TPMA: A two pointers meta-alignment tool to ensemble different multiple nucleic acid sequence alignments.

Accurate multiple sequence alignment (MSA) is imperative for the comprehensive analysis of biological sequences. However, a notable challenge arises as no single MSA tool consistently outperforms its counterparts across diverse datasets. Users often have to try multiple MSA tools to achieve optimal alignment results, which can be time-consuming and memory-intensive. While the overall accuracy of certain MSA results may be lower, there could be local regions with the highest alignment scores, prompting researchers to seek a tool capable of merging these locally optimal results from multiple initial alignments into a globally optimal alignment. In this study, we introduce Two Pointers Meta-Alignment (TPMA), a novel tool designed for the integration of nucleic acid sequence alignments. TPMA employs two pointers to partition the initial alignments into blocks containing identical sequence fragments. It selects blocks with the high sum of pairs (SP) scores to concatenate them into an alignment with an overall SP score superior to that of the initial alignments. Through tests on simulated and real datasets, the experimental results consistently demonstrate that TPMA outperforms M-Coffee in terms of aSP, Q, and total column (TC) scores across most datasets. Even in cases where TPMA's scores are comparable to M-Coffee, TPMA exhibits significantly lower running time and memory consumption. Furthermore, we comprehensively assessed all the MSA tools used in the experiments, considering accuracy, time, and memory consumption. We propose accurate and fast combination strategies for small and large datasets, which streamline the user tool selection process and facilitate large-scale dataset integration. The dataset and source code of TPMA are available on GitHub (https://github.com/malabz/TPMA).

A spray-as-you-go airway topical anesthesia attenuates cardiovascular responses for double-lumen tube tracheal intubation.

BACKGROUND: Spray-as-you-go (SAYGo) airway topical anesthesia and nerve block are common techniques used during awake tracheal intubation. However, their effects have not been described during double-lumen tube intubation. We report on a prospective randomized study that aimed to compare the intubation effects of SAYGo and nerve block patients undergoing thoracic surgery. METHODS: Sixty-six American Society of Anesthesiologists (ASA) physical status I and II patients were scheduled to undergo double-lumen tube (DLT) tracheal intubation for thoracic surgery. The patients were randomly assigned into control (Group C), ultrasound (Group U), and flexible intubation scope (Group F) groups with 22 cases in each group. Patients in Group C were induced with a standard anesthetic regimen. Patients in Groups U and F were treated with superior laryngeal nerve (SLN) block combined with transtracheal injection (TTI) and given a SAYGo airway topical anesthesia before intubation. Hemodynamic variables during intubation process were recorded as the primary outcome. Additional patient data were recorded including the occurrence of adverse events, the level of hoarseness, the occurrence of sore throats, memory function and the level of patient satisfaction with anesthesia. RESULTS: The blood pressure (BP) and heart rate (HR) of patients in group C was significantly increased 1 min after tracheal intubation (P < 0.05) compared to before anesthesia. The BP and HR of patients in Groups U and F remained stable. 10 cases of hypertension were observed in Group C, 6 cases in Group U and 1 case in Group F. In Group C, tachycardia was observed in 9 patients along with 9 cases in Group U and 4 cases in Group F. In Group U, 4 patients experienced puncture and bleeding were and 8 patients had a poor memory of TTI. No significant differences were found in the incidence of hoarseness, sore throats, and satisfaction with anesthesia in postoperative follow-up. CONCLUSIONS: SAYGo airway topical anesthesia and SLN block combined with the TTI technique can inhibit the cardiovascular response during DLT tracheal intubation. The SAYGo technique has fewer complications and more advantages compared to other approaches.

Association of main folate metabolic pathway gene polymorphisms with neural tube defects in Han population of Northern China.

PURPOSE: Neural tube defects (NTDs) are one of the most prevalent and the most severe congenital malformations worldwide. Studies have confirmed that folic acid supplementation could effectively reduce NTDs risk, but the genetic mechanism remains unclear. In this study, we explored association of single nucleotide polymorphisms (SNP) within folate metabolic pathway genes with NTDs in Han population of Northern China. METHODS: We performed a case-control study to compare genotype and allele distributions of SNPs in 152 patients with NTDs and 169 controls. A total of 16 SNPs within five genes were genotyped by the Sequenom MassARRAY assay. RESULTS: Our results indicated that three SNPs associated significantly with NTDs (P<0.05). For rs2236225 within MTHFD1, children with allele A or genotype AA had a high NTDs risk (OR=1.500, 95%CI=1.061~2.120; OR=2.862, 95%CI=1.022~8.015, respectively). For rs1801133 within MTHFR, NTDs risk markedly increased in patients with allele T or genotype TT (OR=1.552, 95%CI=1.130~2.131; OR=2.344, 95%CI=1.233~4.457, respectively). For rs1801394 within MTRR, children carrying allele G and genotype GG had a higher NTDs risk (OR=1.533, 95%CI=1.102~2.188; OR=2.355, 95%CI=1.044~5.312, respectively). CONCLUSIONS: Our results suggest that rs2236225 of MTHFD1 gene, rs1801133 of MTHFR gene and rs1801394 of MTRR gene were associated with NTDs in Han population of Northern China.

Response of energy microalgae Chlamydomonas reinhardtii to nitrogen and phosphorus stress.

Microalgae can effectively absorb nitrogen (N) and phosphorus (P) in wastewater, while growth characteristics can be affected by such nutrients. The influences of the N and P concentration on growth, biomass yield, protein yield, and cell ultrastructure of Chlamydomonas reinhardtii (C. reinhardtii) were investigated in this study. The results showed that, in the optimum conditions (24-72 mg/L for N and 4.5-13.5 mg/L for P), the final biomass and protein content of C. reinhardtii could reach maximum value, and the cell organelles (chloroplast, mitochondria,etc.) showed good structures with larger chloroplasts, and more and neater thylakoids. However, if the concentration of nutrients was much higher or lower than the optimal value, it would cause adverse effects on the growth of C. reinhardtii, especially in high nitrogen (1000 mg/L) and low phosphorus (0.5 mg/L) conditions. Under these extreme conditions, the ultrastructure of the cells was also damaged significantly as follows: the majority of the organelles were deformed, the chloroplast membrane became shrunken, and the mitochondria became swollen, even partial disintegrated (differing slightly under high-N and low-P conditions); furthermore, it is found that C. reinhardtii was more sensitive to low-P stress. On the basis of these results, our findings have general implications in the application of wastewater treatment.

In Vitro Angiogenesis Effect of Xuefu Zhuyu Decoction () and Vascular Endothelial Growth Factor: A Comparison Study.

OBJECTIVE: To compare the angiogenesis behaviors of vascular endothelial growth factor (VEGF) and Chinese medicine Xuefu Zhuyu Decoction (, XZD) treatments. METHODS: Human microvascular endothelial cells (HMEC-1) were treated with various concentrations of either XZD-containing serum (XZD-CS) or VEGF for 24, 48, and 72 h, respectively. Cell viability, proliferation, migration, adhesion, and in vitro tube formation assays were used to assess their angiogenic effects. RESULTS: VEGF promoted all cellular phases involved in angiogenesis including cell viability, proliferation, migration, adhesion, and tube formation (<0.05 or <0.01). Unlike the continuous promotion effects of VEGF at the above stages, XZD inhibited cell viability and proliferation (<0.05 or <0.01) and only promoted tube formation in the early phase of angiogenesis (<0.01). CONCLUSIONS: These two medications promote different angiogenesis behaviors, which might be an important reason for their distinct therapeutic profile in clinical usage.

A unique methylation pattern co-segregates with neural tube defect statuses in Han Chinese pedigrees.

Neural tube defects (NTDs) are a complex trait associated with gene-environment interactions. Folic acid deficiency and planar cell polarity gene mutations account for some NTD cases; however, the etiology of NTDs is still little understood. In this study, in three Han Chinese NTD pedigrees (two with multiple affected children), with no information on folic acid deficiency or supplement, we examined genome-wide methylation profiles of each individual in these families. We further compared methylation status among cases and normal individuals within the pedigrees. A unique methylation pattern co-segregated with affected status: NTD cases had more hypermethylated than hypomethylated CpG islands; genes with different methylations clustered in pathways associated with epithelial-to-mesenchymal transition (ZEB2, SMAD6, and CDH23), folic acid/homocysteine metabolism (MTHFD1L), transcription/nuclear factors (HDAC4, HOXB7, SOX18), cell migration/motility/adhesion, insulin and cell growth, and neuron/axon development. Although the genetics of NTD are likely complex, epigenetic changes may concentrate in certain key pathways.

[Moderate Angiogenic Effect of Xuefu Zhuyu Capsule by Regulating EphB4/EphrinB2].

Objective To observe moderate angiogenic effect of Xuefu Zhuyu Capsule (XFZYC) on human microvascular endothelial cell line 1 ( HMEC-1) , and its regulation effect on expression of EphB4/EphrinB2. Methods The moderate angiogenic effect of XFZYC was clarified by detecting XFZYC containing serum on cell viability, cell cycle, migration, adhesion and in vitro angiogenesis. Its effects on expressions of EphB4/EphrinB2 were detected by Real-time quantitative PCR and Western blot. Results XFZYC containing serum (XFZYC-CS) had no effect on the cell viability or cell ratio in phase S endothelial cells. Cell migration was significantly improved by 1.25% XFZYC-CS after 24, 48, and 72 h of action 2. 50% XFZYC-CS inhibited cell migration at the primary 24 h, but it significantly promoted cell migration at 48 and 72 h afterwards. It showed just an opposite tendency to 5. 00% XFZYC-CS. Cellular adhesion number was significantly reduced by 1. 25% XFZYC-CS at 72 h. Cellular adhesion number was significant- ly increased by 2. 50% XFZYC-CS at 24 and 48 h, but inhibited at 72 h 5. 00% XFZYC-CS showed inhibition at 24 h, but turned to promotion, and disappeared afterwards. In vessel formation aspect, only 2.50% XFZYC-CS showed vessel formation promotion 5. 00% XFZYC-CS showed inhibition on vessel formation at 48 and 72 h. Results of Real-time quantitative PCR and Western blot in 2. 50% XFZYC-CS showed EphB4 expression was up-regulated at 12 h; EphB4 expression was down-regulated while EphrinB2 expression was up-regulated at 24 h. Conclusions Only 2. 50% XFZYC-CS at 48 h had promotion of migration, adhe- sion, and in vitro angiogenesis of HMEC-1 , which was the optimal condition for vessel growth. These re- sults suggested XFZYC promoted angiogenesis in certain conditional limitations. But it regulated the ex- pression of EphB4/EphrinB2, which might be one of important factors.

Effect of EphB4/EphrinB2 reverse signal on angiogenesis induced by Xuefu Zhuyu Capsule () containing serum in human microvascular endothelial cell 1.

OBJECTIVE: To evaluate the effect of Xuefu Zhuyu Capsule ()-containing serum (XFZY-CS) on EphB4/ephrinB2 and its reverse signal in human microvascular endothelial cell-1 (HMEC-1). METHODS: XFZY-CS and the blank control serum were collected. HMEC-1 cells were randomly assigned to 6 groups including the concentration 1.25%, 2.5%, and 5% XFZY-CS groups and their blank serum control ones. The angiogenesis effect of XFZY-CS was tested with an in vitro tube formation assay and the best condition of pro-angiogenesis was determined. The effect of XFZY-CS on EphB4/ephrinB2 and the reverse signal were determined by Western blot and real-time quantitative polymerase chain reaction, respectively; we also confifirmed the results through activating and inhibiting the reverse signal by EphB4/fc and pyrophosphatase/ phosphodiesterase2 (PP2). RESULTS: XFZY-CS promoted angiogenesis at the concentration of 2.5% corresponding serum after being cultured for 48 h, while inhibited angiogenesis at the concentration of 5% after culturing for 48 and 72 h. Under the 2.5% serum concentration, XFZY up-regulated the expression of EphB4-mRNA at 12 h (P<0.05), and down-regulates its expression at 24 h (P<0.01). Protein expression of EphB4 was apparently up-regulated at 12 h and down-regulated at 24 h. The phosphorylation of ephrinB2 increased at 9 h (P<0.05). In addition, 2.5% XFZY-CS played a similar role as the reverse signaling activator EphB4/Fc ranging from 0.5 to 5 µg/mL (P>0.05). XFZY-CS also reduced the inhibitive effect of PP2 in limited periods. CONCLUSIONS: EphB4/ephrinB2 was the upstream signal in the process of angiogenesis and its reverse signaling was responsible for XFZY's effect on promoting angiogenesis.

[Roles of bFGF in endothelial cell tube formation induced by xuefu zhuyu decoction under non-anoxia condition].

OBJECTIVE: To explore the roles of basic fibroblast growth factor (bFGF) on tube formation induced by xuefu zhuyu decoction (XZD) under non-anoxia condition. METHODS: Using serum pharmacology technique, endothelial cell line ECV304 cells were incubated in routine 95% O2. ECV304 cells were intervened by 1.25%, 2.50%, and 5.00% XZD containing serums and the vehicle serum for 48 h. The effects of XZD on tube formation, bFGF contents and its transcription levels were assessed by in vitro tube formation assay, enzyme-linked immunosorbent assay (ELISA), and reverse transcriptase polymerase chain reaction (RT-PCR), respectively. RESULTS: Three concentrations of XZD containing serums could not only obviously promote the tube formation bFGF level, but also up-regulate bFGF contents in the supernate and its transcription levels. The shapes of lumens were more regular in those induced by 1.25% and 2.50% XZD containing serums. CONCLUSION: XZD induced angiogenesis via up-regulating the bFGF expression under non-anoxia condition.

Changes in small intestinal morphology and digestive enzyme activity with oral administration of copper-loaded chitosan nanoparticles in rats.

The experiment was conducted to evaluate the effect of copper-loaded chitosan nanoparticles on the small intestinal morphology and activities of digestive enzyme and mucosal disaccharase in rats. Forty male Sprague-Dawley rats, with average body weight of 82 g, were randomly allotted to five groups (n = 8). All rats were received a basal diet (control) or the same basal diet added with 80 mg/kg BW CuSO(4), 80 mg/kg BW chitosan (CS-I), 80 mg/kg BW copper-loaded chitosan nanoparticles (CSN-I), 160 mg/kg BW copper-loaded chitosan nanoparticles (CSN-II), respectively. The experiment lasted 21 days. The results showed that the villus heights of the small intestinal mucosa in groups CSN-I and CSN-II were higher than those of the control, group CuSO(4) or CS-I. The crypt depth of duodenum and ileum mucosa in group CSN-I or CSN-II was depressed. Compared with the control, there were no significant effects of CuSO(4) or CS-I on the villus height and crypt depth of small intestinal mucosa. Supplementation with CSN improved the activities of trypsin, amylase and lipase in the small intestinal contents and maltase, sucrase and lactase of duodenum, jejunum, and ileum mucosa while there were no significant effects of CuSO(4) on the digestive enzyme activities of the small content compared with the control. The results indicated that intestinal morphology, activities of digestive enzyme in digesta and mucosal disaccharase were beneficially changed by treatment of copper-loaded chitosan nanoparticles.

Effects of osthole on apoptosis and TGF-beta1 of hypertrophic scar fibroblasts.

Osthole, 7-methoxy-8-[3-methylpent-2-enyl]coumarin (1), was extracted from a Chinese herb Cnidium monnieri (L.) Cuss. It showed immunity strengthening, anti-tumor, anti-hepatitis, and anti-osteoporosis activities in previous studies. Our goals are to study the effects of 1 on cell proliferation and TGF-beta of hypertrophic scar fibroblasts. Our results showed that 1 induced apoptosis and inhibited cell proliferation in hypertrophic scar fibroblasts. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay showed that its IC(50) value toward hypertrophic scar fibroblasts was 15.5 +/- 2.2 micromol/l. Furthermore, the results of cell growth curve matched with the above results. Inducing apoptosis by 1 in hypertrophic scar fibroblasts was assessed by various morphological and biochemical characteristics, including cell shrinkage, chromatin condensation, membrane blebbing, formation of apoptotic bodies, and DNA ladder formation. A typical 'Sub-G(1) peak' was also checked through flow cytometry. We used immunohistochemistry to observe the expression of TGF-beta(1). Also, we found that 1 could obviously inhibit the expression of TGF-beta(1) of fibroblasts derived from hypertrophic scar compared with the control group (P < 0.05). These results suggest that 1 inhibits the growth of hypertrophic scar fibroblasts through apoptosis and decreases the expression of TGF-beta(1).

Anti-tumor effect of beta-elemene in glioblastoma cells depends on p38 MAPK activation.

beta-Elemene, a natural plant drug extracted from Curcuma wenyujin, has been used as an antitumor drug for different tumors, including glioblastoma. However, the mechanism of its anti-tumor effect is largely unknown. Here we report that anti-proliferation of glioblastoma cells induced by beta-elemene was dependent on p38 MAPK activation. Treatment of glioblastoma cell lines with beta-elemene, led to phosphorylation of p38 MAPK, cell-cycle arrest in G0/G1 phase and inhibition of proliferation of these cells. Inhibition of p38 MAPK reversed beta-elemene-mediated anti-proliferation effect. Furthermore, the growth of glioblastoma cell-transplanted tumors in nude mice was inhibited by intraperitoneal injection of beta-elemene. Taken together, our findings indicate that activation of p38 MAPK is critical for the anti-proliferation effect of beta-elemene and that p38 MAPK might be a putative pharmacological target for glioblastoma therapy.