Systems Biology
Characterisation of Anopheles species composition and genetic diversity in Meghalaya, northeast India, using molecular identification tools
Infect Genet Evol. 2023 May 23:105450. doi: 10.1016/j.meegid.2023.105450. Online ahead of print.
ABSTRACT
Malaria in India is declining, in part due to the use of long-lasting insecticide-treated nets (LLINs) and vector control. Historically, the north-eastern region of India has contributed ~10%-12% of the nation's malaria burden. The important mosquito vectors in northeast India have long been considered to be Anopheles baimaii and An. minimus, both associated with forest habitats. Local deforestation and increased rice cultivation, along with widespread LLIN use, may be changing vector species composition. Understanding if and how vector species composition is changing is critical to successful malaria control. In Meghalaya state, malaria is now at a low level of endemicity with occasional seasonal outbreaks. In a biodiverse setting like Meghalaya, where >24 Anopheles mosquito species have been recorded, accurate morphological identification of all species is logistically challenging. To accurately determine Anopheles species richness in the West Khasi Hills (WKH) and West Jaintia Hills (WJH) districts, adult and larval mosquitoes were collected and identified using molecular methods of allele-specific PCR and cytochrome oxidase I DNA barcoding. In 14 villages across both districts, we identified high species richness, 19 species in total. Molecular findings indicated that An. minimus and An. baimaii were rare, while four other species (An. maculatus, An. pseudowillmori, An. jeyporiensis and An. nitidus) were abundant. Anopheles maculatus was highly prevalent in WKH (39% of light trap collections) and An. pseudowillmori in WJH (45%). Larvae of these four species were found in rice fields, suggesting that land cover change is influencing species composition change. Our results suggest that rice fields might be contributing to the observed abundance of An. maculatus and An. pseudowillmori, which could be playing a role in malaria transmission, either independently due to their high abundance, or in combination with An. baimaii and/or An. minimus.
PMID:37230159 | DOI:10.1016/j.meegid.2023.105450
Modeling of ionizing radiation-induced chromosome aberration and tumor prevalence based on two classes of DNA double-strand breaks clustering in chromatin domains
Ecotoxicol Environ Saf. 2023 May 23;259:115038. doi: 10.1016/j.ecoenv.2023.115038. Online ahead of print.
ABSTRACT
There has been some controversy over the use of radiobiological models when modeling the dose-response curves of ionizing radiation (IR)-induced chromosome aberration and tumor prevalence, as those curves usually show obvious non-targeted effects (NTEs) at low doses of high linear energy transfer (LET) radiation. The lack of understanding the contribution of NTEs to IR-induced carcinogenesis can lead to distinct deviations of relative biological effectiveness (RBE) estimations of carcinogenic potential, which are widely used in radiation risk assessment and radiation protection. In this work, based on the initial pattern of two classes of IR-induced DNA double-strand breaks (DSBs) clustering in chromatin domains and the subsequent incorrect repair processes, we proposed a novel radiobiological model to describe the dose-response curves of two carcinogenic-related endpoints within the same theoretical framework. The representative experimental data was used to verify the consistency and validity of the present model. The fitting results indicated that, compared with targeted effect (TE) and NTE models, the current model has better fitting ability when dealing with the experimental data of chromosome aberration and tumor prevalence induced by multiple types of IR with different LETs. Notably, the present model without introducing an NTE term was adequate to describe the dose-response curves of IR-induced chromosome aberration and tumor prevalence with NTEs in low-dose regions. Based on the fitting parameters, the LET-dependent RBE values were calculated for three given low doses. Our results showed that the RBE values predicted by the current model gradually decrease with the increase of doses for the endpoints of chromosome aberration and tumor prevalence. In addition, the calculated RBE was also compared with those evaluated from other models. These analyses show that the proposed model can be used as an alternative tool to well describe dose-response curves of multiple carcinogenic-related endpoints and effectively estimate RBE in low-dose regions.
PMID:37229870 | DOI:10.1016/j.ecoenv.2023.115038
Advances in micropropagation, somatic embryogenesis, somatic hybridizations, genetic transformation and cryopreservation for Passiflora improvement
Plant Methods. 2023 May 25;19(1):50. doi: 10.1186/s13007-023-01030-0.
ABSTRACT
Passion fruit is an essential commercial plant in the tropics and subtropics, which has lately seen a rise in demand for high-quality fruits and large-scale production. Generally, different species of passion fruit (Passiflora sp.) are propagated by sexual reproduction. However, asexual reproduction, such as stem cuttings, grafting, or tissue culture, is also available and advantageous in many instances. Recent research on passion fruit has concentrated on improving and establishing methodologies for embryogenesis, clonal proliferation via (somatic embryos), homozygote regeneration (by anther culture), germplasm preservation (via cryopreservation), and genetic transformation. These developments have resulted in potentially new directions for asexual propagation. Even though effective embryo culture and cryogenics are now available, however the limited frequency of embryogenic callus transformation to ex-vitro seedlings still restricts the substantial clonal replication of passion fruit. Here, in this review the advancement related to biotechnological approaches and the current understanding of Passiflora tissue culture. In vitro culture, organogenesis, cryopreservation, breeding, and productivity of Passiflora will significantly improve with novel propagation approaches, which could be applied to a wider range of germplasm.
PMID:37231431 | DOI:10.1186/s13007-023-01030-0
Dictionary learning for integrative, multimodal and scalable single-cell analysis
Nat Biotechnol. 2023 May 25. doi: 10.1038/s41587-023-01767-y. Online ahead of print.
ABSTRACT
Mapping single-cell sequencing profiles to comprehensive reference datasets provides a powerful alternative to unsupervised analysis. However, most reference datasets are constructed from single-cell RNA-sequencing data and cannot be used to annotate datasets that do not measure gene expression. Here we introduce 'bridge integration', a method to integrate single-cell datasets across modalities using a multiomic dataset as a molecular bridge. Each cell in the multiomic dataset constitutes an element in a 'dictionary', which is used to reconstruct unimodal datasets and transform them into a shared space. Our procedure accurately integrates transcriptomic data with independent single-cell measurements of chromatin accessibility, histone modifications, DNA methylation and protein levels. Moreover, we demonstrate how dictionary learning can be combined with sketching techniques to improve computational scalability and harmonize 8.6 million human immune cell profiles from sequencing and mass cytometry experiments. Our approach, implemented in version 5 of our Seurat toolkit ( http://www.satijalab.org/seurat ), broadens the utility of single-cell reference datasets and facilitates comparisons across diverse molecular modalities.
PMID:37231261 | DOI:10.1038/s41587-023-01767-y
You are what you excrete
Nat Microbiol. 2023 May 25. doi: 10.1038/s41564-023-01395-x. Online ahead of print.
NO ABSTRACT
PMID:37231087 | DOI:10.1038/s41564-023-01395-x
3-Hydroxybutyrate ameliorates insulin resistance by inhibiting PPARγ Ser273 phosphorylation in type 2 diabetic mice
Signal Transduct Target Ther. 2023 May 26;8(1):190. doi: 10.1038/s41392-023-01415-6.
ABSTRACT
3-Hydroxybutyrate (3HB) is a small ketone body molecule produced endogenously by the body in the liver. Previous studies have shown that 3HB can reduce blood glucose level in type 2 diabetic (T2D) patients. However, there is no systematic study and clear mechanism to evaluate and explain the hypoglycemic effect of 3HB. Here we demonstrate that 3HB reduces fasting blood glucose level, improves glucose tolerance, and ameliorates insulin resistance in type 2 diabetic mice through hydroxycarboxylic acid receptor 2 (HCAR2). Mechanistically, 3HB increases intracellular calcium ion (Ca2+) levels by activating HCAR2, thereby stimulating adenylate cyclase (AC) to increase cyclic adenosine monophosphate (cAMP) concentration, and then activating protein kinase A (PKA). Activated PKA inhibits Raf1 proto-oncogene serine/threonine-protein kinase (Raf1) activity, resulting in a decrease in extracellular signal-regulated kinases 1/2 (ERK1/2) activity and ultimately inhibiting peroxisome proliferator-activated receptor γ (PPARγ) Ser273 phosphorylation in adipocytes. Inhibition of PPARγ Ser273 phosphorylation by 3HB altered the expression of PPARγ regulated genes and reduced insulin resistance. Collectively, 3HB ameliorates insulin resistance in type 2 diabetic mice through a pathway of HCAR2/Ca2+/cAMP/PKA/Raf1/ERK1/2/PPARγ.
PMID:37230992 | DOI:10.1038/s41392-023-01415-6
Establishment of gastrointestinal assembloids to study the interplay between epithelial crypts and their mesenchymal niche
Nat Commun. 2023 May 25;14(1):3025. doi: 10.1038/s41467-023-38780-3.
ABSTRACT
The cellular organization of gastrointestinal crypts is orchestrated by different cells of the stromal niche but available in vitro models fail to fully recapitulate the interplay between epithelium and stroma. Here, we establish a colon assembloid system comprising the epithelium and diverse stromal cell subtypes. These assembloids recapitulate the development of mature crypts resembling in vivo cellular diversity and organization, including maintenance of a stem/progenitor cell compartment in the base and their maturation into secretory/absorptive cell types. This process is supported by self-organizing stromal cells around the crypts that resemble in vivo organization, with cell types that support stem cell turnover adjacent to the stem cell compartment. Assembloids that lack BMP receptors either in epithelial or stromal cells fail to undergo proper crypt formation. Our data highlight the crucial role of bidirectional signaling between epithelium and stroma, with BMP as a central determinant of compartmentalization along the crypt axis.
PMID:37230989 | DOI:10.1038/s41467-023-38780-3
Demographic reporting and phenotypic exclusion in fNIRS
Front Neurosci. 2023 May 9;17:1086208. doi: 10.3389/fnins.2023.1086208. eCollection 2023.
ABSTRACT
Functional near-infrared spectroscopy (fNIRS) promises to be a leading non-invasive neuroimaging method due to its portability and low cost. However, concerns are rising over its inclusivity of all skin tones and hair types (Parker and Ricard, 2022, Webb et al., 2022). Functional NIRS relies on direct contact of light-emitting optodes to the scalp, which can be blocked more by longer, darker, and especially curlier hair. Additionally, NIR light can be attenuated by melanin, which is accounted for in neither fNIRS hardware nor analysis methods. Recent work has shown that overlooking these considerations in other modalities like EEG leads to the disproportionate exclusion of individuals with these phenotypes-especially Black people-in both clinical and research literature (Choy, 2020; Bradford et al., 2022; Louis et al., 2023). In this article, we sought to determine if (Jöbsis, 1977) biomedical optics developers and researchers report fNIRS performance variability between skin tones and hair textures, (2a) fNIRS neuroscience practitioners report phenotypic and demographic details in their articles, and thus, (2b) is a similar pattern of participant exclusion found in EEG also present in the fNIRS literature. We present a literature review of top Biomedical Optics and Human Neuroscience journals, showing that demographic and phenotypic reporting is unpopular in both fNIRS development and neuroscience applications. We conclude with a list of recommendations to the fNIRS community including examples of Black researchers addressing these issues head-on, inclusive best practices for fNIRS researchers, and recommendations to funding and regulatory bodies to achieve an inclusive neuroscience enterprise in fNIRS and beyond.
PMID:37229429 | PMC:PMC10203458 | DOI:10.3389/fnins.2023.1086208
CO<sub>2</sub> recycling by phospho<em>enol</em>pyruvate carboxylase enables cassava leaf metabolism to tolerate low water availability
Front Plant Sci. 2023 May 9;14:1159247. doi: 10.3389/fpls.2023.1159247. eCollection 2023.
ABSTRACT
Cassava is a staple crop that acclimatizes well to dry weather and limited water availability. The drought response mechanism of quick stomatal closure observed in cassava has no explicit link to the metabolism connecting its physiological response and yield. Here, a genome-scale metabolic model of cassava photosynthetic leaves (leaf-MeCBM) was constructed to study on the metabolic response to drought and stomatal closure. As demonstrated by leaf-MeCBM, leaf metabolism reinforced the physiological response by increasing the internal CO2 and then maintaining the normal operation of photosynthetic carbon fixation. We found that phosphoenolpyruvate carboxylase (PEPC) played a crucial role in the accumulation of the internal CO2 pool when the CO2 uptake rate was limited during stomatal closure. Based on the model simulation, PEPC mechanistically enhanced drought tolerance in cassava by providing sufficient CO2 for carbon fixation by RuBisCO, resulting in high production of sucrose in cassava leaves. The metabolic reprogramming decreased leaf biomass production, which may lead to maintaining intracellular water balance by reducing the overall leaf area. This study indicates the association of metabolic and physiological responses to enhance tolerance, growth, and production of cassava in drought conditions.
PMID:37229106 | PMC:PMC10204807 | DOI:10.3389/fpls.2023.1159247
Genome graphs detect human polymorphisms in active epigenomic state during influenza infection
Cell Genom. 2023 Apr 7;3(5):100294. doi: 10.1016/j.xgen.2023.100294. eCollection 2023 May 10.
ABSTRACT
Genetic variants, including mobile element insertions (MEIs), are known to impact the epigenome. We hypothesized that genome graphs, which encapsulate genetic diversity, could reveal missing epigenomic signals. To test this, we sequenced the epigenome of monocyte-derived macrophages from 35 ancestrally diverse individuals before and after influenza infection, allowing us to investigate the role of MEIs in immunity. We characterized genetic variants and MEIs using linked reads and built a genome graph. Mapping epigenetic data revealed 2.3%-3% novel peaks for H3K4me1, H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq), and ATAC-seq. Additionally, the use of a genome graph modified some quantitative trait loci estimates and revealed 375 polymorphic MEIs in an active epigenomic state. Among these is an AluYh3 polymorphism whose chromatin state changed after infection and was associated with the expression of TRIM25, a gene that restricts influenza RNA synthesis. Our results demonstrate that graph genomes can reveal regulatory regions that would have been overlooked by other approaches.
PMID:37228750 | PMC:PMC10203048 | DOI:10.1016/j.xgen.2023.100294
Suspension feeding in Copepoda (Crustacea) - a numerical model of setae acting in concert
Beilstein J Nanotechnol. 2023 May 17;14:603-615. doi: 10.3762/bjnano.14.50. eCollection 2023.
ABSTRACT
Suspension feeding via setae collecting particles is common within Crustacea. Even though the mechanisms behind it and the structures themselves have been studied for decades, the interplay between the different setae types and the parameters contributing to their particle collecting capacities remain partly enigmatic. Here, we provide a numerical modeling approach to understand the relationship among the mechanical property gradients, the mechanical behavior and the adhesion of setae, and the feeding efficiency of the system. In this context, we set-up a simple dynamic numerical model that takes all of these parameters into account and describes the interaction with food particles and their delivery into the mouth opening. By altering the parameters, it was unraveled that the system performs best when the long and short setae have different mechanical properties and different degrees of adhesion since the long setae generate the feeding current and the short ones establish the contact with the particle. This protocol can be applied to any system in the future as the parameters (i.e., properties and arrangement of particles and setae) can be easily altered. This will shed light on the biomechanical adaptations of these structures to suspension feeding and provide inspiration for biomimetics in the field of filtration technologies.
PMID:37228744 | PMC:PMC10204204 | DOI:10.3762/bjnano.14.50
Topological data analysis of protein structure and inter/intra-molecular interaction changes attributable to amino acid mutations
Comput Struct Biotechnol J. 2023 May 9;21:2950-2959. doi: 10.1016/j.csbj.2023.05.009. eCollection 2023.
ABSTRACT
The presence of some amino acid mutations in the amino acid sequence that determines a protein's structure can significantly affect that 3D structure and its biological function. However, the effects upon structural and functional changes differ for each displaced amino acid, and it is very difficult to predict these changes in advance. Although computer simulations are very effective at predicting conformational changes, they struggle to determine whether the amino acid mutation of interest induces sufficient conformational changes, unless the researcher is a specialist in molecular structure calculations. Therefore, we created a framework that efficiently utilizes molecular dynamics and persistent homology methods to identify amino acid mutations that induce structural changes. We show that this framework can be used not only to predict conformational changes produced by amino acid mutations but also to extract groups of mutations that significantly alter similar molecular interactions, by capturing the resultant protein-protein interaction changes.
PMID:37228703 | PMC:PMC10205437 | DOI:10.1016/j.csbj.2023.05.009
Molecular Dynamics Simulation of Antimicrobial Peptide CM15 in <em>Staphylococcus Aureus</em> and <em>Escherichia coli</em> Model Bilayer Lipid
Iran J Biotechnol. 2023 Apr 1;21(2):e3344. doi: 10.30498/ijb.2023.337246.3344. eCollection 2023 Apr.
ABSTRACT
BACKGROUND: In animals and plants, antimicrobial peptides (AMPs) are crucial components of defense mechanisms, as they play a crucial role in innate immunity, which protects hosts from pathogenic bacteria. The CM15 has attracted considerable interest as a novel antibiotic against gram-negative and positive pathogens.
OBJECTIVE: The aim of this study was to investigate the permeation potential of the CM15 with membrane bilayers of Staphylococcus aureus and Escherichia coli.
MATERIAL AND METHODS: The bilayer membranes of Escherichia coli and Staphylococcus aureus were modelled with the resemblance in lipid composition to its biological sample. This study followed Protein-Membrane Interaction (PMI) through successive applications of molecular dynamics simulation by GROMACS and CHARMM36 force field for two sets of 120-ns simulations.
RESULTS: Significant results were obtained from analyzing the trajectory of the unsuccessful insertion of CM15 during simulation. Our data suggested that Lysine residues in CM15 and Cardiolipins in membrane leaflets play a crucial role in stability and interaction terms.
CONCLUSION: The obtained results strengthen the insertion possibility through the toroidal model, which should consider for further studies on AMPs interaction.
PMID:37228629 | PMC:PMC10203184 | DOI:10.30498/ijb.2023.337246.3344
Weed-induced changes in the maize root transcriptome reveal transcription factors and physiological processes impacted early in crop-weed interactions
AoB Plants. 2023 Apr 6;15(3):plad013. doi: 10.1093/aobpla/plad013. eCollection 2023 Jun.
ABSTRACT
A new paradigm suggests weeds primarily reduce crop yield by altering crop developmental and physiological processes long before the weeds reduce resources through competition. Multiple studies have implicated stress response pathways are activated when crops such as maize are grown in close proximity with weeds during the first 4-8 weeks of growth-the point at which weeds have their greatest impact on subsequent crop yields. To date, these studies have mostly focused on the response of above-ground plant parts and have not examined the early signal transduction processes associated with maize root response to weeds. To investigate the impact of signals from a below-ground competitor on the maize root transcriptome when most vulnerable to weed pressure, a system was designed to expose maize to only below-ground signals. Gene set enrichment analyses identified over-represented ontologies associated with oxidative stress signalling throughout the time of weed exposure, with additional ontologies associated with nitrogen use and transport and abscisic acid (ABA) signalling, and defence responses being enriched at later time points. Enrichment of promoter motifs indicated over-representation of sequences known to bind FAR-RED IMPAIRED RESPONSE 1 (FAR1), several AP2/ERF transcription factors and others. Likewise, co-expression networks were identified using Weighted-Gene Correlation Network Analysis (WGCNA) and Spatiotemporal Clustering and Inference of Omics Networks (SC-ION) algorithms. WGCNA highlighted the potential roles of several transcription factors including a MYB 3r-4, TB1, WRKY65, CONSTANS-like5, ABF3, HOMEOBOX 12, among others. These studies also highlighted the role of several specific proteins involved in ABA signalling as being important for the initiation of the early response of maize to weeds. SC-ION highlighted potential roles for NAC28, LOB37, NAC58 and GATA2 transcription factors, among many others.
PMID:37228420 | PMC:PMC10202722 | DOI:10.1093/aobpla/plad013
Scoping review of genetic databases for rare dermatologic diseases: Opportunity for artificial intelligence and machine learning
JAAD Int. 2023 Mar 31;12:24-31. doi: 10.1016/j.jdin.2023.02.017. eCollection 2023 Sep.
NO ABSTRACT
PMID:37228361 | PMC:PMC10203757 | DOI:10.1016/j.jdin.2023.02.017
Hierarchical association of COPD to principal genetic components of biological systems
PLoS One. 2023 May 25;18(5):e0286064. doi: 10.1371/journal.pone.0286064. eCollection 2023.
ABSTRACT
Many disease-causing genetic variants converge on common biological functions and pathways. Precisely how to incorporate pathway knowledge in genetic association studies is not yet clear, however. Previous approaches employ a two-step approach, in which a regular association test is first performed to identify variants associated with the disease phenotype, followed by a test for functional enrichment within the genes implicated by those variants. Here we introduce a concise one-step approach, Hierarchical Genetic Analysis (Higana), which directly computes phenotype associations against each function in the large hierarchy of biological functions documented by the Gene Ontology. Using this approach, we identify risk genes and functions for Chronic Obstructive Pulmonary Disease (COPD), highlighting microtubule transport, muscle adaptation, and nicotine receptor signaling pathways. Microtubule transport has not been previously linked to COPD, as it integrates genetic variants spread over numerous genes. All associations validate strongly in a second COPD cohort.
PMID:37228113 | DOI:10.1371/journal.pone.0286064
Toward High-Throughput Analysis of Aroma Compounds Using Ultrahigh-Performance Liquid Chromatography-Tandem Mass Spectrometry: Screening of Key Food Odorants in Various Foods
J Agric Food Chem. 2023 May 25. doi: 10.1021/acs.jafc.3c00935. Online ahead of print.
ABSTRACT
Recent studies show the immense capacities of the unified quantitation of aroma and taste compounds using liquid chromatography-mass spectrometry (LC-MS). The goal of this study was to highlight the broad application of this unified method. Thus, a stable isotope dilution analysis quantification method of the most important key food odorants in various food categories by LC-MS was developed. Using the well-known derivatization agent 3-nitrophenylhydrazine for carbonyl derivatization and a newly developed approach for alcohol and thiol derivatization, a method for the quantitation of 20 key food odorants was established. Intraday precision was determined to be ≤26%, and interday precision was between 24 and 31%. Limits of quantitation were determined between 0.014 and 283 μg/kg. The work shows that a wide array of aroma compounds can be analyzed accurately by LC-MS.
PMID:37228041 | DOI:10.1021/acs.jafc.3c00935
A Dynamic Genome-Scale Model Identifies Metabolic Pathways Associated with Cold Tolerance in Saccharomyces kudriavzevii
Microbiol Spectr. 2023 May 25:e0351922. doi: 10.1128/spectrum.03519-22. Online ahead of print.
ABSTRACT
Saccharomyces kudriavzevii is a cold-tolerant species identified as a good alternative for industrial winemaking. Although S. kudriavzevii has never been found in winemaking, its co-occurrence with Saccharomyces cerevisiae in Mediterranean oaks is well documented. This sympatric association is believed to be possible due to the different growth temperatures of the two yeast species. However, the mechanisms behind the cold tolerance of S. kudriavzevii are not well understood. In this work, we propose the use of a dynamic genome-scale model to compare the metabolic routes used by S. kudriavzevii at two temperatures, 25°C and 12°C, to decipher pathways relevant to cold tolerance. The model successfully recovered the dynamics of biomass and external metabolites and allowed us to link the observed phenotype with exact intracellular pathways. The model predicted fluxes that are consistent with previous findings, but it also led to novel results which we further confirmed with intracellular metabolomics and transcriptomic data. The proposed model (along with the corresponding code) provides a comprehensive picture of the mechanisms of cold tolerance that occur within S. kudriavzevii. The proposed strategy offers a systematic approach to explore microbial diversity from extracellular fermentation data at low temperatures. IMPORTANCE Nonconventional yeasts promise to provide new metabolic pathways for producing industrially relevant compounds and tolerating specific stressors such as cold temperatures. The mechanisms behind the cold tolerance of S. kudriavzevii or its sympatric relationship with S. cerevisiae in Mediterranean oaks are not well understood. This study proposes a dynamic genome-scale model to investigate metabolic pathways relevant to cold tolerance. The predictions of the model would indicate the ability of S. kudriavzevii to produce assimilable nitrogen sources from extracellular proteins present in its natural niche. These predictions were further confirmed with metabolomics and transcriptomic data. This finding suggests that not only the different growth temperature preferences but also this proteolytic activity may contribute to the sympatric association with S. cerevisiae. Further exploration of these natural adaptations could lead to novel engineering targets for the biotechnological industry.
PMID:37227304 | DOI:10.1128/spectrum.03519-22
Statistical inference reveals the role of length, GC content, and local sequence in V(D)J nucleotide trimming
Elife. 2023 May 25;12:e85145. doi: 10.7554/eLife.85145.
ABSTRACT
To appropriately defend against a wide array of pathogens, humans somatically generate highly diverse repertoires of B cell and T cell receptors (BCRs and TCRs) through a random process called V(D)J recombination. Receptor diversity is achieved during this process through both the combinatorial assembly of V(D)J-genes and the junctional deletion and insertion of nucleotides. While the Artemis protein is often regarded as the main nuclease involved in V(D)J recombination, the exact mechanism of nucleotide trimming is not understood. Using a previously published TCRβ repertoire sequencing data set, we have designed a flexible probabilistic model of nucleotide trimming that allows us to explore various mechanistically interpretable sequence-level features. We show that local sequence context, length, and GC nucleotide content in both directions of the wider sequence, together, can most accurately predict the trimming probabilities of a given V-gene sequence. Because GC nucleotide content is predictive of sequence-breathing, this model provides quantitative statistical evidence regarding the extent to which double-stranded DNA may need to be able to breathe for trimming to occur. We also see evidence of a sequence motif that appears to get preferentially trimmed, independent of GC-content-related effects. Further, we find that the inferred coefficients from this model provide accurate prediction for V- and J-gene sequences from other adaptive immune receptor loci. These results refine our understanding of how the Artemis nuclease may function to trim nucleotides during V(D)J recombination and provide another step toward understanding how V(D)J recombination generates diverse receptors and supports a powerful, unique immune response in healthy humans.
PMID:37227256 | DOI:10.7554/eLife.85145
Integrating intracellular and extracellular proteomic profiling for in-depth investigations of cellular communication in a model of prostate cancer
Proteomics. 2023 May 24:e2200287. doi: 10.1002/pmic.202200287. Online ahead of print.
ABSTRACT
Cellular communication is essential for cell-cell interactions, maintaining homeostasis and progression of certain disease states. While many studies examine extracellular proteins, the holistic extracellular proteome is often left uncaptured, leaving gaps in our understanding of how all extracellular proteins may impact communication and interaction. We used a cellular-based proteomics approach to more holistically profile both the intracellular and extracellular proteome of prostate cancer. Our workflow was generated in such a manner that multiple experimental conditions can be observed with the opportunity for high throughput integration. Additionally, this workflow is not limited to a proteomic aspect, as metabolomic and lipidomic studies can be integrated for a multi-omics workflow. Our analysis showed coverage of over 8000 proteins while also garnering insights into cellular communication in the context of prostate cancer development and progression. Identified proteins covered a variety of cellular processes and pathways, allowing for the investigation of multiple aspects into cellular biology. This workflow demonstrates advantages for integrating intra- and extracellular proteomic analyses as well as potential for multi-omics researchers. This approach possesses great value for future investigations into the systems biology aspects of disease development and progression.
PMID:37226375 | DOI:10.1002/pmic.202200287