Clinical, immunohistochemical, and genetic characterization of splice-altering biallelic DES variants: Therapeutic implications.

Pathogenic variants in the DES gene clinically manifest as progressive skeletal muscle weakness, cardiomyopathy with associated severe arrhythmias, and respiratory insufficiency, and are collectively known as desminopathies. While most DES pathogenic variants act via a dominant mechanism, recessively acting variants have also been reported. Currently, there are no effective therapeutic interventions for desminopathies of any type. Here, we report an affected individual with rapidly progressive dilated cardiomyopathy, requiring heart transplantation at age 13 years, in the setting of childhood-onset skeletal muscle weakness. We identified biallelic DES variants (c.640-13 T>A and c.1288+1 G>A) and show aberrant DES gene splicing in the affected individual's muscle. Through the generation of an inducible lentiviral system, we transdifferentiated fibroblast cultures derived from the affected individual into myoblasts and validated this system using RNA sequencing. We tested rationally designed, custom antisense oligonucleotides to screen for splice correction in these transdifferentiated cells and a functional minigene splicing assay. However, rather than correctly redirecting splicing, we found them to induce undesired exon skipping. Our results indicate that, while an individual precision-based molecular therapeutic approach to splice-altering pathogenic variants is promising, careful preclinical testing is imperative for each novel variant to test the feasibility of this type of approach for translation.

Engineering metal-carbide hydrogen traps in steels.

Hydrogen embrittlement reduces the durability of the structural steels required for the hydrogen economy. Understanding how hydrogen interacts with the materials plays a crucial role in managing the embrittlement problems. Theoretical models have indicated that carbon vacancies in metal carbide precipitates are effective hydrogen traps in steels. Increasing the number of carbon vacancies in individual metal carbides is important since the overall hydrogen trapping capacity can be leveraged by introducing abundant metal carbides in steels. To verify this concept, we compare a reference steel containing titanium carbides (TiCs), which lack carbon vacancies, with an experimental steel added with molybdenum (Mo), which form Ti-Mo carbides comprising more carbon vacancies than TiCs. We employ theoretical and experimental techniques to examine the hydrogen trapping behavior of the carbides, demonstrating adding Mo alters the hydrogen trapping mechanism, enabling hydrogen to access carbon vacancy traps within the carbides, leading to an increase in trapping capacity.

Identifying weak signals to prepare for uncertainty in the energy sector.

This study aims to prepare the energy sector for uncertainty using a foresight tool known as weak signals. Weak signals (subtle signs of emerging issues with significant impact potential) are often overlooked during strategic planning due to their inherent predictive uncertainty. However, the value does not lie in precise forecasting but in broadening the consideration of future possibilities. By proactively monitoring and addressing these otherwise neglected developments, stakeholders can gain early awareness of threats and opportunities and enhance their resilience, adaptability, and innovation. A panel of technology experts identified eight weak signals in this study: 1) growing mistrust and local grid security measures, 2) consumer reactions to overly prescriptive policies, 3) long-term forecasting errors for thin-margin projects, 4) emergence of variable power industries, and 5) establishment of intercontinental transmission precedence; including three potential 'wild cards' requiring proactive mitigation: 6) escalating electrical generation dependence on continued imports, 7) a new threat surpassing climate change, and 8) mass deployment of low-emissions technology triggering a runaway loss of social license. Political factors were the predominant source of uncertainty, as decisions can suddenly transform the energy landscape. Economic, technological, and social factors followed closely behind, generally through the emergence of new industries and behavioural responses. While environmental and legal factors were less frequent, stakeholders should still adopt a holistic approach, as the signals were found to be highly interconnected. Organisations should also assess their local context when applying these findings and continuously update and respond to their own list of weak signals.

Designing 3d metal oxides: selecting optimal density functionals for strongly correlated materials.

Transition metal oxides (TMOs) have remarkable physicochemical properties, are non-toxic, and have low cost and high annual production, thus they are commonly studied for various technological applications. Density functional theory (DFT) can help to optimize TMO materials by providing insights into their electronic, optical and thermodynamic properties, and hence into their structure-performance relationships, over a wide range of solid-state structures and compositions. However, this is underpinned by the choice of the exchange-correlation (XC) functional, which is critical to accurately describe the highly localized and correlated 3d-electrons of the transition metals in TMOs. This tutorial review presents a benchmark study of density functionals (DFs), ranging from generalized gradient approximation (GGA) to range-separated hybrids (RSH), with the all-electron def2-TZVP basis set, comparing magneto-electro-optical properties of 3d TMOs against experimental observations. The performance of the DFs is assessed by analyzing the band structure, density of states, magnetic moment, structural static and dynamic parameters, optical properties, spin contamination and computational cost. The results disclose the strengths and weaknesses of the XC functionals, in terms of accuracy, and computational efficiency, suggesting the unprecedented PBE0-1/5 as the best candidate. The findings of this work contribute to necessary developments of XC functionals for periodic systems, and materials science modelling studies, particularly informing how to select the optimal XC functional to obtain the most trustworthy description of the ground-state electron structure of 3d TMOs.

Molecular dynamic simulation on temperature evolution of SiC under directional microwave radiation.

Silicon carbide (SiC) is widely used as the substrate for high power electronic devices as well as susceptors for microwave (MW) heating. The dynamics of microwave interaction with SiC is not fully understood, especially at the material boundaries. In this paper, we used the molecular dynamics simulation method to study the temperature evolution during the microwave absorption of SiC under various amplitudes and frequencies of the microwave electric field. Directional MW heating of a SiC crystal slab bounded by surfaces along [100] crystallographic direction shows significantly faster melting when the field is applied parallel to the surface compared to when applied perpendicular.

Personalized Single-Cell Proteogenomics to Distinguish Acute Myeloid Leukemia from Non-Malignant Clonal Hematopoiesis.

Genetic mutations associated with acute myeloid leukemia (AML) also occur in age-related clonal hematopoiesis, often in the same individual. This makes confident assignment of detected variants to malignancy challenging. The issue is particularly crucial for AML post-treatment measurable residual disease monitoring, where results can be discordant between genetic sequencing and flow cytometry. We show here, that it is possible to distinguish AML from clonal hematopoiesis and to resolve the immunophenotypic identity of clonal architecture. To achieve this, we first design patient-specific DNA probes based on patient's whole-genome sequencing, and then use them for patient-personalized single-cell DNA sequencing with simultaneous single-cell antibody-oligonucleotide sequencing. Examples illustrate AML arising from DNMT3A and TET2 mutated clones as well as independently. The ability to personalize single-cell proteogenomic assessment for individual patients based on leukemia-specific genomic features has implications for ongoing AML precision medicine efforts.

Evidence of hydrogen trapping at second phase particles in zirconium alloys.

Zirconium alloys are used in safety-critical roles in the nuclear industry and their degradation due to ingress of hydrogen in service is a concern. In this work experimental evidence, supported by density functional theory modelling, shows that the α-Zr matrix surrounding second phase particles acts as a trapping site for hydrogen, which has not been previously reported in zirconium. This is unaccounted for in current models of hydrogen behaviour in Zr alloys and as such could impact development of these models. Zircaloy-2 and Zircaloy-4 samples were corroded at 350 °C in simulated pressurised water reactor coolant before being isotopically spiked with 2H2O in a second autoclave step. The distribution of 2H, Fe and Cr was characterised using nanoscale secondary ion mass spectrometry (NanoSIMS) and high-resolution energy dispersive X-ray spectroscopy. 2H- was found to be concentrated around second phase particles in the α-Zr lattice with peak hydrogen isotope ratios of 2H/1H = 0.018-0.082. DFT modelling confirms that the hydrogen thermodynamically favours sitting in the surrounding zirconium matrix rather than within the second phase particles. Knowledge of this trapping mechanism will inform the development of current understanding of zirconium alloy degradation through-life.

Atomistic Insights into Lithium Storage Mechanisms in Anatase, Rutile, and Amorphous TiO2 Electrodes.

Density functional theory calculations were used to investigate the phase transformations of LixTiO2 (at 0 ≤ x ≤ 1), solid-state Li+ diffusion, and interfacial charge-transfer reactions in both crystalline and amorphous forms of TiO2. It is shown that in contrast to crystalline TiO2 polymorphs, the energy barrier to Li+ diffusion in amorphous TiO2 decreases with increasing mole fraction of Li+ due to the changes of chemical species pair interactions following the progressive filling of low-energy Li+ trapping sites. Sites with longer Li-Ti and Li-O interactions exhibit lower Li+ insertion energies and higher migration energy barriers. Due to its disordered atomic arrangement and increasing Li+ diffusivity at higher mole fractions, amorphous TiO2 exhibits both surface and bulk storage mechanisms. The results suggest that nanostructuring of crystalline TiO2 can increase both the rate and capacity because the capacity dependence on the bulk storage mechanism is minimized and replaced with the surface storage mechanism. These insights into Li+ storage mechanisms in different forms of TiO2 can guide the fabrication of TiO2 electrodes to maximize the capacity and rate performance in the future.

Evidence for Fast Lithium-Ion Diffusion and Charge-Transfer Reactions in Amorphous TiO x Nanotubes: Insights for High-Rate Electrochemical Energy Storage.

The charge-storage kinetics of amorphous TiO x nanotube electrodes formed by anodizing three-dimensional porous Ti scaffolds are reported. The resultant electrodes demonstrated not only superior storage capacities and rate capability to anatase TiO x nanotube electrodes but also improved areal capacities (324 µAh cm-2 at 50 µA cm-2 and 182 µAh cm-2 at 5 mA cm-2) and cycling stability (over 2000 cycles) over previously reported TiO x nanotube electrodes using planar current collectors. Amorphous TiO x exhibits very different electrochemical storage behavior from its anatase counterpart as the majority of its storage capacity can be attributed to capacitive-like processes with more than 74 and 95% relative contributions being attained at 0.05 and 1 mV s-1, respectively. The kinetic analysis revealed that the insertion/extraction process of Li+ in amorphous TiO x is significantly faster than in anatase structure and controlled by both solid-state diffusion and interfacial charge-transfer kinetics. It is concluded that the large capacitive contribution in amorphous TiO x originates from its highly defective and loosely packed structure and lack of long-range ordering, which facilitate not only a significantly faster Li+ diffusion process (diffusion coefficients of 2 × 10-14 to 3 × 10-13 cm2 s-1) but also more facile interfacial charge-transfer kinetics than anatase TiO x.

Resolving the structure of TiBe12.

There has been considerable controversy regarding the structure of TiBe12, which is variously reported as hexagonal and tetragonal. Lattice dynamics simulations based on density functional theory (DFT) show the tetragonal phase space group I4/mmm to be more stable over all temperatures, while the hexagonal phase exhibits an imaginary phonon mode, which, if followed, would lead to the cell adopting the tetragonal structure. We then report the predicted ground state elastic constants and temperature dependence of the bulk modulus and thermal expansion for the tetragonal phase.

Reprogramming of Polycomb-Mediated Gene Silencing in Embryonic Stem Cells by the miR-290 Family and the Methyltransferase Ash1l.

Members of the miR-290 family are the most abundantly expressed microRNAs (miRNAs) in mouse embryonic stem cells (ESCs). They regulate aspects of differentiation, pluripotency, and proliferation of ESCs, but the molecular program that they control has not been fully delineated. In the absence of Dicer, ESCs fail to express mature miR-290 miRNAs and have selective aberrant overexpression of Hoxa, Hoxb, Hoxc, and Hoxd genes essential for body plan patterning during embryogenesis, but they do not undergo a full differentiation program. Introduction of mature miR-291 into DCR(-/-) ESCs restores Hox gene silencing. This was attributed to the unexpected regulation of Polycomb-mediated gene targeting by miR-291. We identified the methyltransferase Ash1l as a pivotal target of miR-291 mediating this effect. Collectively, our data shed light on the role of Dicer in ESC homeostasis by revealing a facet of molecular regulation by the miR-290 family.

A forward genetic screen reveals novel independent regulators of ULBP1, an activating ligand for natural killer cells.

Recognition and elimination of tumor cells by the immune system is crucial for limiting tumor growth. Natural killer (NK) cells become activated when the receptor NKG2D is engaged by ligands that are frequently upregulated in primary tumors and on cancer cell lines. However, the molecular mechanisms driving NKG2D ligand expression on tumor cells are not well defined. Using a forward genetic screen in a tumor-derived human cell line, we identified several novel factors supporting expression of the NKG2D ligand ULBP1. Our results show stepwise contributions of independent pathways working at multiple stages of ULBP1 biogenesis. Deeper investigation of selected hits from the screen showed that the transcription factor ATF4 drives ULBP1 gene expression in cancer cell lines, while the RNA-binding protein RBM4 supports ULBP1 expression by suppressing a novel alternatively spliced isoform of ULBP1 mRNA. These findings offer insight into the stress pathways that alert the immune system to danger.

miR-155 activates cytokine gene expression in Th17 cells by regulating the DNA-binding protein Jarid2 to relieve polycomb-mediated repression.

Specification of the T helper 17 (Th17) cell lineage requires a well-defined set of transcription factors, but how these integrate with posttranscriptional and epigenetic programs to regulate gene expression is poorly understood. Here we found defective Th17 cell cytokine expression in miR-155-deficient CD4+ T cells in vitro and in vivo. Mir155 was bound by Th17 cell transcription factors and was highly expressed during Th17 cell differentiation. miR-155-deficient Th17 and T regulatory (Treg) cells expressed increased amounts of Jarid2, a DNA-binding protein that recruits the Polycomb Repressive Complex 2 (PRC2) to chromatin. PRC2 binding to chromatin and H3K27 histone methylation was increased in miR-155-deficient cells, coinciding with failure to express Il22, Il10, Il9, and Atf3. Defects in Th17 cell cytokine expression and Treg cell homeostasis in the absence of Mir155 could be partially suppressed by Jarid2 deletion. Thus, miR-155 contributes to Th17 cell function by suppressing the inhibitory effects of Jarid2.

Identification of competence pheromone responsive genes in Streptococcus pneumoniae by use of DNA microarrays.

Natural genetic transformation in Streptococcus pneumoniae is controlled in part by a quorum-sensing system mediated by a peptide pheromone called competence-stimulating peptide (CSP), which acts to coordinate transient activation of genes required for competence. To characterize the transcriptional response and regulatory events occurring when cells are exposed to competence pheromone, we constructed DNA microarrays and analysed the temporal expression profiles of 1817 among the 2129 unique predicted open reading frames present in the S. pneumoniae TIGR4 genome (84%). After CSP stimulation, responsive genes exhibited four temporally distinct expression profiles: early, late and delayed gene induction, and gene repression. At least eight early genes participate in competence regulation including comX, which encodes an alternative sigma factor. Late genes were dependent on ComX for CSP-induced expression, many playing important roles in transformation. Genes in the delayed class (third temporal wave) appear to be stress related. Genes repressed during the CSP response include ribosomal protein loci and other genes involved in protein synthesis. This study increased the number of identified CSP-responsive genes from approximately 40 to 188. Given the relatively large number of induced genes (6% of the genome), it was of interest to determine which genes provide functions essential to transformation. Many of the induced loci were subjected to gene disruption mutagenesis, allowing us to establish that among 124 CSP-inducible genes, 67 were individually dispensable for transformation, whereas 23 were required for transformation.

Phylogenetic analysis of the microbial populations in the wild herbivore gastrointestinal tract: insights into an unexplored niche.

At present, there is little information on the phylogenetic diversity of microbial species that inhabit the gastrointestinal tracts of wildlife. To increase understanding in this area, we initiated a characterization of the bacterial diversity in the digestive tracts of three wild African ruminant species namely eland (Taurotragus oryx), Thompson's gazelle (Gazella rufifrons) and Grant's gazelle (Gazella granti), together with a domesticated ruminant species, zebu cattle (Bos indicus), and a non-ruminant species, zebra (Equus quagga). Bacterial diversity was analysed by PCR amplification, sequencing and phylogenetic analysis of 16S ribosomal DNA (rDNA) sequences. A total of 252 full-length 16S rDNA sequences averaging 1,500 base pairs (bp) in length, and an additional 27 partial sequences were obtained and subject to phylogenetic analysis. Using a 98% criterion for similarity, all except for one of the sequences were derived from distinct phylotypes. At least 24 distinct operational taxonomic units (OTU's) could be identified, with the majority of these sequences representing hitherto uncharacterized species and genera. The sequences were generally affiliated with four major bacterial phyla, the majority being members of the Firmicutes (low G+C Gram-positives) related to the genera Clostridium and Ruminococcus. By contrast, with earlier studies using 16S rDNA sequences to assess biodiversity in Bos taurus dairy cattle, Gram-negative bacteria in the Bacteroidales (Prevotella-Bacteroides group) were poorly represented. The lack of redundancy in the 16S rDNA dataset from the five African ungulate species, and the presence of novel sequences not previously described from the gastrointestinal tract of any animal species, highlights the level of diversity that exists in these ecosystems and raises the question as to the functional role of these species in the gastrointestinal tract.