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1.  Two new species of Stenochironomus Kieffer (Diptera, Chironomidae) from Zhejiang, China 
ZooKeys  2015;109-119.
Two new species of Stenochironomus Kieffer (Diptera: Chironomidae: Chironominae), Stenochironomus brevissimus sp. n. and Stenochironomus linanensis sp. n., are described from China and the male imagines are illustrated. Stenochironomus brevissimus sp. n. can be separated from the so far known species by having very short and small, spatulate superior volsella with two long setae, whereas Stenochironomus linanensis sp. n. is easily separated from the other species of Stenochironomus by the following characters: wings transparent, body yellow, superior volsella finger-like, with nine long setae, elongated inferior volsella with four long setae and one well developed terminal spine; tergite IX with 10−15 long setae medially. A key to the males of Stenochironomus occurring in China is given.
doi:10.3897/zookeys.479.8364
PMCID: PMC4319065
Stenochironomus; new species; key; China
2.  Distinct Conformational Transition Patterns of Noncoding 7SK snRNA and HIV TAR RNAs upon Tat Binding 
Biochemistry  2014;53(4):675-681.
Noncoding 7SK snRNA is believed to play an important role in the recruitment of P-TEFb by viral protein Tat to stimulate HIV processive transcription. Because HIV-2 TAR RNA and 7SK both evolved to feature a dinucleotide bulge region, compared to the trinucleotide bulge for HIV-1 TAR, ultrafast time-resolved fluorescence spectroscopy has been used to probe the conformational landscape of HIV-2 TAR and 7SK-SL4 RNA to monitor the conformational changes upon Tat binding. Our studies demonstrate that both HIV-1/2 TAR and 7SK-SL4 sample heterogeneous ensembles in the free state and undergo distinct conformational transitions upon Tat binding. These findings provide exquisite knowledge on the conformational complexity and intricate mechanism of molecular recognition and pave the way for drug design and discovery that incorporate dynamics information.
doi:10.1021/bi401131z
PMCID: PMC3985858  PMID: 24422492
3.  Optimal contouring of seminal vesicle for definitive radiotherapy of localized prostate cancer: comparison between EORTC prostate cancer radiotherapy guideline, RTOG0815 protocol and actual anatomy 
Background
Intermediate- to-high-risk prostate cancer can locally invade seminal vesicle (SV). It is recommended that anatomic proximal 1-cm to 2-cm SV be included in the clinical target volume (CTV) for definitive radiotherapy based on pathology studies. However, it remains unclear whether the pathology indicated SV extent is included into the CTV defined by current guidelines. The purpose of this study is to compare the volume of proximal SV included in CTV defined by EORTC prostate cancer radiotherapy guideline and RTOG0815 protocol with the actual anatomic volume.
Methods
Radiotherapy planning CT images from 114 patients with intermediate- (36.8%) or high-risk (63.2%) prostate cancer were reconstructed with 1-mm-thick sections. The starting and ending points of SV and the cross sections of SV at 1-cm and 2-cm from the starting point were determined using 3D-view. Maximum (D1H, D2H) and minimum (D1L, D2L) vertical distance from these cross sections to the starting point were measured. Then, CTV of proximal SV defined by actual anatomy, EORTC guideline and RTOG0815 protocol were contoured and compared (paired t test).
Results
Median length of D1H, D1L, D2H and D2L was 10.8 mm, 2.1 mm, 17.6 mm and 8.8 mm (95th percentile: 13.5mm, 5.0mm, 21.5mm and 13.5mm, respectively). For intermediate-risk patients, the proximal 1-cm SV CTV defined by EORTC guideline and RTOG0815 protocol inadequately included the anatomic proximal 1-cm SV in 62.3% (71/114) and 71.0% (81/114) cases, respectively. While for high-risk patients, the proximal 2-cm SV CTV defined by EORTC guideline inadequately included the anatomic proximal 2-cm SV in 17.5% (20/114) cases.
Conclusions
SV involvement indicated by pathology studies was not completely included in the CTV defined by current guidelines. Delineation of proximal 1.4 cm and 2.2 cm SV in axial plane may be adequate to include the anatomic proximal 1-cm and 2-cm SV. However, part of SV may be over-contoured.
doi:10.1186/s13014-014-0288-1
PMCID: PMC4299806  PMID: 25526901
Prostate cancer; Radiotherapy; Seminal vesicle; Target delineation; CT reconstruction
4.  Anticancer efficacy and absorption, distribution, metabolism, and toxicity studies of Aspergiolide A in early drug development 
Since the first anthracycline was discovered, many other related compounds have been studied in order to overcome its defects and improve efficacy. In the present paper, we investigated the anticancer effects of a new anthracycline, aspergiolide A (ASP-A), from a marine-derived fungus in vitro and in vivo, and we evaluated the absorption, distribution, metabolism, and toxicity drug properties in early drug development. We found that ASP-A had activity against topoisomerase II that was comparable to adriamycin. ASP-A decreased the growth of various human cancer cells in vitro and induced apoptosis in BEL-7402 cells via a caspase-dependent pathway. The anticancer efficacy of ASP-A on the growth of hepatocellular carcinoma xenografts was further assessed in vivo. Results showed that, compared with the vehicle group, ASP-A exhibited significant anticancer activity with less loss of body weight. A pharmacokinetics and tissue distribution study revealed that ASP-A was rapidly cleared in a first order reaction kinetics manner, and was enriched in cancer tissue. The maximal tolerable dose (MTD) of ASP-A was more than 400 mg/kg, and ASP-A was not considered to be potentially genotoxic or cardiotoxic, as no significant increase of micronucleus rates or inhibition of the hERG channel was seen. Finally, an uptake and transport assay of ASP-A was performed in monolayers of Caco-2 cells, and ASP-A was shown to be absorbed through the active transport pathway. Altogether, these results indicate that ASP-A has anticancer activity targeting topoisomerase II, with a similar structure and mechanism to adriamycin, but with much lower toxicity. Nonetheless, further molecular structure optimization is necessary.
doi:10.2147/DDDT.S64989
PMCID: PMC4207554  PMID: 25378909
aspergiolide A; anticancer; anthracyclines; ADMT; drug activity
5.  The identification of high-affinity G protein-coupled receptor ligands from large combinatorial libraries using multicolor quantum dot-labeled cell-based screening 
Future medicinal chemistry  2014;6(7):809-823.
G protein-coupled receptors (GPCRs), which are involved in virtually every biological process, constitute the largest family of transmembrane receptors. Many top-selling and newly approved drugs target GPCRs. In this review, we aim to recapitulate efforts and progress in combinatorial library-assisted GPCR ligand discovery, particularly focusing on one-bead-one-compound library synthesis and quantum dot-labeled cell-based assays, which both effectively enhance the rapid identification of GPCR ligands with higher affinity and specificity.
doi:10.4155/fmc.14.38
PMCID: PMC4172322  PMID: 24941874
6.  Timosaponin A3 induces hepatotoxicity in rats through inducing oxidative stress and down-regulating bile acid transporters 
Acta Pharmacologica Sinica  2014;35(9):1188-1198.
Aim:
To investigate the mechanisms underlying the hepatotoxicity of timosaponin A3 (TA3), a steroidal saponin from Anemarrhena asphodeloides, in rats.
Methods:
Male SD rats were administered TA3 (100 mg·kg−1·d−1, po) for 14 d, and the blood and bile samples were collected after the final administration. The viability of a sandwich configuration of cultured rat hepatocytes (SCRHs) was assessed using WST-1. Accumulation and biliary excretion index (BEI) of d8-TCA in SCRHs were determined with LC-MS/MS. RT-PCR and Western blot were used to analyze the expression of relevant genes and proteins. ROS and ATP levels, and mitochondrial membrane potential (MMP) were measured. F-actin cytoskeletal integrity was assessed under confocal microscopy.
Results:
TA3 administration in rats significantly elevated the total bile acid in serum, and decreased bile acid (BA) component concentrations in bile. TA3 inhibited the viability of the SCRHs with an IC50 value of 15.21±1.73 μmol/L. Treatment of the SCRHs with TA3 (1–10 μmol/L) for 2 and 24 h dose-dependently decreased the accumulation and BEI of d8-TCA. The TA3 treatment dose-dependently decreased the expression of BA transporters Ntcp, Bsep and Mrp2, and BA biosynthesis related Cyp7a1 in hepatocytes. Furthermore, the TA3 treatment dose-dependently increased ROS generation and HO-1 expression, decreased the ATP level and MMP, and disrupted F-actin in the SCRHs. NAC (5 mmol/L) significantly ameliorated TA3-induced effects in the SCRHs, whereas mangiferin (10–200 μg/mL) almost blocked TA3-induced ROS generation.
Conclusion:
TA3 triggers liver injury through inducing ROS generation and suppressing the expression of BA transporters. Mangiferin, an active component in Anemarrhena, may protect hepatocytes from TA3-induced hepatotoxicity.
doi:10.1038/aps.2014.65
PMCID: PMC4155534  PMID: 25087997
timosaponin A3; hepatotoxicity; cholestasis; bile acid; transporter; Cyp7a1; ROS; N-acetyl-L- cysteine; mangiferin
7.  A dimeric equilibrium intermediate nucleates Drp1 reassembly on mitochondrial membranes for fission 
Molecular Biology of the Cell  2014;25(12):1905-1915.
Drp1 catalyzes mitochondrial division, but the mechanisms remain elusive. The mitochondrial lipid cardiolipin stimulates Drp1 activity and supports membrane constriction. In addition, Drp1 populates two polymeric states that equilibrate via a dimeric intermediate. Dimers nucleate Drp1 reassembly on mitochondria for fission.
The GTPase dynamin-related protein 1 (Drp1) catalyzes mitochondrial division, but the mechanisms remain poorly understood. Much of what is attributed to Drp1’s mechanism of action in mitochondrial membrane fission parallels that of prototypical dynamin in endocytic vesicle scission. Unlike the case for dynamin, however, no lipid target for Drp1 activation at the mitochondria has been identified. In addition, the oligomerization properties of Drp1 have not been well established. We show that the mitochondria-specific lipid cardiolipin is a potent stimulator of Drp1 GTPase activity, as well as of membrane tubulation. We establish further that under physiological conditions, Drp1 coexists as two morphologically distinct polymeric species, one nucleotide bound in solution and the other membrane associated, which equilibrate via a dimeric assembly intermediate. With two mutations, C300A and C505A, that shift Drp1 polymerization equilibria in opposite directions, we demonstrate that dimers, and not multimers, potentiate the reassembly and reorganization of Drp1 for mitochondrial membrane remodeling both in vitro and in vivo.
doi:10.1091/mbc.E14-02-0728
PMCID: PMC4055269  PMID: 24790094
8.  Content-based histopathology image retrieval using CometCloud 
BMC Bioinformatics  2014;15(1):287.
Background
The development of digital imaging technology is creating extraordinary levels of accuracy that provide support for improved reliability in different aspects of the image analysis, such as content-based image retrieval, image segmentation, and classification. This has dramatically increased the volume and rate at which data are generated. Together these facts make querying and sharing non-trivial and render centralized solutions unfeasible. Moreover, in many cases this data is often distributed and must be shared across multiple institutions requiring decentralized solutions. In this context, a new generation of data/information driven applications must be developed to take advantage of the national advanced cyber-infrastructure (ACI) which enable investigators to seamlessly and securely interact with information/data which is distributed across geographically disparate resources. This paper presents the development and evaluation of a novel content-based image retrieval (CBIR) framework. The methods were tested extensively using both peripheral blood smears and renal glomeruli specimens. The datasets and performance were evaluated by two pathologists to determine the concordance.
Results
The CBIR algorithms that were developed can reliably retrieve the candidate image patches exhibiting intensity and morphological characteristics that are most similar to a given query image. The methods described in this paper are able to reliably discriminate among subtle staining differences and spatial pattern distributions. By integrating a newly developed dual-similarity relevance feedback module into the CBIR framework, the CBIR results were improved substantially. By aggregating the computational power of high performance computing (HPC) and cloud resources, we demonstrated that the method can be successfully executed in minutes on the Cloud compared to weeks using standard computers.
Conclusions
In this paper, we present a set of newly developed CBIR algorithms and validate them using two different pathology applications, which are regularly evaluated in the practice of pathology. Comparative experimental results demonstrate excellent performance throughout the course of a set of systematic studies. Additionally, we present and evaluate a framework to enable the execution of these algorithms across distributed resources. We show how parallel searching of content-wise similar images in the dataset significantly reduces the overall computational time to ensure the practical utility of the proposed CBIR algorithms.
doi:10.1186/1471-2105-15-287
PMCID: PMC4161917  PMID: 25155691
Histopathology; Digital pathology; Content-based image retrieval; High performance computing
9.  Dynamic pattern of suicide in Australia, 1986–2005: a descriptive-analytic study 
BMJ Open  2014;4(7):e005311.
Objective
This study explores the spatiotemporal variations of suicide across Australia from 1986 to 2005, discusses the reasons for dynamic changes, and considers future suicide research and prevention strategies.
Design
Suicide (1986–2005) and population data were obtained from the Australian Bureau of Statistics. A series of analyses were conducted to examine the suicide pattern by sex, method and age group over time and geography.
Results
Differences in suicide rates across sex, age groups and suicide methods were found across geographical areas. Male suicides were mainly completed by hanging, firearms, gases and self-poisoning. Female suicides were primarily completed by hanging and self-poisoning. Suicide rates were higher in rural areas than in urban areas (capital cities and regional centres). Suicide rates by firearms were higher in rural areas than in urban areas, while the pattern for self-poisoning showed the reverse trend. Suicide rates had relatively stable trend for the total population and those aged between 15 and 54, while suicide decreased among 55 years and over during the study period. There was a decrease in suicides by firearms during the study period especially after 1996 when a new firearm control law was implemented, while suicide by hanging continued to increase. Areas with a high proportion of indigenous population (eg, northwest of Queensland and top north of the Northern Territory) had shown a substantial increase in suicide incidence after 1995.
Conclusions
Suicide rates varied over time and space and across sexes, age groups and suicide methods. This study provides detailed patterns of suicide to inform suicide control and prevention strategies for specific subgroups and areas of high and increased risk.
doi:10.1136/bmjopen-2014-005311
PMCID: PMC4120400  PMID: 25079935
Australia; Suicide; Pattern
10.  Socio-environmental drivers and suicide in Australia: Bayesian spatial analysis 
BMC Public Health  2014;14:681.
Background
The impact of socio-environmental factors on suicide has been examined in many studies. Few of them, however, have explored these associations from a spatial perspective, especially in assessing the association between meteorological factors and suicide. This study examined the association of meteorological and socio-demographic factors with suicide across small areas over different time periods.
Methods
Suicide, population and socio-demographic data (e.g., population of Aboriginal and Torres Strait Islanders (ATSI), and unemployment rate (UNE) at the Local Government Area (LGA) level were obtained from the Australian Bureau of Statistics for the period of 1986 to 2005. Information on meteorological factors (rainfall, temperature and humidity) was supplied by Australian Bureau of Meteorology. A Bayesian Conditional Autoregressive (CAR) Model was applied to explore the association of socio-demographic and meteorological factors with suicide across LGAs.
Results
In Model I (socio-demographic factors), proportion of ATSI and UNE were positively associated with suicide from 1996 to 2000 (Relative Risk (RR)ATSI = 1.0107, 95% Credible Interval (CI): 1.0062-1.0151; RRUNE = 1.0187, 95% CI: 1.0060-1.0315), and from 2001 to 2005 (RRATSI = 1.0126, 95% CI: 1.0076-1.0176; RRUNE = 1.0198, 95% CI: 1.0041-1.0354). Socio-Economic Index for Area (SEIFA) and IND, however, had negative associations with suicide between 1986 and 1990 (RRSEIFA = 0.9983, 95% CI: 0.9971-0.9995; RRATSI = 0.9914, 95% CI: 0.9848-0.9980). Model II (meteorological factors): a 1°C higher yearly mean temperature across LGAs increased the suicide rate by an average by 2.27% (95% CI: 0.73%, 3.82%) in 1996–2000, and 3.24% (95% CI: 1.26%, 5.21%) in 2001–2005. The associations between socio-demographic factors and suicide in Model III (socio-demographic and meteorological factors) were similar to those in Model I; but, there is no substantive association between climate and suicide in Model III.
Conclusions
Proportion of Aboriginal and Torres Strait Islanders, unemployment and temperature appeared to be statistically associated with of suicide incidence across LGAs among all selected variables, especially in recent years. The results indicated that socio-demographic factors played more important roles than meteorological factors in the spatial pattern of suicide incidence.
doi:10.1186/1471-2458-14-681
PMCID: PMC4226967  PMID: 24993370
Suicide; Spatial; Socio-environmental; Australia
11.  Rare giant cell tumor involvement of the olecranon bone 
Giant cell tumor (GCT) of bone is a relatively common benign bone lesion and is usually located in long bones, but involvement of the olecranon is extremely rare. Here, we present a case of solitary GCT of bone in the olecranon that was confirmed by preoperative needle biopsy and postoperative histological examination. The treatment included intralesional curettage, allogeneic bone grafting, and plating. At 26 months follow-up, the patient had no local recurrence.
PMCID: PMC4155716  PMID: 25197303
Bone; giant cell tumor; olecranon
12.  Functional Principal Component Analysis Reveals Discriminating Categories of Retinal Pigment Epithelial Morphology in Mice 
Purpose.
To determine whether multivariate, functional principal component analysis of the size and shape of retinal pigment epithelial (RPE) cell morphology allows discrimination of mouse RPE genotypes and age.
Methods.
Flatmounts of RPE sheets obtained from C57BL/6J (n = 50) and rd10 (n = 61) mice at postnatal days 30 to 720 were stained for zonula occludens-1 (ZO-1) and imaged with confocal microscopy. A total of 111 flatmounts were prepared. Twenty-one morphometric measurements were made on tiled, composite images of complete flatmounts, including cell location, area, and eccentricity, using automated image analysis software for quantitatively measuring cell phenotypes.
Results.
In young (≤61-day-old) C57BL/6J mice, the RPE morphology resembled a regular hexagonal array of cells of uniform size throughout the retina, except near the ciliary body, where the shapes of RPE resembled a soft network. Old (≥180-day-old) C57BL/6J eyes had a subpopulation of large cells. A clear disruption of the regular cell size and shape appeared in rd10 mutants. Aspect ratio and cell area gave rise to principal components that predictively classified mouse age and genotype.
Conclusions.
Quantitative differences in the RPE sheet morphology allowed discrimination of rd10 from C57BL/6J strains despite the confounding effect of aging. This has implications for RPE sheet morphology as a potential early biomarker for diagnosis of eye disease and prognosis of the eye at early stages when disease is subtle. We conclude that an RPE cell's area and aspect ratio are very early quantitative indicators that predict progression to advanced RPE disease as manifested in rd10.
We established baseline morphological measurements in wild-type mouse RPE and quantified the difference in morphology due to aging and the rd10 mutation. Multivariate, functional principal component analysis and classification of cell size and cell shape discriminate RPE genotypes and age.
doi:10.1167/iovs.13-12450
PMCID: PMC4086880  PMID: 24114543
RPE; image analysis; retinal degeneration
13.  The challenge in translating basic research discoveries to treatment of Huntington disease 
Rare Diseases  2014;2:e28637.
Huntington disease is a rare neurodegenerative disease resulting from insertion and/or expansion of a polyglutamine repeats close to the N-terminal of the huntingtin protein. Although unequivocal genetic tests have been available for about 20 years, current pharmacological treatments do not prevent or slow down disease progression. Recent basic research identified potential novel drug targets for the treatment of Huntington disease. However, there are clear challenges in translating these discoveries into treatment strategies for these patients. The following is a brief discussion of these challenges using our recent experience as an example.
doi:10.4161/rdis.28637
PMCID: PMC4091548  PMID: 25054095
Huntington disease; neurodegeneration; mitochondria; polyglutamine; animal model; protein-protein interactions; P110 peptide inhibitor; Drp1
14.  Population Explosion in the Yellow-Spined Bamboo Locust Ceracris kiangsu and Inferences for the Impact of Human Activity 
PLoS ONE  2014;9(3):e89873.
Geographic distance and geographical barriers likely play a considerable role in structuring genetic variation in species, although some migratory species may have less phylogeographic structure on a smaller spatial scale. Here, genetic diversity and the phylogenetic structure among geographical populations of the yellow-spined bamboo locust, Ceracris kiangsu, were examined with 16S rDNA and amplified fragment length polymorphisms (AFLPs). In this study, no conspicuous phylogeographical structure was discovered from either Maximum parsimony (MP) and Neighbor-joining (NJ) phylogenetic analyses. The effect of geographical isolation was not conspicuous on a large spatial scale.At smaller spatial scales local diversity of some populations within mountainous areas were detected using Nei's genetic distance and AMOVA. There is a high level of genetic diversity and a low genetic differentiation among populations in the C. kiangsu of South and Southeast China. Our analyses indicate that C. kiangsu is a monophyletic group. Our results also support the hypothesis that the C. kiangsu population is in a primary differentiation stage. Given the mismatch distribution, it is likely that a population expansion in C. kiangsu occurred about 0.242 Ma during the Quaternary interglaciation. Based on historical reports, we conjecture that human activities had significant impacts on the C. kiangsu gene flow.
doi:10.1371/journal.pone.0089873
PMCID: PMC3946154  PMID: 24603526
15.  A strong ‘filter’ effect of the East China Sea land bridge for East Asia’s temperate plant species: inferences from molecular phylogeography and ecological niche modelling of Platycrater arguta (Hydrangeaceae) 
Background
In East Asia, an increasing number of studies on temperate forest tree species find evidence for migration and gene exchange across the East China Sea (ECS) land bridge up until the last glacial maximum (LGM). However, it is less clear when and how lineages diverged in this region, whether in full isolation or in the face of post-divergence gene flow. Here, we investigate the effects of Quaternary changes in climate and sea level on the evolutionary and demographic history of Platycrater arguta, a rare temperate understorey shrub with disjunct distributions in East China (var. sinensis) and South Japan (var. arguta). Molecular data were obtained from 14 P. arguta populations to infer current patterns of molecular structure and diversity in relation to past (Last Interglacial and Last Glacial Maximum) and present distributions based on ecological niche modelling (ENM). A coalescent-based isolation-with-migration (IM) model was used to estimate lineage divergence times and population demographic parameters.
Results
Combining information from nuclear/chloroplast sequence data with nuclear microsatellites, our IM analyses identify the two varieties as genetically distinct units that evolved in strict allopatry since the mid-Pleistocene, c. 0.89 (0.51–1.2) Ma. Together with Bayesian Skyeline Plots, our data further suggest that both lineages experienced post-divergence demographic growth, followed by refugial isolation, divergence, and in the case of var. arguta post-glacial admixture. However, past species distribution modelling indicates that the species’ overall distribution has not greatly changed over the last glacial cycles.
Conclusions
Our findings highlight the important influence of ancient sea-level changes on the diversification of East Asia’s temperate flora. Implicitly, they challenge the notion of general temperate forest expansion across the ECS land bridge, demonstrating instead its ‘filter’ effect owing to an unsuitable environment for certain species and their biological (e.g., recruitment) properties.
doi:10.1186/1471-2148-14-41
PMCID: PMC4015774  PMID: 24593236
16.  Sparse principal component analysis by choice of norm 
Recent years have seen the developments of several methods for sparse principal component analysis due to its importance in the analysis of high dimensional data. Despite the demonstration of their usefulness in practical applications, they are limited in terms of lack of orthogonality in the loadings (coefficients) of different principal components, the existence of correlation in the principal components, the expensive computation needed, and the lack of theoretical results such as consistency in high-dimensional situations. In this paper, we propose a new sparse principal component analysis method by introducing a new norm to replace the usual norm in traditional eigenvalue problems, and propose an efficient iterative algorithm to solve the optimization problems. With this method, we can efficiently obtain uncorrelated principal components or orthogonal loadings, and achieve the goal of explaining a high percentage of variations with sparse linear combinations. Due to the strict convexity of the new norm, we can prove the convergence of the iterative method and provide the detailed characterization of the limits. We also prove that the obtained principal component is consistent for a single component model in high dimensional situations. As illustration, we apply this method to real gene expression data with competitive results.
doi:10.1016/j.jmva.2012.07.004
PMCID: PMC3601508  PMID: 23524453
sparse principal component analysis; high-dimensional data; uncorrelated or orthogonal principal components; iterative algorithm; consistency in high-dimensional
17.  Genome-wide characterization of microRNA in foxtail millet (Setaria italica) 
BMC Plant Biology  2013;13:212.
Background
MicroRNAs (miRNAs) are a class of short non-coding, endogenous RNAs that play key roles in many biological processes in both animals and plants. Although many miRNAs have been identified in a large number of organisms, the miRNAs in foxtail millet (Setaria italica) have, until now, been poorly understood.
Results
In this study, two replicate small RNA libraries from foxtail millet shoots were sequenced, and 40 million reads representing over 10 million unique sequences were generated. We identified 43 known miRNAs, 172 novel miRNAs and 2 mirtron precursor candidates in foxtail millet. Some miRNA*s of the known and novel miRNAs were detected as well. Further, eight novel miRNAs were validated by stem-loop RT-PCR. Potential targets of the foxtail millet miRNAs were predicted based on our strict criteria. Of the predicted target genes, 79% (351) had functional annotations in InterPro and GO analyses, indicating the targets of the miRNAs were involved in a wide range of regulatory functions and some specific biological processes. A total of 69 pairs of syntenic miRNA precursors that were conserved between foxtail millet and sorghum were found. Additionally, stem-loop RT-PCR was conducted to confirm the tissue-specific expression of some miRNAs in the four tissues identified by deep-sequencing.
Conclusions
We predicted, for the first time, 215 miRNAs and 447 miRNA targets in foxtail millet at a genome-wide level. The precursors, expression levels, miRNA* sequences, target functions, conservation, and evolution of miRNAs we identified were investigated. Some of the novel foxtail millet miRNAs and miRNA targets were validated experimentally.
doi:10.1186/1471-2229-13-212
PMCID: PMC3878754  PMID: 24330712
miRNA; Foxtail millet; Expression pattern; Mirtron; miRNA*; Targets; Synteny
18.  An Alternative Model for the Role of RP2 Protein in Flagellum Assembly in the African Trypanosome* 
The Journal of Biological Chemistry  2013;289(1):464-475.
Background: RP2 function in ciliogenesis is enigmatic.
Results: Basal body tethering of TbRP2 depends only on N-terminal TOF-LisH motifs, TbRP2 depletion affects recruitment of transition zone proteins, and TbRP2 encodes the epitope recognized by YL1/2, a monoclonal antibody classically used to detect tyrosinated α-tubulin.
Conclusion: The previous model for RP2 function in trypanosomatids is questioned.
Significance: We give new insight into the assembly of the ciliary transition zone.
The tubulin cofactor C domain-containing protein TbRP2 is a basal body (centriolar) protein essential for axoneme formation in the flagellate protist Trypanosoma brucei, the causal agent of African sleeping sickness. Here, we show how TbRP2 is targeted and tethered at mature basal bodies and provide novel insight into TbRP2 function. Regarding targeting, understanding how several hundred proteins combine to build a microtubule axoneme is a fundamental challenge in eukaryotic cell biology. We show that basal body localization of TbRP2 is mediated by twinned, N-terminal TOF (TON1, OFD1, and FOP) and LisH motifs, motifs that otherwise facilitate localization of only a few conserved proteins at microtubule-organizing centers in animals, plants, and flagellate protists. Regarding TbRP2 function, there is a debate as to whether the flagellar assembly function of specialized, centriolar tubulin cofactor C domain-containing proteins is processing tubulin, the major component of axonemes, or general vesicular trafficking in a flagellum assembly context. Here we report that TbRP2 is required for the recruitment of T. brucei orthologs of MKS1 and MKS6, proteins that, in animal cells, are part of a complex that assembles at the base of the flagellum to regulate protein composition and cilium function. We also identify that TbRP2 is detected by YL1/2, an antibody classically used to detect α-tubulin. Together, these data suggest a general processing role for TbRP2 in trypanosome flagellum assembly and challenge the notion that TbRP2 functions solely in assessing tubulin “quality” prior to tubulin incorporation into the elongating axoneme.
doi:10.1074/jbc.M113.509521
PMCID: PMC3879569  PMID: 24257747
Centriole; Cilia; Protein Targeting; Trypanosoma Brucei; Tubulin; GTPase-activating Protein; Axoneme
19.  Inhibition of mitochondrial fragmentation diminishes Huntington’s disease–associated neurodegeneration 
The Journal of Clinical Investigation  2013;123(12):5371-5388.
Huntington’s disease (HD) is the result of expression of a mutated Huntingtin protein (mtHtt), and is associated with a variety of cellular dysfunctions including excessive mitochondrial fission. Here, we tested whether inhibition of excessive mitochondrial fission prevents mtHtt-induced pathology. We developed a selective inhibitor (P110-TAT) of the mitochondrial fission protein dynamin-related protein 1 (DRP1). We found that P110-TAT inhibited mtHtt-induced excessive mitochondrial fragmentation, improved mitochondrial function, and increased cell viability in HD cell culture models. P110-TAT treatment of fibroblasts from patients with HD and patients with HD with iPS cell–derived neurons reduced mitochondrial fragmentation and corrected mitochondrial dysfunction. P110-TAT treatment also reduced the extent of neurite shortening and cell death in iPS cell–derived neurons in patients with HD. Moreover, treatment of HD transgenic mice with P110-TAT reduced mitochondrial dysfunction, motor deficits, neuropathology, and mortality. We found that p53, a stress gene involved in HD pathogenesis, binds to DRP1 and mediates DRP1-induced mitochondrial and neuronal damage. Furthermore, P110-TAT treatment suppressed mtHtt-induced association of p53 with mitochondria in multiple HD models. These data indicate that inhibition of DRP1-dependent excessive mitochondrial fission with a P110-TAT–like inhibitor may prevent or slow the progression of HD.
doi:10.1172/JCI70911
PMCID: PMC3859413  PMID: 24231356
20.  Acute Inhibition of Excessive Mitochondrial Fission After Myocardial Infarction Prevents Long‐term Cardiac Dysfunction 
Background
Ischemia and reperfusion (IR) injury remains a major cause of morbidity and mortality and multiple molecular and cellular pathways have been implicated in this injury. We determined whether acute inhibition of excessive mitochondrial fission at the onset of reperfusion improves mitochondrial dysfunction and cardiac contractility postmyocardial infarction in rats.
Methods and Results
We used a selective inhibitor of the fission machinery, P110, which we have recently designed. P110 treatment inhibited the interaction of fission proteins Fis1/Drp1, decreased mitochondrial fission, and improved bioenergetics in three different rat models of IR, including primary cardiomyocytes, ex vivo heart model, and an in vivo myocardial infarction model. Drp1 transiently bound to the mitochondria following IR injury and P110 treatment blocked this Drp1 mitochondrial association. Compared with control treatment, P110 (1 μmol/L) decreased infarct size by 28±2% and increased adenosine triphosphate levels by 70+1% after IR relative to control IR in the ex vivo model. Intraperitoneal injection of P110 (0.5 mg/kg) at the onset of reperfusion in an in vivo model resulted in improved mitochondrial oxygen consumption by 68% when measured 3 weeks after ischemic injury, improved cardiac fractional shortening by 35%, reduced mitochondrial H2O2 uncoupling state by 70%, and improved overall mitochondrial functions.
Conclusions
Together, we show that excessive mitochondrial fission at reperfusion contributes to long‐term cardiac dysfunction in rats and that acute inhibition of excessive mitochondrial fission at the onset of reperfusion is sufficient to result in long‐term benefits as evidenced by inhibiting cardiac dysfunction 3 weeks after acute myocardial infarction.
doi:10.1161/JAHA.113.000461
PMCID: PMC3835263  PMID: 24103571
cardiac myocytes; Drp1; heart; mitochondria; protein‐protein interaction inhibitor
21.  ROS generated by CYP450, especially CYP2E1, mediate mitochondrial dysfunction induced by tetrandrine in rat hepatocytes 
Acta Pharmacologica Sinica  2013;34(9):1229-1236.
Aim:
Tetrandrine, an alkaloid with a remarkable pharmacological profile, induces oxidative stress and mitochondrial dysfunction in hepatocytes; however, mitochondria are not the direct target of tetrandrine, which prompts us to elucidate the role of oxidative stress in tetrandrine-induced mitochondrial dysfunction and the sources of oxidative stress.
Methods:
Rat primary hepatocytes were isolated by two-step collagenase perfusion. Mitochondrial function was evaluated by analyzing ATP content, mitochondrial membrane potential (MMP) and the mitochondrial permeability transition. The oxidative stress was evaluated by examining changes in the levels of reactive oxygen species (ROS) and glutathione (GSH).
Results:
ROS scavengers largely attenuated the cytotoxicity induced by tetrandrine in rat hepatocytes, indicating the important role of ROS in the hepatotoxicity of tetrandrine. Of the multiple ROS inhibitors that were tested, only inhibitors of CYP450 (SKF-525A and others) reduced the ROS levels and ameliorated the depletion of GSH. Mitochondrial function assays showed that the mitochondrial permeability transition (MPT) induced by tetrandrine was inhibited by SKF-525A and vitamin C (VC), both of which also rescued the depletion of ATP levels and the mitochondrial membrane potential. Upon inhibiting specific CYP450 isoforms, we observed that the inhibitors of CYP2D, CYP2C, and CYP2E1 attenuated the ATP depletion that occurred following tetrandrine exposure, whereas the inhibitors of CYP2D and CYP2E1 reduced the ROS induced by tetrandrine. Overexpression of CYP2E1 enhanced the tetrandrine-induced cytotoxicity.
Conclusion:
We demonstrated that CYP450 plays an important role in the mitochondrial dysfunction induced by the administration of tetrandrine. ROS generated by CYP450, especially CYP2E1, may contribute to the mitochondrial dysfunction induced by tetrandrine.
doi:10.1038/aps.2013.62
PMCID: PMC4003161  PMID: 23892269
tetrandrine; mitochondria; reactive oxygen species; cytochrome P450
22.  A new species of Polypedilum (Uresipedilum) Oyewo & Sæther, 1998 from Zhejiang Province of Oriental China (Diptera, Chironomidae) 
ZooKeys  2013;43-49.
A new species of Polypedilum (Uresipedilum) Oyewo & Sæther, 1998, Polypedilum (Uresipedilum) minimum sp. n. is described as male. A key to adult males of the subgenus from China is presented.
doi:10.3897/zookeys.320.5147
PMCID: PMC3744150  PMID: 23950682
Chironomidae; Polypedilum (Uresipedilum); key; new species; China
23.  The effect of Chinese Jinzhida recipe on the hippocampus in a rat model of diabetes-associated cognitive decline 
Background
To investigate the effects of treatment with Multi component Chinese Medicine Jinzhida (JZD) on behavioral deficits in diabetes-associated cognitive decline (DACD) rats and verify our hypothesis that JZD treatment improves cognitive function by suppressing the endoplasmic reticulum stress (ERS) and improving insulin signaling transduction in the rats’ hippocampus.
Methods
A rat model of type 2 diabetes mellitus (T2DM) was established using high fat diet and streptozotocin (30 mg/kg, ip). Insulin sensitivity was evaluated by the oral glucose tolerance test and the insulin tolerance test. After 7 weeks, the T2DM rats were treated with JZD. The step-down test and Morris water maze were used to evaluate behavior in T2DM rats after 5 weeks of treatment with JZD. Levels of phosphorylated proteins involved in the ERS and in insulin signaling transduction pathways were assessed by Western blot for T2DM rats’ hippocampus.
Results
Compared to healthy control rats, T2DM rats initially showed insulin resistance and had declines in acquisition and retrieval processes in the step-down test and in spatial memory in the Morris water maze after 12 weeks. Performance on both the step-down test and Morris water maze tasks improved after JZD treatment. In T2DM rats, the ERS was activated, and then inhibited the insulin signal transduction pathways through the Jun NH2-terminal kinases (JNK) mediated. JZD treatment suppressed the ERS, increased insulin signal transduction, and improved insulin resistance in the rats’ hippocampus.
Conclusions
Treatment with JZD improved cognitive function in the T2DM rat model. The possible mechanism for DACD was related with ERS inducing the insulin signal transduction dysfunction in T2DM rats’ hippocampus. The JZD could reduce ERS and improve insulin signal transduction and insulin resistance in T2DM rats’ hippocampus and as a result improved the cognitive function.
doi:10.1186/1472-6882-13-161
PMCID: PMC3735391  PMID: 23829668
Diabetes; Cognitive decline; Step down test; Morris water; Immunobloting analysis; Hippocampus
24.  Regulatory Role of Hypoxia Inducible Factor in the Biological Behavior of Nucleus Pulposus Cells 
Yonsei Medical Journal  2013;54(4):807-812.
Intervertebral disc (IVD) degeneration is implicated as a major cause of low back pain. The alternated phenotypes, reduced cell survival, decreased metabolic activity, loss of matrix production and dystrophic mineralization of nucleus pulposus (NP) cells may be key contributors to progressive IVD degeneration. IVD is the largest avascular structure in the body, characterized by low oxygen tension in vivo. Hypoxia-inducible factor (HIF) is a master transcription factor that is induced upon hypoxia and directs coordinated cellular responses to hypoxic environments. This review summarizes relevant studies concerning the involvement of HIF in the regulation of biological behaviors of NP cells. We describe current data on the expression of HIF in NP cells and further discuss the various roles that HIF plays in the regulation of the phenotype, survival, metabolism, matrix production and dystrophic mineralization of NP cells. Here, we conclude that HIF may be a promising target for the prevention and treatment of IVD degeneration.
doi:10.3349/ymj.2013.54.4.807
PMCID: PMC3663214  PMID: 23709411
Hypoxia inducible factor; intervertebral disc degeneration; nucleus pulposus
25.  Undecylprodigiosin Induced Apoptosis in P388 Cancer Cells Is Associated with Its Binding to Ribosome 
PLoS ONE  2013;8(6):e65381.
Prodigiosins (PGs) are a family of natural red pigments with anticancer activity, and one member of the family has entered clinical phase II trials. However, the anticancer mechanisms of PGs remain largely unclear. This study was designed to investigate the molecular basis of anticancer activity of UP, a derivative of PGs, in P388 cells. By introducing pharmacological inhibitors and utilizing a variety of analytical approaches including western blotting, flow cytometry and confocal laser microscopy, we found that UP inhibited proliferation of P388 via arresting cells at G2/M phase and inducing cells apoptosis, which was related to the activation of P38, JNK rather than ERK1/2 signaling. ROS regeneration and acidification in cells appear not involved in UP induced apoptosis. Furthermore, utilizing mass spectrometry, sucrose density gradient fractionation and immunofluorescence staining, we discovered that UP was apparently located at ribosome. These results together indicate that ribosome may be the potential target of UP in cancer cells, which opened a new avenue in delineating the anticancer mechanism of PGs.
doi:10.1371/journal.pone.0065381
PMCID: PMC3682955  PMID: 23799011

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