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Spectrochim Acta A Mol Biomol Spectrosc ; 265: 120328, 2022 Jan 15.
Article En | MEDLINE | ID: mdl-34481146

Macrophages are key cells in the immune inflammatory response that can be differentiated into M1 and M2 phenotypes. Polarization has a critical therapeutic value, especially in diseases in which an M1/M2 imbalance plays a pathophysiological role. Raman spectroscopy has proven to be a promising bioanalytical technique for discriminating different cell types. However, to our knowledge, its application to identify the functional polarization of macrophages into M1 or M2 cells is yet to be investigated. In this work, Raman spectroscopy was applied to the analysis of macrophage polarization, and the spectral datasets were analyzed using principal component analysis (PCA). In vitro, resting J774.1 macrophages were treated with LPS/IFN-γ to induce the M1 phenotype or with IL-4 to induce the M2 phenotype. The resulting Raman spectra showed sufficient biochemical information to distinguish between M1 and M2 phenotypes when analyzed by PCA, reflecting the changes in cell markers caused by differentiation. The Raman spectra collected from LPS-stimulated M1 and M2 macrophages were more intense. The functional phenotype of M1 macrophages was confirmed by IL-6 secretion and TNF-α mRNA expression, while M2 macrophages produced IL-10 and Arg-1 mRNA, as well as by the morphological changes observed by scanning electron microscopy. Taken together, the results indicate that Raman spectroscopy combined with PCA analysis is a useful tool to identify the functional phenotypes of macrophages, providing an alternative way to distinguish between cells in distinct differentiation stages.

Macrophages , Spectrum Analysis, Raman , Animals , Cell Differentiation , Cell Line , Lipopolysaccharides/pharmacology , Mice , Phenotype
Gene ; 807: 145950, 2022 Jan 10.
Article En | MEDLINE | ID: mdl-34481003

This population-based longitudinal study is the first investigation that assesses the association of common MC4R SNPs with the obesity-related parameters over time and determines the effect of risk alleles during the three adulthood life periods (early, middle, and late) in a large Iranian cohort, a population with a unique genetic make-up that has been understudied and relatively unexplored. We obtained the genotype of 5370 unrelated adults who participated in the ongoing Tehran Cardiometabolic Genetic Study (TCGS) cohort project for the common MC4R SNPs. Linear regression and linear mixed model analyses were performed to examine the effect of MC4R polymorphisms on maximum BMI and other obesity-related factors over time. We recognized that several SNPs associated with the maximum BMI and the increased BMI, waist circumference, and waist-hip ratio across Iranian adults over a lifetime. Interestingly, we found that rs9954571-A has a yet unreported protective role against obesity-related factors, including BMI, waist circumference, waist-hip ratio, and triglyceride level. Additionally, a survey of the impact of the MC4R risk score throughout the adulthood life periods indicated that the MC4R risk score is influenced both the elevated BMI and waist circumference only during the early adulthood period. Our findings can expand our knowledge about the MC4R genetic variant's contributions to adulthood obesity and highlight the importance of evaluating the genetic components affecting obesity over a lifetime, which could be considered for obesity clinical screening and treatment.

Obesity/genetics , Receptor, Melanocortin, Type 4/genetics , Adult , Alleles , Body Mass Index , Cohort Studies , Female , Gene Frequency/genetics , Genetic Predisposition to Disease/genetics , Genotype , Humans , Iran/epidemiology , Longitudinal Studies , Male , Mass Screening/methods , Middle Aged , Obesity/metabolism , Phenotype , Polymorphism, Single Nucleotide/genetics , Receptor, Melanocortin, Type 4/metabolism , Risk Factors , Waist Circumference/genetics , Waist-Hip Ratio/methods
Heart Fail Clin ; 18(1): 1-8, 2022 Jan.
Article En | MEDLINE | ID: mdl-34776071

Genetic testing in children with hypertrophic cardiomyopathy (HCM) can modify clinical management and lifestyle counseling. However, predicting long-term outcome and response to management in individual patients remains challenging, because of the peculiar genetic heterogeneity of the disease in the pediatric age range. Children with HCM secondary to an inborn error of metabolism or malformation syndromes tend to have a worse outcome compared with those with the classic sarcomeric form. Among the latter, adverse genetic features are represented by the identification of a pathogenic variant in MYH7, often associated with severe hypertrophy, a complex genotype, or a de novo variant.

Cardiac Myosins , Cardiomyopathy, Hypertrophic , Cardiac Myosins/genetics , Cardiomyopathy, Hypertrophic/genetics , Child , Genotype , Humans , Myosin Heavy Chains/genetics , Phenotype
Heart Fail Clin ; 18(1): 101-113, 2022 Jan.
Article En | MEDLINE | ID: mdl-34776072

In the wide phenotypic spectrum of cardiomyopathies, sudden cardiac death (SCD) has always been the most visible and devastating disease complication. The introduction of implantable cardioverter-defibrillators for SCD prevention by the late 1980s has moved the question from how to whom we should protect from SCD, leaving clinicians with a measure of uncertainty regarding the most reliable option to guide identification of the highest-risk patients. In this review, we will go through all the available evidence in the field of arrhythmic expression and arrhythmic risk stratification in the different phenotypes of cardiomyopathies to provide practical suggestions in daily clinical management.

Cardiomyopathies , Defibrillators, Implantable , Cardiomyopathies/genetics , Death, Sudden, Cardiac/etiology , Death, Sudden, Cardiac/prevention & control , Humans , Phenotype
Parasitol Int ; 86: 102483, 2022 Feb.
Article En | MEDLINE | ID: mdl-34678492

This study examines the biological efficacy of four mosquito mat vaporizers each containing different active ingredients: prallethrin with PBO, dimefluthrin, prallethrin, and d-allethrin. The glass chamber assay was used to evaluate their efficacy on Aedes albopictus (Skuse) (Diptera: Culicidae) from nine districts in Selangor, Malaysia. Aedes albopictus exhibited different knockdown rates, with 50% knockdown times, KT50, varying from 1.19 to 2.00 min, 1.22 to 2.20 min, 1.39 to 5.85 min, and 1.39 to 1.92 min for prallethrin with PBO, dimefluthrin, prallethrin and d-allethrin, respectively. In general, all populations of Ae. albopictus were completely knocked down after exposure to all active ingredients except Hulu Selangor population, which showed 96.00% knockdown against d-allethrin. On the contrary, mortality rates were observed from 84.00-100.00%, 84.00-100.00%, 90.67-100.00% and 90.67-100.00% in populations tested with prallethrin with PBO, dimefluthrin, prallethrin and d-allethrin, respectively. Moreover, significant correlations between mortality rates of prallethrin with PBO vs dimefluthrin (r = 0.836, P = 0.003), prallethrin with PBO vs prallethrin (r = 0.760, P = 0.011), and prallethrin vs d-allethrin (r = 0.694, P = 0.026) were also observed, suggesting cross-resistance among pyrethroids. d-allethrin was found to be high in insecticidal activity, followed by prallethrin, prallethrin with PBO, and dimefluthrin. In consistent with mortality due to insecticide exposure, elevated levels of enzyme activities were also demonstrated in Sabak Bernam, Hulu Selangor, Gombak, Petaling, Hulu Langat and Klang populations.

Aedes , Insecticides , Mosquito Control , Nebulizers and Vaporizers , Aedes/genetics , Animals , Inactivation, Metabolic , Malaysia , Phenotype
Gene ; 807: 145949, 2022 Jan 10.
Article En | MEDLINE | ID: mdl-34481004

Growth traits is a critical economic trait for animal husbandry. In this study, the SNPs of CTNNA3 and CAP2 genes were investigated to check whether they are associated with growth traits (body weight, body height, body length and chest circumference) in Hu sheep. The result of the association analysis indicated that the mutation in CTNNA3 (g.2018018 A > G) were associated significantly with body weight, body height, body length and chest circumference (P < 0.05), the mutation in CAP2 (g.8588 T > C) were associated significantly with body height at 140, 160, 180 days (P < 0.05), AA and CC of CTNNA3 and CAP2 were the dominant genotypes associated with growth traits in Hu sheep. Moreover, combined effect analyses indicated that the growth traits with combined genotypes AACTNNA3-CCCAP2 and AACTNNA3-CTCAP2 were higher than those with genotype GGCTNNA3-CTCAP2. RT-qPCR indicated that CTNNA3 expression levels were significantly higher in liver and lung than in other nine tissues (P < 0.05), CAP2 expression levels were significantly higher in bone, heart, liver, lung and duodenum than in other six tissues (P < 0.05). In conclusion, CTNNA3 and CAP2 polymorphisms could be used as genetic markers for improving growth traits in Hu sheep husbandry.

Adaptor Proteins, Signal Transducing/genetics , Body Weight/genetics , Sheep/growth & development , Animals , China , Genetic Markers/genetics , Genotype , Haplotypes/genetics , Humans , Linkage Disequilibrium , Male , Membrane Proteins/genetics , Membrane Proteins/metabolism , Phenotype , Polymorphism, Single Nucleotide/genetics , Sheep/genetics , alpha Catenin/genetics , alpha Catenin/metabolism
Chemosphere ; 287(Pt 3): 132262, 2022 Jan.
Article En | MEDLINE | ID: mdl-34543897

Coastal marine systems are the most sensitive zones to emerging pollutants. The present study aims to investigate the effect of Diuron on the meiofaunal assemblages, collected from the Bizerte channel (Tunisia). Microcosm experiments were set up using four increasing Diuron concentrations [D1 (10 ng g-1 dry weight (DW)), D2 (50 ng g-1 DW), D3 (250 ng g-1 DW) and (1250 ng g-1 DW)] compared to non-contaminated sediments (controls) and all plots were incubated for 30 days. Our results show that Diuron-supplemented sediments provoked the significant decrease of meiofaunal abundance as well as a change in nematodes' diversity and structure composition. All univariate indices, as well as the cumulative k-dominance, were lower in the Diuron than the control plot. Additionally, the ordination of treatments according to the two-dimensional nMDS plots analysis showed a clear structural separation of the Diuron treated replicates from the controls based on the functional groups lists. These current data emphasize the utility of the use of biological traits in the detection of disturbances in the aquatic biotope.

Nematoda , Water Pollutants, Chemical , Animals , Climate , Diuron/toxicity , Environmental Monitoring , Geologic Sediments , Phenotype , Tunisia , Water Pollutants, Chemical/analysis , Water Pollutants, Chemical/toxicity
Trop Anim Health Prod ; 53(6): 546, 2021 Nov 15.
Article En | MEDLINE | ID: mdl-34779908

The purpose of this work was to establish DNA marker frequencies for genetic disorders, colour, horned/polled trait, and major genes of importance for productive and reproductive traits in Blanco Orejinegro (BON) cattle. The Blanco Orejinegro breed is a Colombian creole breed characterized by a white hair coat on black skin with black ears, black hair on the middle part of the legs, and absence of horns. We genotyped 420 animals of Colombia, 70 with the GGP-Bovine 150 K chip and 350 with the GGP-Bovine 50 K chip. The markers were associated with 50 genetic diseases, 52 major gene variants related to productive traits, and 12 variants related to coat coloration, presence of horns, and adaptation, selected from the information contained in the chips. Genotype frequencies were estimated using the R statistical program. Genetic disorder annotations were derived using the Online Mendelian Inheritance in Animals tool (OMIA) and the average inbreeding coefficient (F) (n = 7799) using the MTDFNRM program. Carriers were found for 16 of the genetic disorders evaluated but with low frequencies (0.24 to 2.46%); no homozygous animals were found for the disorders. Carriers were associated with disorders such as bovine leukocyte adhesion deficiency (BLAD), deficiency of uridine monophosphate synthase (DUMPS), syndactyly, and epidermolysis bullosa (EB). The F was 4.41%. Concerning the genes associated with colour (TYR, MC1R, and PMEL), alleles related to black pigmentation, the absence of horns (polledness), and slick coat (an adaptive trait) were highly frequent (> 81.90%). Markers associated with milk production and quality, yellow fat, and fertility showed variable frequencies, indicating selection potential. Allele frequency of genetic disorders in BON cattle was low, suggesting few genetic disorder problems, with syndactyly being the most frequent condition. The markers associated with colour and polledness were almost fixed, with a frequency at or near 100%. Production and reproduction markers showed variability for selection.

Inbreeding , Animals , Cattle/genetics , Color , Gene Frequency , Genotype , Phenotype
Clin Dermatol ; 39(4): 738-742, 2021.
Article En | MEDLINE | ID: mdl-34809785

The complete or partial meeting of medial eyebrows at midline above the bridge of nose, forming a single band of hair, is known as synophrys or unibrow. With a few rare exceptions, when it may serve as a cutaneous marker lesion of several genetic disorders, with Cornelia De Lange syndrome being the commonest, synophrys is usually a normal variation. Although various cultures have prized synophrys as an attractive physical trait throughout history, in modern Western culture, the unibrow is frequently regarded as an undesirable and unappealing feature with negative connotations. Synophrys, derived from the Ancient Greek σύν (together, with) and ὀφρύς (eyebrow), meaning "with meeting eyebrows," refers to the complete or partial fusion of medial eyebrows at midline. The hair above the nasal bridge is often of the same color and thickness as the eyebrows, thus giving the appearance that they converge to form one uninterrupted line of hair, a single eyebrow.

Eyebrows , Nose , Hair , Humans , Phenotype
Zootaxa ; 5052(2): 111-129, 2021 Oct 14.
Article En | MEDLINE | ID: mdl-34810875

It is widely accepted among the Cladocera (Crustacea) taxonomists that almost all cosmopolitan taxa are represented by some un-revised complexes of cryptic species. But many macro taxa of the cladocerans are still unrevised. The aim of this work is to analyze the taxonomic status of Oriental populations of the genus Bosminopsis Richard, 1895 (Anomopoda: Bosminidae) based on morphological characters. We have studied populations from India, Myanmar, Cambodia, Thailand, Laos, Vietnam, Philippines, Malaysia and Papua New Guinea and concluded that Oriental populations belong to a single species, Bosminopsis africanus (Daday, 1908), initially described from Africa. Analysis of literature data confirms that is widely distributed through whole Oriental zone. A single large mucro, or the mucro accompanied by an additional small spine in both sexes, is the main trait which differentiates B. africanus from B. zernowi Linko, 1901 distributed in more northern regions of Eurasia.

Cladocera , Animals , Female , Male , Phenotype
Zootaxa ; 5055(1): 1-137, 2021 Oct 19.
Article En | MEDLINE | ID: mdl-34811227

This paper provides a taxonomic revision of the Neotropical ant genus Hylomyrma Forel (1912) (Myrmicinae: Pogonomyrmecini). Morphological traits combined with geographical data and natural history information led to the recognition of 30 species, fourteen of them described here as new: Hylomyrma adelae sp. n., Hylomyrma dandarae sp. n., Hylomyrma jeronimae sp. n., Hylomyrma lispectorae sp. n., Hylomyrma lopesi sp. n., Hylomyrma macielae sp. n., Hylomyrma margaridae sp. n., Hylomyrma mariae sp. n., Hylomyrma marielleae sp. n., Hylomyrma mitiae sp. n., Hylomyrma peetersi sp. n., Hylomyrma primavesi sp. n., Hylomyrma virginiae sp. n. and Hylomyrma wachiperi sp. n. Lectotypes for H. speciosa (junior synonym of H. balzani) and H. reitteri are here designated from syntypes to improve nomenclatural stability. Except for the three species most recently described (H. montana, H. plumosa, and H. villemantae), the external morphology of workers is described or redescribed, as well as for the known males and queens, most described here for the first time. Of the 30 recognized species herein, 11 present intercastes; at least three of them present female specimens with queen-like traits that may be understood as ergatoids. An updated identification key for Hylomyrma workers is provided, as well as high resolution photographs of all known sexes and castes, species distribution maps, and a summary of what is known from the biology of all species.

Ants , Orthoptera , Animals , Female , Geography , Male , Phenotype , Social Class
Stud Health Technol Inform ; 285: 141-146, 2021 Oct 27.
Article En | MEDLINE | ID: mdl-34734865

In this paper we propose a new definition of digital phenotype to enrich the formulation with information stored in the Electronic Health Records (EHR) plus data obtained using wearables. On this basis, we describe how to use this formalism to represent the health state of a patient in a given moment (retrospective, present, or future) and how can it be applied for personalized medicine to find out the mutations that should be introduced at present to reach a better health status in the future.

Electronic Health Records , Precision Medicine , Humans , Phenotype , Retrospective Studies
An Acad Bras Cienc ; 93(suppl 4): e20210047, 2021.
Article En | MEDLINE | ID: mdl-34730621

The Agaricomycetes fungi produce various compounds with pharmaceutical, medicinal, cosmetic, environmental and biotechnological properties. In addition, some polysaccharides extracted from the fungal cell wall have antitumor and immunomodulatory actions. The aim of this study was to use genetic modification to transform Schizophyllum commune and identify if the phenotype observed (different from the wild type) resulted in changes of the cell wall polysaccharides. The plasmid pUCHYG-GPDGLS, which contains the Pleurotus ostreatus glucan synthase gene, was used in S. commune transformations. Polysaccharides from cell wall of wild (ScW) and mutants were compared in this study. Polysaccharides from the biomass and culture broth were extracted with hot water. One of the mutants (ScT4) was selected for further studies and, after hydrolysis/acetylation, the GLC analysis showed galactose as the major component in polysaccharide fraction from the mutant and glucose as the major monomer in the wild type. Differences were also found in the elution profiles from HPSEC and NMR analyses. From the monosaccharide composition it was proposed that mannogalactans are components of S. commune cell wall for both, wild and mutant, but in different proportions. To our knowledge, this is the first time that mannogalactans are isolated from S. commune liquid culture.

Schizophyllum , Cell Wall , Mutation/genetics , Phenotype , Polysaccharides , Schizophyllum/genetics
Sensors (Basel) ; 21(21)2021 Oct 31.
Article En | MEDLINE | ID: mdl-34770574

The speed and accuracy of phenotype detection from medical images are some of the most important qualities needed for any informed and timely response such as early detection of cancer or detection of desirable phenotypes for animal breeding. To improve both these qualities, the world is leveraging artificial intelligence and machine learning against this challenge. Most recently, deep learning has successfully been applied to the medical field to improve detection accuracies and speed for conditions including cancer and COVID-19. In this study, we applied deep neural networks, in the form of a generative adversarial network (GAN), to perform image-to-image processing steps needed for ovine phenotype analysis from CT scans of sheep. Key phenotypes such as gigot geometry and tissue distribution were determined using a computer vision (CV) pipeline. The results of the image processing using a trained GAN are strikingly similar (a similarity index of 98%) when used on unseen test images. The combined GAN-CV pipeline was able to process and determine the phenotypes at a speed of 0.11 s per medical image compared to approximately 30 min for manual processing. We hope this pipeline represents the first step towards automated phenotype extraction for ovine genetic breeding programmes.

Artificial Intelligence , COVID-19 , Animals , Computers , Humans , Image Processing, Computer-Assisted , Phenotype , SARS-CoV-2 , Sheep
BMC Musculoskelet Disord ; 22(1): 962, 2021 Nov 17.
Article En | MEDLINE | ID: mdl-34789204

BACKGROUND: Up to 25% of people who have had carpal tunnel release surgery (CTR) fail to report improvement; however, evidence for prognostic indicators in this surgical cohort is limited. To identify candidate prognostic factors, this study investigated the association of quantitative sensory testing (QST) derived sensory phenotype and attendant impairment with patient-reported surgical outcome. METHODS: With ethical approval and informed consent, this prospective observational longitudinal study recruited patients from two London hospitals. Multimodal phenotyping measures including quantitative sensory testing (QST), pain parameters, insomnia, pain-related worry, mood and function, were evaluated prior to; and at 3- and 6-months post-surgery. Pain in median nerve distribution with electrophysiologically confirmed conduction delay and DN4 score ≥ 4 was defined as neuropathic. Primary outcome was patient-rated change at 6 months, dichotomised as poor outcome; "worse" or "no change" and good outcome; "slightly better", "much better" or "completely cured". RESULTS: Seventy-six patients participated. Prior to surgery, substantial heterogeneity in established categories of somatosensory function was observed with 21% of participants categorised as having a healthy sensory phenotype; 29% with thermal hyperalgesia; 32% mechanical hyperalgesia and 18% sensory loss. Seventy six percent of participants were classified as having neuropathic pain, 33% with high levels of pain related worry and 64% with clinical insomnia. Observed differences in pain, sleep impairment, psychological factors and function, between sensory phenotypic groups, was not significant. At 3- and 6-months post-surgery there was significant improvement in all phenotyping measures with a moderate to large effect size. Thermal and mechanical measures of somatosensation improved (p < 0.001), as did functional ability (p < 0.001). Symptom severity diminished (p < 0.001), as did pain-related worry (p < 0.001), anxiety (p = 0.02) and insomnia (p < 0.001). Patient-rated surgical outcome was good in 92% of the cohort, poor in 8%. Baseline sensory phenotype category was not associated with surgical outcome however pain-related worry, anxiety and functional interference were significantly associated with outcome (p ≤ 0.05). CONCLUSION: In patients undergoing carpal tunnel surgery, pain-related worry, anxiety and pain functional interference are candidate prognostic outcome factors and require further elucidation.

Carpal Tunnel Syndrome , Neuralgia , Carpal Tunnel Syndrome/diagnosis , Carpal Tunnel Syndrome/epidemiology , Carpal Tunnel Syndrome/surgery , Humans , Longitudinal Studies , Phenotype , Sleep
BMJ ; 375: e066288, 2021 11 03.
Article En | MEDLINE | ID: mdl-34732400

OBJECTIVE: To determine whether whole genome sequencing can be used to define the molecular basis of suspected mitochondrial disease. DESIGN: Cohort study. SETTING: National Health Service, England, including secondary and tertiary care. PARTICIPANTS: 345 patients with suspected mitochondrial disorders recruited to the 100 000 Genomes Project in England between 2015 and 2018. INTERVENTION: Short read whole genome sequencing was performed. Nuclear variants were prioritised on the basis of gene panels chosen according to phenotypes, ClinVar pathogenic/likely pathogenic variants, and the top 10 prioritised variants from Exomiser. Mitochondrial DNA variants were called using an in-house pipeline and compared with a list of pathogenic variants. Copy number variants and short tandem repeats for 13 neurological disorders were also analysed. American College of Medical Genetics guidelines were followed for classification of variants. MAIN OUTCOME MEASURE: Definite or probable genetic diagnosis. RESULTS: A definite or probable genetic diagnosis was identified in 98/319 (31%) families, with an additional 6 (2%) possible diagnoses. Fourteen of the diagnoses (4% of the 319 families) explained only part of the clinical features. A total of 95 different genes were implicated. Of 104 families given a diagnosis, 39 (38%) had a mitochondrial diagnosis and 65 (63%) had a non-mitochondrial diagnosis. CONCLUSION: Whole genome sequencing is a useful diagnostic test in patients with suspected mitochondrial disorders, yielding a diagnosis in a further 31% after exclusion of common causes. Most diagnoses were non-mitochondrial disorders and included developmental disorders with intellectual disability, epileptic encephalopathies, other metabolic disorders, cardiomyopathies, and leukodystrophies. These would have been missed if a targeted approach was taken, and some have specific treatments.

Genetic Testing/methods , Mitochondrial Diseases/diagnosis , Mitochondrial Diseases/genetics , Whole Genome Sequencing , Adolescent , Adult , Aged , Aged, 80 and over , Child , Child, Preschool , DNA, Mitochondrial/genetics , Female , Follow-Up Studies , Genetic Markers , Humans , Infant , Infant, Newborn , Male , Middle Aged , Mutation , Phenotype , Young Adult
Neurol India ; 69(5): 1400-1401, 2021.
Article En | MEDLINE | ID: mdl-34747823

Mutations in KMT2B (lysine-specific methyltransferase 2B) gene, which is primarily involved in methylation of Histone3lys4 (H3K4), has been recently described to cause early-onset generalized progressive dystonia (DYT28) by two independent researchers. Unlike other primary dystonias, mutations in KMT2B gene is associated with additional features like dysmorphism (elongated face, bulbous nose), microcephaly, short stature, and multisystemic involvement. Herein, we describe a 13-year-old boy with early-onset, generalized, progressive complex severe dystonia, along with mild intellectual disability, dysmorphism, and dermatological manifestations associated with a novel missense variation in KMT2B gene and also expand the phenotypic spectrum of the same.

Dystonic Disorders , Histone-Lysine N-Methyltransferase , Adolescent , Dystonic Disorders/genetics , Histone-Lysine N-Methyltransferase/genetics , Humans , India , Male , Mutation , Phenotype
Georgian Med News ; (319): 102-108, 2021 Oct.
Article En | MEDLINE | ID: mdl-34749332

There are several pathogenetic models of localized scleroderma. At the same time, studies examining the role of endothelin-1, vascular endothelial growth factor (VEGF-A) and cell adhesion molecule-1 (VCAM) are limited. Objectives - to learn the nature of disorders of vascular, proliferative, adhesive functions of the endothelium on the content of endothelin-1, VEGF-A and VCAM-1 in localized scleroderma. The study included 78 patients with localized scleroderma and 35 healthy individuals (mean age - 44.2±17.6 years, 73 women (64.6%), 40 men (35.4%). All patients underwent clinical, laboratory, enzyme-linked immunosorbent assay examination (endothelin-1, VEGF-A, VCAM-1). In the local form of scleroderma, there are the number of disorders of vascular, proliferative and adhesive functions of the endothelium, with an increase in endothelin-1 (p<0.05), VEGF-A (p<0.05) and VCAM-1 (p<0.05) content. In idiopathic atrophodermia, the level of endothelin-1 was probably higher (p<0.05). The vasospastic type of pathogenesis of localized scleroderma was established in patients under 20 years of age (p<0.05) and in patients older than 70 years (p<0.05). U-shaped age dependence of pathogenesis was noted: high content of VEGF-A in patients under 20 years of age (p<0.05) and after 35 years (p<0.05). Higher levels of VCAM-1 were found in women compared to men (p<0.05). The analysis of the age dependence of the content revealed a U-shaped dependence of VCAM-1 - the highest content in patients under 20 years (p<0.05) and in patients 55-70 years (p<0.05). The level of biomarkers of endothelial dysfunction in patients with localized scleroderma - endothelin-1, VEGF and VCAM is associated with different phenotypes of the disease course - vasospastic, proliferative or adhesive.

Endothelin-1 , Endothelium, Vascular/physiopathology , Scleroderma, Localized , Vascular Cell Adhesion Molecule-1 , Vascular Endothelial Growth Factor A , Adult , Aged , Female , Humans , Male , Middle Aged , Phenotype , Scleroderma, Localized/physiopathology , Young Adult
BMC Genomics ; 22(1): 805, 2021 Nov 08.
Article En | MEDLINE | ID: mdl-34749647

BACKGROUND: Intramuscular fat (IMF) content is a determining factor for meat taste. The Luchuan pig is a fat-type local breed in southern China that is famous for its desirable meat quality due to high IMF, however, the crossbred offspring of Luchuan sows and Duroc boars displayed within-population variation on meat quality, and the reason remains unknown. RESULTS: In the present study, we identified 212 IMF-correlated genes (FDR ≤ 0.01) using correlation analysis between gene expression level and the value of IMF content. The IMF-correlated genes were significantly enriched in the processes of lipid metabolism and mitochondrial energy metabolism, as well as the AMPK/PPAR signaling pathway. From the IMF-correlated genes, we identified 99 genes associated with expression quantitative trait locus (eQTL) or allele-specific expression (ASE) signals, including 21 genes identified by both cis-eQTL and ASE analyses and 12 genes identified by trans-eQTL analysis. Genome-wide association study (GWAS) of IMF identified a significant QTL on SSC14 (p-value = 2.51E-7), and the nearest IMF-correlated gene SFXN4 (r = 0.28, FDR = 4.00E-4) was proposed as the candidate gene. Furthermore, we highlighted another three novel IMF candidate genes, namely AGT, EMG1, and PCTP, by integrated analysis of GWAS, eQTL, and IMF-gene correlation analysis. CONCLUSIONS: The AMPK/PPAR signaling pathway together with the processes of lipid and mitochondrial energy metabolism plays a vital role in regulating porcine IMF content. Trait correlated expression combined with eQTL and ASE analysis highlighted a priority list of genes, which compensated for the shortcoming of GWAS, thereby accelerating the mining of causal genes of IMF.

Meat , Quantitative Trait Loci , Swine , Adipose Tissue , Alleles , Animals , Female , Genetic Association Studies/veterinary , Male , Meat/analysis , Phenotype , Swine/genetics
BMC Genomics ; 22(1): 823, 2021 Nov 15.
Article En | MEDLINE | ID: mdl-34781903

BACKGROUND: Feed efficiency is one of the key determinants of beef industry profitability and sustainability. However, the cellular and molecular background behind feed efficiency is largely unknown. This study combines imputed whole genome DNA variants and 31 plasma metabolites to dissect genes and biological functions/processes that are associated with residual feed intake (RFI) and its component traits including daily dry matter intake (DMI), average daily gain (ADG), and metabolic body weight (MWT) in beef cattle. RESULTS: Regression analyses between feed efficiency traits and plasma metabolites in a population of 493 crossbred beef cattle identified 5 (L-valine, lysine, L-tyrosine, L-isoleucine, and L-leucine), 4 (lysine, L-lactic acid, L-tyrosine, and choline), 1 (citric acid), and 4 (L-glutamine, glycine, citric acid, and dimethyl sulfone) plasma metabolites associated with RFI, DMI, ADG, and MWT (P-value < 0.1), respectively. Combining the results of metabolome-genome wide association studies using 10,488,742 imputed SNPs, 40, 66, 15, and 40 unique candidate genes were identified as associated with RFI, DMI, ADG, and MWT (P-value < 1 × 10-5), respectively. These candidate genes were found to be involved in some key metabolic processes including metabolism of lipids, molecular transportation, cellular function and maintenance, cell morphology and biochemistry of small molecules. CONCLUSIONS: This study identified metabolites, candidate genes and enriched biological functions/processes associated with RFI and its component traits through the integrative analyses of metabolites with phenotypic traits and DNA variants. Our findings could enhance the understanding of biochemical mechanisms of feed efficiency traits and could lead to improvement of genomic prediction accuracy via incorporating metabolite data.

Animal Feed , Genome-Wide Association Study , Animal Feed/analysis , Animals , Cattle , Eating , Genome , Phenotype