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Background Bacteria and their viruses, bacteriophages, are the most abundant entities of the gut microbiota, a complex community of microorganisms associated with human health and disease. In this ecosystem, the interactions between these two key components are still largely unknown. In particular, the impact of the gut environment on bacteria and their associated prophages is yet to be deciphered. Results To gain insight into the activity of lysogenic bacteriophages within the context of their host genomes, we performed proximity ligation-based sequencing (Hi-C) in both in vitro and in vivo conditions on the 12 bacterial strains of the OMM12 synthetic bacterial community stably associated within mice gut (gnotobiotic mouse line OMM12). High-resolution contact maps of the chromosome 3D organization of the bacterial genomes revealed a wide diversity of architectures, differences between environments, and an overall stability over time in the gut of mice. The DNA contacts pointed at 3D signatures of prophages leading to 16 of them being predicted as functional. We also identified circularization signals and observed different 3D patterns between in vitro and in vivo conditions. Concurrent virome analysis showed that 11 of these prophages produced viral particles and that OMM12 mice do not carry other intestinal viruses. Conclusions The precise identification by Hi-C of functional and active prophages within bacterial communities will unlock the study of interactions between bacteriophages and bacteria across conditions (healthy vs disease).

International audience; In recent years, significant technical advances have been made to better observe the structure and the organization of chromatin. Many Hi-C data are now available in public databases, at different accuracy and resolution and for various species. Generally, the final results of Hi-C data analyses are summarized with the representation of “contact maps”. Using a color scale, these maps (heat-maps) show the frequency of contacts observed between different portions of a genome, both at short-rangeand long-range distances.Even if they are widely used, our observation is that the biological interpretation of contact maps is not trivial. It requires training and significant experience to be useful to validate or invalidate hypotheses concerning the overall organization of the studied genome. In this context, alternative tools have been developed. Some of them produce 3D models ofcontact networks, as a substitute for visualization of Hi-C outputs. By 3D models, we mean representations in a 3D space of a genome, in which euclidean distances are derived from the contact frequency matrices. The information contained in the Hi-C data is thus directly translated into distances in a 3D space. Although care must be taken in interpreting these models (they are not “pictures” of the interior of a cell), we observed they are very helpful to highlight specific structural patterns in chromatin organization, originally hidden in contact maps.Developing new strategies to visualize and integrate large scale multi-omics data is the major objective of Thibault Poinsignon’s thesis (ANR MinOmics). These led us to start building 3D models of yeasts andfilamentous fungi genomes, from Hi-C raw sequencing data. We present here our evaluations of the biological significance and the interest to use these models for projecting heterogeneous epigenomics data and hence better support their biological interpretations.

Ce travail avait pour objectif d’identifier les correspondances possibles entre Habitats d’IntérêtCommunautaire (HIC) marins (Tableau 1) et unités d’habitats des typologies nationales (NatHab-Med et NatHab-Atl), typologies EUNIS (EUNIS version 2022) et listes des conventions de mersrégionales (OSPAR et Barcelone) en se basant sur la réinterprétation nationale des Habitats d’IntérêtCommunautaire (HIC) marins (de Bettignies et al., 2021) et les descriptions des unités d’habitats destypologies nationales (La Rivière et al., 2021 ; 2022). Il constitue une mise à jour du travaild’établissement des correspondances réalisé en 2012 (Michez et al., 2012) en suivantglobalement la même méthodologie.Cette note apporte des précisions sur le cadre méthodologique suivi pour établir cescorrespondances et sur la structuration des données. Pour chaque HIC, des explications sontdonnées pour assurer une bonne compréhension des correspondances établies, notamment en cequi concerne les conditions de correspondances résultant du travail de réinterprétation.

Germ cells reflect the evolutionary history and future potential of a species. Understanding how the genome is organised in gametocytes is fundamental to understanding fertility and its impact on genetic diversity and evolution of species. Here, we explore principles of chromatin remodelling during the formation of germ cells and how these are affected by genome reshuffling.

Hydrogen-Induced Cracking (HIC) is a primary failure mechanism of pipeline-welded joints in the absence of external loading in the oil and gas exploration industries. Three different cooling rates after austenitization were used to simulate in the laboratory different regions of the heat-affected zone (HAZ) formed when welding an API X80 pipeline steel specially designed to enhance the HIC resistance. The samples were characterized with regard to microstructure and crystallography as well as HIC resistance. The HIC resistance test used NACE TM0284-2011 methodology. The microstructure and its homogeneity varied as a function of cooling rates. Samples containing inclusions and segregation zone from the segregation bands of specimens showed reduced HIC resistance, while specimens containing only acicular ferrite and granular bainite coupled with the absence of segregation zone showed significant improvement in HIC resistance. The best HIC resistance results came from samples presenting fine acicular ferrite consisting of fine interlocking plates, with divergent crystallographic orientations, preventing the formation of localized strain distribution inside the grain and at grain boundaries. It was also found that a large proportion of medium-angle boundaries prevent microcrack initiation and the transgranular mode of crack propagation.

In the present study, we successfully assembled a high-quality genome of Planiliza haematocheila (redlip mullet) based on Oxford Nanopore long read, single-tube long fragment read (stLFR), and Hi-C chromatin interaction sequencing. The size of the P. haematocheila genome was 652.91 Mb. More than 93.8% of BUSCO genes were detected, and the N50 lengths of contigs and scaffolds reached 7.21 Mb and 28.01 Mb, respectively, thus demonstrating outstanding genome completeness and sequence continuity. A total of 21 045 protein-coding genes were predicted in the assembled genome, and 99.77% of those genes were functionally annotated. Comparative genomic and phylogenetic analyses revealed the adaptability of P. haematocheila to complex living environments at the genomic level, highlighting its broad adaptability and resistance to multiple stresses as an important economic fish. The high-quality reference chromosome-level genome of P. haematocheila provides a powerful genomic resource for further systematic study of Mugilidae.

The gray mangrove [Avicennia marina (Forsk.) Vierh.] is the most widely distributed mangrove species, ranging throughout the Indo-West Pacific. It presents remarkable levels of geographic variation both in phenotypic traits and habitat, often occupying extreme environments at the edges of its distribution. However, subspecific evolutionary relationships and adaptive mechanisms remain understudied, especially across populations of the West Indian Ocean. High-quality genomic resources accounting for such variability are also sparse. Here we report the first chromosome-level assembly of the genome of A. marina. We used a previously release draft assembly and proximity ligation libraries Chicago and Dovetail HiC for scaffolding, producing a 456,526,188-bp long genome. The largest 32 scaffolds (22.4–10.5 Mb) accounted for 98% of the genome assembly, with the remaining 2% distributed among much shorter 3,759 scaffolds (62.4–1 kb). We annotated 45,032 protein-coding genes using tissue-specific RNA-seq data in combination with de novo gene prediction, from which 34,442 were associated to GO terms. Genome assembly and annotated set of genes yield a 96.7% and 95.1% completeness score, respectively, when compared with the eudicots BUSCO dataset. Furthermore, an FST survey based on resequencing data successfully identified a set of candidate genes potentially involved in local adaptation and revealed patterns of adaptive variability correlating with a temperature gradient in Arabian mangrove populations. Our A. marina genomic assembly provides a highly valuable resource for genome evolution analysis, as well as for identifying functional genes involved in adaptive processes and speciation.

Sadece dış dünya değil, düşünülebilir şeyler de ‘var’dır. Bu durumda Varlık ile belirlenmemiş olan, yolu Varlık’tan geçmemiş olan bir şey düşünülemez. Düşünülebilir şeyler arasında yalnızca Hiç’e varlık atfedilemez, zira ona varlık atfedildiği anda o, artık Hiç olmayacaktır. Bu nedenle Heidegger Hiç için ‘Hiçer’ ifadesini kullanır. Yine de bu, Hiçin Varlık soruşturmasında dışarıda bırakılması gerektiği anlamına gelmez. Hiç tam da ‘varlık-sız’ olduğundan Varlığın anlamını soruşturmak için önemli bir perspektif imkânı sunar. Heidegger, ‘varolanlar vardır’ denildiğinde, asıl üzerinde durulması gerekenin ‘vardır’ ifadesi olduğunu düşündüğünden Varlığın anlamını, ‘varolanlardan soyarak’ daha önce yapılmamış bir tarzda soruşturur. Biz de burada onun bu soruşturmada başvurduğu en önemli kavramlardan biri olan Hiç üzerinde duracağız. Heidegger, Varlığın anlamını soruşturmak için Hiçi öyle bir tarzda ele alır ki bu Hiçin sonunda Hiç olarak kalıp kalmayacağından şüphe edebilir ve şunu sorabiliriz: Bir fenomen olarak ele alınan Hiç, tamamen boş ve hatta üzerinde düşünülemeyecek bir Hiçliği mi işaret eder, yoksa o, bir şekilde ele geçirilebilir bir ‘şey’ midir? Bir şekilde tecrübe edilebiliyorsa o, artık Hiç olarak kalabilir mi? Heidegger’e göre Hiç, bir şekilde dünyaya gelerek insan varlığında ele geçirilebilir, öyleyse biz de burada onun Hiçi, Hiç olarak bırakmadığını ve Varlığa taşıdığını savunacağız.

Nowadays, fuel consumption and exhaust emissions are topical issues in the automotive field, as environmental safeguard legislation constraints are going to get tougher. Indeed, one of the most efficient methods to contain fuel consumption and emissions is the weight reduction of the vehicle. In this paper, a feasibility study on the lightweight redesign of a metallic car hood by using composite materials is presented. In particular, two different configurations, employing composite laminates and sandwich structures, are investigated. The feasibility of each configuration is assessed in terms of stiffness specifications and pedestrian safety requirement. Hence, Head Injury Criteria are employed, according to regulations. Finally, an optimization procedure on the stacking sequence of the composite laminates is performed, to determine, among the feasible solutions, the one characterized by the minimum weight.

International audience; While many computational methods have been proposed for 3D chromosome reconstruction from chromosomal contact maps, these methods are rarely used for the interpretation of such experimental data, in particular Hi-C data. We posit that this is due to the lack of an easy-to-use implementation of the proposed algorithms, as well as to the important computational cost of most methods. We here give a detailed implementation of the fast ShRec3D algorithm. We provide a tutorial that will enable the reader to reconstruct 3D consensus structures for human chromosomes and to decorate these structures with chromatin epigenetic states. We use this methodology to show that the bivalent chromatin, including Polycomb-rich domains, is spatially segregated and located in between the active and the quiescent chromatin compartments.

Northern bobwhites (Colinus virginianus) are small quails in the New World Quail family (Odontophoridae) and are one of the most phenotypically diverse avian species. Despite extensive research on bobwhite ecology, genomic studies investigating the evolution of phenotypic diversity in this species are lacking. Here, we present a new, highly contiguous assembly for bobwhites using tissue samples from a vouchered, wild, female bird collected in Louisiana. By performing a de novo assembly and scaffolding the assembly with Dovetail Chicago and HiC libraries and the HiRise pipeline, we produced an 866.8 Mb assembly including 1,512 scaffolds with a scaffold N50 of 66.8 Mb, a scaffold L90 of 17, and a BUSCO completeness score of 90.8%. This new assembly represents approximately 96% of the non-repetitive and 84% of the entire bobwhite genome size, greatly improves scaffold lengths and contiguity compared to an existing draft bobwhite genome, and provides an important tool for future studies of evolutionary and functional genomics in bobwhites.

Health insurance is an important social policy with humanitarian meaning and profound community sharing, which is highly valued and promoted by the Vietnamese Government in the social security policy system. Therefore, it is necessary to study users’ satisfaction to medical examination and treatment services with health insurance cards. Based on the questionnaire surveys, the research team conducted Cronbach's Alpha analysis of each factor, assessed the scale reliability. Multivariate regression and ANOVA test showed that all four components: health services, human resources, medical examination and treatment costs, medical information and medical products positively affected users’ satisfaction to medical examination and treatment services with health insurance cards in Ninh Binh province, Vietnam. Based on the survey results and the information exchanged directly with people who came for medical examination and treatment, the research team drew out shortcomings in medical examination and treatment for users of health insurance card sin Ninh Binh province. Shortcomings in medical examination and treatment with health insurance cards were pointed out as an important basis for proposals to improve the medical examination and treatment quality for insured subjects including: Health insurance costs and response levels; Medical examination and treatment process with health insurance and doctor’s responsibility. Reasonable waiting time and hospital environment; Health insurance-based drug delivery.&nbsp

Falls within children’s playgrounds result in long bone and serious injuries. To lower the likelihood and severity of injury, impact attenuating surfaces (IAS) are installed within the impact area (fall zone). There are three primary IAS materials used, namely: granulated rubber products, wood fibre products, and sand. There is a deficiency with existing IAS test methods in that they do not take account of sand degradation over time. When children use the playground, sand degradation can occur when sand produces fines and smaller particles with low sphericity and angular which fill the voids between the sand particles. These fines and smaller particles tend to bind the sand and lower its impact attenuating performance. This paper proposes an additional IAS test to eliminate sands that degrade above an established threshold rate after installation due to normal usage. IAS degradation properties of fifteen IAS sands were tested including sand particle shape, sand particle distribution, percentage fines and sand particle degradation. This accelerated ageing test method is applicable only to sands and not rubber or wood fibre IAS products. The best IAS sands were sourced from quarries located on rivers that had eroded volcanic outcrops. These sands were shown to degrade the least and had little to no fines, and their particle shape was rounded to well-rounded. The most reliable source for good quality IAS sands on these rivers was on specific bends. The sand mined at these locations consistently had a tight particle size distribution.

This study reports on the assessment of the separation performance of hydrophobic interaction chromatography for intact protein analysis using non-porous butyl polymethacrylate phases. The maximum peak capacity in inverse gradient mode was reached at a volumetric flow rate which was significantly (10–20 times) higher than the flow rate yielding the minimum plate height in isocratic mode, as the gradient volume dominates the peak-capacity generation. The flow rate yielding the maximum peak capacity increased with decreasing gradient volume, i.e., steeper gradients, and also depends on the magnitude of the mass-transfer contribution to peak dispersion (affected by particle size and molecular diffusion coefficient of proteins) at these high flow rates. The maximum peak capacity using a 100 mm long column packed with 4 µm particles for steep 7.5 min gradients was determined to be 60. Increasing the column length by coupling columns leads to better gradient performance than increasing the gradient duration for gradients of 60 min and longer. Using a coupled column system (2 × 100 mm long columns packed with 4 µm particles), the maximum peak capacity was determined to be 105, which was 33% higher compared to that of a single column while applying a similar gradient volume. Decreasing the particle size to 2.3 µm leads to higher peak capacities even though the column was operated at lower volumetric flow rate. The maximum peak capacity obtained with the 2.3 µm column was 128% higher than was obtained with the coupled column. Even at suboptimal conditions, the 2.3 µm column yields a higher peak capacity (14%) than when using two coupled columns packed with 4 µm at optimal conditions (gradient time of 120 min and a flow rate of 0.5 mL/min).

Lo scopo principale di questa tesi consiste nella valutazione dei danni provocati da un utente debole della strada in un incidente con un veicolo e allo sviluppo di un metodo versatile che possa simulare qualsiasi circostanza. I danni vengono quantificati sulla base di alcuni criteri di lesione quali HIC, TTI, criterio dei 3 ms, forze di contatto, ecc… Inoltre è stato eseguito un modello teorico per la validazione dei risultati ottenuti dal punto di vista matematico e una serie di confronti, dei dati ottenuti con delle fonti presenti in bibliografia. A tal fine verranno valutati quelle che sono le condizioni più gravose per questo genere di impatto e alcuni suggerimenti atti a limitarli.

One of the most fascinating aspects of meiosis is the extensive reorganization of the genome at the prophase of the first meiotic division (prophase I). The first steps of this reorganization are observed with the establishment of an axis structure, that connects sister chromatids, from which emanate arrays of chromatin loops. This axis structure, called the axial element, consists of various proteins, such as cohesins, HORMA-domain proteins, and axial element proteins. In many organisms, axial elements are required to set the stage for efficient sister chromatid cohesion and meiotic recombination, necessary for the recognition of the homologous chromosomes. Here, we review the different actors involved in axial element formation inSaccharomyces cerevisiaeand in mouse. We describe the current knowledge of their localization pattern during prophase I, their functional interdependence, their role in sister chromatid cohesion, loop axis formation, homolog pairing before meiotic recombination, and recombination. We also address further challenges that need to be resolved, to fully understand the interplay between the chromosome structure and the different molecular steps that take place in early prophase I, which lead to the successful outcome of meiosis I.

Legumes are of great interest for sustainable agricultural production as they fix atmospheric nitrogen to improve the soil. Medicago truncatula is a well-established model legume, and extensive studies in fundamental molecular, physiological, and developmental biology have been undertaken to translate into trait improvements in economically important legume crops worldwide. However, M. truncatula reference genome was generated in the accession Jemalong A17, which is highly recalcitrant to transformation. M. truncatula R108 is more attractive for genetic studies due to its high transformation efficiency and Tnt1-insertion population resource for functional genomics. The need to perform accurate synteny analysis and comprehensive genome-scale comparisons necessitates a chromosome-length genome assembly for M. truncatula cv. R108. Here, we performed in situ Hi-C (48×) to anchor, order, orient scaffolds, and correct misjoins of contigs in a previously published genome assembly (R108 v1.0), resulting in an improved genome assembly containing eight chromosome-length scaffolds that span 97.62% of the sequenced bases in the input assembly. The long-range physical information data generated using Hi-C allowed us to obtain a chromosome-length ordering of the genome assembly, better validate previous draft misjoins, and provide further insights accurately predicting synteny between A17 and R108 regions corresponding to the known chromosome 4/8 translocation. Furthermore, mapping the Tnt1 insertion landscape on this reference assembly presents an important resource for M. truncatula functional genomics by supporting efficient mutant gene identification in Tnt1 insertion lines. Our data provide a much-needed foundational resource that supports functional and molecular research into the Leguminosae for sustainable agriculture and feeding the future.

Legumes are of great interest for sustainable agricultural production as they fix atmospheric nitrogen to improve the soil. Medicago truncatula is a well-established model legume, and extensive studies in fundamental molecular, physiological, and developmental biology have been undertaken to translate into trait improvements in economically important legume crops worldwide. However, M. truncatula reference genome was generated in the accession Jemalong A17, which is highly recalcitrant to transformation. M. truncatula R108 is more attractive for genetic studies due to its high transformation efficiency and Tnt1-insertion population resource for functional genomics. The need to perform accurate synteny analysis and comprehensive genome-scale comparisons necessitates a chromosome-length genome assembly for M. truncatula cv. R108. Here, we performed in situ Hi-C (48×) to anchor, order, orient scaffolds, and correct misjoins of contigs in a previously published genome assembly (R108 v1.0), resulting in an improved genome assembly containing eight chromosome-length scaffolds that span 97.62% of the sequenced bases in the input assembly. The long-range physical information data generated using Hi-C allowed us to obtain a chromosome-length ordering of the genome assembly, better validate previous draft misjoins, and provide further insights accurately predicting synteny between A17 and R108 regions corresponding to the known chromosome 4/8 translocation. Furthermore, mapping the Tnt1 insertion landscape on this reference assembly presents an important resource for M. truncatula functional genomics by supporting efficient mutant gene identification in Tnt1 insertion lines. Our data provide a much-needed foundational resource that supports functional and molecular research into the Leguminosae for sustainable agriculture and feeding the future.

Electrochemical H charging, hydrogen permeation, and hydrogen-induced cracking (HIC) behavior of 690 MPa grade steel substrate and different heat-treatment states (annealed, quenched, normalized, tempered) are investigated by cyclic voltammetry (CV), hydrogen permeation, electrochemical H charging, and slow strain rate tensile test (SSRT). The results show that hydrogen diffuses through the steel with the highest rate in base metal and the lowest rate in annealed steel. The hydrogen-induced cracks in base metal show obvious step shape with tiny cracks near the main crack. The cracks of annealed steel are mainly distributed along pearlite. The crack propagation of quenched steel is mainly transgranular, while the hydrogen-induced crack propagation of tempered steel is along the prior austenite grain boundary. HIC sensitivity of base metal is the lowest due to its fine homogeneous grain structure, small hydrogen diffusion coefficient, and small hydrogen diffusion rate. There are many hydrogen traps in annealed steel, such as the two-phase interface which provides accommodation sites for H atoms and increases the HIC susceptibility.

Maytenus senegalensis s.l. es un arbusto tropical afro-asiático, relicto en la Península Ibérica, protegido por las normativas de Andalucía, Valencia y Murcia con la categoría VU. Está considerado uno de los taxones directrices del Hábitat de Interés Comunitario (HIC) 5220* (Matorrales arborescentes de Ziziphus lotus), circunscrito principalmente al extremo sureste de la Península Ibérica. Su límite occidental ibérico lo forman algunas poblaciones en la provincia de Málaga aisladas del resto (Manzano 2020, Acta Bot Malacit 45: 7-25). Estas poblaciones están fitosociológicamente caracterizadas (Pérez Latorre et al. 2008, Acta Bot Malacit 33: 215- 270), pero solo parcialmente cartografiadas por la Red de Información Ambiental de Andalucía (REDIAM, www.juntadeandalucia.es/medioambiente/ site/rediam). El objetivo es cartografiar en detalle las poblaciones conocidas de M. senegalensis en su límite occidental y su HIC asociado y realizar una valoración del estado de conservación (EC) de dichas poblaciones. Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech.

Made available in DSpace on 2022-04-28T19:41:37Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-08-10 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Laboratório Nacional de Nanotecnologia The use of friction stir welding (FSW) has proven to be an excellent alternative to join engineering components. Although FSW has had a significant development in recent years, challenges for new applications have been raised, such as offshore steel parts suffering hydrogen embrittlement in the gas and oil industry. Therefore, in this work, the microstructure, corrosion, and hydrogen-induced cracking were investigated in a two-pass FSW welded joint of API 5L X70 pipeline steel. The electrochemical results indicate an inhibitory effect on corrosion reaction because of a carbonate product generation in the steel surface. The polygonal ferritic and degenerated pearlite bands microstructure in the base metal fixed carbonate deposits in the steel surface. In the welded regions, the bainitic microstructure and the carbide particle distribution are less efficient in setting the weld surface carbonate deposit. HIC tests showed cracks initiation and propagation to be more prone in hard phases. USP – University of São Paulo, Av. Trabalhador São Carlense 400 USP – University of São Paulo, Av. Prof. Luciano Gualberto, 380 - Butantã UNESP – São Paulo State University, Campus of São João da Boa Vista UNSA-National University of San Agustín de Arequipa Materials Engineering, Av. Venezuela S/N UNESP – São Paulo State University, Campus of São João da Boa Vista CNPq: 165065/2017-6

This article belongs to the Special Issue Armour and Protection Systems New threats are a challenge for the design and manufacture of modern combat helmets. These helmets must satisfy a wide range of impact velocities from ballistic impacts to blunt impacts. In this paper, we analyze European Regulation ECE R22.05 using a standard surrogate head and a human head model to evaluate combat helmet performance. Two critical parameters on traumatic brain analysis are studied for different impact locations, i.e., peak linear acceleration value and head injury criterion (HIC). The results obtained are compared with different injury criteria to determine the severity level of damage induced. Furthermore, based on different impact scenarios, analyses of the influence of impact velocity and the geometry impact surface are performed. The results show that the risks associated with a blunt impact can lead to a mild traumatic brain injury at high impact velocities and some impact locations, despite satisfying the different criteria established by the ECE R22.05 standard. The results reveal that the use of a human head for the estimation of brain injuries differs slightly from the results obtained using a surrogate head. Therefore, the current combat helmet configuration must be improved for blunt impacts. Further standards should take this into account and, consequently, combat helmet manufacturers on their design process. This work has been carried out within the framework of the research project DPI2017-88166-R of the FEDER program financed by the Ministerio de Economía, Industria y Competitividad and the Spanish Ministry of Education, Culture and Sports for the professor's mobility program José Castillejo's 2018 grant (CAS18/00292).

Background The persistence of HIV-1 in reservoir cells is one of the major obstacles to eradicating the virus in infected individuals receiving combination antiretroviral therapy (ART). HIV-1 persists in infected cells as a stable integrated genome and more labile unintegrated DNA (uDNA), which includes linear, 1-LTR and 2-LTR circular DNA. 2-LTR circle DNA, although less abundant, is considered a surrogate marker of recent infection events and is currently used instead of the other unintegrated species as a diagnostic tool. This pilot study aimed to investigate how to best achieve the measurement of uDNA. Methods A comparative analysis of two qPCR-based methods (U-assay and 2-LTR assay) was performed on the blood of 12 ART-naïve, 14 viremic and 29 aviremic On-ART patients and 20 untreated spontaneous controllers (HIC), sampled at a single time point. Results The U-assay, which quantified all unintegrated DNA species, showed greater sensitivity than the 2-LTR assay (up to 75%, p Conclusions The great advantage of the U-assay is that, unlike the 2-LTR assay, it allows the accurate evaluation of the totality of uDNA that can still be measured even during successful ART when plasma viremia is below the cut-off of common clinical tests (

Background Enhancers play a fundamental role in orchestrating cell state and development. Although several methods have been developed to identify enhancers, linking them to their target genes is still an open problem. Several theories have been proposed on the functional mechanisms of enhancers, which triggered the development of various methods to infer promoter–enhancer interactions (PEIs). The advancement of high-throughput techniques describing the three-dimensional organization of the chromatin, paved the way to pinpoint long-range PEIs. Here we investigated whether including PEIs in computational models for the prediction of gene expression improves performance and interpretability. Results We have extended our $$\textsc{TEPIC}$$TEPIC framework to include DNA contacts deduced from chromatin conformation capture experiments and compared various methods to determine PEIs using predictive modelling of gene expression from chromatin accessibility data and predicted transcription factor (TF) motif data. We designed a novel machine learning approach that allows the prioritization of TFs binding to distal loop and promoter regions with respect to their importance for gene expression regulation. Our analysis revealed a set of core TFs that are part of enhancer–promoter loops involving YY1 in different cell lines. Conclusion We present a novel approach that can be used to prioritize TFs involved in distal and promoter-proximal regulatory events by integrating chromatin accessibility, conformation, and gene expression data. We show that the integration of chromatin conformation data can improve gene expression prediction and aids model interpretability.

International audience; High-resolution native mass spectrometry (MS) provides accurate mass measurements (within 30 ppm) of intact ADCs and can also yield drug load distribution (DLD) and average drug to antibody ratio (DAR) in parallel with hydrophobic interaction chromatography (HIC). Native MS is furthermore unique in its ability to simultaneously detect covalent and noncovalent species in a mixture and for HIC peak identity assessment offline or online.As an orthogonal method described in this chapter, LC-MS following ADC reduction or IdeS (Fabricator) digestion and reduction can also be used to measure the DLD of light chain and Fd fragments for hinge native cysteine residues such as brentuximab vedotin. Both methods allow also the measurement of average DAR for both monomeric and multimeric species. In addition, the Fc fragments can be analyzed in the same run, providing a complete glycoprofile and the demonstration or absence of additional conjugation of this subdomain involved in FcRn and Fc-gammaR binding.

The haptic system has two key performance issues: stability and transparency. A haptic interface controller (HIC) is designed to address these issues. Addressing these issues becomes a complex problem as both are complementary to each other. Here, when transparency of the system is increased, its stability degrades and vice-versa. To overcome this problem, intelligent optimized solutions are used in this paper to design a HIC controller for the haptic system. SVM and NN techniques have been employed to identify the performance of the controller, ensuring stability and transparency both. The disadvantages of NN in terms of the number of neurons and hidden layers are overcome by SVM. Further, the performance of SVM is highly dependent upon the selection of free parameters. So, further, a modified PSO technique is employed for the optimal selection of these parameters to enhance the performance of SVM. Hence, this novel proposed hybrid technique of m-PSO optimized SVM is applied for the optimal design of the HIC to find out an optimal solution between trade-off the transparency and stability of the haptic device simultaneously. To appreciate the efficacy of the proposed technique, the result obtained with this is compared with HIC design using neural network and conventional ZN method also. This designed controller ensures stability as well as transparency, even under the presence of uncertainty, delay, and quantization error.

Dissertation, Rheinisch-Westfälische Technische Hochschule Aachen, 2020; Aachen 1 Online-Ressource (XIV, 124 Seiten) : Illustrationen, Diagramme (2020). = Dissertation, Rheinisch-Westfälische Technische Hochschule Aachen, 2020, In the present work, the microstructural influence on hydrogen-induced cracking is described using a three-dimensional numerical modelling approach with the commercial software ABAQUS FEA. The two-dimensional model according to Oriani and Barrera, which previously has been published in literature, was replicated, validated with an analytical solution and extended to the three-dimensional application. The resulting problem of meshing complex geometries with hexahedral elements could be counteracted by the use of tetrahedral elements. The mathematical deviation between the local hydrogen concentration of the analytically validated hexahedral elements and the tetrahedral elements was solved by a developed linear element compensation function. Furthermore, the HEDE and HELP mechanisms were implemented in the form of a concentration-dependent stress or strain-controlled damage criterion. On the basis of real permeation tests, the newly developed three-dimensional material model could successfully generate virtual permeation measurements hence enable the derivation of the effective diffusion coefficient of the investigated low alloy pipeline steel. The investigations of inclusion-affected representative submodels with different fictional as well as real inclusion characteristics showed that a strong correlation between the development of the local hydrogen concentration and the existing inclusion chemistry can be observed. Additionally, the influence of size and shape of the inclusions could be shown. The model for the description of the stress-dependent hydrogen diffusion was applied to determine the critical non-metallic inclusions. The comparison of different inclusion systems showed that inclusions with the chemical composition Al2O3 in particular led to a significant increase in the local hydrogen concentration. Thus, proving that especially these inclusions contribute critically to the hydrogen-induced crack initiation., Published by Aachen

The retention behavior of polyethylene glycol (PEG) on different types of hydrophobic interaction chromatography (HIC) resins containing butyl, octyl, and phenyl ligands was analyzed. An incomplete elution or splitting of the polymer peak into two parts was observed, where the first one was eluted at the dead time of the column, whereas the second one was strongly retained. The phenomenon was attributed to conformation changes of the polymer upon its adsorption on hydrophobic surface. The effect enhanced with increasing molecular weight of the polymer and hydrophobicity of the HIC media. Addition of PEG to the mobile phase reduced binding of proteins to HIC resins, which was demonstrated with two model systems: lysozyme (LYZ) and immunoglobulin G (IgG), and their mixtures. In case of LYZ, the presence of PEG caused reduction in the protein retention, whereas for IgG-a decrease in efficiency of the protein capture. The effect depended on the adsorption pattern of PEG; it was pronounced in the systems in which conformational changes of the polymer were suggested to occur.

Background As the COVID-19 pandemic rages on, reports on disparities in vaccine roll out alongside COVID-19 reinfection have been emerging. We conducted a systematic review to assess the determinants and disease spectrum of COVID-19 reinfection. Materials and methods A comprehensive search covering relevant databases was conducted for observational studies reporting Polymerase Chain Reaction (PCR) confirmed infection and reinfection cases. A quality assessment tool developed by the National Institute of Health (NIH) for the assessment of case series was utilized. Meta-analyses were performed using RevMan 5.3 for pooled proportions of findings in first infection and reinfection with a 95% confidence interval (CI). Results Eighty-one studies reporting 577 cases were included from 22 countries. The mean age of patients was 46.2 ± 18.9 years and 179 (31.0%) cases of comorbidities were reported. The average time duration between first infection and reinfection was 63.6 ± 48.9 days. During first infection and reinfection, fever was the most common symptom (41.4% and 36.4%, respectively) whilst anti-viral therapy was the most common treatment regimen administered (44.5% and 43.0%, respectively). Comparable odds of symptomatic presentation and management were reported for the two infections. However, a higher Intensive Care Unit (ICU) admission rate was observed in reinfection compared to first infection (10 vs 3). Ten deaths were reported with respiratory failure being the most common cause of death (7/10 deaths). Conclusion Our findings support immunization practices given increased ICU admissions and mortality in reinfections. Our cohort serves as a guide for clinicians and authorities in devising an optimal strategy for controlling the pandemic. (249 words)

Northern bobwhites (Colinus virginianus) are small quails in the New World Quail family (Odontophoridae) and are one of the most phenotypically diverse avian species. Despite extensive research on bobwhite ecology, genomic studies investigating the evolution of phenotypic diversity in this species are lacking. Here, we present a new, highly contiguous assembly for bobwhites using tissue samples from a vouchered, wild, female bird collected in Louisiana. By performing a de novo assembly and scaffolding the assembly with Dovetail Chicago and HiC libraries and the HiRise pipeline, we produced an 866.8 Mb assembly including 1,512 scaffolds with a scaffold N50 of 66.8 Mb, a scaffold L90 of 17, and a BUSCO completeness score of 90.8%. This new assembly represents approximately 96% of the non-repetitive and 84% of the entire bobwhite genome size, greatly improves scaffold lengths and contiguity compared to an existing draft bobwhite genome, and provides an important tool for future studies of evolutionary and functional genomics in bobwhites.

Genome rearrangements that occur during evolution impose major challenges on regulatory mechanisms that rely on three-dimensional genome architecture. Here, we developed a scaffolding algorithm and generated chromosome-length assemblies from Hi-C data for studying genome topology in three distantly relatedDrosophilaspecies. We observe extensive genome shuffling between these species with one synteny breakpoint after approximately every six genes. A/B compartments, a set of large gene-dense topologically associating domains (TADs) and spatial contacts between high-affinity sites (HAS) located on the X chromosome are maintained over 40 million years, indicating architectural conservation at various hierarchies. Evolutionary conserved genes cluster in the vicinity of HAS, while HAS locations appear evolutionarily flexible, thus uncoupling functional requirement of dosage compensation from individual positions on the linear X chromosome. Therefore, 3D architecture is preserved even in scenarios of thousands of rearrangements highlighting its relevance for essential processes such as dosage compensation of the X chromosome.

Background Macaque species share >93% genome homology with humans and develop many disease phenotypes similar to those of humans, making them valuable animal models for the study of human diseases (e.g., HIV and neurodegenerative diseases). However, the quality of genome assembly and annotation for several macaque species lags behind the human genome effort. Results To close this gap and enhance functional genomics approaches, we used a combination of de novo linked-read assembly and scaffolding using proximity ligation assay (HiC) to assemble the pig-tailed macaque (Macaca nemestrina) genome. This combinatorial method yielded large scaffolds at chromosome level with a scaffold N50 of 127.5 Mb; the 23 largest scaffolds covered 90% of the entire genome. This assembly revealed large-scale rearrangements between pig-tailed macaque chromosomes 7, 12, and 13 and human chromosomes 2, 14, and 15. We subsequently annotated the genome using transcriptome and proteomics data from personalized induced pluripotent stem cells derived from the same animal. Reconstruction of the evolutionary tree using whole-genome annotation and orthologous comparisons among 3 macaque species, human, and mouse genomes revealed extensive homology between human and pig-tailed macaques with regards to both pluripotent stem cell genes and innate immune gene pathways. Our results confirm that rhesus and cynomolgus macaques exhibit a closer evolutionary distance to each other than either species exhibits to humans or pig-tailed macaques. Conclusions These findings demonstrate that pig-tailed macaques can serve as an excellent animal model for the study of many human diseases particularly with regards to pluripotency and innate immune pathways.

U ovome radu opisan je kriterij za kvantitativno određivanje rizika nastanka ozljede glave kod udarca, tzv. kriterij HIC („Head Injury Criterion“) koji se u većini slučajeva u današnje vrijeme koristi za postizanje što veće sigurnosti svih sudionika u prometu te utječe i na sami dizajn vozila. Objašnjeni su biomehanički mehanizmi nastanka ozljede mozga kod tupog udarca, primjena, prednosti i nedostaci kriterija HIC te su obrađeni i mogući zamjenski kriteriji. This paper describes the criterion for the quantitative determination of the risk of a head injury on impact, so called HIC („Head Injury Criterion“) which in most cases today is used to maximize the safety of all traffic participants and also affect the design of the vehicle itself. The biomechanical mechanisms of the occurrence of brain injury in blunt impact, applications, advantages and disadvantages of the HIC criteria are explained and possible replacement criteria are discussed.

International audience; Mildly acidic water containing dissolved H 2 S presents a strong risk in the cracking of low-carbon steels. Several studies on H 2 S cracking mechanisms have shown that the main driving force is linked to the ability of H 2 S to promote hydrogen entry into the bulk material. Standard test methods have been developed and published as NACE technical standards (e.g. NACE TM0284 and NACE TM0177) to aid materials selection in the oil and gas sector. Though it is recognized that oxygen pollution should be avoided during H 2 S cracking tests, there is a lack of experimental data to illustrate the effects of a small oxygen pollution. Dissolved oxygen concentrations greater than the recommended upper limit (50 parts per billion) can easily be obtained in the case of poor laboratory practices. This paper will focus on the interactions between oxygen and H 2 S on electrochemical behavior of unalloyed steel. A continuous O 2 injection at a level corresponding to 500 ppb is applied, together with H 2 S bubbling in our test solutions, for periods lasting the same order as SSC standard tests. Steel surface reaction phenomena/corrosion rates in H 2 S saturated solution, with or without oxygen pollution, are studied using electrochemical impedance spectroscopy. The evolution of corrosion rates obtained from impedance analysis was compared to two other independent methods: i/ weight loss measurements and, ii/ hydrogen permeation. Without O 2 pollution, a permeation efficiency of 100% was obtained, as expected. Permeation current density was thus found to match precisely with the corrosion current density determined by impedance analysis at different times. On the other hand, when a continuous O 2 pollution was added in the system, significantly higher corrosion rates were observed, associated with test solution acidification. At the same time, permeation efficiency was decreased by up to one order of magnitude.

Three-dimensional spatial organization of chromosomes is defined by highly self-interacting regions 0.1-1 Mb in size termed Topological Associating Domains (TADs). Genetic factors that explain dynamic variation in TAD structure are not understood. We hypothesize that common structural variation (SV) in the human population; including deletions, insertions and inversions of >50 bp; can disrupt regulatory sequences and thereby influence TAD formation. To determine the effects of SVs on 3D chromatin organization, we performed chromosome conformation capture sequencing (Hi-C) of lymphoblastoid cell lines from 19 subjects for which SVs had been previously characterized in the 1000 genomes project. Large (>10kb) deletions had significant effects on long-range chromatin interactions. Deletions overall were associated with increased contacts that span the deleted region but had a modest effect on contacts in adjacent regions. Deletions at TAD boundaries were associated with diminished contacts in the adjacent domains, consistent with the structure of TADs being dependent on regulatory sequences at their boundaries. Large inversions in the population had a common signature characterized by a rearrangement of contacts that span its breakpoints. Our results suggest that common SVs in the population impact long range chromatin structure.

Head Injury Criterion (HIC) is the most important parameter in terms of human survival; it is indicative of brain injuries due to the impact of the head in numerous cases, with a vehicle. This index can be estimated by integrating the resulting acceleration of the head (measured in its gravity center) in a time window

High strength low alloy (HSLA) steels are used for the construction of pipelines for oil and natural gas transportation. For such applications pipelines must exhibit mechanical resistance and resistance to corrosion and hydrogen induced cracking (HIC). API 5L X65 steels are the main materials used for this purpose. However, for economic reasons, the use of steels of superior grades would be of interest. This work presents a comparative study of the corrosion and HIC resistances of an API 5L X65 and an API 5L X80 steel in deaerated solution A of NACE TM0284 standard. Electrochemical impedance spectroscopy (EIS) and potentiodynamic polarization experiments were performed in non-sour and sour (H2S-saturated) media, and HIC resistance tests were carried out in the sour medium. Scanning electron microscopy (SEM) and optical microscopy (OM) characterizations of polished and corroded samples were also done. Electrochemical tests showed that the API 5L X80 steel is slightly more susceptible to surface corrosion, which can be probably linked to its higher inclusion content and smaller grain sizes, it was also susceptible to HIC. Mn and S-rich inclusions found in the crack path indicate that this microstructural feature may play a key role in crack propagation and HIC susceptibility

It is a well admitted fact that oxygen contamination shall be avoided during H 2 S cracking tests of low alloy steels. In the 2016 revisions of NACE TM0177 and NACE TM0284 documents, quantitative limits of O 2 contamination were included with thresholds at 10 and 50 ppb of dissolved oxygen depending on the considered mechanical properties of the tested grade. However, the scientific basis of these values are not well established and there is still a lack of experimental data to illustrate the potential impacts of an oxygen pollution. In addition, while the revised test methods explicitly address initial contamination of the test solution before H 2 S introduction, they do not consider a continuous oxygen supply during testing. Yet, continuous contamination is extremely difficult to be completely eliminated. In order to better understand the impact of O 2 contamination on H 2 S cracking, a 3-years Joint Industrial Project was launched at the end of 2015. The objectives were to evaluate if O 2 contamination can affect H 2 S cracking test results. A range of steel grades covering different types of O&G applications for High H 2 S content were used. SSC (uniaxial tensile tests as well as 4 point-bend) and HIC tests were conducted, with well controlled and continuous O 2 contamination. Three levels of O 2 partial pressures in the gas feed corresponding to 300 ppb, 50 ppb and less than 10 ppb dissolved O 2 were used. In parallel to the standard qualification tests, hydrogen permeation and weight-loss corrosion experiments were performed with the same test matrix, covering all regions of the SSC severity diagram. This paper aims at sharing the main results of this project for high H 2 S content.

Human infection studies (HIS) have generally been used as a tool in the pathway for vaccine development in high income settings. Over the last decade, this model has been implemented in LMICs with the aim of accelerating development of next generation vaccines that would perform better in these settings. However, in most LMICs, the ethics and regulatory framework for the conduct of these studies are not in place. In Zambia, these studies are yet to be conducted and thus we conducted a stakeholder engagement workshop in October 2019. We engaged with bioethicists, regulatory authority officials, and scientists from within Zambia and other African countries to anticipate and address foreseeable ethical and regulatory issues when conducting HIS in Zambia for the first time. The workshop largely focused on sensitizing the stakeholders on the benefits of these studies with the following main points for consideration on the implementation of these studies in Zambia: need for in-country legal framework and guidelines; need for adequate informed consent based on comprehensive understanding of the concept of HIS and study requirements; and requirements for heightened vigilance to assure participant safety including good ethical and clinical practice with regulatory, ethical, data safety, and community oversight. Additionally, the workshop emphasized the need for rigorous health screening prior to enrolment; suitable infrastructure for containment; and personnel to provide appropriate treatment including emergency resuscitation and evacuation if indicated. Specific recommendations included compensation for burden of participation; access to care and provision for study related injury (e.g. no-fault insurance); and withdrawal and exit procedures to preserve individual and community safety. Finally, the meeting concluded that researchers should actively engage key gate keepers including civic leaders such as parliamentarians, universities, researchers, potential participants and laypersons to avoid circulation of misinformation.

The rail industry has been significantly affected by the passive safety technology in the last few years. The tram front-end design must fulfill the new requirements for pedestrian passive safety performance in the near future. The requirements are connected with a newly prepared technical guide &ldquo, Tramway front end design&rdquo, prepared by Technical Agency for ropeways and Guided Transport Systems. This paper describes research connected with new tram front-end design safe for pedestrians. The brief description of collision scenario and used human-body model &ldquo, Virthuman&rdquo, is provided. The numerical simulations (from field of passive safety) are supported by experiments. The interesting part is the numerical model of the tram windshield experimentally validated here. The results of simulations are discussed at the end of paper.

Background: Literature suggests that the presence of the current Bacillus Calmette Guerin (BCG) policy appears to mitigate COVID-19 disease burden but no information exists on the nature of the BCG strain and disease burden. Objectives: To study the association between type of BCG strain, BCG coverage (%), and COVID-19 disease burden. Methodology: An audit of global data on strains and disease burden was done. Country-specific data for COVID-19 cases and deaths, BCG-related data, and income level were obtained from the online databases, and the association was analyzed using linear regression. Results: Data of 139 countries were studied and 117 (84%) had a current BCG policy. Data on BCG strains were available for 51 countries and 18/51 (35%) used the Danish strain. While the choice of strain did not impact COVID-19-related disease burden, the presence of a current BCG policy was significantly associated with lower COVID-19 mortality. Conclusion: The presence of current BCG policy is associated with decreased COVID-19-related disease burden, but the type of strain used by a country in its vaccination program does not impact disease burden.

Background With the developments of DNA sequencing technology, large amounts of sequencing data have been produced that provides unprecedented opportunities for advanced association studies between somatic mutations and cancer types/subtypes which further contributes to more accurate somatic mutation based cancer typing (SMCT). In existing SMCT methods however, the absence of high-level feature extraction is a major obstacle in improving the classification performance. Results We propose DeepCNA, an advanced convolutional neural network (CNN) based classifier, which utilizes copy number aberrations (CNAs) and HiC data, to address this issue. DeepCNA first pre-process the CNA data by clipping, zero padding and reshaping. Then, the processed data is fed into a CNN classifier, which extracts high-level features for accurate classification. Experimental results on the COSMIC CNA dataset indicate that 2D CNN with both cell lines of HiC data lead to the best performance. We further compare DeepCNA with three widely adopted classifiers, and demonstrate that DeepCNA has at least 78% improvement of performance. Conclusions This paper demonstrates the advantages and potential of the proposed DeepCNA model for processing of somatic point mutation based gene data, and proposes that its usage may be extended to other complex genotype-phenotype association studies.

PEGylated proteins are an increasing important class of therapeutic drugs due to their improved pharmacokinetic characteristics and solubility over their corresponding native forms. PEGylation is the covalent attachment of one or more polyethylene glycol (PEG) molecules to a protein. Despite the many advantages of PEGylated drugs, one of the major challenges is the purification step after the chemical reaction. The main purpose of this project is to determine the nature of chemical interactions between a modified resin with PEG 5000 g/mol and PEGylated proteins that results in a previously demonstrated ability of such resins for the resolution of PEGylated proteins. A chromatographical separation of PEGylated proteins was additionally demonstrated for lysozyme using the modified resin Sepharose 6B-PEG5000 previously reported for PEGylated RNase A. Fourier Transform Infrared (FTIR) spectroscopy provided insight of the resin modification. The interaction thermodynamics associated with PEGylated proteins in hydrophobic interaction chromatography (HIC) with modified resin was carried out in with an ITC (Isothermal Titration Calorimetry) analysis. The specific enthalpy (∆G) was found to be exothermic for both proteins in potassium phosphate buffer with 1.5 M ammonium sulfate at 25ºC. MonoPEGylated proteins showed large negative entropy (-T∆S) values, related to the enhanced hydrophobic interaction between PEG5000 molecules from the resin and PEGylated protein forms. In addition, binding constants (K) of PEGylated proteins to modified resin were slightly higher compared to unmodified proteins.

International audience; This paper examines the influence of traces of oxygen on corrosion and hydrogen charging of steel in an H 2 S containing environment. It is well known that H 2 S promotes hydrogen entry into steels, that may result in many types of steel failures such as Hydrogen Induced Cracking (HIC), Sulfide Stress Cracking (SSC), and Stress-Oriented Hydrogen Induced Cracking (SOHIC). Since it is a huge concern for oil and gas industries, standard test methods have been developed and published as NACE technical methods (e.g. NACE TM0284 and NACE TM0177). Though it is recognized that oxygen pollution should be avoided during H 2 S cracking tests, there is still a lack of experimental data to illustrate the potential impacts of a small oxygen pollution. The aim of the present study is to check if oxygen traces can modify the mechanisms of corrosion and hydrogen charging of steel in H 2 S containing medium. Experiments consisted of hydrogen permeation measurements through a thin pure iron membrane. They were performed at free potential circuit in order to ensure more realistic environmental conditions. The corrosion rate was also evaluated and test solutions analyzed.

International audience; Cet article se propose d’établir une différence entre les emplois anaphoriques des adverbes de lieu formés sur hic et ceux des adverbes formés sur is. Dans le cas des phrases présentatives, la reprise anaphorique privilégie hic, à même d’installer un nouveau thème (§ 2). Le paramètre stylistique, invoqué par les études précédentes, ne vaut que pour les autres chaînes référentielles (§ 3) ; il semble possible d’en rendre compte en termes linguistiques. L’emploi de hic se justifie par la référence indexicale construite qu’il construit. Ce mode de référence, qui s’explique par la valeur déictique de hic, rend l’anaphore plus ‘puissante’ en individuant le référent (§ 4).

Increased accumulation and/or impaired utilization of fatty acid in extra-adipose tissues are implicated in the pathogenesis of insulin resistance and type 2 diabetes. Pyruvate dehydrogenase kinase 4 (Pdk4) is a key enzyme involved in fatty oxidation and energy expenditure, and its expression can be repressed by pro-inflammatory stimuli. Previously, we have shown that class II transactivator (CIITA) mediates the adverse effect of interferon gamma (IFN-γ) in skeletal muscle cells by cooperating with hypermethylated in cancer 1 (HIC1) to repress silent information regulator 1 (SIRT1) transcription. Building upon this finding, we report here that CIITA interacted with HIC1 via the GTP-binding domain (GBD) while HIC1 interacted with CIITA via the BTB/POZ domain. The GBD domain was required for CIITA to repress SIRT1 transcription probably acting as a bridge for CIITA to bind to HIC1 and consequently to bind to the SIRT1 promoter. IFN-γ stimulation, CIITA over-expression, or HIC1 over-expression repressed Pdk4 promoter activity while silencing either CIITA or HIC1 normalized Pdk4 expression in the presence of IFN-γ. An increase in SIRT1 expression or activity partially rescued Pdk4 expression in the presence of CIITA, but SIRT1 inhibition abrogated Pdk4 normalization even in the absence of CIITA. Taken together, our data have identified a HIC1-CIITA-SIRT1 axis that regulates Pdk4 transcription in response to IFN-γ stimulation.

The effectiveness of therapeutic monoclonal antibodies (mAbs) is governed not only by their bioactivity, but also by their biophysical properties. Assays for rapidly evaluating the biophysical properties of mAbs are valuable for identifying those most likely to exhibit superior properties such as high solubility, low viscosity and slow serum clearance. Analytical hydrophobic interaction chromatography (HIC), which is performed at high salt concentrations to enhance hydrophobic interactions, is an attractive assay for identifying mAbs with low hydrophobicity. However, this assay is low throughput and thus not amenable to processing the large numbers of mAbs that are commonly generated during antibody discovery. Therefore, we investigated whether an alternative, higher throughput, assay could be developed that is based on evaluating antibody self-association at high salt concentrations using affinity-capture self-interaction nanoparticle spectroscopy (AC-SINS). Our approach is to coat gold nanoparticles with polyclonal anti-human antibodies, use these conjugates to immobilize human mAbs, and evaluate mAb self-interactions by measuring the plasmon wavelengths of the antibody conjugates as a function of ammonium sulfate concentration. We find that hydrophobic mAbs, as identified by HIC, generally show significant self-association at low to moderate ammonium sulfate concentrations, while hydrophilic mAbs typically show self-association only at high ammonium sulfate concentrations. The correlation between AC-SINS and HIC measurements suggests that our assay, which can evaluate tens to hundreds of mAbs in a parallel manner and requires only small (microgram) amounts of antibody, will enable early identification of mAb candidates with low hydrophobicity and improved biophysical properties.

We can now sequence and identify genome wide epigenetic patterns and perform a variety of “genomic experiments” within relatively short periods of time—ranging from days to weeks. Yet, despite these technological advances, we have a poor understanding of the inter-relationships between epigenetics, genome structure-function, and nutrition. Perhaps this limitation lies, in part, in our propensity to study epigenetics in terms of the linear arrangement of elements and genes. Here we propose that a more complete understanding of how nutrition impacts on epigenetics and cellular development resides within the inter-relationships between DNA and histone modification patterns and genome function, in the context of spatial organization of chromatin and the epigenome.