Hidden antibiotics: Where to uncover?

The struggle of humans versus pathogens is a never ending battle. Since the discovery of antibiotics humans have tipped the scales in their favour, but today bacteria are nullifying this advantage by developing resistance mechanisms against these molecules. The plethora of different antibiotics active against pathogens is shrinking while the discovery of new molecules is arduous. Especially the development of drugs active against Gram^? pathogens continues slowly. New strategies to discover novel, potent antibiotics are hence needed. Adopting the optimistic view of technological singularity, innovative and disruptive approaches are required and hence proposed to lift the current conundrum. In this review, questions are answered on where and how to look for new natural product hit molecules with antibacterial activity, on how the field of synthetic biology can aid the contemporary pharmaceutical challenge and whether we are ready to make the transition towards other approaches, such as narrow-spectrum antibiotics and phage therapy.     

Ratiometric fluorescence imaging of nuclear pH in living cells using Hoechst-tagged fluorescein

Small-molecule fluorescent sensors that allow specific measurement of nuclear pH in living cells will be valuable for biological research. Here we report that Hoechst-tagged fluorescein (hoeFL), which we previously developed as a green fluorescent DNA-staining probe, can be used for this purpose. Upon excitation at 405 nm, the hoeFL–DNA complex displayed two fluorescence bands around 460 nm and 520 nm corresponding to the Hoechst and fluorescein fluorescence, respectively. When pH was changed from 8.3 to 5.5, the fluorescence intensity ratio (F₅₂₀/F₄₆₀) significantly decreased, which allowed reliable pH measurement. Moreover, because hoeFL binds specifically to the genomic DNA in cells, it was applicable to visualize the intranuclear pH of nigericin-treated and intact living human cells by ratiometric fluorescence imaging.     

Using Flatbed Scanners to Collect High-resolution Time-lapsed Images of the Arabidopsis Root Gravitropic Response

Research efforts in biology increasingly require use of methodologies that enable high-volume collection of high-resolution data. A challenge laboratories can face is the development and attainment of these methods. Observation of phenotypes in a process of interest is a typical objective of research labs studying gene function and this is often achieved through image capture. A particular process that is amenable to observation using imaging approaches is the corrective growth of a seedling root that has been displaced from alignment with the gravity vector. Imaging platforms used to measure the root gravitropic response can be expensive, relatively low in throughput, and/or labor intensive. These issues have been addressed by developing a high-throughput image capture method using inexpensive, yet high-resolution, flatbed scanners. Using this method, images can be captured every few minutes at 4,800 dpi. The current setup enables collection of 216 individual responses per day. The image data collected is of ample quality for image analysis applications.     

MALDI-Mass Spectrometric Imaging for the Investigation of Metabolites in Medicago truncatula Root Nodules

Most techniques used to study small molecules, such as pharmaceutical drugs or endogenous metabolites, employ tissue extracts which require the homogenization of the tissue of interest that could potentially cause changes in the metabolic pathways being studied¹. Mass spectrometric imaging (MSI) is a powerful analytical tool that can provide spatial information of analytes within intact slices of biological tissue samples^1-5. This technique has been used extensively to study various types of compounds including proteins, peptides, lipids, and small molecules such as endogenous metabolites. With matrix-assisted laser desorption/ionization (MALDI)-MSI, spatial distributions of multiple metabolites can be simultaneously detected. Herein, a method developed specifically for conducting untargeted metabolomics MSI experiments on legume roots and root nodules is presented which could reveal insights into the biological processes taking place. The method presented here shows a typical MSI workflow, from sample preparation to image acquisition, and focuses on the matrix application step, demonstrating several matrix application techniques that are useful for detecting small molecules. Once the MS images are generated, the analysis and identification of metabolites of interest is discussed and demonstrated. The standard workflow presented here can be easily modified for different tissue types, molecular species, and instrumentation.     

《名古屋议定书》背景下我国传统知识的保护:以德昂族酸茶为例

中国于2016年9月6日成为《名古屋议定书》缔约方, 意味着遗传资源及相关传统知识的保护以及获取与惠益分享制度, 在国际和国内层面已经步入履行阶段。传统知识的防御性保护是防范生物剽窃, 建设性保护是促进惠益分享。本研究通过多年的实地调研发现, 德昂族酸茶作为一类与遗传资源相关的传统知识, 在原持有方不知情同意的情况下, 被某利用方申请了专利, 构成了生物剽窃。本研究指出, 传统知识防御性保护可考虑修订国内专利法, 将传统知识强制性来源披露要求纳入其中, 进而防范生物剽窃。为促进传统知识的持有方分享应得惠益和可持续利用, 本研究建议依据《名古屋议定书》精神, 通过立法制定特殊制度, 创造性地发展出可行的惠益分享制度, 区分不同的传统知识主体资格, 以事先知情同意程序和共同商定条件为途径, 以补偿责任或知识共享许可协议为手段, 来实现《生物多样性公约》的保护与可持续利用两大目标, 方能达成传统知识的建设性保护。     

A new global 1-km dataset of percentage tree cover derived from remote sensing

Accurate assessment of the spatial extent of forest cover is a crucial requirement for quantifying the sources and sinks of carbon from the terrestrial biosphere. In the more immediate context of the United Nations Framework Convention on Climate Change, implementation of the Kyoto Protocol calls for estimates of carbon stocks for a baseline year as well as for subsequent years. Data sources from country level statistics and other ground‐based information are based on varying definitions of ‘forest’ and are consequently problematic for obtaining spatially and temporally consistent carbon stock estimates. By combining two datasets previously derived from the Advanced Very High Resolution Radiometer (AVHRR) at 1 km spatial resolution, we have generated a prototype global map depicting percentage tree cover and associated proportions of trees with different leaf longevity (evergreen and deciduous) and leaf type (broadleaf and needleleaf). The product is intended for use in terrestrial carbon cycle models, in conjunction with other spatial datasets such as climate and soil type, to obtain more consistent and reliable estimates of carbon stocks. The percentage tree cover dataset is available through the Global Land Cover Facility at the University of Maryland at http://glcf.umiacs.umd.edu .     

Evaluation of the anti-fatigue effects of a traditional herbal drug,Gongjin-dan,under insufficient sleep conditions: study protocol for a randomised controlled trial

BackgroundMany herbal medicines are traditionally used as anti-fatigue agents in east Asian countries; however, there is a dearth of clinical evidence supporting the anti-fatigue effects of such medicines and their mechanisms. This study is a feasibility trial to assess the clinical efficacy of Gongjin-dan (GJD) and verify its mechanisms by exploring fatigue outcomes, including endocrine and immunological biomarkers in humans.Methods/DesignTo investigate the anti-fatigue effects of GJD and the mechanism underlying these effects, a randomised, double-blind, placebo-controlled crossover clinical trial was designed. Participants (24 healthy male volunteers) will be hospitalised for 4 days (3 nights), during which acute fatigue and stress conditions will be induced by sleep deprivation, and GJD or a placebo will be administered (twice daily). The primary outcome will be changes in serum cortisol levels, measured in the morning, as an objective biomarker of sleep deprivation-induced fatigue and stress. The secondary outcomes will include: the Fatigue Severity Scale; the Brief Fatigue Inventory, and the Leeds Sleep Evaluation Questionnaire scores; levels of salivary cortisol, epinephrine, norepinephrine, oxidative stress-related biomarkers, homocysteine, and immunological factors; and heart rate variability. After a washout period of more than 4 weeks, a second treatment phase will commence in which participants who were previously administered the placebo will receive the drug and vice versa, following the same treatment regime as in the first phase.DiscussionThis study protocol provides a unique opportunity to enhance our understanding of fatigue and the effects of GJD on fatigue in terms of endocrine and immunological mechanisms by validating the study design and determining feasibility. Findings from this trial will help researchers to design a pilot or definitive clinical trial of traditional herbal medicine for chronic fatigue.

Trial registration

Korean National Clinical Trial Registry CRIS; KCT0001681, registered on 29 October 2015.     

Preparation of Primary Myogenic Precursor Cell/Myoblast Cultures from Basal Vertebrate Lineages

Due to the inherent difficulty and time involved with studying the myogenic program in vivo, primary culture systems derived from the resident adult stem cells of skeletal muscle, the myogenic precursor cells (MPCs), have proven indispensible to our understanding of mammalian skeletal muscle development and growth. Particularly among the basal taxa of Vertebrata, however, data are limited describing the molecular mechanisms controlling the self-renewal, proliferation, and differentiation of MPCs. Of particular interest are potential mechanisms that underlie the ability of basal vertebrates to undergo considerable postlarval skeletal myofiber hyperplasia (i.e. teleost fish) and full regeneration following appendage loss (i.e. urodele amphibians). Additionally, the use of cultured myoblasts could aid in the understanding of regeneration and the recapitulation of the myogenic program and the differences between them. To this end, we describe in detail a robust and efficient protocol (and variations therein) for isolating and maintaining MPCs and their progeny, myoblasts and immature myotubes, in cell culture as a platform for understanding the evolution of the myogenic program, beginning with the more basal vertebrates. Capitalizing on the model organism status of the zebrafish (Danio rerio), we report on the application of this protocol to small fishes of the cyprinid clade Danioninae. In tandem, this protocol can be utilized to realize a broader comparative approach by isolating MPCs from the Mexican axolotl (Ambystomamexicanum) and even laboratory rodents. This protocol is now widely used in studying myogenesis in several fish species, including rainbow trout, salmon, and sea bream^1-4.     

The use of out-of-plane high Z patient shielding for fetal dose reduction in computed tomography: Literature review and comparison with Monte-Carlo calculations of an alternative optimisation technique

When performing CT examinations on pregnant patients, great effort should be dedicated towards optimising the exposure of the mother and the conceptus. For this purpose, many radiology departments use high-Z garments to be wrapped around the patient's lower abdomen for out-of-plane organ shielding to protect the fetus. To assess their current protection efficiency, we performed a literature review and compared the efficiencies mentioned in the literature to Monte-Carlo calculations of CT protocols for which the overall scan length was reduced. We found 11 relevant articles, all of them reporting uterus exposure due to CT imaging performed for exclusion of pulmonary embolism, one of the leading causes of peripartum deaths in western countries. Uterus doses ranged between 60 and 660 µGy per examination, and relative dose reductions to the uterus due to high-Z garments were between 20 and 56%. Calculations showed that reducing the scan length by one to three centimetres could potentially reduce uterus dose up to 24% for chest imaging, and even 47% for upper abdominal imaging. These dose reductions were in the order of those achieved by high-Z garments. However, using the latter may negatively influence the diagnostic image quality and even interfere with the automatic exposure control system thus increasing patient dose if positioned in the primary beam, for example in the overranging length in helical acquisition. We conclude that efforts should be concentrated on positioning the patient correctly in the gantry and optimising protocol parameters, rather than using high-Z garments for out-of-plane uterus shielding.