Real-time relative qPCR without reference to control samples and estimation of run-specific PCR parameters from run-internal mini-standard curves

Light Intensity-A Key Factor Affecting Flavonoid Content and Expression of Key Enzyme Genes of Flavonoid Synthesis in Tartary Buckwheat

Tartary buckwheat, a polygonaceae family plant, is rich in abundant flavonoids, high-quality protein, and well-balanced essential amino acids. This study aimed to investigate the effects of climatic variables on the quality of Tartary buckwheat. In this study, six distinct types of Tartary buckwheat collected from the Sichuan Basin, Western Sichuan Plateau, and Yunnan-Guizhou Plateau in southwest China were chosen to investigate the impact of climatic conditions from the grain-filling stage to the harvest stage on the concentration of flavonoids and expression of key enzyme genes involved the synthesis of flavonoids. Meteorological data of three producing areas were collected from the China Meteorological Network, mainly including maximum temperature (Tmax), minimum temperature (Tmin), diurnal temperature difference (Tdif), and light intensity. Then, the contents of rutin, kaempferol-3-O-rutin glycoside, quercetin, and kaempferol in 30 batches of Tartary buckwheat from 6 varieties including Chuanqiao No. 1, Chuanqiao No. 2, Xiqiao No. 1, Xiqiao No. 2, Miqiao No. 1 and Di ku were determined by ultra performance liquid chromatography-mass spectrometry (UPLC-MS/MS). Furthermore, the expression levels of phenylalanine ammonia lyase (PAL), 4-coumaric acid coenzyme A ligase (4CL), and anthocyanin synthase (ANS) in six kinds of Tartary buckwheat were detected by real-time polymerase chain reaction (PCR). The seed photos were processed by ImageJ processing software. The partial least squares method was used to analyze the correlation. As a result, light intensity can promote the accumulation of flavonoids and the expression of key enzyme genes. Miqiao No. 1, which grows in Liangshan Prefecture, Sichuan Province, has the highest light intensity and is the dominant variety with flavonoid content. More importantly, the expression levels of PAL and 4CL in the secondary metabolic pathway of flavonoids were positively correlated with the content of Tartary buckwheat flavonoids. Interestingly, the expression level of ANS was negatively correlated with the content of PAL, 4CL, and flavonoids. In addition, ANS is a key gene affecting the seed coat color of Tartary buckwheat. The higher the expression of ANS, the darker the seed coat color. These findings provide a theoretical basis and reference for the breeding of fine buckwheat varieties.

Protective effect of GYY4137, a water‑soluble hydrogen sulfide‑releasing molecule, on intestinal ischemia‑reperfusion

The present study aimed to clarify the protective effects of p‑methoxyphenyl morpholino‑phosphinodithioic acid (GYY4137), a water‑soluble hydrogen sulfide‑releasing molecule, on a rat model of intestinal ischemia‑reperfusion (IIR). A total of 40 healthy male Sprague Dawley (SD) rats were randomly divided into four groups (n=10/group): Group A, a sham‑surgery group; Group B, the IIR group; group C, rats with IIR that were administered an abdominal injection of low‑dose GYY4137 (40 mg/kg); and group D, rats with IIR that were administered high‑dose GYY4137 (80 mg/kg). Intestinal histomorphology was observed using hematoxylin and eosin staining, and the concentrations of malondialdehyde (MDA) and superoxide dismutase (SOD) were measured. Apoptotic index (AI) was determined by terminal deoxynucleotidyl‑transferase‑mediated dUTP nick end labeling. Reverse transcription‑quantitative PCR analysis was performed to assess the expression levels of intestinal caspase‑3, Bax and Bcl‑2. Notably, disordered arrangement of intestinal villi and mucosal necrosis were detected in group B, which was substantially improved by GYY4137 treatment (groups C and D). MDA content (nmol/mg) was 2.83±0.36, 9.23±0.78, 4.97±0.45 and 3.51±1.05 nmol/mg in groups A, B, C and D, respectively. In addition, SOD concentration (U/mg) was 135.37±3.34, 76.45±1.39, 95.13±1.64 and 115.13±2.54 in groups A, B, C and D, respectively. Furthermore, AI in group B (21.73±1.17%) was markedly higher than that in group A (4.53±0.28%) and in the GYY4137 intervention groups (9.53±0.96 and 6.53±0.76% in groups C and D, respectively). Compared with in group A, the mRNA expression levels of Bax and caspase‑3 were markedly higher in group B (P<0.05), whereas the expression of Bcl‑2 was significantly lower (P<0.05). Furthermore, compared with in group B, Bcl‑2 expression was higher, and Bax and caspase‑3 expression was lower in groups C and D (P<0.05). In conclusion, GYY4137 may alleviate IIR‑induced damage in SD rats.

Hormonal behavior correlates with follicular recruitment at mid-gestation in the South American plains vizcacha, Lagostomus maximus (Rodentia, Caviomorpha)

In mammals, hormonal regulation during gestation is crucial for embryo implantation and pregnancy success. This regulation is controlled through the level of progesterone (P4) that blocks the activity of the hypothalamic-hypophyseal-gonadal (HHG) axis. Previous studies in the pregnant South American plains vizcacha, Lagostomus maximus, have shown that the HHG axis activates around mid-gestation, promoting pre-ovulatory follicle formation. However, the characterization of the hormonal dynamics throughout gestation and its ovarian correlation has not been studied in depth. We studied the ovarian dynamics of L. maximus and its correlation with the hormonal profile during gestation, analyzing serum levels of P4, 17β-estradiol (E2), 4Δ-androstenedione (A4), luteinizing hormone (LH) and follicle stimulating hormone (FSH) as well as the ovarian distribution and expression of their receptors. Additionally, we have analyzed the folliculogenesis and accessory corpora lutea (ACL) formation. P4 showed two concentration peaks reaching its highest level at mid-gestation decreasing at 91-100days post-coitum. P4 decrease is followed by an increase of circulating levels of A4, E2, FSH and LH and with an elevated number of antral/pre-ovulatory follicles which express PGR, ESR1, ESR2, AR, LHR and FSHR. In addition, ACL with oocyte retention and cytoplasmic lipid droplets in luteal cells were detected at this time point. These results show that in L. maximus the decrease of P4 level from mid-gestation enables follicular recruitment until pre-ovulatory stage and the development of functional ACL.

Adjusting MtDNA Quantification in Whole Blood for Peripheral Blood Platelet and Leukocyte Counts

Alterations of mitochondrial DNA copy number (mtDNAcn) in the blood (mitochondrial to nuclear DNA ratio) appear associated with several systemic diseases, including primary mitochondrial disorders, carcinogenesis, and hematologic diseases. Measuring mtDNAcn in DNA extracted from whole blood (WB) instead of from peripheral blood mononuclear cells or buffy coat may yield different results due to mitochondrial DNA present in platelets. The aim of this work is to quantify the contribution of platelets to mtDNAcn in whole blood [mtDNAcn(WB)] and to propose a correction formula to estimate leukocytes' mtDNAcn [mtDNAcn(L)] from mtDNAcn(WB). Blood samples from 10 healthy adults were combined with platelet-enriched plasma and saline solution to produce artificial blood preparations. Aliquots of each sample were combined with five different platelet concentrations. In 46 of these blood preparations, mtDNAcn was measured by qPCR. MtDNAcn(WB) increased 1.07 (95%CI 0.86, 1.29; p<0.001) per 1000 platelets present in the preparation. We proved that leukocyte count should also be taken into account as mtDNAcn(WB) was inversely associated with leukocyte count; it increased 1.10 (95%CI 0.95, 1.25, p<0.001) per unit increase of the ratio between platelet and leukocyte counts. If hematological measurements are available, subtracting 1.10 the platelets/leukocyte ratio from mtDNAcn(WB) may serve as an estimation for mtDNAcn(L). Both platelet and leukocyte counts in the sample are important sources of variation if comparing mtDNAcn among groups of patients when mtDNAcn is measured in DNA extracted from whole blood. Not taking the platelet/leukocyte ratio into account in whole blood measurements, may lead to overestimation and misclassification if interpreted as leukocytes' mtDNAcn.

Elucidating the genetic basis of antioxidant status in lettuce (Lactuca sativa)

A diet rich in phytonutrients from fruit and vegetables has been acknowledged to afford protection against a range of human diseases, but many of the most popular vegetables are low in phytonutrients. Wild relatives of crops may contain allelic variation for genes determining the concentrations of these beneficial phytonutrients, and therefore understanding the genetic basis of this variation is important for breeding efforts to enhance nutritional quality. In this study, lettuce recombinant inbred lines, generated from a cross between wild and cultivated lettuce (Lactuca serriola and Lactuca sativa, respectively), were analysed for antioxidant (AO) potential and important phytonutrients including carotenoids, chlorophyll and phenolic compounds. When grown in two environments, 96 quantitative trait loci (QTL) were identified for these nutritional traits: 4 for AO potential, 2 for carotenoid content, 3 for total chlorophyll content and 87 for individual phenolic compounds (two per compound on average). Most often, the L. serriola alleles conferred an increase in total AOs and metabolites. Candidate genes underlying these QTL were identified by BLASTn searches; in several cases, these had functions suggesting involvement in phytonutrient biosynthetic pathways. Analysis of a QTL on linkage group 3, which accounted for >30% of the variation in AO potential, revealed several candidate genes encoding multiple MYB transcription factors which regulate flavonoid biosynthesis and flavanone 3-hydroxylase, an enzyme involved in the biosynthesis of the flavonoids quercetin and kaempferol, which are known to have powerful AO activity. Follow-up quantitative RT-PCR of these candidates revealed that 5 out of 10 genes investigated were significantly differentially expressed between the wild and cultivated parents, providing further evidence of their potential involvement in determining the contrasting phenotypes. These results offer exciting opportunities to improve the nutritional content and health benefits of lettuce through marker-assisted breeding.

How much metagenomic sequencing is enough to achieve a given goal?

Metagenomic studies have dramatically expanded our knowledge of the microbial world. Furthermore, the amount of sample for sequencing has significantly increased with the development of high-throughput sequencing technologies. However, fully capturing all DNA sequences carried by every microorganism in the environment is still impossible. Therefore, estimating a reasonable and practical amount for sequencing to achieve the objectives is particularly necessary. In the present study, we introduce a novel method for estimating the required minimum amount for metagenomic sequencing for a given goal. We also calculated the genomic proportion of each operational taxonomic unit and the detection efficiency of a specific gene (we have used SSU rRNA gene as an example) based on a given amount for random metagenomic sequencing. The reasonable and practical estimated amount for sequencing in metagenomic studies will provide good reference information when applying high-throughput sequencing for a given goal.