keyword
MENU ▼
Read by QxMD icon Read
search

Molecular profiling

keyword
https://www.readbyqxmd.com/read/28330247/production-of-glucosinolates-phenolic-compounds-and-associated-gene-expression-profiles-of-hairy-root-cultures-in-turnip-brassica-rapa-ssp-rapa
#1
Ill-Min Chung, Kaliyaperumal Rekha, Govindasamy Rajakumar, Muthu Thiruvengadam
Turnip (Brassica rapa ssp. rapa) is an important vegetable crop producing glucosinolates (GSLs) and phenolic compounds. The GSLs, phenolic compound contents and transcript levels in hairy root cultures, as well as their antioxidant, antimicrobial and anticancer activity were studied in turnip. Transgenic hairy root lines were confirmed by polymerase chain reaction (PCR) and reverse transcription-PCR. GSLs levels (glucoallysin, glucobrassicanapin, gluconasturtiin, glucobrassicin, 4-methoxyglucobrassicin, neoglucobrassicin and 4-hydroxyglucobrassicin) and their gene expression levels (BrMYB28, BrMYB29, BrMYB34, BrMYB51, BrMYB122, CYP79 and CYP83) significantly increased in hairy roots compared with that in non-transformed roots...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330195/identification-and-characterization-of-endophytic-bacteria-isolated-from-in-vitro-cultures-of-peach-and-pear-rootstocks
#2
Fakhra Liaqat, Rengin Eltem
Endophytes are microorganisms which live symbiotically with almost all varieties of plant and in turn helping the plant in a number of ways. Instead of satisfactory surface sterilization approaches, repeatedly occurring bacterial growth on in vitro rootstock cultures of peach and pear was identified and isolated as endophytic bacteria in our present study. Five different isolates from peach rootstocks were molecularly identified by 16S rRNA gene sequencing as Brevundimonas diminuta, Leifsonia shinshuensis, Sphingomonas parapaucimobilis Brevundimonas vesicularis, Agrobacterium tumefaciens while two endophytic isolates of pear were identified as Pseudoxanthomonas mexicana, and Stenotrophomonas rhizophilia...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330176/molecular-dissection-of-pathway-components-unravel-atisine-biosynthesis-in-a-non-toxic-aconitum-species-a-heterophyllum-wall
#3
Varun Kumar, Nikhil Malhotra, Tarun Pal, Rajinder Singh Chauhan
Aconitum heterophyllum is an important component for various herbal drug formulations due to the occurrence of non-toxic aconites including marker compound, atisine. Despite huge pharmacological potential, the reprogramming of aconites production is limited due to lack of understanding on their biosynthesis. To address this problem, we have proposed here the complete atisine biosynthetic pathway for the first time connecting glycolysis, MVA/MEP, serine biosynthesis and diterpene biosynthetic pathways. The transcript profiling revealed phosphorylated pathway as a major contributor towards serine production in addition to repertoire of genes in glycolysis (G6PI, PFK, ALD and ENO), serine biosynthesis (PGDH and PSAT) and diterpene biosynthesis (KO and KH) sharing a similar pattern of expression (2-4-folds) in roots compared to shoots vis-à-vis atisine content (0-0...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330089/discovery-of-potential-alk-inhibitors-by-virtual-screening-approach
#4
Anish Kumar, V Shanthi, K Ramanathan
Crizotinib is an anticancer drug used for the treatment of non-small cell lung cancer. Evidences available suggest that there is a development of an acquired resistance against crizotinib action due to the emergence of several mutations in the ALK gene. It is therefore necessary to develop potent anti-cancer drugs for the treatment of crizotinib resistance non-small cell lung cancer types. In the present study, a novel class of lead molecule was identified using virtual screening, molecular docking and molecular dynamic approach...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329763/the-allosteric-inhibitor-abl001-enables-dual-targeting-of-bcr-abl1
#5
Andrew A Wylie, Joseph Schoepfer, Wolfgang Jahnke, Sandra W Cowan-Jacob, Alice Loo, Pascal Furet, Andreas L Marzinzik, Xavier Pelle, Jerry Donovan, Wenjing Zhu, Silvia Buonamici, A Quamrul Hassan, Franco Lombardo, Varsha Iyer, Michael Palmer, Giuliano Berellini, Stephanie Dodd, Sanjeev Thohan, Hans Bitter, Susan Branford, David M Ross, Timothy P Hughes, Lilli Petruzzelli, K Gary Vanasse, Markus Warmuth, Francesco Hofmann, Nicholas J Keen, William R Sellers
Chronic myeloid leukaemia (CML) is driven by the activity of the BCR-ABL1 fusion oncoprotein. ABL1 kinase inhibitors have improved the clinical outcomes for patients with CML, with over 80% of patients treated with imatinib surviving for more than 10 years. Second-generation ABL1 kinase inhibitors induce more potent molecular responses in both previously untreated and imatinib-resistant patients with CML. Studies in patients with chronic-phase CML have shown that around 50% of patients who achieve and maintain undetectable BCR-ABL1 transcript levels for at least 2 years remain disease-free after the withdrawal of treatment...
March 22, 2017: Nature
https://www.readbyqxmd.com/read/28329733/comparison-of-transcriptional-expression-patterns-of-carotenoid-metabolism-in-cabernet-sauvignon-grapes-from-two-regions-with-distinct-climate
#6
Wei-Kai Chen, Ke-Ji Yu, Bin Liu, Yi-Bin Lan, Run-Ze Sun, Qiang Li, Fei He, Qiu-Hong Pan, Chang-Qing Duan, Jun Wang
The downstream flux of carotenoid metabolism in grape berries includes the biosynthesis of norisoprenoids, a group of important aroma compounds, and the production of ABA, a well-known plant hormone. This study focused on the transcriptional profiling comparison of genes participating in the biosynthesis of carotenoids, norisoprenoids, and ABA in Vitis vinifera 'Cabernet Sauvignon' grapes at pea size, veraison, and ripening stages. The grapes were obtained from Changli (CL, eastern China) and Gaotai (GT, western China) regions and analyzed using RNA-sequencing technology...
March 9, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28329689/the-human-cchc-type-zinc-finger-nucleic-acid-binding-protein-binds-g-rich-elements-in-target-mrna-coding-sequences-and-promotes-translation
#7
Daniel Benhalevy, Sanjay K Gupta, Charles H Danan, Suman Ghosal, Hong-Wei Sun, Hinke G Kazemier, Katrin Paeschke, Markus Hafner, Stefan A Juranek
The CCHC-type zinc finger nucleic acid-binding protein (CNBP/ZNF9) is conserved in eukaryotes and is essential for embryonic development in mammals. It has been implicated in transcriptional, as well as post-transcriptional, gene regulation; however, its nucleic acid ligands and molecular function remain elusive. Here, we use multiple systems-wide approaches to identify CNBP targets and function. We used photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) to identify 8,420 CNBP binding sites on 4,178 mRNAs...
March 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28328988/molecular-mechanisms-of-thermal-resistance-of-the-insect-trypanosomatid-crithidia-thermophila
#8
Aygul Ishemgulova, Anzhelika Butenko, Lucie Kortišová, Carolina Boucinha, Anastasiia Grybchuk-Ieremenko, Karina A Morelli, Martina Tesařová, Natalya Kraeva, Danyil Grybchuk, Tomáš Pánek, Pavel Flegontov, Julius Lukeš, Jan Votýpka, Márcio Galvão Pavan, Fred R Opperdoes, Viktoria Spodareva, Claudia M d'Avila-Levy, Alexei Yu Kostygov, Vyacheslav Yurchenko
In the present work, we investigated molecular mechanisms governing thermal resistance of a monoxenous trypanosomatid Crithidia luciliae thermophila, which we reclassified as a separate species C. thermophila. We analyzed morphology, growth kinetics, and transcriptomic profiles of flagellates cultivated at low (23°C) and elevated (34°C) temperature. When maintained at high temperature, they grew significantly faster, became shorter, with genes involved in sugar metabolism and mitochondrial stress protection significantly upregulated...
2017: PloS One
https://www.readbyqxmd.com/read/28328502/spatial-statistics-for-segmenting-histological-structures-in-h-e-stained-tissue-images
#9
Luong Nguyen, A Burak Tosun, Jeffrey Fine, Adrian Lee, D Lansing Taylor, Chakra Chennubhotla
Segmenting a broad class of histological structures in transmitted light and/or fluorescence-based images is a prerequisite for determining the pathological basis of cancer, elucidating spatial interactions between histological structures in tumor microenvironments (e.g. tumor infiltrating lymphocytes), facilitating precision medicine studies with deep molecular profiling, and providing an exploratory tool for pathologists. Our paper focuses on segmenting histological structures in hematoxylin and eosin (H&E) stained images of breast tissues, e...
March 16, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28327901/data-resources-for-the-identification-and-interpretation-of-actionable-mutations-by-clinicians
#10
A Prawira, T J Pugh, T L Stockley, L L Siu
Following initial characterization of the reference human genome, initiatives have evolved worldwide to identify genomic aberrations in cancer with the aim of deriving diagnostic, prognostic and predictive information. However, the functional and clinical relevance of many somatic variants in cancer are presently unknown and there is no consensus definition of "actionability" for genomic aberrancies. Therefore, while robust detection of a variety of genetic aberrations in clinical specimens remains a technical hurdle, the greater challenge lies in the interpretation of these alterations...
January 24, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28327752/umbrella-sampling-molecular-dynamics-simulations-reveal-concerted-ion-movement-through-g-quadruplex-dna-channels
#11
Parisa Akhshi, Gang Wu
We have applied the umbrella sampling (US) method in all-atom molecular dynamics (MD) simulations to obtain potential of mean force (PMF) profiles for ion transport through three representative G-quadruplex DNA channels: [d(TG4T)]4, [d(G3T4G4)]2, and d[G4(T4G4)3]. The US MD results are in excellent agreement with those obtained previously with the adaptive biasing force (ABF) method. We then utilized the unique features in the US MD method to investigate multi-ion effects in [d(G3T4G4)]2 and discovered that the concerted ion movement is crucial for fully explaining the unusual experimental results on ion movement in this particular G-quadruplex system...
March 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28327647/microrna-expression-profiles-during-cotton-gossypium-hirsutum-l-fiber-early-development
#12
Min Wang, Runrun Sun, Chao Li, Qinglian Wang, Baohong Zhang
The role of microRNAs (miRNAs) during cotton fiber development remains unclear. Here, a total of 54 miRNAs belonging to 39 families were selected to characterize miRNA regulatory mechanism in eight different fiber development stages in upland cotton cv BM-1. Among 54 miRNAs, 18 miRNAs were involved in cotton fiber initiation and eight miRNAs were related to fiber elongation and secondary wall biosynthesis. Additionally, 3,576 protein-coding genes were candidate target genes of these miRNAs, which are potentially involved in cotton fiber development...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28327201/detecting-gene-signature-activation-in-breast-cancer-in-an-absolute-single-patient-manner
#13
E R Paquet, R Lesurf, A Tofigh, V Dumeaux, M T Hallett
BACKGROUND: The ability to reliably identify the state (activated, repressed, or latent) of any molecular process in the tumor of a patient from an individual whole-genome gene expression profile obtained from microarray or RNA sequencing (RNA-seq) promises important clinical utility. Unfortunately, all previous bioinformatics tools are only applicable in large and diverse panels of patients, or are limited to a single specific pathway/process (e.g. proliferation). METHODS: Using a panel of 4510 whole-genome gene expression profiles from 10 different studies we built and selected models predicting the activation status of a compendium of 1733 different biological processes...
March 21, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28327131/transcriptome-analysis-of-pancreatic-cells-across-distant-species-highlights-novel-important-regulator-genes
#14
Estefania Tarifeño-Saldivia, Arnaud Lavergne, Alice Bernard, Keerthana Padamata, David Bergemann, Marianne L Voz, Isabelle Manfroid, Bernard Peers
BACKGROUND: Defining the transcriptome and the genetic pathways of pancreatic cells is of great interest for elucidating the molecular attributes of pancreas disorders such as diabetes and cancer. As the function of the different pancreatic cell types has been maintained during vertebrate evolution, the comparison of their transcriptomes across distant vertebrate species is a means to pinpoint genes under strong evolutionary constraints due to their crucial function, which have therefore preserved their selective expression in these pancreatic cell types...
March 21, 2017: BMC Biology
https://www.readbyqxmd.com/read/28326890/functional-and-molecular-correlates-following-single-and-repeated-rat-closed-head-concussion-indices-of-vulnerability-following-brain-injury
#15
Andrea Mountney, Angela Boutte, Casandra M Cartagena, William J Flerlage, David Johnson, Chanyang Rho, Xi-Chun M Lu, Angela M Yarnell, Sean R Marcsisin, Jason Sousa, Chau Vuong, Victor E Zottig, Lai Yee Leung, Ying Deng-Bryant, Janice Gilsdorf, Frank C Tortella, Deborah A Shear
Closed-head concussive injury is one of the most common causes of traumatic brain injury (TBI). Isolated concussions frequently produce acute neurological impairments; however, individuals typically recover spontaneously within a short time frame. In contrast, brain injuries resulting from multiple concussions can result in cumulative damage and elevated risk of developing chronic brain pathologies, including chronic traumatic encephalopathy (CTE). Increased attention has focused on identification of diagnostic markers that can prognostically serve as indices of brain health after injury, revealing the temporal profile of vulnerability to a second insult...
March 22, 2017: Journal of Neurotrauma
https://www.readbyqxmd.com/read/28326551/cyclic-imine-toxins-from-dinoflagellates-a-growing-family-of-potent-antagonists-of-the-nicotinic-acetylcholine-receptors
#16
REVIEW
Jordi Molgó, Pascale Marchot, Rómulo Aráoz, Evelyne Benoit, Bogdan I Iorga, Armen Zakarian, Palmer Taylor, Yves Bourne, Denis Servent
We present an overview of the toxicological profile of the fast-acting, lipophilic macrocyclic imine toxins, an emerging family of organic compounds associated with algal blooms, shellfish contamination and neurotoxicity. Worldwide, shellfish contamination incidents are expanding; therefore, the significance of these toxins for the shellfish food industry deserves further study. Emphasis is directed to the dinoflagellate species involved in their production, their chemical structures, and their specific mode of interaction with their principal natural molecular targets, the nicotinic acetylcholine receptors, or with the soluble acetylcholine-binding protein, used as a surrogate receptor model...
March 21, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28326488/is-lmwh-sufficient-for-anticoagulant-prophylaxis-in-bariatric-surgery-prospective-study
#17
Farraj Moaad, Bramnik Zakhar, Kvasha Anton, Merie Moner, Sbeit Wisam, Farraj Safy, Waksman Igor
BACKGROUND: The objective of this study was to evaluate the coagulation profile by thromboelastography in morbidly obese patients who undergo bariatric surgery. Morbid obesity entails increased risk for thromboembolic events. There is no clear protocol for thromboembolic prophylaxis, regarding timing and length of treatment, in bariatric surgery. Thromboelastography provides data on a coagulation process from creation of the clot until the fibrinolysis. METHODS: Ninety-three morbidly obese patients were prospectively recruited within a 2-year period...
March 22, 2017: Obesity Surgery
https://www.readbyqxmd.com/read/28326469/hsv-1-interaction-to-3-o-sulfated-heparan-sulfate-in-mouse-derived-drg-explant-and-profiles-of-inflammatory-markers-during-virus-infection
#18
Harsh Sharthiya, Chanmoly Seng, T H Van Kuppevelt, Vaibhav Tiwari, Michele Fornaro
The molecular mechanism of herpes simplex virus (HSV) entry and the associated inflammatory response in the nervous system remain poorly understood. Using mouse-derived ex vivo dorsal root ganglia (DRG) explant model and single cell neurons (SCNs), in this study, we provided a visual evidence for the expression of heparan sulfate (HS) and 3-O-sulfated heparan sulfate (3-OS HS) followed by their interactions with HSV-1 glycoprotein B (gB) and glycoprotein D (gD) during cell entry. Upon heparanase treatment of DRG-derived SCN, a significant inhibition of HSV-1 entry was observed suggesting the involvement of HS role during viral entry...
March 21, 2017: Journal of Neurovirology
https://www.readbyqxmd.com/read/28326094/selection-and-validation-of-reference-genes-for-accurate-rt-qpcr-data-normalization-in-coffea-spp-under-a-climate-changes-context-of-interacting-elevated-co2-and-temperature
#19
Madlles Q Martins, Ana S Fortunato, Weverton P Rodrigues, Fábio L Partelli, Eliemar Campostrini, Fernando C Lidon, Fábio M DaMatta, José C Ramalho, Ana I Ribeiro-Barros
World coffee production has faced increasing challenges associated with ongoing climatic changes. Several studies, which have been almost exclusively based on temperature increase, have predicted extensive reductions (higher than half by 2,050) of actual coffee cropped areas. However, recent studies showed that elevated [CO2] can strongly mitigate the negative impacts of heat stress at the physiological and biochemical levels in coffee leaves. In addition, it has also been shown that coffee genotypes can successfully cope with temperatures above what has been traditionally accepted...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28326074/diversity-and-biomineralization-potential-of-the-epilithic-bacterial-communities-inhabiting-the-oldest-public-stone-monument-of-cluj-napoca-transylvania-romania
#20
Adrian-Ştefan Andrei, Manuela R Păuşan, Tudor Tămaş, Nicolae Har, Lucian Barbu-Tudoran, Nicolae Leopold, Horia L Banciu
In this study, we investigated the biomineralization potential and diversity of the epilithic bacterial communities dwelling on the limestone statue of Saint Donatus, the oldest public monument of Cluj-Napoca city (Transylvania region, NW Romania). Their spatial distribution together with phylogenetic and metabolic diversity, as well as their capacity to precipitate calcium carbonate was evaluated by combining molecular and phenotypic fingerprinting methods with X-ray diffraction, Fourier transform infrared spectroscopy, and scanning electron-microscopy analyses...
2017: Frontiers in Microbiology
keyword
keyword
17809
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"