Reconstructing terrestrial nutrient cycling using stable nitrogen isotopes in wood

Although recent anthropogenic effects on the global nitrogen (N) cycle have been significant, the consequences of increased anthropogenic N on terrestrial ecosystems are unclear. Studies of the impact of increased reactive N on forest ecosystems—impacts on hydrologic and gaseous loss pathways, retention capacity, and even net primary productivity— have been particularly limited by a lack of long-term baseline biogeochemical data. Stable nitrogen isotope analysis (ratio of ¹⁵N to ¹⁴N, termed δ¹⁵N) of wood chronologies offers the potential to address changes in ecosystem N cycling on millennial timescales and across broad geographic regions. Currently, nearly 50 studies have been published utilizing wood δ¹⁵N records; however, there are significant differences in study design and data interpretation. Here, we identify four categories of wood δ¹⁵N studies, summarize the common themes and primary findings of each category, identify gaps in the spatial and temporal scope of current wood δ¹⁵N chronologies, and synthesize methodological frameworks for future research by presenting eight suggestions for common methodological approaches and enhanced integration across studies. Wood δ¹⁵N records have the potential to provide valuable information for interpreting modern biogeochemical cycling. This review serves to advance the utility of this technique for long-term biogeochemical reconstructions

A degenerate primer MOB typing (DPMT) method to classify gamma-proteobacterial plasmids in clinical and environmental settings

Transmissible plasmids are responsible for the spread of genetic determinants, such as antibiotic resistance or virulence traits, causing a large ecological and epidemiological impact. Transmissible plasmids, either conjugative or mobilizable, have in common the presence of a relaxase gene. Relaxases were previously classified in six protein families according to their phylogeny. Degenerate primers hybridizing to coding sequences of conserved amino acid motifs were designed to amplify related relaxase genes from γ-Proteobacterial plasmids. Specificity and sensitivity of a selected set of 19 primer pairs were first tested using a collection of 33 reference relaxases, representing the diversity of γ-Proteobacterial plasmids. The validated set was then applied to the analysis of two plasmid collections obtained from clinical isolates. The relaxase screening method, which we call "Degenerate Primer MOB Typing" or DPMT, detected not only most known Inc/Rep groups, but also a plethora of plasmids not previously assigned to any Inc group or Rep-type

Optimizing convolutional neural networks architecture using a modified particle swarm optimization for image classification

International audienceAlthough Convolutional Neural Networks (CNNs) have been shown to be highly effective in image classificationtasks, designing their architecture to achieve optimal results is often challenging. This process is time consuming, requires significant effort and expertise, and is complicated by the large number of hyperparameters. Toaddress this problem, in this work we propose an approach that reduces human intervention and automaticallygenerates the best CNN design. Our approach uses a variant of Particle Swarm Optimization (PSO), calledParticle Swarm Optimization without Velocity (PSWV), to speed up convergence and reduce the numberof iterations required to determine the optimal CNN hyperparameters. We developed a novel strategy todetermine the updated position of each particle using a linear combination of the best position of the particleand the best position of the swarm without relying on the velocity equation. Our algorithm harnesses thepower of the variable-length encoding strategy to represent particles within the population, thereby providingswift convergence towards the best architecture. We evaluate our proposed algorithm against several recentalgorithms in the literature by using nine benchmark datasets for classification tasks and comparing it to 27other algorithms, including state-of-the-art ones. Our experimental results show that our proposed method,pswvCNN, is able to quickly find effective CNN architectures that provide comparable performance to the bestcurrently available designs, indicating its significant potential

Molecular epidemiology of extended-spectrum beta-lactamase-producing Klebsiella pneumoniae strains in a university hospital in Tunis, Tunisia, 1999-2005.

International audienceDuring a period of 6 years and 5 months (January 1999 to May 2005), 103 extended-spectrum beta-lactamase (ESBL)-producing Klebsiella pneumoniae isolates, each from an individual patient or site, were collected at Mongi Slim University Hospital Centre, Tunis, Tunisia. The objectives of our work were the characterization of the bla genes encoding ESBLs, the investigation of clonal diversity of strains, and identification of the transmission modes of the resistance genes. We carried out detection by PCR and sequencing of the bla(SHV), bla(CTX-M) and bla(TEM) genes, transferability studies, plasmid replicon typing, and analysis by multilocus sequence typing (MLST) on selected isolates. Forty-seven isolates were found to be producers of CTX-M-type ESBLs, of which 43 were CTX-M-15, two CTX-M-14 and two CTX-M-27. Fifty-eight isolates were producers of SHV-12, and three were producers of SHV-2a. More than one ESBL was detected in seven isolates, as five produced both CTX-M-15 and SHV-12, and two produced both CTX-M-27 and SHV-12. By a PCR-based replicon typing method, the plasmids carrying the bla(SHV-2a) or bla(CTX-M-15) genes were assigned to IncFII or, more rarely, to IncL/M types. Of 12 plasmids carrying the bla(SHV-12) gene, only one could be typed: it was positive for the HI2 replicon. The MLST results showed large genetic background diversity in the SHV-12-producing isolates and dissemination of specific clones of the CTX-M-15-producing isolates within the same ward and among wards, and suggested endemicity with horizontal dissemination of the bla(CTX-M-15) and the bla(SHV-12) genes

Clonal lineages detected amongst tetracyclineresistant meticillin-resistant Staphylococcus aureus isolates of a Tunisian hospital, with detection of lineage ST398

Tetracycline resistance has been postulated as a potential phenotypic marker of livestockassociated lineage ST398 amongst meticillin-resistant Staphylococcus aureus (MRSA) clinical isolates in some European hospitals. The objective of this study was to determine if this marker could also be applied to Maghrebian countries. In total, 99 MRSA isolates were collected in a Tunisian hospital during January 2011October 2012, and 24 tetracycline-resistant MRSA isolates of this collection were characterized. All isolates were tested for antimicrobial resistance phenotypes and genotypes, molecular typing, and virulence genes. Multilocus sequence typing showed that the majority of the isolates (19/24) belonged to clonal complex CC8 (ST247, n512 isolates; ST239, n56isolates; ST241, n51 isolate). The remaining isolates belonged to CC398 (ST398, n51 isolate), CC5 (ST5 and ST641, n52 isolates), and CC80 (ST728, n52 isolates). Spa typing discriminated MRSA in eight spa types: t052 (n512 isolates), t037 (n55 isolates), t044 (n52 isolates), and t899, t129, t311, t1744 and the new t14712 (n51 isolate each). Three agr groups were found amongst the studied isolates: agr group I (n520 isolates), agr group II (n52) and agr group III (n52 isolates). We report the detection of one MRSA ST398t899 isolate in the nasal sample of a farmer patient in Tunisia, representing the first report of ST398 in humans in Africa. Tetracycline resistance seems not to be a good phenotypic marker for MRSA ST398 strains in Tunisia, where CC8 was the most prevalent lineage. Continuous efforts to understand the changing epidemiology of this micro-organism are necessary not only for appropriate antimicrobial treatment and effective infection control, but also to monitor its evolution. © 2015 The Authors