Visualizing biomolecular electrostatics in virtual reality with UnityMol‐APBS

Virtual reality is a powerful tool with the ability to immerse a user within a completely external environment. This immersion is particularly useful when visualizing and analyzing interactions between small organic molecules, molecular inorganic complexes, and biomolecular systems such as redox proteins and enzymes. A common tool used in the biomedical community to analyze such interactions is the Adaptive Poisson‐Boltzmann Solver (APBS) software, which was developed to solve the equations of continuum electrostatics for large biomolecular assemblages. Numerous applications exist for using APBS in the biomedical community including analysis of protein ligand interactions and APBS has enjoyed widespread adoption throughout the biomedical community. Currently, typical use of the full APBS toolset is completed via the command line followed by visualization using a variety of two‐dimensional external molecular visualization software. This process has inherent limitations: visualization of three‐dimensional objects using a two‐dimensional interface masks important information within the depth component. Herein, we have developed a single application, UnityMol‐APBS, that provides a dual experience where users can utilize the full range of the APBS toolset, without the use of a command line interface, by use of a simple graphical user interface (GUI) for either a standard desktop or immersive virtual reality experience.     

Systematic review of the “Chromodoris quadricolor group” of East Africa,with descriptions of two new species of the genus Chromodoris Alder & Hancock, 1855 (Heterobranchia,Nudibranchia)

The similarities and variations in nudibranch species of the “Chromodoris quadricolor group” (Heterobranchia, Nudibranchia) have historically created identification problems among both nudibranch enthusiasts and experts. In this study, we combine molecular genetic analyses using one nuclear gene (histone h3) and two mitochondrial genes (cytochrome c oxidase subunit I and ribosomal 16S RNA) with morphological data to ameliorate the identification of specimens from this complex in East Africa. We include a detailed examination of polymorphisms within the group. As a result, Chromodoris boucheti is synonymized with Chromodoris lochi, and two new species are described, Chromodoris celinae sp. nov. and Chromodoris helium sp. nov. Chromodoris celinae sp. nov. is a common shallow water species that was previously misidentified as C. hamiltoni. Chromodoris helium sp. nov. is a species that appears to be restricted to depths below 30 m. This study agrees with previous research indicating the recent divergence of the genus Chromodoris.     

Overexpression of the persimmon abscisic acid β‐glucosidase gene (DkBG1) alters fruit ripening in transgenic tomato

β‐Glucosidases (BG) are present in many plant tissues. Among these, abscisic acid (ABA) β‐glucosidases are thought to take part in the adjustment of cellular ABA levels, however the role of ABA‐BG in fruits is still unclear. In this study, through RNA‐seq analysis of persimmon fruit, 10 full‐length DkBG genes were isolated and were all found to be expressed. In particular, DkBG1 was highly expressed in persimmon fruits with a maximum expression 95 days after full bloom (DAFD). We verified that, in vitro, DkBG1 protein can hydrolyze ABA‐glucose ester (ABA‐GE) to release free ABA. Compared with wild‐type, tomato plants that overexpressed DkBG1 significantly upregulated the expression of ABA receptor PYL3/7 genes and showed typical symptoms of ABA hypersensitivity in fruits. DkBG1 overexpression (DkBG1‐OE) accelerated fruit ripening onset by 3–4 days by increasing ABA levels at the pre‐breaker stage and induced early ethylene release compared with wild‐type fruits. DkBG1‐OE altered the expression of ripening regulator NON‐RIPENING (NOR) and its target genes; this in turn altered fruit quality traits such as coloration. Our results demonstrated that DkBG1 plays an important role in fruit ripening and quality by adjusting ABA levels via hydrolysis of ABA‐GE.     

唾液菌群特征分析对儿童龋齿复发的预测价值

目的探究唾液菌群特征对儿童龋齿复发的预测价值。方法收集2017年1月至2018年1月在中铁十七局集团有限公司中心医院诊断及治疗的龋齿患儿94例,在进行龋齿治疗后第4周搜集唾液样本,并根据12个月后的龋齿发生情况分为复发组及未复发组,对比两组微生物检测结果,并使用ROC曲线评估微生物指标对龋齿复发的预测效能。结果本研究随访结束时,龋齿复发23例(25.84%)。龋齿复发与未复发组的唾液微生物组成存在显著差异:复发组的变形链球菌(Streptococcus mutans)、内氏放线菌(Actinomyces naeslundii)、普雷沃氏菌属(Prevotella)、二氧化碳噬纤维菌属(Capnocytophaga)、普雷沃氏菌科(Prevotellaceae)、放线菌属(Actinobacillus)的相对丰度显著高于未复发组(均P<0.05),未复发组在纤毛杆菌属(Leptotrichia)、奈瑟氏菌属(Neisseria)、链球菌属(Streptococcus)的相对丰度显著高于复发组(均P<0.05)。纤毛杆菌属、内氏放线菌、普雷沃氏菌属、变形链球菌载量预测龋齿复发的AUC值分别为0.753、0.715、0.680、0.940,其中变形链球菌的AUC值显著高于其他三种菌属(均P<0.05)。结论分析唾液菌群对儿童龋齿的复发具有一定的预测价值,其中变形链球菌的预测效能较好。     

Optimization of the enzymatic synthesis of structured triacylglycerols rich in docosahexaenoic acid at sn-2 position by acidolysis of Aurantiochytrium limacinum SR21 oil and caprylic acid using response surface methodology

Journal of Applied Phycology - The thraustochytrid Aurantiochytrium limacinum SR21 is a promising source of docosahexaenoic acid (DHA) for human consumption as dietary supplement, replacing...     

Plant apocarotenoids: from retrograde signaling to interspecific communication

Carotenoids are isoprenoid compounds synthesized by all photosynthetic and some non-photosynthetic organisms. They are essential for photosynthesis and contribute to many other aspects of a plant's life. The oxidative breakdown of carotenoids gives rise to the formation of a diverse family of essential metabolites called apocarotenoids. This metabolic process either takes place spontaneously through reactive oxygen species or is catalyzed by enzymes generally belonging to the CAROTENOID CLEAVAGE DIOXYGENASE family. Apocarotenoids include the phytohormones abscisic acid and strigolactones (SLs), signaling molecules and growth regulators. Abscisic acid and SLs are vital in regulating plant growth, development and stress response. SLs are also an essential component in plants’ rhizospheric communication with symbionts and parasites. Other apocarotenoid small molecules, such as blumenols, mycorradicins, zaxinone, anchorene, β-cyclocitral, β-cyclogeranic acid, β-ionone and loliolide, are involved in plant growth and development, and/or contribute to different processes, including arbuscular mycorrhiza symbiosis, abiotic stress response, plant–plant and plant–herbivore interactions and plastid retrograde signaling. There are also indications for the presence of structurally unidentified linear cis-carotene-derived apocarotenoids, which are presumed to modulate plastid biogenesis and leaf morphology, among other developmental processes. Here, we provide an overview on the biology of old, recently discovered and supposed plant apocarotenoid signaling molecules, describing their biosynthesis, developmental and physiological functions, and role as a messenger in plant communication.