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Jesper Eisfeldt, Daniel Nilsson, Johanna C Andersson-Assarsson, Anna Lindstrand
Copy number variations (CNVs) within the human genome have been linked to a diversity of inherited diseases and phenotypic traits. The currently used methodology to measure copy numbers has limited resolution and/or precision, especially for regions with more than 4 copies. Whole genome sequencing (WGS) offers an alternative data source to allow for the detection and characterization of the copy number across different genomic regions in a single experiment. A plethora of tools have been developed to utilize WGS data for CNV detection...
2018: PloS One
Elin Byman, Nina Schultz, Malin Fex, Malin Wennström
Reduced glucose metabolism and formation of polyglucosan bodies (PGB) are, beside amyloid beta plaques and neurofibrillary tangles, well-known pathological findings associated with Alzheimer's disease (AD). Since both glucose availability and PGB are regulated by enzymatic degradation of glycogen, we hypothesize that dysfunctional glycogen degradation is a critical event in AD progression. We therefore investigated whether alpha (α)-amylase, an enzyme known to efficiently degrade polysaccharides in the gastrointestinal tract, is expressed in the hippocampal CA1/subiculum and if the expression is altered in AD patients...
February 27, 2018: Brain Pathology
Katarina Davalieva, Sanja Kiprijanovska, Ivana Maleva Kostovska, Sotir Stavridis, Oliver Stankov, Selim Komina, Gordana Petrusevska, Momir Polenakovic
Detecting prostate cancer (PCa) using non-invasive diagnostic markers still remains a challenge. The aim of this study was the identification of urine proteins that are sufficiently sensitive and specific to detect PCa in the early stages. Comparative proteomics profiling of urine from patients with PCa, benign prostate hyperplasia, bladder cancer, and renal cancer, coupled with bioinformatics analysis, were performed. Statistically significant difference in abundance showed 20 and 85 proteins in the 2-D DIGE/MS and label-free LC-MS/MS experiments, respectively...
December 29, 2017: Proteomes
Yingliang Li, Guohua Rong, Hua Kang
Breast cancer is the most common malignant tumor in women worldwide, and accounts for an estimated 29% of new cases and 15% of cancer-associated mortalities each year. Invasive ductal carcinoma represents 70-80% of all breast cancer cases, which are responsible for the majority of breast cancer fatalities. Though great progress has been made in understanding the tumorigenesis and development of breast cancer, problems surrounding treatment persist. It was previously reported that carcinoma-associated fibroblasts (CAFs) may be closely associated with chemotherapy resistance...
March 2017: Oncology Letters
Amélie Bonnefond, Loïc Yengo, Aurélie Dechaume, Mickaël Canouil, Maxime Castelain, Estelle Roger, Frédéric Allegaert, Robert Caiazzo, Violeta Raverdy, Marie Pigeyre, Abdelilah Arredouani, Jean-Michel Borys, Claire Lévy-Marchal, Jacques Weill, Ronan Roussel, Beverley Balkau, Michel Marre, François Pattou, Thierry Brousseau, Philippe Froguel
BACKGROUND: Salivary (AMY1) and pancreatic (AMY2) amylases hydrolyze starch. Copy number of AMY1A (encoding AMY1) was reported to be higher in populations with a high-starch diet and reduced in obese people. These results based on quantitative PCR have been challenged recently. We aimed to re-assess the relationship between amylase and adiposity using a systems biology approach. METHODS: We assessed the association between plasma enzymatic activity of AMY1 or AMY2, and several metabolic traits in almost 4000 French individuals from D...
February 23, 2017: BMC Medicine
Padma Pradeepa Srinivasan, Vaishali N Patel, Shuang Liu, Daniel A Harrington, Matthew P Hoffman, Xinqiao Jia, Robert L Witt, Mary C Farach-Carson, Swati Pradhan-Bhatt
Radiotherapy for head and neck cancer often has undesirable effects on salivary glands that lead to xerostomia or severe dry mouth, which can increase oral infections. Our goal is to engineer functional, three-dimensional (3D) salivary gland neotissue for autologous implantation to provide permanent relief. An immediate need exists to obtain autologous adult progenitor cells as the use of embryonic and induced pluripotent stem cells potentially pose serious risks such as teratogenicity and immunogenic rejection...
January 2017: Stem Cells Translational Medicine
Padma Pradeepa Srinivasan, Vaishali N Patel, Shuang Liu, Daniel A Harrington, Matthew P Hoffman, Xinqiao Jia, Robert L Witt, Mary C Farach-Carson, Swati Pradhan-Bhatt
: Radiotherapy for head and neck cancer often has undesirable effects on salivary glands that lead to xerostomia or severe dry mouth, which can increase oral infections. Our goal is to engineer functional, three-dimensional (3D) salivary gland neotissue for autologous implantation to provide permanent relief. An immediate need exists to obtain autologous adult progenitor cells as the use of embryonic and induced pluripotent stem cells potentially pose serious risks such as teratogenicity and immunogenic rejection...
August 18, 2016: Stem Cells Translational Medicine
María A Mejía-Benítez, Amélie Bonnefond, Loïc Yengo, Marlène Huyvaert, Aurélie Dechaume, Jesús Peralta-Romero, Miguel Klünder-Klünder, Jaime García Mena, Julia S El-Sayed Moustafa, Mario Falchi, Miguel Cruz, Philippe Froguel
AIMS/HYPOTHESIS: Childhood obesity is a major public health problem in Mexico, affecting one in every three children. Genome-wide association studies identified genetic variants associated with childhood obesity, but a large missing heritability remains to be elucidated. We have recently shown a strong association between a highly polymorphic copy number variant encompassing the salivary amylase gene (AMY1 also known as AMY1A) and obesity in European and Asian adults. In the present study, we aimed to evaluate the association between AMY1 copy number and obesity in Mexican children...
February 2015: Diabetologia
Sarika Jain, Somak Roy, Milon Amin, Marie Acquafondata, Ming Yin, William Laframboise, Sheldon Bastacky, Liron Pantanowitz, Rajiv Dhir, Anil Parwani
Chromophobe renal cell carcinoma (ChRCC) and oncocytoma present with a perplexing overlap of morphologic and immunohistochemical features. ChRCC have deletions in the 1p21.1 region including the amylase α-1A gene (AMY1A). No such deletions are found in oncocytoma. Instead, oncocytomas shared other deletions on chromosome 1: 1p31.3, 1q25.2, and 1q44. We performed AMY1A immunostaining on 75 oncocytomas (57 tissue microarray [TMA] cores, 18 whole slides) and 54 ChRCCs (20 TMA cores, 34 whole slides). Staining was assessed using the H-score method...
December 2013: American Journal of Surgical Pathology
Makoto Hakata, Masaharu Kuroda, Tomomi Miyashita, Takeshi Yamaguchi, Mikiko Kojima, Hitoshi Sakakibara, Toshiaki Mitsui, Hiromoto Yamakawa
High temperature impairs rice (Oryza sativa) grain filling by inhibiting the deposition of storage materials such as starch, resulting in mature grains with a chalky appearance, currently a major problem for rice farming in Asian countries. Such deterioration of grain quality is accompanied by the altered expression of starch metabolism-related genes. Here we report the involvement of a starch-hydrolyzing enzyme, α-amylase, in high temperature-triggered grain chalkiness. In developing seeds, high temperature induced the expression of α-amylase genes, namely Amy1A, Amy1C, Amy3A, Amy3D and Amy3E, as well as α-amylase activity, while it decreased an α-amylase-repressing plant hormone, ABA, suggesting starch to be degraded by α-amylase in developing grains under elevated temperature...
December 2012: Plant Biotechnology Journal
Tom R Gaunt, Santiago Rodriguez, Philip A I Guthrie, Ian N M Day
Copy number variations (CNVs) are a common form of genetic variation in which the allelic population contains a distribution of copy numbers of a particular gene (or other large sequence/region). The simplest forms describe deletion (0 vs. 1 copy) or duplication (1 vs. 2) events. However, some CNV loci contain a much wider range of copy numbers, such as that seen for the CCL3L1 locus. CNV classification methods typically only describe the total (diploid) copy number, leaving the underlying genotypic and allelic frequency distribution unknown...
April 2010: Human Mutation
Sofia D Baltova
INTRODUCTION: The paper presents data on population distribution of individual phenotypes and gene frequencies of alpha-amylase in random serum samples from the population of the South-Western regions of Bulgaria. MATERIAL AND METHODS: We studied 1939 individuals of both sexes aged between 18 and 45 years from the South-Western regions of Bulgaria. They were clinically healthy and without kinship ties. The blood was obtained by venous puncture. The amylase phenotypes were established by horizontal electrophoresis of blood serum on agar gel (1%) after the J...
2005: Folia Medica
Y S Hwang, B R Thomas, R L Rodriguez
The unique capability of rice (Oryza sativa L.) seedlings to grow under anoxic conditions may result in part from their ability to express alpha-amylase and maintain the supply of sugar needed for energy metabolism. Previous studies have demonstrated that under aerobic conditions the Amy1 and Amy2 subfamily genes are regulated primarily by phytohormones while the Amy3 subfamily genes are induced during sugar starvation. The expression patterns for these alpha-amylase genes were considerably different in anoxic vs...
August 1999: Plant Molecular Biology
M Terashima, M Hosono, S Katoh
Characteristics of two rice alpha-amylases Amy1A and Amy3D, and those of two chimeric enzymes Amy1A/3D and Amy3D/1A, engineered from the two isozymes, were compared in the light of the functional roles of protein domains in alpha-amylase. The enzymes that have an Amy1A-type N-terminal domain, Amy1A and Amy1A/3D, showed high activity against soluble starch, while the enzymes that have an Amy3D-type barrel structure, Amy3D and Amy1A/3D, showed high activity in oligosaccharide hydrolysis. Rigidity of protein folding also significantly affected the enzyme activity in both soluble starch and oligosaccharide hydrolysis...
April 1997: Applied Microbiology and Biotechnology
M Terashima, S Katoh, B R Thomas, R L Rodriguez
Two rice alpha-amylase isozymes, AmylA and Amy3D, were produced by secretion from genetically engineered strains of Saccharomyces cerevisiae. They have distinct differences in enzymatic characteristics that can be related to the physiology of the germinating rice seed. The rice isozymes were purified with immunoaffinity chromatography. The pH optima for Amy3D (pH optimum 5.5) and Amy1A (pH optimum 4.2) correlate with the pH of the endosperm tissue at the times in rice seedling development when these isozymes are produced...
November 1995: Applied Microbiology and Biotechnology
D S Threadgill, D W Threadgill, Y D Moll, J A Weiss, N Zhang, H W Davey, A G Wildeman, J E Womack
Three mouse chromosomes (MMU 1, 3, and 4) carry homologs of human chromosome 1 (HSA 1) genes. A similar situation is found in the bovine, where five bovine chromosomes (BTA 2, 3, 5, 16, and unassigned syntenic group U25) contain homologs of HSA 1 loci. To evaluate further the syntenic relationship of HSA 1 homologs in cattle, 10 loci have been physically mapped through segregation analysis in bovine-rodent hybrid somatic cells. These loci, chosen for their location on HSA 1, are antithrombin 3 (AT3), renin (REN), complement component receptor 2 (CR2), phosphofructokinase muscle type (PFKM), Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog (FGR), alpha fucosidase (FUCA1), G-protein beta 1 subunit (GNB1), alpha 1A amylase, (AMY1), the neuroblastoma RAS viral (v-ras) oncogene homolog (NRAS), and alpha skeletal actin (ACTA1)...
August 1994: Genomics
M Terashima, A Kubo, M Suzawa, Y Itoh, S Katoh
The thermostability and kinetics of starch hydrolysis were compared between a rice alpha-amylase isozyme Amy1A and its mutant enzyme that lacks an N-linked carbohydrate chain. Elimination of the N-glycosylation site in Amy1A reduced the thermostability of the enzyme. The temperature dependence of the kinetic parameters (Vm and Km) and substrate recognition of the enzymes were also affected by elimination of the N-glycosylation site. These results suggest that the N-linked carbohydrate chain of Amy1A has important roles in the thermostability and reaction kinetics of the enzyme...
November 15, 1994: European Journal of Biochemistry
R A Young, O Hagenbüchle, U Schibler
The alpha-amylase mRNAs which accumulate in two different tissues of the mouse, the salivary gland and the liver, are identical except for their 5' non-translated sequences: the 5' terminal 158 nucleotides of the major liver alpha-amylase mRNA are unrelated to the 5' terminal 47 nucleotides found in its salivary gland counterpart. DNA that specifies the 5'terminal one-quarter of these mRNAs has been isolated through genomic cloning and sequenced. The initial 161 nucleotides of the liver alpha-amylase mRNA are specified by DNA sequences that lie 4...
February 1981: Cell
P C Groot, M J Bleeker, J C Pronk, F Arwert, W H Mager, R J Planta, A W Eriksson, R R Frants
Polymorphic amylase protein patterns have suggested the presence in the human genome of various haplotypes encoding these allozymes. To investigate the genomic organization of the human alpha-amylase genes, we isolated the pertinent genes from a cosmid library constructed of DNA from an individual expressing three different salivary amylase allozymes. From the restriction maps of the overlapping cosmids and a comparison of these maps with the restriction enzyme patterns of DNA from the donor and family members, we were able to identify two haplotypes consisting of very different numbers of salivary amylase genes...
July 1989: Genomics
P C Groot, W H Mager, R R Frants
Previous molecular studies have clearly shown that the human amylase locus has a very complicated structure. Multiple salivary and pancreatic amylase genes are present on haplotypes with variable numbers of genes. To study the population heterogeneity, human genomic DNA from family members and random individuals was digested with a number of different restriction enzymes and hybridized with probes representing various parts of the human pancreatic amylase cDNA. The complex patterns obtained were, in most cases, compatible with predictions from the restriction enzyme maps of cloned human amylase genes...
July 1991: Genomics
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