Feeding Different Omega-3 Polyunsaturated Fatty Acid Sources Influences Renal Fatty Acid Composition, Inflammation, and Occurrence of Nephrocalcinosis in Female Sprague-Dawley Rats

The general population is encouraged to increase omega-3 polyunsaturated fatty acid (n-3 PUFA) intake in order to optimize health for preventative health care. Consumers are typically unaware that different amounts, types, and structural forms of n-3 PUFA have different efficacy. Therefore, the objectives of this study were to characterize different sources of n-3 PUFAs and to determine whether consumption of these oils influences renal fatty acid composition and renal health. Lipid classes and fatty acid profile of corn (CO), flaxseed (FO), menhaden (MO), salmon (SO), tuna (TO) or krill (KO) oils were determined by thin-layer and gas chromatography. All dietary oils consisted of >65% triglyceride with the exception of KO. KO and FO also contained phospholipids. FO was rich in the n-3 PUFA, alpha-linolenic acid (18:3n-3) whereas, the marine oils were rich in the long-chain n-3 PUFAs (>18 carbons). Following characterization of the oil sources, female Sprague-Dawley rats (age 28 d) were randomly assigned (n = 10/group) to be fed a high fat 12% (wt) diet consisting of these different oil sources for 8 weeks. Rats fed MO, TO, and SO had significantly higher renal eicosapentaenoic acid (20:5n-3) and docosahexaenoic acid (22:6n-3) deposition and this in turn, modulated inflammatory responses. Feeding rats MO, SO and TO reduced urinary excretion of 13,14-dihydro-15-keto prostaglandin E2. Feeding rats TO and SO reduced (P ≤ 0.002) nuclear factor kappa B activity and circulating TNFα (P < 0.05). In contrast, rats consuming KO had heavier kidney weights (P < 0.001), total calcium content, and histological evidence of renal calcification and tubulo-interstitial injury. This was due to increased (P < 0.001) urinary phosphorus excretion associated with the phospholipids content of KO. The study results indicated that consumption of n-3 PUFAs influences renal health and the effects varied depending on the n-3 PUFA source consumed.

An Observation Data Driven Simulation and Analysis Framework for Early Stage <i>C. elegans</i>Embryogenesis

Recent developments in cutting-edge live microscopy and image analysis provide a unique opportunity to systematically investigate individual cell’s dynamics as well as simulation-based hypothesis testing. After a summary of data generation and analysis in the observation and modeling efforts related to C. elegans embryogenesis, we develop a systematic approach to model the basic behaviors of individual cells. Next, we present our ideas to model cell fate, division, and movement using 3D time-lapse images within an agent-based modeling framework. Then, we summarize preliminary result and discuss efforts in cell fate, division, and movement modeling. Finally, we discuss the ongoing efforts and future directions for C. elegans embryo modeling, including an inferred developmental landscape for cell fate, a quasi-equilibrium model for cell division, and multi-agent, deep reinforcement learning for cell movement.

Inflammatory diseases modelling in zebrafish

The ingest of diets with high content of fats and carbohydrates, low or no physical exercise and a stressful routine are part of the everyday lifestyle of most people in the western world. These conditions are triggers for different diseases with complex interactions between the host genetics, the metabolism, the immune system and the microbiota, including inflammatory bowel diseases(IBD), obesity and diabetes. The incidence of these disorders is growing worldwide; therefore, new strategies for its study are needed. Nowadays, the majority of researches are in use of murine models for understand the genetics, physiopathology and interaction between cells and signaling pathways to find therapeutic solutions to these diseases. The zebrafish, a little tropical water fish, shares 70% of our genes and conserves anatomic and physiological characteristics, as well as metabolical pathways, with mammals, and is rising as a new complementary model for the study of metabolic and inflammatory diseases. Its high fecundity, fast development, transparency, versatility and low cost of maintenance makes the zebrafish an interesting option for new researches. In this review, we offer a discussion of the existing genetic and induced zebrafish models of two important Western diseases that have a strong inflammatory component, the IBD and the obesity.

Visualization of 3-Dimensional Vectors in a Dynamic Embryonic System—WormGUIDES

WormGUIDES is an open-source dynamic embryonic system designed to facilitate global understanding of cellular decisions in the developing nervous system of the nematode C. elegans. WormGUIDES was designed to allow investigation and exploration of the observational results of the C. elegans life cycle from laboratory experiments. In the process of a mechanistic C. elegans model development, some functionalities of WormGUIDES needed to be enhanced to support model validation and verification. In this study, a new way to visualize 3-dimentional vectors within WormGUIDES was investigated and presented. Then, the practical values of this method were demonstrated by visualizing two biologically significant directions (i.e., division orientation and cell polarity) of individual embryonic cells in C. elegans. Lastly, a mathematic approach was designed to illustrate the differences between these two sets of vectors and provide easy indications of the location of these individual cells that have large data discrepancies within the C. elegans embryonic system.

Baculovirus RNA Polymerase: Activities, Composition, and Evolution

Baculoviruses are the only nuclear replicating DNA-containing viruses that encode their own DNA-directed RNA polymerase (RNAP). The baculovirus RNAP is specific for the transcription of genes expressed after virus DNA replication. It is composed of four subunits, making it the simplest multisubunit RNAP known. Two subunits contain motifs found at the catalytic center of other RNAPs and a third has capping enzyme functions. The function of the fourth subunit is not known. Structural studies on this unique RNAP will provide new insights into the functions of this enzyme and the regulation of viral genes and may be instrumental to optimize the baculovirus gene expression system.

Osteogenesis imperfecta mutations in plastin 3 lead to impaired calcium regulation of actin bundling

Mutations in actin-bundling protein plastin 3(PLS3)emerged as a cause of congenital osteoporosis,but neither the role of PLS3 in bone development nor the mechanisms underlying PLS3-dependent osteoporosis are understood.Of the over 20 identified osteoporosis-linked PLS3 mutations,we investigated all five that are expected to produce full-length protein.One of the mutations distorted an actin-binding loop in the second actin-binding domain of PLS3 and abolished F-actin bundling as revealed by cryo-EM reconstruction and protein interaction assays.Surprisingly,the remaining four mutants fully retained F-actin bundling ability.However,they displayed defects in Ca2+sensitivity:two of the mutants lost the ability to be inhibited by Ca2+;while the other two became hypersensitive to Ca2a.Each group of the mutants with similar biochemical properties showed highly characteristic cellular behavior.Wild-type PLS3 was distributed between lamellipodia and focal adhesions.In striking contrast,the Ca2+-hyposensitive mutants were not found at the leading edge but localized exclusively at focal adhesions/stress fibers,which displayed reinforced morphology.Consistently,the Ca2+-hypersensitive PLS3 mutants were restricted to lamellipodia,while chelation of Ca2+caused their redistribution to focal adhesions.Finally,the bundling-deficient mutant failed to co-localize with any F-actin structures in cells despite a preserved F-actin binding through a non-mutation-bearing actin-binding domain.Our findings revealed that severe osteoporosis can be caused by a mutational disruption of the Ca2+-controlled PLS3’s cycling between adhesion complexes and the leading edge.Integration of the structural,biochemical,and cell biology insights enabled us to propose a molecular mechanism of plastin activity regulation by Ca2+.

Histone modification as a drug resistance driver in brain tumors

Patients with brain tumors,specifically,malignant forms such as glioblastoma,medulloblastoma and ependymoma,exhibit dismal survival rates despite advances in treatment strategies.Chemotherapeutics,the primary adjuvant treatment for human brain tumors following surgery,commonly lack efficacy due to either intrinsic or acquired drug resistance.New treatments targeting epigenetic factors are being explored.Post-translational histone modification provides a critical regulatory platform for processes such as chromosome condensation and segregation,apoptosis,gene transcription,and DNA replication and repair.This work reviews how aberrant histone modifications and alterations in histone-modifying enzymes can drive the acquisition of drug resistance in brain tumors.Elucidating these mechanisms should lead to new treatments for overcoming drug resistance.

Control of Directional Macromolecular Trafficking Across Specific Cellular Boundaries:A Key to Integrative Plant Biology

There is now solid evidence that cell-to-cell trafficking of certain proteins and RNAs plays a critical role in trans-cellular regulation of gene expression to coordinate cellular differentiation and development. Such trafficking also is critical for viral infection and plant defense. The mechanisms of trafficking remain poorly understood. Although some proteins may move between cells by diffusion, many proteins and RNAs move in a highly regulated fashion. Regulation is likely achieved through interactions between distinct protein or RNA motifs and cellular factors. Some motifs and factors have been identified. One of the major focuses for future studies is to identify all motifs and their cognate factors and further elucidate their roles in trafficking between specific cells. With increasing information from such studies, we should be able to develop an understanding of the mechanisms that regulate trafficking of various proteins and RNAs across all and specific cellular boundaries. On the basis of such mechanistic knowledge, we can further investigate how the trafficking machinery has evolved to regulate developmental and physiological processes in a plant, how pathogens have co-evolved to use this machinery for systemic spread in a plant, and how plants use this machinery for counterdefense.

植物CRISPR/Cas9多基因编辑载体构建和突变分析的操作方法

CRISPR/Cas9基因组编辑技术是植物基因功能研究与作物改良的有效工具.为此,本实验室开发了高效的CRISPR/Cas9植物多基因编辑载体系统.本载体系统包括6个双元载体和12个含有不同U3/U6启动子的sg RNA中间载体,可满足对单子叶和双子叶植物的遗传转化以及不同抗生素筛选的要求,具有简便、高效,可同时对多基因进行编辑的特点.此外,为了能更高效地应用基因组编辑技术,还开发了一站式在线分析工具包CRISPR-GE.为方便研究人员利用CRISPR/Cas9系统进行植物基因组编辑,本文提供了从靶点选择、CRISPR/Cas9多靶点双元载体构建,以及对靶点突变序列的测序分析等详细的操作方法,以及常见的问题解答.

Viroids:Small Probes for Exploring the Vast Universe of RNA Trafficking in Plants

Cell-to-cell and long-distance trafficking of RNA is a rapidly evolving frontier of integrative plant biology that broadly impacts studies on plant growth and development, spread of infectious agents and plant defense responses. The fundamental questions being pursued at the forefronts revolve around function, mechanism and evolution. In the present review, we will first use specific examples to illustrate the biological importance of cell-to-cell and long-distance trafficking of RNA. We then focus our discussion on research findings obtained using viroids that have advanced our understanding of the underlying mechanisms involved in RNA trafficking. We further use viroid examples to illustrate the great diversity of trafficking machinery evolved by plants, as well as the promise for new insights in the years ahead. Finally, we discuss the prospect of integrating findings from different experimental systems to achieve a systems-based understanding of RNA trafficking function, mechanism and evolution.

Nature子刊：研究揭示咖啡因等24种化合物阻止痴呆症的潜在机制，促进大脑中的酶NMNAT2产生

在一项新的研究中。来自美国印第安纳大学伯明顿分校的研究人员鉴定出24种化合物（包括咖啡因）有潜力增加大脑中的一种经证实抵抗痴呆症的酶的水平。相关研究结果在线发表在ScientificReports期刊上。

Chemotherapy-induced immunological breast cancer dormancy: a new function for old drugs?

Breast cancer remains the main cause of cancer-related mortality for women world-wide. Main cause of death is the development of therapy-resistant metastases. Relapses occur with a bimodal temporal distribution, with a first peak at 1-2 years after initial therapy and a second peak 2-3 years later. This discontinuous growth kinetics is consistent with the notion that disseminated cancer cells can remain dormant over a prolonged period of time before resuming growth. How cancer cells enter, sustain and exit dormancy, are unanswered questions with relevance to cancer biology, monitoring and therapy. Investigating mechanisms of breast cancer dormancy remains challenging, as in patients the condition is elusive and experimentally there are only a few models that recapitulate the clinical condition. Thus, developing new models to identify clinically relevant mechanisms and candidate therapeutic targets may open new avenues for novel therapies to induce and prolong dormancy. We have observed that cells surviving chemotherapy can enter a state of immunological dormancy. Using this model, we identified IRF-7/Interferon type I/IFNRA as signaling axis essential for this effect. Here we will review concepts and recent developments in cancer metastasis and dormancy with emphasis on breast cancer, and elaborate strategies to exploit them therapeutically.

A targetable pathway to eliminate TRA-1-60^(+)/TRA-1-81^(+)chemoresistant cancer cells

Chemoresistance is a primary cause of treatment failure in pancreatic cancer.Identifying cell surface markers specifically expressed in chemoresistant cancer cells(CCCs)could facilitate targeted therapies to overcome chemoresistance.We performed an antibody-based screen and found that TRA-1-60 and TRA-1-81,two‘stemness’cell surface markers,are highly enriched in CCCs.Further-more,TRA-1-60^(+)/TRA-1-81^(+)cells are chemoresistant compared to TRA-1-60^(-)/TRA-1-81^(-)cells.Transcriptome profiling identified UGT1A10,shown to be both necessary and sufficient to maintain TRA-1-60/TRA-1-81 expression and chemoresistance.From a high-content chemical screen,we identified Cymarin,which downregulates UGT1A10,eliminates TRA-1-60/TRA-1-81 expression,and increases chemosensitivity both in vitro and in vivo.Finally,TRA-1-60/TRA-1-81 expression is highly specific in primary cancer tissue and positively correlated with chemoresistance and short survival,which highlights their potentiality for targeted therapy.Therefore,we discovered a novel CCC surface marker regulated by a pathway that promotes chemoresistance,as well as a leading drug candidate to target this pathway.