An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole‐genome sequencing data

Ancient DNA research has developed rapidly over the past few decades due to improvements in PCR and next‐generation sequencing (NGS) technologies, but challenges still exist. One major challenge in relation to ancient DNA research is to recover genuine endogenous ancient DNA sequences from raw sequencing data. This is often difficult due to degradation of ancient DNA and high levels of contamination, especially homologous contamination that has extremely similar genetic background with that of the real ancient DNA. In this study, we collected whole‐genome sequencing (WGS) data from 6 ancient samples to compare different mapping algorithms. To further explore more effective methods to separate endogenous DNA from homologous contaminations, we attempted to recover reads based on ancient DNA specific characteristics of deamination, depurination, and DNA fragmentation with different parameters. We propose a quick and improved pipeline for separating endogenous ancient DNA while simultaneously decreasing homologous contaminations to very low proportions. Our goal in this research was to develop useful recommendations for ancient DNA mapping and for separation of endogenous DNA to facilitate future studies of ancient DNA.     

PRGmatic: an efficient pipeline for collating genome-enriched second-generation sequencing data using a 'provisional-reference genome'

Second-generation sequencing is increasingly being used in combination with genome-enrichment techniques to amplify a large number of loci in many individuals for the purpose of population genetic and phylogeographic analysis. Compiling all the necessary tools to analyse these data is complex and time-consuming. Here, we assemble a set of programs and pipe them together with Perl, enabling research laboratories without a dedicated bioinformatician to utilize second-generation sequencing. User input is a folder of the second-generation sequencing reads sorted by individual (in FASTA format) and pipeline output is a folder of multi-FASTA files that correspond to loci (with 2 alleles called per individual). Additional output includes a summary file of the number of individuals per locus, observed and expected heterozygosity for each locus, distribution of multiple hits and summary statistics (θ, Tajima's D, etc.). This user-friendly, open source pipeline, which requires no a priori reference genome because it constructs its own, allows the user to set various parameters (e.g. minimum coverage) in the dependent programs (CAP3, BWA, SAMtools and VarScan) and facilitates evaluation of the nature and quality of data collected prior to analysis in software packages.     

Functional assessment of hepatobiliary secretion by 11C-cholylsarcosine positron emission tomography

Positron emission tomography (PET) with ¹¹C-cholylsarcosine (¹¹C-CSar), a radiolabelled synthetic N-methylglycine (sarcosine) conjugate of cholic acid, is a novel molecular imaging technique that enables quantitative assessment of the individual transport steps involved in hepatic secretion of conjugated bile acids. Here, we present the method and discuss its potential clinical and scientific applications based on findings in the first human study of healthy subjects and patients with cholestasis. We also present a clinical example of a patient studied during and six months after an episode of drug-induced cholestatic liver injury.     

A novel mutation of the SLC25A13 gene in a Chinese patient with citrin deficiency detected by target next-generation sequencing

Type II citrullinaemia, also known as citrin deficiency, is an autosomal recessive metabolic disorder, which is caused by pathogenic mutations in the SLC25A13 gene on chromosome 7q21.3. One of the clinical manifestations of type II citrullinaemia is neonatal intrahepatic cholestatic hepatitis caused by citrin deficiency (NICCD, OMIM# 605814). In this study, a 5-month-old female Chinese neonate diagnosed with type II citrullinaemia was examined. The diagnosis was based on biochemical and clinical findings, including organic acid profiling using a gas chromatography mass spectrometry (GC/MS), and the patient's parents were unaffected. Approximately 14 kb of the exon sequences of the SLC25A13 and two relative genes (ASS1 and FAH) from the proband and 100 case-unrelated controls were captured by array-based capture method followed by high-throughput next-generation sequencing. Two single-nucleotide mutations were detected in the proband, including the previous reported c.1177+1G>A mutation and a novel c.754G>A mutation in the SLC25A13 gene. Sanger sequence results showed that the patient was a compound heterozygote for the two mutations. The novel mutation (c.754G>A), which is predicted to affect the normal structure and function of citrin, is a candidate pathogenic mutation. Target sequence capture combined with high-throughput next-generation sequencing technologies is proven to be an effective method for molecular genetic testing of type II citrullinaemia.     

A new mutational mechanism for hypertrophic cardiomyopathy

We describe a male patient affected by hypertrophic cardiomyopathy (HCM) with no point mutations in the eight sarcomeric genes most commonly involved in the disease. By multiple ligation-dependent probe amplification (MLPA) we have identified a multi-exons C-terminus deletion in the cardiac myosin binding protein C (MYBPC3) gene. The rearrangement has been confirmed by long PCR and breakpoints have been defined by sequencing. The 3.5kb terminal deletion is mediated by Alu-repeat elements and is predicted to result in haploinsufficiency of MYBPC3. To exclude the presence of other rare pathogenic variants in additional HCM genes, we performed targeted next-generation sequencing (NGS) of 88 cardiomyopathy-associated genes but we did not identify any further mutation. Interestingly, the MYBPC3 multi-exons deletion was detectable by NGS. This finding broadens the range of mutational spectrum observed in HCM, contributing to understanding the genetic basis of the most common inherited cardiovascular disease. Moreover, our data suggest that NGS may represent a new tool to achieve a deeper insight into molecular basis of complex diseases, allowing to detect in a single experiment both point mutations and gene rearrangements.     

Integration of Controlled Intracellular Pressure Microinjection, lontophoresis, and Membrane Potential Measurement

Abstract: A novel device for intracellular microinjection was designed to integrate controlled pressure microinjection and electrical microinjection (iontophoresis) with membrane poten tial recording and a limited capacity for turgor measurement. The validity of the device was verified by microinjection of a mixture of the fluorescent probes, Texas Red sulfonyl chloride and 10 kDa-LYCH-dextran conjugate, into epidermal cells of var iegated Coleus blumei leaves. Continuous monitoring of the fluorochrome movement by confocal laser scanning microscopy evidenced that the novel device succeeded in differential micro-injection of the fluorescent probes by pressure and iontophor esis. The multifunctionality of the microinjection system was further demonstrated by showing that both microinjection methods functioned in parallel with cellular membrane poten tial measurements in Vicia faba stem tissue. Advantages and prospective applications of the integrated microinjectionjmem-brane potential measurement system are briefly discussed.     

Molecularly imprinted nanopatterns for the recognition of biological warfare agent ricin

Molecularly imprinted polymer (MIP) for biological warfare agent (BWA) ricin was synthesized using silanes in order to avoid harsh environments during the synthesis of MIP. The synthesized MIP was utilized for the recognition of ricin. The complete removal of ricin from polymer was confirmed by fluorescence spectrometer and SEM–EDAX. SEM and EDAX studies confirmed the attachment of silane polymer on the surface of silica gel matrix. SEM image of Ricin-MIP exhibited nanopatterns and it was found to be entirely different from the SEM image of non-imprinted polymer (NIP). BET surface area analysis revealed more surface area (227 m²/g) for Ricin-MIP than that of NIP (143 m²/g). In addition, surface area study also showed more pore volume (0.5010 cm³/g) for Ricin-MIP than that of NIP (0.2828 cm³/g) at 12 nm pore diameter confirming the presence of imprinted sites for ricin as the reported diameter of ricin is 12 nm. The recognition and rebinding ability of the Ricin-MIP was tested in aqueous solution. Ricin-MIP rebound more ricin when compared to the NIP. Chromatogram obtained with Ricin-MIP exhibited two peaks due to imprinting, however, chromatogram of NIP exhibited only one peak for free ricin. SDS-PAGE result confirmed the second peak observed in chromatogram of Ricin-MIP as ricin peak. Ricin-MIP exhibited an imprinting efficiency of 1.76 and it also showed 10% interference from the structurally similar protein abrin.     

慢性动脉血压监测模型在惊恐条件反射中的应用

目的：探索一种新的、可靠的模型,用于惊恐条件反射的相关研究。方法：通过使用条件刺激(声音)和非条件刺激(足部电击)相结合的方法,可使动物对条件刺激产生惊恐反应。同时对动脉血压进行长期监测并测定利多卡因阻断杏仁基底外侧核群前后的血压变化。结果：该惊恐条件反射建立后(需经4d训练),单独给予动物条件刺激即可引起血压明显升高。我们将它作为条件反射已形成的标志。此时,用利多卡因阻断杏仁基底外侧核群的作用,单独给予动物条件刺激不再引起血压明显升高。结论：慢性动脉血压监测模型在惊恐条件反射的研究中是一种可靠的动物模型。