A Highly Contiguous Genome Assembly of Arthrinium puccinoides

The phylogenetic relationship of the Arthrinium genus has changed throughout the years. For many years, the Arthrinium genus included the Apiospora genus as well. New evidence has now showed that these two genera in fact are phylogenetically different and belong to two different clades. Here, we present the first genome draft within the Arthrinium genus. This genome was sequenced using the MinION platform from Oxford Nanopore Technologies and the assembly was contiguous. The assembly comprises ten contigs totaling 39.8 Mb with an N50 length of 7.9. In the assembly, 11,602 genes were predicted whereof 10,784 were functionally annotated. A total of 37 rRNA genes were observed in the assembly and repeat elements spanning 7.39% of the genome were found. A total of 99 secondary metabolite gene clusters were predicted, showing a high potential of novel secondary metabolites. This genome sequence will not only be useful for further investigation of the Arthrinium clade, but also for discovery of novel secondary metabolite compounds that could be of high interest for the food, agricultural, or pharmaceutical industry

Increased mid-infrared supercontinuum bandwidth and average power by tapering large-mode-area chalcogenide photonic crystal fibers

The trade-off between the spectral bandwidth and average output power from chalcogenide fiber-based mid-infrared supercontinuum sources is one of the major challenges towards practical application of the technology. In this paper we address this challenge through tapering of large-mode-area chalcogenide photonic crystal fibers. Compared to previously reported step-index fiber tapers the photonic crystal fiber structure ensures single-mode propagation, which improves the beam quality and reduces losses in the taper due to higher-order mode stripping. By pumping the tapered fibers at 4 mu m using a MHz optical parametric generation source, and choosing an appropriate length of the untapered fiber segments, the output could be tailored for either the broadest bandwidth from 1 to 11.5 mu m with 35.4 mW average output power, or the highest output power of 57.3 mW covering a spectrum from 1 to 8 mu m. (C) 2017 Optical Society of Americ

Toxoplasma gondii seroprevalence in extensively farmed wild boars (Sus scrofa) in Denmark

Toxoplasma gondii is a zoonotic parasite of worldwide importance. In this study, we estimated T. gondii seroprevalence in extensively farmed wild boars in Denmark, where little is known about T. gondii in animal hosts. Our study focused on wild boars because they are considered good indicator species for the presence of T. gondii, and wild boar meat is used for human consumption. Serum samples from 101 wild boars collected in 2016-2018 from five different locations from the continental part of Denmark, Jutland, were screened for anti-T. gondii antibodies. The samples were analysed using a commercial indirect enzyme-linked immunosorbent assay (ELISA). Samples from 28 (27.7%) of the 101 wild boars tested positive with the ELISA. The odds for a wild boar to test seropositive were higher if it was sampled during the hunting season 2017-2018 than during 2016-2017 and if it was reported to be at least 1year old than if it was younger (logistic regression model with the two variables: odds ratios 17.5 and 3.9, respectively). A substantial proportion of the investigated extensively farmed wild boars had been exposed to T. gondii. Moreover, the parasite appeared widespread, at least in the continental part of Denmark, Jutland, as seropositive wild boars were found from all five sampled locations. Assuming seropositivity indicates hosting viable parasites, consumption of undercooked wild boar meat from Denmark is a potential source of T. gondii infections to other hosts, including humans.Peer reviewe

Health systems in the Republic of Congo: challenges and opportunities for implementing tuberculosis and HIV collaborative service, research, and training activities

The Republic of Congo is on the World Health Organization (WHO) list of `high burden' countries for tuberculosis (TB) and HIV. TB is the leading cause of death among HIV-infected patients in the Republic of Congo. In this viewpoint, the available data on TB and HIV in the Republic of Congo are reviewed, and the gaps and bottlenecks that the National TB Control Program (NTCP) faces are discussed. Furthermore, priority requirements for developing and implementing TB and HIV collaborative service activities are identified. HIV and TB control programs operate as distinct entities with separate case management plans. The implementation of collaborative TB/HIV activities to evaluate and monitor the management of TB/HIV co-infected individuals remains inefficient in most regions, and these activities are sometimes non-existent. This reveals major challenges that require definition in order to improve the delivery of healthcare. The NTCP lacks adequate resources for optimal implementation of control measures of TB and HIV compliance and outcomes. The importance of aligning and integrating TB and HIV treatment services (including follow-up) and adherence support services through coordinated and collaborative efforts between individual TB and HIV programs is discussed. Aligning and integrating TB and HIV treatment services through coordinated and collaborative efforts between individual TB and HIV programs is required. However, the WHO recommendations are generic, and health services in the Republic of Congo need to tailor their TB and HIV programs according to the availability of resources and operational feasibility. This will also open opportunities for synergizing collaborative TB/HIV research and training activities, which should be prioritized by the donors supporting the TB/HIV programs. (C) 2016 The Author(s). Published by Elsevier Ltd on behalf of International Society for Infectious Diseases. This is an open access article under the CC BY-NC-ND license

High molecular weight DNA extraction methods lead to high quality filamentous ascomycete fungal genome assemblies using Oxford Nanopore sequencing

During the last two decades, whole-genome sequencing has revolutionized genetic research in all kingdoms, including fungi. More than 1000 fungal genomes have been submitted to sequence databases, mostly obtained through second generation short-read DNA sequencing. As a result, highly fragmented genome drafts have typically been obtained. However, with the emergence of third generation long-read DNA sequencing, the assembly challenge can be overcome and highly contiguous assemblies obtained. Such attractive results, however, are extremely dependent on the ability to extract highly purified high molecular weight (HMW) DNA. Extraction of such DNA is currently a significant challenge for all species with cell walls, not least fungi. In this study, four isolates of filamentous ascomycetes (Apiospora pterospermum, Aspergillus sp. (subgen. Cremei), Aspergillus westerdijkiae, and Penicillium aurantiogriseum) were used to develop extraction and purification methods that result in HMW DNA suitable for third generation sequencing. We have tested and propose two straightforward extraction methods based on treatment with either a commercial kit or traditional phenol-chloroform extraction both in combination with a single commercial purification method that result in high quality HMW DNA from filamentous ascomycetes. Our results demonstrated that using these DNA extraction methods and coverage, above 75 x of our haploid filamentous ascomycete fungal genomes result in complete and contiguous assemblies

Microcircuits of excitatory and inhibitory neurons in layer 2/3 of mouse barrel cortex

Avermann M, Tomm C, Mateo C, Gerstner W, Petersen CC. Microcircuits of excitatory and inhibitory neurons in layer 2/3 of mouse barrel cortex. J Neurophysiol 107: 3116-3134, 2012. First published March 7, 2012; doi:10.1152/jn.00917.2011.-Synaptic interactions between nearby excitatory and inhibitory neurons in the neocortex are thought to play fundamental roles in sensory processing. Here, we have combined optogenetic stimulation, whole cell recordings, and computational modeling to define key functional microcircuits within layer 2/3 of mouse primary somatosensory barrel cortex. In vitro optogenetic stimulation of excitatory layer 2/3 neurons expressing channelrhodopsin-2 evoked a rapid sequence of excitation followed by inhibition. Fast-spiking (FS) GABAergic neurons received large-amplitude, fast-rising depolarizing postsynaptic potentials, often driving action potentials. In contrast, the same optogenetic stimulus evoked small-amplitude, subthreshold postsynaptic potentials in excitatory and non-fast-spiking (NFS) GABAergic neurons. To understand the synaptic mechanisms underlying this network activity, we investigated unitary synaptic connectivity through multiple simultaneous whole cell recordings. FS GABAergic neurons received unitary excitatory postsynaptic potentials with higher probability, larger amplitudes, and faster kinetics compared with NFS GABAergic neurons and other excitatory neurons. Both FS and NFS GABAergic neurons evoked robust inhibition on postsynaptic layer 2/3 neurons. A simple computational model based on the experimentally determined electrophysiological properties of the different classes of layer 2/3 neurons and their unitary synaptic connectivity accounted for key aspects of the network activity evoked by optogenetic stimulation, including the strong recruitment of FS GABAergic neurons acting to suppress firing of excitatory neurons. We conclude that FS GABAergic neurons play an important role in neocortical microcircuit function through their strong local synaptic connectivity, which might contribute to driving sparse coding in excitatory layer 2/3 neurons of mouse barrel cortex in vivo

Toxoplasma gondii seroprevalence in extensively farmed wild boars (Sus scrofa) in Denmark

Abstract Toxoplasma gondii is a zoonotic parasite of worldwide importance. In this study, we estimated T. gondii seroprevalence in extensively farmed wild boars in Denmark, where little is known about T. gondii in animal hosts. Our study focused on wild boars because they are considered good indicator species for the presence of T. gondii, and wild boar meat is used for human consumption. Serum samples from 101 wild boars collected in 2016–2018 from five different locations from the continental part of Denmark, Jutland, were screened for anti-T. gondii antibodies. The samples were analysed using a commercial indirect enzyme-linked immunosorbent assay (ELISA). Samples from 28 (27.7%) of the 101 wild boars tested positive with the ELISA. The odds for a wild boar to test seropositive were higher if it was sampled during the hunting season 2017–2018 than during 2016–2017 and if it was reported to be at least 1 year old than if it was younger (logistic regression model with the two variables: odds ratios 17.5 and 3.9, respectively). A substantial proportion of the investigated extensively farmed wild boars had been exposed to T. gondii. Moreover, the parasite appeared widespread, at least in the continental part of Denmark, Jutland, as seropositive wild boars were found from all five sampled locations. Assuming seropositivity indicates hosting viable parasites, consumption of undercooked wild boar meat from Denmark is a potential source of T. gondii infections to other hosts, including humans