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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 -
Environmental Monitoring and Assessment Sep 2023This study evaluated soil erosion rates in the Shaqlawa district using the Geographical Information System (GIS)-based Revised Universal Soil Loss Equation (RUSLE)...
This study evaluated soil erosion rates in the Shaqlawa district using the Geographical Information System (GIS)-based Revised Universal Soil Loss Equation (RUSLE) model. The primary objective was to identify areas within the district that are prone to significant erosion and develop appropriate soil conservation schemes accordingly. A combination of primary and secondary data from diverse sources was utilized to achieve this objective. The GIS-based RUSLE model used variables like soil erodibility (K), soil coverage (C), topographic effect (LS), rainfall runoff (R), and erosion control practices (P) to estimate the amount of soil that had been washed away in the study area. The study provided valuable information that can be used to plan and administer soil protection in the Shaqlawa district. The average yearly soil loss in the study region is estimated to be 65.66 t ha year. The district is experiencing significant soil erosion rates, which may have detrimental effects on agricultural productivity, water quality, and environmental health. The analysis revealed that Balisan, Hiran, Shaqlawa center, and part of the Salahaddin subdistrict are the most affected areas, with high values of LS and R factors contributing to significant soil erosion rates. These results underscore the importance of soil protection and management efforts in the Shaqlawa district. The combination of the RUSLE with GIS and remote sensing techniques has been recognized as an essential, cost-effective, and highly accurate approach for estimating soil erosion.
Topics: Soil; Soil Erosion; Geographic Information Systems; Iraq; Environmental Monitoring
PubMed: 37668802
DOI: 10.1007/s10661-023-11796-4 -
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 -
Inorganic Chemistry Sep 2023Sustainable production of rare earth elements (REEs) is critical for technologies needed for climate change mitigation, including wind turbines and electric vehicles....
Sustainable production of rare earth elements (REEs) is critical for technologies needed for climate change mitigation, including wind turbines and electric vehicles. However, separation technologies currently used in REE production have large environmental footprints, necessitating more sustainable strategies. Aqueous, affinity-based separations are examples of such strategies. To make these technologies feasible, it is imperative to connect aqueous ligand structure to ligand selectivity for individual REEs. As a step toward this goal, we analyzed the extended X-ray absorption fine structure (EXAFS) of four lanthanides (La, Ce, Pr, and Nd) complexed by a common REE chelator, ethylenediaminetetraacetic acid (EDTA) to determine the aqueous-phase structure. Reference structures from density functional theory (DFT) were used to help fit the EXAFS spectra. We found that all four Ln-EDTA coordination complexes formed 9-coordinate structures with 6 coordinating atoms from EDTA (4 carboxyl oxygen atoms and 2 nitrogen atoms) and 3 oxygen atoms from water molecules. All EXAFS fits were of high quality (-factor < 0.02) and showed decreasing average first-shell coordination distance across the series (2.62-2.57 Å from La-Nd), in agreement with DFT (2.65-2.56 Å from La-Nd). The insights determined herein will be useful in the development of ligands for sustainable rare earth elements (REE) separation technologies.
PubMed: 37624729
DOI: 10.1021/acs.inorgchem.3c01334 -
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 -
The Science of the Total Environment Sep 2023In this study, we used a large national database to assess the rainfall erosivity (RE) patterns in time and space over the Brazilian territory. Thereby, RE and erosivity...
In this study, we used a large national database to assess the rainfall erosivity (RE) patterns in time and space over the Brazilian territory. Thereby, RE and erosivity density (ED) values were obtained for 5166 rainfall gauges. Also, the concentration of the RE throughout the year and the RE's gravity center locations were analyzed. Finally, homogeneous regions regarding RE values were delimited and estimative regression models were established. The results show that Brazil's mean annual RE value is 5620 MJ mm ha h year, with considerable spatial variation over the country. The highest RE magnitudes were found for the north region, while the northeast region shows the lowest values. Regarding the RE's distribution throughout the year, in the southern region of Brazil, it is more equitable, while in some spots of the northeastern region, it is irregularly concentrated in specific months. Further analyses revealed that for most of the months, the RE's gravity centers for Brazil are in the Goiás State and that they present a north-south migration pattern throughout the year. Complementarily, the ED magnitudes allowed the identification of high-intensity rainfall spots. Additionally, the Brazilian territory was divided into eleven homogeneous regions regarding the RE patterns and for each defined region, a regression model was established and validated. These models' statistical metrics were considered satisfactory and, thus, can be used to estimate RE values for the whole country using monthly rainfall depths. Finally, all database produced are available for download. Therefore, the values and maps shown in this study are relevant for improving the accuracy of soil loss estimates in Brazil and for the establishment of soil and water conservation planning on a national scale.
PubMed: 37286003
DOI: 10.1016/j.scitotenv.2023.164557 -
Advances in Health Sciences Education :... Dec 2023Q methodology is a unique, yet underutilized methodology designed specifically to scientifically study subjectivity. Q, as it is most often referred to, is an...
Q methodology is a unique, yet underutilized methodology designed specifically to scientifically study subjectivity. Q, as it is most often referred to, is an appropriate methodology whenever a researcher is interested in uncovering and describing the multiple divergent viewpoints on any topic. Such discovery of viewpoints provides insight into the subjectivities related to policies, values, priorities, judgements, opinions, and decisions. The disciplines where Q has been used for research are many, and include health sciences, education, and other social science / behavioral science fields. Because of its rather idiosyncratic place in research, however, many Q methodologists are self-taught or seek education through a few select universities that offer graduate level Q courses. The key to successfully approaching a Q study is to embrace its unique approach to studying subjectivity such that it is a powerful tool in health science education and other fields. It is common to find inconsistencies related to Q terminology, analyses, and decision making across studies. There is often an over reliance on concepts that come from purely quantitative methodologies such as R factor analysis rather than embracing the qualitative-quantitative hybridity of Q. This article is written as a primer with a focus on understanding Q at a deeper level rather than a step-by-step guide.
Topics: Health Education; Research Design
PubMed: 37071262
DOI: 10.1007/s10459-023-10214-1