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Annual Review of Physical Chemistry Jun 2024Crystallographic analysis relies on the scattering of quanta from arrays of atoms that populate a repeating lattice. While large crystals built of lattices that appear... (Review)
Review
Crystallographic analysis relies on the scattering of quanta from arrays of atoms that populate a repeating lattice. While large crystals built of lattices that appear ideal are sought after by crystallographers, imperfections are the norm for molecular crystals. Additionally, advanced X-ray and electron diffraction techniques, used for crystallography, have opened the possibility of interrogating micro- and nanoscale crystals, with edges only millions or even thousands of molecules long. These crystals exist in a size regime that approximates the lower bounds for traditional models of crystal nonuniformity and imperfection. Accordingly, data generated by diffraction from both X-rays and electrons show increased complexity and are more challenging to conventionally model. New approaches in serial crystallography and spatially resolved electron diffraction mapping are changing this paradigm by better accounting for variability within and between crystals. The intersection of these methods presents an opportunity for a more comprehensive understanding of the structure and properties of nanocrystalline materials.
PubMed: 38941528
DOI: 10.1146/annurev-physchem-083122-105226 -
Bioinformatics (Oxford, England) Jun 2024Errors in the processing of genetic information during protein synthesis can lead to phenotypic mutations, such as amino acid substitutions, e.g. by transcription or...
MOTIVATION
Errors in the processing of genetic information during protein synthesis can lead to phenotypic mutations, such as amino acid substitutions, e.g. by transcription or translation errors. While genetic mutations can be readily identified using DNA sequencing, and mutations due to transcription errors by RNA sequencing, translation errors can only be identified proteome-wide using mass spectrometry.
RESULTS
Here, we provide a Python package implementation of a high-throughput pipeline to detect amino acid substitutions in mass spectrometry datasets. Our tools enable users to process hundreds of mass spectrometry datasets in batch mode to detect amino acid substitutions and calculate codon-specific and site-specific translation error rates. deTELpy will facilitate the systematic understanding of amino acid misincorporation rates (translation error rates), and the inference of error models across organisms and under stress conditions, such as drug treatment or disease conditions.
AVAILABILITY
deTELpy is implemented in Python 3 and is freely available with detailed documentation and practical examples at https://git.mpi-cbg.de/tothpetroczylab/detelpy and https://pypi.org/project/deTELpy/ and can be easily installed via pip install deTELpy.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
PubMed: 38941503
DOI: 10.1093/bioinformatics/btae424 -
Science Advances Jun 2024Liver fibrosis is characterized by the activation of perivascular hepatic stellate cells (HSCs), the release of fibrogenic nanosized extracellular vesicles (EVs), and...
Liver fibrosis is characterized by the activation of perivascular hepatic stellate cells (HSCs), the release of fibrogenic nanosized extracellular vesicles (EVs), and increased HSC glycolysis. Nevertheless, how glycolysis in HSCs coordinates fibrosis amplification through tissue zone-specific pathways remains elusive. Here, we demonstrate that HSC-specific genetic inhibition of glycolysis reduced liver fibrosis. Moreover, spatial transcriptomics revealed a fibrosis-mediated up-regulation of EV-related pathways in the liver pericentral zone, which was abrogated by glycolysis genetic inhibition. Mechanistically, glycolysis in HSCs up-regulated the expression of EV-related genes such as Ras-related protein Rab-31 () by enhancing histone 3 lysine 9 acetylation on the promoter region, which increased EV release. Functionally, these glycolysis-dependent EVs increased fibrotic gene expression in recipient HSC. Furthermore, EVs derived from glycolysis-deficient mice abrogated liver fibrosis amplification in contrast to glycolysis-competent mouse EVs. In summary, glycolysis in HSCs amplifies liver fibrosis by promoting fibrogenic EV release in the hepatic pericentral zone, which represents a potential therapeutic target.
Topics: Animals; Glycolysis; Liver Cirrhosis; Hepatic Stellate Cells; Extracellular Vesicles; Mice; rab GTP-Binding Proteins; Humans; Disease Models, Animal; Liver; Mice, Inbred C57BL; Male
PubMed: 38941469
DOI: 10.1126/sciadv.adn5228 -
Science Advances Jun 2024Decades of research have uncovered how plants respond to two environmental variables that change across latitudes and over seasons: photoperiod and temperature. However,...
Decades of research have uncovered how plants respond to two environmental variables that change across latitudes and over seasons: photoperiod and temperature. However, a third such variable, twilight length, has so far gone unstudied. Here, using controlled growth setups, we show that the duration of twilight affects growth and flowering time via the clock genes in the model plant Arabidopsis. Using a series of progressively truncated no-twilight photoperiods, we also found that plants are more sensitive to twilight length compared to equivalent changes in solely photoperiods. Transcriptome and proteome analyses showed that twilight length affects reactive oxygen species metabolism, photosynthesis, and carbon metabolism. Genetic analyses suggested a twilight sensing pathway from the photoreceptors , , , and through to flowering modulation through the pathway. Overall, our findings call for more nuanced models of day-length perception in plants and posit that twilight is an important determinant of plant growth and development.
Topics: Arabidopsis; Flowers; Arabidopsis Proteins; Photoperiod; Gene Expression Regulation, Plant; Transcription Factors; Reactive Oxygen Species; Photosynthesis; Cryptochromes
PubMed: 38941453
DOI: 10.1126/sciadv.adl3199 -
Genome Biology and Evolution Jun 2024Polar regions harbor a diversity of cold-adapted (cryophilic) algae, which can be categorized into psychrophilic (obligate cryophilic) and cryotrophic (non-obligate...
Polar regions harbor a diversity of cold-adapted (cryophilic) algae, which can be categorized into psychrophilic (obligate cryophilic) and cryotrophic (non-obligate cryophilic) snow algae. Both can accumulate significant biomasses on glacier and snow habitats and play major roles in global climate dynamics. Despite their significance, genomic studies on these organisms remain scarce, hindering our understanding of their evolutionary history and adaptive mechanisms in the face of climate change. Here, we present the draft genome assembly and annotation of the psychrophilic snow algal strain CCCryo 101-99 (cf. Sphaerocystis sp.). The draft haploid genome assembly is 122.5 Mb in length and is represented by 664 contigs with an N50 of 0.86 Mb, a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness of 92.9% (n = 1519), a maximum contig length of 5.3 Mb, and a GC content of 53.1%. In total, 28.98% of the genome (35.5 Mb) contains repetitive elements. We identified 417 non-coding RNAs (ncRNAs) and annotated the chloroplast genome. The predicted proteome comprises 14,805 genes with a BUSCO completeness of 97.8%. Our preliminary analyses reveal a genome with a higher repeat content compared to mesophilic chlorophyte relatives, alongside enrichment in gene families associated with photosynthesis and flagella functions. Our current data will facilitate future comparative studies, improving our understanding of the likely response of polar algae to a warming climate as well as their evolutionary trajectories in permanently cold environments.
PubMed: 38941446
DOI: 10.1093/gbe/evae140 -
PloS One 2024A growing increase in the number of serious infections caused by multidrug resistant bacteria (MDR) is challenging our society. Despite efforts to discover novel...
A growing increase in the number of serious infections caused by multidrug resistant bacteria (MDR) is challenging our society. Despite efforts to discover novel therapeutic options, few antibiotics targeting MDR have been approved by the Food and Drug Administration (FDA). Lactic acid bacteria have emerged as a promising therapeutic alternative due to their demonstrated ability to combat MDR pathogens in vitro. Our previous co-culture studies showed Lacticaseibacillus rhamnosus CRL 2244 as having a potent killing effect against carbapenem-resistant Acinetobacter baumannii (CRAB) strains. Here we report that cell-free conditioned media (CFCM) samples obtained from Lcb. rhamnosus CRL 2244 cultures incubated at different times display antimicrobial activity against 43 different pathogens, including CRAB, methicillin-resistant Staphylococcus aureus (MRSA) and carbapenemase Klebsiella pneumoniae (KPC)-positive strains. Furthermore, transwell and ultrafiltration analyses together with physical and chemical/biochemical tests showed that Lcb. rhamnosus CRL 2244 secretes a <3 kDa metabolite(s) whose antimicrobial activity is not significantly impaired by mild changes in pH, temperature and various enzymatic treatments. Furthermore, sensitivity and time-kill assays showed that the bactericidal activity of the Lcb. rhamnosus CRL 2244 metabolite(s) enhances the activity of some current FDA approved antibiotics. We hypothesize that this observation could be due to the effects of Lcb. rhamnosus CRL 2244 metabolite(s) on cell morphology and the enhanced transcriptional expression of genes coding for the phenylacetate (PAA) and histidine catabolic Hut pathways, metal acquisition and biofilm formation, all of which are associated with bacterial virulence. Interestingly, the extracellular presence of Lcb. rhamnosus CRL 2244 induced the transcription of the gene coding for the CidA/LgrA protein, which is involved in programmed cell death in some bacteria. Overall, the findings presented in this report underscore the promising potential of the compound(s) released by Lcb. rhamnosus CRL2244 as an alternative and/or complementary option to treat infections caused by A. baumannii as well as other MDR bacterial pathogens.
Topics: Lacticaseibacillus rhamnosus; Anti-Bacterial Agents; Drug Resistance, Multiple, Bacterial; Microbial Sensitivity Tests; Acinetobacter baumannii; Drug Synergism; Methicillin-Resistant Staphylococcus aureus; Culture Media, Conditioned; Bacterial Proteins
PubMed: 38941324
DOI: 10.1371/journal.pone.0306273 -
Journal of Agricultural and Food... Jun 2024The prohibition of processed animal proteins (PAPs) has been relaxed gradually since 2007. The official control method for PAPs in feedingstuff, a combination of light...
The prohibition of processed animal proteins (PAPs) has been relaxed gradually since 2007. The official control method for PAPs in feedingstuff, a combination of light microscopy (LM) followed by PCR, is no longer sufficient. Thus, a targeted LC-MS/MS method was developed, which enables a tissue-specific distinction between egg and dairy products, gelatine, and PAPs derived from blood or muscle tissue of the species ruminants, pigs, poultry, and fish. Tissue-specific proteins were analyzed after tryptic digestion to peptides with high-resolution ESI-QTOF-MS. A targeted method was developed based on untargeted proteomics approaches and the selection of specific peptides (45 unique peptides in total). Proficiency testing of blank and spiked samples revealed excellent results for trueness and selectivity. Furthermore, sensitivity was achieved at a level of 0.1% (w/w) for assessed peptides. Summing up, the developed method seems to be suitable for routine analysis after verification by ring trials.
PubMed: 38941278
DOI: 10.1021/acs.jafc.4c00516 -
Reproduction (Cambridge, England) Jun 2024There has been remarkable progress in the conservation and reproduction of giant pandas. However, the physiology of the gestation period in pandas remains poorly...
There has been remarkable progress in the conservation and reproduction of giant pandas. However, the physiology of the gestation period in pandas remains poorly understood. The metabolic processes from estrus to pregnancy are dynamic and precisely regulated, playing a crucial role in pregnancy and related dysfunctions. In this study, we conducted a metabolomic analysis of 37 blood samples collected from pandas in estrus, acyclic, potential pregnant states, employing rigorous screening to minimize the influence of diet. Our findings suggest that a reduced appetite can serve as an indicator for evaluating implantation time, representing a characteristic response to pregnancy and aiding in the prediction of delivery time in pregnant pandas. Metabolomic results indicate great metabolism variation from estrus to pregnancy, and highlight the association between amino acid metabolism and pregnancy outcomes. Compared to other pandas, individuals which successfully bred exhibit significantly elevated levels of arginine and histidine, even 2 months before experiencing reduced appetite. Furthermore, the lipid profile undergoes distinct dynamic changes only in estrus samples. In summary, our study comprehensively characterizes the metabolism of giant pandas during gestation and proposes arginine and histidine as potential novel biomarkers for detecting the pregnancy state of giant pandas.
PubMed: 38941177
DOI: 10.1530/REP-23-0480 -
Methods in Molecular Biology (Clifton,... 2024The strong influence of microbiomes on areas such as ecology and human health has become widely recognized in the past years. Accordingly, various techniques for the...
The strong influence of microbiomes on areas such as ecology and human health has become widely recognized in the past years. Accordingly, various techniques for the investigation of the composition and function of microbial community samples have been developed. Metaproteomics, the comprehensive analysis of the proteins from microbial communities, allows for the investigation of not only the taxonomy but also the functional and quantitative composition of microbiome samples. Due to the complexity of the investigated communities, methods developed for single organism proteomics cannot be readily applied to metaproteomic samples. For this purpose, methods specifically tailored to metaproteomics are required. In this work, a detailed overview of current bioinformatic solutions and protocols in metaproteomics is given. After an introduction to the proteomic database search, the metaproteomic post-processing steps are explained in detail. Ten specific bioinformatic software solutions are focused on, covering various steps including database-driven identification and quantification as well as taxonomic and functional assignment.
Topics: Proteomics; Computational Biology; Workflow; Software; Microbiota; Humans; Databases, Protein; Metagenomics
PubMed: 38941024
DOI: 10.1007/978-1-0716-3910-8_16 -
Methods in Molecular Biology (Clifton,... 2024The upper respiratory tract (URT) is home to a diverse range of microbial species. Respiratory infections disturb the microbial flora in the URT, putting people at risk...
The upper respiratory tract (URT) is home to a diverse range of microbial species. Respiratory infections disturb the microbial flora in the URT, putting people at risk of secondary infections. The potential dangers and clinical effects of bacterial and fungal coinfections with SARS-CoV-2 support the need to investigate the microbiome of the URT using clinical samples. Mass spectrometry (MS)-based metaproteomics analysis of microbial proteins is a novel approach to comprehensively assess the clinical specimens with complex microbial makeup. The coronavirus that causes severe acute respiratory syndrome (SARS-CoV-2) is responsible for the COVID-19 pandemic resulting in a plethora of microbial coinfections impeding therapy, prognosis, and overall disease management. In this chapter, the corresponding workflows for MS-based shotgun proteomics and metaproteomic analysis are illustrated.
Topics: Humans; COVID-19; Proteomics; Coinfection; SARS-CoV-2; Microbiota; Respiratory Tract Infections; Mass Spectrometry; Proteome; Respiratory System
PubMed: 38941023
DOI: 10.1007/978-1-0716-3910-8_15