CellBoost: A pipeline for machine assisted annotation in Neuroanatomy.

One of the important yet labor intensive tasks in neuroanatomy is the identification of select populations of cells. Current high-throughput techniques enable marking cells with histochemical fluorescent molecules as well as through the genetic expression of fluorescent proteins. Modern scanning microscopes allow high resolution multi-channel imaging of the mechanically or optically sectioned brain with thousands of marked cells per square millimeter. Manual identification of all marked cells is prohibitively time consuming. At the same time, simple segmentation algorithms suffer from high error rates and sensitivity to variation in fluorescent intensity and spatial distribution. We present a methodology that combines human judgement and machine learning that serves to significantly reduce the labor of the anatomist while improving the consistency of the annotation. As a demonstration, we analyzed murine brains with marked premotor neurons in the brainstem. We compared the error rate of our method to the disagreement rate among human anatomists. This comparison shows that our method can reduce the time to annotate by as much as ten-fold without significantly increasing the rate of errors. We show that our method achieves significant reduction in labor while achieving an accuracy that is similar to the level of agreement between different anatomists.

Research progress on endogenous small-molecule phenolics and the proposal of "phenolomics" / 药学学报

Small-molecule phenolic substances widely exist in animals and plants, and have some shared biological activities. The metabolism of phenylalanine and tyrosine in the human body, and especially the metabolism of catecholamine neurotransmitters, produces endogenous small-molecule phenols. Endogenous small-molecule phenolic substances are functionally related to the important physiological processes and the occurrence of mental diseases in humans and some animals, which are systematically sorts and summarized in this review. Integrating the previous experimental research and literature analysis on natural small-molecule phenols by our research group, the understanding of the hypothesis that "small-molecule phenol are pharmacological signal carriers" was deepened. Based on above, the concept of "phenolomics" was further proposed, analyzed the research direction and research content which can bring into the knowledge framework of phenolomics. The induction of phenolomics will provide wider perspectives on explaining the pharmacological mechanism of drugs, discovering new drug targets, and finding biomarkers of mental diseases.

An exploration of biomarkers for noise exposure: mitochondrial DNA copy number and micronucleus frequencies in Chinese workers.

Few studies have been conducted that use biomarkers as early warning signals for noise-associated health hazards. To explore potentially effective biomarkers for noise-exposed populations, we recruited 218 noise-exposed male workers in China. We calculated cumulative noise exposure (CNE) through noise intensity and noise-exposed duration. When the model was fully adjusted, ln-transformed relative mitochondrial DNA copy number (mtDNAcn) decreased by 0.014 (95% confidence interval (CI): -0.026, -0.003) units with each 1 dB(A)∙year increase in CNE levels. CNE was further included in the model as a grouping variable, and the results showed a negative dose-effect relationship between relative mtDNAcn and CNE (P-trend = 0.045). However, we did not find a correlation between CNE and micronucleus (MN) frequencies. Our findings suggest that CNE in workers was associated with a decrease in relative mtDNAcn which may provide a potential biomarker for noise and for certain health risk but not with MN frequencies.

Reforming the Uniformity of Solid Electrolyte Interphase by Nanoscale Structure Regulation for Stable Lithium Metal Batteries.

The stability of high-energy-density lithium metal batteries depends on the uniformity of solid electrolyte interphase (SEI) on lithium metal anodes. Rationally improving SEI uniformity is hindered by poorly understanding the effect of structure and components of SEI on its uniformity. Herein, a bilayer structure of SEI formed by isosorbide dinitrate (ISDN) additives in localized high-concentration electrolytes was demonstrated to improve SEI uniformity. In the bilayer SEI, LiNx Oy generated by ISDN occupies top layer and LiF dominates bottom layer next to anode. The uniformity of lithium deposition is remarkably improved with the bilayer SEI, mitigating the consumption rate of active lithium and electrolytes. The cycle life of lithium metal batteries with bilayer SEI is three times as that with common anion-derived SEI under practical conditions. A prototype lithium metal pouch cell of 430 Wh kg-1 undergoes 173 cycles. This work demonstrates the effect of a reasonable structure of SEI on reforming SEI uniformity.

Electrolyte Design for Improving Mechanical Stability of Solid Electrolyte Interphase in Lithium-Sulfur Batteries.

Practical lithium-sulfur (Li-S) batteries are severely plagued by the instability of solid electrolyte interphase (SEI) formed in routine ether electrolytes. Herein, an electrolyte with 1,3,5-trioxane (TO) and 1,2-dimethoxyethane (DME) as co-solvents is proposed to construct a high-mechanical-stability SEI by enriching organic components in Li-S batteries. The high-mechanical-stability SEI works compatibly in Li-S batteries. TO with high polymerization capability can preferentially decompose and form organic-rich SEI, strengthening mechanical stability of SEI, which mitigates crack and regeneration of SEI and reduces the consumption rate of active Li, Li polysulfides, and electrolytes. Meanwhile, DME ensures high specific capacity of S cathodes. Accordingly, the lifespan of Li-S batteries increases from 75 cycles in routine ether electrolyte to 216 cycles in TO-based electrolyte. Furthermore, a 417 Wh kg-1 Li-S pouch cell undergoes 20 cycles. This work provides an emerging electrolyte design for practical Li-S batteries.

Nucleic acid aptamer-based traditional Chinese medicine application:therapy,targeting and diagnosis / 中国中药杂志

Nucleic acid aptamers, broad-spectrum target-specific single-stranded oligonucleotides, serve as molecules in targeted therapy, targeted delivery and disease diagnosis for the treatment of tumor or microbial infection and clinical detection. Due to the existence of components in the use of traditional Chinese medicine(TCM), the target is difficult to concentrate and the specificity of treatment is poor. The effective components of TCM are toxic components, so a highly sensitive detection method is urgently needed to reduce the toxicity problem at the same time. The combined application of TCM and modern medical treatment strategy are difficult and cannot improve the therapeutic effect. Aptamers, advantageous in biosensors, aptamer-nanoparticles for targeted drug delivery, and aptamer-siRNA chimeras, are expected to connect Chinese medicinals with nanotechnology, diagnostic technology and combined therapies. We summarized the preparation, screening, and modification techniques of nucleic acid aptamers and the biomedical applications and advantages in therapy, targeting, and diagnosis, aiming at providing a reference for the in-depth research and development in TCM.

Uniform tissue lesion formation induced by high-intensity focused ultrasound along a spiral pathway.

Both theoretical and experimental studies were performed here to investigate the lesion formation induced by high-intensity focused ultrasound (HIFU) operating in continuous scanning mode along a spiral pathway. The Khokhlov-Zabolotskaya-Kuznetsov equation and bio-heat equation were combined in the current model to predict HIFU-induced temperature distribution and lesion formation. The shape of lesion and treatment efficiency were assessed for a given scanning speed at two different grid spacing (3mm and 4mm) in the gel phantom studies and further researched in ex vivo studies. The results show that uniform lesions can be generated with continuous HIFU scanning along a spiral pathway. The complete coverage of the entire treated volume can be achieved as long as the spacing grid of the spiral pathway is small enough for heat to diffuse and deposit, and the treatment efficiency can be optimized by selecting an appropriate scanning speed. This study can provide guidance for further optimization of the treatment efficiency and safety of HIFU therapy.

Low expression levels of putative HPV encoded microRNAs in cervical samples.

Using small RNA sequencing of libraries established from cervical samples and cervical cancer cell lines, we have previously reported identification of nine and validation of five putative microRNA species encoded by human papillomaviruses (HPV) including five microRNAs encoded by HPV 16. Here we have studied the expression of HPV 16 encoded microRNAs in cervical samples and in HPV 16 containing cell lines. Different sample matrices were collected for the study: 20 paraffin embedded cervical tissue samples, 16 liquid cytology samples, and 16 cervical cell samples from women attending colposcopy due to cervical abnormalities, as well as four HPV 16 containing cell lines. Total RNA was extracted, the samples were spiked with small synthetic control RNAs, and the expression of five HPV 16 encoded microRNAs was assessed by real-time PCR amplification. HPV encoded microRNAs could be frequently detected, albeit at high cycle counts. HPV16-miR-H1 was detected in 3.6 %, HPV16-miR-H3 in 23.6 %, HPV16-miR-H5 in 7.3 %, and HPV16-miR-H6 in 18.2 % of all valid samples. True positive signals for HPV16-miR-H2 could not be detected in any of the samples. Viral microRNAs were detected most frequently in paraffin-embedded samples: in one sample representing normal squamous epithelium, in one cervical intraepithelial neoplasia (CIN) grade 1, one CIN2, three CIN3, two squamous cell carcinoma, three adenocarcinoma in situ, and two adenocarcinoma samples. One liquid cytology sample from a patient with CIN3 as well as all four cell lines were positive for HPV16-miR-H3. In all cases HPV encoded microRNAs were expressed at low levels.

NOGO-A/RTN4A and NOGO-B/RTN4B are simultaneously expressed in epithelial, fibroblast and neuronal cells and maintain ER morphology.

Reticulons (RTNs) are a large family of membrane associated proteins with various functions. NOGO-A/RTN4A has a well-known function in limiting neurite outgrowth and restricting the plasticity of the mammalian central nervous system. On the other hand, Reticulon 4 proteins were shown to be involved in forming and maintaining endoplasmic reticulum (ER) tubules. Using comparative transcriptome analysis and qPCR, we show here that NOGO-B/RTN4B and NOGO-A/RTN4A are simultaneously expressed in cultured epithelial, fibroblast and neuronal cells. Electron tomography combined with immunolabelling reveal that both isoforms localize preferably to curved membranes on ER tubules and sheet edges. Morphological analysis of cells with manipulated levels of NOGO-B/RTN4B revealed that it is required for maintenance of normal ER shape; over-expression changes the sheet/tubule balance strongly towards tubules and causes the deformation of the cell shape while depletion of the protein induces formation of large peripheral ER sheets.

HMGB4 is expressed by neuronal cells and affects the expression of genes involved in neural differentiation.

HMGB4 is a new member in the family of HMGB proteins that has been characterized in sperm cells, but little is known about its functions in somatic cells. Here we show that HMGB4 and the highly similar rat Transition Protein 4 (HMGB4L1) are expressed in neuronal cells. Both proteins had slow mobility in nucleus of living NIH-3T3 cells. They interacted with histones and their differential expression in transformed cells of the nervous system altered the post-translational modification statuses of histones in vitro. Overexpression of HMGB4 in HEK 293T cells made cells more susceptible to cell death induced by topoisomerase inhibitors in an oncology drug screening array and altered variant composition of histone H3. HMGB4 regulated over 800 genes in HEK 293T cells with a p-value ≤0.013 (n = 3) in a microarray analysis and displayed strongest association with adhesion and histone H2A -processes. In neuronal and transformed cells HMGB4 regulated the expression of an oligodendrocyte marker gene PPP1R14a and other neuronal differentiation marker genes. In conclusion, our data suggests that HMGB4 is a factor that regulates chromatin and expression of neuronal differentiation markers.

Obesity and Bariatric Surgery Drive Epigenetic Variation of Spermatozoa in Humans.

Obesity is a heritable disorder, with children of obese fathers at higher risk of developing obesity. Environmental factors epigenetically influence somatic tissues, but the contribution of these factors to the establishment of epigenetic patterns in human gametes is unknown. Here, we hypothesized that weight loss remodels the epigenetic signature of spermatozoa in human obesity. Comprehensive profiling of the epigenome of sperm from lean and obese men showed similar histone positioning, but small non-coding RNA expression and DNA methylation patterns were markedly different. In a separate cohort of morbidly obese men, surgery-induced weight loss was associated with a dramatic remodeling of sperm DNA methylation, notably at genetic locations implicated in the central control of appetite. Our data provide evidence that the epigenome of human spermatozoa dynamically changes under environmental pressure and offers insight into how obesity may propagate metabolic dysfunction to the next generation.

[Phytoplankton community structure and its succession in isolated lakes of Poyang-Junshan Lake].

As one of the human activities that transform nature, construction of dams and dykes may impose significant effects on lake ecosystems. Due to lacking of comparative data for ecological monitoring, how the changes of phytoplankton community structure respond to altered hydrological connectivity between lakes and other water bodies is still unknown. This work chose Junshan Lake, the typical isolated lake from Poyang Lake floodplain, to investigate the succession in phytoplankton communities responding to altered connectivity. Phytoplankton samples were collected during the wet and dry seasons in Junshan Lake, to analyze the phytoplankton community structure. The results showed that, fifty three genera from six phyta were identified in Junshan Lake, with Chlorophyta (47.2%), Bacillariophyta (22.2%), Cyanophyta (14.8%) and Euglenophyta (9.3%) being the main phyta. The dominant species were Ceratium hirundinella (20.5%), Anabeana spp. (18.5%) and Microcystis spp. (12.9%) during the wet seasons. Cryptomonas ovate (38.4%), Aulacoseira granulata (15.2%) and Microcystis spp. (10.5%) dominated during the whole dry seasons. The total phytoplankton abundance was mainly composed of Cyanophyta (85.4% -87.0%). The total phytoplankton biomass was dominantly made up of Cyanophyta (45.0%), Dinophyta (21.1%), Bacillariophyta (15.6%) and Chlorophyta (11.5%) during the wet seasons. Cryptophyta (38.2%), Bacillariophyta (31.3%) and Cyanophyta (21.1%) were the main contributors of the total phytoplankton biomass during the dry seasons. The phytoplankton community structure changed from Dinophyta-Bacillariophyta type during the wet seasons of 2007-2008 to Cyanophyta- Dinophyta type during the wet seasons of 2012-2013, and changed from Dinophyta- Bacillariophyta type during the dry seasons of 2007-2008 to Cryptophyta- Bacillariophyta- Cyanophyta type during the dry seasons of 2012-2013. The abundance and biomass increased from 2.66 x 10(6) cell L(-1) during 2007-2008 to 6.77 x 10(7) cell x L(-1) during 2012- 2013, and from 0.72 mg x L(-1) during 2007-2008 to 12.30 mg x L(-1) during 2012-2013, respectively. The succession pattern of phytoplankton community in the Junshan Lake showed a decrease in the proportion of oligotrophic species as Chrysophyta and Dinophyta, and an increase in eutrophic species as Cyanophyta and Cryptophyta. Thus, being isolated from Poyang Lake might alter hydrologic factors so that the water exchange time became longer and the water flow became slower which could promote the growth and aggregation of phytoplankton eutrophication indicator species in Junshan Lake.

The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera.

Previous studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we report the genome (393 Mb) of the Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae), a widely recognized model species in metapopulation biology and eco-evolutionary research, which has the putative ancestral karyotype of n=31. Using a phylogenetic analyses of Nymphalidae and of other Lepidoptera, combined with orthologue-level comparisons of chromosomes, we conclude that the ancestral lepidopteran karyotype has been n=31 for at least 140 My. We show that fusion chromosomes have retained the ancestral chromosome segments and very few rearrangements have occurred across the fusion sites. The same, shortest ancestral chromosomes have independently participated in fusion events in species with smaller karyotypes. The short chromosomes have higher rearrangement rate than long ones. These characteristics highlight distinctive features of the evolutionary dynamics of butterflies and moths.

Gene expression profiles in human and mouse primary cells provide new insights into the differential actions of vitamin D3 metabolites.

1α,25-Dihydroxyvitamin D3 (1α,25(OH)2D3) had earlier been regarded as the only active hormone. The newly identified actions of 25-hydroxyvitamin D3 (25(OH)D3) and 24R,25-dihydroxyvitamin D3 (24R,25(OH)2D3) broadened the vitamin D3 endocrine system, however, the current data are fragmented and a systematic understanding is lacking. Here we performed the first systematic study of global gene expression to clarify their similarities and differences. Three metabolites at physiologically comparable levels were utilized to treat human and mouse fibroblasts prior to DNA microarray analyses. Human primary prostate stromal P29SN cells (hP29SN), which convert 25(OH)D3 into 1α,25(OH)2D3 by 1α-hydroxylase (encoded by the gene CYP27B1), displayed regulation of 164, 171, and 175 genes by treatment with 1α,25(OH)2D3, 25(OH)D3, and 24R,25(OH)2D3, respectively. Mouse primary Cyp27b1 knockout fibroblasts (mCyp27b1 (-/-)), which lack 1α-hydroxylation, displayed regulation of 619, 469, and 66 genes using the same respective treatments. The number of shared genes regulated by two metabolites is much lower in hP29SN than in mCyp27b1 (-/-). By using DAVID Functional Annotation Bioinformatics Microarray Analysis tools and Ingenuity Pathways Analysis, we identified the agonistic regulation of calcium homeostasis and bone remodeling between 1α,25(OH)2D3 and 25(OH)D3 and unique non-classical actions of each metabolite in physiological and pathological processes, including cell cycle, keratinocyte differentiation, amyotrophic lateral sclerosis signaling, gene transcription, immunomodulation, epigenetics, cell differentiation, and membrane protein expression. In conclusion, there are three distinct vitamin D3 hormones with clearly different biological activities. This study presents a new conceptual insight into the vitamin D3 endocrine system, which may guide the strategic use of vitamin D3 in disease prevention and treatment.

Identification and validation of human papillomavirus encoded microRNAs.

We report here identification and validation of the first papillomavirus encoded microRNAs expressed in human cervical lesions and cell lines. We established small RNA libraries from ten human papillomavirus associated cervical lesions including cancer and two human papillomavirus harboring cell lines. These libraries were sequenced using SOLiD 4 technology. We used the sequencing data to predict putative viral microRNAs and discovered nine putative papillomavirus encoded microRNAs. Validation was performed for five candidates, four of which were successfully validated by qPCR from cervical tissue samples and cell lines: two were encoded by HPV 16, one by HPV 38 and one by HPV 68. The expression of HPV 16 microRNAs was further confirmed by in situ hybridization, and colocalization with p16INK4A was established. Prediction of cellular target genes of HPV 16 encoded microRNAs suggests that they may play a role in cell cycle, immune functions, cell adhesion and migration, development, and cancer. Two putative viral target sites for the two validated HPV 16 miRNAs were mapped to the E5 gene, one in the E1 gene, two in the L1 gene and one in the LCR region. This is the first report to show that papillomaviruses encode their own microRNA species. Importantly, microRNAs were found in libraries established from human cervical disease and carcinoma cell lines, and their expression was confirmed in additional tissue samples. To our knowledge, this is also the first paper to use in situ hybridization to show the expression of a viral microRNA in human tissue.

Leptin-induced mTOR activation defines a specific molecular and transcriptional signature controlling CD4+ effector T cell responses.

The sensing by T cells of metabolic and energetic changes in the microenvironment can determine the differentiation, maturation, and activation of these cells. Although it is known that mammalian target of rapamycin (mTOR) gauges nutritonal and energetic signals in the extracellular milieu, it is not known how mTOR and metabolism influence CD4+CD25-FOXP3- effector T cell (Teff) responses. In this article, we show that leptin-induced activation of mTOR, which, in turn, controls leptin production and signaling, causes a defined cellular, biochemical, and transcriptional signature that determine the outcome of Teff responses, both in vitro and in vivo. The blockade of leptin/leptin receptor signaling, induced by genetic means or by starvation, leads to impaired mTOR activity that inhibits the proliferation of Teffs in vivo. Notably, the transcriptional signature of Teffs in the presence of leptin blockade appears similar to that observed in rapamycin-treated Teffs. These results identify a novel link between nutritional status and Teff responses through the leptin-mTOR axis and define a potential target for Teff modulation in normal and pathologic conditions.

miRSeqNovel: an R based workflow for analyzing miRNA sequencing data.

We present miRSeqNovel, an R based workflow for miRNA sequencing data analysis. miRSeqNovel can process both colorspace (SOLiD) and basespace (Illumina/Solexa) data by different mapping algorithms. It finds differentially expressed miRNAs and gives conservative prediction of novel miRNA candidates with customized parameters. miRSeqNovel is freely available at http://sourceforge.net/projects/mirseq/files.

Re-analysis of bipolar disorder and schizophrenia gene expression complements the Kraepelinian dichotomy.

The differential diagnosis of schizophrenia (SZ) and bipolar disorder (BD) is based solely on clinical features and upon a subset of overlapping symptoms. Within the last years, an increasing amount of clinical, epidemiological and genetic data suggested inconsistent with the Kraepelinian dichotomy. We performed re-analysis of genome-wide gene expression data obtained from postmortem prefrontal cortex (PEC) of both BD and SZ patients with matched controls from four independent microarray experiments. We found 2,577 and 477 genes specifically altered in BD and SZ, respectively. Of these, 164 genes were shared between the syndromes. We identified genes of the transcriptional and post-transcriptional machineries altered in BD and genes of the development changed in SZ. Our results showed that the genomic expression profile of BD and SZ had some similarity but still could be well-distinguished by suitable statistical test.