Detection and Removal of Aristolochic Acid in Natural Plants, Pharmaceuticals, and Environmental and Biological Samples: A Review.

Aristolochic acids (AAs) are a toxic substance present in certain natural plants. Direct human exposure to these plants containing AAs leads to a severe and irreversible condition known as aristolochic acid nephropathy (AAN). Additionally, AAs accumulation in the food chain through environmental mediators can trigger Balkan endemic nephropathy (BEN), an environmental variant of AAN. This paper presents a concise overview of the oncogenic pathways associated with AAs and explores the various routes of environmental exposure to AAs. The detection and removal of AAs in natural plants, drugs, and environmental and biological samples were classified and summarized, and the advantages and disadvantages of the various methods were analyzed. It is hoped that this review can provide effective insights into the detection and removal of AAs in the future.

Chromosome-level genome of Camellia lanceoleosa provides a valuable resource for understanding genome evolution and self-incompatibility.

The section Oleifera (Theaceae) has attracted attention for the high levels of unsaturated fatty acids found in its seeds. Here, we report the chromosome-scale genome of the sect. Oleifera using diploid wild Camellia lanceoleosa with a final size of 3.00 Gb and an N50 scaffold size of 186.43 Mb. Repetitive sequences accounted for 80.63% and were distributed unevenly across the genome. Camellia lanceoleosa underwent a whole-genome duplication event approximately 65 million years ago (65 Mya), prior to the divergence of C. lanceoleosa and Camellia sinensis (approx. 6-7 Mya). Syntenic comparisons of these two species elucidated the genomic rearrangement, appearing to be driven in part by the activity of transposable elements. The expanded and positively selected genes in C. lanceoleosa were significantly enriched in oil biosynthesis, and the expansion of homomeric acetyl-coenzyme A carboxylase (ACCase) genes and the seed-biased expression of genes encoding heteromeric ACCase, diacylglycerol acyltransferase, glyceraldehyde-3-phosphate dehydrogenase and stearoyl-ACP desaturase could be of primary importance for the high oil and oleic acid content found in C. lanceoleosa. Theanine and catechins were present in the leaves of C. lanceoleosa. However, caffeine can not be dectected in the leaves but was abundant in the seeds and roots. The functional and transcriptional divergence of genes encoding SAM-dependent N-methyltransferases may be associated with caffeine accumulation and distribution. Gene expression profiles, structural composition and chromosomal location suggest that the late-acting self-incompatibility of C. lanceoleosa is likely to have favoured a novel mechanism co-occurring with gametophytic self-incompatibility. This study provides valuable resources for quantitative and qualitative improvements and genome assembly of polyploid plants in sect. Oleifera.

Triacylglycerol biosynthesis in shaded seeds of tung tree (Vernicia fordii) is regulated in part by Homeodomain Leucine Zipper 21.

Light quantity and quality affect many aspects of plant growth and development. However, few reports have addressed the molecular connections between seed oil accumulation and light conditions, especially dense shade. Shade-avoiding plants can redirect plant resources into extension growth at the expense of leaf and root expansion in an attempt to reach areas containing richer light. Here, we report that tung tree seed oil accumulation is suppressed by dense shade during the rapid oil accumulation phase. Transcriptome analysis confirmed that oil accumulation suppression due to dense shade was attributed to reduced expression of fatty acid and triacylglycerol biosynthesis-related genes. Through weighted gene co-expression network analysis, we identified 32 core transcription factors (TFs) specifically upregulated in densely shaded seeds during the rapid oil accumulation period. Among these, VfHB21, a class I homeodomain leucine zipper TF, was shown to suppress expression of FAD2 and FADX, two key genes related to α-eleostearic acid, by directly binding to HD-ZIP I/II motifs in their respective promoter regions. VfHB21 also binds to similar motifs in the promoters of VfWRI1 and VfDGAT2, two additional key seed lipid regulatory/biosynthetic genes. Functional conservation of HB21 during plant evolution was demonstrated by the fact that AtWRI1, AtSAD1, and AtFAD2 were downregulated in VfHB21-overexpressor lines of transgenic Arabidopsis, with concomitant seed oil reduction, and the fact that AtHB21 expression also was induced by shade. This study reveals some of the regulatory mechanisms that specifically control tung tree seed oil biosynthesis and more broadly regulate plant storage carbon partitioning in response to dense shade conditions.

The genomic origins of the Bronze Age Tarim Basin mummies.

The identity of the earliest inhabitants of Xinjiang, in the heart of Inner Asia, and the languages that they spoke have long been debated and remain contentious1. Here we present genomic data from 5 individuals dating to around 3000-2800 BC from the Dzungarian Basin and 13 individuals dating to around 2100-1700 BC from the Tarim Basin, representing the earliest yet discovered human remains from North and South Xinjiang, respectively. We find that the Early Bronze Age Dzungarian individuals exhibit a predominantly Afanasievo ancestry with an additional local contribution, and the Early-Middle Bronze Age Tarim individuals contain only a local ancestry. The Tarim individuals from the site of Xiaohe further exhibit strong evidence of milk proteins in their dental calculus, indicating a reliance on dairy pastoralism at the site since its founding. Our results do not support previous hypotheses for the origin of the Tarim mummies, who were argued to be Proto-Tocharian-speaking pastoralists descended from the Afanasievo1,2 or to have originated among the Bactria-Margiana Archaeological Complex3 or Inner Asian Mountain Corridor cultures4. Instead, although Tocharian may have been plausibly introduced to the Dzungarian Basin by Afanasievo migrants during the Early Bronze Age, we find that the earliest Tarim Basin cultures appear to have arisen from a genetically isolated local population that adopted neighbouring pastoralist and agriculturalist practices, which allowed them to settle and thrive along the shifting riverine oases of the Taklamakan Desert.

Tung Tree (Vernicia fordii) Genome Provides A Resource for Understanding Genome Evolution and Improved Oil Production.

Tung tree (Vernicia fordii) is an economically important woody oil plant that produces tung oil rich in eleostearic acid. Here, we report a high-quality chromosome-scale genome sequence of tung tree. The genome sequence was assembled by combining Illumina short reads, Pacific Biosciences single-molecule real-time long reads, and Hi-C sequencing data. The size of tung tree genome is 1.12 Gb, with 28,422 predicted genes and over 73% repeat sequences. The V. fordii underwent an ancient genome triplication event shared by core eudicots but no further whole-genome duplication in the subsequent ca. 34.55 million years of evolutionary history of the tung tree lineage. Insertion time analysis revealed that repeat-driven genome expansion might have arisen as a result of long-standing long terminal repeat retrotransposon bursts and lack of efficient DNA deletion mechanisms. The genome harbors 88 resistance genes encoding nucleotide-binding sites; 17 of these genes may be involved in early-infection stage of Fusarium wilt resistance. Further, 651 oil-related genes were identified, 88 of which are predicted to be directly involved in tung oil biosynthesis. Relatively few phosphoenolpyruvate carboxykinase genes, and synergistic effects between transcription factors and oil biosynthesis-related genes might contribute to the high oil content of tung seed. The tung tree genome constitutes a valuable resource for understanding genome evolution, as well as for molecular breeding and genetic improvements for oil production.

Bacillus camelliae sp. nov., isolated from Pu'er tea.

A novel aerobic, Gram-stain-positive, sporogenous, rod-shaped bacterial strain, 7578-1T, was isolated from ripened Pu'er tea. Based on 16S rRNA gene sequence similarity comparisons, strain 7578-1T was grouped into the genus Bacillus and appeared to be closely related to the type strains Bacillus shackletoniiLMG 18435T (98.4 %), Bacillus acidicolaDSM 14745T (97.6 %), Bacillus paralicheniformis KACC 18426T (97.2 %) and Bacillus ginsengihumi KCTC 13944T (96.7 %). The fatty acid profile containing the major fatty acids, iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0 supported the allocation of strain 7578-1T to the genus Bacillus. The strain had a cell-wall type A1γ peptidoglycan with meso-diaminopimelic acid as the diagnostic diamino acid. The major menaquinone was MK-7 (95 %). The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, one unidentified phospholipid and one unidentified lipid. The average nucleotide identity values between strain 7578-1T and its most closely related species were 67.8-82.4 % by OrthoANIu analysis. The DNA-DNA relatedness value between strain 7578-1T and the type strains of closely related species were 17-39 %, again indicating that strain 7578-1T represented a novel species in the genus Bacillus. The DNA G+C content of strain 7578-1T was 36.0 mol%. On the basis of the presented polyphasic evidence, strain 7578-1T is considered to represent a novel species of the genus Bacillus, for which we propose the name Bacillus camelliae sp. nov. The type strain is 7578-1T (=CGMCC 1.15374T=KCTC 33845T).

Daclatasvir: A Review of Preclinical and Clinical Pharmacokinetics.

Daclatasvir is a first-in-class, highly selective, hepatitis C virus, non-structural protein 5a polymerase replication complex inhibitor with picomolar potency and broad genotypic coverage in vitro. Daclatasvir undergoes rapid absorption, with a time to reach maximum plasma concentration of 1-2 h and an elimination half-life of ~ 10 to 14 h observed in single-ascending dose studies. Steady state was achieved by day 4 in multiple-ascending dose studies. Daclatasvir can be administered without regard to food or pH modifiers. Daclatasvir exposure is similar between healthy subjects and subjects infected with hepatitis C virus. Intrinsic factors such as age, race, or sex do not impact daclatasvir exposure. No dose adjustment is necessary for patients with any degree of hepatic or renal impairment. Daclatasvir has low-to-moderate clearance with the predominant route of elimination via cytochrome P450 3A4-mediated metabolism and P-glycoprotein excretion and intestinal secretion. Renal clearance is a minor route of elimination for daclatasvir. As a result, the dose of daclatasvir should be reduced from 60 to 30 mg once daily when co-administered with strong inhibitors of cytochrome P450 3A4. No dose adjustment is required when daclatasvir is co-administered with moderate inhibitors of cytochrome P450 3A4. The dose of daclatasvir should be increased from 60 to 90 mg once daily when co-administered with moderate inducers of cytochrome P450 3A4. Co-administration of daclatasvir with strong inducers of cytochrome P450 3A4 is contraindicated. Concurrent medications with inhibitory effects on P-glycoprotein without concurrent inhibition of cytochrome P450 3A4 are unlikely to cause marked changes in daclatasvir exposure, as the clearance of daclatasvir is through both cytochrome P450 3A4 and P-glycoprotein. The potential for daclatasvir to affect the pharmacokinetics of concomitantly administered drugs that are substrates of the cytochrome P450 enzyme system is low. In vitro, daclatasvir is a weak-to-moderate inhibitor of transporters including organic cation transporter 1, P-glycoprotein, organic transporting polypeptide 1B1, organic transporting polypeptide 1B3, and breast cancer resistance protein, although in clinical studies, daclatasvir has not altered the pharmacokinetics of concomitantly administered drugs that are substrates of these transporters to an appreciable degree, except for rosuvastatin. In summary, daclatasvir is a hepatitis C virus, non-structural protein 5a-selective inhibitor with a well-characterized pharmacokinetic profile that forms part of potent and well-tolerated all-oral treatment regimens for chronic hepatitis C virus infection.

Pullulanibacillus camelliae sp. nov., isolated from Pu'er tea.

A novel Gram-stain-positive, strictly aerobic, endospore-forming, rod-shaped bacterial strain 7578-24T was isolated from ripened Pu'er tea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 7578-24T clustered with species of the genus Pullulanibacillus in the family Sporolactobacillaceae with 97.8-95.2 % sequence similarities, and was most closely related to Pullulanibacillus pueri YN3T with 97.8 % 16S rRNA gene sequence similarity. The DNA-DNA relatedness value between strain 7578-24T and P. pueri YN3T was 35 %. Strain 7578-24T had a cell-wall type A1γ peptidoglycan with meso-diaminopimelic acid as the diagnostic diamino acid. The major menaquinone was menaquinone 7 (MK-7). C18 : 1ω7c (45.4 %), anteiso-C17 : 0 (30.6 %) and anteiso-C15 : 0 (10.1 %) were the predominant fatty acids, and diphosphatidylglycerol, phosphatidylglycerol, five unknown phospholipids and one unknown aminolipid were the major polar lipids. The DNA G+C content of strain 7578-24T was 45.2 mol%. Strain 7578-24T could be differentiated from other related species of the genus Pullulanibacillus based on phenotypic characteristics, chemotaxonomic differences, phylogenetic analysis and DNA-DNA hybridization data. On the basis of polyphasic evidence from this study, a novel species of the genus Pullulanibacillus named Pullulanibacillus camelliae sp. nov. is proposed, with strain 7578-24T (=CGMCC 1.15371T=JCM 31236T) as the type strain.

A fluorescence turn-on detection of copper(II) based on the template-dependent click ligation of oligonucleotides.

In this work, a fluorescence turn-on method for copper(II) detection is reported. A molecular beacon (MB) was designed as a template. Cu(2+) was reduced to Cu(+) in the presence of a reductant (ascorbic acid). Two short single-stranded oligonucleotides one was labeled with a 5'-alkyne and the other with 3'-azide group, proceeded a template-dependent chemical ligation through the Cu(I)-catalyzed azide-alkyne cycloaddition. The newly generated click-ligated long chain oligonucleotide, which was complementary to the MB, opened the MB hairpin structure and resulted in a turn on fluorescence. The increase in fluorescence intensity is directly proportional to the amount of Cu(2+) added to the assay solution. The present assay is quite sensitive and allows the detection of 2 nM Cu(2+). The described assay also exhibits high selectivity over other metal ions.

Discovery and early clinical evaluation of BMS-605339, a potent and orally efficacious tripeptidic acylsulfonamide NS3 protease inhibitor for the treatment of hepatitis C virus infection.

The discovery of BMS-605339 (35), a tripeptidic inhibitor of the NS3/4A enzyme, is described. This compound incorporates a cyclopropylacylsulfonamide moiety that was designed to improve the potency of carboxylic acid prototypes through the introduction of favorable nonbonding interactions within the S1' site of the protease. The identification of 35 was enabled through the optimization and balance of critical properties including potency and pharmacokinetics (PK). This was achieved through modulation of the P2* subsite of the inhibitor which identified the isoquinoline ring system as a key template for improving PK properties with further optimization achieved through functionalization. A methoxy moiety at the C6 position of this isoquinoline ring system proved to be optimal with respect to potency and PK, thus providing the clinical compound 35 which demonstrated antiviral activity in HCV-infected patients.

Real-time fluorometric turn-on assay for protease activity and inhibitor screening with a benzoperylene probe.

A real-time fluorescence turn-on strategy for protease activity and inhibitor screening has been developed. A negatively charged benzo[ghi]perylene derivative (probe 1) was employed. Protamine is a cationic protein which can induce aggregation of probe 1 via strong electrostatic and hydrophobic interactions. The fluorescence of probe 1 was efficiently quenched. In the presence of a protease, protamine was enzymatically hydrolyzed and probe 1 de-aggregated. The recovery of the probe 1 monomer fluorescence could be detected. The protease activity could be monitored in real-time. In addition, upon addition of a protease inhibitor, the protease-catalyzed hydrolysis was inhibited, which led to a decreased fluorescence recovery. The fluorometric assay thus could also be employed for screening protease inhibitors.

[Wastewater pollution characteristics from typical intensive pig farms in the Pearl River Delta and its ecological risk assessment].

Based on the wastewater quality investigation data from March 2009 to November 2011, wastewater qualities from typical intensive pig farms were assessed in the Pearl River Delta by single and comprehensive pollution index model. The results showed that key pollutants of piggery wastewater were fecal coliform (FC), total phosphorus (TP), chemical oxygen demand (COD) and biochemical oxygen demand (BOD), with their average mass concentrations of 1.98 x 10(9) CFU.L-1, 158.61 mg.L-1, 5 608.68 mg.L-1 and 1984.34 mg.L-1, respectively; key pollutants of biogas slurry were FC, TP, ammonia nitrogen (NH+4 -N) and suspended substance (SS), with their average mass concentrations of 8. 10 x 10(6) CFU.L-1, 81.76 mg.L-1, 476.24 mg.L-1 and 464.58 mg.L-1, respectively. Under the effect of wastewater pollutants, environment surrounding of typical intensive pig farms was seriously polluted, which decreased gradually from piggery wastewater to biogas slurry, and comprehensive pollution indices were 11.41, 6.91, 5.27, respectively. The risk analysis showed that the high-risk wastewater could never be discharged directly and irrigated crops. After the anaerobic treatment, FC, TP, NH+4 -N and SS were still strong factors with the potential ecological risk in the biogas slurry. In the long run, the ecological risk still exists for direct discharge or irrigation of them, and it is necessary to apply further treatment.

Selenium speciation in flue desulfurization residues.

Flue gas from coal combustion contains significant amounts of volatile selenium (Se). The capture of Se in the flue gas desulfurization (FGD) scrubber unit has resulted in a generation of metal-laden residues. It is important to determine Se speciation to understand the environmental impact of its disposal. A simple method has been developed for selective inorganic Se(IV), Se(VI) and organic Se determination in the liquid-phase FGD residues by hydride generation atomic fluorescence spectrometry (AFS). It has been determined that Se(IV), Se(VI) and organic Se can be accurately determined with detection limits (DL) of 0.05, 0.06 and 0.06 microg/L, respectively. The accuracy of the proposed method was evaluated by analyzing the certified reference material, NIST CRM 1632c, and also by analyzing spiked tap-water samples. Analysis indicates that the concentration of Se is high in FGD liquid residues and primarily exists in a reduced state as selenite (Se(IV)). The toxicity of Se(IV) is the strongest of all Se species. Flue gas desulfurization residues pose a serious environmental risk.

Folate and fiber in the prevention of colorectal cancer: between shadows and the light.

Colorectal cancer (CRC) is one of the most common malignancies and causes of cancer deaths throughout the world. Endoscopy has its functional and financial limitations; therefore, chemoprevention might be crucial in reducing the incidence of CRC. Although a number of studies have demonstrated the potential chemopreventive effects of folate (or folic acid), many challenges still remain. The relationship between folate intake and CRC risk is a complex association that might depend on many factors including gender, age, alcohol consumption, and smoking, all of which interfere with folate metabolism. The supplementary dose of fiber, the length of time required to observe the effects, and confounding factors exposed during the trial might also influence these findings. Therefore, more evidence from clinical studies is needed regarding the mechanisms that underlie the actions of bioactive food components in minimizing the risk of CRC.

Evidence that a West-East admixed population lived in the Tarim Basin as early as the early Bronze Age.

BACKGROUND: The Tarim Basin, located on the ancient Silk Road, played a very important role in the history of human migration and cultural communications between the West and the East. However, both the exact period at which the relevant events occurred and the origins of the people in the area remain very obscure. In this paper, we present data from the analyses of both Y chromosomal and mitochondrial DNA (mtDNA) derived from human remains excavated from the Xiaohe cemetery, the oldest archeological site with human remains discovered in the Tarim Basin thus far. RESULTS: Mitochondrial DNA analysis showed that the Xiaohe people carried both the East Eurasian haplogroup (C) and the West Eurasian haplogroups (H and K), whereas Y chromosomal DNA analysis revealed only the West Eurasian haplogroup R1a1a in the male individuals. CONCLUSION: Our results demonstrated that the Xiaohe people were an admixture from populations originating from both the West and the East, implying that the Tarim Basin had been occupied by an admixed population since the early Bronze Age. To our knowledge, this is the earliest genetic evidence of an admixed population settled in the Tarim Basin.