Avanti lipid tools: Connecting lipids,technology, and cell biology

Lipid research is challenging owing to the complexity and diversity of the lipidome. Here we review a set of experimental tools developed for the seasoned lipid researcher, as well as, those who are new to the field of lipid research. Novel tools for probing protein–lipid interactions, applications for lipid binding antibodies, enhanced systems for the cellular delivery of lipids, improved visualization of lipid membranes using gold-labeled lipids, and advances in mass spectrometric analysis techniques will be discussed. Because lipid mediators are known to participate in a host of signal transduction and trafficking pathways within the cell, a comprehensive lipid toolbox that aids the science of lipidomics research is essential to better understand the molecular mechanisms of interactions between cellular components. This article is part of a Special Issue entitled Tools to study lipid functions.     

Detecting and Measuring Selection from Gene Frequency Data

The recent advent of high-throughput sequencing and genotyping technologies makes it possible to produce, easily and cost effectively, large amounts of detailed data on the genotype composition of populations. Detecting locus-specific effects may help identify those genes that have been, or are currently, targeted by natural selection. How best to identify these selected regions, loci, or single nucleotides remains a challenging issue. Here, we introduce a new model-based method, called SelEstim, to distinguish putative selected polymorphisms from the background of neutral (or nearly neutral) ones and to estimate the intensity of selection at the former. The underlying population genetic model is a diffusion approximation for the distribution of allele frequency in a population subdivided into a number of demes that exchange migrants. We use a Markov chain Monte Carlo algorithm for sampling from the joint posterior distribution of the model parameters, in a hierarchical Bayesian framework. We present evidence from stochastic simulations, which demonstrates the good power of SelEstim to identify loci targeted by selection and to estimate the strength of selection acting on these loci, within each deme. We also reanalyze a subset of SNP data from the Stanford HGDP–CEPH Human Genome Diversity Cell Line Panel to illustrate the performance of SelEstim on real data. In agreement with previous studies, our analyses point to a very strong signal of positive selection upstream of the LCT gene, which encodes for the enzyme lactase–phlorizin hydrolase and is associated with adult-type hypolactasia. The geographical distribution of the strength of positive selection across the Old World matches the interpolated map of lactase persistence phenotype frequencies, with the strongest selection coefficients in Europe and in the Indus Valley.     

CT检查中造影剂不良反应的预防、处理及对影像学检查的影响分析

目的：在CT等医学影像检查过程中,常需要应用造影剂。在造影剂的使用常常发生不良反应,掌握不良反应的发生率,减少或减轻患者的不良反应,能够使CT增强扫描顺利进行,提高检查安全性。方法：搜集我院2011年10月至2012年9月间的1500例CT造影增强检查患者,包括冠状动脉CT血管成像（冠脉CTA）、头部CT血管成像（头CTA）、肝脏增强、泌尿系三维成像（CTU）以及双下肢血管成像（双下肢CTA）,进行造影剂的不良反应类型、造影剂药物剂量、注射速度等统计分析,总结造成不良反应发生的因素及处理方法。结果：不良反应的类型包括发热、呕吐、荨麻疹、面色潮红、局部疼痛、流泪、血压下降、喉头水肿、休克等。使用非离子型造影剂出现不良反应者85例,占5．67％。其中轻度反应65例,占4．33％;中度反应16例,占1．06％;重度4例,占0．27％。结论：在CT增强扫描过程中,造影剂的用量及注射速度与不良反应的发生有相关性。cT检查过程总应该认真执行操作流程,密切观察病人情况,积极防治,正确处理,将造影剂不良反应降低到最低程度,使患者更加安全。     

脑梗死后智能障碍影响因素分析

目的 探讨影响脑梗死后智能障碍的因素。方法 应用长谷川痴呆量表对249例经CT证实的脑梗死患者进行智能测评,评分0～21．5为智能障碍组,22～32．5为正常组,探讨智能障碍的发生与性别、年龄、文化程度、卒中主要危险因素(高血压和糖尿病)、梗死灶数量及体积,以及脑萎缩和脑白质疏松之间的相互关系．结果 249例脑梗死患者中有106例(42．6％)出现智能障碍．并发现年龄、性别、文化程度、高血压病、糖尿病与智能障碍的发生有关;梗死灶的数量越多、体积越大其智能障碍发生率越高;脑萎缩及脑白质疏松与智能障碍关系密切．结论 脑梗死后智能障碍是多因素相互作用的结果,与梗死灶数量、体积、脑萎缩及脑白质疏松等多种因素有关．     

A heterogeneous thermal environment enables remarkable behavioral thermoregulation in Uta stansburiana

Ectotherms can attain preferred body temperatures by selecting specific temperature microhabitats within a varied thermal environment. The side‐blotched lizard, Uta stansburiana may employ microhabitat selection to thermoregulate behaviorally. It is unknown to what degree habitat structural complexity provides thermal microhabitats for thermoregulation. Thermal microhabitat structure, lizard temperature, and substrate preference were simultaneously evaluated using thermal imaging. A broad range of microhabitat temperatures was available (mean range of 11°C within 1–2 m²) while mean lizard temperature was between 36°C and 38°C. Lizards selected sites that differed significantly from the mean environmental temperature, indicating behavioral thermoregulation, and maintained a temperature significantly above that of their perch (mean difference of 2.6°C). Uta's thermoregulatory potential within a complex thermal microhabitat structure suggests that a warming trend may prove advantageous, rather than detrimental for this population.     

The role of subcellular organelles in hormone secretion : The interactions of calcium, vitamin A, vinblastine, and cytochalasin B in PTH secretion

To determine the role of subcellular organelles in hormone secretion, we studied the interaction of low calcium concentration (low Ca), retinol (vitamin A, vit A), vinblastine (VB), and cytochalasin B (CB) in parathyroid hormone (PTH) secretion. Bovine parathyroid tissue pieces were incubated in media containing the above agents. Vit A stimulated PTH release to a mean of 170% of control. This effect of vit A was diminished when tissues were simultaneously stimulated with low Ca and, furthermore, absent when tissues were pre-incubated in low Ca.VB had no effect on low Ca-stimulated secretion, but did inhibit vit A-induced secretion in the presence of low Ca.CB stimulated PTH secretion to a mean of 150% of control during the second and third hours of incubation. CB had at least an additive effect with low Ca in stimulating PTH secretion, with a more prompt and greater response than seen in normal calcium. VB did not inhibit the acute effect of CB on secretion in normal calcium media, but did inhibit CB-induced secretion during the third hour of incubation.None of the agents stimulated the release of lysosomal cathepsin D, and vit A and CB did not stimulate the release of LDH.Our results suggest that; (1) vit A and low Ca stimulate PTH secretion through a common pathway involving the cell membrane; (2) CB stimulates PTH secretion through a separate effect on the cell membrane or submembrane microfilaments, which normally retards secretion of PTH; and (3) microtubular proteins may facilitate basal secretion of PTH, but are not involved in low Ca-stimulated secretion of PTH.     

能谱CT优化胃肿瘤扫描辐射剂量对肾上腺嗜铬细胞瘤的诊断价值

目的:探讨能谱CT优化胃肿瘤扫描辐射剂量对肾上腺嗜铬细胞瘤的诊断价值。方法:采用回顾性、抽样、随机研究方法选择2012年9月到2017年2月在我院诊治的肾上腺嗜铬细胞瘤患者59例作为研究对象,所有患者都给予常规CT扫描与能谱CT优化胃肿瘤扫描,记录和比较辐射剂量与图像质量。结果:所有病例包膜均完整,边缘清楚,肿瘤内见单发或多发低密度区,肿瘤实质区呈不均匀显著强化。常规CT与能谱CT的图像质量主观评分分别为3.89±0.45分和4.54±0.34分;常规CT与能谱CT图像的胃肿瘤CT值分别为31.94±6.39HU和35.29±5.19HU,对比都有显著差异(P0.05)。能谱CT图像的膀胱和皮下脂肪图像噪声值都显著低于常规CT图像,对比差异都有统计学意义(P0.05);能谱CT扫描的CTDIvol和DLP分别为12.39±3.48mGy和624.10±39.19mGy.cm,都显著低于常规CT扫描的14.09±4.13mGy和653.92±56.29mGy.cm(P0.05)。结论:能谱CT优化胃肿瘤扫描在肾上腺嗜铬细胞瘤诊断中的应用能有效减少辐射剂量与图像噪声,提高图像CT值与主观质量,临床应用价值更高。     

Chromosomal inversions and ecotypic differentiation in Anopheles gambiae: the perspective from whole‐genome sequencing

The molecular mechanisms and genetic architecture that facilitate adaptive radiation of lineages remain elusive. Polymorphic chromosomal inversions, due to their recombination‐reducing effect, are proposed instruments of ecotypic differentiation. Here, we study an ecologically diversifying lineage of Anopheles gambiae, known as the Bamako chromosomal form based on its unique complement of three chromosomal inversions, to explore the impact of these inversions on ecotypic differentiation. We used pooled and individual genome sequencing of Bamako, typical (non‐Bamako) An. gambiae and the sister species Anopheles coluzzii to investigate evolutionary relationships and genomewide patterns of nucleotide diversity and differentiation among lineages. Despite extensive shared polymorphism and limited differentiation from the other taxa, Bamako clusters apart from the other taxa, and forms a maximally supported clade in neighbour‐joining trees based on whole‐genome data (including inversions) or solely on collinear regions. Nevertheless, F_ST outlier analysis reveals that the majority of differentiated regions between Bamako and typical An. gambiae are located inside chromosomal inversions, consistent with their role in the ecological isolation of Bamako. Exceptionally differentiated genomic regions were enriched for genes implicated in nervous system development and signalling. Candidate genes associated with a selective sweep unique to Bamako contain substitutions not observed in sympatric samples of the other taxa, and several insecticide resistance gene alleles shared between Bamako and other taxa segregate at sharply different frequencies in these samples. Bamako represents a useful window into the initial stages of ecological and genomic differentiation from sympatric populations in this important group of malaria vectors.     

Auditory anatomy of beaked whales and other odontocetes: Potential for cochlear stimulation via a “vibroacoustic duct mechanism”

Computed tomography (CT) and microcomputed tomography (microCT) were used to examine the structures involved in cochlear stimulation in odontocetes and terrestrial mammals. Cranial CT examined the osseous attachment of the skull to the tympanoperiotic complex (TPC) and the path of the endocranial foramen of the vestibulocochlear nerve (EFVN), which was assumed to contain the perilymphatic duct. Additional CTs of TPC were taken postextraction to examine the gross morphology of this structure. MicroCT was used to examine the acoustic windows of the cochlea, including the round and oval windows and the apertures of the cochlear and vestibular aqueducts. Cranial CT scans demonstrated an osseous connection between the skull and TPC in beaked whales and Physeter macrocephalus. EFVN traveled through a greater length of cranial bone and communicated more closely with the periotic bone in beaked whales than in other species. Ziphius cavirostris was observed to have a reduced medial sulcus of the mallear ridge (MSMR) and tympanic plate and an enlarged aperture of the cochlear aqueduct, respectively. The potential significance of these findings, including the role of the perilymphatic duct as a novel route of cochlear stimulation referred to as the “vibroacoustic duct mechanism,” are discussed.     

Targeted resequencing reveals geographical patterns of differentiation for loci implicated in parallel evolution

Parallel divergence and speciation provide evidence for the role of divergent selection in generating biological diversity. Recent studies indicate that parallel phenotypic divergence may not have the same genetic basis in different geographical locations – ‘outlier loci’ (loci potentially affected by divergent selection) are often not shared among parallel instances of phenotypic divergence. However, limited sharing may be due, in part, to technical issues if false‐positive outliers occur. Here, we test this idea in the marine snail Littorina saxatilis, which has evolved two partly isolated ecotypes (adapted to crab predation vs. wave action) in multiple locations independently. We argue that if the low extent of sharing observed in earlier studies in this system is due to sampling effects, we expect outliers not to show elevated F_ST when sequenced in new samples from the original locations and also not to follow predictable geographical patterns of elevated F_ST. Following a hierarchical sampling design (within vs. between country), we applied capture sequencing, targeting outliers from earlier studies and control loci. We found that outliers again showed elevated levels of F_ST in their original location, suggesting they were not generated by sampling effects. Outliers were also likely to show increased F_ST in geographically close locations, which may be explained by higher levels of gene flow or shared ancestral genetic variation compared with more distant locations. However, in contrast to earlier findings, we also found some outlier types to show elevated F_ST in geographically distant locations. We discuss possible explanations for this unexpected result.