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RNA-Seq Analysis of lncRNAs and cisNATs in the Tomato Genome 番茄基因组lncrna和cisNATs的RNA-Seq分析
Pub Date : 2015-06-01 DOI: 10.14434/IUJUR.V1I1.13244
S. H. Ather
Since the sequencing of the human genome, it has been revealed that the vast majority of DNA does not code for proteins. Instead, these regions of DNA produce long noncoding RNAs (lncRNAs), which have recently been reported to play important roles such as protein regulation and small RNA processing (Wilusz, Sunwoo, & Spector, 2009). The catalog and functions of lncRNAs in the ripening of tomato species ( Solanum lycopersicum ) are largely unknown. Similarly, the mechanisms of cis-natural antisense transcripts (cisNATs) of proximal complementary RNA strings, which function to inhibit transcription, are also poorly understood (Wang, Gaasterland, & Chua, 2005). Global issues in food production and malnutrition exacerbate the relevance of understanding these biological mechanisms central to the development of fruit. We identified certain functions of lncRNAs and cisNATs in the tomato ripening process using an RNA-Seq pipeline (Wang, Gerstein, & Snyder, 2005). Raw reads from two different stages in the tomato ripening cycle were aligned to a reference genome to test the hypothesis that there would be different expression levels for certain lncRNAs and cis-NATs between the two stages. The two stages were Mature Green, the stage in which the tomato is completely green, and Breaker, the stage in which the tomato shows initial colors of red. Then, the reads were de novo assembled, assessed for coding potential, and annotated by transcript and function. Finally, the results were filtered for lncRNAs (length > 200 bp, ORF 0) and cis-NATs (sense-antisense pairs, overlap length > 50 bp, differential splice patterns, expression value = 0). Differentially-expressed lncRNAs and cis-NATs between the two stages of development were identified, and their functions were analyzed. However, experimental evidence is necessary to confirm our findings and hypothesize models of cis-NAT mechanisms for further classification and identification.
自从人类基因组测序以来,已经揭示了绝大多数DNA不编码蛋白质。相反,这些DNA区域产生长链非编码RNA (lncRNAs),最近有报道称,lncRNAs在蛋白质调控和小RNA加工等方面发挥着重要作用(Wilusz, Sunwoo, & Spector, 2009)。在番茄成熟过程中lncrna的目录和功能在很大程度上是未知的。同样,近端互补RNA串的顺式天然反义转录物(cisNATs)具有抑制转录的功能,其机制也知之甚少(Wang, Gaasterland, & Chua, 2005)。粮食生产和营养不良的全球性问题加剧了理解这些对水果发育至关重要的生物机制的相关性。我们使用RNA-Seq管道确定了lncrna和cisNATs在番茄成熟过程中的某些功能(Wang, Gerstein, & Snyder, 2005)。研究人员将番茄成熟周期中两个不同阶段的原始读数与一个参考基因组进行比对,以检验在两个阶段之间某些lncrna和顺式nats的表达水平是否存在差异。这两个阶段分别是“成熟绿”(Mature Green)和“破碎绿”(Breaker),这两个阶段的番茄完全是绿色的,而“破碎绿”是番茄最初呈现红色的阶段。然后,重新组装这些reads,评估编码潜力,并通过转录和功能进行注释。最后,筛选lncRNAs(长度> 200 bp, ORF为0)和顺式nats(正反义对,重叠长度> 50 bp,差异剪接模式,表达值为0),鉴定两个发育阶段差异表达的lncRNAs和顺式nats,并分析其功能。然而,需要实验证据来证实我们的发现,并对顺式nat机制的模型进行假设,以进一步分类和鉴定。
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引用次数: 0
Cardiac Myocardial Hypertrophy and Altered Swimming Behavior in Xenopus laevis Embryos in Incrementally Increasing Hypergravity 逐渐增加的超重条件下非洲爪蟾胚胎心肌肥大和游泳行为的改变
Pub Date : 2015-01-30 DOI: 10.33697/AJUR.2015.005
Stacey Howes, D. Wiens
Every living organism on earth has developed and evolved in unit gravity (1G) conditions. It is likely that any deviation from earth’s standard gravity will influence development, particularly at early stages. Previous reports from this lab showed that total length is reduced and that ventricle size is increased during development at 7G. The objective of the present study was to investigate the effect of increasing levels of hypergravity on the development of the ventricular myocardial wall and the neuromuscular responsiveness of Xenopus laevis. At early gastrulation, embryos were placed in a centrifuge simulating 7G, 10G, 15G or 17G until they reached stage 45 (feeding tadpole stage, approximately 72 hours from initiation of gastrulation). Mortality was low and only the 17G exposure induced significant mortality. Immediately following centrifugation, the embryos were stimulated by touching with a probe to test neuromuscular responsiveness. With increasing G forces, responsiveness to this test was incrementally reduced. A quarter of the embryos were fixed and their body dimensions were measured. One group of remaining live embryos, those exposed to 7G, was maintained and swimming behavior was observed during daily 5-minute periods for 52 days. Overall, abnormal swimming behavior was found in 33% of 7G embryos and in 2% of controls during this time. These embryos were later subjected to an orientation-swimming test. Hypergravity-exposed embryos required, on average, one second longer (9% of time required) to become oriented. From the embryos exposed to increasing G levels and then fixed, we found that total length was reduced successively at increasing hypergravity levels, but the snout-vent proportion of total length increased. Stained sections of the fixed embryos revealed that the thickness of the ventricle wall was increased, especially the interior ridge component (trabeculae/papillary muscles). The data demonstrates that hypergravity has persistent effects on the development of the ventricular myocardial wall, neuromuscular responsiveness, and equilibrium organs.
地球上的每一种生物都是在单位重力(1G)条件下发展和进化的。任何偏离地球标准重力的情况都可能影响发展,特别是在早期阶段。本实验室以前的报告显示,在7G发育期间,总长度减少,心室大小增加。本研究的目的是探讨增加的超重力水平对非洲爪蟾心室心肌壁发育和神经肌肉反应的影响。在早期原肠胚形成时,将胚胎置于模拟7G、10G、15G或17G的离心机中,直到它们达到第45期(饲养蝌蚪期,距原肠胚形成开始约72小时)。死亡率低,只有17G暴露引起显著死亡率。离心后,立即用探针触摸刺激胚胎,以测试神经肌肉反应。随着G力的增加,对该测试的响应性逐渐降低。四分之一的胚胎是固定的,并测量了它们的身体尺寸。其中一组存活的胚胎暴露于7G环境中,并在52天内每天5分钟的时间内观察其游泳行为。总的来说,在这段时间里,33%的7G胚胎和2%的对照组发现了异常的游泳行为。这些胚胎随后接受定向游泳测试。暴露在超重力环境下的胚胎平均需要多一秒钟(9%的时间)才能定向。从G水平先增加再固定的胚胎中,我们发现,随着重力水平的增加,总长度逐渐减少,但总长度中嘴部排出的比例增加。固定胚胎的染色切片显示脑室壁厚度增加,特别是内部脊部(小梁/乳头肌)。数据表明,超重力对心室心肌壁、神经肌肉反应性和平衡器官的发育有持续的影响。
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引用次数: 0
2015 Year in Review 2015年回顾
Pub Date : 2015-01-01 DOI: 10.24839/2164-8204.JN20.4.264
Melanie M. Domenech Rodríguez
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引用次数: 8
Stealing is Stealing: A Cross-Cultural Analysis on the Perception of Criminality for Physical Theft Versus Illegal Downloading 偷窃就是偷窃:盗窃与非法下载犯罪认知的跨文化分析
Pub Date : 2014-11-11 DOI: 10.14434/IUJUR.V1I1.13320
Alexius Q. Babb
In our technology-driven world, consumers have access to a wealth of product options, but this access also allows consumers the opportunity to obtain purchasable content through illegal means. Past studies have addressed the perceptions of the criminality of online versus face-to-face theft, but limitations have been consistent across studies with the frequent use of collegiate sample pools. It was important for this experiment to gather data from a broader world population to make results more generalizable. Therefore, we examined a total of 589 participants from a global participant pool to evaluate their perceptions of the criminality of online piracy or physical theft of music or software. This experiment hypothesized that (1) the perception of the criminality of illegal downloading of media would be assessed higher ratings by South Asian participants than North American participants, and (2) criminality ratings would be assessed higher ratings by females than males. Participants were randomly assigned to one of four vignettes. They were then asked a series of questions using semantic differential and Likert scales to assess their perception of the criminal act committed in the randomly selected vignette. A one-way ANCOVA and a multiple regression test were performed to test the hypotheses.
在我们这个技术驱动的世界里,消费者可以获得丰富的产品选择,但这种访问也使消费者有机会通过非法手段获得可购买的内容。过去的研究已经解决了在线盗窃与面对面盗窃的犯罪观念,但由于频繁使用大学样本池,研究的局限性一直是一致的。这项实验从更广泛的世界人口中收集数据,使结果更具普遍性,这一点很重要。因此,我们对来自全球参与者池的589名参与者进行了调查,以评估他们对在线盗版或实体盗窃音乐或软件的犯罪行为的看法。本实验假设:(1)南亚受试者对非法下载媒体的犯罪认知评分高于北美受试者,(2)女性受试者对犯罪评分高于男性受试者。参与者被随机分配到四个小插曲中的一个。然后用语义差异和李克特量表向他们提出一系列问题,以评估他们对随机选择的小插图中犯罪行为的看法。采用单因素方差分析和多元回归检验对假设进行检验。
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引用次数: 0
Great indexing news for Psi Chi Journal 伟大的索引新闻Psi气杂志
Pub Date : 2014-01-01 DOI: 10.24839/2164-8204.JN19.1.2
M. Rodríguez
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引用次数: 0
Another year of great strides 又是大踏步前进的一年
Pub Date : 2014-01-01 DOI: 10.24839/2164-8204.JN19.4.225
M. Rodríguez
COPYRIGHT 2014 BY PSI CHI, THE INTERNATIONAL HONOR SOCIETY IN PSYCHOLOGY (VOL. 19, NO. 4/ISSN 2164-8204) Four more issues of the Psi Chi Journal of Psychological Research have been printed. I have exciting updates to share and new developments to report, but above all, I want to take a moment to thank the authors for submitting their fine work to our Journal. They provide the content that is critical to the advancement of science. I also want to thank reviewers for their tireless work on behalf of Psi Chi Journal. Their excellent peer reviews provide the feedback necessary for us to meet the Journal’s mission “to foster and reward the scholarly efforts of psychology students as well as to provide them with a valuable learning experience” (Psi Chi, 2014). Our publication standards are high. In the fiscal 2013–2014 year, 54 editorial decisions were made. Only eight manuscripts were conditionally accepted at the first submission. This represents an acceptance rate of 14.8%, which is comparable to rates for American Psychological Association (APA) journals (APA, 2013). However, a majority of first submissions were invited to return major revisions (n = 31, 57.4%) providing ample evidence of our efforts to support burgeoning authors in strengthening their publication skills. The Journal is growing in multiple ways. Our manuscript submissions are up. In 2013, we received 64 original manuscripts. As of September 15, 2014, we have received 69 manuscripts. At this printing, 75% of the manuscripts processed in 2014 were submitted by undergraduate students, 18% by graduate students, and 7% by faculty. The numbers are similar to 2013 when the proportions were 79%, 13%, and 8% respectively. Psi Chi Journal is also literally growing in size. For the past two years, we have published five manuscripts per issue. This was a deliberate decision intended to provide our members with a high-quality, consistent product. Due to the increase in submissions and improved manuscript management system, we have increased the number of original empirical articles to seven per issue, starting with the 19.3 issue. Finally, our Journal team has grown. Last year, we had three excellent Associate Editors, Drs. Debi Brannan, Carlos Escoto, and Shelia Kennison. This summer we added a fourth Associate Editor to our team, Dr. Steven Rouse. Dr. Rouse is a Professor of Psychology at Pepperdine University (CA) whose work focuses on personality assessment, positive psychology, and spirituality-based conceptions of self-worth. He brings strong quantitative skills to the position. Dr. Rouse teaches Introductory Psychology, Psychological Testing and Measurement, Personality, and Psychology and Religion. We also have a new editorial assistant at Utah State University (USU) to support new projects for the Journal. Jeisianne Rosario Colón is a first-year doctoral student in the Clinical, Counseling, and School Psychology program at USU. Her scholarship is focused on Latino mental health with a
国际心理学荣誉学会(第19卷第19号)2014年版权所有。4/ISSN 2164-8204)《Psi Chi心理学研究杂志》又出版了4期。我有令人兴奋的最新进展要分享,有新的发展要报告,但最重要的是,我想花一点时间感谢作者们向我们的杂志提交了他们出色的工作。它们提供了对科学进步至关重要的内容。我也要感谢评审代表《Psi Chi杂志》孜孜不倦的工作。他们优秀的同行评议为我们提供了必要的反馈,以实现《华尔街日报》“培养和奖励心理学学生的学术努力,并为他们提供宝贵的学习经验”的使命(Psi Chi, 2014)。我们的出版标准很高。在2013-2014财年,共做出了54项编辑决定。只有8份手稿在第一次提交时被有条件地接受。这代表了14.8%的接受率,与美国心理学会(APA)期刊的接受率相当(APA, 2013)。然而,大多数首次提交的论文被邀请进行重大修订(n = 31, 57.4%),这充分证明了我们为支持新兴作者加强出版技能所做的努力。《华尔街日报》正在以多种方式发展。我们的稿子提交完了。2013年共收到原创稿件64篇。截至2014年9月15日,共收到稿件69篇。在本次印刷中,2014年处理的手稿中有75%是由本科生提交的,18%是由研究生提交的,7%是由教师提交的。这些数字与2013年的比例相似,当时的比例分别为79%、13%和8%。《Psi Chi杂志》的规模也在不断扩大。在过去的两年里,我们每期出版五篇稿件。这是一个深思熟虑的决定,旨在为我们的成员提供高质量,一致的产品。由于投稿量的增加和稿件管理系统的完善,我们从19.3期开始,每期的原创实证文章增加到7篇。最后,我们的Journal团队壮大了。去年,我们有三位优秀的副主编。黛比·布兰南,卡洛斯·埃斯科托,还有希拉·肯尼森。今年夏天,我们的团队增加了第四位副主编,史蒂文·劳斯博士。劳斯博士是佩珀代因大学(CA)的心理学教授,他的工作重点是人格评估、积极心理学和基于灵性的自我价值观念。他为这个职位带来了很强的定量分析能力。他教授心理学入门、心理测试与测量、人格、心理学与宗教。我们还在犹他州立大学(USU)聘请了一位新的编辑助理来支持《华尔街日报》的新项目。Jeisianne Rosario Colón是USU临床,咨询和学校心理学项目的一年级博士生。她的奖学金专注于拉丁裔心理健康,对家庭和育儿特别感兴趣。我们对期刊处理做了一些显著的改变,最明显的是APA风格和抄袭检查。我们有一位才华横溢的内部APA风格编辑,他现在系统地审查所有提交的APA风格。所有作者,不管编辑的决定,都会收到关于APA格式的实质性反馈。这也使我们的审稿人能够更深入地关注手稿的科学内容,同时放心所有的出版风格问题都将得到解决。我们的APA风格编辑在投稿时仔细检查稿件以及随后的每一次修改。从今年秋天开始,所有的手稿也将通过TurnItIn®进行抄袭检查,以确认每一篇文章的原创性。我很高兴地报告,每一份被检查过的手稿都已作为原创作品返回!《华尔街日报》的一个关键目标是传播我们作者的工作,以造福于心理科学。为了更好地了解我们的影响,《Psi Chi Journal》现在有了一个GoogleScholarTM账户,所以我们的社论:又一年的伟大进步
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引用次数: 0
The Effects of Hypergravity on Xenopus Embryo Growth and Cardiac Hypertrophy 超重力对爪蟾胚胎生长和心脏肥厚的影响
Pub Date : 2012-09-17 DOI: 10.33697/AJUR.2012.008
B. Duchman, D. Wiens
All life on earth has developed and evolved in a unity gravity (1G) environment. Any deviation below or above 1G could affect animal development, a period when much change occurs and sensitivity is high. We imposed simulated hypergravity through centrifugation and analyzed the effects on the overall body length and cardiac growth of Xenopus laevis embryos. We predicted that increased contractile force would be required from the heart to adequately circulate blood, dispersing nutrients, and that this would inhibit organism growth and possibly induce a state of hypertrophy. Embryos reaching gastrulation stage were exposed to a 7G or 1G (control) field via centrifugation for 96 hours. We then recorded behavior, mortality and took body length measurements. We found no significant differences in behavior or mortality, however, body length was significantly reduced by an average of 6.8% in the 7G group. We then fixed, embedded, sectioned and stained embryos in order to investigate the dimensions of cardiac tissue and of the cardiac region of the body using image analysis software. We found the 7G group had a significantly reduced average body cross-sectional area (-18%) and yet a significantly larger ventricular cross-sectional area (+36%) when compared to the 1G group. The average ratio of ventricle cross-sectional area to average body cross-sectional area was significantly higher in the 7G group when compared to the 1G. From these data, we conclude that hypergravity has a significant inhibitory impact on the Xenopus laevis embryo growth and causes a significant increase in ventricle size.
地球上的所有生命都是在统一重力(1G)的环境中发展和进化的。任何低于或高于1G的偏差都可能影响动物的发育,这是一个变化多、敏感性高的时期。通过离心施加模拟超重力,分析超重力对非洲爪蟾胚胎体长和心脏生长的影响。我们预测心脏需要更大的收缩力来充分循环血液,分散营养物质,这将抑制有机体的生长,并可能诱发肥厚状态。将达到原肠胚期的胚胎置于7G或1G(对照)环境中离心96小时。然后我们记录了它们的行为、死亡率,并测量了它们的体长。我们发现,在行为和死亡率方面没有显著差异,然而,7G组的体长平均显著缩短了6.8%。然后,我们固定、嵌入、切片和染色胚胎,以便使用图像分析软件研究心脏组织和身体心脏区域的尺寸。我们发现,与1G组相比,7G组的平均身体横截面积明显减少(-18%),但心室横截面积明显增大(+36%)。7G组脑室平均横截面积与体平均横截面积之比明显高于1G组。从这些数据中,我们得出结论,超重力对非洲爪蟾胚胎的生长有显著的抑制作用,并导致脑室大小的显著增加。
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引用次数: 5
Guidance for reviewers: Observations after a year as editor 对审稿人的指导:担任编辑一年后的观察
Pub Date : 2012-01-01 DOI: 10.24839/2164-8204.JN17.4.182
M. Rodríguez
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引用次数: 0
How does Psi Chi Journal of Undergraduate Research measure up 《Psi Chi本科生研究杂志》的表现如何
Pub Date : 2011-01-01 DOI: 10.24839/1089-4136.JN16.2.95
M. Rodríguez
Understanding the complexities inherent in descriptions of research journals can take significant time and energy, and in the end leave the average psychologist and psychology student wondering—what does it all mean? Why does this matter? In this column, I attempt to provide information to illuminate how journals are described and why we care. Additionally, I will review how our own journal, Psi Chi Journal of Undergraduate Research, measures up on these criteria. In short, Psi Chi Journal of Undergraduate Research is a scholarly journal that is peer-reviewed and indexed. Let’s explore these areas so you will feel very excited about this description!
理解研究期刊描述中固有的复杂性需要花费大量的时间和精力,最终会让普通的心理学家和心理学专业的学生想知道——这一切都意味着什么?为什么这很重要?在这个专栏中,我试图提供一些信息来阐明期刊是如何被描述的,以及我们为什么要关注它。此外,我还将回顾我们自己的杂志《Psi Chi本科生研究杂志》是如何达到这些标准的。简而言之,Psi Chi本科生研究期刊是一本经过同行评审和索引的学术期刊。让我们来探索这些领域,这样你就会对这个描述感到非常兴奋!
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引用次数: 0
Psi Chi Journal now serves all Psi Chi members Psi气杂志现在为所有Psi气成员服务
Pub Date : 2011-01-01 DOI: 10.24839/1089-4136.JN16.4.156
M. Rodríguez
The Psi Chi Journal of Undergraduate Research has undergone an exciting transformation into the Psi Chi Journal of Psychological Research, a peer-reviewed, indexed journal, that now accepts manuscripts from all Psi Chi members. This change provides an excellent opportunity to review the evolution of the Journal and submission criteria as well as the twists and turns that the life of a submitted manuscript takes potential authors through once manuscripts are entrusted to the Psi Chi Journal team.
《Psi Chi本科生研究期刊》经历了令人兴奋的转变,成为《Psi Chi心理学研究期刊》,这是一本同行评议的、有索引的期刊,现在接受所有Psi Chi成员的手稿。这一变化提供了一个极好的机会来回顾期刊的发展和提交标准,以及一旦手稿被委托给Psi Chi期刊团队,提交的手稿所需要的潜在作者的生命曲折。
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引用次数: 0
期刊
The Journal of Undergraduate Research
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