BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
Gromacs
Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Unread 09-24-2017, 06:16 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,135
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default Renal Cell Carcinoma: A Study through NMR-Based Metabolomics Combined with Transcriptomics.

Renal Cell Carcinoma: A Study through NMR-Based Metabolomics Combined with Transcriptomics.

Related Articles Renal Cell Carcinoma: A Study through NMR-Based Metabolomics Combined with Transcriptomics.

Diseases. 2016 Jan 22;4(1):

Authors: Ragone R, Sallustio F, Piccinonna S, Rutigliano M, Vanessa G, Palazzo S, Lucarelli G, Ditonno P, Battaglia M, Fanizzi FP, Schena FP

Abstract
Renal cell carcinoma (RCC) is a heterogeneous cancer often showing late symptoms. Until now, some candidate protein markers have been proposed for its diagnosis. Metabolomics approaches have been applied, predominantly using Mass Spectrometry (MS), while Nuclear Magnetic Resonance (NMR)-based studies remain limited. There is no study about RCC integrating NMR-based metabolomics with transcriptomics. In this work, ¹H-NMR spectroscopy combined with multivariate statistics was applied on urine samples, collected from 40 patients with clear cell RCC (ccRCC) before nephrectomy and 29 healthy controls; nine out of 40 patients also provided samples one-month after nephrectomy. We observed increases of creatine, alanine, lactate and pyruvate, and decreases of hippurate, citrate, and betaine in all ccRCC patients. A network analysis connected most of these metabolites with glomerular injury, renal inflammation and renal necrosis/cell death. Interestingly, intersecting metabolites with transcriptomic data from CD133+/CD24+ tumoral renal stem cells isolated from ccRCC patients, we found that both genes and metabolites differentially regulated in ccRCC patients belonged to HIF-? signaling, methionine and choline degradation, and acetyl-CoA biosynthesis. Moreover, when comparing urinary metabolome of ccRCC patients after nephrectomy, some processes, such as the glomerular injury, renal hypertrophy, renal necrosis/cell death and renal proliferation, were no more represented.


PMID: 28933387 [PubMed]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] NMR spectroscopy-based metabolomics of Drosophila model of Huntington's disease suggests altered cell energetics.
NMR spectroscopy-based metabolomics of Drosophila model of Huntington's disease suggests altered cell energetics. Related Articles NMR spectroscopy-based metabolomics of Drosophila model of Huntington's disease suggests altered cell energetics. J Proteome Res. 2017 Sep 05;: Authors: Singh V, Sharma RK, Athilingam T, Sinha P, Sinha N, Thakur AK Abstract Huntington's disease (HD) is a neurodegenerative disorder induced by aggregation of the pathological form of Huntingtin protein that has expanded polyglutamine (polyQ) repeats. In...
nmrlearner Journal club 0 09-06-2017 04:13 PM
[NMR paper] Metabolic Effects of a 24-Week Energy-Restricted Intervention Combined with Low or High Dairy Intake in Overweight Women: An NMR-Based Metabolomics Investigation.
Metabolic Effects of a 24-Week Energy-Restricted Intervention Combined with Low or High Dairy Intake in Overweight Women: An NMR-Based Metabolomics Investigation. Related Articles Metabolic Effects of a 24-Week Energy-Restricted Intervention Combined with Low or High Dairy Intake in Overweight Women: An NMR-Based Metabolomics Investigation. Nutrients. 2016;8(3) Authors: Zheng H, Lorenzen JK, Astrup A, Larsen LH, Yde CC, Clausen MR, Bertram HC Abstract We investigated the effect of a 24-week energy-restricted intervention with low...
nmrlearner Journal club 0 02-27-2016 12:52 AM
[NMR paper] (1) H NMR Metabolomics analysis of renal cell carcinoma cells: Effect of VHL inactivation on metabolism.
(1) H NMR Metabolomics analysis of renal cell carcinoma cells: Effect of VHL inactivation on metabolism. (1) H NMR Metabolomics analysis of renal cell carcinoma cells: Effect of VHL inactivation on metabolism. Int J Cancer. 2015 Dec 1; Authors: Cuperlovic-Culf M, Cormier K, Touaibia M, Reyjal J, Robichaud S, Belbraouet M, Turcotte S Abstract Von Hippel-Lindau (VHL) is an onco-suppressor involved in oxygen and energy-dependent promotion of protein ubiquitination and proteosomal degradation. Loss of function mutations of VHL (VHL-...
nmrlearner Journal club 0 12-02-2015 11:37 AM
[NMR paper] NMR ((1)H and (13)C) based Signatures of Abnormal Choline Metabolism in Oral Squamous Cell Carcinoma with no Prominent Warburg Effect.
NMR ((1)H and (13)C) based Signatures of Abnormal Choline Metabolism in Oral Squamous Cell Carcinoma with no Prominent Warburg Effect. NMR ((1)H and (13)C) based Signatures of Abnormal Choline Metabolism in Oral Squamous Cell Carcinoma with no Prominent Warburg Effect. Biochem Biophys Res Commun. 2015 Mar 10; Authors: Bag S, Banerjee DR, Basak A, Das AK, Pal M, Banerjee R, Paul RR, Chatterjee J Abstract At functional levels, besides genes and proteins, changes in metabolome profiles are instructive for a biological system...
nmrlearner Journal club 0 03-15-2015 09:36 PM
[NMR paper] NMR metabolomics of human lung tumours reveals distinct metabolic signatures for adenocarcinoma and squamous cell carcinoma.
NMR metabolomics of human lung tumours reveals distinct metabolic signatures for adenocarcinoma and squamous cell carcinoma. Related Articles NMR metabolomics of human lung tumours reveals distinct metabolic signatures for adenocarcinoma and squamous cell carcinoma. Carcinogenesis. 2014 Nov 3; Authors: Rocha CM, Barros AS, Goodfellow BJ, Carreira IM, Gomes A, Sousa V, Bernardo J, Carvalho L, Gil AM, Duarte IF Abstract Lung tumour subtyping, particularly the distinction between adenocarcinoma (AdC) and squamous cell carcinoma...
nmrlearner Journal club 0 11-05-2014 04:04 PM
[NMR paper] Metabolomics of the rat lens: a combined LC-MS and NMR study.
Metabolomics of the rat lens: a combined LC-MS and NMR study. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Metabolomics of the rat lens: a combined LC-MS and NMR study. Exp Eye Res. 2014 Aug;125:71-8 Authors: Yanshole VV, Snytnikova OA, Kiryutin AS, Yanshole LV, Sagdeev RZ, Tsentalovich YP Abstract This work is the first comprehensive report on the quantitative metabolomic composition of the rat lens. Quantitative metabolomic profiles...
nmrlearner Journal club 0 09-27-2014 05:14 PM
NMR-based metabolomics of mammalian cell and tissue cultures
NMR-based metabolomics of mammalian cell and tissue cultures Abstract NMR spectroscopy was used to evaluate growth media and the cellular metabolome in two systems of interest to biomedical research. The first of these was a Chinese hamster ovary cell line engineered to express a recombinant protein. Here, NMR spectroscopy and a quantum mechanical total line shape analysis were utilized to quantify 30 metabolites such as amino acids, Krebs cycle intermediates, activated sugars, cofactors, and others in both media and cell extracts. The impact of bioreactor scale and addition of...
nmrlearner Journal club 0 03-09-2011 04:19 AM
NMR-based metabolomics of mammalian cell and tissue cultures.
NMR-based metabolomics of mammalian cell and tissue cultures. NMR-based metabolomics of mammalian cell and tissue cultures. J Biomol NMR. 2011 Mar 4; Authors: Aranibar N, Borys M, Mackin NA, Ly V, Abu-Absi N, Abu-Absi S, Niemitz M, Schilling B, Li ZJ, Brock B, Russell RJ, Tymiak A, Reily MD NMR spectroscopy was used to evaluate growth media and the cellular metabolome in two systems of interest to biomedical research. The first of these was a Chinese hamster ovary cell line engineered to express a recombinant protein. Here, NMR spectroscopy and a...
nmrlearner Journal club 0 03-05-2011 01:02 PM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This Thread:

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is On
Trackbacks are Off
Pingbacks are Off
Refbacks are Off



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2024, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 01:25 AM.


Map