Teleseismic tomography: Equation one is wrong

ABSTRACT Seismic tomography methods that use waves originating outside the volume being studied are subject to bias caused by unknown structure outside this volume. The bias is of the same mathematical order and similar magnitude as the local-structure effects being studied; failure to account for it can significantly corrupt derived structural models. This bias can be eliminated by adding to the inverse problem three unknown parameters specifying the direction and time for each incident wave, a procedure analogous to solving for event locations in local-earthquake and whole-mantle tomography. The forward problem is particularly simple: The first-order change in the arrival time at an observation point resulting from a perturbation to the incident-wave direction and time equals the change in the time of the perturbed incident wave at the point where the unperturbed ray entered the study volume. This consequence of Fermat’s principle apparently has not previously been recognized. Published teleseismic tomography models probably contain significant artifacts and need to be recomputed using the more complete theory.

Validated Determination of NRG1 Ig-like Domain Structure by Mass Spectrometry Coupled with Computational Modeling

High resolution hydroxyl radical protein footprinting (HR-HRPF) is a mass spectrometry-based method that measures the solvent exposure of multiple amino acids in a single experiment, offering constraints for experimentally-informed computational modeling. HR-HRPF-based modeling has previously been used to accurately model the structure of proteins of known structure, but the technique has never been used to determine the structure of a protein of unknown structure leaving questions of unintentional bias and applicability to unknown structures unresolved. Here, we present the use of HR-HRPF-based modeling to determine the structure of the Ig-like domain of NRG1, a protein with no close homolog of known structure. Independent determination of the protein structure by both HR-HRPF-based modeling and heteronuclear NMR was carried out, with results compared only after both processes were complete. The HR-HRPF-based model was highly similar to the lowest energy NMR model, with a backbone RMSD of 1.6 Å. To our knowledge, this is the first use of HR-HRPF-based modeling to determine a previously uncharacterized protein structure.

Molecular architecture of nucleosome remodeling and deacetylase sub-complexes by integrative structure determination

The Nucleosome Remodeling and Deacetylase (NuRD) complex is a chromatin-modifying assembly that regulates gene expression and DNA damage repair. Despite its importance, limited structural information is available on the complex and a detailed understanding of its mechanism is lacking. We investigated the molecular architecture of three NuRD sub-complexes: MTA1-HDAC1-RBBP4 (MHR), MTA1N-HDAC1-MBD3GATAD2CC (MHM), and MTA1-HDAC1-RBBP4-MBD3-GATAD2 (NuDe) using Bayesian integrative structure determination with IMP (Integrative Modeling Platform), drawing on information from SEC-MALLS, DIA-MS, XLMS, negative stain EM, X-ray crystallography, NMR spectroscopy, secondary structure and homology predictions. The structures were corroborated by independent cryo-EM maps, biochemical assays, and known cancer-associated mutations. Our integrative structure of the 2:2:2 MHM complex shows asymmetric binding of MBD3, whereas our structure of the NuDe complex shows MBD3 localized precisely to a single position distant from the MTA1 dimerization interface. Our models suggest a possible mechanism by which asymmetry is introduced in NuRD, and indicate three previously unrecognized subunit interfaces in NuDe: HDAC1C-MTA1BAH, MTA1BAH-MBD3, and HDAC160-100-MBD3. We observed that a significant number of cancer-associated mutations mapped to protein-protein interfaces in NuDe. Our approach also allows us to localize regions of unknown structure, such as HDAC1C and MBD3IDR, thereby resulting in the most complete structural characterization of these NuRD sub-complexes so far.

Characterizing disease-associated human proteins without available protein structures or homologues

Mutations in human proteins lead to diseases. The structure of these proteins can help understand the mechanism of such diseases and develop therapeutics against them. With improved deep learning techniques such as RoseTTAFold and AlphaFold, we can predict the structure of these proteins even in the absence of structural homologues. We modeled and extracted the domains from 553 disease-associated human proteins. We noticed that the model quality was higher and the RMSD lower between AlphaFold and RoseTTAFold models for domains that could be assigned to CATH families as compared to those which could be assigned to Pfam families of unknown structure or could not be assigned to either. We predicted ligand-binding sites, protein-protein interfaces, conserved residues and destabilising effects caused by residue mutations in these predicted structures. We then explored whether the disease-associated mutations were in the proximity of these predicted functional sites or if they destabilized the protein structure based on ddG calculations. We could explain 80% of these disease-associated mutations based on proximity to functional sites or structural destabilization. Usage of models from the two state-of-the-art techniques provide better confidence in our predictions, and we explain 93 additional mutations based on RoseTTAFold models which could not be explained based solely on AlphaFold models.

Halomonas jincaotanensis sp. nov., a 1-naphthylamine degrading bacterium isolated from Pamir Plateau

A Gram-staining-negative, aerobic, rod-shaped bacterium, designated strain TRM 85114 T , was isolated from Jincaotan wetland in Pamir Plateau, PR China. According to the study, we found it have an ability to degrade 1-naphthylamine. Strain TRM 85114 T grow at 4-35 ℃ (optimum, 30 ℃), pH of 6.0-9.0 (optimum, pH 6.0) and can tolerate 1%-10% (w/v) NaCl (optimum, 3%). Phylogenetic analysis of 16S rRNA gene sequences revealed that strain TRM 85114 T was affiliated of the genus Halomonas , sharing high sequence similarity (97.3%) with the type strain of Halomonas korlensis XK1 T . The primary cellular fatty acids of strain TRM 85114 T were C 16:0 and C 19:0 cyclo ω 8 c . The predominate respiratory quinone was Q-9. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, lyso-phospatidylglycerol, phospholipids of unknown structure containing glucosarmine, and five unidentified lipids. The genomic DNA G+C content of strain TRM 85114 T was 61.6 mol%. Calculated the average nucleotide identities and the digital DNA-DNA hybridization values between strain TRM 85114 T and the related type Halomonas strains further revealed that TRM 85114 T represented a novel species of the genus Halomonas , for which the name Halomonas jincaotanensis sp. nov. is proposed. The type strain is TRM 85114 T (CCTCC AB 2021006 T =LMG 32311 T ).

Crustacean cardiac ganglion model reveals constraints on morphology and conductances

The crustacean cardiac ganglion (CG) network coordinates the rhythmic contractions of the heart muscle to control the circulation of blood. The network consists of 9 cells, 5 large motor cells (LC1-5) and 4 small endogenous pacemaker cells (SCs). We report a new three-compartmental biophysical model of an LC that is morphologically realistic and includes provision for inputs from the SCs via a gap-junction coupled spike-initiation-zone (SIZ) compartments. To determine physiologically viable LC models in this realistic configuration, maximal conductances in three compartments of an LC are determined by random sampling from a biologically-characterized 9D-parameter space, followed by a three stage rejection protocol that checks for conformity with electrophysiological features from single cell traces. LC models that pass the single cell rejection protocol are then incorporated into a network model which is then used in a final rejection protocol stage. Using disparate experimental data, the study provides hitherto unknown structure-function insights related to the crustacean cardiac ganglion large cell, including predictions about morphology including the role of its SIZ, and the differential roles of active conductances in the three compartments. Further, we extend analyses of emergent conductance relationships and correlations in model neurons relative to their biological counterparts, allowing us to make inferences both with respect to the biological system as well as the implications of the ability to detect such relationships in populations of model neurons going forward.

Molecular Diagnosis and Prenatal Phenotype Analysis of Eight Fetuses With Ciliopathies

Human ciliopathies are hereditary conditions caused by variants in ciliary-associated genes. Ciliopathies are often characterized by multiple system defects. However, it is not easy to make a definite diagnosis in the prenatal period only based on the imageology. In this report, eight new prenatal cases from five unrelated families diagnosed with ciliopathies were systematically examined. The clinical manifestations of these fetuses showed such prenatal diagnostic features as occipital encephalocele, and polydactyly and polycystic kidneys. Situs inversus caused by CPLANE1 variant was first reported. In Family 1 and Family 3, homozygous variants of CPLANE1 and NPHP4 caused by consanguineous marriage and uniparental disomy were detected by whole-exome sequencing, respectively. In Family 2, Family 4 and Family 5, compound heterozygotes of TMEM67 and DYNC2H1 including two novel missense variants and one novel nonsense variant were identified. The distribution of pathogenic missense variants along TMEM67 gene mainly clustered in the extracellular cysteine rich region, extracellular area with unknown structure, and the transmembrane regions. Genotype-phenotype relationship between CPLANE1 and TMEM67 genes was concluded. This report describes new clinical manifestations and novel variants in CPLANE1, TMEM67, NPHP4, and DYNC2H1.

Synthesis and analytical characterization of all N–N-coupled, dimeric oxidation products of α-tocopheramine: hydrazo-, azo-, and azoxy-tocopherol

Tocopherols are a mixture of antioxidants which are commonly referred to as vitamin E. Tocopheramines differ from tocopherols by an amino function in lieu of the phenolic OH group. They are potent antioxidants which are used in biomedical scenarios as well as stabilizers for polymers against aging. While in aqueous media α-tocopheramine is mainly oxidized to α-tocopherylquinone and N-oxidized by-products, oxidation in apolar media or in polymeric matrices mainly leads to dimeric compounds of hitherto unknown structure. In the present study, we synthesized the whole array of N,N-dimerization product of α-tocopheramine, including the hydrazo, azo, and azoxy derivatives for the first time, and provided comprehensive analytical data as well as general protocols to access the compounds in straightforward syntheses. These results can now be used to identify the common oxidation by-products of α -tocopheramine in different reaction systems. Graphic abstract

Interior of sand fly (Diptera: Psychodidae) abdomen reveals novel structures involved in pheromone release: discovering the Manifold.

The males of many species of New World Phlebotomines produce volatile terpenoid chemicals which have been shown in Lutzomyia longipalpis s.l. and L. cruciata to be sex/aggregation pheromones which attract female and male conspecifics. Pheromone is produced in secretory cells surrounding a cuticular reservoir which collects the pheromone and passes it through a cuticular duct to the surface of the insect. On the surface the pheromone passes through a specialised structure prior to evaporation. The shape and distribution of the structures are highly diverse and differ according to species. They range in appearance from slightly raised domes (papules) to almost spherical apple shaped structures to slight depressions with central spikes and all with a central pore. They can occur either singly or in many hundreds distributed on most abdominal tergites or grouped on one. The pheromone secreting apparatus in sand flies and other insects have historically been examined from the exterior using scanning electron microscopy (SEM) and from the interior using transmission electron microscopy. In this study we used SEM to examine the interior cuticular structure of 3 members of the Lutzomyia longipalpis s.l. species complex and Migonemyia migonei and found a new structure associated with pheromone release which we have called the Manifold. The Manifold is a substantial structure siting in-line between the cuticular duct and the underside of the tergite. Differences in the size and shape of the Manifold may be related to the chemical structure of the pheromone. In addition to the importance of this hitherto unknown structure in the production, dissemination and ecology of the pheromone, as well as its potential taxonomic value, examination of the interior cuticle by SEM may help locate the secretory apparatus in important vector species where pheromonal activity has been inferred from behavioural studies but the external secretory structures or potential pheromones have not been found.

A Capped Tudor Domain within a Core Subunit of the Sin3L/Rpd3L Histone Deacetylase Complex Binds Nucleic Acids

Chromatin-modifying complexes containing histone deacetylase (HDAC) activities play critical roles in the regulation of gene transcription in eukaryotes. These complexes are thought to lack intrinsic DNA-binding activity, but according to a well-established paradigm, they are recruited via protein-protein interactions by gene-specific transcription factors and post-translational histone modifications to their sites of action on the genome. The mammalian Sin3L/Rpd3L complex, comprising more than a dozen different polypeptides, is an ancient HDAC complex found in diverse eukaryotes. The subunits of this complex harbor conserved domains and motifs of unknown structure and function. Here we show that Sds3, a constitutively associated subunit critical for the proper functioning of the complex, harbors a type of Tudor domain that we designate the capped Tudor domain (CTD). Unlike canonical Tudor domains that bind modified histones, the Sds3 CTD binds to nucleic acids that can form higher-order structures such as G-quadruplexes, and shares similarities with the knotted Tudor domain of the Esa1 histone acetyltransferase (HAT) that was previously shown to bind single-stranded RNA. Our findings expand the range of macromolecules capable of recruiting the Sin3L/Rpd3L complex and draws attention to potentially new roles for this HDAC complex in transcription biology.