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Tea, one of the world's most important beverage crops, provides numerous secondary metabolites that account for its rich taste and health benefits. Here we present a high-quality sequence of the genome of tea, Camellia sinensis var. sinensis (CSS), using both Illumina and PacBio sequencing technologies. At least 64% of the 3.1-Gb genome assembly consists of repetitive sequences, and the rest yields 33,932 high-confidence predictions of encoded proteins. Divergence between two major lineages, CSS and Camellia sinensis var. assamica (CSA), is calculated to ∼0.38 to 1.54 million years ago (Mya). Analysis of genic collinearity reveals that the tea genome is the product of two rounds of whole-genome duplications (WGDs) that occurred ∼30 to 40 and ∼90 to 100 Mya. We provide evidence that these WGD events, and subsequent paralogous duplications, had major impacts on the copy numbers of secondary metabolite genes, particularly genes critical to producing three key quality compounds: catechins, theanine, and caffeine. Analyses of transcriptome and phytochemistry data show that amplification and transcriptional divergence of genes encoding a large acyltransferase family and leucoanthocyanidin reductases are associated with the characteristic young leaf accumulation of monomeric galloylated catechins in tea, while functional divergence of a single member of the glutamine synthetase gene family yielded theanine synthetase. This genome sequence will facilitate understanding of tea genome evolution and tea metabolite pathways, and will promote germplasm utilization for breeding improved tea varieties., Competing Interests: The authors declare no conflict of interest., (Copyright © 2018 the Author(s). Published by PNAS.)

Red blood cells (RBCs) are known to function as a refuge for providing food resources and as a shelter against the host's immune system after malaria parasite (Plasmodium) infection. Recent studies have reported significant production of extracellular vesicles (microparticles, MPs) in the circulation of malaria patients. However, it is unclear how these extracellular vesicles are generated and what their biological functions are. In this study, we isolated the MPs from a culture medium of normal RBCs and malaria parasite-infected RBCs (iRBCs), compared their quantity and origins, and profiled their miRNAs by deep sequencing. We found a much larger number of MPs released in the culture of iRBCs than in the culture of normal RBCs. Further investigation indicated that, in these MPs, human argonaute 2 (hAgo2) was found to bind to hundreds of miRNAs. These hAgo2-miRNA complexes were transferred into the parasites, and the expression of an essential malaria antigen, PfEMP1, was downregulated by miR-451/140 through its binding to the A and B subgroups of var genes, a family of genes encoding PfEMP1. Our data suggest for the first time that, through the release of MPs, mature RBCs present an innate resistance to malaria infection. These studies also shed new light on the reason why RBCs' genetic mutation occurs mainly in populations living in intensive malaria endemic areas and on the possibility of using miRNAs as novel medicines for malaria patients.

A spatially varying effective refractive index gradient using chalcogenide glass layers is printed on a silicon wafer using an optimized electrospray (ES) deposition process. Using solution-derived glass precursors, IR-transparent Ge 23 Sb 7 S 70 and As 40 S 60 glass films of programmed thickness are fabricated to yield a bilayer structure, resulting in an effective gradient refractive index (GRIN) film. Optical and compositional analysis tools confirm the optical and physical nature of the gradient in the resulting high-optical-quality films, demonstrating the power of direct printing of multimaterial structures compatible with planar photonic fabrication protocols. The potential application of such tailorable materials and structures as they relate to the enhancement of sensitivity in chalcogenide glass based planar chemical sensor device design is presented. This method, applicable to a broad cross section of glass compositions, shows promise in directly depositing GRIN films with tunable refractive index profiles for bulk and planar optical components and devices.

The Kernel-RX detector (KRXD) has attracted widespread interest in hyperspectral image processing with the utilization of nonlinear information. However, the kernelization of hyperspectral data leads to poor execution efficiency in KRXD. This paper presents an approach to the progressive line processing of KRXD (PLP-KRXD) that can perform KRXD line by line (the main data acquisition pattern). Parallel causal sliding windows are defined to ensure the causality of PLP-KRXD. Then, with the employment of the Woodbury matrix identity and the matrix inversion lemma, PLP-KRXD has the capacity to recursively update the kernel matrices, thereby avoiding a great many repetitive calculations of complex matrices, and greatly reducing the algorithm's complexity. To substantiate the usefulness and effectiveness of PLP-KRXD, three groups of hyperspectral datasets are used to conduct experiments., Competing Interests: The authors declare no conflict of interest.

An increase in global temperatures will impact future crop yields. In the cereal crops wheat and barley, high temperatures accelerate reproductive development, reducing the number of grains per plant and final grain yield. Despite this relationship between temperature and cereal yield, it is not clear what genes and molecular pathways mediate the developmental response to increased temperatures. The plant circadian clock can respond to changes in temperature and is important for photoperiod-dependent flowering, and so is a potential mechanism controlling temperature responses in cereal crops. This study examines the relationship between temperature, the circadian clock, and the expression of flowering-time genes in barley (Hordeum vulgare), a crop model for temperate cereals. Transcript levels of barley core circadian clock genes were assayed over a range of temperatures. Transcript levels of core clock genes CCA1, GI, PRR59, PRR73, PRR95, and LUX are increased at higher temperatures. CCA1 and PRR73 respond rapidly to a decrease in temperature whereas GI and PRR59 respond rapidly to an increase in temperature. The response of GI and the PRR genes to changes in temperature is lost in the elf3 mutant indicating that their response to temperature may be dependent on a functional ELF3 gene., (© The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.)

The transcription factor AP-1 plays an important role in inflammation and cell survival. Using a dual-luciferase reporter assay system and a library of 940 candidate human secretory protein cDNA clones, we identified that CGREF1 can inhibit the transcriptional activity of AP-1. We demonstrated that CGREF1 is secreted via the classical secretory pathway through the ER-to-Golgi apparatus. Functional investigations revealed that overexpression of CGREF1 can significantly inhibit the phosphorylation of ERK and p38 MAPK, and suppress the proliferation of HEK293T and HCT116 cells. Conversely, specific siRNAs against CGREF1 can increase the transcriptional activity of AP-1. These results clearly indicated that CGREF1 is a novel secretory protein, and plays an important role in regulation of AP-1 transcriptional activity and cell proliferation., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

The authors present a tablet-based image-guided neurosurgery system that transmits navigation information from a host to a movable tablet PC via a wireless local area network, and displays this information on the tablet screen. With this new system, surgeons can obtain standard navigation information on the tablet screen to avoid large view switching between the surgical field and the navigation screen of the computer monitor. In addition, this system can also provide additional navigation information by displaying arbitrary sectional images and maximum intensity projection images on the tablet screen. These images are generated according to the position and orientation of the tablet screen, and can be used to locate intracranial tumor for preoperative planning and intraoperative procedures in neurosurgery. The average tracking error was approximately 1.25 mm. A dry skull specimen study verified the feasibility of the proposed system. Furthermore, an actual patient's surgery with this system showed its clinical applicability.

The transcription factor p53 and AP-1 play an important role in cellular proliferation, transformation and death. In this study, we investigated the role of a novel human gene, TTC5 (tetratricopeptide repeat domain 5), in the regulation of cell signaling pathway and cell viability. TTC5 is a member of the TTC family of proteins and has previously been shown to participate in cellular stress response. Here we demonstrate for the first time that TTC5 significantly activates p53 pathway and inhibits AP-1 transcriptional activity. Further investigation revealed that overexpression of TTC5 up-regulated p53 and p21 expression, and significantly inhibited transcriptional activity, expression and phosphorylation of c-Jun. As for the upstream of signaling pathway of AP-1, our study demonstrated that overexpression of TTC5 significantly down-regulated the expression and phosphorylation of JNK/SAPK. Moreover, overexpression of TTC5 repressed cell proliferation and induced S phase cell cycle arrest. These results indicated that TTC5 may regulate cell viability by p53 and AP-1 signaling pathway.

Transcriptional activation of the VERNALIZATION1 gene mediates the acceleration of flowering by prolonged cold (vernalization) in temperate cereals. This study examined the earliest stages of the transcriptional response of VRN1 to low temperatures. Time-course analyses, using a sensitive quantitative PCR assay, showed that in sprouting barley seedlings VRN1 transcripts begin to accumulate within 24 hours of the onset of cold. The kinetics of the initial transcriptional response of VRN1 to cold was similar to the cold-induced genes DEHYDRIN5 (DHN5) and COLD REGULATED 14B (COR14B), but occurred at lower levels compared to cold acclimation genes or the response to longer cold treatments. Temperatures between 15 and -2 °C induced expression of VRN1 within 24 hours, with a maximal response observed between 2 and -2 °C. Transcriptional induction was also observed in undifferentiated callus cells. There were significant increases in histone acetylation levels at the VRN1 locus in response to 24-hour cold treatment. Sodium butyrate, a histone deacetylation inhibitor, triggered an increase in histone acetylation at VRN1 chromatin and elevated VRN1 transcript levels. The transcriptional response of VRN1 to short-term cold treatment was examined in near-isogenic lines that have different VRN1 genotypes, showing that an allele of the barley VRN1 gene with an insertion in the first intron and high basal expression levels has a reduced transcriptional response to short term cold treatment. This study suggests that low-temperature induction of VRN1 is a cellular response to cold triggered by the same mechanisms that mediate low-temperature induction of cold acclimation genes.

FLOWERING LOCUS C (FLC) has a key role in the timing of the initiation of flowering in Arabidopsis. FLC binds and represses two genes that promote flowering, FT and SOC1. We show that FLC binds to many other genes, indicating that it has regulatory roles other than the repression of flowering. We identified 505 FLC binding sites, mostly located in the promoter regions of genes and containing at least one CArG box, the motif known to be associated with MADS-box proteins such as FLC. We examined 40 of the target genes, and 20 showed increased transcript levels in an flc mutant compared with the wild type. Five genes showed decreased expression in the mutant, indicating that FLC binding can result in either transcriptional repression or activation. The genes we identified as FLC targets are involved in developmental pathways throughout the life history of the plant, many of which are associated with reproductive development. FLC is also involved in vegetative development, as evidenced by its binding to SPL15, delaying the progression from juvenile to adult phase. Some of the FLC target genes are also bound by two other MADS-box proteins, AP1 and SEP3, suggesting that MADS-box genes may operate in a network of control at different stages of the life cycle, many ultimately contributing to the development of the reproductive phase of the plant.

We developed a well-controlled method to generate PLGA microparticles of different morphologies using the electrospray drying route. By judiciously selecting polymer molecular weight, concentration, and solution flow rate, we can control the order in which polymer entanglements and Coulomb fission occur in the droplets and their relative importance, and subsequently govern the morphology of the resulting polymer particles. We show that spherical, monodisperse particles are generated when sufficiently strong polymer entanglements set in the evaporating droplets before they undergo any Coulomb fission. On the other hand, tailed and elongated particles are obtained if the Coulomb fission occurs first and if the droplets/particles are sufficiently evaporated to freeze in their irregular shape. Strictly spherical particles are unachievable for polymer solutions below a critical concentration, because the onset of Coulomb fission always sets in prior to the development of a sufficiently entangled polymer network. An extension of a simple model, originally used to determine the onset of electrospinning of polymer solutions, adequately predicts when non-spherical particles are produced. We conclude by demonstrating the scale-up of this approach to the synthesis of polymer particles using a compact, microfabricated, multiplexed electrospray system, which would make it suitable for practical applications., (2009 Elsevier Inc. All rights reserved.)

Autophagy, a tightly regulated process responsible for the bulk degradation of most long-lived proteins and some organelles, is associated with several forms of human diseases including cancer, neurodegenerative disease and cardiomyopathies. However, the molecular machinery involved in autophagy in mammalian cells remains poorly understood. Here, we describe a high-throughput, cell-based functional screening platform, based on an automated fluorescence microscopy system, which enables acquiring and quantitatively analyzing images of GFP-LC3 dots in cotransfected cells. From a library of 1,050 human cDNA clones, we identified three genes (TM9SF1, TMEM166 and TMEM74) whose overexpression induced high levels of autophagosome formation. In particular, overexpression of TM9SF1, which colocalized with LC3 according to the confocal assay, led to a significant increase in the number of GFP-LC3 dots. The results of transmission electron microscopy and immunoblotting to examine LC3-II levels further confirmed the ability of TM9SF1 to induce autophagy. Furthermore, knockdown of TM9SF1 expression by RNA interference could hamper starvation-induced autophagy. The functional screening platform therefore can be applied to high-throughput genomic screening candidate autophagy-related genes, which would provide new insights into underlying molecular mechanisms that may regulate autophagy in mammalian cells.

DCUN1D3 (DCN1, defective in cullin neddylation 1, domain containing 3) was found during the process of high throughput screening of novel human genes associated with serum response element (SRE) pathway activation. The DCUN1D3 gene is highly conserved among vertebrates. Human DCUN1D3 complementary DNA (cDNA) encodes 304 amino acids with an apparent molecular mass of 34 kDa. However, there has been no report about the function of DCUN1D3. This study detected that DCUN1D3 was broadly expressed in several tumor tissues and cultured cell lines; however, UVC irradiation of different doses significantly increased DCUN1D3 expression level in these cancer cell lines. Over-expression of the DCUN1D3 inhibits cell growth in HeLa. When the DCUN1D3 gene was silenced by siRNA in UVC-treated HeLa, the cell cycle in S phase was remarkably blocked; furthermore, the UVC-induced cell death was inhibited. In addition, DCUN1D3 localized mainly in the cytoplasm and perinuclear, but after UVC treatment, the DCUN1D3 gradually entered the nucleus. All the results above indicate that DCUN1D3 is a novel UVC-response gene involved in cell cycle regulation and cell survival.

Histone acetylation is an important posttranslational modification correlated with gene activation. In Arabidopsis (Arabidopsis thaliana), the histone acetyltransferase AtHAC1 is homologous to animal p300/CREB (cAMP-responsive element-binding protein)-binding proteins, which are the main histone acetyltransferases participating in many physiological processes, including proliferation, differentiation, and apoptosis. The functions of p300/CREB-binding proteins in animals are well characterized, whereas little is known about the roles of AtHAC1 in developmental control in Arabidopsis. Lesions in AtHAC1 caused pleiotropic developmental defects, including delayed flowering, a shortened primary root, and partially reduced fertility. Analysis of the molecular basis of late flowering in hac1 mutants showed that the hac1 plants respond normally to day length, gibberellic acid treatment, and vernalization. Furthermore, the expression level of the flowering repressor FLOWERING LOCUS C (FLC) is increased in hac1 mutants, indicating that the late-flowering phenotype of hac1 mutants is mediated by FLC. Since histone acetylation is usually associated with the activation of gene expression, histone modifications of FLC chromatin are not affected by mutations in HAC1 and expression levels of all known autonomous pathway genes are unchanged in hac1 plants, we propose that HAC1 affects flowering time by epigenetic modification of factors upstream of FLC.

In the present study, a cell-based high-throughput assay is established to identify novel human genes associated with cell viability. The assay relies on the down-regulation of Renilla luciferase (pRL) activity in a 96-well format. In addition, 2-color fluorescence probes were used to distinguish living and dead cells. As the positive control, the authors used the expression vectors encoding Bax, TNFRSF1A, and TAJ, which were widely known to effectively induce programmed cell death. They screened 409 novel genes (including alternative mRNA splicing forms) cloned in their laboratory and found that 39 genes could significantly down-regulate pRL activity. A subsequent fluorescence-based assay revealed that 4 of the 39 genes (PIP5KL1, OLFM1, RNF122, FAM26B) were associated with cell viability. Further function assays validated that the 4 genes were able to induce both necrosis and apoptosis. These results therefore indicate that a rapid and effective screening system has been developed, which should shed light on some functions of novel genes.