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Intermediate phenotypes

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https://www.readbyqxmd.com/read/29159761/nestin-expression-in-breast-cancer-association-with-prognosis-and-subtype-on-3641-cases-with-long-term-follow-up
#1
Karama Asleh, Jennifer R Won, Dongxia Gao, K David Voduc, Torsten O Nielsen
BACKGROUND: Basal-like breast cancers, originally recognized by gene expression profiling, can be clinically identified using immunohistochemical (IHC) definitions that require estrogen receptor (ER) negativity. However, some basal cases are ER positive and are mistakenly considered to be luminal by standard IHC approaches, leading to suboptimal treatment choices. Nestin, an intermediate filament expressed in many stem cells, is a recently identified positive marker of basal-like phenotype independent of ER status...
November 20, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/29158965/colour-change-of-twig-mimicking-peppered-moth-larvae-is-a-continuous-reaction-norm-that-increases-camouflage-against-avian-predators
#2
Amy Eacock, Hannah M Rowland, Nicola Edmonds, Ilik J Saccheri
Camouflage, and in particular background-matching, is one of the most common anti-predator strategies observed in nature. Animals can improve their match to the colour/pattern of their surroundings through background selection, and/or by plastic colour change. Colour change can occur rapidly (a few seconds), or it may be slow, taking hours to days. Many studies have explored the cues and mechanisms behind rapid colour change, but there is a considerable lack of information about slow colour change in the context of predation: the cues that initiate it, and the range of phenotypes that are produced...
2017: PeerJ
https://www.readbyqxmd.com/read/29157227/metabolic-adaptation-of-two-in-silico-mutants-of-mycobacterium-tuberculosis-during-infection
#3
Víctor A López-Agudelo, Andres Baena, Howard Ramirez-Malule, Silvia Ochoa, Luis F Barrera, Rigoberto Ríos-Estepa
BACKGROUND: Up to date, Mycobacterium tuberculosis (Mtb) remains as the worst intracellular killer pathogen. To establish infection, inside the granuloma, Mtb reprograms its metabolism to support both growth and survival, keeping a balance between catabolism, anabolism and energy supply. Mtb knockouts with the faculty of being essential on a wide range of nutritional conditions are deemed as target candidates for tuberculosis (TB) treatment. Constraint-based genome-scale modeling is considered as a promising tool for evaluating genetic and nutritional perturbations on Mtb metabolic reprogramming...
November 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29154293/the-changing-landscape-of-parkinson-epidemiologic-research
#4
Honglei Chen
Despite recent successes in understanding the genetics of Parkinson's disease (PD), the causes of late-onset sporadic PD remain elusive. Many of the epidemiologic findings on PD etiology have been challenged by alternative explanations such as reverse causation. This is mainly because PD often takes decades to develop before it can be diagnosed late in life. Convincing evidence shows that this prodromal stage of PD is characterized by various prodromal symptoms such as olfactory impairment and rapid-eye-movement sleep behavior disorder (RBD)...
November 14, 2017: Journal of Parkinson's Disease
https://www.readbyqxmd.com/read/29154286/clinic-based-validation-of-cerebrospinal-fluid-biomarkers-with-florbetapir-pet-for-diagnosis-of-dementia
#5
Ignacio Álvarez, Miquel Aguilar, Jose Manuel González, Montse Ysamat, Carles Lorenzo-Bosquet, Alvaro Alonso, Juan Pablo Tartari, Silvia Romero, Monica Diez-Fairen, Maria Carcel, Francisco Pujalte, Pau Pastor
BACKGROUND: Cerebrospinal fluid (CSF) biomarker studies have shown variable accuracy for diagnosis of Alzheimer's disease (AD); therefore, internal validation is recommended. OBJECTIVE: To investigate the correlation between CSF biomarkers and cerebral 18-Florbetapir positron emission tomography (Amyloid-PET) and calculate their sensitivity and specificity to obtain the optimal clinical cut-off points to diagnose the etiology of cognitive impairment. METHODS: We performed Amyloid-PET scans and CSF biomarker levels analyses in 68 subjects (50 with mild cognitive impairment, 11 with AD dementia, and 7 with non-AD dementia)...
November 14, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/29154026/inhibitors-of-metallo-%C3%AE-lactamases
#6
REVIEW
Caitlyn M Rotondo, Gerard D Wright
The β-lactams are the most successful class of antibiotic drugs but they are vulnerable to inactivation by a growing cadre of β-lactamases that now number more than a thousand variants. β-Lactamases operate by one of two general chemical mechanisms either catalyzing β-lactam ring hydrolysis via a covalent enzyme intermediate through the aegis of an active site serine residue or through a noncovalent Zn-dependent mechanism. The Ser-β-lactamases are currently dominant in the clinic and consequently, there has been great effort to identify inhibitors and to co-formulate these with β-lactam antibiotics...
November 15, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/29146812/evolution-of-flower-color-pattern-through-selection-on-regulatory-small-rnas
#7
Desmond Bradley, Ping Xu, Irina-Ioana Mohorianu, Annabel Whibley, David Field, Hugo Tavares, Matthew Couchman, Lucy Copsey, Rosemary Carpenter, Miaomiao Li, Qun Li, Yongbiao Xue, Tamas Dalmay, Enrico Coen
Small RNAs (sRNAs) regulate genes in plants and animals. Here, we show that population-wide differences in color patterns in snapdragon flowers are caused by an inverted duplication that generates sRNAs. The complexity and size of the transcripts indicate that the duplication represents an intermediate on the pathway to microRNA evolution. The sRNAs repress a pigment biosynthesis gene, creating a yellow highlight at the site of pollinator entry. The inverted duplication exhibits steep clines in allele frequency in a natural hybrid zone, showing that the allele is under selection...
November 17, 2017: Science
https://www.readbyqxmd.com/read/29141026/in-depth-phenotypic-characterization-of-multicellular-tumor-spheroids-effects-of-5-fluorouracil
#8
Angélique Virgone-Carlotta, Manon Lemasson, Hichem C Mertani, Jean-Jacques Diaz, Sylvain Monnier, Thomas Dehoux, Hélène Delanoë-Ayari, Charlotte Rivière, Jean-Paul Rieu
MultiCellular Tumor Spheroids (MCTS), which mimic the 3-Dimensional (3D) organization of a tumor, are considered as better models than conventional cultures in 2-Dimensions (2D) to study cancer cell biology and to evaluate the response to chemotherapeutic drugs. A real time and quantitative follow-up of MCTS with simple and robust readouts to evaluate drug efficacy is still missing. Here, we evaluate the chemotherapeutic drug 5-Fluorouracil (5-FU) response on the growth and integrity of MCTS two days after treatment of MCTS and for three colorectal carcinoma cell lines with different cohesive properties (HT29, HCT116 and SW480)...
2017: PloS One
https://www.readbyqxmd.com/read/29138350/the-dead-box-rna-helicase-rh50-is-a-23s-4-5s-rrna-maturation-factor-that-functionally-overlaps-with-the-plastid-signaling-factor-gun1
#9
Francesca Paieri, Luca Tadini, Nikolay Manavski, Tatjana Kleine, Roberto Ferrari, Pietro Angelo Morandini, Paolo Pesaresi, Jörg Meurer, Dario Leister
DEAD-box RNA helicases (DBRHs) modulate RNA secondary structure, allowing RNA molecules to adopt the conformations required for interaction with their target proteins. RH50 is a chloroplast-located DBRH that co-localizes and is co-expressed with GUN1, a central factor in chloroplast-to-nucleus signaling. When combined with mutations that impair plastid gene expression (prors1-1, prpl11-1, prps1-1, prps21-1, prps17-1 and prpl24-1), rh50 and gun1 mutations evoke similar patterns of epistatic effects. These observations, together with the synergistic growth phenotype of the double mutant rh50-1 gun1-102, suggest that RH50 and GUN1 are functionally related and that this function is associated with plastid gene expression, in particular ribosome functioning...
November 14, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29136549/the-spectrum-of-charcot-marie-tooth-disease-due-to-myelin-protein-zero-an-electrodiagnostic-nerve-ultrasound-and-histological-study
#10
Gian Maria Fabrizi, Stefano Tamburin, Tiziana Cavallaro, Ilaria Cabrini, Moreno Ferrarini, Federica Taioli, Francesca Magrinelli, Giampietro Zanette
OBJECTIVE: Nerve ultrasound (US) data on myelin protein zero (MPZ)-related Charcot-Marie-Tooth disease (CMT) are lacking. To offer a comprehensive perspective on MPZ-related CMTs, we combined nerve US with clinics, electrodiagnosis and histopathology. METHODS: We recruited 36 patients (12 MPZ mutations), and correlated nerve US to clinical, electrodiagnostic measures, and sural nerve biopsy. RESULTS: According to motor nerve conduction velocity (MNCV) criteria, nine patients were categorized as "demyelinating" CMT1B, 17 as "axonal" CMT2I/J, and 10 as dominant "intermediate" CMTDID...
October 20, 2017: Clinical Neurophysiology: Official Journal of the International Federation of Clinical Neurophysiology
https://www.readbyqxmd.com/read/29134233/-genuine-motor-phenomena-in-schizophrenia-neuronal-correlates-and-pathomechanisms
#11
REVIEW
D Hirjak, G Northoff, P A Thomann, K M Kubera, R C Wolf
Despite a growing body of evidence on motor dysfunction in schizophrenia spectrum disorders, the neuronal correlates of genuine motor abnormalities (GMA) are not fully elucidated at present. Moreover, the clinical relevance of a potential "motor intermediate phenotype" remains controversial. This systematic review aims at characterizing a "motor intermediate phenotype" in schizophrenia spectrum disorders. The second goal of this systematic review is to discuss GMA-associated brain alterations as potential biomarkers of psychosis risk syndrome and manifest motor symptoms against the background of current neuroimaging evidence...
November 13, 2017: Der Nervenarzt
https://www.readbyqxmd.com/read/29133223/phenotypical-differences-of-childhood-and-adult-onset-atopic-dermatitis
#12
Jonathan I Silverberg, Paras P Vakharia, Rishi Chopra, Ryan Sacotte, Neha Patel, Supriya Immaneni, Takeisha White, Robert Kantor, Derek Y Hsu
BACKGROUND: Little is known about adult-onset atopic dermatitis (AD). OBJECTIVE: To determine the associations and clinical characteristics of adult-onset AD. METHODS: A prospective study of 356 adults with AD (age ≥18 years) was performed using standardized questionnaires and examination. AD severity was assessed using the Patient-Oriented Eczema Measure, Eczema Area and Severity Index, Scoring Atopic Dermatitis, body surface area, and numeric rating scale for itch and sleeplessness...
November 10, 2017: Journal of Allergy and Clinical Immunology in Practice
https://www.readbyqxmd.com/read/29133218/cluster-analysis-identifies-3-phenotypes-within-allergic-asthma
#13
María Paz Sendín-Hernández, Carmelo Ávila-Zarza, Catalina Sanz, Asunción García-Sánchez, Elena Marcos-Vadillo, Francisco J Muñoz-Bellido, Elena Laffond, Christian Domingo, María Isidoro-García, Ignacio Dávila
BACKGROUND: Asthma is a heterogeneous chronic disease with different clinical expressions and responses to treatment. In recent years, several unbiased approaches based on clinical, physiological, and molecular features have described several phenotypes of asthma. Some phenotypes are allergic, but little is known about whether these phenotypes can be further subdivided. OBJECTIVE: We aimed to phenotype patients with allergic asthma using an unbiased approach based on multivariate classification techniques (unsupervised hierarchical cluster analysis)...
November 10, 2017: Journal of Allergy and Clinical Immunology in Practice
https://www.readbyqxmd.com/read/29127260/an-improved-brome-mosaic-virus-silencing-vector-greater-insert-stability-and-more-extensive-vigs
#14
Xin Shun Ding, Stephen W Mannas, Bethany A Bishop, Xiaolan Rao, Mitchell Lecoultre, Soonil Kwon, Richard S Nelson
Virus-induced gene silencing (VIGS) is used extensively for gene function studies in plants. VIGS is inexpensive and rapid compared with silencing conducted through stable transformation, but many virus silencing vectors, especially in grasses, induce only transient silencing phenotypes. A major reason for transient phenotypes is instability of the foreign gene fragment (insert) in the vector during VIGS. Here we report the development of a Brome mosaic virus (BMV)-based vector that better maintains inserts through modification of the original BMV vector RNA sequence...
November 10, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29122363/clustering-of-multi-parametric-functional-imaging-to-identify-high-risk-subvolumes-in-non-small-cell-lung-cancer
#15
Aniek J G Even, Bart Reymen, Matthew D La Fontaine, Marco Das, Felix M Mottaghy, José S A Belderbos, Dirk De Ruysscher, Philippe Lambin, Wouter van Elmpt
BACKGROUND AND PURPOSE: We aimed to identify tumour subregions with characteristic phenotypes based on pre-treatment multi-parametric functional imaging and correlate these subregions to treatment outcome. The subregions were created using imaging of metabolic activity (FDG-PET/CT), hypoxia (HX4-PET/CT) and tumour vasculature (DCE-CT). MATERIALS AND METHODS: 36 non-small cell lung cancer (NSCLC) patients underwent functional imaging prior to radical radiotherapy...
November 6, 2017: Radiotherapy and Oncology: Journal of the European Society for Therapeutic Radiology and Oncology
https://www.readbyqxmd.com/read/29119593/prediction-of-cognitive-worsening-in-de-novo-parkinson-s-disease-clinical-use-of-biomarkers
#16
Dario Arnaldi, Fabrizio De Carli, Francesco Famà, Andrea Brugnolo, Nicola Girtler, Agnese Picco, Matteo Pardini, Jennifer Accardo, Luca Proietti, Federico Massa, Matteo Bauckneht, Silvia Morbelli, Gianmario Sambuceti, Flavio Nobili
BACKGROUND: Cognitive impairment is a frequent and disabling feature of Parkinson's disease. Identifying the factors able to predict cognitive worsening since the early stage may improve disease management. The objective of this study was to define the best predictors of future cognitive worsening in a group of patients with newly diagnosed PD and to propose cutoff values potentially useful at the individual level. METHODS: Fifty-four consecutive drug-naive patients with de novo PD were prospectively evaluated by clinical and neuropsychological assessment, resting EEG, and (123) I-FP-CIT-SPECT and clinically classified into mainly motor, diffuse/malignant, and intermediate PD subtypes; they were then followed up for an average of 5 years...
November 9, 2017: Movement Disorders: Official Journal of the Movement Disorder Society
https://www.readbyqxmd.com/read/29116131/context-dependent-compensation-among-phosphatidylserine-recognition-receptors
#17
Kristen K Penberthy, Claudia Rival, Laura S Shankman, Michael H Raymond, Jianye Zhang, Justin S A Perry, Chang Sup Lee, Claudia Z Han, Suna Onengut-Gumuscu, Krzysztof Palczewski, Jeffrey J Lysiak, Kodi S Ravichandran
Phagocytes express multiple phosphatidylserine (PtdSer) receptors that recognize apoptotic cells. It is unknown whether these receptors are interchangeable or if they play unique roles during cell clearance. Loss of the PtdSer receptor Mertk is associated with apoptotic corpse accumulation in the testes and degeneration of photoreceptors in the eye. Both phenotypes are linked to impaired phagocytosis by specialized phagocytes: Sertoli cells and the retinal pigmented epithelium (RPE). Here, we overexpressed the PtdSer receptor BAI1 in mice lacking MerTK (Mertk (-/-) Bai1 (Tg) ) to evaluate PtdSer receptor compensation in vivo...
November 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29113992/axonemal-dynein-assembly-requires-the-r2tp-complex-component-pontin
#18
Yuanyuan Li, Lu Zhao, Shiaulou Yuan, Jiefang Zhang, Zhaoxia Sun
Pontin (Ruvbl1) and Reptin (Ruvbl2) are closely related AAA ATPases. They are components of the Ruvbl1-Rvubl2-Tah1-Pih1 (R2TP) complexes that function as co-chaperones for the assembly of multiple macromolecular protein complexes. Here, we show that Pontin is essential for cilia motility in both zebrafish and mouse and that Pontin and Reptin function cooperatively in this process. pontin zebrafish mutants display phenotypes tightly associated with cilia defects and cilia motility is lost in a number of ciliated tissues along with a reduction in the number of both outer and inner dynein arms (ODAs and IDAs)...
November 7, 2017: Development
https://www.readbyqxmd.com/read/29113978/additive-phenotypes-underlie-epistasis-of-fitness-effects
#19
Andrew M Sackman, Darin R Rokyta
Gene interactions, or epistasis, play a large role in determining evolutionary outcomes. The ruggedness of fitness landscapes, and thus the predictability of evolution and the accessibility of high-fitness genotypes, is determined largely by the pervasiveness of epistasis and the degree of correlation between similar genotypes. We created all possible pairings of three sets of five beneficial first-step mutations fixed during adaptive walks under three different regimes: selection on growth rate alone, on growth rate and thermal stability, and on growth rate and pH stability...
November 7, 2017: Genetics
https://www.readbyqxmd.com/read/29113020/the-genetics-of-obstructive-sleep-apnoea
#20
REVIEW
Sutapa Mukherjee, Richa Saxena, Lyle J Palmer
Obstructive sleep apnoea (OSA) is a common chronic disease and is associated with high social and economic costs. OSA is heritable, and there is evidence of both direct genetic contributions to OSA susceptibility and indirect contributions via 'intermediate' phenotypes such as obesity, craniofacial structure, neurological control of upper airway muscles and of sleep and circadian rhythm. Investigation of the genetics of OSA is an important research area and may lead to improved understanding of disease aetiology, pathogenesis, adverse health consequences and new preventive strategies and treatments...
November 7, 2017: Respirology: Official Journal of the Asian Pacific Society of Respirology
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