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https://www.readbyqxmd.com/read/28231577/response-evaluation-in-head-and-neck-oncology-definition-and-prediction
#1
T K Hoffmann, P J Schuler, S Laban, R Grässlin, M Beer, A J Beer, U Friebe-Hoffmann, L Bullinger, P Möller, T Wiegel
Curative treatment of head and neck squamous cell carcinoma includes surgery and/or (chemo)radiation, whereas in the palliative setting, chemotherapy and/or immunotherapy represent(s) the standard approach. With regard to quality control, methods for determining treatment response are sorely needed. For surgical therapy, histopathology is the standard quality control. Established criteria for high-risk patients include resection margins of the primary tumor and extracapsular extension of lymph node metastases...
February 24, 2017: ORL; Journal for Oto-rhino-laryngology and its related Specialties
https://www.readbyqxmd.com/read/28230703/omics-and-cachexia
#2
Brigitte Twelkmeyer, Nicolas Tardif, Olav Rooyackers
PURPOSE OF REVIEW: The purpose of this review is to recapture recent advances in cachexia-related diseases, mainly cancer cachexia, and treatment using genomic, transcriptomics, proteomic, and metabolomics-related techniques. RECENT FINDINGS: From recent studies in the cancer cachexia field it is clear that the tumor has a direct effect on distant organs via its secretome. The affected pathways on the other hand were largely known from earlier studies with changes in energy-related pathways (mainly lipid metabolism) and the protein degradation pathways...
February 21, 2017: Current Opinion in Clinical Nutrition and Metabolic Care
https://www.readbyqxmd.com/read/28230319/depletion-of-abundant-human-serum-proteins-by-per-se-imprinted-cryogels-based-on-sample-heterogeneity
#3
Chun Yang, Ya-Ru Liu, Yan Zhang, Jian Wang, Li-Li Tian, Ya-Nan Yan, Wei-Qin Cao, Yu-Yang Wang
Macroporous cryogels were prepared and used to deplete abundant proteins. It was accomplished based on the sample heterogeneity rather than any exogenous assistance. Human serum was added in monomer solutions to synthesize molecularly imprinted polymers (MIPs); therein some abundant proteins were imprinted in the polyacrylamide cryogels. Meanwhile the rare components remained aqueous. Chromatography and electrophoresis showed that albumin, serotransferrin and most globulins were depleted by columns packed with the MIPs...
February 23, 2017: Proteomics
https://www.readbyqxmd.com/read/28229048/anaplasma-phagocytophilum-infection-subverts-carbohydrate-metabolic-pathways-in-the-tick-vector-ixodes-scapularis
#4
Alejandro Cabezas-Cruz, Pilar Alberdi, James J Valdés, Margarita Villar, José de la Fuente
The obligate intracellular pathogen, Anaplasma phagocytophilum, is the causative agent of human, equine, and canine granulocytic anaplasmosis and tick-borne fever (TBF) in ruminants. A. phagocytophilum has become an emerging tick-borne pathogen in the United States, Europe, Africa, and Asia, with increasing numbers of infected people and animals every year. It has been recognized that intracellular pathogens manipulate host cell metabolic pathways to increase infection and transmission in both vertebrate and invertebrate hosts...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28227691/understanding-the-cochlear-implant-environment-by-mapping-perilymph-proteomes-from-different-species
#5
Jonathan C Palmer, Megan S Lord, Jeremy L Pinyon, Andrew K Wise, Nigel H Lovell, Paul M Carter, Ya Lang Enke, Gary D Housley, Rylie A Green, Jonathan C Palmer, Megan S Lord, Jeremy L Pinyon, Andrew K Wise, Nigel H Lovell, Paul M Carter, Ya Lang Enke, Gary D Housley, Rylie A Green, Ya Lang Enke, Rylie A Green, Jonathan C Palmer, Nigel H Lovell, Paul M Carter, Jeremy L Pinyon, Gary D Housley, Andrew K Wise, Megan S Lord
Cochlear implants operate within a bony channel of the cochlea, bathed in a fluid known as the perilymph. The perilymph is a complex fluid containing ions and proteins, which are known to actively interact with metallic electrodes. To improve our understanding of how cochlear implant performance varies in preclinical in vivo studies in comparison to human trials and patient outcomes, the protein composition (or perilymph proteome) is needed. Samples of perilymph were gathered from feline and guinea pig subjects and analyzed using liquid chromatography with tandem mass spectrometry (LC-MS/MS) to produce proteomes and compare against the recently published human proteome...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227017/reconfigurable-hardware-software-codesign-methodology-for-protein-identification
#6
Venkateshwarlu Y Gudur, Sandeep Thallada, Abhinay R Deevi, Venkata Krishna Gande, Amit Acharyya, Vasundhra Bhandari, Paresh Sharma, Saqib Khursheed, Ganesh R Naik, Venkateshwarlu Y Gudur, Sandeep Thallada, Abhinay R Deevi, Venkata Krishna Gande, Amit Acharyya, Vasundhra Bhandari, Paresh Sharma, Saqib Khursheed, Ganesh R Naik, Saqib Khursheed, Paresh Sharma, Vasundhra Bhandari, Venkata Krishna Gande, Venkateshwarlu Y Gudur, Abhinay R Deevi, Amit Acharyya, Sandeep Thallada, Ganesh R Naik
In this paper we propose an on-the-fly reconfigurable hardware-software codesign based reconfigurable solution for real-time protein identification. Reconfigurable string matching is performed in the disciplines of protein identification and biomarkers discovery. With the generation of plethora of sequenced data and number of biomarkers for several diseases, it is becoming necessary to have an accelerated processing and on-the-fly reconfigurable system design methodology to bring flexibility to its usage in the medical science community without the need of changing the entire hardware every time with the advent of new biomarker or protein...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28225606/effect-of-astringent-stimuli-on-salivary-protein-interactions-elucidated-by-complementary-proteomics-approaches
#7
Judith Delius, Guillaume Médard, Bernhard Kuster, Thomas Hofmann
The interaction of astringent substances with salivary proteins, which results in protein precipitation, is considered a key event in the molecular mechanism underlying the oral sensation of puckering astringency. As the chemical nature of orally active astringents is diverse and the knowledge on their interactions with salivary proteins rather fragmentary, human whole saliva samples were incubated with supra-threshold and iso-intensity solutions of the astringent polyphenol (-)-epigallocatechin gallate, the multivalent metal salt iron(III) sulfate, the amino-functionalized polysaccharide chitosan, and the basic protein lysozyme...
February 22, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28224116/persistence-of-functional-protein-domains-in-mycoplasma-species-and-their-role-in-host-specificity-and-synthetic-minimal-life
#8
Tjerko Kamminga, Jasper J Koehorst, Paul Vermeij, Simen-Jan Slagman, Vitor A P Martins Dos Santos, Jetta J E Bijlsma, Peter J Schaap
Mycoplasmas are the smallest self-replicating organisms and obligate parasites of a specific vertebrate host. An in-depth analysis of the functional capabilities of mycoplasma species is fundamental to understand how some of simplest forms of life on Earth succeeded in subverting complex hosts with highly sophisticated immune systems. In this study we present a genome-scale comparison, focused on identification of functional protein domains, of 80 publically available mycoplasma genomes which were consistently re-annotated using a standardized annotation pipeline embedded in a semantic framework to keep track of the data provenance...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28224023/evaluation-of-liver-cirrhosis-and-hepatocellular-carcinoma-using-protein-protein-interaction-networks
#9
Mohammad Javad Ehsani Ardakani, Akram Safaei, Afsaneh Arefi Oskouie, Hesam Haghparast, Mehrdad Haghazali, Hamid Mohaghegh Shalmani, Hassan Peyvandi, Nosratollah Naderi, Mohammad Reza Zali
AIM: In the current study, we analysised only the articles that investigate serum proteome profile of cirrhosis patients or HCC patients versus healthy controls. BACKGROUND: Increased understanding of cancer biology has enabled identification of molecular events that lead to the discovery of numerous potential biomarkers in diseases. Protein-protein interaction networks is one of aspect that could elevate the understanding level of molecular events and protein connections that lead to the identification of genes and proteins associated with diseases...
December 2016: Gastroenterology and Hepatology From Bed to Bench
https://www.readbyqxmd.com/read/28223859/histatin-peptides-pharmacological-functions-and-their-applications-in-dentistry
#10
REVIEW
Zohaib Khurshid, Shariq Najeeb, Maria Mali, Syed Faraz Moin, Syed Qasim Raza, Sana Zohaib, Farshid Sefat, Muhammad Sohail Zafar
There are many human oral antimicrobial peptides responsible for playing important roles including maintenance, repairing of oral tissues (hard or soft) and defense against oral microbes. In this review we have highlighted the biochemistry, physiology and proteomics of human oral histatin peptides, secreted from parotid and submandibular salivary glands in human. The significance of these peptides includes capability for ionic binding that can kill fungal Candida albicans. They have histidine rich amino acid sequences (7-12 family members; corresponding to residues 12-24, 13-24, 12-25, 13-25, 5-11, and 5-12, respectively) for Histatin-3...
January 2017: Saudi Pharmaceutical Journal: SPJ: the Official Publication of the Saudi Pharmaceutical Society
https://www.readbyqxmd.com/read/28223351/in-vivo-and-in-vitro-proteome-analysis-of-hiv-1-infected-human-cd4-t-cells
#11
Johannes Nemeth, Valentina Vongrad, Karin J Metzner, Victoria Strouvelle, Rainer Weber, Patrick Pedrioli, Ruedi Aebersold, Huldrych Guenthard, Ben C Collins
Host directed therapies against HIV-1 are thought to be critical for long term containment of the HIV-1 pandemic but remain elusive. Since HIV-1 infects and manipulates important effectors of both the innate and adaptive immune system, identifying modulations of the host cell systems in humans during HIV-1 infection may be crucial for the development of immune based therapies. Here, we quantified the changes of the proteome in human CD4+ T cells upon HIV-1 infection, both in vitro and in vivo. A SWATH-MS approach was used to measure the proteome of human primary CD4+ T cells infected with HIV-1 in vitro as well as CD4+ T cells from HIV-1 infected patients with paired samples on and off antiretroviral treatment...
February 21, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28223350/mapping-atheroprotective-functions-and-related-proteins-lipoproteins-in-size-fractionated-human-plasma
#12
Debi K Swertfeger, Hailong Li, Sandra Rebholz, Xiaoting Zhu, Amy S Shah, W Sean Davidson, L Jason Lu
HDL has been shown to possess a variety of cardio-protective functions, including removal of excess cholesterol from the periphery, and inhibition of lipoprotein oxidation. It has been proposed that various HDL subparticles exist, each with distinct protein and lipid compositions, which may be responsible for HDL's many functions. We hypothesized that HDL functions will co-migrate with the operational lipoprotein subspecies when separated by gel filtration chromatography. Plasma from 10 healthy male donors was fractionated and the protein composition of the phospholipid containing fractions was analyzed by mass spectrometry (MS)...
February 21, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28223226/targeted-protein-degradation-by-protacs
#13
REVIEW
Taavi K Neklesa, James D Winkler, Craig M Crews
Targeted protein degradation using the PROTAC technology is emerging as a novel therapeutic method to address diseases driven by the aberrant expression of a disease-causing protein. PROTAC molecules are bifunctional small molecules that simultaneously bind a target protein and an E3-ubiquitin ligase, thus causing ubiquitination and degradation of the target protein by the proteasome. Like small molecules, PROTAC molecules possess good tissue distribution and the ability to target intracellular proteins. Herein, we highlight the advantages of protein degradation using PROTACs, and provide specific examples where degradation offers therapeutic benefit over classical enzyme inhibition...
February 13, 2017: Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/28223137/human-clec16a-regulates-autophagy-through-modulating-mtor-activity
#14
Rachel Chun Yee Tam, Michelle Wing Man Li, Yan Pan Gao, Yuen Ting Pang, Sheng Yan, Wei Ge, Chak Sing Lau, Vera Sau Fong Chan
CLEC16A is genetically linked with multiple autoimmune disorders but its functional relevance in autoimmunity remains obscure. Recent evidence has signposted the emerging role of autophagy in autoimmune disease development. Here, by ectopic expression and siRNA silencing, we show that CLEC16A has an inhibitory role in starvation-induced autophagy in human cells. Combining quantitative proteomics and immunoblotting analyses, we found that CLEC16A likely regulates autophagy by activating mTOR pathway. Overexpression of CLEC16A was found to sensitize cells towards the availability of nutrients, resulting in a heightened mTOR activity, which in turn diminished LC3 autophagic activity following nutrient deprivation...
February 18, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/28222503/selenium-levels-in-serum-red-blood-cells-and-cerebrospinal-fluid-of-alzheimer-s-disease-patients-a-report-from-the-australian-imaging-biomarker-lifestyle-flagship-study-of-ageing-aibl
#15
Bárbara R Cardoso, Dominic J Hare, Ashley I Bush, Qiao-Xin Li, Christopher J Fowler, Colin L Masters, Ralph N Martins, Katherine Ganio, Amber Lothian, Soumya Mukherjee, Eugene A Kapp, Blaine R Roberts
Selenium (Se) protects cells against oxidative stress damage through a range of bioactive selenoproteins. Increased oxidative stress is a prominent feature of Alzheimer's disease (AD), and previous studies have shown that Se deficiency is associated with age-related cognitive decline. In this study, we assessed Se status in different biofluids from a subgroup of participants in the Australian Imaging, Biomarkers and Lifestyle Flagship Study of Ageing. As Se in humans can either be an active component of selenoproteins or inactive via non-specific incorporation into other proteins, we used both size exclusion chromatography-inductively coupled plasma-mass spectrometry (SEC-ICP-MS) and tandem mass spectrometry to characterize selenoproteins in serum...
February 10, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28221766/proteoform-profile-mapping-of-the-human-serum-complement-component-c9-reveals-unexpected-new-features-of-n-o-and-c-glycosylation
#16
Vojtech Franc, Yang Yang, Albert J R Heck
The human complement C9 protein (~65 kDa) is a member of the complement pathway. It plays an essential role in the membrane attack complex (MAC), which forms a lethal pore on the cellular surface of pathogenic bacteria. Here, we charted in detail the structural micro-heterogeneity of C9 purified from human blood serum, using an integrative workflow combining high-resolution native mass spectrometry and (glyco)peptide-centric proteomics. The proteoform profile of C9 was acquired by high-resolution native mass spectrometry, which revealed the co-occurrence of ~50 distinct MS signals...
February 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28221718/quantitative-analysis-of-shigella-flexneri-protein-expression-under-acid-stress
#17
Kaiwen Yu, Zhen Wang, Fan Zhou, Jiezhang Jiang, Yanhua Liu, Mo Hu, Xiaoyun Liu
As an important foodborne pathogen, Shigella flexneri can cause widespread enteric infection with bacteria as few as hundreds. This is, at least in part, attributed to its robust anti-acid strategies because passage through the highly acidic human digestive tract is a prerequisite for successful bacterial infection. Nevertheless, our understanding of these mechanisms and the impact of acid stress on Shigella protein expression still remains largely incomplete. Herein we conducted a proteomic survey of Shigella spp...
February 21, 2017: Proteomics
https://www.readbyqxmd.com/read/28221344/chemoproteomic-profiling-and-discovery-of-protein-electrophiles-in-human-cells
#18
Megan L Matthews, Lin He, Benjamin D Horning, Erika J Olson, Bruno E Correia, John R Yates, Philip E Dawson, Benjamin F Cravatt
Activity-based protein profiling (ABPP) serves as a chemical proteomic platform to discover and characterize functional amino acids in proteins on the basis of their enhanced reactivity towards small-molecule probes. This approach, to date, has mainly targeted nucleophilic functional groups, such as the side chains of serine and cysteine, using electrophilic probes. Here we show that 'reverse-polarity' (RP)-ABPP using clickable, nucleophilic hydrazine probes can capture and identify protein-bound electrophiles in cells...
March 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28221173/new-developments-in-transplant-proteomics
#19
Julie Ho, Patricia Hirt-Minkowski, John A Wilkins
PURPOSE OF REVIEW: Despite modern immunosuppression, renal allograft rejection remains a major contributor to graft loss. Novel biomarkers may help improve posttransplant outcomes through the early detection and treatment of rejection. Our objective is to provide an overview of proteomics, review recent discovery-based rejection studies, and explore innovative approaches in biomarker development. RECENT FINDINGS: Urine MMP7 was identified as a biomarker of subclinical and clinical rejection using two-dimensional liquid chromatography tandem-mass spectrometry (LC-MS/MS) and improved the overall diagnostic discrimination of urine CXCL10 : Cr alone for renal allograft inflammation...
February 17, 2017: Current Opinion in Nephrology and Hypertension
https://www.readbyqxmd.com/read/28218651/proteome-characteristics-of-non-alcoholic-steatohepatitis-liver-tissue-and-associated-hepatocellular-carcinomas
#20
Anna Kakehashi, Vasily E Stefanov, Naomi Ishii, Takahiro Okuno, Hideki Fujii, Kazuaki Kawai, Norifumi Kawada, Hideki Wanibuchi
To uncover mechanisms of nonalcoholic steatohepatitis (NASH) associated hepatocarcinogenesis, we compared the proteomes of human NASH-associated liver biopsies, resected hepatocellular carcinomas (HCCs) and HCCs of HCV⁺ patients with normal liver tissue of patients with gastrointestinal tumor metastasis, in formalin-fixed paraffin-embedded samples obtained after surgery in our hospital during the period from 2006 to 2011. In addition, proteome analysis of liver tumors in male STAM NASH-model mice was performed...
February 17, 2017: International Journal of Molecular Sciences
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