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Journal of Microbiology and... Dec 2023The recently published high-resolution R388 T4SS structure provides exciting new details about the complete complex of T4SS, including the components making up the stalk... (Review)
Review
The recently published high-resolution R388 T4SS structure provides exciting new details about the complete complex of T4SS, including the components making up the stalk and arches, numerous symmetry mismatches between regions of the complex, and an intriguing interpretation of the closed stalk and radial symmetry of the inner membrane complex, which is related to pilus biogenesis assembly. However, there are a few unidentified densities in the electron microscopy map and portions of the identified component sequences for which the structure is not yet known. It is also unclear how well this minimized DNA-transporting T4SS predicts the structure of other T4SSs, such as expanded systems and those that transport proteins rather than DNA. In this review, we evaluate what can be inferred from the recent high-resolution structure of the R388 T4SS with respect to the Cag and Dot/Icm systems. These systems were selected because, given what is currently known about these systems, we expect them to present most structural differences compared to the R388 T4SS structure. Furthermore, we discuss bacterial physiology and diversity, the T4SS structures and their variations between different bacterial species. These insights may prove beneficial for researchers who elucidate the structure and functions of T4SS in different bacterial species.
Topics: Type IV Secretion Systems; Biological Transport; DNA; Bacterial Proteins
PubMed: 37528551
DOI: 10.4014/jmb.2307.07006 -
Acta Crystallographica. Section E,... Feb 2024The ()-(+)-1-(4-bromo-phen-yl)--[(4-methoxyphen-yl)methyl-idene]ethyl-amine ligand, CHBrNO, (I), was synthesized through the reaction of 4-meth-oxy-anisaldehyde with...
()-(+)-1-(4-Bromo-phen-yl)--[(4-methoxyphen-yl)methyl-idene]ethyl-amine and bis-{()-(+)-1-(4-bromo-phen-yl)--[(4-methoxyphen-yl)methyl-idene]ethyl-amine-κ}di-chlorido-palladium(II).
The ()-(+)-1-(4-bromo-phen-yl)--[(4-methoxyphen-yl)methyl-idene]ethyl-amine ligand, CHBrNO, (I), was synthesized through the reaction of 4-meth-oxy-anisaldehyde with ()-(-)-1-(4-bromo-phen-yl)ethyl-amine. It crystallizes in the ortho-rhom-bic space group 222 belonging to the Sohncke group, featuring a single mol-ecule in the asymmetric unit. The refinement converged successfully, achieving an factor of 0.0508. The Pd com-plex bis-{()-(+)-1-(4-bromo-phen-yl)--[(4-methoxyphen-yl)methyl-idene]ethyl-amine-κ}di-chlorido-pal-ladium(II), [PdCl(CHBrNO)], (II), crystallizes in the monoclinic space group 2 belonging to the Sohncke group, with two mol-ecules in the asymmetric unit. The central atom is tetra-coordinated by two N atoms and two Cl atoms, resulting in a square-planar configuration. The imine moieties exhibit a configuration around the Pd centre, with average Cl-Pd-N angles of approximately 89.95 and 90°. The average distances within the palladium com-plex for the two mol-ecules are ∼2.031 Å for Pd-N and ∼2.309 Å for Pd-Cl.
PubMed: 38333132
DOI: 10.1107/S2056989024000690 -
Data in Brief Oct 2023Here, we present and release the Global Rainfall Erosivity Database (GloREDa), a multi-source platform containing rainfall erosivity values for almost 4000 stations...
Here, we present and release the Global Rainfall Erosivity Database (GloREDa), a multi-source platform containing rainfall erosivity values for almost 4000 stations globally. The database was compiled through a global collaboration between a network of researchers, meteorological services and environmental organisations from 65 countries. GloREDa is the first open access database of rainfall erosivity (R-factor) based on hourly and sub-hourly rainfall records at a global scale. This database is now stored and accessible for download in the long-term European Soil Data Centre (ESDAC) repository of the European Commission's Joint Research Centre. This will ensure the further development of the database with insertions of new records, maintenance of the data and provision of a helpdesk. In addition to the annual erosivity data, this release also includes the mean monthly erosivity data for 94% of the GloREDa stations. Based on these mean monthly R-factor values, we predict the global monthly erosivity datasets at 1 km resolution using the ensemble machine learning approach (ML) as implemented in the mlr package for R. The produced monthly raster data (GeoTIFF format) may be useful for soil erosion prediction modelling, sediment distribution analysis, climate change predictions, flood, and natural disaster assessments and can be valuable inputs for Land and Earth Systems modelling.
PubMed: 37636128
DOI: 10.1016/j.dib.2023.109482 -
Cureus Dec 2023Hepatic injuries attributable to terbinafine usage are a well-documented yet infrequent phenomenon. This case study details the clinical presentation and management of a...
Hepatic injuries attributable to terbinafine usage are a well-documented yet infrequent phenomenon. This case study details the clinical presentation and management of a 70-year-old Hispanic female, with no previous medical history, subsequently hospitalized for progressive jaundice, right upper quadrant abdominal discomfort, and worsening pruritus. A comprehensive review of her prior records revealed a recent terbinafine prescription for onychomycosis, which she took consistently for five weeks and then self-discontinued four weeks before her current admission. Laboratory tests on admission revealed a cholestatic pattern of liver injury, evident by transaminitis and conjugated hyperbilirubinemia. The R factor used to determine whether a liver injury is hepatocellular or cholestatic was 0.9. Further diagnostic imaging, including abdominal ultrasound, CT of the abdomen, and magnetic resonance cholangiopancreatography, failed to disclose an obstructive pathology, revealing only cholelithiasis and chronic cholecystitis. Therapeutically, the patient was initiated on hydroxyzine to address symptoms of pruritus, and then subsequently underwent a liver biopsy. Histopathologic findings from the biopsy revealed benign hepatic parenchyma demonstrating focal canalicular cholestasis, mild chronic inflammation involving select portal tracts, and chronic lobular inflammation, suggesting terbinafine-induced hepatotoxicity. This case highlights the challenges of diagnosing terbinafine-induced liver injury, emphasizing the need for a high index of clinical suspicion and recognizing the potential for prolonged symptomatic manifestation after drug discontinuation. This article provides valuable insights into the complexities inherent in such diagnoses and significantly enriches a medical provider's approach to diagnosing and treating unexplained liver injuries.
PubMed: 38239534
DOI: 10.7759/cureus.50749 -
Acta Crystallographica Section B,... Oct 2023Five different electron density datasets obtained from conventional and synchrotron single crystal X-ray diffraction experiments are compared. The general aim of the...
Five different electron density datasets obtained from conventional and synchrotron single crystal X-ray diffraction experiments are compared. The general aim of the study is to investigate the quality of data for electron density analysis from current state-of-the-art conventional sources, and to see how the data perform in comparison with high-quality synchrotron data. A molecular crystal of melamine was selected as the test compound due to its ability to form excellent single crystals, the light atom content, and an advantageous suitability factor of 3.6 for electron density modeling. These features make melamine an optimal system for conventional X-ray diffractometers since the inherent advantages of synchrotron sources such as short wavelength and high intensity are less critical in this case. Data were obtained at 100 K from new in-house diffractometers Rigaku Synergy-S (Mo and Ag source, HyPix100 detector) and Stoe Stadivari (Mo source, EIGER2 1M CdTe detector), and an older Oxford Diffraction Supernova (Mo source, Atlas CCD detector). The synchrotron data were obtained at 25 K from BL02B1 beamline at SPring-8 in Japan (λ = 0.2480 Å, Pilatus3 X 1M CdTe detector). The five datasets were compared on general quality parameters such as resolution, ⟨I/σ⟩, redundancy and R factors, as well as the more model specific fractal dimension plot and residual density maps. Comparison of the extracted electron densities reveals that all datasets can provide reliable multipole models, which overall convey similar chemical information. However, the new laboratory X-ray diffractometers with advanced pixel detector technology clearly measure data with significantly less noise and much higher reliability giving densities of higher quality, compared to the older instrument. The synchrotron data have higher resolution and lower measurement temperature, and they allow for finer details to be modeled (e.g. hydrogen κ parameters).
PubMed: 37669152
DOI: 10.1107/S2052520623006625 -
IEEE Transactions on Medical Imaging Jan 2024Our lab at the University of Pennsylvania (UPenn) is investigating novel designs for digital breast tomosynthesis. We built a next-generation tomosynthesis system with a...
Our lab at the University of Pennsylvania (UPenn) is investigating novel designs for digital breast tomosynthesis. We built a next-generation tomosynthesis system with a non-isocentric geometry (superior-to-inferior detector motion). This paper examines four metrics of image quality affected by this design. First, aliasing was analyzed in reconstructions prepared with smaller pixelation than the detector. Aliasing was assessed with a theoretical model of r -factor, a metric calculating amplitudes of alias signal relative to input signal in the Fourier transform of the reconstruction of a sinusoidal object. Aliasing was also assessed experimentally with a bar pattern (illustrating spatial variations in aliasing) and 360°-star pattern (illustrating directional anisotropies in aliasing). Second, the point spread function (PSF) was modeled in the direction perpendicular to the detector to assess out-of-plane blurring. Third, power spectra were analyzed in an anthropomorphic phantom developed by UPenn and manufactured by Computerized Imaging Reference Systems (CIRS), Inc. (Norfolk, VA). Finally, calcifications were analyzed in the CIRS Model 020 BR3D Breast Imaging Phantom in terms of signal-to-noise ratio (SNR); i.e., mean calcification signal relative to background-tissue noise. Image quality was generally superior in the non-isocentric geometry: Aliasing artifacts were suppressed in both theoretical and experimental reconstructions prepared with smaller pixelation than the detector. PSF width was also reduced at most positions. Anatomic noise was reduced. Finally, SNR in calcification detection was improved. (A potential trade-off of smaller-pixel reconstructions was reduced SNR; however, SNR was still improved by the detector-motion acquisition.) In conclusion, the non-isocentric geometry improved image quality in several ways.
Topics: Humans; Image Processing, Computer-Assisted; Breast; Mammography; Computer Simulation; Models, Theoretical; Calcinosis; Phantoms, Imaging; Algorithms
PubMed: 37603482
DOI: 10.1109/TMI.2023.3307004 -
Frontiers in Microbiology 2023Metaproteomics is a subfield in meta-omics that is used to characterize the proteome of a microbial community. Despite its importance and the plethora of publications in...
BACKGROUND
Metaproteomics is a subfield in meta-omics that is used to characterize the proteome of a microbial community. Despite its importance and the plethora of publications in different research area, scientists struggle to fully comprehend its functional impact on the study of microbiomes. In this study, bibliometric analyses are used to evaluate the current state of metaproteomic research globally as well as evaluate the specific contribution of Africa to this burgeoning research area. In this study, we use bibliometric analyses to evaluate the current state of metaproteomic research globally, identify research frontiers and hotspots, and further predict future trends in metaproteomics. The specific contribution of Africa to this research area was evaluated.
METHODS
Relevant documents from 2004 to 2022 were extracted from the Scopus database. The documents were subjected to bibliometric analyses and visualization using VOS viewer and Biblioshiny package in R. Factors such as the trends in publication, country and institutional cooperation networks, leading scientific journals, author's productivity, and keywords analyses were conducted. The African publications were ranked using Field-Weighted Citation Impact (FWCI) scores.
RESULTS
A total of 1,138 documents were included and the number of publications increased drastically from 2004 to 2022 with more publications (170) reported in 2021. In terms of publishers, had the highest number of total publications (62). The United States of America (USA), Germany, China, and Canada, together with other European countries were the most productive. Institution-wise, the Helmholtz Zentrum für Umweltforschung, Germany had more publications while Max Plank Institute had the highest total collaborative link strength. Jehmlich N. was the most productive author whereas Hettich RL had the highest h-index of 63. Regarding Africa, only 2.2% of the overall publications were from the continent with more publication outputs from South Africa. More than half of the publications from the continent had an FWCI score ≥ 1.
CONCLUSION
The scientific outputs of metaproteomics are rapidly evolving with developed countries leading the way. Although Africa showed prospects for future progress, this could only be accelerated by providing funding, increased collaborations, and mentorship programs.
PubMed: 37476667
DOI: 10.3389/fmicb.2023.1217727 -
Chemosphere Jul 2024Arsenic, ubiquitous in various industrial processes and consumer products, presents both essential functions and considerable toxicity risks, driving extensive research...
Arsenic, ubiquitous in various industrial processes and consumer products, presents both essential functions and considerable toxicity risks, driving extensive research into safer applications. Our investigation, drawing from 7182 arsenic-containing molecules in the Cambridge Structural Database (CSD), outlines their diverse bonding patterns. Notably, 51% of these molecules exhibit cyclic connections, while 49% display acyclic ones. Arsenic forms eight distinct bonding types with other elements, with significant interactions observed, particularly with phenyl rings, O and F moieties. Top interactions involve carbon, nitrogen, oxygen, fluorine, sulfur, and arsenic itself. We meticulously evaluated average bond lengths under three conditions: without an R-factor cut-off, with R-factor ≤0.075, and with R-factor ≤0.05, supporting the credibility of our results. Comparative analysis with existing literature data enriches our understanding of arsenic's bonding behaviour. Our findings illuminate the structural attributes, molecular coordination, geometry, and bond lengths of arsenic with 68 diverse atoms, enriching our comprehension of arsenic chemistry. These revelations not only offer a pathway for crafting innovative and safer arsenic-based compounds but also foster the evolution of arsenic detoxification mechanisms, tackling pivotal health and environmental challenges linked to arsenic exposure across different contexts.
Topics: Arsenic; Data Mining; Databases, Chemical; Molecular Structure; Arsenicals
PubMed: 38763400
DOI: 10.1016/j.chemosphere.2024.142349 -
Acta Crystallographica. Section D,... Dec 2023Hydrogen (H) atoms are abundant in macromolecules and often play critical roles in enzyme catalysis, ligand-recognition processes and protein-protein interactions....
Hydrogen (H) atoms are abundant in macromolecules and often play critical roles in enzyme catalysis, ligand-recognition processes and protein-protein interactions. However, their direct visualization by diffraction techniques is challenging. Macromolecular X-ray crystallography affords the localization of only the most ordered H atoms at (sub-)atomic resolution (around 1.2 Å or higher). However, many H atoms of biochemical significance remain undetectable by this method. In contrast, neutron diffraction methods enable the visualization of most H atoms, typically in the form of deuterium (H) atoms, at much more common resolution values (better than 2.5 Å). Thus, neutron crystallography, although technically demanding, is often the method of choice when direct information on protonation states is sought. REFMAC5 from the Collaborative Computational Project No. 4 (CCP4) is a program for the refinement of macromolecular models against X-ray crystallographic and cryo-EM data. This contribution describes its extension to include the refinement of structural models obtained from neutron crystallographic data. Stereochemical restraints with accurate bond distances between H atoms and their parent atom nuclei are now part of the CCP4 Monomer Library, the source of prior chemical information used in the refinement. One new feature for neutron data analysis in REFMAC5 is refinement of the protium/deuterium (H/H) fraction. This parameter describes the relative H/H contribution to neutron scattering for hydrogen isotopes. The newly developed REFMAC5 algorithms were tested by performing the (re-)refinement of several entries available in the PDB and of one novel structure (FutA) using either (i) neutron data only or (ii) neutron data supplemented by external restraints to a reference X-ray crystallographic structure. Re-refinement with REFMAC5 afforded models characterized by R-factor values that are consistent with, and in some cases better than, the originally deposited values. The use of external reference structure restraints during refinement has been observed to be a valuable strategy, especially for structures at medium-low resolution.
Topics: Proteins; Deuterium; Models, Molecular; Crystallography, X-Ray; Neutron Diffraction; Hydrogen; Neutrons; Macromolecular Substances
PubMed: 37921806
DOI: 10.1107/S2059798323008793 -
Scientific Reports Sep 2023Most civil structures exhibit nonlinear behavior during moderate to severe earthquakes. Consequently, inelastic analysis is needed for seismic design. Several dynamic...
Most civil structures exhibit nonlinear behavior during moderate to severe earthquakes. Consequently, inelastic analysis is needed for seismic design. Several dynamic and static analysis methods are available for the assessment and design of engineering structures. Two of the available methods in terms of nonlinear dynamic time history analysis and nonlinear static analysis, which is known as pushover analysis, are employed herein to comprehensively study and investigate the seismic performance of multi-story building structures with different floor systems. Moreover, the study is extended to assess the actual values of the response reduction/modification factor (R-factor) for each building model, then evaluate the values with the code-recommended design values. Three-dimensional finite element building models with 5, 10 and 15 stories are developed for the evaluation process. The advanced computer program ETABS is used for developing and analyzing the buildings considering material and geometrical nonlinearity. A suit of seven earthquake records is considered and scaled according to the ASCE-16 seismic design code to excite the building models. The obtained results evidently reveal that the type of floor slab significantly impacts the seismic response of the building. More specifically, the effects of floor slabs on seismic demands are more evident in low- and mid-rise buildings. In addition, the type of slab system and height of the building have more influence on the response modification factors, especially for low-rise building models.
PubMed: 37697013
DOI: 10.1038/s41598-023-41656-7