er octobre 2008. La tourbière de Rogersville, un site actif avec un réseau de drainage à grande échelle, possède un bassin de sédimentation de taille qui ne correspond pas aux lignes directrices du Nouveau-Brunswick. Le bassin est situé à environ 78 m en aval de la zone de récolte de tourbe. Sa longueur, de 170 m ainsi que la profondeur de 0.5 m ne correspondent pas aux normes recommandées au Nouveau-Brunswick. Le suivi des sédiments à Rogersville, qui a eu lieu du 27 juin au 25 novembre en 2008 et du 7 mai au 9 décembre en 2009, a été l'une des premières études à mesurer les CSS simultanément à l’entrée et à la sortie du bassin de sédimentation. Les CSS ont été mesurées également dans le cours d’eau récepteur, à 1,16 km en aval du bassin de sédimentation. Des épis ont été installés dans le bassin de sédimentation à la mi-octobre en 2008 pour déterminer si ces structures pouvaient améliorer l'efficacité du bassin en ralentissant l’écoulement. Ces épis sont restés en place pendant le reste de 2008 et tout au long de la période d'étude en 2009 et n'ont jamais été enlevés. Pour le suivi de la sédimentation en aval des bassins, cinq sites ont été équipés de quatre trappes à sédiments chacun pour la tourbière Hardwood et ce durant les deux années de suivi. Quatre sites, avec 3 trappes à sédiments chacun, ont été mis en place pour la tourbière de Rogersville durant la période d’étude. À la tourbière Hardwood, un site de suivi de la sédimentation a été placé dans une zone tampon qui est entre le bassin de sédimentation et la rivière. Dans les deux tourbières, il a été constaté que les CSS n'étaient ni significativement corrélées avec la précipitation, ni avec les débits. Cependant, des séries chronologiques des CSS, débits et des précipitations ont montré que certains niveaux élevés des CSS ont été causés par des événements importants des débits et/ou précipitations. À la tourbière de Rogersville, il a été conclu que les mesures négatives de l’efficacité du bassin de sédimentation ont été associées à de fortes précipitations, mais seulement une très faible corrélation existait entre les précipitations et l'efficacité du bassin. Les activités de nettoyage du bassin de sédimentation ont eu une influence assez importante sur les niveaux des CSS, mais l’entretien des bassins n'a pas été suffisant pour assurer l’efficacité optimale du bassin de sédimentation. Dans les deux tourbières, la norme néo-brunswickoise des CSS de 25mg/L a été dépassée à chaque station et à chaque année. À la tourbière Hardwood, la station la plus affectée a été la station 2, située immédiatement en aval de la tourbière. La norme y a été dépassée 47% du temps en 2007 et 52% du temps en 2008. À Rogersville, les plus faibles taux de dépassements de la norme ont été trouvés à la station 1 avec un taux de dépassement de 64% du temps en 2008 et 62% du temps en 2009. À Rogersville, il n’a pas été possible de conclure que les épis ont contribué à améliorer l'efficacité du bassin de sédimentation. Une fois installés, les épis n'ont jamais été nettoyés. Une meilleure efficacité du bassin aurait pu éventuellement avoir été enregistrée si les épis avaient été correctement entretenus. Le faible volume du bassin de sédimentation et le fait qu’il ne corresponde pas aux lignes directrices du Nouveau-Brunswick ont également été des facteurs contribuant à la faible performance des épis. Le sable était le type de sédiment dominant déposé en aval des tourbières exploitée (Hardwood et Rogersville) durant les deux années, avec des quantités croissantes trouvées dans les sites les plus en aval. En outre, le pourcentage du contenu organique pour les sédiments inférieurs à 2 mm a été plus élevé que le pourcentage du contenu organique pour les sédiments supérieurs à 2 mm dans les deux tourbières pendant les deux années. À la tourbière Hardwood, le contenu organique était plus important dans les sédiments déposés dans le site 5 que sur les sites moins affectés de 1 à 4. Le contenu organique pour le site 5, pour les sédiments de tailles inférieures à 2 mm en 2007, a été significativement différent de celui des autres sites. À Rogersville, le contenu organique des sédiments inférieurs à 2 mm en 2008 a diminué progressivement de l’amont vers l’aval (sites 4 à 1), mais aucune différence significative n'a été trouvée entre les sites. En 2009, le site 2 a eu la plus haute valeur pour le contenu organique des sédiments inférieurs à 2 mm et le site 1 a le contenu organique le moins élevé.Peat harvesting is a growing industry in Canada. Peat harvesting is also carried out in several Nordic countries to meet the demand for horticultural grade peat moss. However, harvesting has some undesirable side effects such as drainage water containing peat sediment that flows into streams and rivers downstream of the harvested area. These sediments have been shown to negatively affect the natural environment. The aim of the project is to conduct a comparative study of the effectiveness of different methods of attenuation of sediment load produced by harvested peat bogs, with a special emphasis on the effectiveness of sedimentation ponds. Two different peat bogs, both operated by Premier Horticulture, in New Brunswick, Canada were studied for the current project; the Hardwood and Rogersville peat bogs. One objective of the study was to investigate if a relationship existed between discharge and suspended sediment concentration (SSC) and between rainfall and SSC on the East Branch Portage River and at the Rogersville peat bog. Other objectives were to determine if relationships existed between the efficiency of the sedimentation pond and harvesting activities or maintenance. In addition, one pond was modified during the study and baffles were added to verify if such structures would increase pond efficiency. Finally, data about the type and size of sediment deposited in the rivers downstream of the sedimentation ponds as well as the organic content of those deposits were gathered and analyzed. The Hardwood peatland has a sedimentation pond which meets the New Brunswick design guidelines. Three stations were monitored during the ice-free period of 2007 and 2008. Stations 1 and 2 were located respectively 2 km and 200 m downstream of the harvested peatland and Station 3 was located approximately 600 m upstream of all operational activities. Data were gathered at these sites from May 11th to November 9th in 2007 and from May 28th to October 1st in 2008. The Rogersville peatland, a well established and active harvested site with extensive drainage, had a sedimentation pond size that did not correspond to New Brunswick standards. The pond is located approximately 78 m downstream of the peat production area. Its length of 170 m was much higher than the recommended standard. This study, which took place from June 27th to November 25th in 2008 and from May 7th to December 9th in 2009, was one of the first to measure SSC at both the inflow and outflow of the sedimentation pond. SSC was also measured at Station 1 at a point approximately 1.16 km downstream of the sedimentation pond. At the Rogersville bog, baffles were installed in mid-October 2008 in the sedimentation pond to determine if they would improve the efficiency of the pond. These baffles remained in place for the remainder of 2008 and throughout the study period in 2009 and were never removed. Five sites with four sediment traps each were established at Hardwood in both years and four sites with three sediment traps each were set up at Rogersville in both years. At each peat bog, site 1 was located the furthest downstream of the sedimentation pond with each subsequent site moving further upstream. At Portage, site 5 was located in the buffer zone between the sedimentation pond and river, in an area close to harvesting activities. In both study areas, it was found that SSC levels were neither significantly correlated with precipitation nor discharge, although time series of SSC, discharge and rainfall suggested that some of the high SSC events were triggered by high discharge and/or precipitation. At Rogersville, it was found that negative pond efficiency measurements were triggered by heavy rainfall, but only a very weak correlation existed between rain and pond efficiency. Pond cleaning activities, however, had an important influence on SSC levels but cleaning on its own was not enough to ensure optimal sedimentation pond efficiency. Although pond cleaning did eventually decrease SSC levels at both the Rogersville and Hardwood settling ponds, pond maintenance can induce an increase in SSC for a period of up to one month. At both Rogersville and Hardwood, the New Brunswick SSC maximum threshold of 25mg/L was exceeded at each station in each year. At Hardwood, the most impacted station was Station 2, which exceeded the threshold 47% of the time in 2007 and 52% of the time in 2008. At Rogersville, lower exceedances were found at Station 1 with the threshold being exceeded 64% of the time in 2008 and 62% of the time in 2009. At Rogersville, no conclusive evidence was obtained indicating that the baffles helped to improve the efficiency of the pond. Once installed, the baffles were never cleaned. Better pond efficiency may possibly have been recorded, had the baffles been properly maintained. Small pond volume and the fact that the sedimentation pond did not conform to the New Brunswick guidelines were also likely factors in poor basin performance. Sand was the dominant sediment type deposited downstream of the harvested peat bogs (Hardwood and Rogersville) in both years with increasing quantities found further downstream. As well, the percentage organic matter < 2 mm was higher than the percentage organic content > 2 mm at both bogs in both years. At Hardwood, more organic content was found in the deposited sediment at site 5 than at the less impacted sites 1 through 4. Organic content at site 5, for grain sizes < 2 mm in 2007 was found to be significantly different then sites downstream of the harvested area. At Rogersville, in 2008, organic content < 2mm was found in diminishing quantities from site 4 to 1 but no significant differences were noted between sites. In 2009, for organic content < 2 mm, site 2 had the highest organic content and site 1 had the least. The two sites were found to be significantly different from each other

FUNGSI PENGAWASAN EFEKTIF PADA PELAYANAN PUBLIK MENURUT AL-QUR’AN: Konsep dan Implementasinya di Indonesia

Pelayanan publik yang diselenggarakan pemerintah belum efektif dalam mewujudkan kesejahteraan masyarakat Indonesia sesuai amanat UUD 1945, ditandai masih maraknya kasus penyimpangan prosedur, penyimpangan, penyalahgunaan wewenang, penyelewengan, serta praktek mal-administasi lainnya sebagaimana ditunjukkan fakta pengaduan di Lembaga-lembaga yang kompeten. Untuk tindakan perefentif dan korektif perlu ditegakkannya fungsi pengawasan yang efektif, yang konsep dan implementasinya didasarkan pada nilai-nilai yangdiisayaratkan Al-Qur’an sebagai sumber kebenaran absolut. Karena itu, penelitian ini bertujuan: (1) Memahami ayat-ayat Al-Qur’an tentang arti penting pengawasan, (2) Menemukan konsep yang diisyaratkan Al-Qur’an dalam implementasi fungsi pengawasan yang efektif pada pelayanan publik. Untuk mencapai tujuan dimaksud dilakukan penelitian dengan metode kualitatif berbasis library research, Data primer adalah ayat-ayat Al-Qur’an, dengan mengkaji kitab-kitab Tafsir melalui pendekatan Maudhu’i, dan interview dengan para Ahli Tafsir, Ahli bahasa Arab Al-Qur’an, serta Lembaga-lembaga yang kompeten dalam tugas pengawasan sebagai Narasumber (Prof. Nazaruddin Umar, MA, PhD.; Prof. Dr. KH. Quraish Shihab, MA; Prof. Dr. Aziz Fackrurrozi, MA; Prof. Dr. Rachmat Syafe’i Lc, MA), Pimpinan OMBUDSMAN RI dan Perwakilan Jawa Barat serta Pimpinan BPKP RI. Teknik Analisis dengan prosedur content analysis, langkah-langkah: Data Reduction (Reduksi Data), Data Display (Penyajian Data) serta Conclusion Drawing / Verification. Hasil penelitian dapat disimpulan bahwa: (1) Manusia tidak dapat dipercaya untuk kerja keras dalam bekerja maupun beribadah kepada Allah, karena itu penting ditegakkannya fungsi pengawasan yang konsepnya bersumber dari Al-Qur’an. Makna Pengawasan dalam perspektif ini memiliki dua makna, yaitu: pengawasan melekat yang bersifat Ilahiyah, dan makna pengawasan kolektif bersifat materi dalam bentuk amar maruf nahi munkar. (2) Implementasi fungsi pengawasan pada pelayanan publik diwujudkan melalui tiga pilar, yaitu: (a) Keimanan dan ketaqwaan individu, (b) Kontrol anggota, (c) Penerapan atau supremasi aturan, organisasi ditegakkan dengan aturan main yang jelas dan transparan, dan tidak bertentangan dengan syariah. Didukung oleh perangkat-perangkat: berlaku jujur, amanah, integritas, bil-hikmah, menegakkan etik, bersahabat dengan spiritual, dan pemberian sanksi yang tegas manakala melakukan penyimpanga

Correlation Between Tumor Necrosis Factor Alpha and Proteinuria in Type-2 Diabetic Patients

Introduction: Diabetic Nephropathy (DN) is the single most common cause of end stage renal disease (ESRD) in many countries. Inflammation is a potential factor in the development and progression of DN and recent data indicate that diabetes includes an inflammatory component which may contribute to diabetic complications. Methods: This study was conducted at Ain Shams University Hospital on 95 patients with type-2 diabetes mellitus complicated with retinopathy and fifteen age- and sex-matched healthy volunteers. Diabetic patients were divided into 4 groups according to the degree of proteinuria. Serum tumor necrosis factor-α (TNF-α), urine TNF-α and C-reactive protein (CRP) levels were measured in all subjects. Correlations between these inflammatory parameters and degree of proteinuria, duration of diabetes and degree of glycemic control were examined. Results: Levels of the three inflammatory parameters were significantly higher in diabetic patients when compared to control subjects, and they were positively correlated to urinary protein excretion. There was significant positive correlation between serum and urine TNF-α and duration of diabetes, as well as between serum TNF-α and glycemic control. Serum and urine TNF-α remained as independent predictors of urine protein excretion in diabetic patients with overt proteinuria after forward stepwise multiple regression analysis. Conclusion: Serum and urine TNF-α and CRP levels are significantly elevated in this group of diabetic patients, and correlate positively with severity of proteinuria. This suggests a significant role for TNF-α in the pathogenesis and progression of renal injury in diabetes mellitus. Keywards: Diabetic nephropathy; Proteinuria; Tumor necrosis factor-

Study of hadronic event-shape variables in multijet final states in pp collisions at √s=7 TeV

Peer reviewe

Investigating International Time Trends in the Incidence and Prevalence of Atopic Eczema 1990-2010: A Systematic Review of Epidemiological Studies

The prevalence of atopic eczema has been found to have increased greatly in some parts of the world. Building on a systematic review of global disease trends in asthma, our objective was to study trends in incidence and prevalence of atopic eczema. Disease trends are important for health service planning and for generating hypotheses regarding the aetiology of chronic disorders. We conducted a systematic search for high quality reports of cohort, repeated cross-sectional and routine healthcare database-based studies in seven electronic databases. Studies were required to report on at least two measures of the incidence and/or prevalence of atopic eczema between 1990 and 2010 and needed to use comparable methods at all assessment points. We retrieved 2,464 citations, from which we included 69 reports. Assessing global trends was complicated by the use of a range of outcome measures across studies and possible changes in diagnostic criteria over time. Notwithstanding these difficulties, there was evidence suggesting that the prevalence of atopic eczema was increasing in Africa, eastern Asia, western Europe and parts of northern Europe (i.e. the UK). No clear trends were identified in other regions. There was inadequate study coverage worldwide, particularly for repeated measures of atopic eczema incidence. Further epidemiological work is needed to investigate trends in what is now one of the most common long-term disorders globally. A range of relevant measures of incidence and prevalence, careful use of definitions and description of diagnostic criteria, improved study design, more comprehensive reporting and appropriate interpretation of these data are all essential to ensure that this important field of epidemiological enquiry progresses in a scientifically robust manner

Constraints on parton distribution functions and extraction of the strong coupling constant from the inclusive jet cross section in pp collisions at √s=7 TeV

Peer reviewe

Peste des petits ruminants in large ruminants, camels and unusual hosts

Since its first report in 1942, peste-des-petits-ruminants virus (PPRV) has caused several epidemics in a wide range of susceptible hosts around the world. In the last 30 years, the evidence of natural and experimental infections and virus isolation were reported from novel but unusual hosts such as camel, cattle, buffalo, dogs, Asiatic lion and pigs. In addition, PPRV in a potential vector, biting midges (Culicoides imicola), has been reported. Either presented as clinical and/or subclinical infections, the presence of the virus in an extended range of susceptible hosts highlights the cross-species transmission and supports the hypothesis of an endemic circulation of PPRV among susceptible hosts. However, the potential role of large ruminants, camels and unusual hosts for PPRV epidemiology is still obscure. Therefore, there is a need for molecular and epidemiological investigations of the disease among usual and unusual hosts to achieve the goals of disease control and eradication programmes initiated by national and international organisations, such as the FAO and OIE. This review is the first to summarise the scattered data on PPR in large ruminants, camels and unusual hosts to obtain the global scientific communities' attention for further research on epidemiological aspects, not only in its native hosts, but also in large ruminants, camels and other unusual hosts

High OGT activity is essential for MYC-driven proliferation of prostate cancer cells

O-GlcNAc transferase (OGT) is overexpressed in aggressive prostate cancer. OGT modifies intra-cellular proteins via single sugar conjugation (O-GlcNAcylation) to alter their activity. We recently discovered the first fast-acting OGT inhibitor OSMI-2. Here, we probe the stability and function of the chromatin O-GlcNAc and identify transcription factors that coordinate with OGT to promote proliferation of prostate cancer cells. Methods: Chromatin immunoprecipitation (ChIP) coupled to sequencing (seq), formaldehyde-assisted isolation of regulatory elements, RNA-seq and reverse-phase protein arrays (RPPA) were used to study the importance of OGT for chromatin structure and transcription. Mass spectrometry, western blot, RT-qPCR, cell cycle analysis and viability assays were used to establish the role of OGT for MYC-related processes. Prostate cancer patient data profiled for both mRNA and protein levels were used to validate findings. Results: We show for the first time that OGT inhibition leads to a rapid loss of O-GlcNAc chromatin mark. O-GlcNAc ChIP-seq regions overlap with super-enhancers (SE) and MYC binding sites. OGT inhibition leads to down-regulation of SE-dependent genes. We establish the first O-GlcNAc chromatin consensus motif, which we use as a bait for mass spectrometry. By combining the proteomic data from oligonucleotide enrichment with O-GlcNAc and MYC ChIP-mass spectrometry, we identify host cell factor 1 (HCF-1) as an interaction partner of MYC. Inhibition of OGT disrupts this interaction and compromises MYC's ability to confer androgen-independent proliferation to prostate cancer cells. We show that OGT is required for MYC-mediated stabilization of mitotic proteins, including Cyclin B1, and/or the increased translation of their coding transcripts. This implies that increased expression of mRNA is not always required to achieve increased protein expression and confer aggressive phenotype. Indeed, high expression of Cyclin B1 protein has strong predictive value in prostate cancer patients (p=0.000014) while mRNA does not. Conclusions: OGT promotes SE-dependent gene expression. OGT activity is required for the interaction between MYC and HCF-1 and expression of MYC-regulated mitotic proteins. These features render OGT essential for the androgen-independent, MYC-driven proliferation of prostate cancer cells. Androgen-independency is the major mechanism of prostate cancer progression, and our study identifies OGT as an essential mediator in this process.</p