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The potential protective or pathogenic role of the adaptive immune response to SARS‐CoV‐2 infection has been vigorously debated. While COVID‐19 patients consistently generate a T lymphocyte response to SARS‐CoV‐2 antigens, evidence of significant immune dysregulation in these patients continues to accumulate. In this study, next generation sequencing of the T cell receptor beta chain (TRB) repertoire was conducted in hospitalized COVID‐19 patients to determine if immunogenetic differences of the TRB repertoire contribute to disease course severity. Clustering of highly similar TRB CDR3 amino acid sequences across COVID‐19 patients yielded 781 shared TRB sequences. The TRB sequences were then filtered for known associations with common diseases such as EBV and CMV. The remaining sequences were cross‐referenced to a publicly accessible dataset that mapped COVID‐19 specific TCRs to the SARS‐CoV‐2 genome. We identified 158 SARS‐CoV‐2 specific TRB sequences belonging to 134 clusters in our COVID‐19 patients. Next, we investigated 113 SARS‐CoV‐2 specific clusters binding only one peptide target in relation to disease course. Distinct skewing of SARS‐CoV‐2 specific TRB sequences toward the nonstructural proteins (NSPs) encoded within ORF1a/b of the SARS‐CoV‐2 genome was observed in clusters associated with critical disease course when compared to COVID‐19 clusters associated with a severe disease course. These data imply that T‐lymphocyte reactivity towards peptides from NSPs of SARS‐CoV‐2 may not constitute an effective adaptive immune response and thus may negatively affect disease severity., Graphical Abstract The T cell receptor beta chain (TRB) repertoire of hospitalized COVID‐19 patients revealed that TRB sequences targeting nonstructural proteins of SARS‐CoV‐2 may negatively affect disease severity.

A major contributor to coronavirus disease 2019 (COVID-19) progression and severity is a dysregulated innate and adaptive immune response. Interleukin-38 (IL-38) is an IL-1 family member with broad anti-inflammatory properties, but thus far little is known about its role in viral infections. Recent studies have shown inconsistent results, as one study finding an increase in circulating IL-38 in COVID-19 patients in comparison to healthy controls, whereas two other studies report no differences in IL-38 concentrations.Here, we present an exploratory, retrospective cohort study of circulating IL-38 concentrations in hospitalized COVID-19 patients admitted to two Dutch hospitals (discovery n = 148 and validation n = 184) and age- and sex-matched healthy subjects. Plasma IL-38 concentrations were measured by enzyme-linked immunosorbent assay, disease-related proteins by proximity extension assay, and clinical data were retrieved from hospital records.IL-38 concentrations were stable during hospitalization and similar to those of healthy control subjects. IL-38 was not associated with rates of intensive care unit admission or mortality. Only in men in the discovery cohort, IL-38 concentrations were positively correlated with hospitalization duration. A positive correlation between IL-38 and the inflammatory biomarker d-dimer was observed in men of the validation cohort. In women of the validation cohort, IL-38 concentrations correlated negatively with thrombocyte numbers. Furthermore, plasma IL-38 concentrations in the validation cohort correlated positively with TNF, TNFRSF9, IL-10Ra, neurotrophil 3, polymeric immunoglobulin receptor, CHL1, CD244, superoxide dismutase 2, and fatty acid binding protein 2, and negatively with SERPINA12 and cartilage oligomeric matrix protein.These data indicate that IL-38 is not associated with disease outcomes in hospitalized COVID-19 patients. However, moderate correlations between IL-38 concentrations and biomarkers of disease were identified in one of two cohorts. While we demonstrate that IL-38 concentrations are not indicative of COVID-19 severity, its anti-inflammatory effects may reduce COVID-19 severity and should be experimentally investigated.

BACKGROUND: The Transfusion Register of Irregular Antibodies and Cross-match Problems (TRIX) is a unique national database in the Netherlands that was launched in 2007. Transfusion laboratories register the presence of irregular RBC alloantibodies for their patients and can consult the database for information that is relevant for pretransfusion testing, unknown in their own laboratory information system. STUDY DESIGN AND METHODS: Data from the TRIX database 10 years after implementation have been analyzed to demonstrate the added value of TRIX for transfusion practice. TRIX antibody registration, antibody disappearance likelihood, and differences between men and women have been analyzed and evaluated. RESULTS: In the 10-year period 2007 to 2016, a total of 80,164 alloantibodies have been identified and registered in 62,110 individuals. Of the antibodies, 81% were reported in women and 19% in men (female:male, 4.3:1). Rh (DCcEe and C w), K, Fy a, and Jk a antibodies account for 65.6% of all antibody registrations. M and Lewis antibodies account for 18.6% of all antibodies. Antibody disappearance likelihood is relatively high for the clinically relevant antibodies directed against Jk b, s, Fy b, and e. Antibodies directed against D, Fy a, and K have a relatively low antibody disappearance likelihood. CONCLUSION: TRIX is a unique and useful tool for transfusion laboratories for timely and up-to-date information on the presence of erythrocyte antibodies, which improves pretransfusion testing and compatible blood selection. TRIX also provides macro data on the prevalence of individual antibodies and antibody disappearance likelihoods that can be used for developing blood type matching strategies for patient groups at risk.

Background: Both one-stage (OSA) and chromogenic substrate assays (CSA) are used to measure factor VIII (FVIII) activity. Factors explaining analytical variation in FVIII activity levels are still to be completely elucidated. Aim: The aim of this study was to investigate and quantify the analytical variation in OSA and CSA. Methods: Factors determining analytical variation were studied in sixteen lyophilized plasma samples (FVIII activity

We describe a first Dutch case of Hb M Saskatoon (HBB:c.190C > T p.His64Tyr) in a 47-year-old female Dutch patient who presented with cyanosis, hemolysis, and abnormal co-oximetry. A mean corpuscular volume (MCV) of 105 fL caused by reticulocytosis (160 x 10(9)/L) and low red blood cell count (3.6 x 10(12)/L) suggested an increased erythrocyte turnover. An HPLC glyco-globin analysis revealed a decreased HbA1c fraction of 12.3 mmol/mmol, HbA0 of 93.3% and an additional unidentified fraction at 1.2 min. DNA sequencing revealed a missense mutation in the HBB gene, (HBB:c.190C > T p.His64Tyr), known as Hb M Saskatoon, a variant which has been previously identified as an unstable hemoglobin variant leading to methemoglobinemia and anemia. In this report, we describe the clinical and remarkable laboratory aspects of our patient with Hb M Saskatoon, and the consequences for treatment and drug use.

Background: Older patients often have iron deficiency anemia before surgery, which can be effectively treated with intravenous iron supplementation (IVIS). Anemia and blood transfusions are associated with an increased risk of delirium. The aim of this research was to assess the effectiveness and safety of using IVIS in a prehabilitation program. Material and methods: Patients ≥70 y who underwent abdominal surgery between November 2015 and June 2018 were included in this single-center prospective cohort study. All patients were prehabilitated; however, only anemic patients received a single dose of 1000 mg intravenous iron (ferric carboxymaltose) to increase preoperative hemoglobin levels (IVIS group). Nonanemic patients received standard care (SC). The hemoglobin levels (primary outcome) were assessed at the outpatient clinic visit, at admission, and at discharge. Secondary outcomes were postoperative delirium, postoperative anemia, blood transfusion, complications other than delirium, and length of hospital stay. All outcomes were compared between the IVIS group and SC group. Results: Of all patients (n = 248), 97 anemic patients received IVIS (39%). Of the anemic patients, 50 patients (52%) had iron deficiency. Initial differences in hemoglobin concentrations between the IVIS group and SC group at T1 and T2 (7.2 versus 8.8; P < 0.001 and 7.4 versus 8.6; P = 0.023, respectively) were no longer present at discharge (6.6 versus 7.2; P = 0.35). No statistically significant differences were observed for all secondary outcomes between the IVIS group and the SC group. No infusion-related adverse events occurred. Conclusions: Adding IVIS to prehabilitation programs is safe and diminishes differences in these concentrations between preoperatively anemic and nonanemic patients. IVIS may be worthwhile as an additional component of prehabilitation programs. Results merit further investigation.

We report a newborn with a compound heterozygosity for Hb O-Arab (

We report a newborn with a compound heterozygosity for Hb O-Arab (HBB: 364G>A) and Hb D-Los Angeles (HBB: 364G>C). To the best of our knowledge, the combination of these two hemoglobin (Hb) variants has not been identified and reported before. The variants of the proband and parents were identified by high-performance liquid chromatography (HPLC) and capillary electrophoresis (CE). DNA analysis was performed to confirm the variants. The levels of Hb variants of the proband were determined post-partum, at 3 months and 1 year after birth. Blood count analysis after 1 year revealed that the proband had a mild microcytic anemia. Furthermore, HPLC and CE analysis revealed an equal distribution of Hb D-Los Angeles compared to Hb O-Arab at the age of 1 year. The follow-up of the patient, suggested that the Hb combination is clinically silent or mild.

BACKGROUND Extension of storage time of platelet (PLT) concentrates may result in an increased risk of bacteremia, directly via transfusion of contaminated products or indirectly via transfusion-related immunomodulation. We aimed to quantify the association of storage time of PLT concentrates and all-cause bacteremia in hematologic patients. STUDY DESIGN AND METHODS We established a cohort of hematologic patients who received a PLT transfusion between 2005 and 2015. Cases were defined as patients with a bacteremia the day after transfusion and matched to as many controls as possible. A conditional logistic regression was performed, stratified by storage medium. RESULTS Among 3514 patients receiving 36,032 PLT concentrates stored in plasma, 613 cases of bacteremia were found. The relative risk of all-cause bacteremia the day after transfusion was 0.80 (95% confidence interval [CI], 0.58-1.12) for PLT concentrates stored 3 to 4 days and 0.67 (95% CI, 0.49-0.92) for at least 5 days, compared to no more than 2 days. Among 1527 patients receiving 11,822 PLT concentrates stored in PLT additive solution, 182 cases of bacteremia were found. The relative risk of all-cause bacteremia was 1.14 (95% CI, 0.70-1.84) for PLT concentrates stored for 3 to 4 days and 1.19 (95% CI, 0.70-2.01) for at least 5 days, compared to not more than 2 days. CONCLUSION Storage time of PLT concentrates was not associated with increased occurrence of all-cause bacteremia the day after transfusion. If anything, fewer cases of bacteremia occurred with increasing storage time of PLT concentrates in plasma. These bacteremias are not directly caused by transfusion of a contaminated product and the underlying mechanism warrants further research.

BACKGROUND: Due to the increase in elderly patients who undergo major abdominal surgery there is a subsequent increase in postoperative complications, prolonged hospital stays, health-care costs and mortality rates. Delirium is a frequent and severe complication in the 'frail' elderly patient. Different preoperative approaches have been suggested to decrease incidence of delirium by improving patients' baseline health. Studies implementing these approaches are often heterogeneous, have a small sample and do not provide high-quality or successful strategies. The aim of this study is to prevent postoperative delirium and other complications by implementing a unique multicomponent and multidisciplinary prehabilitation program. METHODS: This is a single-center controlled before-and-after study. Patients aged ≥70 years in need of surgery for colorectal cancer or an abdominal aortic aneurysm are considered eligible. Baseline characteristics (such as factors of frailty, physical condition and nutritional state) are collected prospectively. During 5 weeks prior to surgery, patients will follow a prehabilitation program to optimize overall health, which includes home-based exercises, dietary advice and intravenous iron infusion in case of anaemia. In case of frailty, a geriatrician will perform a comprehensive geriatric assessment and provide additional preoperative interventions when deemed necessary. The primary outcome is incidence of delirium. Secondary outcomes are length of hospital stay, complication rate, institutionalization, 30-day, 6- and 12-month mortality, mental health and quality of life. Results will be compared to a retrospective control group, meeting the same inclusion and exclusion criteria, operated on between January 2013 and October 2015. Inclusion of the prehabilitation cohort started in November 2015; data collection is ongoing. DISCUSSION: This is the first study to investigate the effect of prehabilitation on postoperative delirium. The aim is to provide evidence, based on a large sample size, for a standardized multicomponent strategy to improve patients' preoperative physical and nutritional status in order to prevent postoperative delirium and other complications. A multimodal intervention was implemented, combining physical, nutritional, mental and hematinic optimization. This research involves a large cohort, including patients most at risk for postoperative adverse outcomes. TRIAL REGISTRATION: The protocol is retrospectively registered at the Netherlands National Trial Register (NTR) number: NTR5932 . Date of registration: 05-04-2016. ispartof: BMC GERIATRICS vol:19 issue:1 ispartof: location:England status: published

Background: Genotyping of HLA-DQ2.2, HLA-DQ2.5, and HLA-DQ8 is important in celiac disease (CD). The absence of these three genotypes has a strong negative predictive value. Methods: We designed multiplex ligation-dependent probe amplification (MLPA) for the combined detection of HLA-DQ2.2, HLA-DQ2.5, and HLA-DQ8. The MLPA probe mix was validated against a set of 59 samples characterized by conventional techniques. Results: The MLPA assay genotyped all 59 samples correctly when compared to the results obtained by PCR-SSCP/HD or PCR-SSO and PCR-SSP. Conclusion: The MLPA assay provides a reliable single-reaction analysis of the CD risk genotypes HLA-DQ2.2, HLA-DQ2.5, and HLA-DQ8 allowing for stratification or exclusion of disease risk.

Background: A flow cytometry score (FCS) based on four parameters has been proposed for analysis of myelodysplastic syndromes patients with

Extension of storage time of platelet (PLT) concentrates may result in an increased risk of bacteremia, directly via transfusion of contaminated products or indirectly via transfusion-related immunomodulation. We aimed to quantify the association of storage time of PLT concentrates and all-cause bacteremia in hematologic patients.We established a cohort of hematologic patients who received a PLT transfusion between 2005 and 2015. Cases were defined as patients with a bacteremia the day after transfusion and matched to as many controls as possible. A conditional logistic regression was performed, stratified by storage medium.Among 3514 patients receiving 36,032 PLT concentrates stored in plasma, 613 cases of bacteremia were found. The relative risk of all-cause bacteremia the day after transfusion was 0.80 (95% confidence interval [CI], 0.58-1.12) for PLT concentrates stored 3 to 4 days and 0.67 (95% CI, 0.49-0.92) for at least 5 days, compared to no more than 2 days. Among 1527 patients receiving 11,822 PLT concentrates stored in PLT additive solution, 182 cases of bacteremia were found. The relative risk of all-cause bacteremia was 1.14 (95% CI, 0.70-1.84) for PLT concentrates stored for 3 to 4 days and 1.19 (95% CI, 0.70-2.01) for at least 5 days, compared to not more than 2 days.Storage time of PLT concentrates was not associated with increased occurrence of all-cause bacteremia the day after transfusion. If anything, fewer cases of bacteremia occurred with increasing storage time of PLT concentrates in plasma. These bacteremias are not directly caused by transfusion of a contaminated product and the underlying mechanism warrants further research.

An increase in urine calcium compared to the consensus value was observed in some urine samples of the Dutch External Quality Assessment Scheme (EQAS). It appeared that the increase was due to the addition of oxalate by the EQAS organizers and preanalytical acidification of the samples by some of the participants. Because of this observation, the effect of urine acidification on urine calcium level in EQAS and patient samples with added oxalate was investigated.Twenty-four EQAS urine samples and 20 patient urine samples were subject to recovery measurements of urine calcium before and after addition of sodium oxalate and acidification.Differences in urine calcium between acidified and non-acidified samples up to 30.9% have been observed in EQAS samples with added oxalate. Patient samples show differences up to 80%. Differences between acidified and non-acidified samples are minimal for low calcium oxalate levels but increase with higher levels. Samples without added oxalate show equal urine calcium results between acidified and non-acidified samples.Urine calcium results are decreased in non-acidified samples with an excess of oxalate. In case of hyperoxaluria, acidification of patient urine collections and EQAS samples is recommended for correct urine calcium values.

Protein nuclear magnetic resonance (NMR) secondary chemical shifts are widely used to predict the secondary structure, and in solid-state NMR, they are often the only unambiguous structural parameters available. However, the employed prediction methods are empirical in nature, relying on the assumption that secondary shifts are only affected by shielding effects of neighboring atoms. We analyzed the secondary shifts of a photosynthetic membrane protein with a high density of chromophores and very tight packing, the light-harvesting 2 (LH2) complex of Rhodopseudomonas acidophila. A relation was found between secondary shift anomalies and protein-protein or pigment-protein tertiary and quaternary contacts. For several residues, including the bacteriochlorophyll-coordinating histidines (alphaH31 and betaH30) and the phenylalanine alphaF41 that has strongly twisted C(b)-C(a)-C and C(a)-C-N conformations in the LH2 crystal structure, the perturbing effects on the backbone chemical shifts were tested by density functional theory (DFT) calculations. We propose that higher-order interactions in the tightly packed complex can induce localized perturbations of the backbone conformation and electronic structure, related to functional pigment-protein or protein-protein interactions.

Magic-angle spinning (MAS) (13)C-(13)C correlation NMR spectroscopy was used to resolve the electronic ground state characteristics of the bacteriochlorophyll a (BChl a) cofactors in light-harvesting 1 (LH1) complexes of Rhodopseudomonas acidophila (strain 10050). The BChl a (13)C isotropic chemical shifts of the LH1 complexes are compared to the (13)C chemical shifts for BChl a dissolved in acetone-d(6) and to (13)C NMR data that has been obtained for the B800 and B850 BChl molecules in Rps. acidophila peripheral light-harvesting complexes (LH2). Since both complexes contain BChl a cofactors, we can address the chemical shift variability for specific carbon responses between the two types of antennae. The global shift pattern of the LH1 BChl's resembles the shift patterns of the LH2 alpha- and beta-B850 BChl's, while some carbon responses, in particular the C3 and C3(1), show significant deviations. A comparison with density functional theory (DFT) shift calculations provides insight into the BChl concomitant structural and electronic interactions in the ground state. The differences in the LH1 BChl observed chemical shifts relative to the (13)C responses of BChl a in solution cannot be explained by local side chain interactions, such as hydrogen bonding or nonplanarity of the C3 acetyl, but appear to be dominated by protein-induced macrocycle distortion. Such shaping of the macrocycle will contribute significantly to the red shift of the BChl Q(y) absorbance band in purple bacterial light-harvesting complexes.

Background Consolidation of analyzers is an emerging issue in clinical chemistry. We evaluated the analytical performance of the Cobas 6,000 analyzer (Roche Diagnostics), which is considered a candidate for replacement of current Hitachi 917 analyzers and for consolidation of chemistry and immunochemistry. Methods The precision, accuracy, linearity and correlation with current field methods were evaluated according to Clinical and Laboratory Standards Institute protocols EP5, EP9 and EP10. A total of 31 routine chemistry assays and 18 immunoassays were studied. Accuracy and linearity were verified for 24 chemistry parameters using value-assigned trueness controls from the Dutch External Quality Assessment Scheme organizers. In addition, traceability to methods endorsed by the Joint Committee of Traceability in Laboratory Medicine was examined. Results All analytes met allowable precision criteria, apart from the low level for sodium and folate. Total coefficients of variation ranged between 0.6% and 4.4% for routine chemistry and between 0.8% and 5.8% for immunochemistry, apart from folate (12% at the low end). The correlation coefficients for comparison to current field methods were >0.975, except for magnesium and for six out of 18 immunochemistries. Recovery experiments indicated high recovery for most of the 24 routine chemistry assays. Conclusions Considering the excellent precision data and the result equivalence for most assays, it can be concluded that Cobas 6,000 accommodates robust chemistry and immunochemistry, and has good potential for workstation consolidation in medium-sized laboratories.

Structure determination of membrane proteins with magic angle spinning NMR is rapidly developing. Probing secondary, tertiary, and quaternary structure along with protein−cofactor interactions thro...

The electronic ground states of the bacteriochlorophyll a type B800 and type B850 in the light-harvesting 2 complex of Rhodopseudomonas acidophila strain 10050 have been characterized by magic angle spinning (MAS) dipolar (13)C-(13)C correlation NMR spectroscopy. Uniformly [(13)C,(15)N] enriched light-harvesting 2 (LH2) complexes were prepared biosynthetically, while [(13)C,(15)N]-B800 LH2 complexes were obtained after reconstitution of apoprotein with uniformly [(13)C,(15)N]-enriched bacteriochlorophyll cofactors. Extensive sets of isotropic (13)C NMR chemical shifts were obtained for each bacteriochlorin ring species in the LH2 protein. (13)C isotropic shifts in the protein have been compared to the corresponding shifts of monomeric BChl a dissolved in acetone-d(6). Density functional theory calculations were performed to estimate ring current effects induced by adjacent cofactors. By correction for the ring current shifts, the (13)C shift effects due to the interactions with the protein matrix were resolved. The chemical shift changes provide a clear evidence for a global electronic effect on the B800 and B850 macrocycles, which is attributed to the dielectrics of the protein environment, in contrast with local effects due to interaction with specific amino acid residues. Considerable shifts of -6.2 < Deltasigma < +5.8 ppm are detected for (13)C nuclei in both the B800 and the B850 bacteriochlorin rings. Because the shift effects for the B800 and B850 are similar, the polarization of the electronic ground states induced by the protein environment is comparable for both cofactors and corresponds with a red shift of approximately 30 nm relative to the monomeric BChl dissolved in acetone-d(6). The electronic coupling between the B850 cofactors due to macrocycle overlap is the predominant mechanism behind the additional red shift in the B850.

Mg(II)-porphyrin-ligand and (bacterio)chlorophyl-ligand coordination interactions have been studied by solution and solid-state MAS NMR spectroscopy. (1)H, (13)C and (15)N coordination shifts due to ring currents, electronic perturbations and structural effects are resolved for imidazole (Im) and 1-methylimidazole (1-MeIm) coordinated axially to Mg(II)-OEP and (B)Chl a. As a consequence of a single axial coordination of Im or 1-MeIm to the Mg(II) ion, 0.9-5.2 ppm (1)H, 0.2-5.5 ppm (13)C and 2.1-27.2 ppm (15)N coordination shifts were measured for selectively labeled [1,3-(15)N]-Im, [1,3-(15)N,2-(13)C]-Im and [1,3-(15)N,1,2-(13)C]-1-MeIm. The coordination shifts depend on the distance of the nuclei to the porphyrin plane and the perturbation of the electronic structure. The signal intensities in the (1)H NMR spectrum reveal a five-coordinated complex, and the isotropic chemical shift analysis shows a close analogy with the electronic structure of the BChl a-histidine in natural light harvesting 2 complexes. The line broadening of the ligand responses support the complementary IR data and provide evidence for a dynamic coordination bond in the complex.

Multiple segmental and selective isotope labeling of RNA with three segments has been demonstrated by introducing an RNA segment, selectively labeled with (13)C(9)/(15)N(2)/(2)H((1', 3', 4', 5', 5''))-labeled uridine residues, into the central position of the 20 kDa epsilon-RNA of Duck Hepatitis B Virus. The RNA molecules were produced via two efficient protocols: a two-step protocol, which uses T4 DNA ligase and T4 RNA ligase 1, and a one-pot protocol, which uses T4 RNA ligase 1 alone. With T4 RNA ligase 1 all not-to-be-ligated termini are usually protected to prevent formation of side products. We show that such labor-intensive protection of termini is not required, provided segmentation sites can be chosen such that the segments fold into the target structure or target-like structures and thus are not trapped into stable alternate structures. These sites can be reliably predicted via DINAMelt. The simplified NMR spectrum provided evidence for the presence of a U28 H(3)-imino resonance, previously obscured in the fully labeled sample, and thus of the non-canonical base pair U28:C37. The demonstrated multiple segmental labeling protocols are generally applicable to large RNA molecules and can be extended to more than three segments.