Decadal-centennial scale monsoon variations in the Arabian Sea during the Early Holocene

An essential prerequisite for the prediction of future climate change due to anthropogenic input is an understanding of the natural processes that control Earth's climate on timescales comparable to human-lifespan. The Early Holocene period was chosen to study the natural climate variability in a warm interval when solar insolation was at its maximum. The monsoonal system of the Tropics is highly sensitive to seasonal variations in solar insolation, and consequently marine sediments from the region are a potential monitor of past climate change. Here we show that during the Early Holocene period rapid

Cold hardening protects cereals from oxidative stress and necrotrophic fungal pathogenesis

The effects of cold hardening of cereals on their cross-tolerance to treatments leading to oxidative stress were investigated. Long-term exposure to low non-freezing temperatures provided partial protection to wheat and barley plants from the damage caused by paraquat and hydrogen peroxide treatments. It also conferred resistance in two barley cultivars to the necrotic symptoms and growth of the fungal phytopathogen Pyrenophora teres f. teres . Pathogen-induced oxidative burst was also reduced in cold hardened plants. The possible roles of host-derived redox factors and other signaling components in the observed forms of cereal cross-tolerance are discussed

Inferring viral quasispecies spectra from 454 pyrosequencing reads

<p>Abstract</p> <p>Background</p> <p>RNA viruses infecting a host usually exist as a set of closely related sequences, referred to as quasispecies. The genomic diversity of viral quasispecies is a subject of great interest, particularly for chronic infections, since it can lead to resistance to existing therapies. High-throughput sequencing is a promising approach to characterizing viral diversity, but unfortunately standard assembly software was originally designed for single genome assembly and cannot be used to simultaneously assemble and estimate the abundance of multiple closely related quasispecies sequences.</p> <p>Results</p> <p>In this paper, we introduce a new <b>Vi</b>ral <b>Sp</b>ectrum <b>A</b>ssembler (ViSpA) method for quasispecies spectrum reconstruction and compare it with the state-of-the-art ShoRAH tool on both simulated and real 454 pyrosequencing shotgun reads from HCV and HIV quasispecies. Experimental results show that ViSpA outperforms ShoRAH on simulated error-free reads, correctly assembling 10 out of 10 quasispecies and 29 sequences out of 40 quasispecies. While ShoRAH has a significant advantage over ViSpA on reads simulated with sequencing errors due to its advanced error correction algorithm, ViSpA is better at assembling the simulated reads after they have been corrected by ShoRAH. ViSpA also outperforms ShoRAH on real 454 reads. Indeed, 7 most frequent sequences reconstructed by ViSpA from a real HCV dataset are viable (do not contain internal stop codons), and the most frequent sequence was within 1% of the actual open reading frame obtained by cloning and Sanger sequencing. In contrast, only one of the sequences reconstructed by ShoRAH is viable. On a real HIV dataset, ShoRAH correctly inferred only 2 quasispecies sequences with at most 4 mismatches whereas ViSpA correctly reconstructed 5 quasispecies with at most 2 mismatches, and 2 out of 5 sequences were inferred without any mismatches. ViSpA source code is available at <url>http://alla.cs.gsu.edu/~software/VISPA/vispa.html</url>.</p> <p>Conclusions</p> <p>ViSpA enables accurate viral quasispecies spectrum reconstruction from 454 pyrosequencing reads. We are currently exploring extensions applicable to the analysis of high-throughput sequencing data from bacterial metagenomic samples and ecological samples of eukaryote populations.</p

LICSTER -- A Low-cost ICS Security Testbed for Education and Research

Unnoticed by most people, Industrial Control Systems (ICSs) control entire productions and critical infrastructures such as water distribution, smart grid and automotive manufacturing. Due to the ongoing digitalization, these systems are becoming more and more connected in order to enable remote control and monitoring. However, this shift bears significant risks, namely a larger attack surface, which can be exploited by attackers. In order to make these systems more secure, it takes research, which is, however, difficult to conduct on productive systems, since these often have to operate twenty-four-seven. Testbeds are mostly very expensive or based on simulation with no real-world physical process. In this paper, we introduce LICSTER, an open-source low-cost ICS testbed, which enables researchers and students to get hands-on experience with industrial security for about 500 Euro. We provide all necessary material to quickly start ICS hacking, with the focus on low-cost and open-source for education and research

Operons

Operons (clusters of co-regulated genes with related functions) are common features of bacterial genomes. More recently, functional gene clustering has been reported in eukaryotes, from yeasts to filamentous fungi, plants, and animals. Gene clusters can consist of paralogous genes that have most likely arisen by gene duplication. However, there are now many examples of eukaryotic gene clusters that contain functionally related but non-homologous genes and that represent functional gene organizations with operon-like features (physical clustering and co-regulation). These include gene clusters for use of different carbon and nitrogen sources in yeasts, for production of antibiotics, toxins, and virulence determinants in filamentous fungi, for production of defense compounds in plants, and for innate and adaptive immunity in animals (the major histocompatibility locus). The aim of this article is to review features of functional gene clusters in prokaryotes and eukaryotes and the significance of clustering for effective function

Mechanical stability of the CMS strip tracker measured with a laser alignment system

Peer reviewe

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2–4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease