Nat Commun. 2024 Jul 25;15(1):6271. doi: 10.1038/s41467-024-50588-3.

ABSTRACT

Addressing the global disparity in cancer care necessitates the development of rapid and affordable nucleic acid (NA) testing technologies. This need is particularly critical for cervical cancer, where molecular detection of human papillomavirus (HPV) has emerged as an accurate screening method. However, implementing this transition in low- and middle-income countries has been challenging due to the high costs and centralized facilities required for current NA tests. Here, we present CreDiT (CRISPR Enhanced Digital Testing) for on-site NA detection. The CreDiT platform integrates i) a one-pot CRISPR strategy that simultaneously amplifies both target NAs and analytical signals and ii) a robust fluorescent detection based on digital communication (encoding/decoding) technology. These features enable a rapid assay (<35 minutes) in a single streamlined workflow. We demonstrate the sensitive detection of cell-derived HPV DNA targets down to single copies and accurate identification of HPV types in clinical cervical brushing specimens (n = 121).

PMID:39054353 | DOI:10.1038/s41467-024-50588-3

Dev Cell. 2024 Jul 17:S1534-5807(24)00424-6. doi: 10.1016/j.devcel.2024.07.001. Online ahead of print.

ABSTRACT

Symbiotic nodules comprise two classes, indeterminate and determinate, defined by the presence/absence of apical meristem and developmental zonation. Why meristem and zonation are absent from determinate nodules remains unclear. Here, we define cell types in developing soybean nodules, highlighting the undifferentiated infection zones and differentiated nitrogen-fixation zones. Auxin governs infection zone maintenance. GRETCHEN HAGEN 3 (GH3) enzymes deactivate auxin by conjugation and promote cell differentiation. gh3 mutants increased undifferentiated cells and enlarged infection zones. The central symbiosis-transcription factor NIN2a activates GH3.1 to reduce auxin levels and facilitates cell differentiation. High auxin promotes NIN2a protein accumulation and enhances signaling, further deactivating auxin and depleting infection zones. Our findings shed light on the NIN2a-GH3-auxin module that drives soybean nodule cell differentiation. This study challenges our understanding of determinate nodule development and proposes that the regulation of nodule zonation offers valuable insights into broader mechanisms of cell differentiation across plant species.

PMID:39053471 | DOI:10.1016/j.devcel.2024.07.001

Redox Biol. 2024 Jul 20;75:103276. doi: 10.1016/j.redox.2024.103276. Online ahead of print.

ABSTRACT

Metabolic rewiring is essential for tumor growth and progression to metastatic disease, yet little is known regarding how cancer cells modify their acquired metabolic programs in response to different metastatic microenvironments. We have previously shown that liver-metastatic breast cancer cells adopt an intrinsic metabolic program characterized by increased HIF-1α activity and dependence on glycolysis. Here, we confirm by in vivo stable isotope tracing analysis (SITA) that liver-metastatic breast cancer cells retain a glycolytic profile when grown as mammary tumors or liver metastases. However, hepatic metastases exhibit unique metabolic adaptations including elevated expression of genes involved in glutathione (GSH) biosynthesis and reactive oxygen species (ROS) detoxification when compared to mammary tumors. Accordingly, breast-cancer-liver-metastases exhibited enhanced de novo GSH synthesis. Confirming their increased capacity to mitigate ROS-mediated damage, liver metastases display reduced levels of 8-Oxo-2'-deoxyguanosine. Depletion of the catalytic subunit of the rate-limiting enzyme in glutathione biosynthesis, glutamate-cysteine ligase (GCLC), strongly reduced the capacity of breast cancer cells to form liver metastases, supporting the importance of these distinct metabolic adaptations. Loss of GCLC also affected the early steps of the metastatic cascade, leading to decreased numbers of circulating tumor cells (CTCs) and impaired metastasis to the liver and the lungs. Altogether, our results indicate that GSH metabolism could be targeted to prevent the dissemination of breast cancer cells.

PMID:39053265 | DOI:10.1016/j.redox.2024.103276

Eur J Med Chem. 2024 Jul 19;276:116693. doi: 10.1016/j.ejmech.2024.116693. Online ahead of print.

ABSTRACT

New 2-pyrrolamidobenzothiazole-based inhibitors of mycobacterial DNA gyrase were discovered. Among these, compounds 49 and 51, show excellent antibacterial activity against Mycobacterium tuberculosis and Mycobacterium abscessus with a notable preference for mycobacteria. Both compounds can penetrate infected macrophages and reduce intracellular M. tuberculosis load. Compound 51 is a potent inhibitor of DNA gyrase (M. tuberculosis DNA gyrase IC50 = 4.1 nM, Escherichia coli DNA gyrase IC50 of <10 nM), selective for bacterial topoisomerases. It displays low MIC90 values (M. tuberculosis: 0.63 μM; M. abscessus: 2.5 μM), showing specificity for mycobacteria, and no apparent toxicity. Compound 49 not only displays potent antimycobacterial activity (MIC90 values of 2.5 μM for M. tuberculosis and 0.63 μM for M. abscessus) and selectivity for mycobacteria but also exhibits favorable solubility (kinetic solubility = 55 μM) and plasma protein binding (with a fraction unbound of 2.9 % for human and 4.7 % for mouse). These findings underscore the potential of fine-tuning molecular properties to develop DNA gyrase B inhibitors that specifically target the mycobacterial chemical space, mitigating the risk of resistance development in non-target pathogens and minimizing harm to the microbiome.

PMID:39053193 | DOI:10.1016/j.ejmech.2024.116693

Bioinformatics. 2024 Jul 25:btae471. doi: 10.1093/bioinformatics/btae471. Online ahead of print.

ABSTRACT

SUMMARY: One of the first steps in single-cell omics data analysis is visualization, which allows researchers to see how well-separated cell-types are from each other. When visualizing multiple datasets at once, data integration/batch correction methods are used to merge the datasets. While needed for downstream analyses, these methods modify features space (e.g. gene expression)/PCA space in order to mix cell-types between batches as well as possible. This obscures sample-specific features and breaks down local embedding structures that can be seen when a sample is embedded alone. Therefore, in order to improve in visual comparisons between large numbers of samples (e.g., multiple patients, omic modalities, different time points), we introduce Compound-SNE, which performs what we term a soft alignment of samples in embedding space. We show that Compound-SNE is able to align cell-types in embedding space across samples, while preserving local embedding structures from when samples are embedded independently.

AVAILABILITY AND IMPLEMENTATION: Python code for Compound-SNE is available for download at https://github.com/HaghverdiLab/Compound-SNE.

SUPPLEMENTARY INFORMATION: Available online. Provides algorithmic details and additional tests.

PMID:39052868 | DOI:10.1093/bioinformatics/btae471

PLoS Pathog. 2024 Jul 25;20(7):e1012149. doi: 10.1371/journal.ppat.1012149. Online ahead of print.

ABSTRACT

The intracellular symbiont Wolbachia pipientis evolved after the divergence of arthropods and nematodes, but it reached high prevalence in many of these taxa through its abilities to infect new hosts and their germlines. Some strains exhibit long-term patterns of co-evolution with their hosts, while other strains are capable of switching hosts. This makes strain selection an important factor in symbiont-based biological control. However, little is known about the ecological and evolutionary interactions that occur when a promiscuous strain colonizes an infected host. Here, we study what occurs when two strains come into contact in host cells following horizontal transmission and infection. We focus on the faithful wMel strain from Drosophila melanogaster and the promiscuous wRi strain from Drosophila simulans using an in vitro cell culture system with multiple host cell types and combinatorial infection states. Mixing D. melanogaster cell lines stably infected with wMel and wRi revealed that wMel outcompetes wRi quickly and reproducibly. Furthermore, wMel was able to competitively exclude wRi even from minuscule starting quantities, indicating that this is a nearly deterministic outcome, independent of the starting infection frequency. This competitive advantage was not exclusive to wMel's native D. melanogaster cell background, as wMel also outgrew wRi in D. simulans cells. Overall, wRi is less adept at in vitro growth and survival than wMel and its in vivo state, revealing differences between the two strains in cellular and humoral regulation. These attributes may underlie the observed low rate of mixed infections in nature and the relatively rare rate of host-switching in most strains. Our in vitro experimental framework for estimating cellular growth dynamics of Wolbachia strains in different host species, and cell types provides the first strategy for parameterizing endosymbiont and host cell biology at high resolution. This toolset will be crucial to our application of these bacteria as biological control agents in novel hosts and ecosystems.

PMID:39052691 | DOI:10.1371/journal.ppat.1012149

ACS Synth Biol. 2024 Jul 25. doi: 10.1021/acssynbio.4c00370. Online ahead of print.

ABSTRACT

We recently developed "autonomous hypermutation yeast surface display" (AHEAD), a technology that enables the rapid generation of potent and specific antibodies in yeast. AHEAD pairs yeast surface display with an error-prone orthogonal DNA replication system (OrthoRep) to continuously and rapidly mutate surface-displayed antibodies, thereby enabling enrichment for stronger binding variants through repeated rounds of cell growth and fluorescence-activated cell sorting. AHEAD currently utilizes a standard galactose induction system to drive the selective display of antibodies on the yeast surface. However, achieving maximal display levels can require up to 48 h of induction. Here we report an updated version of the AHEAD platform that utilizes a synthetic β-estradiol-induced gene expression system to regulate the surface display of antibodies and find that induction is notably faster in achieving surface display for both our AHEAD system and traditional yeast surface display from nuclear plasmids that do not hypermutate. The updated AHEAD platform was fully functional in repeated rounds of evolution to drive the rapid evolution of antibodies.

PMID:39052526 | DOI:10.1021/acssynbio.4c00370

Methods Mol Biol. 2024;2823:225-239. doi: 10.1007/978-1-0716-3922-1_14.

ABSTRACT

Quantitative proteomics approaches based on stable isotopic labeling and mass spectrometry have been widely applied to disease research, drug target discovery, biomarker identification, and systems biology. One of the notable stable isotopic labeling approaches is trypsin-catalyzed 18O/16O labeling, which has its own advantages of low sample consumption, simple labeling procedure, cost-effectiveness, and absence of chemical reactions that potentially generate by-products. In this chapter, a protocol for 18O/16O labeling-based quantitative proteomics approach is described with an application to the identification of proteomic biomarkers of acetaminophen (APAP)-induced hepatotoxicity in rats. The protocol involves first the extraction of proteins from liver tissues of control and APAP-treated rats and digestion into peptides by trypsin. After cleaning of the peptides by solid-phase extraction, equal amounts of peptides from the APAP treatment and the control groups are then subject to trypsin-catalyzed 18O/16O labeling. The labeled peptides are combined and fractionated by off-line strong cation exchange liquid chromatography (SCXLC), and each fraction is then analyzed by nanoflow reversed-phase LC coupled online with tandem mass spectrometry (RPLC-MS/MS) for identification and quantification of differential protein expression between APAP-treated rats and controls. The protocol is applicable to quantitative proteomic analysis for a variety of biological samples.

PMID:39052223 | DOI:10.1007/978-1-0716-3922-1_14

Chem Res Toxicol. 2024 Jul 25. doi: 10.1021/acs.chemrestox.4c00085. Online ahead of print.

ABSTRACT

Our purpose was to test the hypothesis that ultrasonic cigarettes (u-cigarettes), which operate at relatively low temperatures, produce aerosols that are less harmful than heated-coil pod-style electronic cigarettes (e-cigarettes). The major chemicals in SURGE u-cigarette fluids and aerosols were quantified, their cytotoxicity and cellular effects were assessed, and a Margin of Exposure risk assessment was performed on chemicals in SURGE fluids. Four SURGE u-cigarette flavor variants ("Blueberry Ice," "Watermelon Ice," "Green Mint," and "Polar Mint") were evaluated. Flavor chemicals were quantified in fluids and aerosols using gas chromatography/mass spectrometry. Cytotoxicity and cell dynamics were assessed using the MTT assay, live-cell imaging, and fluorescence microscopy. WS-23 (a coolant) and total flavor chemical concentrations in SURGE were similar to e-cigarettes, while SURGE nicotine concentrations (13-19 mg/mL) were lower than many fourth generation e-cigarettes. Transfer efficiencies of dominant chemicals to aerosols in SURGE ranged from 44-100%. SURGE fluids and aerosols had four dominant flavor chemicals (>1 mg/mL). Toxic aldehydes were usually higher in SURGE aerosols than in SURGE fluids. SURGE fluids and aerosols had aldehyde concentrations significantly higher than pod-style e-cigarettes. Chemical constituents, solvent ratios, and aldehydes varied among SURGE flavor variants. SURGE fluids and aerosols inhibited cell growth and mitochondrial reductases, produced attenuated and round cells, and depolymerized actin filaments, effects that depended on pod flavor, chemical constituents, and concentration. The MOEs for nicotine, WS-23, and propylene glycol were <100 based on consumption of 1-2 SURGE u-cigarettes/day. Replacing the heating coil with a sonicator did not eliminate chemicals, including aldehydes, in aerosols or diminish toxicity in comparisons between SURGE and other e-cigarette pod products. The high concentrations of nicotine, WS-23, flavor chemicals, and aldehydes and the cytotoxicity of SURGE aerosols do not support the hypothesis that aerosols from u-cigarettes are less harmful than those from e-cigarettes.

PMID:39051826 | DOI:10.1021/acs.chemrestox.4c00085

BioTech (Basel). 2024 Jul 1;13(3):22. doi: 10.3390/biotech13030022.

ABSTRACT

Predictive tools provide a unique opportunity to explain the observed differences in outcome between patients of the COVID-19 pandemic. The aim of this study was to associate individual demographic and clinical characteristics with disease severity in COVID-19 patients and to highlight the importance of machine learning (ML) in disease prognosis. The study enrolled 344 unvaccinated patients with confirmed SARS-CoV-2 infection. Data collected by integrating questionnaires and medical records were imported into various classification machine learning algorithms, and the algorithm and the hyperparameters with the greatest predictive ability were selected for use in a disease outcome prediction web tool. Of 111 independent features, age, sex, hypertension, obesity, and cancer comorbidity were found to be associated with severe COVID-19. Our prognostic tool can contribute to a successful therapeutic approach via personalized treatment. Although at the present time vaccination is not considered mandatory, this algorithm could encourage vulnerable groups to be vaccinated.

PMID:39051337 | DOI:10.3390/biotech13030022

J Appl Phycol. 2024;36(4):2161-2172. doi: 10.1007/s10811-024-03222-0. Epub 2024 Apr 3.

ABSTRACT

Sea lettuce (Ulva) is recognised for its potential in food, pharmaceutical, nutraceutical, biorefinery and bioremediation industries and is increasingly being cultivated. The requirements of those industries vary widely in terms of biomass composition. Ulva biomass composition and growth is known to be directly influenced by environmental factors, e.g., temperature, light, salinity, nutrient availability as well as by genetic factors and likely by microbiome composition. In order to select for the highest yielding strains in a given environment, we tested the suitability of common-garden experiments, i.e., the co-cultivation of different strains grown under shared conditions. Fifteen strains from six different foliose Ulva species were grown together under two different salinities, 35 ppt and 15 ppt. After 32 days, only U. australis strains remained at both salinities. If selection at low salinity was mostly based on survival, the selection process at seawater salinity was driven by competition, largely based on growth performance. Growth rates after a month were very similar at both salinities, suggesting the U. australis strains cope equally well in either condition. However, the composition of the biomass produced in both environments varied, with the content of all organic compounds being higher at low salinity, and the ash content being reduced in average by 66%. To summarize, this study provides an established bulk-selection protocol for efficiently screening large numbers of locally-sourced strains and highlights the potential of low salinity treatments for increased organic matter content, particularly in carbohydrates.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10811-024-03222-0.

PMID:39050553 | PMC:PMC11263424 | DOI:10.1007/s10811-024-03222-0

J Trop Med. 2024 Jul 17;2024:6735764. doi: 10.1155/2024/6735764. eCollection 2024.

ABSTRACT

BACKGROUND: Parasitic infection remains a serious health trade for humans and livestock. The purpose of this study was to present scientific proof of the anthelmintic properties of Khaya grandifoliola, which the native population uses to cure helminthiasis.

METHOD: Fresh Heligmosomoides polygyrus eggs were isolated from faecal samples of experimentally infected mice. The faecal material was cultured, and L1 and L2 larval stages were recovered after 48 and 120 hours, respectively. Using the worm microtracker, the anthelminthic efficacy of the extracts against H. polygyrus was assessed. Two different extracts (aqueous and ethanol extracts) were prepared. For the ovicidal and larvicidal activities, 100 µL of various concentrations of plant extracts, levamisole and 1.5% dimethyl sulfoxide (DMSO), were introduced into a 96-well microplate titer followed by the addition of 100 µL of embryonated eggs (60 eggs) for the ovicidal activity and 100 µL of L 1 or L 2 larvae (50 larvae) for the larvicidal activity. The movement of the worm was monitored for 24 hours in the worm microtracker at 27°C. The Glide module of the Schrodinger Maestro software was used to perform docking studies.

RESULTS: For the aqueous extracts, the highest percentage of inhibition of hatching was 42.77 ± 12% at 7.5 mg/mL. The IC50 values for the ethanol (0.36 mg/mL) extract showed that the ethanol extract had a good inhibitory effect on the ability of parasites to hatch from eggs. The inhibition percentage of L1 larvae motility at 7.5 mg/mL was 98.0 ± 1.66% and 83.33 ± 1.66% for ethanol and aqueous extracts, respectively. The negative controls, distilled water and 1.5% DMSO, had no inhibitory impact on larvae. On L1-larvae, the drug of choice levamisole (positive control) had the highest percentage effect (100.0%). Six compounds had the highest docking score and their interactions with the receptor as well. Grandiamide A interacts most with tyrosine, glycine, phenylalanine, asparagine, and serine, and its benzene ring and oxygens inhibit these receptors. Carbonyl and hydroxyl (OH) groups connect grandiamide D to asparagine, isoleucine, and phenylalanine, respectively. By donating hydrogen to the receptor through OH groups, D-glucopyranose-6-phosphate also forms relatively strong hydrogen bonds with its oxygen-bound phosphorus and the receptor. 1-O-deacetylkhayanolide E interacts most with serine and glutamic acid. The carbamic acid benzyl ester of carbamic acid [(1S)-1-phenyl-2-[(4-methylphenyl) sulfinyl] ethyl] interacts most with the receptor with carbonyl groups and with asparagine and serine. With its abundant hydroxide, D-mannitol acts as a hydrogen donor and acceptor and interacts most strongly with amino acids such as glycine, asparagine, aspartic acid, alanine, and glutamic acid.

CONCLUSIONS: K. grandifoliola extracts possess anthelminthic properties. However, in vivo studies are still necessary to demonstrate the effectiveness of this plant for the treatment of helminthiasis.

PMID:39050406 | PMC:PMC11268970 | DOI:10.1155/2024/6735764

Mol Ther Nucleic Acids. 2024 Jun 17;35(3):102260. doi: 10.1016/j.omtn.2024.102260. eCollection 2024 Sep 10.

ABSTRACT

Space particle radiation is a major environmental factor in spaceflight, and it is known to cause body damage and even trigger cancer, but with unknown molecular etiologies. To examine these causes, we developed a systems biology approach by focusing on the co-expression network analysis of transcriptomics profiles obtained from single high-dose (SE) and multiple low-dose (ME) α-particle radiation exposures of BEAS-2B human bronchial epithelial cells. First, the differential network and pathway analysis based on the global network and the core modules showed that genes in the ME group had higher enrichment for the extracellular matrix (ECM)-receptor interaction pathway. Then, collagen gene COL1A1 was screened as an important gene in the ME group assessed by network parameters and an expression study of lung adenocarcinoma samples. COL1A1 was found to promote the emergence of the neoplastic characteristics of BEAS-2B cells by both in vitro experimental analyses and in vivo immunohistochemical staining. These findings suggested that the degree of malignant transformation of cells in the ME group was greater than that of the SE, which may be caused by the dysregulation of the ECM-receptor pathway.

PMID:39049874 | PMC:PMC11268105 | DOI:10.1016/j.omtn.2024.102260

Nature. 2024 Jul 24. doi: 10.1038/s41586-024-07606-7. Online ahead of print.

ABSTRACT

Alzheimer's disease is the leading cause of dementia worldwide, but the cellular pathways that underlie its pathological progression across brain regions remain poorly understood1-3. Here we report a single-cell transcriptomic atlas of six different brain regions in the aged human brain, covering 1.3 million cells from 283 post-mortem human brain samples across 48 individuals with and without Alzheimer's disease. We identify 76 cell types, including region-specific subtypes of astrocytes and excitatory neurons and an inhibitory interneuron population unique to the thalamus and distinct from canonical inhibitory subclasses. We identify vulnerable populations of excitatory and inhibitory neurons that are depleted in specific brain regions in Alzheimer's disease, and provide evidence that the Reelin signalling pathway is involved in modulating the vulnerability of these neurons. We develop a scalable method for discovering gene modules, which we use to identify cell-type-specific and region-specific modules that are altered in Alzheimer's disease and to annotate transcriptomic differences associated with diverse pathological variables. We identify an astrocyte program that is associated with cognitive resilience to Alzheimer's disease pathology, tying choline metabolism and polyamine biosynthesis in astrocytes to preserved cognitive function late in life. Together, our study develops a regional atlas of the ageing human brain and provides insights into cellular vulnerability, response and resilience to Alzheimer's disease pathology.

PMID:39048816 | DOI:10.1038/s41586-024-07606-7

Nat Struct Mol Biol. 2024 Jul 24. doi: 10.1038/s41594-024-01353-z. Online ahead of print.

ABSTRACT

Cell size is tightly controlled in healthy tissues and single-celled organisms, but it remains unclear how cell size influences physiology. Increasing cell size was recently shown to remodel the proteomes of cultured human cells, demonstrating that large and small cells of the same type can be compositionally different. In the present study, we utilize the natural heterogeneity of hepatocyte ploidy and yeast genetics to establish that the ploidy-to-cell size ratio is a highly conserved determinant of proteome composition. In both mammalian and yeast cells, genome dilution by cell growth elicits a starvation-like phenotype, suggesting that growth in large cells is restricted by genome concentration in a manner that mimics a limiting nutrient. Moreover, genome dilution explains some proteomic changes ascribed to yeast aging. Overall, our data indicate that genome concentration drives changes in cell composition independently of external environmental cues.

PMID:39048803 | DOI:10.1038/s41594-024-01353-z

Nat Genet. 2024 Jul 24. doi: 10.1038/s41588-024-01830-7. Online ahead of print.

ABSTRACT

Contiguous genome sequence assemblies will help us to realize the full potential of crop translational genomics. Recent advances in sequencing technologies, especially long-read sequencing strategies, have made it possible to construct gapless telomere-to-telomere (T2T) assemblies, thus offering novel insights into genome organization and function. Plant genomes pose unique challenges, such as a continuum of ancient to recent polyploidy and abundant highly similar and long repetitive elements. Owing to progress in sequencing approaches, for most crop plants, chromosome-scale reference genome assemblies are available, but T2T assembly construction remains challenging. Here we describe methods for haplotype-resolved, gapless T2T assembly construction in plants, including various crop species. We outline the impact of T2T assemblies in elucidating the roles of repetitive elements in gene regulation, as well as in pangenomics, functional genomics, genome-assisted breeding and targeted genome manipulation. In conjunction with sequence-enriched germplasm repositories, T2T assemblies thus hold great promise for basic and applied plant sciences.

PMID:39048791 | DOI:10.1038/s41588-024-01830-7

EMBO Rep. 2024 Jul 24. doi: 10.1038/s44319-024-00206-6. Online ahead of print.

ABSTRACT

The Bcl-2 family controls apoptosis by direct interactions of pro- and anti-apoptotic proteins. The principle mechanism is binding of the BH3 domain of pro-apoptotic proteins to the hydrophobic groove of anti-apoptotic siblings, which is therapeutically exploited by approved BH3-mimetic anti-cancer drugs. Evidence suggests that also the transmembrane domain (TMD) of Bcl-2 proteins can mediate Bcl-2 interactions. We developed a highly-specific split luciferase assay enabling the analysis of TMD interactions of pore-forming apoptosis effectors BAX, BAK, and BOK with anti-apoptotic Bcl-2 proteins in living cells. We confirm homotypic interaction of the BAX-TMD, but also newly identify interaction of the TMD of anti-apoptotic BCL-2 with the TMD of BOK, a peculiar pro-apoptotic Bcl-2 protein. BOK-TMD and BCL-2-TMD interact at the endoplasmic reticulum. Molecular dynamics simulations confirm dynamic BOK-TMD and BCL-2-TMD dimers and stable heterotetramers. Mutation of BCL-2-TMD at predicted key residues abolishes interaction with BOK-TMD. Also, inhibition of BOK-induced apoptosis by BCL-2 depends specifically on their TMDs. Thus, TMDs of Bcl-2 proteins are a relevant interaction interface for apoptosis regulation and provide a novel potential drug target.

PMID:39048751 | DOI:10.1038/s44319-024-00206-6

Sci Rep. 2024 Jul 24;14(1):17067. doi: 10.1038/s41598-024-66851-y.

ABSTRACT

Breath analysis is an area of significant interest in medical research as it allows for non-invasive sampling with exceptional potential for disease monitoring and diagnosis. Volatile organic compounds (VOCs) found in breath can offer critical insight into a person's lifestyle and/or disease/health state. To this end, the development of a rapid, sensitive, cost-effective and potentially portable method for the detection of key compounds in breath would mark a significant advancement. Herein, we have designed, built and tested a novel reagent-less atmospheric pressure photoionisation (APPI) source, coupled with mass spectrometry (MS), utilising a bespoke bias electrode within a custom 3D printed sampling chamber for direct analysis of VOCs. Optimal APPI-MS conditions were identified, including bias voltage, cone voltage and vaporisation temperature. Calibration curves were produced for ethanol, acetone, 2-butanone, ethyl acetate and eucalyptol, yielding R2 > 0.99 and limits of detection < 10 pg. As a pre-clinical proof of concept, this method was applied to bacterial headspace samples of Escherichia coli (EC), Pseudomonas aeruginosa (PSA) and Staphylococcus aureus (SA) collected in 1 L Tedlar bags. In particular, PSA and SA are commonly associated with lung infection in cystic fibrosis patients. The headspace samples were classified using principal component analysis with 86.9% of the total variance across the first three components and yielding 100% classification in a blind-sample study. All experiments conducted with the novel APPI arrangement were carried out directly in real-time with low-resolution MS, which opens up exciting possibilities in the future for on-site (e.g., in the clinic) analysis with a portable system.

PMID:39048618 | DOI:10.1038/s41598-024-66851-y

Carbohydr Polym. 2024 Oct 15;342:122399. doi: 10.1016/j.carbpol.2024.122399. Epub 2024 Jun 15.

ABSTRACT

This work demonstrates that sesame (Sesamum indicum L.) hull, an unexploited food industrial waste, can be used as an efficient source for the extraction of hemicellulose and/or pectin polysaccharides to further obtain functional oligosaccharides. Different polysaccharides extraction methods were surveyed including alkaline and several enzymatic treatments. Based on the enzymatic release of xylose, arabinose, glucose, and galacturonic acid from sesame hull by using different enzymes, Celluclast®1.5 L, Pectinex®Ultra SP-L, and a combination of them were selected for the enzymatic extraction of polysaccharides at 50 °C, pH 5 up to 24 h. Once the polysaccharides were extracted, Ultraflo®L was selected to produce arabinoxylo-oligosaccharides (AXOS) at 40 °C up to 24 h. Apart from oligosaccharides production from extracted polysaccharides, alternative approaches for obtaining oligosaccharides were also explored. These were based on the analysis of the supernatants resulting from the polysaccharide extraction, alongside a sequential hydrolysis performed with Celluclast®1.5 L and Ultraflo®L of the starting raw sesame hull. The different fractions obtained were comprehensively characterized by determining low molecular weight carbohydrates and monomeric compositions, average Mw and dispersity, and oligosaccharide structure by MALDI-TOF-MS. The results indicated that sesame hull can be a useful source for polysaccharides extraction (pectin and hemicellulose) and derived oligosaccharides, especially AXOS.

PMID:39048235 | DOI:10.1016/j.carbpol.2024.122399

J Proteomics. 2024 Jul 22:105262. doi: 10.1016/j.jprot.2024.105262. Online ahead of print.

ABSTRACT

Gastric cancer (GC) is a global health concern. To facilitate improved management of GCs protein biomarkers have been identified through mass spectrometry-based proteomics platforms. In order to exhibit clinical utility of such data, we congregated over 6800 differentially regulated proteins in GCs from proteomics studies and recorded the mass spectrometry platforms, association of the protein with infectious agents, protein identifiers, sample size and clinical characters of samples used with details on validation. Development of targeted proteomics methods is the cornerstone for pursuing these markers into clinical utility. Therefore, we developed Protein Biomarker Matrix for Gastric Cancer (PBMGC), a simple catalogue of robustness of each protein. This analysis yielded the identification of robust tissue, serum, urine and prognostic protein panels which can be further tested for their clinical utility. We also ascertained proteotypic tryptic peptides of 5631 proteins suitable for developing MRM assays. Extensive characterization of these peptides was carried out to record peptide ions, mass/charge and enhanced specific peptide features. With the vision of catering to proteomics researchers, the data generated through this analysis has been catalogued at Gastric Cancer Proteomics DataBase (GCPDB) (https://ciods.in/gcpdb/). Users can browse and download the data and improve GCPDB by submitting recently published data. SIGNIFICANCE: Mass spectrometry-based proteomics platforms have accumulated substantial data on protein differential regulation in gastric cancer (GC) clinical samples. The utility of such data in clinical applications is limited by search for suitable biomarker panels for assessing GCs. We assembled over 6800 differentially regulated proteins in GCs from proteomics studies and recorded the corresponding details including mass spectrometry platforms, status on the association of the protein with infectious agents, protein identifiers from different databases, sample size and clinical characters of samples used in test and control conditions along with details on their validation. Towards the vision of utilizing these markers in clinical assays, Protein Biomarker Matrix for Gastric Cancer (PBMGC) was developed and clinically relevant multi-protein panels were identified. We also demonstrated identification and characterization of tryptic proteotypic tryptic peptides of 5631 proteins biomarkers of GCs which are suitable for development of multiple reaction monitoring (MRM) assays in a SCIEX QTRAP instrument. With the moto of catering to proteomics researchers, the data generated through this analysis has been catalogued at Gastric Cancer Proteomics DataBase (GCPDB) (https://ciods.in/gcpdb/). The users can browse and download details on different markers and improve GCPDB by submitting recently published data. Such an analysis could lay a cornerstone for building more such resources or conduct such analysis in different clinical conditions to uptake and develop targeted proteomics as the method of choice for clinical applications.

PMID:39047941 | DOI:10.1016/j.jprot.2024.105262