An Optimized Proteomics Approach Reveals Novel Alternative Proteins in Mouse Liver Development

Alternative ORFs (AltORFs) are unannotated sequences in genome that encode novel peptides or proteins named alternative proteins (AltProts). Although ribosome profiling and bioinformatics predict a large number of AltProts, mass spectrometry as the only direct way of identification is hampered by the short lengths and relative low abundance of AltProts. There is an urgent need for improvement of mass spectrometry methodologies for AltProt identification. Here, we report an approach based on size-exclusion chromatography for simultaneous enrichment and fractionation of AltProts from complex proteome. This method greatly simplifies the variance of AltProts discovery by enriching small proteins smaller than 40 kDa. In a systematic comparison between 10 methods, the approach we reported enabled the discovery of more AltProts with overall higher intensities, with less cost of time and effort compared to other workflows. We applied this approach to identify 89 novel AltProts from mouse liver, 39 of which were differentially expressed between embryonic and adult mice. During embryonic development, the upregulated AltProts were mainly involved in biological pathways on RNA splicing and processing, whereas the AltProts involved in metabolisms were more active in adult livers. Our study not only provides an effective approach for identifying AltProts but also novel AltProts that are potentially important in developmental biology.     

The influence of feeding,enrichment, and seasonal context on the behavior of Pacific Walruses (Odobenus rosmarus divergens)

Though some research exists concerning general behavior and activity patterns of Walruses in zoos or aquariums, less is known about how these patterns change in response to various environmental and temporal contexts. This study presents two studies assessing behavioral changes in relation to feeding period, object enrichment (OE), and season in a social group of four Pacific Walruses at the New York Aquarium. Study 1 examined behavior in relation to feeding context (nonfeed, prefeed, postfeed); data were collected over a three‐week period, resulting in 47 observation sessions for each feeding context. Study 2 examined behavior in relation to OE and season; data were collected in two phases resulting in 12 enrichment and 9 no‐enrichment (NE) observation sessions (Phase 1), and 21 enrichment and 18 NE observation sessions (Phase 2). Study 1 showed that after feeding, oral behavior increased while social behavior and total swim frequency decreased. In Study 2, both swim frequency and social behavior were found to interact with OE and phase, while oral behavior remained constant across all conditions. As in the wild, both studies found all animals to be swimming the majority of the time. Though every animal spent much of its swim time engaged in an Individual Swimming Pattern (ISP), both studies showed that the proportion of ISP (in relation to total time swimming) remained stable across all contexts, suggesting a potential functional role of the ISPs. These results are discussed in light of the ongoing debate over the role of stereotypies in welfare assessment. Zoo Biol 29:397–404, 2010. © 2009 Wiley‐Liss, Inc.     

基于脂质组学技术研究急性缺血性脑卒中临床诊断标志物

目的:急性缺血性脑卒中(Acute ischemic stroke, AIS)是由于血流减少导致的脑功能突然丧失。由于AIS发病机制是异质性和多因素的,我们建立全面的脂质组学方法来阐明AIS进程相关的脂质变化和复杂的脂质代谢网络。方法:选取26例AIS患者血液标本和27例健康志愿者血清作为研究对象,进行总脂抽提,通过基于LC-MS策略的非靶向脂质组学方法进行规模性、整体性的脂质组学分析。结果:对AIS患者和健康志愿者血浆进行大规模脂质定性定量分析,通过Progenesis~? QI软件分析Xevo~? G2-XS QTOF质谱系统MSE采集的子离子数据,精确定量到1054个脂质特征差异,准确定性得到368个脂质分子,多变量统计分析中差异脂质组成能将AIS患者和健康志愿者区分开来,通路富集分析图显示差异脂质主要参与甘油磷脂代谢的紊乱。结论:AIS患者血浆脂质组成与健康志愿者存在显著差异,差异表达的脂质可能与AIS发生有关。这些发现有助于开发新的诊断标志物和AIS治疗靶点。     

Improved expansion of T cells in culture when isolated with an equipment-free,high-throughput,flow-through microfluidic module versus traditional density gradient centrifugation

Background

The isolation of lymphocytes – and removal of platelets (PLTs) and red blood cells (RBCs) – from an initial blood sample prior to culture is a key enabling step for effective manufacture of cellular therapies. Unfortunately, currently available methods suffer from various drawbacks, including low cell recovery, need for complex equipment, potential loss of sterility and/or high materials/labor cost.

31° South: The physiology of adaptation to arid conditions in a passerine bird

Arid environments provide ideal ground for investigating the mechanisms of adaptive evolution. High temperatures and low water availability are relentless stressors for many endotherms, including birds; yet birds persist in deserts. While physiological adaptation probably involves metabolic phenotypes, the underlying mechanisms (plasticity, genetics) are largely uncharacterized. To explore this, we took an intraspecific approach that focused on a species that is resident over a mesic to arid gradient, the Karoo scrub‐robin (Cercotrichas coryphaeus). Specifically, we integrated environmental (climatic and primary productivity), physiological (metabolic rates: a measure of energy expenditure), genotypic (genetic variation underlying the machinery of energy production) and microbiome (involved in processing food from where energy is retrieved) data, to infer the mechanism of physiological adaptation. We that found the variation in energetic physiology phenotypes and gut microbiome composition are associated with environmental features as well as with variation in genes underlying energy metabolic pathways. Specifically, we identified a small list of candidate adaptive genes, some of them with known ties to relevant physiology phenotypes. Together our results suggest that selective pressures on energetic physiology mediated by genes related to energy homeostasis and possibly microbiota composition may facilitate adaptation to local conditions and provide an explanation to the high avian intraspecific divergence observed in harsh environments.     

CO2加富对盐胁迫下黄瓜幼苗叶片光合特性及活性氧代谢的影响

以‘津优35号’黄瓜(Cucumis sativus L.)水培苗为试材,采用裂区设计,主区因素为CO_2浓度处理,设大气CO_2浓度(Symbol{B@400μmol/mol)和CO_2加富[(800±40)μmol/mol]2个CO_2浓度水平,裂区因素为盐胁迫处理,用NaCl模拟盐胁迫,设对照(0 mmol/L NaCl)、盐胁迫(80 mmol/L NaCl)2个盐分水平,研究了CO_2加富对盐胁迫下黄瓜幼苗生长、光合特性及活性氧代谢的影响。结果表明:盐胁迫显著抑制黄瓜幼苗的生长,并降低了叶绿素含量、ETR、Φ_(PSII)、核酮糖-1,5-二磷酸羧化酶(RuBPCase)活性及净光合速率;盐胁迫增加了丙二醛及活性氧的累积,与此同时也提高了脯氨酸含量及超氧化物歧化酶(SOD)、过氧化氢酶(CAT)活性,但降低了过氧化物酶(POD)活性。CO_2加富显著提高了盐胁迫下黄瓜幼苗的株高、茎粗、叶面积及地上部鲜重,降低了叶绿素a、叶绿素b、类胡萝卜素及叶绿素(a+b)含量,但显著提高了净光合速率和RuBPCase活性,同时降低了气孔导度及蒸腾速率,并且使其具有较高的表观电子传递速率及PSII实际光化学效率;CO_2加富显著提高了盐胁迫下黄瓜幼苗叶片脯氨酸含量及SOD、POD、CAT活性,丙二醛、过氧化氢含量和超氧阴离子产生速率显著降低。综上所述,CO_2加富可通过提高幼苗叶片净光合速率、脯氨酸含量及抗氧化酶活性,降低蒸腾速率、减少丙二醛含量及活性氧的积累,从而缓解盐胁迫对黄瓜植株造成的伤害。     

镉胁迫对紫花苜蓿幼苗生理特性和镉富集的影响

以"甘农三号"紫花苜蓿幼苗为材料,在水培条件下,探究了在10 d内不同浓度(0～2.0 mmol·L^-1)镉(Cd)胁迫对其根长、茎长、生物量、叶绿素和丙二醛(MDA)含量、超氧化物歧化酶(SOD)和过氧化物酶(POD)活性、Cd富集及其亚细胞分布的影响。结果表明:低浓度(0.125 mmol·L^-1) Cd能促进幼苗根和茎的生长,增加叶片叶绿素含量,较高浓度(0.5～2.0 mmol·L^-1) Cd显著抑制幼苗根和茎的生长,叶绿素及生物量显著降低; Cd胁迫使MDA含量显著增加,而SOD和POD活性显著增强,其中Cd胁迫浓度为0.5mmol·L^-1时,SOD和POD活性达到最大值,这可能是植物对环境胁迫的一种应激保护反应; Cd在各亚细胞组分中的含量依次为细胞壁>细胞质>线粒体>叶绿体,且均随Cd胁迫浓度的升高而增加。当Cd胁迫浓度为0.125 mmol·L^-1时,水培10 d的紫花苜蓿幼苗单株地上部对Cd的净化率最高可达0.214%,而整盆植株在单位体积内对Cd的净化率最高可达15.5%;当Cd胁迫浓度为2.0 mmol·L^-1时,紫花苜蓿幼苗地上部Cd含量达89.36μg·g-1。这些结果表明紫花苜蓿对Cd具有很强的富集能力,虽未达到Cd超富集植物的临界标准,但从植株生物量、耐Cd能力、富集Cd量及对Cd的净化率等方面综合考虑,紫花苜蓿在Cd污染土壤的植物修复中具备良好的应用价值。     

Evaluation of Enrichment for Reptiles in Zoos

Studies on environmental enrichment for reptiles are lacking in the scientific literature. Although the literature reflects a limited take on reptile enrichment in the zoological community, it may not be the case in reality as enrichment is generally considered an important aspect of the care of nonhuman animals in captivity. This project investigated the current state of reptile enrichment as it is being used in zoos. Although respondents were disproportionately accredited by the Association of Zoos and Aquariums, the results showed many forms of enrichment being used for reptiles in zoos and happening at much greater levels than what has been suggested in the scientific literature. There were significant differences between a) reptile groups for each form of enrichment, and b) enrichment forms within each reptile group, except with the use of natural enrichment devices and structural/habitat design, which did not differ across all reptile groups. Enrichment goals, assessment methods, and sources of information for reptile enrichment used by zoos suggest the need for more scientific publications for facilities to make evidence-based decisions to improve the welfare of reptiles in captivity.     

Microbial enrichment and multiplexed microfiltration for accelerated detection of Salmonella in spinach

To attain Salmonella detection thresholds in spinach suspensions using enrichment media requires at least 24 hr. Separation and concentration of selected microorganisms via microfiltration and microfugation reduce time for sample preparation, especially when working with large volumes of vegetable suspensions. This facilitates accelerated detection of Salmonella in spinach suspensions, and may contribute to effectively monitoring this pathogen before it reaches the consumer. We report a microfiltration-based protocol for accelerated sample preparation to concentrate and recover ≤1 colony forming unit (CFU) Salmonella/g pathogen-free spinach. Store-bought samples of spinach and a spinach plant subjected to two environmental conditions (temperature and light exposure) during its production were tested. The overall procedure involves extraction with buffer, a short enrichment step, prefiltration using a nylon filter, crossflow hollow fiber microfiltration, and retentate centrifugation to bring microbial cells to detection levels. Based on 1 CFU Salmonella/g frozen spinach, and a Poisson distribution statistical analyses with 99% probability, we calculated that 3 hr of incubation, when followed by microfiltration, is sufficient to reach the 2 log concentration required for Salmonella detection within 7 hr. Longer enrichment times (5 hr or more) is needed for concentrations lower than 1 CFU Salmonella/g of ready to eat spinach. The recovered microbial cells were identified and confirmed as Salmonella using both polymerase chain reaction (PCR) and plating methods. Different environmental conditions tested during production did not affect Salmonella viability; this demonstrated the broad adaptability of Salmonella and emphasized the need for methods that enable efficient monitoring of production for the presence of this pathogen.