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BACKGROUND: FMRI resting state networks (RSNs) are used to characterize brain disorders. They also show extensive heterogeneity across patients. Identifying systematic differences between RSNs in patients, i.e. discovering neurofunctional subtypes, may further increase our understanding of disease heterogeneity. Currently, no methodology is available to estimate neurofunctional subtypes and their associated RSNs simultaneously. NEW METHOD: We present an unsupervised learning method for fMRI data, called Clusterwise Independent Component Analysis (C-ICA). This enables the clustering of patients into neurofunctional subtypes based on differences in shared ICA-derived RSNs. The parameters are estimated simultaneously, which leads to an improved estimation of subtypes and their associated RSNs. RESULTS: In five simulation studies, the C-ICA model is successfully validated using both artificially and realistically simulated data (N = 30-40). The successful performance of the C-ICA model is also illustrated on an empirical data set consisting of Alzheimer's disease patients and elderly control subjects (N = 250). C-ICA is able to uncover a meaningful clustering that partially matches (balanced accuracy = .72) the diagnostic labels and identifies differences in RSNs between the Alzheimer and control cluster. COMPARISON WITH OTHER METHODS: Both in the simulation study and the empirical application, C-ICA yields better results compared to competing clustering methods (i.e., a two step clustering procedure based on single subject ICA's and a Group ICA plus dual regression variant thereof) that do not simultaneously estimate a clustering and associated RSNs. Indeed, the overall mean adjusted Rand Index, a measure for cluster recovery, equals 0.65 for C-ICA and ranges from 0.27 to 0.46 for competing methods. CONCLUSIONS: The successful performance of C-ICA indicates that it is a promising method to extract neurofunctional subtypes from multi-subject resting state-fMRI data. This method can be applied on fMRI scans of patient groups to study (neurofunctional) subtypes, which may eventually further increase understanding of disease heterogeneity. ispartof: JOURNAL OF NEUROSCIENCE METHODS vol:382 ispartof: location:Netherlands status: published

Radioactive iodine isotopes play a pivotal role in radiopharmaceuticals. Large-scale production of multi-patient dose of radioiodinated nuclear medicines requires high concentration of radioiodine. We demonstrate that tetrabutylammonium chloride and methyltrioctylamonium chloride are effective phase transfer reagents to concentrate iodide-124, iodide-125 and iodide-131 from the corresponding commercial water solutions. The resulting concentrated radioiodide, in the presence of either phase transfer reagent, does not hamper the chemical reactivity of aqueous radioiodide in the copper (II)-mediated one-pot three-component click chemistry to produce radioiodinated iodotriazoles.

Physarum polycephalum is a species of slime mold that spends most of its life cycle as a plasmodium, a unicellular multinucleated amoeboid. This species of slime mold is well known for its spatial memory. Oats, quinoa, and barley have a lot of protein and nutrients; therefore, they were used to feed the slime mold. Other studies tested the memory or growth of slime mold. This experiment compared both slime mold growth and memory using oats, quinoa, and barley. It was hypothesized that barley would make the slime mold grow the quickest and largest due to its high protein concentration. Into 3 Petri dishes a drop of water, a culture of slime mold, and each food source was placed. The slime mold was then placed in a shoebox, with graph paper taped to the bottom, to make sure there was minimal light on it. After sections were cut out and placed into the remaining petri dishes with the same food sources it grew in and then placed into a Legomaze with the food sources to track the time of its memory. While barley and oats tied for overall growth after 48-hours, barley-fed plasmodium grew much faster than oats-fed. For the maze and memory part of the experiment, due to timing, that part could not yet be done. Future work includes testing the slime mold's growth in a maze to discover how long it takes for the slime mold to find its food, depending on the food source.

Efficient transcriptional terminators are essential for the performance of genetic circuitry in microbial SynBio hosts. In recent years, several libraries of characterized strong terminators have become available for model organisms such as Escherichia coli. Conversely, terminator libraries for nonmodel species remain scarce, and individual terminators are often ported over from model systems, leading to unpredictable performance in their new hosts. In this work, we mined the genomes of Pseudomonas infecting phages LUZ7 and LUZ100 for transcriptional terminators utilizing the full-length RNA sequencing technique "ONT-cappable-seq" and validated these terminators in three Gram-negative hosts using a terminator trap assay. Based on these results, we present nine terminators for E. coli, Pseudomonas putida, and Pseudomonas aeruginosa, which outperform current reference terminators. Among these, terminator LUZ7 T50 displays potent bidirectional activity. These data further support that bacteriophages, as evolutionary-adapted natural predators of the targeted bacteria, provide a valuable source of microbial SynBio parts. ispartof: ACS SYNTHETIC BIOLOGY vol:12 issue:5 pages:1415-1423 ispartof: location:United States status: published

Summary 1H nuclear magnetic resonance (NMR) spectroscopy is an established bioanalytical technology for metabolic profiling of biofluids in both clinical and large-scale population screening applications. Recently, urinary protein quantification has been demonstrated using the same 1D 1H NMR experimental data captured for metabolic profiling. Here, we introduce NMRpQuant, a freely available platform that builds on these findings with both novel and further optimized computational NMR approaches for rigorous, automated protein urine quantification. The results are validated by interlaboratory comparisons, demonstrating agreement with clinical/biochemical methodologies, pointing at a ready-to-use tool for routine protein urinalyses. Availability and implementation NMRpQuant was developed on MATLAB programming environment. Source code and Windows/macOS compiled applications are available at https://github.com/pantakis/NMRpQuant, and working examples are available at https://doi.org/10.6084/m9.figshare.18737189.v1. Supplementary information Supplementary data are available at Bioinformatics online.

COVID-19 symptoms and mortality are largely due to its devastating effects in the lungs. The disease is caused by the SARS (Severe Acute Respiratory Syndrome)-CoV-2 coronavirus, which requires host cell proteins such as ACE2 (angiotensin-converting enzyme 2) and TMPRSS2 (transmembrane serine protease 2) for infection of lung epithelia. The expression and function of the steroid hormone receptor family is important in many aspects that impact on COVID-19 effects in the lung – notably lung development and function, the immune system, and expression of TMPRSS2 and ACE2. This review provides a brief summary of current knowledge on the roles of the steroid hormone receptors [androgen receptor (AR), glucocorticoid receptor (GR), progesterone receptor (PR), mineralocorticoid receptor (MR) and oestrogen receptor (ER)] in the lung, their effects on host cell proteins that facilitate SARS-CoV-2 uptake, and provides a snapshot of current clinical trials investigating the use of steroid receptor (SR) ligands to treat COVID-19.

Motivation Genome-wide association studies (GWAS) summary statistics have popularized and accelerated genetic research. However, a lack of standardization of the file formats used has proven problematic when running secondary analysis tools or performing meta-analysis studies. Results To address this issue, we have developed MungeSumstats, a Bioconductor R package for the standardization and quality control of GWAS summary statistics. MungeSumstats can handle the most common summary statistic formats, including variant call format (VCF) producing a reformatted, standardized, tabular summary statistic file, VCF or R native data object. Availability and implementation MungeSumstats is available on Bioconductor (v 3.13) and can also be found on Github at: https://neurogenomics.github.io/MungeSumstats. Supplementary information Supplementary data are available at Bioinformatics online.

We aimed to evaluate how different types of toothpaste (TP) for children affected molecular mechanisms of odontogenesis in zebrafish embryos. Commercially available TPs were selected according to their detergent contents as the cocamidopropyl betaine (CAPB) containing TP (TP1) and sodium lauryl sulfate (SLS) containing TP (TP2). TP3 contained no detergent. Effects of SLS, and CAPB alone were also examined. TP and detergent concentrations affecting development were determined as 750 mg/L and 4 mg/L, respectively. Embryos were exposed to TP1, TP2, TP3, SLS, CAPB, and embryo medium (control) for 72 h post fertilization. Acetylcholinesterase (AChE) activity and oxidant–antioxidant parameters were analyzed spectrophotometrically. Expressions of tooth development genes were evaluated by reverse transcription PCR (RT-PCR). Intraocular distance, lower jaw, and ceratohyal cartilage length were displayed using Alcian Blue staining.axin2andwnt10aexpressions increased in SLS and TP2 groups.igf2aandeve1expressions decreased in all groups except TP3.nrOb1expression decreased in TP1, SLS, and CAPB groups. Oxidant–antioxidant balance was disturbed in all groups except TP3, evidenced by increased lipid peroxidation, nitric oxide. SLS, and CAPB groups were more affected in terms of AChE, glutathione-S-transferase, and superoxide dismutase; perturbations were observed in cartilage structures. Altered expression of tooth development geneaxin2correlated withwnt10a, and with changes in cartilage structures in SLS and TP2 groups. TP3 group presented no disruptions in oxidant–antioxidant balance. Our study shows the availability of externally developing zebrafish embryos in examining the effects of TP’ contents on embryogenesis.

RATIONALE: Cassava production faces challenges in a changing climate. Pulse labelling cassava with 13 C-CO2 has the potential to elucidate carbon allocation mechanisms of cassava under drought stress and with potassium application. Understanding these mechanisms could guide efforts to mitigate effects of drought in cassava cropping systems. METHODS: Forty-eight cassava plants received a nutrient solution high or low in potassium. Water deficit was imposed on half of the plants at bulk root initiation stage, after which they were labelled for 8 h with 13 C-CO2 in a 15 m3 growth chamber. Plants were harvested 8 h, 9 days and 24 days after labelling, and separated into leaves, stems and roots. δ13 C values of the different parts were measured using an isotope ratio mass spectrometer, from which 13 C excess was calculated. RESULTS: Water deficit decreased transpiration (P

Amyloid-like aggregation of proteins is induced by short amyloidogenic sequence segments within a specific protein sequence resulting in self-assembly into β-sheets. We recently validated a technology platform in which synthetic amyloid peptides ("Pept-ins") containing a specific aggregation-prone region (APR) are used to induce specific functional knockdown of the target protein from which the APR was derived, including bacterial, viral, and mammalian cell proteins. In this work, we investigated if Pept-ins can be used as vector probes for in vivo Positron Emission Tomography (PET) imaging of intracellular targets. The radiolabeled Pept-ins [68Ga]Ga-NODAGA-PEG4-vascin (targeting VEGFR2) and [68Ga]Ga-NODAGA-PEG2-P2 (targeting E. coli) were evaluated as PET probes. The Pept-in based radiotracers were cross-validated in a murine tumor and muscle infection model, respectively, and were found to combine target specificity with favorable in vivo pharmacokinetics. When the amyloidogenicity of the interacting region of the peptide is suppressed by mutation, cellular uptake and in vivo accumulation are abolished, highlighting the importance of the specific design of synthetic Pept-ins. The ubiquity of target-specific amyloidogenic sequence segments in natural proteins, the straightforward sequence-based design of the Pept-in probes, and their spontaneous internalization by cells suggest that Pept-ins may constitute a generic platform for in vivo PET imaging of intracellular targets. ispartof: BIOCONJUGATE CHEMISTRY vol:32 issue:9 pages:2052-2064 ispartof: location:United States status: published

For yeast cells, tolerance to high levels of ethanol is vital both in their natural environment and in industrially relevant conditions. We recently genotyped experimentally evolved yeast strains adapted to high levels of ethanol and identified mutations linked to ethanol tolerance. In this study, by integrating genomic sequencing data with quantitative proteomics profiles from six evolved strains (data set identifier PXD006631) and construction of protein interaction networks, we elucidate exactly how the genotype and phenotype are related at the molecular level. Our multi-omics approach points to the rewiring of numerous metabolic pathways affected by genomic and proteomic level changes, from energy-producing and lipid pathways to differential regulation of transposons and proteins involved in cell cycle progression. One of the key differences is found in the energy-producing metabolism, where the ancestral yeast strain responds to ethanol by switching to respiration and employing the mitochondrial electron transport chain. In contrast, the ethanol-adapted strains appear to have returned back to energy production mainly via glycolysis and ethanol fermentation, as supported by genomic and proteomic level changes. This work is relevant for synthetic biology where systems need to function under stressful conditions, as well as for industry and in cancer biology, where it is important to understand how the genotype relates to the phenotype. ispartof: JOURNAL OF PROTEOME RESEARCH vol:20 issue:8 pages:3840-3852 ispartof: location:United States status: published

Terahertz imaging is becoming a biological imaging modality in its own right, alongside the more mature infrared and X-ray techniques. Nevertheless, extraction of hyperspectral, biometric information of samples is limited by experimental challenges. Terahertz time domain spectroscopy reflection measurements demand highly precise alignment and suffer from limitations of the sample thickness. In this work, a novel hybrid Kramers-Kronig and Fabry-Pérot based algorithm has been developed to overcome these challenges. While its application is demonstrated through dielectric retrieval of glass-backed human bone slices for prospective characterisation of metastatic defects or osteoporosis, the generality of the algorithm offers itself to wider application towards biological materials.

Motivation Single-cell/nuclei RNA-sequencing (scRNA-seq) technologies can simultaneously quantify gene expression in thousands of cells across the genome. However, the majority of the noncoding RNAs, such as microRNAs (miRNAs), cannot currently be profiled at the same scale. MiRNAs are a class of small noncoding RNAs and play an important role in gene regulation. MiRNAs originate from the processing of primary transcripts, known as primary-microRNAs (pri-miRNAs). The pri-miRNA transcripts, independent of their cognate miRNAs, can also function as long noncoding RNAs, code for micropeptides or even interact with DNA, acting like enhancers. Therefore, it is apparent that the significance of scRNA-seq pri-miRNA profiling expands beyond using pri-miRNA as proxies of mature miRNAs. However, there are no computational methods that allow profiling and quantification of pri-miRNAs at the single-cell-type resolution. Results We have developed a simple yet effective computational framework to profile pri-MiRNAs from single-cell RNA-sequencing datasets (PPMS). Based on user input, PPMS can profile pri-miRNAs at cell-type resolution. PPMS can be applied to both newly produced and publicly available datasets obtained via single cell or single-nuclei RNA-seq. It allows users to (i) investigate the distribution of pri-miRNAs across cell types and cell states and (ii) establish a relationship between the number of cells/reads sequenced and the detection of pri-miRNAs. Here, to demonstrate its efficacy, we have applied PPMS to publicly available scRNA-seq data generated from (i) individual chambers (ventricles and atria) of the human heart, (ii) human pluripotent stem cells during their differentiation into cardiomyocytes (the heart beating cells) and (iii) hiPSCs-derived cardiomyocytes infected with severe acute respiratory syndrome coronavirus 2.

Objective: It is known that exercise has positive effects on inflammatory biomarkers. However, the results on the effect of specific exercises such as core exercises on inflammatory markers are limited. Therefore, the aim of this study is to examine the acute effects of core exercise on inflammatory biomarkers interleukin 6 (IL-6), C-reactive protein (CRP) and albumin.Materials and Methods: In this study, the experimental method, one of the quantitative data collection methods, was used. The research sample consists of 11 elite amputee football players aged between 19-36. Participants were randomly divided into two groups as core exercise group (EG) and control group (KG). At week 0 of the study, blood samples of the participants were taken before and after the aerobic exercise (AY). The same procedure was repeated after an 8-week (3 days a week) exercise program. Within the scope of blood measurements, IL-6, CRP and albumin values were checked. SPSS package program 25 was used for the statistical processes of the research. As a result of the normality analysis of the data, it was determined that the data were not normally distributed and the Wilcoxon Test, one of the non-parametric tests, was applied. The level of significance in the study was determined as p=0.05.Results: According to the results of the study, a significant difference was found between the levels of p=0.043 and p=0.028 between acute IL-6 levels before and after the 0th and 8th weeks of EG, respectively. A significant difference was found between the levels of acute albumin before and after the 0th and 8th weeks of AR at the level of p=0.041 before the AR. Acute CRP levels did not change before and after 0th and 8th weeks (p>0.05). A significant difference was found between the levels of p=0.043 and p=0.043 between acute IL-6 levels before and after the 0th and 8th weeks of CG, respectively. No statistically significant difference was found between the albumin and CRP levels of KG.Conclusion: Core exercise had a positive effect on IL-6 and albumin levels in amputee football players. For this reason, it is recommended to include core exercises in the routine football training program of amputee football players., Amaç: Egzersizin inflamatuar biyo-belirteçler üzerine olumlu etkileri olduğu bilinmektedir. Fakat core egzersiz gibi spesifik egzersizlerin inflamatuar belirteçler üzerindeki etkisine yönelik sonuçlar sınırlıdır. Bu nedenle bu çalışmanın amacı, core egzersizin inflamatuar biyo-belirteçler olan interlökin 6 (IL-6), C-reaktif protein (CRP) ve albümine akut etkisinin incelenmesidir. Materyal ve Metot: Bu çalışmada nicel veri toplama metotlarından deneysel yöntem kullanılmıştır. Araştırma örneklemini, yaşları 19-36 arasında değişen 11 elit ampute futbolcu oluşturmaktadır. Katılımcılar core egzersiz grubu (EG) ve kontrol grubu (KG) olarak iki gruba rastgele yöntemle ayrıldı. Araştırmanın 0.haftasında, katılımcıların kan örnekleri aerobik yüklenme (AY) öncesinde ve sonrasında alındı. 8 haftalık (haftada 3 gün) egzersiz programı sonrasında aynı işlem tekrarlandı. Kan ölçümleri kapsamında IL-6, CRP ve albümin değerlerine bakılmıştır. Araştırmanın istatistiksel işlemleri için SPSS paket program 25 kullanılmıştır. Verilerin normallik analizi sonucunda verilerin normal dağılmadı tespit edilmiş ve non-parametrik testlerden Wilcoxon Testi uygulanmıştır. Araştırmada anlamlılık düzeyi p=0,05 olarak belirlenmiştir. Bulgular: Araştırma sonuçlarına göre EG’nun 0. ve 8. hafta AY öncesi ve sonrası akut IL-6 seviyeleri arasında sırasıyla p=0.043 ve p=0.028 düzeyinde anlamlı fark tespit edilmiştir. 0. ve 8. hafta AY öncesi ve sonrası akut albümin seviyeleri arasında AY öncesi p=0.041 düzeyinde anlamlı fark tespit edilmiştir. 0. ve 8. hafta AY öncesi ve sonrası akut CRP seviyeleri değişmemiştir (p>0.05). KG’nun 0. ve 8. hafta AY öncesi ve sonrası akut IL-6 seviyeleri arasında sırasıyla p=0.043 ve p=0.043 düzeyinde anlamlı fark tespit edilmiştir. KG’nun albümin ve CRP seviyeleri arasında istatistiksel olarak anlamlı fark tespit edilmemiştir. Sonuçlar: Core egzersiz ampute futbolcularda IL-6 ve albumin değerlerine olumlu etki etmiştir. Bu nedenle core egzersizlerin, ampute futbolcuların rütin futbol antrenman programına dahil edilmesi önerilmektedir.

Demand for accurate SARS-CoV-2 diagnostics is high. Most samples in the UK are collected in the community and rely on the postal service for delivery to the laboratories. The current recommendation remains that swabs should be collected in Viral Transport Media (VTM) and transported with a cold chain to the laboratory for RNA extraction and RT-qPCR. This is not always possible. We aimed to test the stability of SARS-CoV-2 RNA subjected to different pre-analytical conditions. Swabs were dipped into PBS containing cultured SARS-CoV-2 and placed in either a dry tube or a tube containing either normal saline or VTM. The tubes were then stored at different temperatures (20-50 °C) for variable periods (8 h to 5 days). Samples were tested by RT-qPCR targeting SARS-CoV-2 E gene. VTM outperformed swabs in saline and dry swabs in all conditions. Samples in VTM were stable, independent of a cold chain, for 5 days, with a maximum increase in cycle threshold (Ct) of 1.34 when held at 40 °C. Using normal saline as the transport media resulted in a loss of sensitivity (increased Ct) over time and with increasing temperature (up to 7.8 cycles compared to VTM). SARS-CoV-2 was not detected in 3/9 samples in normal saline when tested after 120 h incubation. Transportation of samples in VTM provides a high level of confidence in the results despite the potential for considerable, uncontrolled variation in temperature and longer transportation periods. False negative results may be seen after 96 h in saline and viral loads will appear lower.

Photoacoustic (PA) endoscopy has shown significant potential for clinical diagnosis and surgical guidance. Multimode fibres (MMFs) are becoming increasingly attractive for the development of miniature endoscopy probes owing to their ultrathin size, low cost and diffraction-limited spatial resolution enabled by wavefront shaping. However, current MMF-based PA endomicroscopy probes are either limited by a bulky ultrasound detector or a low imaging speed that hindered their usability. In this work, we report the development of a highly miniaturised and high-speed PA endomicroscopy probe that is integrated within the cannula of a 20 gauge medical needle. This probe comprises a MMF for delivering the PA excitation light and a single-mode optical fibre with a plano-concave microresonator for ultrasound detection. Wavefront shaping with a digital micromirror device enabled rapid raster-scanning of a focused light spot at the distal end of the MMF for tissue interrogation. High-resolution PA imaging of mouse red blood cells covering an area 100 µm in diameter was achieved with the needle probe at ∼3 frames per second. Mosaicing imaging was performed after fibre characterisation by translating the needle probe to enlarge the field-of-view in real-time. The developed ultrathin PA endomicroscopy probe is promising for guiding minimally invasive surgery by providing functional, molecular and microstructural information of tissue in real-time. ispartof: BIOMEDICAL OPTICS EXPRESS vol:13 issue:8 pages:4414-4428 ispartof: location:United States status: published

A major challenge in the field of microfluidics is to predict and control drop interactions. This work develops an image-based data-driven model to forecast drop dynamics based on experiments performed on a microfluidics device. Reduced-order modelling techniques are applied to compress the recorded images into low-dimensional spaces and alleviate the computational cost. Recurrent neural networks are then employed to build a surrogate model of drop interactions by learning the dynamics of compressed variables in the reduced-order space. The surrogate model is integrated with real-time observations using data assimilation. In this paper we developed an ensemble-based latent assimilation algorithm scheme which shows an improvement in terms of accuracy with respect to the previous approaches. This work demonstrates the possibility to create a reliable data-driven model enabling a high fidelity prediction of drop interactions in microfluidics device. The performance of the developed system is evaluated against experimental data (i.e., recorded videos), which are excluded from the training of the surrogate model. The developed scheme is general and can be applied to other dynamical systems.

Sodyum Dodesil sülfat poliakrilamid jel elektroforezi (SDS-PAGE), bir protein karışımının bileşenleri ayrı ayrı çözmek için en yaygın kullanılan analitik yöntemdir. Ayrıca bir proteinin saflığını elektroforetik bir yöntemle değerlendirmek neredeyse zorunlu hale gelmiştir. SDS-PAGE, proteinlerin moleküler boyuttaki farklılıkları ile jel matrisi boyunca %1' den daha az farklılık gösteren elektroforetik hareketliliklerini aynı anda kullanarak proteinleri birbirinden ayırır. Teknik aynı zamanda proteinlerin moleküler ağırlıklarını tahmin etme de güçlü bir araçtır.Protein analizinde vazgeçilmez bir araç olarak SDS-PAGE'in başarısı, elektroforetik hareketliliğin bir proteinin moleküler kütlesi ile korelasyonuna izin vermektedir. Ve günümüzde başarılı bir SDS-PAGE analizi sadece ve sadece dikkatli numune hazırlama ve yüklemeden önce işlemlere bağlıdır.Bu makalede en basit SDS-PAGE analizinin farklı et ve sakatat örneklerinin ayrımında kullanılabileceği anlatılmaktadır.

We present a multivariate metabotyping approach to assess the functional recovery of nonhospitalized COVID-19 patients and the possible biochemical sequelae of "Post-Acute COVID-19 Syndrome", colloquially known as long-COVID. Blood samples were taken from patients ca. 3 months after acute COVID-19 infection with further assessment of symptoms at 6 months. Some 57% of the patients had one or more persistent symptoms including respiratory-related symptoms like cough, dyspnea, and rhinorrhea or other nonrespiratory symptoms including chronic fatigue, anosmia, myalgia, or joint pain. Plasma samples were quantitatively analyzed for lipoproteins, glycoproteins, amino acids, biogenic amines, and tryptophan pathway intermediates using Nuclear Magnetic Resonance (NMR) spectroscopy and mass spectrometry. Metabolic data for the follow-up patients (n = 27) were compared with controls (n = 41) and hospitalized severe acute respiratory syndrome SARS-CoV-2 positive patients (n = 18, with multiple time-points). Univariate and multivariate statistics revealed variable patterns of functional recovery with many patients exhibiting residual COVID-19 biomarker signatures. Several parameters were persistently perturbed, e.g., elevated taurine (p = 3.6 × 10-3 versus controls) and reduced glutamine/glutamate ratio (p = 6.95 × 10-8 versus controls), indicative of possible liver and muscle damage and a high energy demand linked to more generalized tissue repair or immune function. Some parameters showed near-complete normalization, e.g., the plasma apolipoprotein B100/A1 ratio was similar to that of healthy controls but significantly lower (p = 4.2 × 10-3) than post-acute COVID-19 patients, reflecting partial reversion of the metabolic phenotype (phenoreversion) toward the healthy metabolic state. Plasma neopterin was normalized in all follow-up patients, indicative of a reduction in the adaptive immune activity that has been previously detected in active SARS-CoV-2 infection. Other systemic inflammatory biomarkers such as GlycA and the kynurenine/tryptophan ratio remained elevated in some, but not all, patients. Correlation analysis, principal component analysis (PCA), and orthogonal-partial least-squares discriminant analysis (O-PLS-DA) showed that the follow-up patients were, as a group, metabolically distinct from controls and partially comapped with the acute-phase patients. Significant systematic metabolic differences between asymptomatic and symptomatic follow-up patients were also observed for multiple metabolites. The overall metabolic variance of the symptomatic patients was significantly greater than that of nonsymptomatic patients for multiple parameters (χ2 p = 0.014). Thus, asymptomatic follow-up patients including those with post-acute COVID-19 Syndrome displayed a spectrum of multiple persistent biochemical pathophysiology, suggesting that the metabolic phenotyping approach may be deployed for multisystem functional assessment of individual post-acute COVID-19 patients.

The generation of tissue and organs requires close interaction with vasculature from the earliest moments of embryonic development. Tissue-specific organoids derived from pluripotent stem cells allow for the in vitro recapitulation of elements of embryonic development. However, they are not intrinsically vascularized, which poses a major challenge for their sustained growth, and for understanding the role of vasculature in fate specification and morphogenesis. Current organoid vascularization strategies do not recapitulate the temporal synchronization and spatial orientation needed to ensure in vivo-like early co-development. Here, we developed a human pluripotent stem cell (hPSC)-based approach to generate organoids which interact with vascular cells in a spatially determined manner. The spatial interaction between organoid and vasculature is enabled by the use of a custom designed 3D printed microfluidic chip which allows for a sequential and developmentally matched co-culture system. We show that on-chip hPSC-derived pericytes and endothelial cells sprout and self-assemble into organized vascular networks, and use cerebral organoids as a model system to explore interactions with this de novo generated vasculature. Upon co-development, vascular cells physically interact with the cerebral organoid and form an integrated neurovascular organoid on chip. This 3D printing-based platform is designed to be compatible with any organoid system and is an easy and highly cost-effective way to vascularize organoids. The use of this platform, readily performed in any lab, could open new avenues for understanding and manipulating the co-development of tissue-specific organoids with vasculature. ispartof: LAB ON A CHIP vol:22 issue:8 pages:1615-1629 ispartof: location:England status: published

Confocal laser endomicroscopy (CLE) offers imaging of tissue microarchitecture and has emerged as a promising tool for in vivo clinical diagnosis of cancer across many organs. CLE, however, can show high inter-observer dependency and does not provide information about tissue molecular composition. In contrast, Raman spectroscopy is a label-free optical technique that provides detailed biomolecular compositional information but offers limited or no morphological information. Here we present a novel hybrid fiber-optic confocal Raman endomicroscopy system for morpho-chemical tissue imaging and analysis. The developed confocal endomicroscopy system is based on a novel detection scheme for rejecting Raman silica fiber interference permitting simultaneous CLE imaging and Raman spectral acquisition of tissues through a coherent fiber bundle. We show that this technique enables real-time microscopic visualization of tissue architecture as well as simultaneous pointwise label-free biomolecular characterization and fingerprinting of tissue paving the way for multimodal diagnostics at endoscopy. ispartof: BIOMEDICAL OPTICS EXPRESS vol:13 issue:4 pages:2278-2285 ispartof: location:United States status: published

Background: Antibody validation for tissue staining is required for reproducibility; criteria to ensure validity have been published recently. The majority of these recommendations imply the use of routinely processed (formalin-fixed, paraffin-embedded) tissue. Materials & methods: We applied to lightly fixed frozen sections a panel of 126 antibodies validated for formalin-fixed, paraffin-embedded tissue with extended criteria. Results: Less than 30% of the antibodies performed as expected with all fixations. 35% preferred one fixation over another, 13% gave nonspecific staining and 23% did not stain at all. Conclusion: Individual antibody variability of the paratope's fitness for the fixed antigen may be the cause. Revalidation of established antibody panels is required when they are applied to sections whose fixation and processing are different from the tissue where they were initially validated. ispartof: BIOTECHNIQUES vol:70 issue:3 pages:137-148 ispartof: location:England status: published

Antibodies (Abs) are among the most important class of biologicals, showcasing a high therapeutic and diagnostic value. In the global therapeutic Ab market, fully-human monoclonal Abs (FH-mAbs) are flourishing thanks to their low immunogenicity and high specificity. The rapidly emerging field of single-cell technologies has paved the way to efficiently discover mAbs by facilitating a fast screening of the antigen (Ag)-specificity and functionality of Abs expressed by B cells. This review summarizes the principles and challenges of the four key concepts to discover mAbs using these technologies, being confinement of single cells using either droplet microfluidics or microstructure arrays, identification of the cells of interest, retrieval of those cells and single-cell sequence determination required for mAb production. This review reveals the enormous potential for mix-and-matching of the above-mentioned strategies, which is illustrated by the plethora of established, highly integrated devices. Lastly, an outlook is given on the many opportunities and challenges that still lie ahead to fully exploit miniaturized single-cell technologies for mAb discovery. ispartof: LAB ON A CHIP vol:21 issue:19 pages:3627-3654 ispartof: location:England status: published

The advent of high-dimensional single-cell data has necessitated the development of dimensionality-reduction tools. t-Distributed stochastic neighbor embedding (t-SNE) and uniform manifold approximation and projection (UMAP) are the two most frequently used approaches, allowing clear visualization of complex single-cell datasets. Despite the need for quantitative comparison, t-SNE and UMAP have largely remained visualization tools due to the lack of robust statistical approaches. Here, we have derived a statistical test for evaluating the difference between dimensionality-reduced datasets using the Kolmogorov-Smirnov test on the distributions of cross entropy of single cells within each dataset. As the approach uses the inter-relationship of single cells for comparison, the resulting statistic is robust and capable of identifying true biological variation. Further, the test provides a valid distance between single-cell datasets, allowing the organization of multiple samples into a dendrogram for quantitative comparison of complex datasets. These results demonstrate the largely untapped potential of dimensionality-reduction tools for biomedical data analysis beyond visualization. ispartof: CELL REPORTS METHODS vol:3 issue:1 ispartof: location:United States status: published

Ölçüm belirsizliği, bir sonucun kalitesinin kantitatif bir göstergesi olup, ölçüm sonuçlarının güvenilirlik düzeyinde gerçekleştirildiğini gösterir. Çalışmamızda laboratuvarımızda sık istenen testlerden olan total kolesterol (TK), HDL-kolesterol (HDL-K), trigliserid (Tg), hesaplanmış LDL-kolesterol (LDL-K) ve HDL dışı-kolesterol (HDL dışı-K) için ölçüm belirsizliğini hesaplamak ve bu değerleri CLIA 2019 toplam izin verilen hata (%TEa) değerleriyle karşılaştırmak amaçlandı. Çalışmamız Karacabey Devlet Hastanesi Merkez Laboratuvarı’nda gerçekleştirildi. Nordtest kılavuzunda tanımlanan ve 6 adımdan oluşan hesaplama modeli ile ölçüm belirsizliği belirlendi. Mart-Ağustos 2020 dönemine ait iç ve dış kalite kontrol verileri kullanıldı. Ölçüm belirsizliği, TK, HDL-K ve Tg için %7, LDL-K için %12, HDL dışı-K için %10 olarak hesaplandı. TK, HDL-K ve Tg testleri için hesaplanan ölçüm belirsizliği, hedef %TEa değerinin altındadır. Ölçüm belirsizliğinin belirlenmesi ve düzenli olarak izlenmesi, laboratuvar içinde doğru sonuçlar üretmeyi ve kullanıcılara sonuçları yorumlamak için objektif bir araç sağlamayı amaçlar., Measurement uncertainty is a quantitative indicator of the quality of a result, indicates that the measurement results are performed at the level of reliability. It was aimed to calculate the measurement uncertainty for total cholesterol, HDL-cholesterol, triglycerides, calculated LDL-cholesterol, and non-HDL-cholesterol, which are frequently ordered tests in our laboratory, and to compare these values with CLIA 2019 allowable total error (TEa%) values. Our study was performed in the Central Laboratory of Karacabey State Hospital. The measurement uncertainty was determined with the calculation model defined in the Nordtest guide consisting of 6 steps. Internal and external quality control data were recorded from March to August 2020. The measurement uncertainty was calculated as 7% for total cholesterol, HDL-cholesterol and triglycerides, 12% for LDL-cholesterol and 10% for non-HDL-cholesterol. Measurement uncertainty for total cholesterol, HDL-cholesterol and triglycerides was found below the targeted TEa%. Measurement uncertainty estimation and its periodical verification aim to produce accurate results within the laboratory and provide users with an objective tool to interpret the results.

Reversed-phase high performance thin-layer chromatography (RP-HPTLC) on C18 bonded silica gel was combined with desorption electrospray ionization (DESI) and high resolution time of flight mass spectrometry (HRToFMS) to detect, characterize and image (MSI) phytoecdysteroids (plant-derived insect moulting hormones) in ethanolic extracts of members of the Silene plant family. As seen previously for silica gel, DESI provided a simple and convenient method for recovering polar polyhydoxysteroids from RP-HPTLC plates for the purposes of both the MS and MSI of extracts obtained from three species of the Silene family (Silene otites, S. nutans and S. viridiflora). Using RP-HPTLC/DESI/MSI/HRToFMS a number of ecdysteroids, including 20-hydroxyecdysone, polypodine-B, 2-deoxy-20-hydroxyecdysone and 2-deoxyecdysone were identified in these extracts. Differences were noted in the mass spectra obtained depending upon both the stationary phase on which they were separated, and the temperatures used in the heated transfer line used for introduction into the ion source. Ecdysteroids detected after chromatography on C18 bonded silica showed increased fragmentation due to water loss compared to those imaged from silica. In addition, the benefits of the additional resolution provided by 2-dimensional TLC for increasing spectral quality compared to a 1-dimensional separation are demonstrated.

Brain networks store new memories using functional and structural synaptic plasticity. Memory formation is generally attributed to Hebbian plasticity, while homeostatic plasticity is thought to have an ancillary role in stabilizing network dynamics. Here we report that homeostatic plasticity alone can also lead to the formation of stable memories. We analyze this phenomenon using a new theory of network remodeling, combined with numerical simulations of recurrent spiking neural networks that exhibit structural plasticity based on firing rate homeostasis. These networks are able to store repeatedly presented patterns and recall them upon the presentation of incomplete cues. Storage is fast, governed by the homeostatic drift. In contrast, forgetting is slow, driven by a diffusion process. Joint stimulation of neurons induces the growth of associative connections between them, leading to the formation of memory engrams. These memories are stored in a distributed fashion throughout connectivity matrix, and individual synaptic connections have only a small influence. Although memory-specific connections are increased in number, the total number of inputs and outputs of neurons undergo only small changes during stimulation. We find that homeostatic structural plasticity induces a specific type of “silent memories”, different from conventional attractor states.

Objective: Cystatin C is considered an important marker for the detection of renal dysfunction. It was aimed to determine cystatin C levels, status of oxidant-antioxidant and inflammation in hemodialysis (HD) patients.Methods: The study groups consisted of 20 HD patients and 20 healthy controls. Blood samples were obtained from the control group and from the HD group before hemodialysis. Serum cystatin C, total antioxidant capacity (TAC), total oxidative state (TOS), tumor necrosis factor-alpha (TNF-α), interleukin 6 (IL-6) interleukin 18 (IL-18) levels were detected by Enzyme Linked Immunosorbent Assay (ELISA), C-reactive protein (CRP) and some biochemical parameters were analyzed by autoanalyser.Results: Cystatin C, TOS, TNF-α, IL-6, IL-18 and CRP levels of the HD group were significantly higher than the control group.Conclusion: As a result; oxidative stress and inflammation were increased in patients with chronic renal failure undergoing hemodialysis. New strategies and new studies are needed to reduce the increase in oxidative stress and inflammation in HD patients., Amaç: Sistatin C, böbrek fonksiyon bozukluğunun saptanması için önemli bir belirteç olarak kabul edilir. Hemodiyaliz (HD) hastalarında sistatin C düzeylerinin, oksidan-antioksidan ve inflamasyon durumunun belirlenmesi amaçlandı.Yöntem: Çalışma grupları 20 HD hastası ve 20 sağlıklı kontrolden oluşturuldu. Hemodiyaliz öncesi kontrol grubundan ve HD grubundan kan örnekleri alındı. Serum sistatin C, total antioksidan kapasite (TAC), total oksidatif durum (TOS), tümör nekroz faktör alfa (TNF-α), interlökin 6 (IL-6), interlökin 18 (IL-18) seviyeleri ELISA ile C- reaktif protein (CRP) ve bazı biyokimyasal parametreler ise otoanalizörde analiz edildi.Bulgular: HD grubunun sistatin C, TOS, TNF-α, IL-6, IL-18 ve CRP düzeyleri kontrol grubuna göre anlamlı derecede yüksekti.Sonuç: Sonuç olarak; hemodiyaliz uygulanan kronik böbrek yetmezliği olan hastalarda oksidatif stres ve inflamasyon artmıştır. Hemodiyaliz hastalarında oksidatif stres ve inflamasyonu azaltmak için yeni stratejilere ve yeni çalışmalara ihtiyaç vardır.

Traditional breeding techniques, applied incrementally over thousands of years, have yielded huge benefits in the characteristics of agricultural animals. This is a result of significant, measurable changes to the genomes of those animal species and breeds. Genome editing techniques may now be applied to achieve targeted DNA sequence alterations, with the potential to affect traits of interest to production of agricultural animals in just one generation. New opportunities arise to improve characteristics difficult to achieve or not amenable to traditional breeding, including disease resistance, and traits that can improve animal welfare, reduce environmental impact, or mitigate impacts of climate change. Countries and supranational institutions are in the process of defining regulatory approaches for genome edited animals and can benefit from sharing approaches and experiences to institute progressive policies in which regulatory oversight is scaled to the particular level of risk involved. To facilitate information sharing and discussion on animal biotechnology, an international community of researchers, developers, breeders, regulators, and communicators recently held a series of seven virtual workshop sessions on applications of biotechnology for animal agriculture, food and environmental safety assessment, regulatory approaches, and market and consumer acceptance. In this report, we summarize the topics presented in the workshop sessions, as well as discussions coming out of the breakout sessions. This is framed within the context of past and recent scientific and regulatory developments. This is a pivotal moment for determination of regulatory approaches and establishment of trust across the innovation through-chain, from researchers, developers, regulators, breeders, farmers through to consumers. Published version

Standardized DNA assembly methods utilizing modular components provide a powerful framework to explore design spaces and iterate through Design-Build-Test-Learn cycles. Biopart Assembly Standard for Idempotent Cloning (BASIC) DNA assembly uses modular parts and linkers, is highly accurate, easy to automate, free for academic and commercial use, while enabling simple hierarchical assemblies through an idempotent format. These features facilitate various applications including pathway engineering, ribosome binding site tuning, fusion protein engineering and multiplexed gRNA expression. In this work we present basicsynbio, an open-source software encompassing a Web App (https://basicsynbio.web.app/) and Python Package (https://github.com/LondonBiofoundry/basicsynbio). With basicsynbio, users can access commonly used BASIC parts and linkers while robustly designing new parts and assemblies with exception handling for common design errors. Users can export sequence data and create build instructions for manual or acoustic liquid-handling platforms. The generation of build instructions relies on the BasicBuild Open Standard which is easily parsed for bespoke workflows and is serializable in Java Script Object Notation for transfer and storage. We demonstrate basicsynbio by assembling a collection of 30 vectors using various sequences including modules from the Standard European Vector Architecture (SEVA). The BASIC SEVA collection is compatible with BASIC and Golden Gate using BsaI. It encompasses vectors containing six antibiotic resistance markers and five origins of replication from different compatibility groups, including a temperature-sensitive variant. To make the collection accessible we deposited it on Addgene under an OpenMTA agreement. Furthermore, vector sequences are accessible from within the basicsynbio application programming interface along with other collections of parts and linkers, providing an ideal environment to design assemblies for bioengineering applications using BASIC.

Simple diffusion of molecular entities through a phospholipid bilayer, is a phenomenon of great importance to the pharmaceutical and agricultural industries. Current model lipid systems to probe this typically only employ fluorescence as a readout, thus limiting the range of assessable chemical matter that can be studied. We report a new technology platform, the UV-DIB, which facilitates label free measurement of small molecule translocation rates. This is based upon the coupling of droplet interface bilayer technology with implemented fiber optics to facilitate analysis via ultraviolet spectroscopy, in custom designed PMMA wells. To improve on current DIB technology, the platform was designed to be reusable, with a high sampling rate and a limit of UV detection in the low μM regime. We demonstrate the use of our system to quantify passive diffusion in a reproducible and rapid manner where the system was validated by investigating multiple permeants of varying physicochemical properties across a range of lipid interfaces, each demonstrating differing kinetics. Our system permits the interrogation of structural dependence on the permeation rate of a given compound. We present this ability from two structural perspectives, that of the membrane, and the permeant. We observed a reduction in permeability between pure DOPC and DPhPC interfaces, concurring with literature and demonstrating our ability to study the effects of lipid composition on permeability. In relation to the effects of permeant structure, our device facilitated the rank ordering of various compounds from the xanthine class of compounds, where the structure of each permeant differed by a single group alteration. We found that DIBs were stable up to 5% DMSO, a molecule often used to aid solubilisation of pharmaceutical and agrochemical compounds. The ability of our device to rank-order compounds with such minor structural differences provides a level of precision that is rarely seen in current, industrially applied technologies.

Typical protocols to differentiate induced pluripotent stem cells (iPSCs) from hepatocyte-like cells (HLCs) imply complex strategies that include transfection with key hepatic transcription factors and the addition to culture media of nutrients, growth factors, and cytokines. A main constraint to evaluate the hepatic phenotype achieved arises from the way the grade of differentiation is determined. Currently, it relies on the assessment of the expression of a limited number of hepatic gene transcripts, less frequently by assessing certain hepatic metabolic functions, and rarely by the global metabolic performance of differentiated cells. We envisaged a new strategy to assess the extent of differentiation achieved, based on the analysis of the cellular metabolome along the differentiation process and its quantitative comparison with that of primary human hepatocytes (PHHs). To validate our approach, we examined the changes in the metabolome of three iPSC progenies (transfected with/without key transcription factors), cultured in three differentiation media, and compared them to PHHs. Results revealed consistent metabolome changes along differentiation and evidenced the factors that more strongly promote changes in the metabolome. The integrated dissimilarities between the PHHs and HLCs retrieved metabolomes were used as a numerical reference for quantifying the degree of iPSCs differentiation. This newly developed metabolome-analysis approach evidenced its utility in assisting us to select a cell's source, culture conditions, and differentiation media, to achieve better-differentiated HLCs. ispartof: JOURNAL OF PROTEOME RESEARCH vol:21 issue:3 pages:702-712 ispartof: location:United States status: published

Motivation: dataset sizes in computational biology have been increased drastically with the help of improved data collection tools and increasing size of patient cohorts. Previous kernel-based machine learning algorithms proposed for increased interpretability started to fail with large sample sizes, owing to their lack of scalability. To overcome this problem, we proposed a fast and efficient multiple kernel learning (MKL) algorithm to be particularly used with large-scale data that integrates kernel approximation and group Lasso formulations into a conjoint model. Our method extracts significant and meaningful information from the genomic data while conjointly learning a model for out-of-sample prediction. It is scalable with increasing sample size by approximating instead of calculating distinct kernel matrices. Results: to test our computational framework, namely, Multiple Approximate Kernel Learning (MAKL), we demonstrated our experiments on three cancer datasets and showed that MAKL is capable to outperform the baseline algorithm while using only a small fraction of the input features. We also reported selection frequencies of approximated kernel matrices associated with feature subsets (i.e. gene sets/pathways), which helps to see their relevance for the given classification task. Our fast and interpretable MKL algorithm producing sparse solutions is promising for computational biology applications considering its scalability and highly correlated structure of genomic datasets, and it can be used to discover new biomarkers and new therapeutic guidelines., Scientific and Technological Research Council of Turkey (TÜBİTAK); Turkish Academy of Sciences (TÜBA) Young Outstanding Researcher Support Programme (GEBIP); Science Academy of Turkey (BAGEP The Young Scientist Award Program)

Control-Based Continuation (CBC) is a general and systematic method to carry out the bifurcation analysis of physical experiments. CBC does not rely on a mathematical model and thus overcomes the uncertainty introduced when identifying bifurcation curves indirectly through modelling and parameter estimation. We demonstrate, in silico, CBC applicability to biochemical processes by tracking the equilibrium curve of a toggle switch which includes additive process noise and exhibits bistability. We compare results obtained when CBC uses a model-free and model-based control strategy and show that both can track stable and unstable solutions, revealing bistability. We then demonstrate CBC in conditions more representative of a real experiment using an agent-based simulator describing cells growth and division, cell-to-cell variability, spatial distribution, and diffusion of chemicals. We further show how the identified curves can be used for parameter estimation and discuss how CBC can significantly accelerate the prototyping of synthetic gene regulatory networks.

Human health is at risk from environmental exposures to a wide range of chemical toxicants and endocrine-disrupting chemicals (EDCs). As part of understanding this risk, the U.S. Environmental Protection Agency (EPA) has been pursuing new high-throughput in vitro assays and computational models to characterize EDCs. EPA models have incorporated our high-content analysis-based green fluorescent protein estrogen receptor (GFP-ER): PRL-HeLa assay, which allows direct visualization of ER binding to DNA regulatory elements. Here, we characterize a modified functional assay based on the stable expression of a chimeric androgen receptor (ARER), wherein a region containing the native AR DNA-binding domain (DBD) was replaced with the ERα DBD (amino acids 183-254). We demonstrate that the AR agonist dihydrotestosterone induces GFP-ARER nuclear translocation, PRL promoter binding, and transcriptional activity at physiologically relevant concentrations (

Purpose: The purpose of this study is to investigate the preoperative hemogram and biochemistry values of patients who undergo oral and dental surgical operations under local anesthesia.Materials and Methods: The study included 1598 patients who visited the Faculty of Dentistry at Adıyaman University. The patients’ demographic information as age and sex and biochemistry values as blood glucose level (BGL), Aspartate Aminotransferase (AST), Alanine Aminotransferase (ALT), Gama-Glutamyl Transpeptidase (GGT), sodium (Na), potassium (K) and calcium (Ca) and hemogram values as white blood cell count (WBC), Hemoglobin (HGB), Hematocrit (HCT) and Platelet count (PLT) were recorded and statistically analyzed.Results: There were abnormal values outside the normal limits in all hemogram and biochemical values that were examined. Among these, high values of BGL, AST, ALT, GGT and WBC and low values of Na, Ca, HGB and HCT were more frequent. When the values measured outside the reference ranges were examined in terms of sex, it was seen that the GGT values were significantly higher in the men, while the HGB and PLT values were significantly higher in the women. The abnormal values were distributed significantly more among the age group of 21-40.Conclusion: In patients from whom detailed medical anamnesis is not collected, it is believed that taking hemogram and biochemical tests before oral surgical procedures is important in terms of elimination of negative issues that may arise., Amaç: Bu çalışmanın amacı lokal anestezi altında oral cerrahi işlem geçiren hastaların preoperatif hemogram ve biyokimya değerlerinin araştırılmasıdır.Gereç ve Yöntem: Çalışmaya Adıyaman Üniversitesi Diş Hekimliği Fakültesi’ne başvuran 1598 hasta dahil edildi. Hastalara ait yaş, cinsiyet gibi demografik bilgiler ile kan glukoz seviyesi (KGS), Aspartat Aminotransferaz (AST), Alanin Aminotransferaz (ALT), Gama-Glutamil Transpeptidaz (GGT), sodyum (Na), potasyum (K) ve kalsiyum (Ca) gibi biyokimya değerleri ve beyaz küre sayısı (WBC), Hemoglobin (HGB), Hemotaktit (HCT), Trombosit sayısı (PLT) gibi hemogram değerleri kaydedildi ve istatistiksel olarak analiz edildi.Bulgular: İncelenen tüm hemogram ve biyokimyasal değerlerin hepsinde normal sınırların dışında seyreden anormal değerler görüldü. Bunlardan KGS, AST, ALT, GGT, WBC değerlerinde yüksek değerler; Na, Ca, HGB, HCT değerlerinde ise düşük değerler sayıca daha fazla bulundu. Referans aralığının dışında ölçülen anormal değerler cinsiyet bakımından değerlendirildiğinde istatistiksel olarak GGT’nin anlamlı şekilde erkeklerde; HGB ve PLT’nin ise anlamlı şekilde kadınlarda daha fazla sayıda görüldüğü bulundu. Anormal değerlerin yaş grupları bakımından ise istatistiksel olarak anlamlı şeklide 21-40 yaş arasında dağılım gösterdiği görüldü. Sonuç: Detaylı tıbbi anamnez alınamayan hastalarda oral cerrahi işlemler öncesinde hemogram ve biyokimyasal testlerin alınmasının oluşabilecek olumsuz durumların eliminasyonu açısından önem arz ettiğini düşünmekteyiz.

A rapid reversed-phase gradient method employing a 50 mm × 1 mm i.d., C18 microbore column, combined with ion mobility and high-resolution mass spectrometry, was applied to the metabolic phenotyping of urine samples obtained from rats receiving different diets. This method was directly compared to a “conventional” method employing a 150 × 2.1 mm i.d. column packed with the same C18 bonded phase using the same samples. Multivariate statistical analysis of the resulting data showed similar class discrimination for both microbore and conventional methods, despite the detection of fewer mass/retention time features by the former. Multivariate statistical analysis highlighted a number of ions that represented diet-specific markers in the samples. Several of these were then identified using the combination of mass, ion-mobility-derived collision cross section and retention time including N-acetylglutamate, urocanic acid, and xanthurenic acid. Kynurenic acid was tentatively identified based on mass and ion mobility data.

Circular DNA is ubiquitous in nature in the form of plasmids, circular DNA viruses, and extrachromosomal circular DNA (eccDNA) in eukaryotes. Sequencing of such molecules is essential to profiling virus distributions, discovering new viruses and understanding the roles of eccDNAs in eukaryotic cells. Circular DNA enrichment sequencing (CIDER-Seq) is a technique to enrich and accurately sequence circular DNA without the need for polymerase chain reaction amplification, cloning, and computational sequence assembly. The approach is based on randomly primed circular DNA amplification, which is followed by several enzymatic DNA repair steps and then by long-read sequencing. CIDER-Seq includes a custom data analysis package (CIDER-Seq Data Analysis Software 2) that implements the DeConcat algorithm to deconcatenate the long sequencing products of random circular DNA amplification into the intact sequences of the input circular DNA. The CIDER-Seq data analysis package can generate full-length annotated virus genomes, as well as circular DNA sequences of novel viruses. Applications of CIDER-Seq also include profiling of eccDNA molecules such as transposable elements (TEs) from biological samples. The method takes ~2 weeks to complete, depending on the computational resources available. Owing to the present constraints of long-read single-molecule sequencing, the accuracy of circular virus and eccDNA sequences generated by the CIDER-Seq method scales with sequence length, and the greatest accuracy is obtained for molecules

Pain and emotional distress have a reciprocal relation. The amygdala has been implicated in emotional processing. The central nucleus of the amygdala (CeA) receives nociceptive information from the dorsal horn of spinal cord and is responsible for the central plasticity in chronic pain. Neuropathic pain is a type of severe chronic pain and can be strongly influenced by emotional components. Plastic changes in the CeA may play a key role in the development or maintenance or both of neuropathic pain. We studied the expression levels of proteins in the CeA of spinal nerve transection (SNT) model rats. Total tissue lysate proteins were separated by two-dimensional-gel electrophoresis (2D-PAGE). Gels from different time points were compared using Progenesis SameSpot software, and the spots with Fold Change greater than 2 were excised for protein identification by mass spectrometry. We identified more than 50 cytosolic proteins as significantly altered in their expression levels in the CeA of SNT rats, and most of these changes have been validated at mRNA levels by qRT-PCR. We also identified more than 40 membrane proteins as notably up- or down-regulated in the CeA of SNT model rats relative to a control using stable isotope dimethyl labeling nano-LC-MS/MS based proteomics and found that one such protein, doublecortin (DCX), a microtubule-associated protein expressed by neuronal precursor cells during development, is specifically localized in the membrane fraction without changes in total amount of the protein. Immunohistochemistry showed that doublecortin is expressed in processes in the CeA of rats 7 and 21 days after SNT surgery, suggesting that doublecortin is one of the proteins that may contribute to the plastic changes, namely, redevelopment or rewiring of neural networks, in the CeA in the neuropathic pain model. These dysregulated proteins may play roles in reciprocal relationships between pain and psychological distress in the amygdala and contribute to central sensitization. Data are available via ProteomeXchange with identifier PXD017473.

Thin layer chromatography–flame ionization detection (TLC–FID) is a versatile analytical technique that can be used for fast analysis of organic compounds. It has been implemented in past decades for the analysis of lipids and petrochemical products, but rarely in other fields. Despite the improvement in the latest Iatroscan model and the introduction of an automatic programmable sample spotter, this system is still struggling to gain acceptance in universities and major research laboratories. The reason behind this might be a lack of awareness on the potential application of this system to other fields of analytical chemistry. This review presents TLC–FID as a mature and reliable, state of the art technique that combines the separation power of TLC with FID as a universal detector, which can be applied to the analysis of a wide variety of organic compounds. Basic operational procedures and previous literature, including its potential for ultrafast analysis of commercial samples, are discussed in order to create awareness on the potentials of this piece of equipment to other fields.

ispartof: JOURNAL OF MASS SPECTROMETRY vol:54 issue:12 pages:1013-1018 ispartof: location:England status: published

To increase the scope of natural biosystem, nucleic acids have been intensively modified. One direction includes the development of a synthetic alternative to the native DNA and RNA, denoted Xenobiotic nucleic acids (XNAs) that are able to store and transfer genetic information either by base-modification or backbone-modification. Another line of research aims to develop alternative third base pair additional to natural A:T and G:C. These unnatural base pairs (UBPs) can store increased information content encoded in three base pairs. This review outlines the recent progress made towards XNA and UBP applications as new components of the genomic DNA as well as biostable aptamers. New achievements in the replacement of a bacterial genome by unnatural non-canonical nucleotides are also described. ispartof: Current Opinion In Biotechnology vol:60 pages:259-267 ispartof: location:England status: published

Reversed-phase UHPLC-MS is extensively employed for both the profiling of biological fluids and tissues to characterize lipid dysregulation in disease and toxicological studies. With conventional LC-MS systems the chromatographic performance and throughput are limited due to dispersion from the fluidic connections as well as radial and longitudinal thermal gradients in the LC column. In this study vacuum jacketed columns (VJC), positioned at the source of the mass spectrometer, were applied to the lipidomic analysis of plasma extracts. Compared to conventional UHPLC, the VJC-based methods offered greater resolution, faster analysis, and improved peak intensity. For a 5 min VJC analysis, the peak capacity increased by 66%, peak tailing reduced by up to 34%, and the number of lipids detected increased by 30% compared to conventional UHPLC. The narrower peaks, and thus increased resolution, compared to the conventional system resulted in a 2-fold increase in peak intensity as well a significant improvement in MS and MS/MS spectral quality resulting in a 22% increase in the number of lipids identified. When applied to mouse plasma samples, reproducibility of the lipid intensities in the pooled QC ranged from 1.8–12%, with no related drift in tR observed.

Neuro-oncology surgery would benefit from detailed intraoperative tissue characterization provided by noncontact, contrast-agent-free, noninvasive optical imaging methods. In-depth knowledge of target tissue optical properties across a wide-wavelength spectrum could inform the design of optical imaging and computational methods to enable robust tissue analysis during surgery. We adapted a dual-beam integrating sphere to analyse small tissue samples and investigated ex vivo optical properties of five types of human brain tumour (meningioma, pituitary adenoma, schwannoma, low- and high-grade glioma) and nine different types of healthy brain tissue across a wavelength spectrum of 400 to 1800 nm. Fresh and frozen tissue samples were analysed. All tissue types demonstrated similar absorption spectra, but the reduced scattering coefficients of tumours show visible differences in the obtained optical spectrum compared to those of surrounding normal tissue. These results underline the potential of optical imaging technologies for intraoperative tissue characterization. ispartof: JOURNAL OF BIOPHOTONICS vol:15 issue:4 ispartof: location:Germany status: published