75 research outputs found
Labolmage: a workstation environment for research in image processing and analysis
- Publication venue
- Publication date
- 02/08/2017
- Field of study
Numerous images are produced daily in biomedical research. In order to extract relevant and useful results, various processing and analysis steps are mandatory. The present paper describes a new, powerful and user-friendly image analysis system: Labolmage. In addition to standard image processing modules, Labolmage also contains various specialized tools. These multiple processing modules and tools are first introduced. A one-dimensional gel analysis method is then described. The new concept of ‘normalized virtual one-dimensional gel' is introduced, making comparisons between gels particularly easy. This normalized gel is obtained by compensating for the bending of the lanes automatically; no information loss is incurred in the process. Finally, the model of interaction in a multi-window environment is discussed. Labolmage is designed to run in two ways: interactively, using menus and panels; and in batch mode by means of user-defined macros. Examples are given to illustrate the potentialities of the softwar
The SWISS-2DPAGE database: what has changed during the last year
- Author
- Publication venue
- Publication date
- 02/08/2017
- Field of study
Swiss-2DPAGE (http://www.expasy.ch/ch2d/) is an annotated two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) database established in 1993. The current release contains 21 reference maps from human and mouse biological samples, as well as from Saccharomyces cerevisiae, Escherichia coli and Dictyostelium discoideum origin. These reference maps now have 2480 identified spots, corresponding to 528 separate protein entries in the database, in addition to virtual entries for each SWISS-PROT sequence. During the last year, the SWISS-2DPAGE has undergone major changes. Six new maps have been added, and new functions to access the data have been provided through the ExPASy server. Finally, an important change concerns the database funding sourc
Ubiquitin Fusion Degradation Protein 1 as a Blood Marker for The Early Diagnosis of Ischemic Stroke
- Author
- Publication venue
- Libertas Academica
- Publication date
- 01/01/2007
- Field of study
Background: Efficacy of thrombolysis in acute ischemic stroke is strongly related to physician’s ability to make an accurate diagnosis and to intervene within 3–6 h after event onset. In this context, the discovery and validation of very early blood markers have recently become an urgent, yet unmet, goal of stroke research. Ubiquitin fusion degradation protein 1 is increased in human postmortem CSF, a model of global brain insult, suggesting that its measurement in blood may prove useful as a biomarker of stroke.Methods: Enzyme-linked immunosorbent assay (ELISA) was used to measure UFD1 in plasma and sera in three independent cohorts, European (Swiss and Spanish) and North-American retrospective analysis encompassing a total of 123 consecutive stroke and 90 control subjects.Results: Highly significant increase of ubiquitin fusion degradation protein 1 (UFD1) was found in Swiss stroke patients with 71% sensitivity (95% CI, 52–85.8%), and 90% specificity (95% CI, 74.2–98%) (N = 31, p < 0.0001). Significantly elevated concentration of this marker was then validated in Spanish (N = 39, p < 0.0001, 95% sensitivity (95% CI, 82.7–99.4%)), 76% specificity (95% CI, 56.5–89.7%)) and North-American stroke patients (N = 53, 62% sensitivity (95% CI, 47.9–75.2%), 90% specificity (95% CI, 73.5–97.9%), p < 0.0001). Its concentration was increased within 3 h of stroke onset, on both the Swiss (p < 0.0001) and Spanish (p = 0.0004) cohorts.Conclusions: UFD1 emerges as a reliable plasma biomarker for the early diagnosis of stroke, and in the future, might be used in conjunction with clinical assessments, neuroimaging and other blood markers.Abbreviations: AUC: area under curve; BBB: blood–brain barrier; CO: cut-off; CSF: cerebrospinal fluid; CT: computerized tomography; H-FABP: heart-fatty acid binding protein; MMP9: matrix metalloproteinase 9; MRI: magnetic resonance imaging; NDKA: nucleotide diphosphate kinase A; OR: odds ratio; RFU: relative fluorescence units; ROC: receiver operating characteristic; rtPA: recombinant tissue plasminogen activator; SE: sensitivity; SP: specificity; TIA: transient ischemic attack; UFD1: ubiquitin fusion degradation protein
Exploring glycopeptide-resistance in Staphylococcus aureus: a combined proteomics and transcriptomics approach for the identification of resistance-related markers
- Author
- Bento Manuela
- Binz Pierre-Alain
- Charbonnier Yvan
- Deshusses Jacques M
- Fischer Adrien
- François Patrice
- Gallé Francesca
- Hochstrasser Denis F
- Huyghe Antoine
- Koessler Thibaud
- Lew Daniel
- Masselot Alexandre
- Renzoni Adriana
- Sanchez Jean-Charles
- Scherl Alexander
- Schrenzel Jacques
- Stahl-Zeng Jianru
- Vaezzadeh Alireza
- Vaudaux Pierre
- Zimmermann-Ivol Catherine G
- Publication venue
- BioMed Central
- Publication date
- 01/01/2006
- Field of study
BACKGROUND: To unravel molecular targets involved in glycopeptide resistance, three isogenic strains of Staphylococcus aureus with different susceptibility levels to vancomycin or teicoplanin were subjected to whole-genome microarray-based transcription and quantitative proteomic profiling. Quantitative proteomics performed on membrane extracts showed exquisite inter-experimental reproducibility permitting the identification and relative quantification of >30% of the predicted S. aureus proteome. RESULTS: In the absence of antibiotic selection pressure, comparison of stable resistant and susceptible strains revealed 94 differentially expressed genes and 178 proteins. As expected, only partial correlation was obtained between transcriptomic and proteomic results during stationary-phase. Application of massively parallel methods identified one third of the complete proteome, a majority of which was only predicted based on genome sequencing, but never identified to date. Several over-expressed genes represent previously reported targets, while series of genes and proteins possibly involved in the glycopeptide resistance mechanism were discovered here, including regulators, global regulator attenuator, hyper-mutability factor or hypothetical proteins. Gene expression of these markers was confirmed in a collection of genetically unrelated strains showing altered susceptibility to glycopeptides. CONCLUSION: Our proteome and transcriptome analyses have been performed during stationary-phase of growth on isogenic strains showing susceptibility or intermediate level of resistance against glycopeptides. Altered susceptibility had emerged spontaneously after infection with a sensitive parental strain, thus not selected in vitro. This combined analysis allows the identification of hundreds of proteins considered, so far as hypothetical protein. In addition, this study provides not only a global picture of transcription and expression adaptations during a complex antibiotic resistance mechanism but also unravels potential drug targets or markers that are constitutively expressed by resistant strains regardless of their genetic background, amenable to be used as diagnostic targets
Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)
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- Abdel-Aziz A. K.
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- Zhang Z.
- Zhang Z.
- Zhang Z.
- Zhang Z.
- Zhang Z.
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- Zorzano A.
- Zou W.
- Zou Z.
- Zou Z.
- Zuryn S.
- Zwerschke W.
- Publication venue
- 'Informa UK Limited'
- Publication date
- 01/01/2021
- Field of study
Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.
- Author
- Abdel-Aziz AK
- Abdelfatah S
- Abdellatif M
- Abdoli A
- Abel S
- Abeliovich H
- Abildgaard MH
- Abudu YP
- Acevedo-Arozena A
- Adamopoulos IE
- Adeli K
- Adolph TE
- Adornetto A
- Aflaki E
- Agam G
- Agarwal A
- Aggarwal BB
- Agnello M
- Agostinis P
- Agrewala JN
- Agrotis A
- Aguilar PV
- Ahmad ST
- Ahmed ZM
- Ahumada-Castro U
- Aits S
- Aizawa S
- Akkoc Y
- Akoumianaki T
- Akpinar HA
- Al-Abd AM
- Al-Akra L
- Al-Gharaibeh A
- Alaoui-Jamali MA
- Alberti S
- Alcocer-Gómez E
- Alessandri C
- Ali M
- Alim Al-Bari MA
- Aliwaini S
- Alizadeh J
- Almacellas E
- Almasan A
- Alonso A
- Alonso GD
- Altan-Bonnet N
- Altieri DC
- Alves da Costa C
- Alves S
- Alzaharna MM
- Amadio M
- Amantini C
- Amaral C
- Ambrosio S
- Amer AO
- Ammanathan V
- An Z
- Andersen SU
- Andrabi SA
- Andrade-Silva M
- Andres AM
- Angelini S
- Ann D
- Anozie UC
- Ansari MY
- Antas P
- Antebi A
- Antón Z
- Anwar T
- Apetoh L
- Apostolova N
- Araki T
- Araki Y
- Arasaki K
- Araya J
- Araújo WL
- Arden C
- Arguelles S
- Arias E
- Arikkath J
- Arimoto H
- Ariosa AR
- Armstrong-James D
- Arnauné-Pelloquin L
- Aroca A
- Arroyo DS
- Arsov I
- Artero R
- Arévalo M-A
- Asaro DML
- Aschner M
- Ashrafizadeh M
- Ashur-Fabian O
- Atanasov AG
- Au AK
- Auberger P
- Auner HW
- Aurelian L
- Autelli R
- Avagliano L
- Aveic S
- Aveleira CA
- Avin-Wittenberg T
- Aydin Y
- Ayton S
- Ayyadevara S
- Azzopardi M
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- Backer JM
- Backues SK
- Bae D-H
- Bae O-N
- Bae SH
- Baehrecke EH
- Baek A
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- Baek SH
- Bagetta G
- Bagniewska-Zadworna A
- Bai H
- Bai J
- Bai X
- Bai Y
- Bairagi N
- Baksi S
- Balazadeh S
- Balbi T
- Baldari CT
- Balduini W
- Ballabio A
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- Baptista MS
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- Barmada SJ
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- Bassham DC
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- Bhaskar K
- Bhatia-Kissova I
- Bhattacharya R
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- Bultynck G
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- Burón MI
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- Camara NO
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- Chang H-C
- Chang K
- Chao J
- Chapman T
- Charlet-Berguerand N
- Chatterjee S
- Chaube SK
- Chaudhary A
- Chauhan S
- Chaum E
- Checler F
- Cheetham ME
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- Chen Q
- Chen R-H
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- Chen W
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- Chen X
- Chen X-M
- Chen X-W
- Chen Y
- Chen Y
- Chen Y
- Chen Y-G
- Chen Y-J
- Chen Y-Q
- Chen Z
- Chen Z
- Chen Z
- Chen Z-H
- Chen ZJ
- Chen ZS
- Cheng H
- Cheng J
- Cheng S-Y
- Cheng W
- Cheng X
- Cheng X-T
- Cheng Y
- Cheng Z
- Cheong H
- Cheong JK
- Chernyak BV
- Cherry S
- Cheung CFR
- Cheung CHA
- Cheung K-H
- Chevet E
- Chi RJ
- Chiang AKS
- Chiaradonna F
- Chiarelli R
- Chiariello M
- Chica N
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- Chiong M
- Chiou S-H
- Chiramel AI
- Chiurchiù V
- Cho D-H
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- Choudhury KR
- Chow NS
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- Cianfanelli V
- Ciechomska IA
- Cifuentes M
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- Cirone M
- Clague MJ
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- Clementi E
- Coccia EM
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- Cohen MM
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- Colasuonno F
- Colbert RA
- Colell A
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- Collins MO
- Colombo MI
- Colón-Ramos DA
- Combaret L
- Comincini S
- Cominetti MR
- Consiglio A
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- Coombs KM
- Coppens I
- Corasaniti MT
- Cordes N
- Corkery DP
- Cortese K
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- Costantino S
- Costelli P
- Coto-Montes A
- Crack PJ
- Crespo JL
- Criollo A
- Crippa V
- Cristofani R
- Csizmadia T
- Cuadrado A
- Cui B
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- Cybulsky AV
- Czaja MJ
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- Dal Col J
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- Dando I
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- Darling AL
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- de Mattos Barbosa MG
- De Meyer GRY
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- DeBosch BJ
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- Delpino MV
- Demarchi F
- Dembitz V
- Demers ND
- Deng H
- Deng Z
- Dengjel J
- Dent P
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- Der CJ
- Deretic V
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- Devis L
- Devkota S
- Devuyst O
- Dewson G
- Dharmasivam M
- Dhiman R
- di Bernardo D
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- Diallinas G
- Diao J
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- Dickinson JM
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- Dieudé M
- Dikic I
- Ding S
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- Dini L
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- Dinkova-Kostova AT
- Dionne MS
- Distler JHW
- Diwan A
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- Djavaheri-Mergny M
- Dobrinski I
- Dobrovinskaya O
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- Dobson RCJ
- Dokmeci Emre S
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- Drucker L
- du Toit A
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- Dubrovska A
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- Dwarakanath BS
- Dyshlovoy SA
- Dávila VA
- Díaz-Laviada I
- Ebrahimi-Fakhari D
- Eckhart L
- Edelstein CL
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- Eftekharpour E
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- Eid N
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- Emerling BM
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- Ávalos Y
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- Čolić M
- Đokić J
- Žerovnik E
- Publication venue
- 'Informa UK Limited'
- Publication date
- 01/01/2021
- Field of study
In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field
Analysis of plasma/serum immunoglobulins by two-dimensional polyacrylamide gel electrophoresis
- Publication venue
- 'Elsevier BV'
- Publication date
- 01/08/1993
- Field of study
Enhanced protein recovery after electrotransfer using square wave alternating voltage
- Publication venue
- 'Elsevier BV'
- Publication date
- 01/01/2002
- Field of study
Protein identification is becoming a complement to the available fully sequenced genomes. To meet the challenge, newly developed techniques for high throughput protein identification using matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-MS) and peptide mass fingerprint are needed. Two years ago, a parallel protein digestion process was proposed. It provided a collecting polyvinylidene difluoride (PVDF) membrane able to be scanned by MALDI. Acquired data were used to recreate a virtual multidimensional image. Voltage used during this protein electroblotting technique was an unusual square wave alternative voltage (SWAV). The goal of the current study is to evaluate quantitatively the efficiency of the SWAV compared with a classical electroblot process on intact proteins. The effect of the pulsed electric field and the buffer composition were compared to a standard continuous transblotting process defined as the gold standard. Combination of the pulsed asymmetric electric field with 3-(cyclohexylamino)-1-propane-sulfonique acid (CAPS) buffers showed an average 65% increase of protein recovery. Moreover, a strongest effect is observed for high M(r) proteins. In conclusion, the present study highlighted a positive influence of the "shaking" effect of the asymmetric alternative voltage on gel protein extraction
Labolmage: a workstation environment for research in image processing and analysis
- Publication venue
- 'Oxford University Press (OUP)'
- Publication date
- 01/01/1991
- Field of study
- …