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Nov. 2018, Volume 9 Issue 11

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It’s well accepted that the secondary structures of HCV RNA and the cellular proteins that bind to them modulate both translation and RNA replication together. In this paper, we identified RNA binding motif protein 24 (RBM24) as a novel host factor participated in HCV life cycle which binds to the 5′ and 3′ UTRs in the HCV genome, and may function at the switch from translation to replication as silencing of RBM24 stimulated the initial translation of HCV proteins but inhibited and delayed replication of HCV genome. Mechanically, RBM24 could interrupt the assembly of the 80S ribosome on the HCV IRES and enhance the interaction between the 5′ and 3′ UTRs in the HCV genome.

Aug. 2018, Volume 9 Issue 8

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“Hypertonia-linked protein Trak1 functions with mitofusins to promote mitochondrial tethering and fusion”

Hypertonia is a neurological dysfunction in several central nervous system disorders, including cerebral palsy, Parkinson’s disease, and epilepsy. In this issue, Lee et al report that hypertonia-linked protein Trak1 is a new regulator of mitochondrial tethering and fusion with a critical role in maintaining mitochondrial and cell health under stress conditions. Their study reveals that hypertonia-associated mutation impairs the mitochondrial localization and function of Trak1 and provides evidence linking dysregulated mitochondrial dynamics to hypertonia pathogenesis. This cover image shows the intracellular localization of hypertonia-associated Trak1 mutant protein (green) with reduced association with mitochondria (red) captured by three-dimensional structured illumination microscopy.

Jun. 2018, Volume 9 Issue 6

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Say bye to crude FMT by targeting purified microbial cells from donated healthy stool using an automatic purification system. Scanning electron microscope confirmed the “clean” bacteria from the frozen fecal microbiota suspension which was provided by fmtBank as a national non-profit stool bank.

By Faming Zhang

Mar. 2018, Volume 9 Issue 3

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Lung regeneration is the major challenge of modern medicine. In this issue, Ma et.al. identified a previously unknown population of adult human lung stem cells, which locates at the basal layer of airway epithelium and could be marked by SOX9 gene expression. Culture and orthotopic transplantation of such cells generated functional human alveoli and bronchioles in mouse model. In a pilot clinical trial, after autologous transplantation of such cells, two patients with chronic lung diseases demonstrated recovery of pulmonary structure and function. This is the first evidence showing that human lung tissue could be regenerated by adult stem cell transplantation. The cover picture illustrated the re-growth of “respiratory tree”.
Lung-related diseases are the third-leading cause of human death throughout the world. Lethal lung diseases such as chronic obstructive pulmonary disease (COPD), pulmonary fibrosis and bronchiectasis are characterized by irreversible, progressive damage of the lung tissue. The ability to regenerate human lung tissue, if successful, would constitute a breakthrough in modern medicine. Despite years of research, however, currently there is no effective strategy to regenerate lost bronchioles or alveoli in humans. Stem cell-based regenerative medicine holds great potential for combating tissue damage in lung diseases and other disorders by providing unlimited materials for transplant (Liu et al., 2012; Liu et al., 2014; Wu and Izpisua Belmonte, 2016; Shi et al., 2017; Yang et al., 2017). Induced pluripotent stem cells (iPSCs) could be the source of cells for autologous transplantation. iPSC has been successfully differentiated to alveolar and airway lineage (Huang et al., 2014; McCauley et al., 2017). It remains unknown however, whether these iPSC-derivatives can form lung tissue in vivo, and/or functionally contribute to gas-blood air exchange. In addition, undifferentiated iPSCs in the differentiation culture generate safety concerns. On the other hand, somatic stem cells or progenitors—if can be identified, isolated and expanded—could offer a better and safer choice for regenerative medicine.
Different types of lung stem/progenitor cells have been identified and extensively studied in rodents (Hogan et al., 2014; Vaughan et al., 2015; Zuo et al., 2015). To date, however, human lung stem/progenitor cells remain elusive (Kajstura et al., 2011). Given the vast differences between human and mouse in the development, tissue architecture (e.g., lobulation and branching pattern) and cell composition of the respiratory system, existing information in the rodents may not be directly translated into humans. Therefore, additional efforts are needed to identify and characterize human lung stem/progenitor cells. In this issue of Protein & Cell, Ma et al. identified a previously unknown population of adult human lung stem cells, which were successfully used for generating functional human lung air exchanging units following their transplantation to a mouse model and also in a pilot human clinical trial.
The putative adult human lung stem cells discovered by Ma et al. are located to the bottom of rugae in 2–4 order airway and could be distinguished from airway basal cells (BCs) by SOX9 expression. SOX9 is a known marker for embryonic lung progenitor cells and also stem/progenitor cells of other tissues such as liver and gut. Interestingly, in gut the SOX9+ progenitors reside in the crypt, an invaginated structure similar to the airway rugae. From a trace amount of bronchoscopic brush-off lung tissues, the authors isolated SOX9+ BCs and expanded them in vitro for a long time. Clonally derived SOX9+ BCs were carefully characterized and then transplanted into injured mouse lung. Following transplantation, SOX9+ BCs could give rise to both human bronchiolar and alveolar epithelium in vivo, demonstrating their generative potential. It is worth noting that SOX9+ BCs could be easily isolated from both normal and diseased patients by routine, bleeding-free bronchoscopic brushing with a high success rate. Also the culture method the authors developed to expand SOX9+ BCs in vitro is pivotal for producing sufficient cells for transplantation. The culture method for adult the putative human lung stem cells developed in this study has certain advantage over the bronchiolar/alveolar organoid culture method reported previously (Nichane et al., 2017), in that it enables the production of a large number of relatively pure population of cells from as few as one single cell, which can maintain their developmental potential even in a feeder-free culture condition.
By transplanting the in vitro expanded cells into immune-deficient mice, Ma et al. generated a chimeric lung with both human and mouse tissues. The regenerated human alveoli established intact vasculature system and were functional. However, human type II alveoli cells were not generated, which is likely due to the limited potency of the human cells and/or species difference. More importantly, in this study, for the first time the authors explored the clinical feasibility of autologous SOX9+ BC transplantation to treat two patients with bronchiectasis. The results showed recovery of patients’ pulmonary function and improvement of bronchi dilation on CT over time. Although it is a very small sample size, the results of this pilot trial are consistent with their observation in the mouse model, and pave the road for a large-scale controlled clinical study in the future. Interestingly, the authors also showed that the anti-lung fibrosis drug Pirfenidone could boost stem cell transplantation efficiency in a TGFβ-dependent manner, suggesting the possible combination of traditional chemical pills and stem cell transplantation for combating lung diseases.
Although Ma et al. established an applicable system for human lung regeneration, there are still several issues remain unsolved—for instance, whether the stem cell transplantation therapy works well in treating other lung-related diseases, such as emphysema or idiopathic pulmonary fibrosis, and the long term effect of stem cell transplantation remains unexplored. In summary, the identification and culture of human lung stem/progenitor cells reported in this study hold great potential for developing regenerative medicine therapy for treating lung diseases. Considering chronic lung diseases are life threatening with only palliative treatments available, the significance of lung stem/progenitor cell-based transplantation would be tremendous, which provides exciting translational opportunities ahead.

Mar. 2018, Volume 9 Issue 2

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Mammalian carboxylesterases (EC 3.1.1.1) have been demonstrated to hydrolyze endogenous esters and thioesters including lipids. Recent studies have revealed the role of carboxylesterases in lipid metabolism and their relevance to metabolic diseases. To translate pre-clinical studies in cellular and mouse models to humans, differences and similarities of carboxylesterases between mice and human need to be elucidated. Jihong Lian and colleagues review current knowledge and research progression in the structure and function of mouse and human carboxylesterases, with emphasis on physiological roles of these enzymes in lipid metabolism and human diseases.

Mar. 2018, Volume 9 Issue 1

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Antibody therapeutics represents a major breakthrough in combating human diseases and the improvement of human health. About 80 antibody therapies have been approved for the treatment of cancer, immune disorders, and metabolic, cardiovascular and infectious diseases. The rapid rise of antibody-based therapies is largely due to their desirable safety profile, target specificity, and efficacy. Antibody-based therapies are engineered into diverse modalities such as naked IgGs, antibody-drug conjugates (ADCs), bispecific antibodies, antibody fragments, and Fc-modified antibodies. Antibody-based therapies often possess multiple modes of actions which include interrupting ligand-receptor interaction and signaling, engaging immune effector functions, and blocking immune check point inhibition. The cover picture illustrates an antibody-binding to a cell surface receptor, thereby inhibiting ligand-receptor interaction and signaling.

Dec. 2017, Volume 8 Issue 12

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A new three-dimensional organoid culture system from iPSCs in vitro has been reported to recapitulate normal cortical development and neural developmental diseases. Organoids derived from this culture system generate ventricle-like cavities surrounded by progenitor cells (green), while new-born neurons (red) locate superficially. In these organoids, ventricular zone (VZ), subventricular zone (SVZ), lower and upper cortical plate (CP) display a well-aligned layer structure, which mimics the developmental structure of the normal human brain. Neurons in organoids undergo a process of maturation and form a functional neuronal network. Furthermore, the authors have developed this culture system for an investigation of the ASPM-dependent pathogenesis of microcephaly. This study has revealed the cortical organoids generated from primary microcephaly patient-derived iPSCs exhibit defective neurogenesis and neuronal network connectivity.

Nov. 2017, Volume 8 Issue 11

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A new three-dimensional organoid culture system from iPSCs in vitro has been reported to recapitulate normal cortical development and neural developmental diseases. Organoids derived from this culture system generate ventricle-like cavities surrounded by progenitor cells (green), while new-born neurons (red) locate superficially. In these organoids, ventricular zone (VZ), subventricular zone (SVZ), lower and upper cortical plate (CP) display a well-aligned layer structure, which mimics the developmental structure of the normal human brain. Neurons in organoids undergo a process of maturation and form a functional neuronal network. Furthermore, the authors have developed this culture system for an investigation of the ASPM-dependent pathogenesis of microcephaly. This study has revealed the cortical organoids generated from primary microcephaly patient-derived iPSCs exhibit defective neurogenesis and neuronal network connectivity.

Nov. 2017, Volume 8 Issue 10

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The enzyme that degrades mitochondrial RNAs in mammalian cells had eluded discovery for decades. It had long been assumed that the degradation happens in mitochondrial matrix where transcription and translation occur. Liu et al. provide compelling evidence that mammalian mitochondrial RNA degradation happens in mitochondrial intermembrane space (IMS) and RNASET2 is the ribonuclease for the process. RNASET2 activity also has an effect on mitochondrial transcription in the matrix, suggesting a compensatory feedback. PNPASE, a previously identified mitochondrial IMS protein that is involved in mitochondrial RNA degradation, possibly functions in transportation of mitochondrial RNAs instead of acting as a ribonuclease. The cover picture demonstrates the degradation machinery together with the transcriptional regulation.

Sep. 2017, Volume 8 Issue 9

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Key mitotic checkpoint kinases Aurora B and C can regulate distinct cell fate in mouse preimplantation embryos. Aurorakinase B or C was overexpressed or knocked-down in one cell of the 4-cell transgenic mouse embryo. The descendent cells of Aurora B or C overexpression cell (green) preferably developed to placenta or embryo proper of the 13.5 dpc embryo. The authors also showed that Aurora B and C differentially regulated Spindle Assembly Checkpoint (SAC) activation, pluripotency transcription factor Oct4 stability and inner cell mass or trophectoderm fate choice in preimplantation mouse embryos. This study revealed new mechanism of how early mammalian embryos prevent abnormal cells entering the embryo lineage and have important implications in assisted human reproduction.

Aug. 2017, Volume 8 Issue 8

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Entero virus 71 (EV71) is a most common causative agent of hand, foot, and mouth disease (HFMD). SCARB2 is the main receptor for EV71 and critical for both viral infection and pathogenesis. In this issue, Zhang and colleagues generated a monoclonal antibody JL2, which binds human but not mouse SCARB2 and blocks EV71 infection effectively. Structural views of SCARB2-JL2 complex reveal that JL2 binds to the apical region of SCARB2 involving α-helices 2, 5, and 14. Three regions of human SCARB2, residues 77–113, 144–151, and 302–478, contribute to the binding of JL2 mAb. These results provide new insights into the potential binding sites for EV71 on SCARB2 and the molecular mechanism of EV71 entry.

Aug. 2017, Volume 8 Issue 7

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T lymphocytes can be genetically modified to specifically target and kill tumors for cancer treatment. Since most current T cell products require ex vivo stimulation and expansion, it is uppermost important to produce T cells with maximal in vivo anti-tumor activities. Improved in vivo anti-tumor function was achieved using T cells generated by a novel method of transferring peripheral blood mononuclear cells (PBMCs) by electroporation with RNA encoding a chimeric membrane protein consisting of a CD3 scFv and the intracellular domains from CD28 and 4-1BB, thus provides a simple, upgradable and easy to scale-up platform for producing high quality T cells for adoptive immunotherapy. The study also suggests that testing T cells in different mouse tumor models is necessary to fully evaluate the quality of the T cell products.

May. 2017, Volume 8 Issue 4

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Cell reprogramming in vitro to generate induced pluripotent stem cells stimulates flourishing of regenerative medicine and comes into focus in decades. Meanwhile, it is still not well known whether cell reprogramming induced or promoted by factors in vivo directly favors tissue regeneration. In this issue, Tang and colleagues report that cocktail of small chemical compounds promoting cell reprogramming, which was identifi ed through in vitro assay, was found to be able to enhance tissue regeneration in mouse model of acute liver injuries, which was induced by partial hepatectomy or toxic treatment. This study not only offers a brand-new strategy for regenerative purpose, but also identifi es clinical drugs protecting liver against damage.

Mar. 2017, Volume 8 Issue 3

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Metastasis is a major death causing factor in breast cancer, lacking effective treatments. Th2 and M2macrophages have been associated with metastasis in breast cancer models and are considered as potential targets for immunotherapy. Here for the first time, we characterized the expression and function of IL-25 in a spontaneous breast cancer model and found its blockade re-shaped tumor microenvironments and reduced tumor metastasis to the lung. Our study thus identified IL-25 as a novel therapeutic target in breast cancer for treatment of metastasis. The cover image shows co-expression of IL-25 and F4/80 in the primary mouse breast tumor.

Mar. 2017, Volume 8 Issue 2

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DEAD-box proteins are named after the strictly conserved sequence Asp-Glu-Ala-Asp (D-E-A-D) and widely found in organisms from bacteria to humans. They are involved in many aspects of RNA metabolism, such as transcription, pre-mRNA splicing, transport, translation, mRNA decay and ribosome biogenesis. DDX41 is a member of the DEAD-box proteins and acts as an intracellular DNA sensor in myeloid dendritic cells. On viral infection, the DDX41 will be phosphorylated by BTK kinase and senses the DNA or c-di-GMP of the invaders, followed by induction of type I interferons. Besides the roles in innate immunity, DDX41 is also related to disease and an increasing number of both inherited and acquired mutations in DDX41 gene are identified from myelodysplastic syndrome and/or acute myeloid leukemia (MDS/AML) patients.

Feb. 2017, Volume 8 Issue 1

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Mitophagy is a critical mechanism for mitochondria quality control. Defective mitophagy has been proved to be highly related to a number of important human diseases including cancer and Parkinson’s disease. Fun14 domain-containing protein 1 (FUNDC1) was reported as a new receptor for hypoxia-induced mitophagy. Its phosphorylation modification affects the binding affinity for microtubule-associated protein light chain 3 beta (LC3B) and regulates selective mitophagy. Here in this research, we present the crystal structure of LC3B in complex with a FUNDC1 LIR peptide phosphorylated at Ser17 (pS17). Together with the in vitro interaction analyses, our results provide a detailed elucidation of the specific recognition of phosphorylated and dephosphorylated FUNDC1 by LC3B, which unveils the precise role of post-translational modification in the elaborate regulation of the selective mitophagy.

Jan. 2017, Volume 7 Issue 12

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Mechanistic target of rapamycin (mTOR) complex 1 (mTORC1) integrates signals from growth factors, cellular energy levels, stress and amino acids to control cell growth and proliferation. Here we determined the cryo-electron microscopy structure of human mTORC1 at 4.4 Å resolution. The mTORC1 comprises a dimer of heterotrimer: mTOR-Raptor-mLST8. The complex adopts a hollow rhomboid shape with 2-fold symmetry. Within the complex, the conserved N-terminal caspase-like domain of Raptor faces toward the catalytic cavity of mTOR’s kinase domain. Raptor shows no caspase activity and may bind to TOS motif for substrate recognition. Structural analysis indicates that FKBP12-Rapamycin may generate steric hindrance for substrate entry to mTORC1’s catalytic cavity. The structure provides a basis to understand the assembly of mTORC1 and a framework to characterize the regulatory mechanism of mTORC1 pathway.

Nov. 2016, Volume 7 Issue 11

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Circadian rhythm is a fundamental biological system that regulates various physiological functions with respect to the solar day. It has been revealed that circadian genes controlled several adult stem cells functions. However, biological rhythms are absent in embryonic stem cells (ESCs). Interestingly, circadian rhythms appear when embryonic stem cells exit the pluripotent state and disappear when adult somatic cells are reprogrammed back into pluripotent state. Lu et al knocked out the core circadian gene Clock in mouse ESCs by CRISPR/CAS9-mediated genetic editing techniques. They found that Clock did not influence the maintenance of the pluripotent state for ESCs. However, Clock was not only required for maintaining regular proliferation but also essential for differentiation of ESCs. Their findings provided interesting new insights into the regulatory mechanisms of biological clock in pluripotent stem cells as well as embryonic development in mammals.

Oct. 2016, Volume 7 Issue 10

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Reproduction, fat metabolism, and longevity are directly coupled; signals from reproductive system can regulate longevity and fat metabolism. Here, we find that an oogenesis-enriched gene, c30f12.4, is specifically expressed and located in germ cells and early embryos. Further identification of the localization of C30F12.4 in germ cells and embryos suggests that C30F12.4 was mainly located in the cytoplasm around the germ cells and everywhere in oocytes. Knocked out of c30f12.4 in worms not only decreases the brood size, but also alters fat metabolism and leads to a shortened lifespan. Our results highlight an important role for c30f12.4 in regulating reproduction, fat homeostasis, and aging in C. elegans, which helps us to better understand the relationship between these processes.

Sep. 2016, Volume 7 Issue 9

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Living organisms are exposed to the geomagnetic fi eld (GMF) throughout their lifespan. Elimination of the GMF, resulting in a hypogeomagnetic fi eld (HMF), leads to central nervous system dysfunction and abnormal development in animals. However, the cellular mechanisms underlying these effects have not been identifi ed so far. In this issue, Fu & Mo et al.show that exposure to an HMF (< 200 nT), produced by a magnetic fi eld shielding chamber, promotes the proliferation of neural progenitor/stem cells from C57BL/6 mice both in vitro and in vivo. HMF-disturbed NPCs/ NSCs production probably affects brain development and function, which provides a novel clue for elucidating the cellular mechanisms of the bio- HMF response. The picture shows the proliferative neural progenitor/stem cells immunostained with anti-BrdU antibody (green) and glia cells with anti-GFAP antibody (red) in the hippocampus of adult mice exposed to the HMF for one month, nuclei were counterstained with Hoechst (blue).

Sep. 2016, Volume 7 Issue 8

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Neonatal microcephaly associated with Zika virus infection has already caused a public health emergency of international concern. The ZIKV helicase, which plays a pivotal role in viral RNA replication, is an attractive target for therapy. We determined the crystal structures of ZIKV helicase-ATP-Mn2+ and ZIKV helicase-RNA. Our fi ndings suggest that fl avivirus helicases could have evolved a conserved engine to convert chemical energy from nucleoside triphosphate to mechanical energy for RNA unwinding, but different motor domain rotations result in variable RNA recognition modes to adapt to individual viral replication.

Jul. 2016, Volume 7 Issue 7

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Werner syndrome (WS) is a premature aging disorder that primarily affects mesodermal tissues. A WS disease model using WRN-deficient MSCs has been recently developed,which recapitulates many phenotypic features of WS. In this issue, by small-molecule screening Li et al. (pp. 478–488) find that Vitamin C exerts most efficient rescue for diverse premature aging defects as shown in WS MSCs. Moreover, Vitamin C restores in vivo viability of WS MSCs in a mouse model. RNA sequencing analysis indicates that Vitamin C inhibits aging related gene expression and pathways in the WS MSC model. These results identify Vitamin C as a geroprotective factor for WS MSCs, which holds the potential of being applied as a novel type of treatment of WS.

Jun. 2016, Volume 7 Issue 6

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Homocysteine (Hcy) is a sulfur-containing non-constitutive amino acid derived from the essential amino acid methionine. Hyperhomocysteinemia (HHcy) accelerates atherosclerosis by promoting immuno-inflammatory responses. Recent studies have revealed the intercrossing of pathways in the regulation of immune and metabolic systems. Feng et al., for the fi rst time, show that Hcy-stimulated T-cell activation in mice was accompanied by increased mitochondrial metabolic reprogramming in vitro and in vivo. Inhibiting mitochondrial calcium signals or blocking mitochondrial respiration blunted Hcy-induced T-cell IFN-γ secretion and proliferation. ER and mitochondria interact with each other physically and functionally. This study suggests that the metabolic axis, consisting of ER stress, ER-mitochondria coupling, and mitochondrial metabolic reprogramming is involved in the Hcy-promoted T-cell early activation, and sheds new light on understanding the mechanisms underlying the pathogenesis of HHcy-accelerated metabolic syndrome.

May. 2016, Volume 7 Issue 5

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On a vast cosmic background with the human form as a constellation, the phylogenetic tree of the G protein-coupled receptor superfamily is presented with structures that have been determined highlighted as red stars. A snake plot diagram that shows the prototypical 7 transmembrane topology of receptors in this superfamily as well as the target locations for insertion of a protein fusion partner (BRIL) that was used in the studies described by Lv et al. in this issue. This cover signifies the importance of GPCR in the human body and the fact that life science constitute a part of the mystery of the universe.

May. 2016, Volume 7 Issue 4

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Meiotic recombination is carried out through a specialized pathway for the formation and repair of DNA double-strand breaks (DSBs) made by the Spo11 protein. The present study shed light on the functional role of cyclin, CYC2, in Tetrahymena thermophila which has transcriptionally high expression level during meiosis process. Knocking out the CYC2 gene results in arrest of meiotic conjugation process at 2.5–3.5 h after conjugation initiation, before the meiosis division starts, and in company with the absence of DSBs. Complete transcriptome profile was performed between wild-type strain and CYC2 knock-out strain. Functional analysis of RNA-Seq results identifies related differentially expressed genes (DEGs) including SPO11 and these DEGs are enriched in DNA repair/mismatch repair (MMR) terms in homologous recombination (HR), which indicates that CYC2 could play a crucial role in meiosis by regulating SPO11 and participating in HR.

Apr. 2016, Volume 07 Issue 03

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The “plum tree blossom” represents in vivo or in vitro differentiation and maturation of human neural stem cells into functional neurons. Underneath the tree, a “dragon”-shaped structure represents single cell RNA-sequencing tethered with electrophysiological recordings. The “dragon head” is a matured single human neuron and the “tail”, an immature neuron. The maturity of the cultured neurons is characterized by neuronal morphology as well as electrophysiological traits. The Chinese auspicious totem dragon signifi es the power and prosperity of the emerging “Patch-seq” technology in future endeavors to decode the secret of human brain functions and hopefully, then the pathology of human brain disorders.

Mar. 2016, Volume 7 Issue 2

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Mutations or inactivation of parkin, an E3 ubiquitin ligase, are associated with familial form or sporadic Parkinson’s disease (PD), respectively. Here we report that p62 is a new substrate of parkin. P62 levels were increased in the SN and STR regions, but not in other brain regions in parkin knockout mice. Parkin directly interacts with and ubiquitinates p62 at the lysine-13 to promote proteasomal degradation of p62 even in the absence of ATG5. Pathogenic mutations, knockdown of parkin or mutation of p62 at lysine 13 prevented the degradation of p62. We further showed that parkin deficiency mice have pronounced loss of Tyrosine hydroxylase positive neurons and have worse performance in motor test when treated with 6-OHDA in aged mice. These results suggest that, in addition to their critical role in regulating autophagy, p62 are subjected to parkin mediated proteasomal degradation and implicate that the dysregulation of parkin/p62 axis may involve in the selective vulnerability of neuronal cells during the onset of PD pathogenesis.

Jan. 2016, Volume 7 Issue 1

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Single particle analysis is an efficient method to study the threedimensional structures of biological macromolecules. While for particles with multiple conformations, inaccurate alignments and orientation parameters will yield an averaged map with diminished resolution and smeared density. Besides extensive classification approaches, here based on the assumption that the macromolecular complex is made up of multiple rigid modules whose relative orientations and positions are in slight fl uctuation around equilibriums, we propose a new method called as local optimization refinement to address this conformational heterogeneity for an improved resolution. The key idea is to optimize the orientation and shift parameters of each rigid module and then reconstruct their three-dimensional structures individually. Using simulated data of 80S/70S ribosomes with relative fl uctuations between the large (60S/50S) and the small (40S/30S) subunits, we tested this algorithm and found that the resolutions of both subunits are signifi cantly improved. Our method provides a proof-of-principle solution for highresolution single particle analysis of macromolecular complexes with dynamic conformations.

Jan. 2016, Volume 06 Issue 12

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MiR-33a was recently reported to play an important role in lipid homeostasis, atherosclerosis and hepatic fibrosis. Here, we found that downregulated miR-33a in breast cancer tissues correlates with lymph node metastasis. MiR-33a expression is significantly lower in the highly metastatic breast cancer cell lines than the noncancerous breast epithelial cells and non-metastatic breast cancer cells. Moreover, the overexpression of miR-33a in metastatic breast cancer cells remarkably decreases cell proliferation and invasion in vitro and significantly inhibits tumor growth and lung metastasis in vivo, whereas its knockdown in non-metastatic breast cancer cells significantly enhances cell proliferation and invasion in vitro and promotes tumor growth and lung metastasis in vivo. Combining bioinformatics prediction and biochemical analyses, we showed that ADAM9 and ROS1 are direct downstream targets of miR-33a. These findings identified miR-33a as a negative regulator of breast cancer cell proliferation and metastasis.

Nov. 2015, Volume 6 Issue 11

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Ebolavirus can cause hemorrhagic fever in humans with a mortality rate of 50%–90%. Currently, no approved vaccines and antiviral therapies are available. Human TIM1 is considered as an attachment factor for EBOV, enhancing viral infection through interaction with PS located on the viral envelope. However, reasons underlying the preferable usage of hTIM-1, but not other PS binding receptors by fi lovirus, remain unknown. We fi rstly demonstrated a direct interaction between hTIM-1 and EBOV GP in vitro and determined the crystal structures of the Ig V domains of hTIM-1 and hTIM-4. The binding region in hTIM-1 to EBOV GP was mapped by chimeras and mutation assays, which were designed based on structural analysis. Pseudovirion infection assays performed using hTIM-1 and its homologs as well as point mutants verified the location of the GP binding site and the importance of EBOV GP-hTIM-1 interaction in EBOV cellular entry.

Oct. 2015, Volume 6 Issue 10

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Recent MSCs gained much attention on myocardial function restore, but the underlying cellular mechanisms of MSC therapy are still not fully understood. In order to decipher the potential mechanism of MSC therapy for cardiac fibrosis, we investigated the interplay between MSCs and cardiac myofibroblasts (mFBs) using interactive co-culture method, with comparison to paracrine approaches, namely treatment by MSC conditioned medium and gap co-culture method. Various fibrotic features of mFBs were analyzed and the most prominent anti-fibrosis effects were always obtained using direct co-culture that allowed cell-to-cell contacts. Hepatocyte growth factor (HGF), a wellknown anti-fibrosis factor, was demonstrated to be a major contributor for MSCs’ anti-fi brosis function. Moreover, physical contacts and tubelike structures between MSCs and mFBs were observed by live cell imaging and TEM which demonstrate the direct cellular interactions.

Sep. 2015, Volume 6 Issue 9

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RXRα and its N-terminally truncated version tRXRα play important roles in tumorigenesis. Here we describe a compound N-6 binds to RXRα and inhibits the transactivation of RXRα homodimer and RXRα/TR3 heterodimer. Mutational analysis and computational study showed that Trp305 and Phe313 in RXRα are crucial for N-6 binding to RXRα by forming extra π-π stacking interactions with N-6. N-6 inhibits TR3-stimulated transactivation of Gal4-DBD-RXRα-LBD by binding to the ligand binding pocket of RXRα-LBD. In addition, N-6 strongly inhibits TNFα-induced AKT activation and stimulates TNFα- mediated apoptosis in cancer cells in an RXRα/tRXRα dependent manner. The inhibition of TNFα-induced tRXRα/p85α complex formation by N-6 implies that N-6 targets tRXRα to inhibit TNFα- induced AKT activation and to induce cancer cell apoptosis. Together, our data illustrate N-6 regulates TR3 activity indirectly and induces TNFα-mediated cancer cell apoptosis by targeting RXRα/tRXRα.

Aug. 2015, Volume 6 Issue 8

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HPV including high-risk (HR) and low-risk (LR) subtypes have distinguishable variation on both genotypes and phenotypes. Here, we found a well-conserved target site of miRNAs in the genomes of most HR-HPVs, not LR-HPVs. The site is targeted by two less common human miRNAs, miR-875 and miR-3144, and is located in E6 oncogene open reading frame (ORF) and overlap with the first alternative splice exon of viral early transcripts. In validation tests, miR-875 and miR-3144 were identified to suppress the target reporter activity markedly and inhibit the expression of both synthetically exogenous E6 and endogenous E6 oncogene. High level of two miRNAs can inhibit cell growth and promote apoptosis in HPV16- positive cervical cancer cells. This study provides a promising common target of miRNAs for most HR-HPVs and highlights the effects of two low expressed human miRNAs on tumour suppression.

Jul. 2015, Volume 6 Issue 7

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Nuclease-based gene editing technologies have opened up opportunities for correcting human genetic diseases. For the first time, scientists achieved targeted gene editing of mitochondrial DNA in mouse oocytes fused with patient cells. This fascinating progression may encourage the development of novel therapy for human maternally inherent mitochondrial diseases.

Jun. 2015, Volume 6 Issue 6

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G-quadruplex is a significant drug target for inhibiting telomerase maintenance of telomeres in cancer, and metal cations play important roles in stabilizing G-quadruplex. To investigate the detailed binding procedures, molecular dynamics simulations were conducted on the hybrid [3+1] form-one human telomeric intra-molecular G-quadruplex. We show here that the binding of a potassium ion to a G-tetrad core is mediated by two alternative pathways. Principal component analysis illustrated the dominant concerted motions of G-quadruplex occurred at the loop domains. MM-PBSA calculations revealed that binding was energetically favorable and driven by the electrostatic interactions. The lower binding site was found more constructive favorable for binding. Our data provide useful information on a potassium-mediated stable structure of human telomeric intra-molecular G-quadruplex, implicating in ion disorder associated conformational changes and targeted drug design.

May. 2015, Volume 6 Issue 5

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Ebola virus (EBOV) cause lethal hemorrhagic fever with extremely high morbidity and mortality. EBOV is typically found in Central Africa, but re-emerged in Western Africa from 2014 to cause a worldwide-spreading outbreak spreading. As of April 15, 2015, the World Health Organization (WHO) have reported a total of 25,890 suspected cases and 10,717 deaths. EBOV encodes nucleocapsid protein (NP) to facilitate viral RNA encapsidation to form ribonucleoprotein complex, which plays essential role in EBOV life cycle. However, the structural detail and molecular mechanism of EBOV RNP formation remains unknown. Here, we report the structure of EBOV NP at 1.8 Å resolution, provides great potential for understanding the mechanism and enables the development of antiviral therapies targeting EBOV RNP formation.

Apr. 2015, Volume 6 Issue 4

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Pyruvate kinase isoform M2 (PKM2) plays an important role in cancer metabolism. In this study, we show that post-translational modifications and a patient-derived mutation regulate pyruvate kinase activity of PKM2 through modulating the conformation of the PKM2 tetramer. We determined crystal structures of human PKM2 mutants and proposed a “seesaw” model to illustrate conformational changes between an inactive T-state and an active R-state tetramers of PKM2. Our study reveals the mechanism for dynamic regulation of PKM2 by post-translational modifications and a patient-derived mutation and provides a structural basis for further investigation of other modifi cations and mutations of PKM2 yet to be discovered.

Apr. 2015, Volume 6 Issue 3

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Dicer is a key player in the small RNA induced gene silencing pathway. The typical feature of a pre-miRNA contains a terminal loop and a stem duplex, which bind to human Dicer’s DExH/D (ATPasehelicase) domain and PAZ domain respectively during the dicing reaction. Here, we show that pre-miRNA’s terminal loop can regulate human Dicer’s enzymatic activity by interacting with the DExH/D domain. We found that various editing products of pre-miR-151 by the ADAR1P110 protein, an A-to-I editing enzyme that modifies pre-miRNAs sequence, have different terminal loop structures and different activity regulatory effects on human Dicer. Single particle electron microscopy reconstruction revealed that pre-miRNAs with different terminal loop structures induce human Dicer’s DExH/D (ATPase-helicase) domain into different conformational states, in correlation with their activity regulatory effects.

Feb. 2015, Volume 6 Issue 2

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Human noroviruses (huNoVs) recognize histo-blood group antigens (HBGAs) as attachment factors, in which genogroup (G) I and GII huNoVs use distinct binding interfaces. The genetic and evolutionary relationships of GI NoVs remain unclear due to the fact that the structures of HBGA-binding interfaces of only three GI NoVs with similar binding profi les are known. In this study the crystal structures of the P dimers of a Lewis-binding strain, the GI.8 Boxer virus (BV) that does not bind the A and H antigens, in complex with the Lewis b (Leb) and Ley antigens, respectively, were determined and compared with those of the three previously known GI huNoVs, i.e. GI.1 Norwalk virus (NV), GI.2 FUV258 (FUV) and GI.7 TCH060 (TCH) that bind the A/H/Le antigens.

Jan. 2015, Volume 6 Issue 1

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Histone deacetylase 6 (HDAC6) participates in a wide range of cellular processes. In an attempt to explore the substrate diversity of HDAC6, we performed quantitative proteomic analyses to monitor changes in the abundance of protein lysine acetylation in response to HDAC6 defi ciency. We identifi ed 107 proteins with elevated acetylation in the liver of HDAC6 knockout mice. Three cytoplasmic proteins, including MYH9, Hsc70 and DNAJA1, were verified to interact with HDAC6. The acetylation levels of these proteins were negatively regulated by HDAC6 both in the mouse liver and in cultured cells. Functional studies reveal that HDAC6-mediated deacetylation modulates the actin-binding ability of MYH9 and the interaction between Hsc70 and DNAJA1. These fi ndings consolidate the notion that HDAC6 serves as a critical regulator of protein acetylation with the capability of coordinating various cellular functions.

Dec. 2014, Volume 5 Issue 12

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In this issue, Chen et al. (pp. 912–927) report that coronavirus PLP2-TM acts as a novel autophagy-inducing protein, and induces incomplete autophagy process by increasing the accumulation of autophagosomes but blocking the fusion of autophagosomes with lysosomes. PLP2-TM interacts with the key autophagy regulators, LC3 and Beclin1, and promotes Beclin1 interaction with STING, the key regulator for antiviral IFN signaling. Knockdown of Beclin1 partially reverses PLP2-TM’s inhibitory effect on innate immunity which resulting in decreased coronavirus replication. The cover shows coronavirus PLP2-TM causes a clear redistribution of eGFP-LC3B to punctate structures, indicative of formation of autophagosomes.

Nov. 2014, Volume 5 Issue 11

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The cover depicts the structural basis how KDM5B PHD1 domain is involved in histone H3K4me2/3 demethylation by KDM5B. KDM5B is up-regulated in breast cancer, and represses transcription of tumor suppressor genes. Its PHD1 domain was found to prevent H3K4 from remethylation by specifically interacting with unmodified H3K4me0 tail. The structure presents the details of this specifi c binding, which was confi rmed by mutation studies on full-length KDM5B. The mutations impact KDM5B binding affi nities to H3K4me0, decrease its demethylase activity, and increase the transcription of tumor suppress genes in vivo. These fi ndings imply that KDM5B PHD1 domain may help maintain KDM5B at the target genes to mediate the demethylase activity. The interaction between PHD1 and histone H3 tail could be disrupted by specifi c compound to inhibit the repression of tumor suppressor genes.

Oct. 2014, Volume 5 Issue 10

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Bacterial cell division is governed by a series of spatial and temporal regulators. Here, we report the requirement of gluconate 5-dehydrogenase (Ga5DH) in cell division of the zoonotic pathogen S. suis. Ga5DH catalyzes the reversible reduction of 5-ketogluconate to D-gluconate and was localized to the site of cell division. The deletion of Ga5DH in S. suis resulted in a plump morphology with aberrant septa joining the progeny. A significant increase was also observed in cell length. These defects were determined to be the consequence of Ga5DH deprivation in S. suis causing FtsZ delocalization. In addition, the interaction of FtsZ with Ga5DH in vitro was confirmed by protein interaction assays. These results indicate that Ga5DH may function to prevent the formation of ectopic Z rings during S. suis cell division.

Sep. 2014, Volume 5 Issue 9

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Unlike the well-established picture for the entry of enveloped viruses, the mechanism of cellular entry of non-enveloped eukaryotic viruses remains largely mysterious. Picornaviruses are representative models for such viruses, and initiate this entry process by their functional receptors. Dang et al. determine two structures of SCARB2, a functional receptor of the important human enterovirus 71 (EV71), under neutral and acidic conditions. Differences in the structures reveal that SCARB2 undergoes a pivotal pH-dependent conformational change which opens a lipid-transfer tunnel to mediate the expulsion of a hydrophobic pocket factor from the virion. The cover picture demonstrates the procedure of SCARB2-mediated EV71 attachment and uncoating.

Aug. 2014, Volume 5 Issue 8

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This is an electron micrograph of human T cells. In human beings, each T cell expresses one or two T cell receptors (TCR) on the surface. TCRs are responsible for recognizing foreign antigens through binding to the peptide-MHC complex. All of the TCRs expressed in a given individual compose the TCR repertoire of this people. As distinct antigen stimulations, MHC background, the TCR repertoire of different people shouldn’t be the same. Our study demonstrated TCRα and TCRβ repertoires of three healthy donors in parallel utilizing deep sequencing and the date indicated that some novel features like D-D fusions in TCRβ were found.

Jul. 2014, Volume 5 Issue 7

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In the cover, the hierarchical packaging of eukaryotic chromatin is merged together with two famous Chinese legends about Nezha and Dragons. In the first story, a dragon is playing with a pearl, which represent a cell nucleus within which 2 meters of genomic DNA have to compact into chromatin to fit into. The other story, Nezha is playing with a dragon king: Nezha is riding on the wind fire wheels (looks like two nucleosomes here), has the universe ring (represent electron microscopy in our study) around his body or in his left hand sometimes, the red amillary Sash around his shoulders and a fire-tipped spear in his right hand.

Jun. 2014, Volume 5 Issue 6

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CD146 is a newly identified endothelial biomarker that has been implicated in angiogenesis. Here, we generated endothelial-specific CD146 knockout (CD146EC-KO) mice using the Tg(Tek-cre) system. These mice did not exhibit any apparent morphological defects in the development of normal retinal vasculature, but in a xenograft tumor model, both tumor volume and vascular density were significantly lower in CD146EC-KO mice when compared to WT littermates. Additionally, the ability for sprouting, migration and tube formation in response to VEGF treatment was impaired in endothelial cells of CD146EC-KO mice. Mechanistic studies further confirmed that VEGF-induced VEGFR-2 phosphorylation and AKT/p38 MAPKs/NF-κB activation were inhibited in these CD146-null ECs, which might present the underlying cause for the observed inhibition of tumor angiogenesis in CD146EC-KO mice. These results suggest that CD146 plays a redundant role in physiological angiogenic processes, but becomes essential during pathological angiogenesis as observed in tumorigenesis.