A simple and accurate SNP scoring strategy based on typeIIS restriction endonuclease cleavage and matrix-assisted laser desorption/ionization mass spectrometry

<p>Abstract</p> <p>Background</p> <p>We describe the development of a novel matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF)-based single nucleotide polymorphism (SNP) scoring strategy, termed Restriction Fragment Mass Polymorphism (RFMP) that is suitable for genotyping variations in a simple, accurate, and high-throughput manner. The assay is based on polymerase chain reaction (PCR) amplification and mass measurement of oligonucleotides containing a polymorphic base, to which a typeIIS restriction endonuclease recognition was introduced by PCR amplification. Enzymatic cleavage of the products leads to excision of oligonucleotide fragments representing base variation of the polymorphic site whose masses were determined by MALDI-TOF MS.</p> <p>Results</p> <p>The assay represents an improvement over previous methods because it relies on the direct mass determination of PCR products rather than on an indirect analysis, where a base-extended or fluorescent report tag is interpreted. The RFMP strategy is simple and straightforward, requiring one restriction digestion reaction following target amplification in a single vessel. With this technology, genotypes are generated with a high call rate (99.6%) and high accuracy (99.8%) as determined by independent sequencing.</p> <p>Conclusion</p> <p>The simplicity, accuracy and amenability to high-throughput screening analysis should make the RFMP assay suitable for large-scale genotype association study as well as clinical genotyping in laboratories.</p

Expression of aldo-keto reductase family 1 member C1 (AKR1C1) gene in porcine ovary and uterine endometrium during the estrous cycle and pregnancy

<p>Abstract</p> <p>Background</p> <p>The aldo-keto reductase family 1 member C1 (AKR1C1) belongs to a superfamily of NADPH-dependent reductases that convert a wide range of substrates, including carbohydrates, steroid hormones, and endogenous prostaglandins. The 20alpha-hydroxysteroid dehydrogenase (20alpha-HSD) is a member of AKR family. The aims of this study were to determine its expression in the ovary and uterus endometrium during the estrous cycle and pregnancy.</p> <p>Methods</p> <p>Rapid amplification of cDNA ends (RACE) experiments were performed to obtain the 5' and 3' ends of the porcine <it>20alpha-HSD </it>cDNA. Reverse-transcriptase-PCR (RT-PCR), real-time PCR, northern blot analysis, and western blot analysis were performed to examine the expression of porcine 20alpha-HSD. Immunohistochemical analysis was also performed to determine the localization in the ovary.</p> <p>Results</p> <p>The porcine 20alpha-HSD cDNA is 957 bp in length and encodes a protein of 319 amino acids. The cloned cDNA was virtually the same as the porcine <it>AKR1C1 </it>gene (337 amino acids) reported recently, and only differed in the C-terminal region (the <it>AKR1C1 </it>gene has a longer C-terminal region than our sequence). The <it>20alpha-HSD </it>gene (from now on referred to as <it>AKR1C1</it>) cloned in this paper encodes a deletion of 4 amino acids, compared with the C-terminal region of <it>AKR1C1 </it>genes from other animals. Porcine AKR1C1 mRNA was expressed on day 5, 10, 12, 15 of the cycle and 0-60 of pregnancy in the ovary. The mRNA was also specifically detected in the uterine endometrium on day 30 of pregnancy. Western blot analysis indicated that the pattern of AKR1C1 protein in the ovary during the estrous cycle and uterus during early pregnancy was similar to that of <it>AKR1C1 </it>mRNA expression. The recombinant protein produced in CHO cells was detected at approximately 37 kDa. Immunohistochemical analysis also revealed that pig AKR1C1 protein was localized in the large luteal cells in the early stages of the estrous cycle and before parturition.</p> <p>Conclusions</p> <p>Our study demonstrated that AKR1C1 mRNA and protein are coordinately expressed in the luteal cell of ovary throughout the estrous cycle and in the uterus on day 30 of pregnancy. Thus, the porcine AKR1C1 gene might control important mechanisms during the estrous cycle.</p

Early Diagnosis of Pseudohypoparathyroidism before the Development of Hypocalcemia in a Young Infant

Pseudohypoparathyroidism (PHP) is a rare, heterogeneous disorder characterized by end-organ resistance to parathyroid hormone (PTH). PTH resistance causes elevated PTH levels, hypocalcemia, and hyperphosphatemia. Since hypocalcemia causes life-threatening events, early diagnosis is crucial. However, the diagnosis of PHP is elusive during infancy because PHP is usually diagnosed with hypocalcemia-induced symptoms, which develop later in childhood when calcium requirements increase. A 1-month-old girl was referred to our clinic for elevated thyroid-stimulating hormone (TSH) levels on newborn screening. When measured 1 month after levothyroxine treatment, her TSH level normalized. At 4-months-old, multiple hard nodules were noted on her trunk. A punch skin biopsy revealed osteoma cutis associated with Albright&rsquo;s hereditary osteodystrophy, a major characteristic of PHP. We performed targeted sanger sequencing of the GNAS gene and detected a heterozygous variant c.150dupA (p.Ser51Ilefs*3) in both the proband and her mother, causing frameshift and premature termination mutations. The patient was diagnosed with PHP Ia when she had normal calcium, phosphorous, and PTH levels. We report the early diagnosis of PHP Ia without hypocalcemia. It emphasizes the importance of meticulous physical examination in patients with congenital hypothyroidism

Metabolic Evidence on Vintage Effect in Tea (Camellia sinensis L.) Plants

Abstract Recent metabolomics studies have reported diverse metabolites of tea depending on tea (Camellia sinensis) cultivars, cultivation conditions and geographical location. However, these studies were limited the effects of these conditions on metabolome of tea leaves in a single year. We explored the year-to-year variations in leaf metabolome of two tea (C. sinensis) cultivars over a period of five successive years from 2015 to 2019 to determine vintage tea products, such as in grapes or wines, and showed a clear metabolic differentiations of fresh tea leaves. Also, the best conditions of climate were suggested through an association of rainfall and sun-expose time with the metabolism of theanine in taste- or flavor-rich tea cultivar and of catechin compounds in EGCG3″Me-rich tea cultivar, thereby providing the potential vintage tea tailored to the cultivar. Since vintage wine is derived from grapes grown in a year under good climatic conditions, which provides high quality of wine in the best year, the current result highlights important information relevant to tea metabolome associated with climatic conditions in a specific year and the manufacture of vintage tea with unique quality. Graphical Abstrac