SF3B1 mutations provide genetic vulnerability to copper ionophores in human acute myeloid leukemia

In a phenotypical screen of 56 acute myeloid leukemia (AML) patient samples and using a library of 10,000 compounds, we identified a hit with increased sensitivity toward SF3B1-mutated and adverse risk AMLs. Through structure-activity relationship studies, this hit was optimized into a potent, specific, and nongenotoxic molecule called UM4118. We demonstrated that UM4118 acts as a copper ionophore that initiates a mitochondrial-based noncanonical form of cell death known as cuproptosis. CRISPR-Cas9 loss-of-function screen further revealed that iron-sulfur cluster (ISC) deficiency enhances copper-mediated cell death. Specifically, we found that loss of the mitochondrial ISC transporter ABCB7 is synthetic lethal to UM4118. ABCB7 is misspliced and down-regulated in SF3B1-mutated leukemia, creating a vulnerability to copper ionophores. Accordingly, ABCB7 overexpression partially rescued SF3B1-mutated cells to copper overload. Together, our work provides mechanistic insights that link ISC deficiency to cuproptosis, as exemplified by the high sensitivity of SF3B1-mutated AMLs. We thus propose SF3B1 mutations as a biomarker for future copper ionophore-based therapies.

Unveiling the evolutionary history of lingonberry (Vaccinium vitis-idaea L.) through genome sequencing and assembly of European and North American subspecies

Lingonberry (Vaccinium vitis-idaea L.) produces tiny red berries that are tart and nutty in flavor. It grows widely in the circumpolar region, including Scandinavia, northern parts of Eurasia, Alaska, and Canada. Although cultivation is currently limited, the plant has a long history of cultural use among indigenous communities. Given its potential as a food source, genomic resources for lingonberry are significantly lacking. To advance genomic knowledge, the genomes for 2 subspecies of lingonberry (V. vitis-idaea ssp. minus and ssp. vitis-idaea var. 'Red Candy') were sequenced and de novo assembled into contig-level assemblies. The assemblies were scaffolded using the bilberry genome (Vaccinium myrtillus) to generate a chromosome-anchored reference genome consisting of 12 chromosomes each with a total length of 548.07 Mb [contig N50 = 1.17 Mb, BUSCO (C%) = 96.5%] for ssp. vitis-idaea and 518.70 Mb [contig N50 = 1.40 Mb, BUSCO (C%) = 96.9%] for ssp. minus. RNA-seq-based gene annotation identified 27,243 and 25,718 genes on the respective assembly, and transposable element detection methods found that 45.82 and 44.58% of the genome were repeats. Phylogenetic analysis confirmed that lingonberry was most closely related to bilberry and was more closely related to blueberries than cranberries. Estimates of past effective population size suggested a continuous decline over the past 1-3 MYA, possibly due to the impacts of repeated glacial cycles during the Pleistocene leading to frequent population fragmentation. The genomic resource created in this study can be used to identify industry-relevant genes (e.g. anthocyanin production), infer phylogeny, and call sequence-level variants (e.g. SNPs) in future research.

Can simple 'molecular' corrections outperform projector augmented-wave density functional theory in the prediction of 35 Cl electric field gradient tensor parameters for chlorine-containing crystalline systems?

Many-body expansion (MBE) fragment approaches have been applied to accurately compute nuclear magnetic resonance (NMR) parameters in crystalline systems. Recent examples demonstrate that electric field gradient (EFG) tensor parameters can be accurately calculated for 14 N and 17 O. A key additional development is the simple molecular correction (SMC) approach, which uses two one-body fragment (i.e., isolated molecule) calculations to adjust NMR parameter values established using 'benchmark' projector augmented-wave (PAW) density functional theory (DFT) values. Here, we apply a SMC using the hybrid PBE0 exchange-correlation (XC) functional to see if this can improve the accuracy of calculated 35 Cl EFG tensor parameters. We selected eight organic and two inorganic crystal structures and considered 15 chlorine sites. We find that this SMC improves the accuracy of computed values for both the 35 Cl quadrupolar coupling constant (CQ ) and the asymmetry parameter ( η Q ) by approximately 30% compared with benchmark PAW DFT values. We also assessed a SMC that offers local improvements not only in terms of the quality of the XC functional but simultaneously in the quality of the description of relativistic effects via the inclusion of spin-orbit effects. As the inorganic systems considered contain heavy atoms bonded to the chlorine atoms, we find further improvements in the accuracy of calculated 35 Cl EFG tensor parameters when both a hybrid functional and spin-orbit effects are included in the SMC. On the contrary, for chlorine-containing organics, the inclusion of spin-orbit relativistic effects using a SMC does not improve the accuracy of computed 35 Cl EFG tensor parameters.

Characterization of runs of homozygosity islands in American mink using whole-genome sequencing data

The genome-wide analysis of runs of homozygosity (ROH) islands can be an effective strategy for identifying shared variants within a population and uncovering important genomic regions related to complex traits. The current study performed ROH analysis to characterize the genome-wide patterns of homozygosity, identify ROH islands and annotated genes within these candidate regions using whole-genome sequencing data from 100 American mink (Neogale vison). After sequence processing, variants were called using GATK and Samtools pipelines. Subsequent to quality control, 8,373,854 bi-allelic variants identified by both pipelines remained for further analysis. A total of 34,652 ROH segments were identified in all individuals, among which shorter segments (0.3-1 Mb) were abundant throughout the genome, approximately accounting for 84.39% of all ROH. Within these segments, we identified 63 ROH islands housing 156 annotated genes. The genes located in ROH islands were associated with fur quality (EDNRA, FGF2, FOXA2 and SLC24A4), body size/weight (MYLK4, PRIM2, FABP2, EYS and PHF3), immune capacity (IL2, IL21, PTP4A1, SEMA4C, JAK2, CCNA2 and TNIP3) and reproduction (ADAD1, KHDRBS2, INSL6, PGRMC2 and HSPA4L). Furthermore, Gene Ontology and KEGG pathway enrichment analyses revealed 56 and 9 significant terms (FDR-corrected p-value < 0.05), respectively, among which cGMP-PKG signalling pathway, regulation of actin cytoskeleton, and calcium signalling pathway were highlighted due to their functional roles in growth and fur characteristics. This is the first study to present ROH islands in American mink. The candidate genes from ROH islands and functional enrichment analysis suggest possible signatures of selection in response to the mink breeding targets, such as increased body length, reproductive performance and fur quality. These findings contribute to our understanding of genetic characteristics, and provide complementary information to assist with implementation of breeding strategies for genetic improvement in American mink.

A high-quality reference genome for the common creek chub, Semotilus atromaculatus

Creek chub (Semotilus atromaculatus) is a leuciscid minnow species commonly found in anthropogenically disturbed environments, making it an excellent model organism to study human impacts on aquatic systems. Genomic resources for creek chub and other leuciscid species are currently limited. However, advancements in DNA sequencing now allow us to create genomic resources at a historically low cost. Here, we present a high quality, 239 contig reference genome for the common creek chub, created with PacBio HiFi sequencing. We compared the assembly quality of two pipelines: Pacific Biosciences' Improved Phase Assembly (873 contigs) and Hifiasm (239 contigs). Quality and completeness of this genome is comparable to the zebrafish (Danioninae) and fathead minnow (Leuciscidae) genomes. The creek chub genome is highly syntenic to the zebrafish and fathead minnow genomes, and while our assembly does not resolve into the expected 25 chromosomes, synteny with zebrafish suggests that each creek chub chromosome is likely represented by 1-4 large contigs in our assembly. This reference genome is a valuable resource that will enhance genomic biodiversity studies of creek chub and other nonmodel leuciscid species common to disturbed environments.

StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses

Generalist microbes have adapted to a multitude of environmental stresses through their integrated stress response system. Individual stress responses have been quantified by E. coli metabolism and expression (ME) models under thermal, oxidative and acid stress, respectively. However, the systematic quantification of cross-stress & cross-talk among these stress responses remains lacking. Here, we present StressME: the unified stress response model of E. coli combining thermal (FoldME), oxidative (OxidizeME) and acid (AcidifyME) stress responses. StressME is the most up to date ME model for E. coli and it reproduces all published single-stress ME models. Additionally, it includes refined rate constants to improve prediction accuracy for wild-type and stress-evolved strains. StressME revealed certain optimal proteome allocation strategies associated with cross-stress and cross-talk responses. These stress-optimal proteomes were shaped by trade-offs between protective vs. metabolic enzymes; cytoplasmic vs. periplasmic chaperones; and expression of stress-specific proteins. As StressME is tuned to compute metabolic and gene expression responses under mild acid, oxidative, and thermal stresses, it is useful for engineering and health applications. The modular design of our open-source package also facilitates model expansion (e.g., to new stress mechanisms) by the computational biology community.

Ebola virus VP35 interacts non-covalently with ubiquitin chains to promote viral replication

Ebolavirus (EBOV) belongs to a family of highly pathogenic viruses that cause severe hemorrhagic fever in humans. EBOV replication requires the activity of the viral polymerase complex, which includes the cofactor and Interferon antagonist VP35. We previously showed that the covalent ubiquitination of VP35 promotes virus replication by regulating interactions with the polymerase complex. In addition, VP35 can also interact non-covalently with ubiquitin (Ub); however, the function of this interaction is unknown. Here, we report that VP35 interacts with free (unanchored) K63-linked polyUb chains. Ectopic expression of Isopeptidase T (USP5), which is known to degrade unanchored polyUb chains, reduced VP35 association with Ub and correlated with diminished polymerase activity in a minigenome assay. Using computational methods, we modeled the VP35-Ub non-covalent interacting complex, identified the VP35-Ub interacting surface, and tested mutations to validate the interface. Docking simulations identified chemical compounds that can block VP35-Ub interactions leading to reduced viral polymerase activity. Treatment with the compounds reduced replication of infectious EBOV in cells and in vivo in a mouse model. In conclusion, we identified a novel role of unanchored polyUb in regulating Ebola virus polymerase function and discovered compounds that have promising anti-Ebola virus activity.

Escherichia coli CRISPR arrays from early life fecal samples preferentially target prophages

CRISPR-Cas systems are defense mechanisms against phages and other nucleic acids that invade bacteria and archaea. In Escherichia coli, it is generally accepted that CRISPR-Cas systems are inactive in laboratory conditions due to a transcriptional repressor. In natural isolates, it has been shown that CRISPR arrays remain stable over the years and that most spacer targets (protospacers) remain unknown. Here, we re-examine CRISPR arrays in natural E. coli isolates and investigate viral and bacterial genomes for spacer targets using a bioinformatics approach coupled to a unique biological dataset. We first sequenced the CRISPR1 array of 1769 E. coli isolates from the fecal samples of 639 children obtained during their first year of life. We built a network with edges between isolates that reflect the number of shared spacers. The isolates grouped into 34 modules. A search for matching spacers in bacterial genomes showed that E. coli spacers almost exclusively target prophages. While we found instances of self-targeting spacers, those involving a prophage and a spacer within the same bacterial genome were rare. The extensive search for matching spacers also expanded the library of known E. coli protospacers to 60%. Altogether, these results favor the concept that E. coli's CRISPR-Cas is an antiprophage system and highlight the importance of reconsidering the criteria use to deem CRISPR-Cas systems active.

OpenProt 2.0 builds a path to the functional characterization of alternative proteins

The OpenProt proteogenomic resource (https://www.openprot.org/) provides users with a complete and freely accessible set of non-canonical or alternative open reading frames (AltORFs) within the transcriptome of various species, as well as functional annotations of the corresponding protein sequences not found in standard databases. Enhancements in this update are largely the result of user feedback and include the prediction of structure, subcellular localization, and intrinsic disorder, using cutting-edge algorithms based on machine learning techniques. The mass spectrometry pipeline now integrates a machine learning-based peptide rescoring method to improve peptide identification. We continue to help users explore this cryptic proteome by providing OpenCustomDB, a tool that enables users to build their own customized protein databases, and OpenVar, a genomic annotator including genetic variants within AltORFs and protein sequences. A new interface improves the visualization of all functional annotations, including a spectral viewer and the prediction of multicoding genes. All data on OpenProt are freely available and downloadable. Overall, OpenProt continues to establish itself as an important resource for the exploration and study of new proteins.

Mock microbial community meta-analysis using different trimming of amplicon read lengths

Trimming of sequencing reads is a pre-processing step that aims to discard sequence segments such as primers, adapters and low quality nucleotides that will interfere with clustering and classification steps. We evaluated the impact of trimming length of paired-end 16S and 18S rRNA amplicon reads on the ability to reconstruct the taxonomic composition and relative abundances of communities with a known composition in both even and uneven proportions. We found that maximizing read retention maximizes recall but reduces precision by increasing false positives. The presence of expected taxa was accurately predicted across broad trim length ranges but recovering original relative proportions remains a difficult challenge. We show that parameters that maximize taxonomic recovery do not simultaneously maximize relative abundance accuracy. Trim length represents one of several experimental parameters that have non-uniform impact across microbial clades, making it a difficult parameter to optimize. This study offers insights, guidelines, and helps researchers assess the significance of their decisions when trimming raw reads in a microbiome analysis based on overlapping or non-overlapping paired-end amplicons.

High diversity, abundance, and expression of hydrogenases in groundwater

Hydrogen may be the most important electron donor available in the subsurface. Here we analyse the diversity, abundance and expression of hydrogenases in 5 proteomes, 25 metagenomes, and 265 amplicon datasets of groundwaters with diverse geochemistry. A total of 1545 new [NiFe]-hydrogenase gene sequences were recovered, which considerably increased the number of sequences (1999) in a widely used database. [NiFe]-hydrogenases were highly abundant, as abundant as the DNA-directed RNA polymerase. The abundance of hydrogenase genes increased with depth from 0 to 129 m. Hydrogenases were present in 481 out of 1245 metagenome-assembled genomes. The relative abundance of microbes with hydrogenases accounted for ~50% of the entire community. Hydrogenases were actively expressed, making up as much as 5.9% of methanogen proteomes. Most of the newly discovered diversity of hydrogenases was in "Group 3b", which has been associated with sulfur metabolism. "Group 3d", facilitating the interconversion of electrons between hydrogen and NAD, was the most abundant and mainly observed in methanotrophs and chemoautotrophs. "Group 3a", associated with methanogenesis, was the most abundant in proteomes. Two newly discovered groups of [NiFe]-hydrogenases, observed in Methanobacteriaceae and Anaerolineaceae, further expanded diversity. Our results highlight the vast diversity, abundance and expression of hydrogenases in groundwaters, suggesting a high potential for hydrogen oxidation in subsurface habitats.

Charge Self-Regulation of Metallic Heterostructure Ni2 P@Co9 S8 for Alkaline Water Electrolysis with Ultralow Overpotential at Large Current Density

Designing cost-effective alkaline water-splitting electrocatalysts is essential for large-scale hydrogen production. However, nonprecious catalysts face challenges in achieving high activity and durability at a large current density. An effective strategy for designing high-performance electrocatalysts is regulating the active electronic states near the Fermi-level, which can improve the intrinsic activity and increase the number of active sites. As a proof-of-concept, it proposes a one-step self-assembly approach to fabricate a novel metallic heterostructure based on nickel phosphide and cobalt sulfide (Ni2 P@Co9 S8 ) composite. The charge transfer between active Ni sites of Ni2 P and Co─Co bonds of Co9 S8 efficiently enhances the active electronic states of Ni sites, and consequently, Ni2 P@Co9 S8 exhibits remarkably low overpotentials of 188 and 253 mV to reach the current density of 100 mA cm-2 for the hydrogen evolution reaction and oxygen evolution reaction, respectively. This leads to the Ni2 P@Co9 S8 incorporated water electrolyzer possessing an ultralow cell voltage of 1.66 V@100 mA cm-2 with ≈100% retention over 100 h, surpassing the commercial Pt/C║RuO2 catalyst (1.9 V@100 mA cm-2 ). This work provides a promising methodology to boost the activity of overall water splitting with ultralow overpotentials at large current density by shedding light on the charge self-regulation of metallic heterostructure.

Wetting vs Droplet Aggregation: A Broadband Rotational Spectroscopic Study of 3-Methylcatechol⋅⋅⋅Water Clusters

Two competing solvation pathways of 3-methylcatechol (MC), an atmospherically relevant aromatic molecule, with up to five water molecules were explored in detail by using a combination of broadband rotational spectroscopy and computational chemistry. Theoretically, two different pathways of solvation emerge: the commonly observed droplet pathway which involves preferential binding among the water molecules while the solute serves as an anchor point for the formation of a water cluster, and an unexpected wetting pathway which involves interactions between the water molecules and the aromatic face of MC, i.e., a wetting of the π-surface. Conclusive identification of the MC hydrate structures, and therefore the wetting pathway, was facilitated by rotational spectra of the parent MC hydrates and several H2 18 O and 13 C isotopologues which exhibit splittings associated with methyl internal rotation and/or water tunneling motions. Theoretical modelling and analyses offer insights into the tunneling and conversion barriers associated with the observed hydrate conformers and the nature of the non-covalent interactions involved in choosing the unusual wetting pathway.

Automated identification of unstandardized medication data: a scalable and flexible data standardization pipeline using RxNorm on GEMINI multicenter hospital data

Objective

Patient data repositories often assemble medication data from multiple sources, necessitating standardization prior to analysis. We implemented and evaluated a medication standardization procedure for use with a wide range of pharmacy data inputs across all drug categories, which supports research queries at multiple levels of granularity.

Methods

The GEMINI-RxNorm system automates the use of multiple RxNorm tools in tandem with other datasets to identify drug concepts from pharmacy orders. GEMINI-RxNorm was used to process 2 090 155 pharmacy orders from 245 258 hospitalizations between 2010 and 2017 at 7 hospitals in Ontario, Canada. The GEMINI-RxNorm system matches drug-identifying information from pharmacy data (including free-text fields) to RxNorm concept identifiers. A user interface allows researchers to search for drug terms and returns the relevant original pharmacy data through the matched RxNorm concepts. Users can then manually validate the predicted matches and discard false positives. We designed the system to maximize recall (sensitivity) and enable excellent precision (positive predictive value) with efficient manual validation. We compared the performance of this system to manual coding (by a physician and pharmacist) of 13 medication classes.

Results

Manual coding was performed for 1 948 817 pharmacy orders and GEMINI-RxNorm successfully returned 1 941 389 (99.6%) orders. Recall was greater than 0.985 in all 13 drug classes, and the F1-score and precision remained above 0.90 in all drug classes, facilitating efficient manual review to achieve 100% precision. GEMINI-RxNorm saved time substantially compared with manual standardization, reducing the time taken to review a pharmacy order row from an estimated 30 to 5 s and reducing the number of rows needed to be reviewed by up to 99.99%.

Discussion and Conclusion

GEMINI-RxNorm presents a novel combination of RxNorm tools and other datasets to enable accurate, efficient, flexible, and scalable standardization of pharmacy data. By facilitating efficient manual validation, the GEMINI-RxNorm system can allow researchers to achieve near-perfect accuracy in medication data standardization.

Infrared and vibrational circular dichroism spectra of methyl β-D-glucopyranose in water: The application of the quantum cluster growth and clusters-in-a-liquid solvation models

The infrared (IR) and vibrational circular dichroism (VCD) spectra of methyl β-D-glucopyranose in water were measured. Both implicit and explicit solvation models were utilized to explain the observed spectra. The vast body of existing experimental and theoretical data suggested that about eight explicit water molecules are needed to account for the solvent effects, supported by the current Quantum Cluster Growth (QCG) analysis. Extensive manual and systematic conformational searches of the molecular target and its water clusters were carried out by using a recently developed conformational searching tool, conformer-rotamer ensemble sampling tool (CREST), and the microsolvation model in the associated QCG code. The Boltzmann averaged IR and VCD spectra of the methyl β-D-glucopyranose-(water)n (n = 8) conformers in the PCM of water provide better agreement with the experimental ones than those with n = 0, 1, and 2. The explicit solvation with eight water molecules was shown to greatly modify the conformational preference of methyl β-D-glucopyranose from its monomeric form. Further analyses show that the result is consistent with the existence of long-lived methyl β-D-glucopyranose monohydrates with the additional explicit water effects being accounted for with the quantum mechanical treatment of the other seven close-by water molecules in the PCM of water.

Measuring small-scale plasma irregularities in the high-latitude E- and F-regions simultaneously

The ionosphere, Earth's space environment, exhibits widespread turbulent structuring, or plasma irregularities, visualized by the auroral displays seen in Earth's polar regions. Such plasma irregularities have been studied for decades, but plasma turbulence remains an elusive phenomenon. We combine scale-dependent measurements from a ground-based radar with satellite observations to characterize small-scale irregularities simultaneously in the bottomside and topside ionosphere and perform a statistical analysis on an aggregate from both instruments over time. We demonstrate the clear mapping of information vertically along the ionospheric altitude column, for field-perpendicular wavelengths down to 1.5 km. Our results paint a picture of the northern hemisphere high-latitude ionosphere as a turbulent system that is in a constant state of growth and decay; energy is being constantly injected and dissipated as the system is continuously attempting an accelerated return to equilibrium. We connect the widespread irregularity dissipation to Pedersen conductance in the E-region, and discuss the similarities between irregularities found in the polar cap and in the auroral region in that context. We find that the effects of a conducting E-region on certain turbulent properties (small-scale spectral index) is near ubiquitous in the dataset, and so we suggest that the electrodynamics of a conducting E-region must be considered when discussing plasma turbulence at high latitudes. This intimate relationship opens up the possibility that E-region conductivity is associated with the generation of F-region irregularities, though further studies are needed to assess that possibility.

Conformational Distributions of Phenyl β-D-Glucopyranoside and Gastrodin in Solution by Vibrational Optical Activity and Theoretical Calculations

The conformational landscapes of two highly flexible monosaccharide derivatives, namely phenyl β-D-glucopyranoside (ph-β-glu) and 4-(hydroxymethyl)phenyl β-D-glucopyranoside, also commonly known as gastrodin, were explored using a combined experimental and theoretical approach. For the infrared, Raman, and the associated vibrational optical activity (VOA), i.e., vibrational circular dichroism and Raman optical activity, experiments of these two compounds in DMSO and in water were carried out. Extensive and systematic conformational searches were performed using a recently developed conformational searching tool called CREST (conformer-rotamer ensemble sampling tool) in the two solvents. Fourteen and twenty-four low-energy conformers were identified at the DFT level for ph-β-glu and gastrodin, respectively. The spectral simulations of individual conformers were done at the B3LYP-D3BJ/def2-TZVPD level with the polarizable continuum model of the solvents. The VOA spectral features exhibit much higher specificity to conformational differences than their parent infrared and Raman. The excellent agreements achieved between the experimental and simulated VOA spectra allow for the extraction of experimental conformational distributions of these two carbohydrates in solution directly. The experimental percentage abundances based on the hydroxymethyl (at the pyranose ring) conformations G+, G-, and T for ph-β-glu were obtained to be 15%, 75%, and 10% in DMSO and 53%, 40%, and 7% in water, respectively, in comparison to the previously reported gas phase values of 68%, 25%, and 7%, highlighting the important role of solvents in conformational preferences. The corresponding experimental distributions for gastrodin are 56%, 22%, and 22% in DMSO and 70%, 21%, and 9% in water.