Protein Concentration Research Articles

Associations of the Serum KL-6 with Severity and Prognosis in Patients with Acute Exacerbation of Chronic Obstructive Pulmonary Disease.

As a biomarker of alveolar-capillary basement membrane injury, Krebs von den Lungen-6 (KL-6) is involved in the occurrence and development of pulmonary diseases. However, the role of the KL-6 in patients with acute exacerbation of chronic obstructive pulmonary disease (AECOPD) has yet to be elucidated. This prospective study was designed to clarify the associations of the serum KL-6 with the severity and prognosis in patients with AECOPD. This study enrolled 199 eligible AECOPD patients. Demographic data and clinical characteristics were recorded. Follow-up was tracked to evaluate acute exacerbation and death. The serum KL-6 concentration was measured via an enzyme-linked immunosorbent assay. Serum KL-6 level at admission was higher in AECOPD patients than in control subjects. The serum KL-6 concentration gradually elevated with increasing severity of AECOPD. Pearson and Spearman analyses revealed that the serum KL-6 concentration was positively correlated with the severity score, monocyte count and concentrations of C-reactive protein, interleukin-6, uric acid, and lactate dehydrogenase in AECOPD patients during hospitalization. A statistical analysis of long-term follow-up data showed that elevated KL-6 level at admission was associated with longer hospital stays, an increased risk of future frequent acute exacerbations, and increased severity of exacerbation in COPD patients. Serum KL-6 level at admission is positively correlated with increased disease severity, prolonged hospital stay and increased risk of future acute exacerbations in COPD patients. There are positive dose-response associations of elevated serum KL-6 with severity and poor prognosis in COPD patients. The serum KL-6 concentration could be a novel diagnostic and prognostic biomarker in AECOPD patients.

Effect of pH and Shear on Heat-Induced Changes in Milk Protein Concentrate Suspensions

The effect of shear on heat-induced changes in milk protein concentrate suspensions was examined at different pH levels, revealing novel insights into micellar dissociation and protein aggregation dynamics. Milk protein concentrate suspensions, adjusted to pH of 6.1, 6.4, 6.8, or 7.5, underwent combined heat (90 °C for 5 min or 121 °C for 2.6 min) and shear (0, 100, or 1000 s−1) treatment. The fragmentation of protein aggregates induced by shear was evident in the control MPC suspensions at pH 6.8, irrespective of the temperature. At pH 7.5, shear increased the heat-induced micellar dissociation. This effect was particularly pronounced at 121 °C and 1000 s−1, resulting in reduced particle size and an elevated concentration of κ-casein (κ-CN) in the non-sedimentable phase. At pH 6.1 or 6.4, shear effects were dependent on sample pH, thereby modifying electrostatic interactions and the extent of whey protein association with the micelles. At pH 6.1, shear promoted heat-induced aggregation, evidenced by an increase in particle size and a significant decline in both whey proteins and caseins in the non-sedimentable phase. At pH 6.4, shear-induced fragmentation of aggregates was observed, prominently due to comparatively higher electrostatic repulsions and fewer protein interactions. The influence of shear on heat-induced changes was considerably impacted by initial pH.

Multiplexing the Identification of Microorganisms via Tandem Mass Tag Labeling Augmented by Interference Removal through a Novel Modification of the Expectation Maximization Algorithm.

Having fast, accurate, and broad spectrum methods for the identification of microorganisms is of paramount importance to public health, research, and safety. Bottom-up mass spectrometer-based proteomics has emerged as an effective tool for the accurate identification of microorganisms from microbial isolates. However, one major hurdle that limits the deployment of this tool for routine clinical diagnosis, and other areas of research such as culturomics, is the instrument time required for the mass spectrometer to analyze a single sample, which can take ∼1 h per sample, when using mass spectrometers that are presently used in most institutes. To address this issue, in this study, we employed, for the first time, tandem mass tags (TMTs) in multiplex identifications of microorganisms from multiple TMT-labeled samples in one MS/MS experiment. A difficulty encountered when using TMT labeling is the presence of interference in the measured intensities of TMT reporter ions. To correct for interference, we employed in the proposed method a modified version of the expectation maximization (EM) algorithm that redistributes the signal from ion interference back to the correct TMT-labeled samples. We have evaluated the sensitivity and specificity of the proposed method using 94 MS/MS experiments (covering a broad range of protein concentration ratios across TMT-labeled channels and experimental parameters), containing a total of 1931 true positive TMT-labeled channels and 317 true negative TMT-labeled channels. The results of the evaluation show that the proposed method has an identification sensitivity of 93-97% and a specificity of 100% at the species level. Furthermore, as a proof of concept, using an in-house-generated data set composed of some of the most common urinary tract pathogens, we demonstrated that by using the proposed method the mass spectrometer time required per sample, using a 1 h LC-MS/MS run, can be reduced to 10 and 6 min when samples are labeled with TMT-6 and TMT-10, respectively. The proposed method can also be used along with Orbitrap mass spectrometers that have faster MS/MS acquisition rates, like the recently released Orbitrap Astral mass spectrometer, to further reduce the mass spectrometer time required per sample.

A novel in-house built printed circuit board-ceria based electrochemical device for rapid detection of Epithelial Sodium Channel (ENaC), a hypertension biomarker

The Epithelial Sodium Channel (ENaC) is a protein that plays a role in the cellular intake of salt and is known as one of the biomarkers for hypertension in the human body. Higher concentrations of sodium lead to increased activity of the ENaC protein in sodium absorption. In this study, a self-made immunosensor was developed using a homemade Printed Circuit Board-Screen Printed Carbon Electrode (PCB-SPCE) modified with cerium oxide. Anti-ENaC was immobilized on the surface of PCB-SPCE/ceria at pH 7.4, relying on the interaction between carboxyl groups of anti-ENaC and cerium oxide to detect the ENaC protein. Additionally, a portable in-house potentiostat named “UnpadStat” was developed for integration with the immunosensor. UnpadStat features a 5-in. touch screen display to showcase measurement data. Cyclic voltammetry measurements using the redox system of K3[Fe(CN)6] were applied to bare PCB-SPCE, PCB-SPCE/Ceria, PCB-SPCE/Ceria/Anti-ENaC, and PCB-SPCE/Ceria/Anti-ENaC/ENaC. Measurement results indicated an increase in current after modification with cerium, reaching 73.805 µA compared to unmodified (63.256 µA). After anti-ENaC immobilization, there was a decrease in current to 64.456 µA, and upon binding with the ENaC protein, a further decrease in current occurred, corresponding to the concentration of the ENaC protein. The detection limit obtained in this study was 0.133 ng/mL, and the quantification limit was 0.444 ng/mL for the concentration range of ENaC protein from 0.375 ng/mL to 6.0 ng/mL. The integration of the PCB-based immunosensor and UnpadStat can be utilized to determine the levels of ENaC protein in non-hypertensive urine samples and hypertensive patients.

Biomarker signatures associated with ageing free of major chronic diseases: results from a population-based sample of the EPIC-Potsdam cohort.

A number of biomarkers denoting various pathophysiological pathways have been implicated in the aetiology and risk of age-related diseases. Hence, the combined impact of multiple biomarkers in relation to ageing free of major chronic diseases, such as cancer, cardiovascular disease and type 2 diabetes, has not been sufficiently explored. We measured concentrations of 13 biomarkers in a random subcohort of 2,500 participants in the European Prospective Investigation into Cancer and Nutrition Potsdam study. Chronic disease-free ageing was defined as reaching the age of 70years within study follow-up without major chronic diseases, including cardiovascular disease, type 2 diabetes or cancer. Using a novel machine-learning technique, we aimed to identify biomarker clusters and explore their association with chronic disease-free ageing in multivariable-adjusted logistic regression analysis taking socio-demographic, lifestyle and anthropometric factors into account. Of the participants who reached the age of 70years, 321 met our criteria for chronic-disease free ageing. Machine learning analysis identified three distinct biomarker clusters, among which a signature characterised by high concentrations of high-density lipoprotein cholesterol, adiponectin and insulin-like growth factor-binding protein 2 and low concentrations of triglycerides was associated with highest odds for ageing free of major chronic diseases. After multivariable adjustment, the association was attenuated by socio-demographic, lifestyle and adiposity indicators, pointing to the relative importance of these factors as determinants of healthy ageing. These data underline the importance of exploring combinations of biomarkers rather than single molecules in understanding complex biological pathways underpinning healthy ageing.

The impacts of pullulan soaking on radish seed germination and seedling growth under salt stress.

Pullulan can not only provide a source of organic carbon but also has excellent properties. However, current research is mostly limited to the physical properties of the high molecular-weight components of pullulan, and little is known of the application of its low molecular-weight components. This study was designed to explore the impact of the pre-soaking of radish seeds in a pullulan solution on seed germination and subsequent seedling growth under salt stress conditions. Pullulan soaking was found to enhance the germination rates of radish seeds subjected to salt stress, while also enhancing the aboveground growth of radish seedlings. Pullulan soaking resulted in increases in chlorophyll, soluble protein, and soluble sugar concentrations in the leaves of these seedlings, together with greater peroxidase activity and root activity as well as decreases in Na+ and malondialdehyde concentrations. This provides an important reference for the application of pullulan in plant protection.

Exercise as an anti-inflammatory Therapy in Axial Spondyloarthritis Therapeutic Intervention (EXTASI study): a randomised control trial

Abstract Objectives Axial Spondyloarthritis (AxSpA) is a chronic inflammatory disease, yet despite known anti-inflammatory effects of exercise, the effect of exercise on inflammatory immune cell populations and associated inflammatory profiles in AxSpA is unknown. This randomised-control trial investigated the effect of 12-weeks of walking on symptom severity, cardiometabolic health, inflammatory biomarkers, and immune cell populations. Methods Twenty people (60% male) living with AxSpA who were on stable dose non-steroidal anti-inflammatory (NSAIDs) medication participated. Participants were randomly assigned to control or exercise (30 min of walking five x per week). Participants were invited back every four-weeks for assessment. Results There was a 0% drop out and no adverse events in the exercise group showing walking exercise was well tolerated. Home-based walking for 12-weeks lowered the proportion of pro-inflammatory monocytes, whereas they increased in the control group. Changes were associated with lower interleukin-6 (IL-6) and C-reactive protein (CRP) concentrations, lower spinal pain, and lower systolic blood pressure in the exercise group, whereas these markers increased in the control group. Reductions in IL-6 and pro-inflammatory monocytes with exercise were independent of lower body fat percentage. Conclusion Supplementing NSAID therapy with walking exercise can improve inflammatory immune profiles in people with AxSpA coinciding with reductions in spinal pain. Importantly, the exercise was well tolerated, suggesting walking exercise can be used as an adjuvant anti-inflammatory therapy for NSAID treatments. This should now be explored in people living with AxSpA who have had high enough disease activity to necessitate the prescription of biologic or synthetic DMARD treatments. Clinical trials registration ClinicalTrials.Gov, NCT04368494

A new strain of Saccharomyces cerevisiae in diets of lactating Holstein cows improved feed efficiency and lactation performance

Abstract This study compared the effects of feeding a new strain of Saccharomyces cerevisiae HSA2020 with a commercial strain on in vitro rumen fermentation and production performance of dairy cows. Permeate was used as a substrate for the laboratory production of the new strain of S. cerevisiae after the hydrolysis by β–galactosidase (5000 µ/mL at 37°C). Two experiments were conducted: in Experiment 1, the effects of three levels (1, 2 and 3 g/kg dry matter) of S. cerevisiae on in vitro ruminal fermentation kinetics were evaluated. In Experiment 2, for 60 days, sixty multiparous Holstein cows (639±24.8 kg BW, 3±1 parity, 7±1 days in milk, with a previous milk production of 23±2.0 kg/d) during the previous lactation, were randomly assigned to 3 treatments in a completely randomized design. Cows were fed without any additives (control treatment) or supplemented with 2 g/kg feed daily of laboratory produced (PY)or commercial (CY) S. cerevisiae. In Experiment 1, inclusion of PY and CY increased (P<0.05) gas production, propionate, and nutrient disappearance, while decreased (P<0.05) methane production and protozoal count. Moreover, in Experiment 2, PY followed by CY increased (P<0.01) nutrient digestibility, and serum concentrations of total protein, albumin, and glucose (P<0.05). Higher daily milk yield, and milk energy output were observed with PY and CY without affecting concentrations of milk components or milk fatty acid profile. Compared to control, increased feed efficiency was observed with PY and CY. Compared to PY, CY increased serum concentrations of urea-N and decreased triglycerides, while PY decreased serum aspartate transaminase and increased concentration of conjugated linoleic acids in milk. In early lactating cow diets, both strains of S. cerevisiae improved production performance at 2 g/kg improved production performance, and minimal differences between strains were found.

Mesenchymal stem cell-derived exosomes decrease Hyperplasia in Psoriasis by inducing transforming growth factor β2 (TGF-β2).

Psoriasis, a chronic inflammatory skin disease, is increasingly effectively managed with the targeted immunotherapy; however, long-term immunotherapy carries health risks, and loss of response. Therefore, we need to develop the alternative treatment strategies. Mesenchymal stem/stromal cell (M.S.C.) exosomes stand out for their remarkable immunomodulatory properties, gaining widespread recognition. This study investigated whether M.S.C. exosomes can reduce psoriasis-induced hyperplasia by inducing Transforming Growth Factor beta 2 (TGF-beta2) signaling. Exosomes were isolated from M.S.C.s by ultracentrifugation. Then, scanning electron microscopy was used for the morphology of exosomes. To ascertain the exosome concentration, the Bradford test was used. To ascertain the cellular toxicity of exosomes in Human Umbilical Vein Endothelial Cells ( H.U.V.E.C), an MTT experiment was then conducted. Real-time PCR was used to quantify TGF beta2 expression levels, whereas an ELISA immunosorbent assay was used to determine the protein concentration of TGF beta2. In this study, the exosomes of 15-30nm in size that were uniform, and cup-shaped were isolated. Moreover, the IC50 value for this Treatment was calculated to be 181.750µg/ml. The concentration of TGF-β2 gene in the target cells significantly increased following Treatment with the exosomes. Furthermore, the expression level of the studied gene significantly increased due to the Treatment. Upregulating the expression of TGF-β2 in psoriatic cells via TGF-β2 signaling is one way exosomes can help reduce hyperplasia.

Fluorescence Sensing of Eclampsia Biomarkers via the Immunosorbent Atom Transfer Radical Polymerization Assay.

Accurate and quantitative detection of pre-eclampsia markers is crucial in reducing pregnancy mortality rates. This study introduces a novel approach utilizing a fluorescent biosensor by the immunosorbent atom transfer radical polymerization (immuno-ATRP) assay to detect the pre-eclampsia protein marker CD81. The critical step used in this sensor is the novel signal amplification strategy of fluorescein polymerization mediated by ferritin-enhanced controlled radical polymerization, which combines with a traditional enzyme-linked immunosorbent assay (ELISA) to further reduce the detection limit of the CD81 protein concentration. The fluorescence intensity was linear versus logarithmic CD81 protein concentration from 0.1 to 10,000 pg mL-1, and the detection limit was 0.067 pg mL-1. Surprisingly, in 30% normal human serum (NHS), the sensor can also detect target protein over 0.1-10,000 pg mL-1, with 0.083 pg mL-1 for the detection limit. Moreover, the proposed biosensor is designed to be cost-effective, making it accessible, particularly in resource-limited settings where expensive detection techniques may not be available. The affordability of this method enables widespread screening and monitoring of preeclampsia, ultimately benefiting many pregnant women by improving their healthcare outcomes. In short, developing of a low-cost and susceptible direct detection method for preeclampsia protein markers, such as CD81, through the use of the immuno-ATRP assay, has significant implications for reducing pregnancy mortality. This method holds promise for early detection, precise treatment, and improved management of preeclampsia, thereby contributing to better maternal and fetal health.

The Influence of Substrate and Strain on Protein Quality of Pleurotus ostreatus

Background: The effect of substrate and strain on the nutritional and functional properties of mushroom flours and protein concentrates (PCs) has not thoroughly been investigated. Methods: The proteins of P. ostreatus flours (strains AMRL144 and 150) were isolated following alkaline extraction (pH 12) and isoelectric precipitation (pH 4) as it was determined by the solubility curves. The protein quality of the flours and PCs were evaluated by determining the protein solubility index (PSI) and their functional properties, such as water (WAC) and oil absorption capacity (OAC), foam capacity (FC), foam stability (FS) and emulsion stability (ES). The amino acid (AA) composition of the flours was determined by reversed-phase liquid chromatography after protein hydrolysis and o-phthalaldehyde derivatization. Results: The PSIs of the flours and PCs of P. ostreatus were comparable to those of soy protein flours and protein concentrates. The highest AA concentration was found for both strains when cultivated on the barley and oat straw (BOS) substrate, showing a similar trend as the protein content. A principal component analysis (PCA) indicated an impact of the strain on the functional properties. Conclusions: Both strains can produce high quality proteins especially when cultivated on wheat straw (WS). The FS was positively correlated with the P. ostreatus strain AMRL150 whereas the FC was positively correlated with AMRL144.

Clinicopathological and Molecular Analysis of Aqueous Humor for the Diagnosis of Feline Infectious Peritonitis

Background: This study was designed to assess the diagnostic utility for FIP of cytology, protein measurement and RT-PCR for feline coronaviruses (FCoV) on aqueous humor (AH), since little information is currently available. Methods: AH samples (n = 85) were collected post-mortem from 13 cats with effusive FIP (E-FIP), 15 with non-effusive FIP (NE-FIP) and 16 without FIP, to perform cytology (n = 83) and RT-PCR (n = 66) and to calculate their sensitivity, specificity and positive and negative likelihood ratios (LR+ and LR−). The protein concentration was measured on 80 fluids. Results: The proportion of RT-PCR positive samples did not differ among groups, while positive cytology was more frequent in samples with FIP (p = 0.042) or positive RT-PCR (p = 0.007). Compared with other groups, the protein concentration was higher in samples with NE-FIP (p = 0.017), positive RT-PCR (p = 0.005) or positive cytology (p < 0.001). The specificity of cytology together with RT-PCR, cytology alone, RT-PCR alone and cytological proteinaceous background were 90.0%, 84.6%, 70.0%, 61.5%, and the LRs 3.48, 2.65, 1.83, 1.64, respectively. However, their sensitivities were low (34.8–63.0%) and their LR− high (0.60–0.72). Conclusions: Based on the LR+, cytology and/or RT-PCR may support the diagnosis when the pre-test probability of FIP is high. The concentration of intraocular protein is a promising marker, especially in NE-FIP.

Pea growth, yield, and quality affected by nitrogen fertilization to previous crop in small grain–pea rotations

AbstractStarter N fertilization at low rates may enhance pea (Pisum sativum L.) performance, but little information exists about the effect of N fertilization rate to previous crop (NRPC) on pea growth, yield, and quality in small grain–pea rotations. We examined the effect of N fertilization rates to barley (Hordeum vulgare L.) and spring wheat (Triticum aestivum L.) on succeeding pea growth, yield, and quality in barley–pea and spring wheat–pea rotations from 2006 to 2019 in the semiarid environment of US northern Great Plains. We measured pea plant density, straw and grain yields, harvest index, straw N concentration, grain protein concentration, grain test weight, straw and grain N uptake, and N harvest index. In the barley–pea rotation, pea grain yield increased with increased NRPC. Grain test weight was greater without than with NRPC in 2008 and 2009. In the spring wheat–pea rotation, straw yield was greater for 50 than 0 kg N ha−1 of NRPC in 2014, 2018, and 2019. Grain yield and N uptake were greater with than without NRPC in 2014, 2015, and 2019, but grain test weight varied with NRPC and year. Plant density, harvest index, straw N concentration, grain protein concentration, straw N uptake, and N harvest index varied with year in both barley–pea and spring wheat–pea rotations. Nitrogen fertilization to barley or spring wheat can enhance succeeding pea grain yield and N uptake during years with normal growing season precipitation in barley–pea and spring–wheat pea rotations in the semiarid region of the US northern Great Plains.

Feeding strategy and feed protein level affect the gut microbiota of common carp (Cyprinus carpio).

Common carp (Cyprinus carpio) were fed food with different protein concentrations following different feeding regimes, which were previously shown to affect growth, nitrogen excretion and amino acid catabolism. 16S rRNA gene amplicon sequencing was performed to investigate the gut microbiota of these fish. Lower dietary protein content increased microbial richness, while the combination of demand feeding and dietary protein content affected the composition of the gut microbiota. Hepatic glutamate dehydrogenase (GDH) activity was correlated to the composition of the gut microbiota in all dietary treatments. We found that demand-fed carp fed a diet containing 39% protein had a significantly higher abundance of Beijerinckiaceae compared to other dietary groups. Network analysis identified this family and two Rhizobiales families as hubs in the microbial association network. In demand-fed carp, the microbial association network had significantly fewer connections than in batch-fed carp. In contrast to the large effects of the feeding regime and protein content of the food on growth and nitrogen metabolism, it had only limited effects on gut microbiota composition. However, correlations between gut microbiota composition and liver GDH activity showed that host physiology and gut microbiota are connected, which warrants functional studies into the role of the gut microbiota in fish physiology.

The biological equivalent and prognostic relevance of c-reactive protein (CRP) velocity in ST segment elevation myocardial infarction

Abstract Funding Acknowledgements None. Background The rate of increase, i.e. the velocity, of circulating C-reactive protein (CRP) concentrations during myocardial infarction has been associated with left ventricular dysfunction. However, the prognostic yield of this biomarker as well as the underlying biological process that links high CRP velocity (CRPv) with increased myocardial injury are not clear. Therefore, we sought to determine the associations between CRPv early during STEMI with short- and long-term mortality and its correlation to myocardial necrosis. Methods We retrospectively examined 1,155 patients with the diagnosis of acute STEMI, who had at least two successive CRP measurements (up to 48 hours apart) and at least one echocardiographic evaluation, all within the first 96 hours of admission. We calculated CRPv and examined its correlation with myocardial injury, measured by cardiac troponin and overall mortality over a median follow-up period of 5.2 years [IQR 3.7-6.5]. Results Patients with high CRPv values (above 90th percentile, > 1 mg/L/h) had higher concentrations of cardiac troponin upon presentation regardless of their left ventricular systolic function (EF above or below 40%; Figure 1). Patients with high CRPv had increased 30-day and long-term mortality rates; OR= 4.6, 95% CI 2.3-9.2, p<0.001 for 30-day mortality and HR= 2.2, 95% CI 1.5-3.2, p<0.001 for long-term mortality. Furthermore, CRPv was associated with increased 30 –day and long term mortality rates even among patients with similar systolic function (EF above or below 40%; Figure 2). Conclusions High levels of CRPv early during STEMI are associated with increased mortality rates and elevated cardiac troponin release across all levels of left ventricular function. The higher mortality risk might be explained by an aggravated systemic inflammatory response to STEMI.CRP velocity and troponinCRP velocity and mortality

Enhancing the usability of pea protein in emulsion applications through modification by various approaches: A comparative study

The extensive utilization in food industry of pea protein is often impeded by its low water solubility, resulting in poor functional properties. Various methods, including pH-shifting (PS), ultrasonication (US), high-pressure micro-fluidization (MF), pH-shifting combined with ultrasonication (PS-US), and pH-shifting with micro-fluidization (PS-MF), were utilized to modify pea protein isolate (PPI) in order to enhance its functionality in emulsion formulation. The physicochemical properties and structural changes of the protein were investigated by assessing solubility, particle size, surface charge, protein profile, surface hydrophobicity, free sulfhydryl groups, and secondary structure content. The extent of modification induced by each treatment method on PPI-stabilized emulsions was compared based on parameters such as adsorbed interfacial protein concentration, particle size, zeta potential, and microstructure of the prepared emulsions. All modification increased the solubility of pea protein in the sequence of PS (4-fold) < MF (7-fold) < US (11-fold) < PS-US (13-fold) < PS-MF (14-fold). For single treatments, proteins dissolved more readily under US, resulting in the most uniform emulsions with small particle. The combined processes of PS-US and PS-MF further improved solubility, decreased emulsions particle size, promoted uniformity of emulsions. PS-US-stabilized emulsions displayed more smaller droplet size, narrower size distribution, and slightly higher stability than those prepared by PS-MF. The relatively higher emulsifying capacity of PPI treated by PS-US than those by PS-MF may be attributed to its higher surface hydrophobicity.

Genome organization around nuclear speckles drives mRNA splicing efficiency.

The nucleus is highly organized, such that factors involved in thetranscription and processing of distinct classes of RNA are confined within specific nuclear bodies1,2. One example is the nuclear speckle, which is defined by high concentrations of protein and noncoding RNA regulators of pre-mRNA splicing3. What functional role, if any, speckles might play in the process of mRNA splicing is unclear4,5. Here we show that genes localized near nuclear speckles display higher spliceosome concentrations, increased spliceosome binding to their pre-mRNAs and higher co-transcriptional splicing levels than genes that are located farther from nuclear speckles. Gene organization around nuclear speckles is dynamic between cell types, and changes in speckle proximity lead to differences in splicing efficiency. Finally, directed recruitment of a pre-mRNA to nuclear speckles is sufficient to increase mRNA splicing levels. Together, our results integrate the long-standing observations of nuclear speckles with the biochemistry of mRNA splicing and demonstrate a crucial role for dynamic three-dimensional spatial organization of genomic DNA in driving spliceosome concentrations and controlling the efficiency of mRNA splicing.

Ultra-Sensitive Detection of the SARS-CoV-2 Nucleocapsid Protein via a Clustered Regularly Interspaced Short Palindromic Repeat/Cas12a-Mediated Immunoassay.

Tracking trace protein analytes in precision diagnostics is an ongoing challenge. Here, we developed an ultrasensitive detection method for the detection of SARS-CoV-2 nucleocapsid (N) protein by combining enzyme-linked immunosorbent assay (ELISA) with the clustered regularly interspaced short palindromic repeat/CRISPR-associated protein (CRISPR/Cas) system. First, the SARS-CoV-2 N protein bound by the capture antibody adsorbed on the well plate was sequentially coupled with the primary antibody, biotinylated secondary antibody, and streptavidin (SA), followed by biotin primer binding to SA. Subsequently, rolling circle amplification was initiated to generate ssDNA strands, which were targeted by CRISPR/Cas12a to cleave the FAM-ssDNA-BHQ1 probe in trans to generate fluorescence signals. We observed a linear relationship between fluorescence intensity and the logarithm of N protein concentration ranging from 3 fg/mL to 3 × 107 fg/mL. The limit of detection (LOD) was 1 fg/mL, with approximately nine molecules in 1 μL of the sample. This detection sensitivity was 4 orders magnitude higher than that of commercially available ELISA kits (LOD: 5.7 × 104 fg/mL). This method was highly specific and sensitive and could accurately detect SARS-CoV-2 pseudovirus and clinical samples, providing a new approach for ultrasensitive immunoassay of protein biomarkers.

C-reactive protein concentrations diverge as a function of substance use disorder: A pre-registered replication in a clinical sample

BackgroundInflammatory biomarkers may differentiate clinical disorders, which could lead to more targeted interventions. Analyses within a clinical sample (May et al., 2021) revealed that females with substance use disorders (SUD) exhibited lower C-reactive protein (CRP) and higher interleukin (IL)-8 and −10 concentrations than females without SUD who met criteria for mood/anxiety disorders. We aimed to replicate these findings in a new sample. MethodsHypotheses and analyses were preregistered. Treatment-seeking individuals with mood/anxiety disorders and/or SUD (N = 184) completed a blood draw, clinical interview, and questionnaires. Participants were categorized as SUD+ (45F, 43M) and SUD- (78F, 18M). Principal component analysis (PCA) of questionnaire data resulted in two factors reflecting appetitive and aversive emotional states. SUD group and nuisance covariates (PCA factors, age, body mass index [BMI], medication, nicotine [and hormones in females]) predicted biomarker concentrations (CRP, IL-8, and IL-10) in regressions. ResultsIn females, the omnibus CRP model [F(8, 114) = 8.02, p <.001, R²-adjusted =.32] indicated that SUD+ exhibited lower CRP concentrations than SUD- (β = −.33, t = −3.09, p =.002, 95% CI [-.54, −.12]) and greater BMI was associated with higher CRP levels (β =.58, t = 7.17, p <.001, 95% CI [.42,.74]). SUD+ exhibited higher IL-8 levels than SUD- in simple but not omnibus regression models. ConclusionFindings across two samples bolster confidence that females with SUD show attenuated CRP-indexed inflammation. As SUD+ comorbidity was high, replication is warranted with respect to specific SUD classes (i.e., stimulants versus cannabis).

Single-Cell Profiling Reveals Immune Aberrations in Progressive Idiopathic Pulmonary Fibrosis.

Changes in peripheral blood cell populations have been observed but not detailed at single-cell resolution in idiopathic pulmonary fibrosis (IPF). To provide an atlas of the changes in the peripheral immune system in stable and progressive IPF. Peripheral blood mononuclear cells (PBMCs) from IPF patients and controls were profiled using 10x Chromium 5' single-cell RNA sequencing (scRNA-seq). Flow cytometry was used for validation. Protein concentrations of Regulatory T-cells (Tregs) and Monocytes chemoattractants were measured in plasma and lung homogenates from patients and controls. Thirty-eight PBMC samples from 25 patients with IPF and 13 matched controls yielded 149,564 cells that segregated into 23 subpopulations. Classical monocytes were increased in progressive and stable IPF compared to controls (32.1%, 25.2%, 17.9%, respectively, p<0.05). Total lymphocytes were decreased in IPF vs controls, and in progressive vs stable IPF (52.6% vs 62.6%, p=0.035). Tregs were increased in progressive vs stable IPF (1.8% vs 1.1% of all PBMC, p=0.007), although not different than controls, and may be associated with decreased survival (P=0.009 in Kaplan-Meier analysis; P=0.069 after adjusting for age, sex, and baseline FVC). Flow cytometry analysis confirmed this finding in an independent cohort of IPF patients. Fraction of Tregs out of all T cells was also increased in two cohorts of lung scRNA-seq. CCL22 and CCL18, ligands for CCR4 and CCR8 Treg chemotaxis receptors, were increased in IPF. The single-cell atlas of the peripheral immune system in IPF, reveals an outcome-predictive increase in classical monocytes and Tregs, as well as evidence for a lung-blood immune recruitment axis involving CCL7 (for classical monocytes) and CCL18/CCL22 (for Tregs).