Individuals with Darier disease have an increased risk of suicide and self-injurious behaviours

In a large population-based registry study of 935 patients in Sweden with Darier disease, we show that patients with the disease display significantly increased risks of suicide and self-injurious behaviours.

Clinical implications of ADHD, ASD, and their co-occurrence in early adulthood-the prospective ABIS-study

BACKGROUND

Attention-deficit/hyperactivity disorder (ADHD) and autism spectrum disorder (ASD) are childhood-onset disorders associated with functional and psychosocial impairments that may persist into adulthood, leading to serious personal and societal costs.

OBJECTIVE

This study aimed to examine the socio-economic difficulties, physical and mental comorbidities, and psycho-social vulnerabilities associated with ADHD, ASD, and their co-occurrence among young adults.

METHODS

16 365 families with children born 1997-1999, were involved in the prospective population-based ABIS study (All Babies in Southeast Sweden). A total of 6 233 ABIS young adults answered the questionnaire at the 17-19-year follow-up and were included in this case-control study. Diagnoses of ADHD and ASD from birth up to 17 years of age were obtained from the Swedish National Diagnosis Register. N=182 individuals received a single diagnosis of ADHD, n=78 of ASD, and n=51 received both diagnoses and were considered the co-occurrence group. Multiple multinomial logistic regression analyses were performed.

RESULTS

In the univariate analyses all three conditions were significantly associated with concentration difficulties, worse health quality, lower socio-economic status, lower faith in the future, less control over life, and lower social support. In the adjusted analyses, individuals with ADHD were almost three-times more likely to have less money compared with their friends (aOR 2.86; p < .001), experienced worse sleep quality (aOR 1.50; p = .043) and concentration difficulties (aOR 1.96; p < .001). ASD group were two-fold more likely to experience concentration difficulties (aOR 2.35; p = .002) and tended not to have faith in the future (aOR .63; p = .055), however, showed lesser risk-taking bahaviours (aOR .40; p < .001). Finally, the co-occurrence was significantly associated with unemployment (aOR 2.64; p = .007) and tended to have a higher risk of autoimmune disorders (aOR 2.41; p = .051), however, showed a 51% lower risk of stomach pain (aOR .49; p = .030).

CONCLUSIONS

All these conditions significantly deteriorated several areas of life. ADHD/ASD co-occurrence is a heavy burden for health associated with several psychosocial vulnerabilities, that shared a similar morbidity pattern with ADHD although showed less risk cognitive and behavioral profile, similar to the ASD group. Long-term follow-up and support for individuals with these conditions over the life course are crucial.

Dynamics of nucleic acid mobility

Advances in sequencing technologies and bioinformatic analyses are accelerating the quantity and quality of data from all domains of life. This rich resource has the potential to reveal a number of important incidences with respect to possible exchange of nucleic acids. Ancient events have impacted species evolution and adaptation to new ecological niches. However, we still lack a full picture of processes ongoing within and between somatic cells, gametes, and different organisms. We propose that events linked to acceptance of alien nucleic acids grossly could be divided into 2 main routes in plants: one, when plants are exposed to extreme challenges and, the second level, a more everyday or season-related stress incited by biotic or abiotic factors. Here, many events seem to comprise somatic cells. Are the transport and acceptance processes of alien sequences random or are there specific regulatory systems not yet fully understood? Following entrance into a new cell, a number of intracellular processes leading to chromosomal integration and function are required. Modification of nucleic acids and possibly exchange of sequences within a cell may also occur. Such fine-tune events are most likely very common. There are multiple questions that we will discuss concerning different types of vesicles and their roles in nucleic acid transport and possible intracellular sequence exchange between species.

Structural insights into CodY activation and DNA recognition

Virulence factors enable pathogenic bacteria to infect host cells, establish infection, and contribute to disease progressions. In Gram-positive pathogens such as Staphylococcus aureus (Sa) and Enterococcus faecalis (Ef), the pleiotropic transcription factor CodY plays a key role in integrating metabolism and virulence factor expression. However, to date, the structural mechanisms of CodY activation and DNA recognition are not understood. Here, we report the crystal structures of CodY from Sa and Ef in their ligand-free form and their ligand-bound form complexed with DNA. Binding of the ligands-branched chain amino acids and GTP-induces conformational changes in the form of helical shifts that propagate to the homodimer interface and reorient the linker helices and DNA binding domains. DNA binding is mediated by a non-canonical recognition mechanism dictated by DNA shape readout. Furthermore, two CodY dimers bind to two overlapping binding sites in a highly cooperative manner facilitated by cross-dimer interactions and minor groove deformation. Our structural and biochemical data explain how CodY can bind a wide range of substrates, a hallmark of many pleiotropic transcription factors. These data contribute to a better understanding of the mechanisms underlying virulence activation in important human pathogens.

Vascular Proteome Responses Precede Organ Dysfunction in a Murine Model of Staphylococcus aureus Bacteremia

Vascular dysfunction and organ failure are two distinct, albeit highly interconnected, clinical outcomes linked to morbidity and mortality in human sepsis. The mechanisms driving vascular and parenchymal damage are dynamic and display significant molecular cross talk between organs and tissues. Therefore, assessing their individual contribution to disease progression is technically challenging. Here, we hypothesize that dysregulated vascular responses predispose the organism to organ failure. To address this hypothesis, we have evaluated four major organs in a murine model of Staphylococcus aureus sepsis by combining in vivo labeling of the endothelial cell surface proteome, data-independent acquisition (DIA) mass spectrometry, and an integrative computational pipeline. The data reveal, with unprecedented depth and throughput, that a septic insult evokes organ-specific proteome responses that are highly compartmentalized, synchronously coordinated, and significantly correlated with the progression of the disease. These responses include abundant vascular shedding, dysregulation of the intrinsic pathway of coagulation, compartmentalization of the acute phase response, and abundant upregulation of glycocalyx components. Vascular cell surface proteome changes were also found to precede bacterial invasion and leukocyte infiltration into the organs, as well as to precede changes in various well-established cellular and biochemical correlates of systemic coagulopathy and tissue dysfunction. Importantly, our data suggest a potential role for the vascular proteome as a determinant of the susceptibility of the organs to undergo failure during sepsis. IMPORTANCE Sepsis is a life-threatening response to infection that results in immune dysregulation, vascular dysfunction, and organ failure. New methods are needed for the identification of diagnostic and therapeutic targets. Here, we took a systems-wide approach using data-independent acquisition (DIA) mass spectrometry to track the progression of bacterial sepsis in the vasculature leading to organ failure. Using a murine model of S. aureus sepsis, we were able to quantify thousands of proteins across the plasma and parenchymal and vascular compartments of multiple organs in a time-resolved fashion. We showcase the profound proteome remodeling triggered by sepsis over time and across these compartments. Importantly, many vascular proteome alterations precede changes in traditional correlates of organ dysfunction, opening a molecular window for the discovery of early markers of sepsis progression.

Nanostructurally Controllable Strong Wood Aerogel toward Efficient Thermal Insulation

Eco-friendly materials with superior thermal insulation and mechanical properties are desirable for improved energy- and space-efficiency in buildings. Cellulose aerogels with structural anisotropy could fulfill these requirements, but complex processing and high energy demand are challenges for scaling up. Here we propose a scalable, nonadditive, top-down fabrication of strong anisotropic aerogels directly from wood with excellent, near isotropic thermal insulation functions. The aerogel was obtained through cell wall dissolution and controlled precipitation in lumen, using an ionic liquid (IL) mixture comprising DMSO and a guanidinium phosphorus-based IL [MTBD][MMP]. The wood aerogel shows a unique structure with lumen filled with nanofibrils network. In situ formation of a cellulosic nanofibril network in the lumen results in specific surface areas up to 280 m²/g and high yield strengths >1.2 MPa. The highly mesoporous structure (average pore diameter ∼20 nm) of freeze-dried wood aerogels leads to low thermal conductivities in both the radial (0.037 W/mK) and axial (0.057 W/mK) directions, showing great potential as scalable thermal insulators. This synthesis route is energy efficient with high nanostructural controllability. The unique nanostructure and rare combination of strength and thermal properties set the material apart from comparable bottom-up aerogels. This nonadditive synthesis approach is believed to contribute significantly toward large-scale design and structure control of biobased aerogels.

Structure of mycobacterial CIII2CIV2 respiratory supercomplex bound to the tuberculosis drug candidate telacebec (Q203)

The imidazopyridine telacebec, also known as Q203, is one of only a few new classes of compounds in more than 50 years with demonstrated antituberculosis activity in humans. Telacebec inhibits the mycobacterial respiratory supercomplex composed of complexes III and IV (CIII2CIV2). In mycobacterial electron transport chains, CIII2CIV2 replaces canonical CIII and CIV, transferring electrons from the intermediate carrier menaquinol to the final acceptor, molecular oxygen, while simultaneously transferring protons across the inner membrane to power ATP synthesis. We show that telacebec inhibits the menaquinol:oxygen oxidoreductase activity of purified Mycobacterium smegmatis CIII2CIV2 at concentrations similar to those needed to inhibit electron transfer in mycobacterial membranes and Mycobacterium tuberculosis growth in culture. We then used electron cryomicroscopy (cryoEM) to determine structures of CIII2CIV2 both in the presence and absence of telacebec. The structures suggest that telacebec prevents menaquinol oxidation by blocking two different menaquinol binding modes to prevent CIII2CIV2 activity.

Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19

Our understanding of protective versus pathological immune responses to SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is limited by inadequate profiling of patients at the extremes of the disease severity spectrum. Here, we performed multi-omic single-cell immune profiling of 64 COVID-19 patients across the full range of disease severity, from outpatients with mild disease to fatal cases. Our transcriptomic, epigenomic, and proteomic analyses revealed widespread dysfunction of peripheral innate immunity in severe and fatal COVID-19, including prominent hyperactivation signatures in neutrophils and NK cells. We also identified chromatin accessibility changes at NF-κB binding sites within cytokine gene loci as a potential mechanism for the striking lack of pro-inflammatory cytokine production observed in monocytes in severe and fatal COVID-19. We further demonstrated that emergency myelopoiesis is a prominent feature of fatal COVID-19. Collectively, our results reveal disease severity-associated immune phenotypes in COVID-19 and identify pathogenesis-associated pathways that are potential targets for therapeutic intervention.

Social cognition in refugee children: an experimental cross-sectional study of emotional processing with Syrian families in Turkish communities

More than 5.6 million people have fled Syria since 2011, about half of them children. These children grow up with parents that often suffer from war-related mental health problems. In this study, we assess emotional processing abilities of 6-18 year-old children growing up in families that have fled from Syria and reside in Turkish communities (100 families, 394 individuals). We demonstrate that mothers', but not fathers', post-traumatic stress (PTS) impacts children's emotional processing abilities. A 4% reduction of mothers' PTS was equivalent to 1 year of development in children, even when controlling for parents' traumatic experiences. Making a small investment in increased mental health of refugee mothers might have a positive impact on the lives of their children.

smartPARE: An R Package for Efficient Identification of True mRNA Cleavage Sites

Degradome sequencing is commonly used to generate high-throughput information on mRNA cleavage sites mediated by small RNAs (sRNA). In our datasets of potato (Solanum tuberosum, St) and Phytophthora infestans (Pi), initial predictions generated high numbers of cleavage site predictions, which highlighted the need of improved analytic tools. Here, we present an R package based on a deep learning convolutional neural network (CNN) in a machine learning environment to optimize discrimination of false from true cleavage sites. When applying smartPARE to our datasets on potato during the infection process by the late blight pathogen, 7.3% of all cleavage windows represented true cleavages distributed on 214 sites in P. infestans and 444 sites in potato. The sRNA landscape of the two organisms is complex with uneven sRNA production and cleavage regions widespread in the two genomes. Multiple targets and several cases of complex regulatory cascades, particularly in potato, was revealed. We conclude that our new analytic approach is useful for anyone working on complex biological systems and with the interest of identifying cleavage sites particularly inferred by sRNA classes beyond miRNAs.

A novel type of colistin resistance genes selected from random sequence space

Antibiotic resistance is a rapidly increasing medical problem that severely limits the success of antibiotic treatments, and the identification of resistance determinants is key for surveillance and control of resistance dissemination. Horizontal transfer is the dominant mechanism for spread of resistance genes between bacteria but little is known about the original emergence of resistance genes. Here, we examined experimentally if random sequences can generate novel antibiotic resistance determinants de novo. By utilizing highly diverse expression libraries encoding random sequences to select for open reading frames that confer resistance to the last-resort antibiotic colistin in Escherichia coli, six de novocolistin resistance conferring peptides (Dcr) were identified. The peptides act via direct interactions with the sensor kinase PmrB (also termed BasS in E. coli), causing an activation of the PmrAB two-component system (TCS), modification of the lipid A domain of lipopolysaccharide and subsequent colistin resistance. This kinase-activation was extended to other TCS by generation of chimeric sensor kinases. Our results demonstrate that peptides with novel activities mediated via specific peptide-protein interactions in the transmembrane domain of a sensory transducer can be selected de novo, suggesting that the origination of such peptides from non-coding regions is conceivable. In addition, we identified a novel class of resistance determinants for a key antibiotic that is used as a last resort treatment for several significant pathogens. The high-level resistance provided at low expression levels, absence of significant growth defects and the functionality of Dcr peptides across different genera suggest that this class of peptides could potentially evolve as bona fide resistance determinants in natura.

We expressed over 100 million randomly generated DNA sequences in Escherichia coli and selected 6 variants that encode peptides that provide resistance to the last-resort antibiotic colistin. We show that the selected peptides are auxiliary activators of the two-component system PmrAB, and that resistance is mediated via modifications of the cell envelope causing decreased antibiotic uptake. This is the first example where random expression libraries have been employed to select for peptides that perform an activating function by direct peptide-protein interactions in vivo, adding support to the idea that non-coding DNA can serve as a substrate for de novo gene evolution. Additionally, the described peptides expand the narrow list of colistin resistance genes and further analyses of clinical isolates will be necessary to determine if similar resistance determinants have evolved in natura.

Critical behavior within 20 fs drives the out-of-equilibrium laser-induced magnetic phase transition in nickel

It has long been known that ferromagnets undergo a phase transition from ferromagnetic to paramagnetic at the Curie temperature, associated with critical phenomena such as a divergence in the heat capacity. A ferromagnet can also be transiently demagnetized by heating it with an ultrafast laser pulse. However, to date, the connection between out-of-equilibrium and equilibrium phase transitions, or how fast the out-of-equilibrium phase transitions can proceed, was not known. By combining time- and angle-resolved photoemission with time-resolved transverse magneto-optical Kerr spectroscopies, we show that the same critical behavior also governs the ultrafast magnetic phase transition in nickel. This is evidenced by several observations. First, we observe a divergence of the transient heat capacity of the electron spin system preceding material demagnetization. Second, when the electron temperature is transiently driven above the Curie temperature, we observe an extremely rapid change in the material response: The spin system absorbs sufficient energy within the first 20 fs to subsequently proceed through the phase transition, whereas demagnetization and the collapse of the exchange splitting occur on much longer, fluence-independent time scales of ~176 fs. Third, we find that the transient electron temperature alone dictates the magnetic response. Our results are important because they connect the out-of-equilibrium material behavior to the strongly coupled equilibrium behavior and uncover a new time scale in the process of ultrafast demagnetization.