Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle

As top predators, falcons possess unique morphological, physiological and behavioral adaptations that allow them to be successful hunters: for example, the peregrine is renowned as the world's fastest animal. To examine the evolutionary basis of predatory adaptations, we sequenced the genomes of both the peregrine (Falco peregrinus) and saker falcon (Falco cherrug), and we present parallel, genome-wide evidence for evolutionary innovation and selection for a predatory lifestyle. The genomes, assembled using Illumina deep sequencing with greater than 100-fold coverage, are both approximately 1.2 Gb in length, with transcriptome-assisted prediction of approximately 16,200 genes for both species. Analysis of 8,424 orthologs in both falcons, chicken, zebra finch and turkey identified consistent evidence for genome-wide rapid evolution in these raptors. SNP-based inference showed contrasting recent demographic trajectories for the two falcons, and gene-based analysis highlighted falcon-specific evolutionary novelties for beak development and olfaction and specifically for homeostasis-related genes in the arid environment–adapted saker

The 5-Hydroxymethylcytosine Landscape of Prostate Cancer

Analysis of DNA methylation is a valuable tool to understand disease progression and is increasingly being used to create diagnostic and prognostic clinical biomarkers. While conversion of cytosine to 5-methylcytosine (5mC) commonly results in transcriptional repression, further conversion to 5-hydroxymethylcytosine (5hmC) is associated with transcriptional activation. Here we perform the first study integrating whole-genome 5hmC with DNA, 5mC, and transcriptome sequencing in clinical samples of benign, localized, and advanced prostate cancer. 5hmC is shown to mark activation of cancer drivers and downstream targets. Furthermore, 5hmC sequencing revealed profoundly altered cell states throughout the disease course, characterized by increased proliferation, oncogenic signaling, dedifferentiation, and lineage plasticity to neuroendocrine and gastrointestinal lineages. Finally, 5hmC sequencing of cell-free DNA from patients with metastatic disease proved useful as a prognostic biomarker able to identify an aggressive subtype of prostate cancer using the genes TOP2A and EZH2, previously only detectable by transcriptomic analysis of solid tumor biopsies. Overall, these findings reveal that 5hmC marks epigenomic activation in prostate cancer and identify hallmarks of prostate cancer progression with potential as biomarkers of aggressive disease. SIGNIFICANCE: In prostate cancer, 5-hydroxymethylcytosine delineates oncogene activation and stage-specific cell states and can be analyzed in liquid biopsies to detect cancer phenotypes. See related article by Wu and Attard, p. 3880.publishedVersionPeer reviewe

Use of indocyanine green for detecting the sentinel lymph node in breast cancer patients: from preclinical evaluation to clinical validation.

Assessment of the sentinel lymph node (SLN) in patients with early stage breast cancer is vital in selecting the appropriate surgical approach. However, the existing methods, including methylene blue and nuclides, possess low efficiency and effectiveness in mapping SLNs, and to a certain extent exert side effects during application. Indocyanine green (ICG), as a fluorescent dye, has been proved reliable usage in SLN detection by several other groups. In this paper, we introduce a novel surgical navigation system to detect SLN with ICG. This system contains two charge-coupled devices (CCD) to simultaneously capture real-time color and fluorescent video images through two different bands. During surgery, surgeons only need to follow the fluorescence display. In addition, the system saves data automatically during surgery enabling surgeons to find the registration point easily according to image recognition algorithms. To test our system, 5 mice and 10 rabbits were used for the preclinical setting and 22 breast cancer patients were utilized for the clinical evaluation in our experiments. The detection rate was 100% and an average of 2.7 SLNs was found in 22 patients. Our results show that the usage of our surgical navigation system with ICG to detect SLNs in breast cancer patients is technically feasible

Ultrasound-assisted pH-shifting to construct a stable aqueous solution of paprika oleoresin using egg yolk low-density lipoprotein as a natural liposome-like nano-emulsifier

In this study, a stable aqueous solution of paprika oleoresin (PO, the natural colorant extracted from the fruit peel of Capsicum annuum L) was constructed. The solubility of PO in an alkline aqueous solution (pH 10.95–11.10) increased rapidly. However, the aqueous solution of PO (pH 12.00) was unstable, obvious stratification was observed, and the color retention rate was only 52.99% after 28 days of storage. Chicken egg yolk low-density lipoprotein (LDL) was added combined with ultrasonic treatment to improve the stability of LDL-PO solution. The method could decrease the turbidity by 17.5 %, reduce the average particle size of the LDL-PO solution (13.9%), and enhance the interaction and combination of LDL and PO. The prepared PO aqueous solution was used in yogurt, egg white gel, fish balls and soymilk, and it could significantly improve the color of products and provided potential health benefits

Seminal plasma metabolomics signatures of normosmic congenital hypogonadotropic hypogonadism

Background: Normosmic congenital hypogonadotropic hypogonadism (nCHH) is a rare disease, whose pathogenesis remains unclear. Here, we conducted untargeted metabolomics and lipidomics to identify seminal plasma signatures of nCHH, and to study the effect of LH and FSH deficiency on semen. Methods: Twenty-five diagnosed patients with nCHH (HH group) and twenty-three healthy participants (HC group) were enrolled. Laboratory parameters, seminal plasma samples and patients’ medical data were collected. Untargeted metabolomics and lipidomic profiling were performed using mass spectrometry (MS). Results: The metabolomics profiling are altered among patients with nCHH and healthy controls. There are 160 kinds of differential metabolites and the main different lipid species are TAG, PC, SM and PE. Conclusions: The metabolomics profiles in patients with nCHH changed. We hope that this work provides important insights into the pathophysiology of nCHH

Planar Laser Induced Fluorescence of OH for Thermometry in a Flow Field Based on Two Temperature Point Calibration Method

In view of the uncertainty in the calibration process of two-color plane laser-induced fluorescence (PLIF) temperature measurement, a new calibration method is proposed, in which the influence of fluorescence yield is considered. The calibration process was carried out at high and low temperature region, respectively. Then, the bias of thermometry results origin from quenching is restrained. This new calibration method is validated in a jet flame with temperature range of 1300–1800 K. Here, the temperature results from Coherent Anti-Stokes Raman scattering (CARS), single-point calibrated PLIF, and two-point calibrated PLIF are all acquired with the maximum standard errors of 13 K, 36 K, and 37 K, respectively. The temperature deviation between the average results from PLIF and Coherent Anti-Stokes Raman scattering (CARS) is 120 K and 10 K, when the two-point and one-point calibration methods are used. Therefore, the two-point calibrated PLIF is preferred in the combustion field, especially with a large temperature range and strong quenching coefficient

The normal and tumor-metastasis pathology slices of SLN dissected by ICG-guided surgery.

<p>All of the dissected SLNs were sent in for pathological examination. After the conventional Hematoxylin-Eosin (HE) staining, the results proved that all of the dissected tissue specimens were lymph nodes. Figure a. shows normal sentinel lymph node cells with no cancer metastasis. Figure b. shows infiltrating ductal breast cancer.</p

Schematic diagram of the surgical navigation system and its application in surgery.

<p>a. The principle figure of the surgical navigation system clarifying the operation course of the system. When the LED light illuminated the surgical area, the ICG dye emitted NIR light. The emission and reflection of the halogen light went through the lens to the prism. Then, the light was equally divided into two beams by the prism. One beam went through the filter to the color CCD and the other to the EMCCD. All of the data collected from the CCD were transferred to the computer, and the computer controlled the CCD. b. The hardware of the surgical navigation system. c. User interface of the software offering exposure time and auto capture interval time parameter settings. d. Image acquisition interface as an example of the capture mode results. e. Preoperative preparation in the operating room. f. Intraoperative diagnosis with a surgical navigation system carried out during the surgery.</p