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The Journal of Biological Chemistry Nov 2023Heavy chain-only antibodies can offer advantages of higher binding affinities, reduced sizes, and higher stabilities than conventional antibodies. To address the...
Heavy chain-only antibodies can offer advantages of higher binding affinities, reduced sizes, and higher stabilities than conventional antibodies. To address the challenge of SARS-CoV-2 coronavirus, a llama-derived single-domain nanobody C5 was developed previously that has high COVID-19 virus neutralization potency. The fusion protein C5-Fc comprises two C5 domains attached to a glycosylated Fc region of a human IgG1 antibody and shows therapeutic efficacy in vivo. Here, we have characterized the solution arrangement of the molecule. Two 1443 Da N-linked glycans seen in the mass spectra of C5-Fc were removed and the glycosylated and deglycosylated structures were evaluated. Reduction of C5-Fc with 2-mercaptoethylamine indicated three interchain Cys-Cys disulfide bridges within the hinge. The X-ray and neutron Guinier R values, which provide information about structural elongation, were similar at 4.1 to 4.2 nm for glycosylated and deglycosylated C5-Fc. To explain these R values, atomistic scattering modeling based on Monte Carlo simulations resulted in 72,737 and 56,749 physically realistic trial X-ray and neutron structures, respectively. From these, the top 100 best-fit X-ray and neutron models were identified as representative asymmetric solution structures, similar to that of human IgG1, with good R-factors below 2.00%. Both C5 domains were solvent exposed, consistent with the functional effectiveness of C5-Fc. Greater disorder occurred in the Fc region after deglycosylation. Our results clarify the importance of variable and exposed C5 conformations in the therapeutic function of C5-Fc, while the glycans in the Fc region are key for conformational stability in C5-Fc.
Topics: Humans; Immunoglobulin G; Immunoglobulin Heavy Chains; Models, Molecular; Polysaccharides; SARS-CoV-2; Antibodies, Viral; Single-Domain Antibodies
PubMed: 37838175
DOI: 10.1016/j.jbc.2023.105337 -
Scientific Reports Sep 2023To explore the connection between chloroplast and coffee resistance factors, designated as S1 to S9, whole genomic DNA of 42 coffee genotypes was sequenced, and entire...
To explore the connection between chloroplast and coffee resistance factors, designated as S1 to S9, whole genomic DNA of 42 coffee genotypes was sequenced, and entire chloroplast genomes were de novo assembled. The chloroplast phylogenetic haplotype network clustered individuals per species instead of S factors. However, for the first time, it allowed the molecular validation of Coffea arabica as the maternal parent of the spontaneous hybrid "Híbrido de Timor". Individual reads were also aligned on the C. arabica reference genome to relate S factors with chloroplast metabolism, and an in-silico analysis of selected nuclear-encoded chloroplast proteins (132 proteins) was performed. The nuclear-encoded thioredoxin-like membrane protein HCF164 enabled the discrimination of individuals with and without the S9 factor, due to specific DNA variants linked to chromosome 7c (from C. canephora-derived sub-genome). The absence of both the thioredoxin domain and redox-active disulphide center in the HCF164 protein, observed in S9 individuals, raises the possibility of potential implications on redox regulation. For the first time, the identification of specific DNA variants of chloroplast proteins allows discriminating individuals according to the S profile. This study introduces an unexplored strategy for identifying protein/genes associated with S factors and candidate targets of H. vastatrix effectors, thereby creating new perspectives for coffee breeding programs.
Topics: Humans; Coffea; Coffee; Phylogeny; R Factors; Plant Breeding; Thioredoxins; Nuclear Proteins; Membrane Proteins; Chloroplast Proteins; Chloroplasts; Complement Factor H
PubMed: 37749157
DOI: 10.1038/s41598-023-41950-4 -
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 -
Nature Communications Sep 2023There is an arms race between beta-lactam antibiotics development and co-evolving beta-lactamases, which provide resistance by breaking down beta-lactam rings. We have...
There is an arms race between beta-lactam antibiotics development and co-evolving beta-lactamases, which provide resistance by breaking down beta-lactam rings. We have observed that certain beta-lactamases tend to aggregate, which persists throughout their evolution under the selective pressure of antibiotics on their active sites. Interestingly, we find that existing beta-lactamase active site inhibitors can act as molecular chaperones, promoting the proper folding of these resistance factors. Therefore, we have created Pept-Ins, synthetic peptides designed to exploit the structural weaknesses of beta-lactamases by causing them to misfold into intracellular inclusion bodies. This approach restores sensitivity to a wide range of beta-lactam antibiotics in resistant clinical isolates, including those with Extended Spectrum variants that pose significant challenges in medical practice. Our findings suggest that targeted aggregation of resistance factors could offer a strategy for identifying molecules that aid in addressing the global antibiotic resistance crisis.
Topics: Anti-Bacterial Agents; Inclusion Bodies; Monobactams; R Factors; beta-Lactamase Inhibitors; beta-Lactamases
PubMed: 37689716
DOI: 10.1038/s41467-023-41191-z -
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 -
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 -
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 -
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 -
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