Arctic introgression and chromatin regulation facilitated rapid Qinghai-Tibet Plateau colonization by an avian predator.

The Qinghai-Tibet Plateau (QTP), possesses a climate as cold as that of the Arctic, and also presents uniquely low oxygen concentrations and intense ultraviolet (UV) radiation. QTP animals have adapted to these extreme conditions, but whether they obtained genetic variations from the Arctic during cold adaptation, and how genomic mutations in non-coding regions regulate gene expression under hypoxia and intense UV environment, remain largely unknown. Here, we assemble a high-quality saker falcon genome and resequence populations across Eurasia. We identify female-biased hybridization with Arctic gyrfalcons in the last glacial maximum, that endowed eastern sakers with alleles conveying larger body size and changes in fat metabolism, predisposing their QTP cold adaptation. We discover that QTP hypoxia and UV adaptations mainly involve independent changes in non-coding genomic variants. Our study highlights key roles of gene flow from Arctic relatives during QTP hypothermia adaptation, and cis-regulatory elements during hypoxic response and UV protection.

RNA-combine: a toolkit for comprehensive analyses on transcriptome data from different sequencing platforms.

BACKGROUND: Understanding the transcriptome has become an essential step towards the full interpretation of the biological function of a cell, a tissue or even an organ. Many tools are available for either processing, analysing transcriptome data, or visualizing analysis results. However, most existing tools are limited to data from a single sequencing platform and only several of them could handle more than one analysis module, which are far from enough to meet the requirements of users, especially those without advanced programming skills. Hence, we still lack an open-source toolkit that enables both bioinformatician and non-bioinformatician users to process and analyze the large transcriptome data from different sequencing platforms and visualize the results. RESULTS: We present a Linux-based toolkit, RNA-combine, to automatically perform the quality assessment, downstream analysis of the transcriptome data generated from different sequencing platforms, including bulk RNA-seq (Illumina platform), single cell RNA-seq (10x Genomics) and Iso-Seq (PacBio) and visualization of the results. Besides, this toolkit is implemented with at least 10 analysis modules more than other toolkits examined in this study. Source codes of RNA-combine are available on GitHub: https://github.com/dongxuemin666/RNA-combine . CONCLUSION: Our results suggest that RNA-combine is a reliable tool for transcriptome data processing and result interpretation for both bioinformaticians and non-bioinformaticians.

Quantitative investigation of factors relevant to the T cell spot test for tuberculosis infection in active tuberculosis.

BACKGROUND: Previous qualitative studies suggested that the false negative rate of the T cell spot test for tuberculosis infection (T-SPOT.TB) is associated with many risk factors in tuberculosis patients. However, more precise quantitative studies are lacking. The purpose of this study was to investigate the factors affecting quantified spot-forming cells (SFCs) to early secreted antigenic target 6 kDa (ESAT-6) or culture filtrate protein 10 kDa (CFP-10) in patients with active tuberculosis. METHODS: We retrospectively analyzed the data of 360 patients who met the inclusion criteria. Using the SFCs to ESAT-6 or CFP-10 levels as dependent variables, variables with statistical significance in the univariate analysis were subjected to optimal scaling regression analysis. The combination of ESAT-6 and CFP-10 (i.e., T-SPOT.TB) was analyzed by the exact logistic regression model. RESULTS: The results showed that the SFCs to ESAT-6 regression model had statistical significance (P < 0.001) and that previous treatment and CD4+ and platelet counts were its independent risk factors (all P < 0.05). Their importance levels were 0.095, 0.596 and 0.100, respectively, with a total of 0.791. The SFCs to CFP-10 regression model also had statistical significance (P < 0.001); platelet distribution width and alpha-2 globulin were its independent risk factors (all P < 0.05). Their importance levels were 0.287 and 0.247, respectively, with a total of 0.534. The quantification graph showed that quantified SFCs to ESAT-6 or CFP-10 grading had a linear correlation with risk factors. Albumin-globulin ratio, CD4+ and CD8+ were independent risk factors for false negative T-SPOT.TB (all P < 0.05). CONCLUSIONS: In T-SPOT.TB-assisted diagnosis of patients with active tuberculosis, previous treatment, decreased CD4+ and platelet count might lead to the decreased SFCs to ESAT-6, decreased alpha-2 globulin and high platelet distribution width might lead to the decreased SFCs to CFP-10, decreased albumin-globulin ratio, CD4+ and CD8+ might lead to an increase in the false negative rate of the T-SPOT.TB.

Understanding the relationships between molecule structure and imprinting effect of two acetyl-nitrogen heterocyclic compounds.

The molecularly imprinted polymers (MIPs) for two structural analogs, 1,3,5-triacetyl-1,3,5-triazacyclohexane (TRAT) and 1,3,5,7-tetraacetyl-1,3,5,7-tetraazacyclooctane (TAT), have been synthesized respectively under the same conditions. The TAT-MIP showed excellent imprinting effect, whereas the TRAT-MIP did not. To understand the different imprinting effects of the MIPs prepared from these two templates, the geometric structures and energetic properties of complexes formed around TAT and TRAT were studied computationally. The results indicate that in liquid phase, for the complexes formed with TAT and its nearest neighbor molecules, the magnitude of the binding energy increases with the number of surrounding TAT, methacrylic acid, and acetonitrile (ACT), whereas for the cases of TRAT, the magnitude of the binding energy increases with the number of surrounding TRAT and trimethylolpropane trimethacrylate. The studied systems form stronger and thus more stable networks encapsulating TAT than with TRAT. ACT may also play an important role in the polymerization phase in stabilizing the shapes of the cavities that TATs reside in. We propose these as the major factors that affect the different imprinting effects of the two MIPs. Copyright © 2016 John Wiley & Sons, Ltd.

Energetic salts based on dipicrylamine and its amino derivative.

Energetic salts based on dipicrylamine and its amino derivative were synthesized. All salts were fully characterized by multinuclear NMR spectroscopy ((1)H, (13)C), vibrational spectroscopy (IR), and elemental analysis. Ethylenediammonium di-DPA (DPA=dipicrylamine) and 1,3-diaminoguanidinium DPA were further confirmed by single-crystal X-ray diffraction. These salts exhibit reasonable physical properties, such as high densities (1.71-1.81 g cm(-3)), good thermal stabilities (T(d) =155-285 °C), and low solubilities in water. The impact sensitivity of 1-methyl-3,4,5-triamino-1,2,4-triazolium DPA is lower than that of 2,4,6-trinitrotoluene (TNT), and for some other energetic salts their impact sensitivities are comparable to that of TNT. Based on experimental densities and theoretical calculations carried out by using the Gaussian 03 suite of programs, all the salts have calculated detonation pressures (22.5-27.8 GPa) and velocities (7226-7917 m s(-1)) that exceed those of conventional TNT. The toxicities of these salts measured by luminescent bacteria toxicity tests are much lower than that of TNT, and two binary eutectic mixtures with melting points that fall between 70 and 100 °C were identified.