Pitfalls of haplotype phasing from amplicon-based long-read sequencing

This is the final version. Available on open access from Nature Research via the DOI in this recordThe long-read sequencers from Pacific Bioscience (PacBio) and Oxford Nanopore Technologies (ONT) offer the opportunity to phase mutations multiple kilobases apart directly from sequencing reads. In this study, we used long-range PCR with ONT and PacBio sequencing to phase two variants 9 kb apart in the RET gene. We also re-analysed data from a recent paper which had apparently successfully used ONT to phase clinically important haplotypes at the CYP2D6 and HLA loci. From these analyses, we demonstrate PCR-chimera formation during PCR amplification and reference alignment bias are pitfalls that need to be considered when attempting to phase variants using amplicon-based long-read sequencing technologies. These methodological pitfalls need to be avoided if the opportunities provided by long-read sequencers are to be fully exploited.Wellcome Trus

New genus of the tribe Ceutorhynchini (Coleoptera: Curculionidae) from the late Oligocene of Enspel, southwestern Germany, with a remark on the role of weevils in the ancient food web

The new weevil genus Igneonasus gen. nov. (type species: I. rudolphi sp. nov.) of the tribe Ceutorhynchini (Curculionidae: Conoderinae: Ceutorhynchitae) is described from the late Oligocene of Fossillagerstätte Enspel, Germany. The new genus differs from the similar genus Stenocarus Thomson, 1859 in the anterior margin of the pronotum, which is not raised, a pronotum without tubercles on the sides, and a femur without teeth. This weevil is the largest representative of this supertribe and the first fossil Curculionidae species described from the paleolake Enspel. In this ancient ecosystem, weevils were at least sometimes an important food resource for the cyprinid fish Palaeorutilus enspelensis.</p

Quantitative insights into the cyanobacterial cell economy

© Zavřel et al. Phototrophic microorganisms are promising resources for green biotechnology. Compared to heterotrophic microorganisms, however, the cellular economy of phototrophic growth is still insufficiently understood. We provide a quantitative analysis of light-limited, light-saturated, and light-inhibited growth of the cyanobacterium Synechocystis sp. PCC 6803 using a reproducible cultivation setup. We report key physiological parameters, including growth rate, cell size, and photosynthetic activity over a wide range of light intensities. Intracellular proteins were quantified to monitor proteome allocation as a function of growth rate. Among other physiological acclimations, we identify an upregulation of the translational machinery and downregulation of light harvesting components with increasing light intensity and growth rate. The resulting growth laws are discussed in the context of a coarse-grained model of phototrophic growth and available data obtained by a comprehensive literature search. Our insights into quantitative aspects of cyanobacterial acclimations to different growth rates have implications to understand and optimize photosynthetic productivity

Ammonia Decomposition in the Process Chain for a Renewable Hydrogen Supply

This review article deals with the challenge to identify catalyst materials from literature studies for the ammonia decomposition reaction with potential for application in large-scale industrial processes. On the one hand, the requirements on the catalyst are quite demanding. Of central importance are the conditions for the primary reaction that have to be met by the catalyst. Likewise, the catalytic performance, i.e., an ideally quantitative conversion, and a high lifetime are critical as well as the consideration of requirements on the product properties in terms of pressure or by-products for potential follow-up processes, in this case synthesis gas applications. On the other hand, the evaluation of the multitude of literature studies poses difficulties due to significant varieties in catalytic testing protocols

An Integrative Omics Approach Reveals Involvement of BRCA1 in Hepatic Metastatic Progression of Colorectal Cancer

(1) Background & Aims: The roles of different cells in the tumor microenvironment (TME) are critical to the metastatic process. The phenotypic transformation of the liver cells is one of the most important stages of the hepatic metastasis progression of colorectal cancer (CRC). Our aim was to identify the major molecules (i.e., genes, miRNAs and proteins) involved in this process. (2) Methods: We isolated and performed whole-genome analysis of gene, miRNA, and protein expression in three types of liver cells (Ito cells, Kupffer cells, and liver sinusoidal endothelial cells) from the TME of a murine model of CRC liver metastasis. We selected the statistically significant differentially expressed molecules using the Student’s t-test with Benjamini-Hochberg correction and performed functional statistically-significant enrichment analysis of differentially expressed molecules with hypergeometric distribution using the curated collection of molecular signatures, MSigDB. To build a gene-miRNA-protein network centered in Brca1, we developed a software package (miRDiana) that collects miRNA targets from the union of the TargetScan, MicroCosm, mirTarBase, and miRWalk databases. This was used to search for miRNAs targeting Brca1. We validated the most relevant miRNAs with real-time quantitative PCR. To investigate BRCA1 protein expression, we built tissue microarrays (TMAs) from hepatic metastases of 34 CRC patients. (3) Results: Using integrated omics analyses, we observed that the Brca1 gene is among the twenty transcripts simultaneously up-regulated in all three types of TME liver cells during metastasis. Further analysis revealed that Brca1 is the last BRCA1-associated genome surveillance complex (BASC) gene activated in the TME. We confirmed this finding in human reanalyzing transcriptomics datasets from 184 patients from non-tumor colorectal tissue, primary colorectal tumor and colorectal liver metastasis of the GEO database. We found that the most probable sequence of cell activation during metastasis is Endothelial→Ito→Kupffer. Immunohistochemical analysis of human liver metastases showed the BRCA1 protein was co-localized in Ito, Kupffer, and endothelial cells in 81.8% of early or synchronous metastases. However, in the greater part of the metachronous liver metastases, this protein was not expressed in any of these TME cells. (4) Conclusions: These results suggest a possible role of the co-expression of BRCA1 in Ito, Kupffer, and sinusoidal endothelial cells in the early occurrence of CRC liver metastases, and point to BRCA1 as a potential TME biomarker.D.G. and M.J.A.-B. have been supported by Grants DFG113/18 from Diputación Foral de Gipuzkoa (DFG), Spain, Ministry of Economy and Competitiveness, Spain, MINECO Grant BFU2016-77987-P and Instituto de Salud Carlos III (AC17/00012) Grant co-funded by the European Union (Eracosysmed/H2020 Grant Agreement No. 643271) and European Union (H2020-FETOPEN, Project 899417). D.G., M.J.A.-B. and I.B. have been supported by Grants Health Department of the Basque Government (Spain), RIS3 call, Exp. No. 2020333039 and 2020333001

Genome-wide DNA methylation profiling identifies convergent molecular signatures associated with idiopathic and syndromic autism in post-mortem human brain tissue

Autism spectrum disorder (ASD) encompasses a collection of complex neuropsychiatric disorders characterized by deficits in social functioning, communication and repetitive behaviour. Building on recent studies supporting a role for developmentally moderated regulatory genomic variation in the molecular aetiology of ASD, we quantified genome-wide patterns of DNA methylation in 223 post-mortem tissues samples isolated from three brain regions [prefrontal cortex, temporal cortex and cerebellum (CB)] dissected from 43 ASD patients and 38 non-psychiatric control donors.We identified widespread differences in DNA methylation associated with idiopathic ASD (iASD), with consistent signals in both cortical regions that were distinct to those observed in the CB. Individuals carrying a duplication on chromosome 15q (dup15q), representing a genetically defined subtype of ASD, were characterized by striking differences in DNA methylation across a discrete domain spanning an imprinted gene cluster within the duplicated region. In addition to the dramatic cis-effects on DNA methylation observed in dup15q carriers, we identified convergent methylomic signatures associated with both iASD and dup15q, reflecting the findings from previous studies of gene expression and H3K27ac. Cortical co-methylation network analysis identified a number of co-methylated modules significantly associated with ASD that are enriched for genomic regions annotated to genes involved in the immune system, synaptic signalling and neuronal regulation. Our study represents the first systematic analysis of DNA methylation associated with ASD across multiple brain regions, providing novel evidence for convergent molecular signatures associated with both idiopathic and syndromic autism

Shuffle and Mix: On the Diffusion of Randomness in Threshold Implementations of Keccak

Threshold Implementations are well-known as a provably firstorder secure Boolean masking scheme even in the presence of glitches. A precondition for their security proof is a uniform input distribution at each round function, which may require an injection of fresh randomness or an increase in the number of shares. However, it is unclear whether violating the uniformity assumption causes exploitable leakage in practice. Recently, Daemen undertook a theoretical study of lossy mappings to extend the understanding of uniformity violations. We complement his work by entropy simulations and practical measurements of Keccak’s round function. Our findings shed light on the necessity of mixing operations in addition to bit-permutations in a cipher’s linear layer to propagate randomness between S-boxes and prevent exploitable leakage. Finally, we argue that this result cannot be obtained by current simulation methods, further stressing the continued need for practical leakage measurements

Homeosis in a scorpion supports a telopodal origin of pectines and components of the book lungs

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ARMADILLO: A Multi-purpose Cryptographic Primitive Dedicated to Hardware

This paper describes and analyzes the security of a general-purpose cryptographic function design, with application in RFID tags and sensor networks. Based on these analyzes, we suggest minimum parameter values for the main components of this cryptographic function, called ARMADILLO. With fully serial architecture we obtain that 2 923 GE could perform one compression function computation within 176 clock cycles, consuming 44 μW at 1 MHz clock frequency. This could either authenticate a peer or hash 48 bits, or encrypt 128 bits on RFID tags. A better tradeoff would use 4 030 GE, 77 μW of power and 44 cycles for the same, to hash (resp. encrypt) at a rate of 1.1 Mbps (resp. 2.9 Mbps). As other tradeoffs are proposed, we show that ARMADILLO offers competitive performances for hashing relative to a fair Figure Of Merit (FOM)