4,501 results match your criteria biologically distinct

Measuring pathway database coverage of the phosphoproteome.

PeerJ 2021 25;9:e11298. Epub 2021 May 25.

Division of Bioinformatics, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.

Protein phosphorylation is one of the best known post-translational mechanisms playing a key role in the regulation of cellular processes. Over 100,000 distinct phosphorylation sites have been discovered through constant improvement of mass spectrometry based phosphoproteomics in the last decade. However, data saturation is occurring and the bottleneck of assigning biologically relevant functionality to phosphosites needs to be addressed. Read More

View Article and Full-Text PDF

Data assimilation of synthetic data as a novel strategy for predicting disease progression in alopecia areata.

Math Med Biol 2021 Jun 10. Epub 2021 Jun 10.

School of Mathematical and Natural Sciences, Arizona State University - West Campus, Glendale, AZ 85306, USA, and Department of Mathematics, North Carolina State University, Raleigh, NC 27695, USA.

The goal of patient-specific treatment of diseases requires a connection between clinical observations with models that are able to accurately predict the disease progression. Even when realistic models are available, it is very difficult to parameterize them and often parameter estimates that are made using early time course data prove to be highly inaccurate. Inaccuracies can cause different predictions, especially when the progression depends sensitively on the parameters. Read More

View Article and Full-Text PDF

Topographic numerosity maps cover subitizing and estimation ranges.

Nat Commun 2021 06 7;12(1):3374. Epub 2021 Jun 7.

Spinoza Centre for Neuroimaging, Amsterdam, Netherlands.

Numerosity, the set size of a group of items, helps guide behaviour and decisions. Non-symbolic numerosities are represented by the approximate number system. However, distinct behavioural performance suggests that small numerosities, i. Read More

View Article and Full-Text PDF

Identification of over 200-fold more hairpin ribozymes than previously known in diverse circular RNAs.

Nucleic Acids Res 2021 Jun 7. Epub 2021 Jun 7.

Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany.

Self-cleaving ribozymes are catalytic RNAs that cut themselves at a specific inter-nucleotide linkage. They serve as a model of RNA catalysis, and as an important tool in biotechnology. For most of the nine known structural classes of self-cleaving ribozymes, at least hundreds of examples are known, and some are present in multiple domains of life. Read More

View Article and Full-Text PDF

HPV-Negative Cervical Cancer: A Narrative Review.

Diagnostics (Basel) 2021 May 26;11(6). Epub 2021 May 26.

Obstetrics and Gynecology Unit, Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", Piazza Giulio Cesare 11, 70124 Bari, Italy.

Cervical cancer (CC) is the fourth most frequent cancer in women worldwide. HPV infection is associated with the majority of CC cases, but a small proportion of CCs actually test negative for HPV. The prevalence of HPV among CC histotypes is very different. Read More

View Article and Full-Text PDF

A new method to visualize CEP peptide-CEP receptor interactions in vascular tissue in vivo.

J Exp Bot 2021 May 31. Epub 2021 May 31.

Division of Plant Sciences, Research School of Biology, College of Medicine, Biology and the Environment, The Australian National University, Canberra, ACT, Australia.

C-TERMINALLY ENCODED PEPTIDEs (CEPs) control diverse responses in plants including root development, root system architecture, nitrogen demand signalling, and nutrient allocation influencing yield and there is evidence that different ligands impart different phenotypic responses. Thus, there is a need for a simple method that identifies bona fide CEP hormone-receptor pairings in vivo and examines if different CEP family peptides bind the same receptor. We used formaldehyde or photo-activation to cross-link fluorescently tagged group 1 or group 2 CEPs to receptors in semi-purified Medicago truncatula or Arabidopsis thaliana leaf vascular tissues to verify that COMPACT ROOT ARCHITECTURE 2 (CRA2) is the Medicago CEP receptor, and to investigate if sequence diversity within the CEP family influences receptor binding. Read More

View Article and Full-Text PDF

Bacterial Peptidoglycan Fragments Differentially Regulate Innate Immune Signaling.

ACS Cent Sci 2021 Apr 23;7(4):688-696. Epub 2021 Mar 23.

Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States.

The human innate immune system responds to both pathogen and commensal bacteria at the molecular level using bacterial peptidoglycan (PG) recognition elements. Traditionally, synthetic and commercially accessible PG monosaccharide units known as muramyl dipeptide (MDP) and -glycolyl MDP (ng-MDP) have been used to probe the mechanism of innate immune activation of pattern recognition receptors, such as NOD-like receptors. However, bacterial PG is a dynamic and complex structure, with various chemical modifications and trimming mechanisms that result in the production of disaccharide-containing elements. Read More

View Article and Full-Text PDF

A framework to decipher the genetic architecture of combinations of complex diseases: Applications in cardiovascular medicine.

Bioinformatics 2021 May 29. Epub 2021 May 29.

School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.

Motivation: Currently, most genome-wide association studies (GWAS) are studies of a single disease against controls. However, an individual is often affected by more than one condition. For example, coronary artery disease (CAD) is often comorbid with type 2 diabetes (T2DM). Read More

View Article and Full-Text PDF

Improving cognitive functioning in major depressive disorder with psychedelics: a dimensional approach.

Neurobiol Learn Mem 2021 May 25:107467. Epub 2021 May 25.

Faculty of Psychology and Neuroscience, Section Neuropsychology & Psychopharmacology, Maastricht University, Maastricht, The Netherlands. Electronic address:

The high symptomatic and biological heterogeneity of major depressive disorder (MDD) makes it very difficult to find broadly efficacious treatments that work against all symptoms. Concentrating on single core symptoms that are biologically well understood might consist of a more viable approach. The Research Domain Criteria (RDoC) framework is a trans-diagnostic dimensional approach that focuses on symptoms and their underlying neurobiology. Read More

View Article and Full-Text PDF

A Rhodamine-based Fluorescent Chemodosimeter for Au in Aqueous Solution and Living Cells.

J Fluoresc 2021 May 27. Epub 2021 May 27.

Department of Chemistry, Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, 10400, Bangkok, Thailand.

A highly selective rhodamine hydrazide-based fluorescent chemosensor for Au detection was developed. The aqueous solution of rhodamine N-hydroxysemicarbazide (RHS), in the presence of Au, exhibited a significant 55-fold turn-on fluorescence response at 591 nm and a colorimetric change from colorless to pink. Other interested ions including Li, Na, K, Cs, Mg, Ca, Ba, Pb, Mn, Co, Ni, Ag, Cd, Cu, Hg, Zn, Sn, Fe, Fe, Cr, Ce did not induce any distinct color/spectral changes. Read More

View Article and Full-Text PDF

Integrative molecular characterization of pediatric spinal ependymoma: the UK Children's Cancer and Leukaemia Group study.

Neurooncol Adv 2021 Jan-Dec;3(1):vdab043. Epub 2021 Mar 8.

Children's Brain Tumour Research Centre, School of Medicine, University of Nottingham, Nottingham, UK.

Background: Pediatric spinal ependymomas (SP-EPNs) are rare primary central nervous system tumors with heterogeneous clinical course. Considering that ependymomas in children are biologically distinct from their adult counterparts, this study aimed to define the molecular landscape of SP-EPNs in children.

Methods: In this retrospective study, we have collected tumor samples from 27 SP-EPN patients younger than 18 years and carried out the histological review, DNA methylation, and gene expression profiling. Read More

View Article and Full-Text PDF

CLUE: Exact maximal reduction of kinetic models by constrained lumping of differential equations.

Bioinformatics 2021 May 25. Epub 2021 May 25.

IMT School for Advanced Studies, Lucca, 55100, Italy.

Motivation: Detailed mechanistic models of biological processes can pose significant challenges for analysis and parameter estimations due to the large number of equations used to track the dynamics of all distinct configurations in which each involved biochemical species can be found. Model reduction can help tame such complexity by providing a lower-dimensional model in which each macro-variable can be directly related to the original variables.

Results: We present CLUE, an algorithm for exact model reduction of systems of polynomial differential equations by constrained linear lumping. Read More

View Article and Full-Text PDF

Phenotypic plasticity underlies local invasion and distant metastasis in colon cancer.

Elife 2021 May 26;10. Epub 2021 May 26.

Department of Pathology, Erasmus MC, Rotterdam, Netherlands.

Phenotypic plasticity represents the most relevant hallmark of the carcinoma cell as it bestows it with the capacity of transiently altering its morphological and functional features while to the metastatic site. However, the study of phenotypic plasticity is hindered by the rarity of these events within primary lesions and by the lack of experimental models. Here, we identified a subpopulation of phenotypic plastic colon cancer cells: EpCAM cells are motile, invasive, chemo-resistant, and highly metastatic. Read More

View Article and Full-Text PDF

Pharmacological inhibition of MDA-9/Syntenin blocks breast cancer metastasis through suppression of IL-1β.

Proc Natl Acad Sci U S A 2021 May;118(21)

Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298;

Melanoma differentiation associated gene-9 (MDA-9), Syntenin-1, or syndecan binding protein is a differentially regulated prometastatic gene with elevated expression in advanced stages of melanoma. MDA-9/Syntenin expression positively associates with advanced disease stage in multiple histologically distinct cancers and negatively correlates with patient survival and response to chemotherapy. MDA-9/Syntenin is a highly conserved PDZ-domain scaffold protein, robustly expressed in a spectrum of diverse cancer cell lines and clinical samples. Read More

View Article and Full-Text PDF

Genetic Architecture of Maize Rind Strength Revealed by the Analysis of Divergently Selected Populations.

Plant Cell Physiol 2021 May 20. Epub 2021 May 20.

Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA.

The strength of the stalk rind, measured as rind penetrometer resistance (RPR), is an important contributor to stalk lodging resistance. To enhance the genetic architecture of RPR, we combined selection mapping on populations developed by 15 cycles of divergent selection for high and low RPR with time-course transcriptomic and metabolic analyses of the stalks. Divergent selection significantly altered allele frequencies of 3,656 and 3,412 single nucleotide polymorphisms (SNPs) in the high and low RPR populations, respectively. Read More

View Article and Full-Text PDF

A Simple and Efficient Method to Generate Dual Site-Specific Conjugation ADCs with Cysteine Residue and an Unnatural Amino Acid.

Bioconjug Chem 2021 May 20. Epub 2021 May 20.

Interdisciplinary Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.

Antibody-drug conjugates (ADCs) are complex pharmaceutical molecules that combine monoclonal antibodies with biologically active drugs through chemical linkers. ADCs are designed to specifically kill disease cells by utilizing the target specificity of antibodies and the cytotoxicity of chemical drugs. However, the traditional ADCs were only applied to a few disease targets because of some limitations such as the huge molecular weight, the uncontrollable coupling reactions, and a single mechanism of action. Read More

View Article and Full-Text PDF

Pediatric ependymoma: an overview of a complex disease.

Childs Nerv Syst 2021 May 18. Epub 2021 May 18.

Department of Neuropathology, DGNN Brain Tumor Reference Centre, University of Bonn Medical Centre, Bonn, Germany.

Pediatric ependymomas comprise biologically distinct tumor entities with different (epi)genetics, age distribution and localization, as well as a different prognosis. Regarding risk stratification within these biologically defined entities, histopathological features still seem to be relevant. The mainstay of treatment is gross total resection (GTR) if possible, achieved with intraoperative monitoring and neuronavigation-and if necessary second surgery-followed by adjuvant radiation therapy. Read More

View Article and Full-Text PDF

Identifying brain networks in synaptic density PET (C-UCB-J) with independent component analysis.

Neuroimage 2021 May 15;237:118167. Epub 2021 May 15.

Yale PET Center, Department of Radiology and Biomedical Imaging, Yale University, 801 Howard Avenue, New Haven, CT 06520, USA.

Background: The human brain is inherently organized into distinct networks, as reported widely by resting-state functional magnetic resonance imaging (rs-fMRI), which are based on blood-oxygen-level-dependent (BOLD) signal fluctuations. C-UCB-J PET maps synaptic density via synaptic vesicle protein 2A, which is a more direct structural measure underlying brain networks than BOLD rs-fMRI.

Methods: The aim of this study was to identify maximally independent brain source networks, i. Read More

View Article and Full-Text PDF

Carbon Nanotube Microelectrode Set: Detection of Biomolecules to Heavy Metals.

Anal Chem 2021 May 14;93(20):7439-7448. Epub 2021 May 14.

Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States.

An ultrasensitive electrochemical microelectrode set (μ-ES), where all three electrodes are made of highly densified carbon nanotube fiber (HD-CNTf) cross sections (length ∼40 μm), embedded in an inert polymer matrix, and exposed open-ended CNTs at the interface, is presented here. Bare open ends of HD-CNTf rods were used as the working (∼40 μm diameter) and counter (∼94 μm diameter) electrodes, while the cross section of a ∼94 μm diameter was electroplated with Ag/AgCl and coated with Nafion to employ as a quasi-reference electrode. The Ag/AgCl/Nafion-coated HD-CNTf rod quasi-reference electrode provided a very stable potential comparable to the commercial porous-junction Ag/AgCl reference electrode. Read More

View Article and Full-Text PDF

Integrative genomics of the mammalian alveolar macrophage response to intracellular mycobacteria.

BMC Genomics 2021 May 12;22(1):343. Epub 2021 May 12.

Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland.

Background: Bovine TB (bTB), caused by infection with Mycobacterium bovis, is a major endemic disease affecting global cattle production. The key innate immune cell that first encounters the pathogen is the alveolar macrophage, previously shown to be substantially reprogrammed during intracellular infection by the pathogen. Here we use differential expression, and correlation- and interaction-based network approaches to analyse the host response to infection with M. Read More

View Article and Full-Text PDF

Cellular and transcriptomic analyses reveal two-staged chloroplast biogenesis underpinning photosynthesis build-up in the wheat leaf.

Genome Biol 2021 May 11;22(1):151. Epub 2021 May 11.

Department of Biological Sciences, Royal Holloway University of London, Egham, UK.

Background: The developmental gradient in monocot leaves has been exploited to uncover leaf developmental gene expression programs and chloroplast biogenesis processes. However, the relationship between the two is barely understood, which limits the value of transcriptome data to understand the process of chloroplast development.

Results: Taking advantage of the developmental gradient in the bread wheat leaf, we provide a simultaneous quantitative analysis for the development of mesophyll cells and of chloroplasts as a cellular compartment. Read More

View Article and Full-Text PDF

Single Hormone Receptor-Positive Metaplastic Breast Cancer: Similar Outcome as Triple-Negative Subtype.

Front Endocrinol (Lausanne) 2021 23;12:628939. Epub 2021 Apr 23.

Department of Vascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.

Background: Metaplastic breast cancer (MBC) is a rare and aggressive subtype of the breast. To understand the characteristics and prognosis of single hormone receptor-positive (HR+) MBC (estrogen receptor-positive [ER+]/progesterone receptor-negative [PR-] and ER-/PR+), we compared these tumors to double HR+ tumors as well as HR- tumors.

Patients And Methods: The Surveillance, Epidemiology, and End Results database was used to analyze MBC between 1975 and 2016. Read More

View Article and Full-Text PDF

Rare Histological Variants of Liver Cancer and Their Management: A Single-Institution Experience.

Case Reports Hepatol 2021 21;2021:6654229. Epub 2021 Apr 21.

Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine/New-York Presbyterian, New York, New York, USA.

Primary liver malignancies, including hepatocellular carcinoma (HCC) and cholangiocarcinoma, are a major cause of cancer-related morbidity and mortality worldwide. There are several histologically and biologically distinct subtypes of liver cancer that have previously been reported. However, literature regarding the nonsurgical management of these patients upon disease recurrence remains limited. Read More

View Article and Full-Text PDF

Silent corticotroph pituitary adenomas: clinical characteristics, long-term outcomes, and management of disease recurrence.

J Neurosurg 2021 May 7:1-8. Epub 2021 May 7.

Departments of1Neurological Surgery.

Objective: Silent corticotroph adenomas (SCAs) are a distinct subtype of nonfunctioning pituitary adenomas (NFAs) that demonstrate positive immunohistochemistry for adrenocorticotropic hormone (ACTH) without causing Cushing's disease. SCAs are hypothesized to exhibit more aggressive behavior than standard NFAs. The authors analyzed their institution's surgical experience with SCAs in an effort to characterize rates of invasion, postoperative clinical outcomes, and patterns of disease recurrence and progression. Read More

View Article and Full-Text PDF

Chromatographic separation of the interconverting enantiomers of imidazo- and triazole-fused benzodiazepines.

J Chromatogr A 2021 Jun 15;1647:462148. Epub 2021 Apr 15.

SapienzaUniversità di Roma, Dipartimento di Chimica e Tecnologie del Farmaco, P.le A. Moro 5, 00185Rome, Italy. Electronic address:

The toolbox of medicinal chemists includes the 1,4-benzodiazepine scaffold as a "privileged scaffold" in drug discovery. Several biologically active small molecules containing a 1,4-benzodiazepine scaffold have been approved by the FDA for the treatment of various diseases, with most of them being used for their psychotropic effects. The therapeutic potential of 1,4-benzodiazepines has stimulated the interest of synthetic chemists in developing new synthetic strategies to a range of substituted analogues for biological evaluation. Read More

View Article and Full-Text PDF

Detection of Genetic Variability in Borrelia miyamotoi (Spirochaetales: Spirochaetaceae) Between and Within the Eastern and Western United States.

J Med Entomol 2021 May 6. Epub 2021 May 6.

Bacterial Diseases Branch, Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, USA.

Borrelia miyamotoi is a hard tick-associated relapsing fever spirochete that is geographically widespread in Ixodes spp. (Acari: Ixodidae) ticks, but typically occurs at low prevalence. Genetic variability has been described among strains derived from Asia, Europe, and North America, and among tick species that carry the infection, but little variability has been described within foci or tick species. Read More

View Article and Full-Text PDF

iTIME.219: An Immortalized KSHV Infected Endothelial Cell Line Inducible by a KSHV-Specific Stimulus to Transition From Latency to Lytic Replication and Infectious Virus Release.

Front Cell Infect Microbiol 2021 14;11:654396. Epub 2021 Apr 14.

Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States.

Kaposi's sarcoma-associated herpesvirus (KSHV/HHV-8) is the causative agent of Kaposi's sarcoma and two B cell lymphoproliferative disorders: primary effusion lymphoma and KSHV-associated multicentric Castleman's disease. These distinct pathologies involve different infected cell types. In Kaposi's sarcoma, the virus is harbored in spindle-like tumor cells of endothelial origin, in contrast with the two pathologies of B cells. Read More

View Article and Full-Text PDF

Neutrophils: Need for Standardized Nomenclature.

Front Immunol 2021 15;12:602963. Epub 2021 Apr 15.

Discipline of Paediatrics, Trinity College, The University of Dublin, Dublin, Ireland.

Neutrophils are the most abundant innate immune cell with critical anti-microbial functions. Since the discovery of granulocytes at the end of the nineteenth century, the cells have been given many names including phagocytes, polymorphonuclear neutrophils (PMN), granulocytic myeloid derived suppressor cells (G-MDSC), low density neutrophils (LDN) and tumor associated neutrophils (TANS). This lack of standardized nomenclature for neutrophils suggest that biologically distinct populations of neutrophils exist, particularly in disease, when in fact these may simply be a manifestation of the plasticity of the neutrophil as opposed to unique populations. Read More

View Article and Full-Text PDF

Myxoepithelioid tumor with chordoid feature: A clinicopathological, immunohistochemical, and genetic study of 14 cases of SMARCB1/INI1-deficient soft-tissue neoplasm.

Histopathology 2021 May 1. Epub 2021 May 1.

Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.

Aims: Complete loss of SMARCB1/INI1 in soft-tissue tumors such as malignant rhabdoid tumor, epithelioid sarcoma, myoepithelial tumor of soft tissue, and extraskeletal myxoid chondrosarcoma is often associated with high-grade malignancy and poor prognosis. The diagnosis is sometimes challenging due to histological similarities, so careful differential diagnosis is required. Therefore, soft-tissue tumors with complete SMARCB1/INI1 loss could potentially include an unknown entity. Read More

View Article and Full-Text PDF

Pathophysiological role of prostaglandin E synthases in liver diseases.

Prostaglandins Other Lipid Mediat 2021 Jun 27;154:106552. Epub 2021 Apr 27.

Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People's Republic of China. Electronic address:

Prostaglandin E synthases (PGESs) convert cyclooxygenase (COX)-derived prostaglandin H (PGH) into prostaglandin E (PGE) and comprise at least three types of structurally and biologically distinct enzymes. Two of these, namely microsomal prostaglandin E synthase-1 (mPGES-1) and mPGES-2, are membrane-bound enzymes. mPGES-1 is an inflammation-inducible enzyme that converts PGH into PGE. Read More

View Article and Full-Text PDF