Recombination dynamics of a human Y-chromosomal palindrome:rapid GC-biased gene conversion, multi-kilobase conversion tracts, and rare inversions

The male-specific region of the human Y chromosome (MSY) includes eight large inverted repeats (palindromes) in which arm-to-arm similarity exceeds 99.9%, due to gene conversion activity. Here, we studied one of these palindromes, P6, in order to illuminate the dynamics of the gene conversion process. We genotyped ten paralogous sequence variants (PSVs) within the arms of P6 in 378 Y chromosomes whose evolutionary relationships within the SNP-defined Y phylogeny are known. This allowed the identification of 146 historical gene conversion events involving individual PSVs, occurring at a rate of 2.9-8.4×10(-4) events per generation. A consideration of the nature of nucleotide change and the ancestral state of each PSV showed that the conversion process was significantly biased towards the fixation of G or C nucleotides (GC-biased), and also towards the ancestral state. Determination of haplotypes by long-PCR allowed likely co-conversion of PSVs to be identified, and suggested that conversion tract lengths are large, with a mean of 2068 bp, and a maximum in excess of 9 kb. Despite the frequent formation of recombination intermediates implied by the rapid observed gene conversion activity, resolution via crossover is rare: only three inversions within P6 were detected in the sample. An analysis of chimpanzee and gorilla P6 orthologs showed that the ancestral state bias has existed in all three species, and comparison of human and chimpanzee sequences with the gorilla outgroup confirmed that GC bias of the conversion process has apparently been active in both the human and chimpanzee lineages

Structure and Barrier Properties of Multinanolayered Biodegradable PLA/PBSA Films: Confinement Effect via Forced Assembly Coextrusion

Multilayer coextrusion processing was applied to produce 2049-layer film of poly(butylene succinate-co-butylene adipate) (PBSA) confined against poly(lactic acid) (PLA) using forced assembly, where the PBSA layer thickness was about 60 nm. This unique technology allowed to process semicrystalline PBSA as confined polymer and amorphous PLA as confining polymer in a continuous manner. The continuity of PBSA layers within the 80/20 wt % PLA/PBSA layered films was clearly evidenced by atomic force microscopy (AFM). Similar thermal events to the reference films were revealed by thermal studies; indicating no diffusion of polymers during the melt-processing. Mechanical properties were measured for the multilayer film and the obtained results were those expected considering the fraction of each polymer, revealing the absence of delamination in the PLA/PBSA multinanolayer film. The confinement effect induced by PLA led to a slight orientation of the crystals, an increase of the rigid amorphous fraction (RAF) in PBSA with a densification of this fraction without changing film crystallinity. These structural changes allowed to strongly improve the water vapor and gas barrier properties of the PBSA layer into the multilayer film up to two decades in the case of CO2 gas. By confining the PBSA structure in very thin and continuous layers, it was then possible to improve the barrier performances of a biodegradable system and the resulting barrier properties were successfully correlated to the effect of confinement on the microstructure and the chain segment mobility of the amorphous phase. Such investigation on these multinanolayers of PLA/PBSA with the aim of evidencing relationships between microstructure implying RAF and barrier performances has never been performed yet. Besides, gas and water permeation results have shown that the barrier improvement obtained from the multilayer was mainly due to the reduction of solubility linked to the reduction of the free volume while the tortuosity effect, as usually expected, was not really observed. This work brings new insights in the field of physicochemical behaviors of new multilayer films made of biodegradable polyesters but also in interfacial processes due to the confinement effect induced in these multinanolayer structures obtained by the forced assembly coextrusion. This original coextrusion process was a very advantageous technique to produce eco-friendly materials with functional properties without the help of tie layer, additives, solvents, surface treatments, or inorganic fillers

Impact of water and thermal induced crystallizations in a PC/MXD6 multilayer film on barrier properties

A multilayer film composed of alternating layers of polycarbonate (PC) and poly(m-xylene adipamide) (MXD6) was elaborated by using an innovative multilayer coextrusion process. Quasi-continuous thin MXD6 layers (nanolayers) alternating with PC layers were successfully obtained. The PC/MXD6 multilayer film showed a confining effect of MXD6 exerted by PC layers leading to an improvement of barrier properties despite a low degree of crystallinity (X c < 10 wt%). In order to further improve the barrier performances, crystallization treatments induced by water and by heating were then applied on the multilayer film and allowed reaching around 30 wt% of crystallinity in MXD6 layers. To decouple crystallization and geometrical constraint effects on the barrier properties in the multilayer films, the two treatments were also applied on MXD6 films. Surprisingly, despite an increase of the degree of crystallinity from 6 to 26%, water crystallization did not permit to improve gas barrier performances of the MXD6 film nor into the PC/MXD6 multilayer film. On the other hand, thermal crystallization of MXD6 in the multilayer film seems to be a more efficient route to strongly decrease the gas and moisture permeability, up to 75% for nitrogen, 58% for oxygen, 84% for carbon dioxide and 43% for water

Structural and Barrier Properties of Compatibilized PE/PA6 Multinanolayer Films

The barrier performance and structural lightening of organic materials are increasingly desired and constitute a major challenge for manufacturers, particularly for transport and packaging. A promising technique which tends to emerge in recent years is that of multinanolayer coextrusion. The advantage is that it can produce multilayers made of thousands of very thin layers, leading to new properties due to crystalline morphology changes induced by confinement. This paper is focusing on the study of multinanolayered films with alternated polyethylene (PE), compatibilizer (PEgMA) and polyamide 6 (PA6) layers and made by a forced assembly coextrusion process equipped with layer multiplying elements (LME). PE/PA6 multilayer films consisting of 5 to 2049 layers (respectively 0 to 9 LME) were successfully obtained with well-organized multilayered structure. The evolution of the morphology and the microstructure of these two semi-crystalline polymers, when the thickness of each polymer layer decreases from micro-scale to nano-scale, was correlated to the water and gas transport properties of the PE/PA multilayers. The expected improvement of barrier properties was limited due to the on-edge orientation of crystals in very thin PE and PA6 layers. Despite this change of crystalline morphology, a slight improvement of the gas barrier properties was shown by comparing experimental results with permeabilities predicted on the basis of a serial model developed by considering a PE/PA6 interphase. This interphase observed by TEM images and the on-edge crystal orientation in multilayers were evidenced from mechanical properties showing an increase of the stiffness and the strength

Definition of Biologically Distinct Groups of Conjunctival Melanomas According to Etiological Factors and Implications for Precision Medicine

From MDPI via Jisc Publications RouterHistory: accepted 2021-07-26, pub-electronic 2021-07-30Publication status: PublishedFunder: European Commission; Grant(s): 667787Funder: European Research Council; Grant(s): ERC-ADG-2014 671262Funder: Cancer Research UK; Grant(s): A27412 and A22902Funder: Institut Curie; Grant(s): #Funder: Ligue Contre le Cancer; Grant(s): #Funder: Institut National de la Santé et de la Recherche Médicale; Grant(s): #Conjunctival melanoma (ConjMel) is a potentially deadly ocular melanoma, originating from partially sunlight-exposed mucosa. We explored the mutational landscape of ConjMel and studied the correlation with etiological factors. We collected 47 primary ConjMel samples and performed next-generation sequencing of 400 genes. Hotspot mutations in BRAF, NRAS, HRAS, and KIT were observed in 16 (34%), 5 (11%), 2, and 2 cases, respectively. Patients with BRAF and CDKN2A-mutated ConjMel tended to be younger while the NF1-mutated one tended to be older. The eight tumors arising from nevi were enriched in CTNNB1 mutations (63% vs. 8%; Fisher’s exact p-test = 0.001) compared to non-nevi ConjMel and five were devoid of BRAF, RAS, NF1, or KIT mutations, suggesting a specific oncogenic process in these tumors. The two KIT-mutated cases carried SF3B1 mutations and were located on sun-protected mucosa, a genotype shared with genital and anorectal mucosal melanomas. Targetable mutations were observed in ERBB2, IDH1, MET, and MAP2K1 (one occurrence each). Mutational landscape of ConjMel characterizes distinct molecular subtypes with oncogenic drivers common with mucosal and skin melanomas. CTNNB1 mutations were associated with nevus-derived ConjMel. Concomitant KIT/SF3B1 mutations in sun-protected cases suggest a common tumorigenic process with genital and anorectal mucosal melanomas

The Genome of Borrelia recurrentis, the Agent of Deadly Louse-Borne Relapsing Fever, Is a Degraded Subset of Tick-Borne Borrelia duttonii

In an effort to understand how a tick-borne pathogen adapts to the body louse, we sequenced and compared the genomes of the recurrent fever agents Borrelia recurrentis and B. duttonii. The 1,242,163–1,574,910-bp fragmented genomes of B. recurrentis and B. duttonii contain a unique 23-kb linear plasmid. This linear plasmid exhibits a large polyT track within the promoter region of an intact variable large protein gene and a telomere resolvase that is unique to Borrelia. The genome content is characterized by several repeat families, including antigenic lipoproteins. B. recurrentis exhibited a 20.4% genome size reduction and appeared to be a strain of B. duttonii, with a decaying genome, possibly due to the accumulation of genomic errors induced by the loss of recA and mutS. Accompanying this were increases in the number of impaired genes and a reduction in coding capacity, including surface-exposed lipoproteins and putative virulence factors. Analysis of the reconstructed ancestral sequence compared to B. duttonii and B. recurrentis was consistent with the accelerated evolution observed in B. recurrentis. Vector specialization of louse-borne pathogens responsible for major epidemics was associated with rapid genome reduction. The correlation between gene loss and increased virulence of B. recurrentis parallels that of Rickettsia prowazekii, with both species being genomic subsets of less-virulent strains

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Malware and Ransomware Detection Models

Cybercrime is one of the major digital threats of this century. In particular, ransomware attacks have significantly increased, resulting in global damage costs of tens of billion dollars. In this paper, we train and test different Machine Learning and Deep Learning models for malware detection, malware classification and ransomware detection. We introduce a novel and flexible ransomware detection model that combines two optimized models. Our detection results on a limited dataset demonstrate good accuracy and F1 scores