Genome-wide DNA polymorphism in the indica rice varieties RGD-7S and Taifeng B as revealed by whole genome re-sequencing.

Next-generation sequencing technologies provide opportunities to further understand genetic variation, even within closely related cultivars. We performed whole genome resequencing of two elite indica rice varieties, RGD-7S and Taifeng B, whose F1 progeny showed hybrid weakness and hybrid vigor when grown in the early- and late-cropping seasons, respectively. Approximately 150 million 100-bp pair-end reads were generated, which covered ∼86% of the rice (Oryza sativa L. japonica 'Nipponbare') reference genome. A total of 2,758,740 polymorphic sites including 2,408,845 SNPs and 349,895 InDels were detected in RGD-7S and Taifeng B, respectively. Applying stringent parameters, we identified 961,791 SNPs and 46,640 InDels between RGD-7S and Taifeng B (RGD-7S/Taifeng B). The density of DNA polymorphisms was 256.8 SNPs and 12.5 InDels per 100 kb for RGD-7S/Taifeng B. Copy number variations (CNVs) were also investigated. In RGD-7S, 1989 of 2727 CNVs were overlapped in 218 genes, and 1231 of 2010 CNVs were annotated in 175 genes in Taifeng B. In addition, we verified a subset of InDels in the interval of hybrid weakness genes, Hw3 and Hw4, and obtained some polymorphic InDel markers, which will provide a sound foundation for cloning hybrid weakness genes. Analysis of genomic variations will also contribute to understanding the genetic basis of hybrid weakness and heterosis.

Preliminary study on the active substances and cellular pathways of lactic acid bacteria for colorectal cancer treatment.

Colorectal cancer (CRC) is a common malignant tumor and is one of the three most common cancers worldwide. Traditional surgical treatment, supplemented by chemotherapy and radiotherapy, has obvious side effects on patients. Immunotherapy may lead to some unpredictable complications. Low introduction rate and high cost are some of the problems of gene therapy, so finding a safe, reliable and least toxic treatment method became the main research direction for this study. Lactic acid bacteria and their metabolites are widely used in functional foods or as adjuvant therapies for various diseases because they are safe to eat and have no adverse reactions. Research has shown that lactic acid bacteria and their metabolites play an auxiliary therapeutic role in colorectal cancer mainly by improving the intestinal flora composition, inhibiting the growth of pathogenic bacteria and inhibiting the proliferation of cancer cells. It is now widely believed that the substances that probiotics such as lactic acid bacteria exert anti-cancer effects are mainly secondary metabolites such as butyric acid. Lb. plantarum AY01 isolated from fermented food has good anti-cancer ability, and its main anti-cancer substance is 2'-deoxyinosine. Through flow cytometry detection, it was found that Lb. plantarum AY01 can block cell proliferation in the S phase. In addition, Lb. plantarum AY01 culture reduces the sensitivity of mice to colitis-associated CRC induced by azoxymethane (AOM)/dextran sulfate sodium salt (DSS) and exhibits the occurrence and promotion of tumors. According to transcriptome analysis, Lb. plantarum AY01 may induce apoptosis of colorectal cancer cells by activating the p38 MAPK pathway. This experiment provided possibilities for the treatment of CRC.

[Evaluation of risk factors for retinopathy of prematurity].

OBJECTIVE: To evaluate the incidence and risk factors of ROP (retinopathy of prematurity) through a prospective multicenter study. METHODS: Eleven children's or maternal & child hospitals participated in a collective network. All infants of birth weight < 2000 g, born in or transferred to one of the participating centers from January 1st 2005 to February 28th 2006 were recruited. Timely ophthalmologic examinations were performed. The relevant data at baseline and endpoints were collected at each unit. RESULTS: A total of 882 preterm infants fulfilled the screening criteria and 752 finished a followup. And 123 infants (16.4%) had some degree of ROP. Infants with ROP had a lower gestational age, birth weight and a longer duration of oxygen versus those without ROP [(30.82 +/- 0.20) weeks vs (32.56 +/- 0.09) weeks, (1430 +/- 25) g vs (1636 +/-10) g, (11.6 +/- 1.4) d vs (4.4 +/- 0.3) d]. Through a univariate analysis, birth weight, gestational age, asphyxia, oxygen duration > 5 days, apnea, surfactant usage, pneumonia, anemia, blood transfusion, acidosis and neonatal respiratory distress syndrome (NRDS) were associated with ROP (P < 0.05). Logistic regression analysis showed that birth weight (OR = 0.998), apnea (OR = 1.653) and blood transfusion (OR = 1.763) were independent risk factors for ROP. CONCLUSION: Asphyxia, oxygen duration > 5 days, surfactant usage, anemia, acidosis and NRDS, lower birth weight, apnea and blood transfusion may improve the risks of ROP.

Protective effect of supplemental anthocyanins on Arabidopsis leaves under high light.

Ten anthocyanin components have been detected in roots of purple sweet potato (Ipomoea batatas Lam.) by high-performance liquid chromatography coupled to diode array detection and electrospray ionization tandem mass spectrometry. All the anthocyanins were exclusively cyanidins or peonidin 3-sophoroside-5-glucosides and their acylated derivatives. The total anthocyanin content in purple sweet potato powder obtained by solid-phase extraction was 66 mg g(-1). A strong capacity of purple sweet potato anthocyanins (PSPA) to scavenge reactive oxygen species (superoxide, hydroxyl radical) and the stable 1,1-diphenyl-2-picrylhydrazyl organic free radical was found in vitro using the electron spin resonance technique. To determine the functional roles of anthocyanins in leaves in vivo, for the first time, supplemental anthocyanins were infiltrated into leaves of Arabidopsis thaliana double mutant of the ecotype Landsberg erecta (tt3tt4) deficient in anthocyanin biosynthesis. Chlorophyll fluorescence imaging showed that anthocyanins significantly ameliorated the inactivation of photosystems II during prolonged high-light (1300 micromol m(-2) s(-1)) exposure. Comet assay of DNA revealed an obvious role of supplemental PSPA in alleviating DNA damage by high light in leaves. Our results suggest that anthocyanins could function in vitro and in vivo to alleviate the direct or indirect oxidative damage of the photosynthetic apparatus and DNA in plants caused by high-light stress.

Transcriptomic analysis of de novo folate biosynthetic genes in Lactobacillus plantarum strain 4_3 in fermented soybean.

Folate is an important intermediate in cellular metabolism. However, because of a lack of key enzymes in the folate biosynthetic pathway, humans require supplementation with dietary folate. Some Lactobacillus plantarum strains have the ability to produce folate. To gain a better understanding of the folate biosynthetic pathway in the L. plantarum strain 4_3, which generates high folate yields, L. plantarum strain 4_3 was grown in folic acid casei medium (FACM) and fermented soybean, after obtaining a draft genome sequence. The pH values and folate yields were monitored during culturing, as were the transcriptomic profiles of cultured bacteria. The folate content increased for 12 h and then decreased before increasing again. All the genes involved in the de novo biosynthesis of folate were detected in both the genomic and transcriptomic data. The upregulation of the para-aminobenzoate biosynthesis pathway could explain the folate production in fermented soybean. Soybeans are a good substrate for the production of functional foods because of their well-suited cultivation and nutritional quality. The results of this study provide a good explanation for the high folate production observed during the fermentation of soybeans.

Is the delivery mode a critical factor for the microbial communities in the meconium?

BACKGROUND: Mothers are the primary source of bacteria for newborns, but it is unclear whether mother-to-newborn transmission occurs prior to, during or after birth. Similarly, the effect of the delivery mode on neonatal microorganisms has been the focus of controversy. METHODS: Healthy maternal and neonatal pairs that underwent vaginal birth and caesarean section were enrolled in this study. Meconium, placenta, membrane and amniotic fluid samples for newborns and vaginal, rectal and oral samples for mothers were collected. All samples were amplified and sequenced by a 16S rRNA gene primer set targeting bacteria and archaea. FINDINGS: A total of 550 samples from 36 mother-neonate pairs with vaginal births and 42 mother-neonate pairs with caesarean sections were included in this study. The negative controls showed that the data analysis in this study was not affected by contamination. There was a high diversity of microbial communities in the pregnancy environment of the foetus. Meconium samples could be divided into three distinct types that were not influenced by the delivery method. INTERPRETATION: The distribution patterns of bacterial communities in the meconium, placenta, and foetal membranes were highly similar and had nothing to do with the mode of delivery. For approximately half of the placental microorganisms, the same sequence could be found in the vaginal, rectal, and oral samples of the mother.

[Anatomical study and clinical applications of the posterior tibial artery intermuscular septum branches island flaps].

OBJECTIVE: To report an anatomical basis for the posterior tibial artery intermuscular septum branches island flaps and its clinical value. METHODS: The origin,course, number, caliber and distribution of the posterior tibial artery intermuscular septum branches were studied in 10 adult cadavers(20 legs). 10 cases of homonymy and opposite side ankle and adjacent soft tissue defects with posterior tibial artery intermuscular septum branches island flaps, aged 20-50 years. Free skin transplantation on the donor sites. RESULTS: The posterior tibial artery gives off 2-7 intermuscular septum branches. Its external diameter was about 0.4-1.8 mm,and the length was about 0.3-4.5 cm. The area of flaps was 7 cm x 6 cm - 20 cm x 8 cm in the group. All the flaps were survived except 1 with partial necrosis in the distant part(3 cm x 1 cm) of the flap. 7 cases were followed up two months to three years. The color, texture and appearance of the flaps were good. CONCLUSIONS: The kind of flap has reliable blood supply, the scope of repairing was wide; avoidance of sacrificing the major artery; the flap was easy to be dissected. It was one of the ideal flaps to repair the ankle and adjacent soft tissue defects.