Analysis of DNA Barcodes Using DNA Subway.

DNA Subway makes bioinformatic analysis of DNA barcodes classroom friendly, eliminating the need for software installations or command line tools. Subway bundles research-grade bioinformatics software into workflows with an easy-to-use interface. This chapter covers DNA Subway's DNA barcoding analysis workflow (Blue Line) starting with one or more Sanger sequence reads. During analysis, users can view trace files and sequence quality, pair and align forward and reverse reads, create and trim consensus sequences, perform BLAST searches, select reference data, align multiple sequences, and compute phylogenetic trees. High-quality sequences with the required metadata can also be submitted as barcode sequences to NCBI GenBank.

Prediction of SMILE surgical cutting formula based on back propagation neural network.

AIM: To predict cutting formula of small incision lenticule extraction (SMILE) surgery and assist clinicians in identifying candidates by deep learning of back propagation (BP) neural network. METHODS: A prediction program was developed by a BP neural network. There were 13 188 pieces of data selected as training validation. Another 840 eye samples from 425 patients were recruited for reverse verification of training results. Precision of prediction by BP neural network and lenticule thickness error between machine learning and the actual lenticule thickness in the patient data were measured. RESULTS: After training 2313 epochs, the predictive SMILE cutting formula BP neural network models performed best. The values of mean squared error and gradient are 0.248 and 4.23, respectively. The scatterplot with linear regression analysis showed that the regression coefficient in all samples is 0.99994. The final error accuracy of the BP neural network is -0.003791±0.4221102 µm. CONCLUSION: With the help of the BP neural network, the program can calculate the lenticule thickness and residual stromal thickness of SMILE surgery accurately. Combined with corneal parameters and refraction of patients, the program can intelligently and conveniently integrate medical information to identify candidates for SMILE surgery.

Rh-Catalyzed Borylative Cyclization of Acrylate-Containing 1,6-Enynes.

A Rh-catalyzed regioselective, stereoselective carbocyclization/borylation of acrylate-containing 1,6-enynes was described, which offers a general and practical method for constructing versatile and densely functionalized pyrrolidines with the (Z) geometry or the uncommon (E) geometry at the double bond with different substituents of the alkyne, with sterically hindered and conjugative aryl groups favoring the latter, featuring a tetrasubstituted vinyl boronate, containing an all-carbon quaternary stereocenter.

Effects of extrusion on physical properties of glutinous rice and its application in the improvement of quality characteristics of glutinous rice products.

This study investigated the effects of extrusion on the physical properties of glutinous rice and addressed the challenges associated with its hardened texture and reduced taste in glutinous rice products by adding extruded glutinous rice to assess their anti-retrogradation effect compared with different improvers. Glutinous rice flour with different gelatinization degrees was obtained by changing the initial moisture content of glutinous rice grains before extrusion, and their physicochemical properties and the effect of adding them to rice products were analyzed. Results showed that with the increase in moisture content, the viscosity, water absorption index of extruded glutinous rice flour, and product viscosity increased, while the gelatinization degree, water solubility index, and product elasticity decreased, and the hardness of the rice products showed a trend of first decreasing and then increasing. Twenty percent moisture content of glutinous rice products showed the best properties mentioned above. The effects of adding different improvers on retrogradation degree, quality characteristics, microstructure, and moisture migration of glutinous rice products were analyzed by texture profile analysis, sensory evaluation, scanning electron microscopy, and low-field nuclear magnetic resonance. It was found that soybean polysaccharides, xanthan gum, and extruded glutinous rice flour had better anti-retrogradation effects, while colloid and soybean polysaccharides provided a tighter and more three-dimensional internal structure to the rice products. Our study showed that extruded glutinous rice flour had good anti-retrogradation properties and little effect on flavor and taste, but it would increase the roughness and viscosity of the products, which had advantages and disadvantages compared with other improvers.

Switch effect on controlled water splitting by biaxial strain regulating the promising two-dimensional Janus X2PAs (X = Si, Ge and Sn) photocatalyst.

Two-dimensional photocatalytic materials with unique properties have been well-reported in recent decades. However, strategies for controlling the photocatalytic process are still ongoing. Herein, Janus X2PAs (X = Si, Ge and Sn) monolayers have been explored by first-principles calculations to meet this challenge. All strain-free X2PAs monolayers exhibit excellent photocatalytic properties with high carrier mobility (2.39 × 102-1.34 × 104 cm2 V-1 s-1), suitable band edge positions straddling the standard redox potential of water and large visible light absorption coefficients (up to 105 cm-1). Most importantly, a reaction switch effect is proposed for the first time towards controlling the microscopic photocatalytic process of water splitting on X2PAs monolayers through macroscopic mechanical strain. This effect renders the Janus X2PAs photocatalytic switches among the states of only oxygen evolution reaction, only hydrogen evolution reaction and the full redox reaction for controlled water splitting. This work not only provides a new avenue for designing highly tunable photocatalysts but also offers new physical insights into controlling the photocatalytic water-splitting reaction.

The highest-elevation frog provides insights into mechanisms and evolution of defenses against high UV radiation.

Defense against ultraviolet (UV) radiation exposure is essential for survival, especially in high-elevation species. Although some specific genes involved in UV response have been reported, the full view of UV defense mechanisms remains largely unexplored. Herein, we used integrated approaches to analyze UV responses in the highest-elevation frog, Nanorana parkeri. We show less damage and more efficient antioxidant activity in skin of this frog than those of its lower-elevation relatives after UV exposure. We also reveal genes related to UV defense and a corresponding temporal expression pattern in N. parkeri. Genomic and metabolomic analysis along with large-scale transcriptomic profiling revealed a time-dependent coordinated defense mechanism in N. parkeri. We also identified several microRNAs that play important regulatory roles, especially in decreasing the expression levels of cell cycle genes. Moreover, multiple defense genes (i.e., TYR for melanogenesis) exhibit positive selection with function-enhancing substitutions. Thus, both expression shifts and gene mutations contribute to UV adaptation in N. parkeri. Our work demonstrates a genetic framework for evolution of UV defense in a natural environment.

Co-Catalyzed Reductive Cyclization of Acrylate-Containing 1,6-Enynes.

A Co-catalyzed reductive cyclization of acrylate-containing 1,6-enynes is reported, providing an approach to construct five-membered carbocyclic and heterocyclic scaffolds containing enol ethers and all-carbon quaternary carbons. This novel process enables an E/Z mixture of 1,6-enynes to react with good functional group tolerance and good isolated yields, in an operationally simple manner.

Pd-Catalyzed Borylsilylative Cyclization of 1,6-Allenynes.

A Pd-catalyzed borylsilylative cyclization of 1,6-allenynes with PhMe2SiBpin was developed. This method provides a practical and general method to afford the carbocycles and heterocycles bearing silyl and boryl groups with excellent regioselectivities and stereoselectivities in high to excellent yields.

Multiple Mechanistic Models Reveal the Neuroprotective Effects of Diterpene Ginkgolides against Astrocyte-Mediated Demyelination via the PAF-PAFR Pathway.

Currently, therapies for ischemic stroke are limited. Ginkgolides, unique Folium Ginkgo components, have potential benefits for ischemic stroke patients, but there is little evidence that ginkgolides improve neurological function in these patients. Clinical studies have confirmed the neurological improvement efficacy of diterpene ginkgolides meglumine injection (DGMI), an extract of Ginkgo biloba containing ginkgolides A (GA), B (GB), and K (GK), in ischemic stroke patients. In the present study, we performed transcriptome analyses using RNA-seq and explored the potential mechanism of ginkgolides in seven in vitro cell models that mimic pathological stroke processes. Transcriptome analyses revealed that the ginkgolides had potential antiplatelet properties and neuroprotective activities in the nervous system. Specifically, human umbilical vein endothelial cells (HUVEC-T1 cells) showed the strongest response to DGMI and U251 human glioma cells ranked next. The results of pathway enrichment analysis via gene set enrichment analysis (GSEA) showed that the neuroprotective activities of DGMI and its monomers in the U251 cell model were related to their regulation of the sphingolipid and neurotrophin signaling pathways. We next verified these in vitro findings in an in vivo cuprizone (CPZ, bis(cyclohexanone)oxaldihydrazone)-induced model. GB and GK protected against demyelination in the corpus callosum (CC) and promoted oligodendrocyte regeneration in CPZ-fed mice. Moreover, GB and GK antagonized platelet-activating factor (PAF) receptor (PAFR) expression in astrocytes, inhibited PAF-induced inflammatory responses, and promoted brain-derived neurotrophic factor (BDNF) and ciliary neurotrophic factor (CNTF) secretion, supporting remyelination. These findings are critical for developing therapies that promote remyelination and prevent stroke progression.

Borylative Cyclization of 1,6-Allenynes Driven by BCl3.

A metal-free intramolecular borylative cyclization of 1,6-allenynes driven by BCl3 was developed. This method provides a general and practical strategy to construct valuable pyrrolidines containing all-carbon quaternary centers or 3,5-dihydroazepine derivatives depending on the substituents of the allene, with conjugative and sterically hindered phenyl groups favoring the latter.

Metal-Free Intramolecular Aminophosphination of Allenes.

A metal-free intramolecular aminophosphination of sulfonamidoallenes with diarylphosphine oxides and Tf2O was developed. This method offers a general and practical procedure to construct valuable alkenylphosphine-substituted N-heterocycles via the bifunctionalization reaction of allenes in good yields under mild conditions.

Direct Intramolecular Aminoboration of Allenes.

Direct intramolecular aminoboration of sulfonamidoallenes was realized using BCl3 as a boron source. The reactions benefited from the interaction between BCl3 and sulfonamides and provided a variety of borylvinyl heterocycles in good isolated yields. When chiral substrates were involved in the reactions, high stereoselectivity was observed, as can be ascertained by single-crystal X-ray diffraction experiments. Derivatization of the thus-obtained borylvinyl compounds proceeded readily, and different functionalities could be obtained via oxidation, halogenation, and Suzuki coupling reactions.

Baicalin Inhibits Coxsackievirus B3 Replication by Reducing Cellular Lipid Synthesis.

Baicalin is a flavonoid extracted from Scutellariae Radix and shows a variety of biological activities as reducing lipids, diminishing inflammation, and inhibiting bacterial infection. However, there is no report of baicalin against CVB3 infection. In this study, we found that baicalin can reduce viral titer in a dose-dependent manner in vitro at a dose with no direct virucidal effect. Moreover, we revealed that baicalin can also improve survival rate, reduce heart weight/body weight ratio, prevent virus replication, and relieve myocardial inflammation in the acute viral myocarditis mouse model induced by CVB3. Then, in order to explore the mechanism of baicalin inhibiting CVB3 replication, we respectively examined the expression of autophagosome marker LC3-II by Western blot, tested the concentration of free fatty acid (FFA) and cholesterol (CHO) by commercial kits, detected the mRNA levels of fatty acid synthase (Fasn) and acetyl coenzyme a carboxylase (ACC) by RT-PCR, and observed the lipid content of cells by fluorescence staining. The results showed that CVB3 infection increased autophagosome formation and lipid content in HeLa cells, but these changes were significantly blocked by baicalin. Finally, in order to confirm that baicalin inhibits viral replication and reduces autophagosome formation by reducing cellular lipids, we added exogenous palmitate to cell culture supernatants to promote intracellular lipid synthesis and found that palmitate did not alter LC3-II and CVB3/VP1 expression in HeLa cells with or without CVB3 infection. Interestingly, palmitate can reverse the inhibitory effect of baicalin on autophagosome formation and viral replication. In conclusion, our results indicated that lipids play an important role in CVB3 replication, and the effect of baicalin against CVB3 was associated with its ability to reduce cellular lipid synthesis to limit autophagosome formation.

Access to Stereodefined (E)-2-Silylallylboronates via Regioselective Chloroboration of Allenylsilanes.

A catalyst-free method for the highly regioselective chloroboration of allenylsilanes is described. In the presence of BCl3 and 2,6-lutidine, chloroboration of allenylsilanes proceeds smoothly without any catalyst, and the product could be treated with pinacol to afford the corresponding pinacol borates in one-pot reaction. This reaction provides a direct approach to construct valuable 2-silylallylboronate frameworks with operational simplicity and high atom-economy.

Direct Access to Allenylphosphine Oxides via a Metal Free Coupling of Propargylic Substrates with P(O)H Compounds.

A direct and convenient approach for the coupling of propargylic substrates with diphenylphosphine oxide in the presence of Tf2O and 2,6-lutidine has been developed. The method provides a general approach for the construction of attractive allenylphosphoryl skeletons with high atom and step economy under metal free conditions.

Genetic distribution analyses and population background explorations of Gansu Yugur and Guizhou Miao groups via InDel markers.

Insertion and deletion markers (InDels) have gained considerable attentions in population genetics and forensic research. In this study, we investigated genetic distributions of 30 InDels in Gansu Yugur and Guizhou Miao groups and evaluated their forensic application values. Genetic relationship analyses between Gansu Yugur, Guizhou Miao groups and other published populations were conducted based on these 30 InDels. Power of discrimination and power of exclusion in trio and duo cases of 30 InDels ranged from 0.3528 to 0.6247, 0.0937 to 0.1873, and 0.0219 to 0.1247 in Gansu Yugur group; and they ranged from 0.2579 to 0.6247, 0.0671 to 0.1874, and 0.0105 to 0.1247 in Guizhou Miao group. Obtained cumulative power of discrimination values indicated these InDels could be used for forensic individual identifications in both ethnic groups. Principal component analysis and phylogenetic reconstruction revealed that Gansu Yugur and Guizhou Miao groups had close affinities with their neighboring populations. Genetic structure analyses among these populations also indicated that studied Gansu Yugur and Guizhou Miao groups showed similar genetic structure with their neighboring populations. Further analyses of Y-STR, mtDNA, and ancestry informative markers should be conducted to better understand genetic backgrounds of Gansu Yugur and Guizhou Miao groups in the future.

Iodine catalyzed reduction of quinolines under mild reaction conditions.

A reduction of quinolines to synthetically versatile tetrahydroquinoline molecules with I2 and HBpin is described. In the presence of iodine (20 mol%) as a catalyst, reduction of quinolines and other N-heteroarenes proceeded readily with hydroboranes as the reducing reagents. The broad functional-group tolerance, good yields and mild reaction conditions imply high practical utility.

Catalyst free annulative thioboration of unfunctionalized olefins.

A direct and catalyst-free annulative thioboration of unfunctionalized olefins has been developed. In the presence of BCl3 as the sole boron source, the boryl group and thiol group are added to the C-C double bonds simultaneously. The boronic acids obtained can be protected to form synthetically ubiquitous pinacol boronate esters.

Genetic variation and forensic efficiency of autosomal insertion/deletion polymorphisms in Chinese Bai ethnic group: phylogenetic analysis to other populations.

Thirty insertion/deletion loci were utilized to study the genetic diversities of 125 bloodstain samples collected from Bai group in Yunnan Dali region, China. The observed heterozygosity and expected heterozygosity of the 30 loci ranged from 0.1520 to 0.5680, and 0.1927 to 0.4997, respectively. No deviations from Hardy-Weinberg equilibrium tests after Bonferroni correction were found at all 30 loci in Bai group. The cumulative probability of exclusion and combined discrimination power were 0.9859 and 0.9999999999887, respectively, which indicated the 30 loci could be used as complementary genetic markers for paternity testing and were qualified for personal identification in forensic cases. We found the studied Bai group had close relationships with Tibetan, Yi and Han groups from China by the population structure, principal component analysis, population differentiations, and phylogenetic reconstruction studies. Even so, for a better understanding of Bai ethnicity's genetic milieu, DNA genotyping at various genetic markers is necessary in future studies.

Relationship between cytotoxic T-lymphocyte antigen 4 -318C/T (rs5742909) gene polymorphism and the risk of acute rejection in renal transplantation.

Results on the relationship between CTLA4 -318C/T (rs5742909) gene polymorphism and risk of acute rejection in renal transplantation are still conflicting. This meta-analysis was performed to update the association between CTLA4 -318C/T and risk of acute rejection in renal transplantation. The association investigations were identified from PubMed and Cochrane Library, and eligible studies were included and synthesized using meta-analysis method. Twelve reports were included in this meta-analysis for the association of CTLA4 -318C/T gene polymorphism with acute rejection risk in renal transplantation, consisting of 728 acute rejection patients and 1628 non-acute rejection controls. The association between CTLA4 -318C/T gene polymorphism and acute rejection risk in renal transplantation for overall populations was not found in this meta-analysis (T allele: OR=0.96, 95% CI: 0.60-1.54, P=.88; TT genotype: OR=0.90, 95% CI: 0.47-1.71, P=.74; CC genotype: OR=1.00, 95% CI: 0.62-1.59, P=.98). Interestingly, T allele was associated with the risk of acute rejection in renal transplantation in African population. In conclusion, CTLA4 -318C/T gene polymorphism is not associated with the risk of acute rejection in renal transplantation in overall populations.