Decreased expression of GEM in osteoarthritis cartilage regulates chondrogenic differentiation via Wnt/β-catenin signaling

BACKGROUND

GEM (GTP-binding protein overexpressed in skeletal muscle) is one of the atypical small GTPase subfamily members recently identified as a regulator of cell differentiation. Abnormal chondrogenesis coupled with an imbalance in the turnover of cartilaginous matrix formation is highly relevant to the onset and progression of osteoarthritis (OA). However, how GEM regulates chondrogenic differentiation remains unexplored.

METHODS

Cartilage tissues were obtained from OA patients and graded according to the ORASI and ICRS grading systems. The expression alteration of GEM was detected in the Grade 4 cartilage compared to Grade 0 and verified in OA mimic culture systems. Next, to investigate the specific function of GEM during these processes, we generated a Gem knockdown (Gem-Kd) system by transfecting siRNA targeting Gem into ATDC5 cells. Acan, Col2a1, Sox9, and Wnt target genes of Gem-Kd ATDC5 cells were detected during induction. The transcriptomic sequencing analysis was performed to investigate the mechanism of GEM regulation. Wnt signaling pathways were verified by real-time PCR and immunoblot analysis. Finally, a rescue model generated by treating Gem-KD ATDC5 cells with a Wnt signaling agonist was established to validate the mechanism identified by RNA sequencing analysis.

RESULTS

A decreased expression of GEM in OA patients' cartilage tissues and OA mimic chondrocytes was observed. While during chondrogenesis differentiation and cartilage matrix formation, the expression of GEM was increased. Gem silencing suppressed chondrogenic differentiation and the expressions of Acan, Col2a1, and Sox9. RNA sequencing analysis revealed that Wnt signaling was downregulated in Gem-Kd cells. Decreased expression of Wnt signaling associated genes and the total β-CATENIN in the nucleus and cytoplasm were observed. The exogenous Wnt activation exhibited reversed effect on Gem loss-of-function cells.

CONCLUSION

These findings collectively validated that GEM functions as a novel regulator mediating chondrogenic differentiation and cartilage matrix formation through Wnt/β-catenin signaling.

Gaseous elemental mercury emissions from informal E-Waste recycling facilities in Pakistan

Detrimental effects of mercury (Hg) on ecosystems and human health have been well-documented. Whereas emissions of gaseous elemental mercury (GEM) from e-waste recycling have been reported in developed countries, much less is known about the situation in the Global South. Using a total of 132 passive air samplers, seasonally resolved concentrations of GEM in air were measured continuously at 32 informal e-waste recycling facilities and background location in Pakistan for a period of one year between September 2020 and December 2021. Annual average GEM concentrations at the studied locations ranged from 1.8 to 92 ng m-3. Among the studied cities, higher concentrations were measured in Karachi (mean ± s.d: 17 ± 22, range: 4.2-92 ng m-3), Lahore (16 ± 4.2, 8.2-22 ng m-3) and Peshawar (15 ± 17, 4.9-80 ng m-3), while lower levels were measured in Hyderabad (6.9 ± 6.2, 3.1-25 ng m-3), consistent with a higher rate of informal recycling activities in metropolitan areas. Seasonally, higher GEM levels occurred during autumn (15 ± 16: 3.3-92 ng m-3) and summer (13 ± 8.7: 1.8-80 ng m-3) than in winter (12 ± 8.4: 2.5-49 ng m-3) and spring (9.2 ± 7.3: 1.8-80 ng m-3), possibly reflecting enhanced volatilization at higher temperatures and/or varying magnitude of recycling operations in different seasons. Policies and strict regulations related to e-waste management should be developed and implemented urgently in the country.

The African Gender and Development Index: an engendered and culturally sensitive statistical tool

In 2004 the African Union adopted an innovative gender index, the Afriacn Gender and Development Index (AGDI). It is composed of the quantitative Gender Status Index (GSI) and the qualitative African Women's Progress Scorecard (AWPS). The tool is built on the use of national data collected by a national team of specialists. Since the beginning three cycles of implementation have occurred. After the last cycle the AGDI was revised. In this article the authors assess the implementation of the AGDI, against the background of other gender indices, and discuss the latest revisions.

Cutaneous Neurofibroma Heterogeneity: Factors that Influence Tumor Burden in Neurofibromatosis Type 1

Neurofibromatosis type 1 is one of the most common genetic disorders of the nervous system and predisposes patients to develop benign and malignant tumors. Cutaneous neurofibromas (cNFs) are NF1-associated benign tumors that affect nearly 100% of patients with NF1. cNFs dramatically reduce patients' QOL owing to their unaesthetic appearance, physical discomfort, and corresponding psychological burden. There is currently no effective drug therapy option, and treatment is restricted to surgical removal. One of the greatest hurdles for cNF management is the variability of clinical expressivity in NF1, resulting in intrapatient and interpatient cNF tumor burden heterogeneity, that is, the variability in the presentation and evolution of these tumors. There is growing evidence that a wide array of factors are involved in the regulation of cNF heterogeneity. Understanding the mechanisms underlying this heterogeneity of cNF at the molecular, cellular, and environmental levels can facilitate the development of innovative and personalized treatment regimens.

Yield prediction through integration of genetic, environment, and management data through deep learning

Accurate prediction of the phenotypic outcomes produced by different combinations of genotypes, environments, and management interventions remains a key goal in biology with direct applications to agriculture, research, and conservation. The past decades have seen an expansion of new methods applied toward this goal. Here we predict maize yield using deep neural networks, compare the efficacy of 2 model development methods, and contextualize model performance using conventional linear and machine learning models. We examine the usefulness of incorporating interactions between disparate data types. We find deep learning and best linear unbiased predictor (BLUP) models with interactions had the best overall performance. BLUP models achieved the lowest average error, but deep learning models performed more consistently with similar average error. Optimizing deep neural network submodules for each data type improved model performance relative to optimizing the whole model for all data types at once. Examining the effect of interactions in the best-performing model revealed that including interactions altered the model's sensitivity to weather and management features, including a reduction of the importance scores for timepoints expected to have a limited physiological basis for influencing yield-those at the extreme end of the season, nearly 200 days post planting. Based on these results, deep learning provides a promising avenue for the phenotypic prediction of complex traits in complex environments and a potential mechanism to better understand the influence of environmental and genetic factors.

Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data

Single-cell RNA sequencing combined with genome-scale metabolic models (GEMs) has the potential to unravel the differences in metabolism across both cell types and cell states but requires new computational methods. Here, we present a method for generating cell-type-specific genome-scale models from clusters of single-cell RNA-Seq profiles. Specifically, we developed a method to estimate the minimum number of cells required to pool to obtain stable models, a bootstrapping strategy for estimating statistical inference, and a faster version of the task-driven integrative network inference for tissues algorithm for generating context-specific GEMs. In addition, we evaluated the effect of different RNA-Seq normalization methods on model topology and differences in models generated from single-cell and bulk RNA-Seq data. We applied our methods on data from mouse cortex neurons and cells from the tumor microenvironment of lung cancer and in both cases found that almost every cell subtype had a unique metabolic profile. In addition, our approach was able to detect cancer-associated metabolic differences between cancer cells and healthy cells, showcasing its utility. We also contextualized models from 202 single-cell clusters across 19 human organs using data from Human Protein Atlas and made these available in the web portal Metabolic Atlas, thereby providing a valuable resource to the scientific community. With the ever-increasing availability of single-cell RNA-Seq datasets and continuously improved GEMs, their combination holds promise to become an important approach in the study of human metabolism.

Optimization and application of passive air sampling method for gaseous elemental mercury in Ulsan, South Korea

We compared uptake rates and concentrations of gaseous elemental mercury (GEM) by passive sampling conditions and investigated the spatial distribution of GEM in Ulsan, the largest industrial city in South Korea. For the optimization of sampling conditions, two outer sampling containers (cylindrical polyethylene terephthalate and two stainless steel bowls), two different sulfur contents of the sorbent (16.3% and 26.3%), and three sampling periods (1, 2, and 3 months) were considered. The uptake rates of GEM were not statistically different by the sampling container, but they were increased with the sulfur contents of activated carbon. A sampling condition using two stainless bowls and lower sulfur contents of activated carbon for 2-3 months was preferred with the highest precision of GEM concentrations. With the same method, passive air samples were collected for 3 months in duplicate from 10 sites in Ulsan. The concentrations of GEM ranged from 3.13 to 11.2 ng/m³ (mean 4.65 ng/m³), and the highest concentration was measured at a non-ferrous industrial complex. A zinc smelter in the non-ferrous industrial complex was identified as a major mercury source in Ulsan. This study is the first passive air sampling study investigating the spatial distributions of GEM in different types of industrial areas as well as residential areas of Ulsan.

A bacterium-like particle vaccine displaying Zika virus prM-E induces systemic immune responses in mice

The emergence of Zika virus (ZIKV) infection, which is unexpectedly associated with congenital defects, has prompted the development of safe and effective vaccines. The Gram-positive enhancer matrix-protein anchor (GEM-PA) display system has emerged as a versatile and highly effective platform for delivering target proteins in vaccines. In this study, we developed a bacterium-like particle vaccine, ZI-△-PA-GEM, based on the GEM-PA system. The fusion protein ZI-△-PA, which contains the prM-E-△TM protein of ZIKV (with a stem-transmembrane region deletion) and the protein anchor PA3, was expressed. The fusion protein was successfully displayed on the GEM surface to form ZI-△-PA-GEM. Moreover, the intramuscular immunization of BALB/c mice with ZI-△-PA-GEM combined with ISA 201 VG and poly(I:C) adjuvants induced durable ZIKV-specific IgG and protective neutralizing antibody responses. Potent B-cell/DC activation was also stimulated early after immunization. Notable, splenocyte proliferation, the secretion of multiple cytokines, T/B-cell activation and central memory T-cell responses were elicited. These data indicate that ZI-△-PA-GEM is a promising bacterium-like particle vaccine candidate for ZIKV.

Continuous and near real-time measurements of gaseous elemental mercury (GEM) from an Unmanned Aerial Vehicle: A new approach to investigate the 3D distribution of GEM in the lower atmosphere

We present the first real attempt to directly and continuously measure GEM through a Lumex RA-915 M, designed for real-time detection of mercury vapor, mounted on an UAV (Unmanned Aerial Vehicle, namely a heavy-lift octocopter), inside and outside the former Hg-mining area of Abbadia San Salvatore (Mt. Amiata, Italy), known as a GEM source. We tested the effectiveness of the UAV-Lumex combination at different heights in selected sites pertaining to both mining facilities and surrounding urban zones, shedding light on the GEM spatial distribution and concentration variability. The Lumex great sensitivity and the octocopter optimal versatility and maneuverability, both horizontally and vertically, allowed to depict the GEM distribution in the atmosphere up to 60 m above the ground. The acquisition system was further optimized by: i) synchronizing Lumex and UAV GPS data by means of a stand-alone GPS that was previously synchronized with Lumex; ii) using a vertical sampling tube (1.20 m high) connected to the Lumex inlet to overcome the rotors strong airflows and turbulence that would have affected GEM measurements; iii) supplying the octocopter with batteries for power supply to avoid the release of exhaust gases; iv) taking the advantage of the UAV ability to land in small spaces and stop at selected altitudes. The resulting dot-map graphical representations, providing a realistic 3D picture of GEM vertical profiling during the flights in near real-time, were useful to verify whether the guideline concentrations indicated by competent authorities were exceeded. The results showed that the GEM concentrations in the urban area, located a few hundred meters from the mining structures, and close to already reclaimed areas remained at relatively low values. Contrarily, GEM contents showed significant variations and the highest concentrations above the facilities containing the old furnaces, where increasing GEM concentrations were recorded at decreasing heights or downwind.

Chronic exposure to volcanic gaseous elemental mercury: using wild Mus musculus to unveil its uptake and fate

Volcanoes are a natural source of gaseous elemental mercury (GEM) (Hg⁰). Monitoring GEM releases of volcanic origin has been widely studied; however, few studies have been performed about the biomonitoring of species exposed to GEM, rendering an unknown risk to the worldwide populations living in the vicinity of an active volcano. In this pilot study, we used Mus musculus as a bioindicator species to understand to what extent lungs are the main route of mercury uptake in populations chronically exposed to active volcanic environments. Autometallographic silver protocol was used to detect mercury deposits in the histological lung slides. Abundant mercury deposits were found in the lungs of specimens captured at the site with volcanic activity (Furnas Village, S. Miguel Island-Azores). The presence of mercury in the lungs could represent not only hazardous effects to the lung itself but also to other tissues and organs, such as brain and kidneys. This study confirms that the main uptake route for GEM is the lungs and that, even at very low concentrations in the environment, a chronic exposure to Hg⁰ results in its bioaccumulation in the lung tissue. These results reinforce that biomonitoring studies should be combined with monitoring classical approaches in order to better characterize the risks of exposure to Hg⁰ in volcanic environments.

Gaseous Elemental Mercury (GEM) in the Mexico City Metropolitan Area

This paper presents atmospheric gaseous elemental mercury (GEM) data recorded during two short-term monitoring surveys in the Mexico City Metropolitan Area (MCMA) at 12th May 2019 and at 22nd May 2020, during conditions of low and high human activity respectively. Results, although they are limited, can be considered as the representative range of exposure to GEM of the inhabitants of MCMA; differences in results reveal the impact of human activities on GEM background levels (2.53 and 3.76 ng m^-3, respectively). GEM concentrations and their spatial distribution does not allow for the identification of important industrial sources and do not reach intervention pollution levels. The activity of the Popocatépetl volcano is not likely to have an effect on GEM in the MCMA. In spite the evident decrease in GEM concentrations compared with data previously reported, monitoring must be carried out routinely given Mexico's participation in the Minamata Convention on Mercury.

Analyzing Metabolic States of Adipogenic and Osteogenic Differentiation in Human Mesenchymal Stem Cells via Genome Scale Metabolic Model Reconstruction

Since their initial discovery in 1976, mesenchymal stem cells (MSCs) have been gathering interest as a possible tool to further the development and enhancement of various therapeutics within regenerative medicine. However, our current understanding of both metabolic function and existing differences within the varying cell lineages (e.g., cells in either osteogenesis or adipogenesis) is severely lacking making it more difficult to fully realize the therapeutic potential of MSCs. Here, we reconstruct the MSC metabolic network to understand the activity of various metabolic pathways and compare their usage under different conditions and use these models to perform experimental design. We present three new genome-scale metabolic models (GEMs) each representing a different MSC lineage (proliferation, osteogenesis, and adipogenesis) that are biologically feasible and have distinctive cell lineage characteristics that can be used to explore metabolic function and increase our understanding of these phenotypes. We present the most distinctive differences between these lineages when it comes to enriched metabolic subsystems and propose a possible osteogenic enhancer. Taken together, we hope these mechanistic models will aid in the understanding and therapeutic potential of MSCs.

Listening to student voice-understanding student and faculty experience at two UK graduate entry programmes

CONTEXT

Shortage of physicians in the UK has been a long-standing issue. Graduate entry medicine (GEM) may offer a second point of entry for potential doctors. However, the challenges of developing and implementing these programmes are still unrecognised. This small-scale study aimed to briefly explore the opportunities and challenges facing students at two UK GEM programmes.

METHODS

Two case studies were conducted at Imperial College and Scotland's GEM (ScotGEM) and used a triangulated qualitative approach via semi-structured and elite interviews. Data analysis, informed by grounded theory, applied thematic and force-field analysis in an empirical approach to generate evidence and instrumental interpretations for Higher Education Institutions.

RESULTS

Although GEM forms an opportunity for graduates to enter medicine, the different drivers of each programme were key in determining entry requirements and challenges experienced by postgraduates. Three key dilemmas seem to influence the experiences of learners in GEM programmes: (a) postgraduate identity and the everchanging sense-of-self; (b)self-directed and self-regulated learning skills, and (c) servicescape, management and marketing concepts.

CONCLUSIONS

Graduate entry programmes may support policy makers and faculty to fill the workforce gap of healthcare professionals. However, their successful implementation requires careful considerations to the needs of graduates to harness their creativity, resilience and professional development as future healthcare workers.

Development and characterization of optical readout well-type glass gas electron multiplier for dose imaging in clinical carbon beams

The use of carbon ion beams in cancer therapy (also known as hadron therapy) is steadily growing worldwide; therefore, the demand for more efficient dosimetry systems is also increasing because daily quality assurance (QA) measurements of hadron radiotherapy is one of the most complex and time consuming tasks. The aim of this study is to develop a two-dimensional dosimetry system that offers high spatial resolution, a large field of view, quick data response, and a linear dose-response relationship. We demonstrate the dose imaging performance of a novel digital dose imager using carbon ion beams for hadron therapy. The dose imager is based on a newly-developed gaseous detector, a well-type glass gas electron multiplier. The imager is successfully operated in a hadron therapy facility with clinical intensity beams for radiotherapy. It features a high spatial resolution of less than 1 mm and an almost linear dose-response relationship with no saturation and very low linear-energy-transfer dependence. Experimental results show that the dose imager has the potential to improve dosimetry accuracy for daily QA.

Common Transcriptional Program of Liver Fibrosis in Mouse Genetic Models and Humans

Multifactorial metabolic diseases, such as non-alcoholic fatty liver disease, are a major burden to modern societies, and frequently present with no clearly defined molecular biomarkers. Herein we used system medicine approaches to decipher signatures of liver fibrosis in mouse models with malfunction in genes from unrelated biological pathways: cholesterol synthesis-Cyp51, notch signaling-Rbpj, nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling-Ikbkg, and unknown lysosomal pathway-Glmp. Enrichment analyses of Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome and TRANScription FACtor (TRANSFAC) databases complemented with genome-scale metabolic modeling revealed fibrotic signatures highly similar to liver pathologies in humans. The diverse genetic models of liver fibrosis exposed a common transcriptional program with activated estrogen receptor alpha (ERα) signaling, and a network of interactions between regulators of lipid metabolism and transcription factors from cancer pathways and the immune system. The novel hallmarks of fibrosis are downregulated lipid pathways, including fatty acid, bile acid, and steroid hormone metabolism. Moreover, distinct metabolic subtypes of liver fibrosis were proposed, supported by unique enrichment of transcription factors based on the type of insult, disease stage, or potentially, also sex. The discovered novel features of multifactorial liver fibrotic pathologies could aid also in improved stratification of other fibrosis related pathologies.

Extracting the GEMs: Genotype, Environment, and Microbiome Interactions Shaping Host Phenotypes

One of the fundamental tenets of biology is that the phenotype of an organism (Y) is determined by its genotype (G), the environment (E), and their interaction (GE). Quantitative phenotypes can then be modeled as Y = G + E + GE + e, where e is the biological variance. This simple and tractable model has long served as the basis for studies investigating the heritability of traits and decomposing the variability in fitness. The importance and contribution of microbe interactions to a given host phenotype is largely unclear, nor how this relates to the traditional GE model. Here we address this fundamental question and propose an expansion of the original model, referred to as GEM, which explicitly incorporates the contribution of the microbiome (M) to the host phenotype, while maintaining the simplicity and tractability of the original GE model. We show that by keeping host, environment, and microbiome as separate but interacting variables, the GEM model can capture the nuanced ecological interactions between these variables. Finally, we demonstrate with an in vitro experiment how the GEM model can be used to statistically disentangle the relative contributions of each component on specific host phenotypes.

The COL11A1/Akt/CREB signaling axis enables mitochondrial-mediated apoptotic evasion to promote chemoresistance in pancreatic cancer cells through modulating BAX/BCL-2 function

Collagen XI, a member of the collagen family, is present in the extracellular matrix (ECM), and high collagen XI/αI (COL11A1) expression in tumor tissue is reportedly correlated with the clinicopathological parameters of pancreatic ductal adenocarcinoma (PDAC). However, the function of COL11A1 in the development of pancreatic cancer cells remains unclear. In the current study, we assessed mRNA expression of COL11A1 and its receptors and created a testing-model of both a COL11A1-overexpressing tumor microenvironment and/or altered-COL11A1 expression in pancreatic cancer cell lines. Next, we investigated the mechanism by which COL11A1 affects growth, gemcitabine (GEM) resistance and apoptosis in pancreatic cancer cells. We demonstrated that COL11A1 phosphorylated Akt^Ser473, promoting proliferation of cancer cells and inhibiting their apoptosis. Additionally, our data showed that COL11A1/Akt/CREB altered the balance between BCL-2 and BAX and mediated their mitochondrial translocation in pancreatic cancer cells. The COL11A1/Akt axis induced disruption of mitochondrial transmembrane function, enabling mitochondria-mediated apoptotic evasion to promote chemoresistance. We also explored the regulatory effect of COL11A1/Akt on molecular signaling in the mitochondria-mediated apoptotic program. COL11A1/Akt disturbed the BCL-2/BAX balance, inhibiting cytochrome c (Cyt-C) release and binding of Apaf-1/procaspase-9/Cyt-C, which suppressed the apoptotic program and induced GEM resistance in pancreatic cancer cells. In conclusion, COL11A1 modulates apoptotic inhibition and chemoresistance in pancreatic cancer cells by activating the Akt/CREB/BCL-2/BAX signaling pathway. COL11A1 may represent a distinct prognostic indicator and may be an attractive therapeutic target for PDAC.

Evaluation of possible impact on human health of atmospheric mercury emanations from the Popocatépetl volcano

The contribution of Hg from volcanic emanations is decisive for assessing global mercury emissions given the impact of this highly toxic contaminant on human health and ecosystems. Atmospheric Hg emissions from Popocatépetl volcano and their dispersion were evaluated carrying out two gaseous elemental mercury (GEM) surveys during a period of intense volcanic activity. Continuous GEM measurements were taken for 24 h using a portable mercury vapor analyzer (Lumex RA-915M) at the Altzomoni Atmospheric Observatory (AAO), 11 km from the crater. In addition, a long-distance survey to measure GEM was conducted during an automobile transect around the volcano, covering a distance of 129 km. The evaluation of the GEM data registered in the fixed location showed that heightened volcanic activity clearly intensifies the concentration of atmospheric Hg, extreme values around 5 ng m^-3. Highest concentrations of GEM recorded during the mobile survey were about 10 ng m^-3. In both surveys, the recorded concentrations during most of the measurement time were below 2 ng m^-3, but measurements were taken at a considerable distance from the crater, and GEM is subject to dilution processes. During both surveys, recorded GEM did not exceed the 200 ng m^-3 concentration recommended by the WHO (Air quality guidelines for Europe, 2000) as the regulatory limits for Hg in the atmospheric environment for long-term inhalation. Because this study was carried out in inhabited areas around the volcano during a period of intense volcanic activity, it can be concluded that the Popocatépetl does not represent a risk to human health in terms of Hg.

Expression profile analysis to predict potential biomarkers for glaucoma: BMP1, DMD and GEM

Purpose

Glaucoma is the second commonest cause of blindness. We assessed the gene expression profile of astrocytes in the optic nerve head to identify possible prognostic biomarkers for glaucoma.

Method

A total of 20 patient and nine normal control subject samples were derived from the GSE9944 (six normal samples and 13 patient samples) and GSE2378 (three normal samples and seven patient samples) datasets, screened by microarray-tested optic nerve head tissues, were obtained from the Gene Expression Omnibus (GEO) database. We used a weighted gene coexpression network analysis (WGCNA) to identify coexpressed gene modules. We also performed a functional enrichment analysis and least absolute shrinkage and selection operator (LASSO) regression analysis. Genes expression was represented by boxplots, functional geneset enrichment analyses (GSEA) were used to profile the expression patterns of all the key genes. Then the key genes were validated by the external dataset.

Results

A total 8,606 genes and 19 human optic nerve head samples taken from glaucoma patients in the GSE9944 were compared with normal control samples to construct the co-expression gene modules. After selecting the most common clinical traits of glaucoma, their association with gene expression was established, which sorted two modules showing greatest correlations. One with the correlation coefficient is 0.56 (P = 0.01) and the other with the correlation coefficient is −0.56 (P = 0.01). Hub genes of these modules were identified using scatterplots of gene significance versus module membership. A functional enrichment analysis showed that the former module was mainly enriched in genes involved in cellular inflammation and injury, whereas the latter was mainly enriched in genes involved in tissue homeostasis and physiological processes. This suggests that genes in the green–yellow module may play critical roles in the onset and development of glaucoma. A LASSO regression analysis identified three hub genes: Recombinant Bone Morphogenetic Protein 1 gene (BMP1), Duchenne muscular dystrophy gene (DMD) and mitogens induced GTP-binding protein gene (GEM). The expression levels of the three genes in the glaucoma group were significantly lower than those in the normal group. GSEA further illuminated that BMP1, DMD and GEM participated in the occurrence and development of some important metabolic progresses. Using the GSE2378 dataset, we confirmed the high validity of the model, with an area under the receiver operator characteristic curve of 85%.

Conclusion

We identified several key genes, including BMP1, DMD and GEM, that may be involved in the pathogenesis of glaucoma. Our results may help to determine the prognosis of glaucoma and/or to design gene- or molecule-targeted drugs.

Encapsulation of gemcitabine in RGD-modified nanoliposomes improves breast cancer inhibitory activity

In this study, RGD coated GEM liposomes were prepared by the emulsification-solvent evaporation method. The in vitro and in vivo characterizations were done to evaluate the feasibility of application. The mean particle size of the prepared liposomes was found to be 165.6 ± 15.7 nm. The entrapment efficiency and drug loading of the formulation were 82.4% ± 7.2% and 10.1% ± 1.4%, respectively. The liposomes were negatively charged with a zeta potential of -25.8 mV. The surface morphology of RGD-GEM liposomes was spherical and smooth. After three months of storage at different conditions, lyophilized liposomes appeared to be stable since they showed no collapse or contraction. The Weibull model was the most appropriate kinetic model for RGD-GEM liposomes, showing that the release of GEM from the liposomes was in the manners of both dissolution and diffusion. In vivo, the additive cytotoxicity of RGD-GEM-LPs in our study was caused by the presence of RGD which is more effective in the treatment of breast cancer devoid of toxicity to normal cells. Liposomes could also significantly extend the role of GEM in vivo and showed higher bioavailability than solution.

Paired-end mappability of transposable elements in the human genome

Though transposable elements make up around half of the human genome, the repetitive nature of their sequences makes it difficult to accurately align conventional sequencing reads. However, in light of new advances in sequencing technology, such as increased read length and paired-end libraries, these repetitive regions are now becoming easier to align to. This study investigates the mappability of transposable elements with 50 bp, 76 bp and 100 bp paired-end read libraries. With respect to those read lengths and allowing for 3 mismatches during alignment, over 68, 85, and 88% of all transposable elements in the RepeatMasker database are uniquely mappable, suggesting that accurate locus-specific mapping of older transposable elements is well within reach.

Consistency, Inconsistency, and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome-Scale Metabolic Modelling

Genome-scale metabolic models (GEMs) are manually curated repositories describing the metabolic capabilities of an organism. GEMs have been successfully used in different research areas, ranging from systems medicine to biotechnology. However, the different naming conventions (namespaces) of databases used to build GEMs limit model reusability and prevent the integration of existing models. This problem is known in the GEM community, but its extent has not been analyzed in depth. In this study, we investigate the name ambiguity and the multiplicity of non-systematic identifiers and we highlight the (in)consistency in their use in 11 biochemical databases of biochemical reactions and the problems that arise when mapping between different namespaces and databases. We found that such inconsistencies can be as high as 83.1%, thus emphasizing the need for strategies to deal with these issues. Currently, manual verification of the mappings appears to be the only solution to remove inconsistencies when combining models. Finally, we discuss several possible approaches to facilitate (future) unambiguous mapping.

Molecular characterization of GTP binding protein overexpressed in skeletal muscle (GEM) and its role in promoting adipogenesis in goat intramuscular preadipocytes

GTP binding protein overexpressed in skeletal muscle (GEM) is an important gene with many functions, such as regulating the rearrangement of cytoskeleton and the activity of voltage-dependent calcium channel, and GEM was regarded as a candidate gene for obesity. However, little investigation has been carried out to explore whether GEM affected the intramuscular fat (IMF) deposition of goat. To explore the role of GEM gene in goat, this gene was cloned and its tissue and temporal expression profile were detected. Effect of GEM on adipogenesis was examined by losing function of GEM in vitro. Thereafter, several lipid metabolism-related genes were examined, including CCAAT/enhancing-binding protein α (C/EBPα), CCAAT/enhancing-binding protein β (C/EBPβ), lipoprotein lipase (LPL), preadipocyte factor 1 (Pref-1), peroxisome proliferator activated receptor γ (PPARγ) and sterol regulatory element binding protein 1 (SREBP1). We found that the goat GEM gene consisted of 936 bp, which encoded a protein of 311 amino acids. The expression of GEM was higher in spleen, lung and large intestine and it appeared sharp in the interim stage of differentiation. Furthermore, GEM knockdown blocked adipogenesis and the expression of C/EBPα, C/EBPβ, LPL, PPARγ and SREBP1. These results indicated that GEM might promote lipid accumulation and adipogenesis.

AMPK-related kinase 5 (ARK5) enhances gemcitabine resistance in pancreatic carcinoma by inducing epithelial-mesenchymal transition

AMPK-related kinase 5 (ARK5) is a member of the human AMP-activated protein kinase (AMPK) family, which is associated with increased tumor survival and drug resistance in many cancers. However, the function of ARK5 in pancreatic carcinoma (PC) is unclear. Our study investigated the role of ARK5 in the chemo-resistance of PC and its underlying mechanism. PC cell lines that displayed high expression levels of ARK5 had low sensitivity to gemcitabine (GEM). Suppression of ARK5 increased sensitivity to GEM in PC cell lines. Western blotting and immunofluorescence showed that suppression of ARK5 upregulated expression of E-cadherin and downregulated vimentin expression. Suppression of ARK5 also inhibited the epithelial-mesenchymal transition (EMT) efficiency associated with GEM in PC cell lines and upregulation of ARK5 expression enhanced GEM resistance in PC cell lines by inducing Twist-mediated EMT. In addition, we found that suppression of ARK5 increased GEM sensitivity in PC cell lines under hypoxic conditions. ARK5 increases GEM resistance in PC cell lines via EMT, and suppression of ARK5 increases sensitivity to GEM under both normoxic and hypoxic conditions.

Carrier-free Janus nano-prodrug based on camptothecin and gemcitabine: Reduction-triggered drug release and synergistic in vitro antiproliferative effect in multiple cancer cells

A carrier-free and reduction-degradable Janus prodrug, termed as CPT-SS-GEM, was fabricated by redox-sensitive disulfide bond linked gemcitabine and camptothecin. This amphiphilic prodrug showed high drug loading capacity, 42.6% of CPT and 32.2% of GEM, respectively. Benefiting from its amphiphilic property, CPT-SS-GEM prodrug could self-assemble into Janus nano-prodrug in water without aid of any excipient. The morphology of the nano-prodrug was spherical particle confirmed by TEM. The rapid drug release from the nano-prodrug proceeded in a reduction-dependent manner, more than 90% of the native CPT and GEM were released in the mimic microenvironment of tumor cells (pH 6.5 PBS containing 2 mM DTT) within a period of 3 h. The concurrent and ratio-metric release of CPT and GEM endowed the Janus nano-prodrug CPT-SS-GEM with pronounced in vitro synergistic antiproliferative effect in multiple cancer cell lines when the inhibition rate of cancer cell proliferation exceeded 50%, including A549, NCI-H460, HCT116, HT-29, and MCF-7/ADR. The combination index values showed as followings, 1.04-0.4 (A549), 0.24-0.60 (NCI-H460), 0.42-0.16 (HCT116), 1.98-0.15 (HT-29), 0.36-0.19 (MCF-7/ADR). Taken together, the carrier-free, redox-sensitive Janus nano-prodrug CPT-SS-GEM is a promising candidate as synergistic combination of chemotherapeutics.

Transgenic Mouse Models of Tumor Virus Action

Genetically engineered mice (GEMs) have provided valuable insights into the carcinogenic properties of various human tumor viruses, which, in aggregate, are etiologically associated with over 15% of all human cancers. This review provides an overview of seminal discoveries made through the use of GEM models for human DNA tumor viruses. Emphasis is placed on the discoveries made in the study of human papillomaviruses, Merkel cell carcinoma-associated polyomavirus, Epstein-Barr virus, and Kaposi's sarcoma-associated herpesvirus, because GEMs have contributed extensively to our understanding of how these DNA tumor viruses directly contribute to human cancers.

Associative transcriptomics study dissects the genetic architecture of seed glucosinolate content in Brassica napus

Breeding new varieties with low seed glucosinolate (GS) concentrations has long been a prime target in Brassica napus. In this study, a novel association mapping methodology termed 'associative transcriptomics' (AT) was applied to a panel of 101 B. napus lines to define genetic regions and also candidate genes controlling total seed GS contents. Over 100,000 informative single-nucleotide polymorphisms (SNPs) and gene expression markers (GEMs) were developed for AT analysis, which led to the identification of 10 SNP and 7 GEM association peaks. Within these peaks, 26 genes were inferred to be involved in GS biosynthesis. A weighted gene co-expression network analysis provided additional 40 candidate genes. The transcript abundance in leaves of two candidate genes, BnaA.GTR2a located on chromosome A2 and BnaC.HAG3b on C9, was correlated with seed GS content, explaining 18.8 and 16.8% of phenotypic variation, respectively. Resequencing of genomic regions revealed six new SNPs in BnaA.GTR2a and four insertions or deletions in BnaC.HAG3b. These deletion polymorphisms were then successfully converted into polymerase chain reaction-based diagnostic markers that can, due to high linkage disequilibrium observed in these regions of the genome, be used for marker-assisted breeding for low seed GS lines.

Comparison of the GEM and the ECAL indirect calorimeters against the Deltatrac for measures of RMR and diet-induced thermogenesis

The Deltatrac™ II Metabolic Monitor (Datex-Ohmeda Inc.) is considered the standard reference machine in indirect calorimetry; however, it is no longer commercially available thus there is a need for new machines. The gas exchange measurement (GEM; GEM Nutrition Ltd) and the ECAL (Health Professional Solutions) are alternative measuring systems. The aim of this study was to compare the ECAL and GEM with Deltatrac for measures of RMR and the GEM to the Deltatrac for measures of diet-induced thermogenesis (DIT). Twenty healthy participants were tested on test day 1 (T1) and test day 2 (T2). RMR was measured in a randomised order for 30 min on the Deltatrac, the GEM and the ECAL. Following this, a 1553 kJ meal was consumed and DIT was measured on the Deltatrac and the GEM in alternating 15 min intervals for 4 h. The GEM reported consistently higher values than the Deltatrac for VO2, VCO2, RMR and fat oxidation (P < 0·005). The ECAL was significantly higher than the Deltatrac for measures of VO2, RMR, carbohydrate oxidation (T2) and respiratory quotient and fat oxidation (T1, T2) (P < 0·05). There were no significant differences within repeated RMR measures on the ECAL, the GEM or the Deltatrac. DIT measures were consistently higher on the GEM (T1) (P < 0·005); however, there were no significant differences between repeated measures. The findings suggest that while the GEM and the ECAL were not accurate alternatives to the Deltatrac, they may be reliable for repeated measures.

Model based engineering of Pichia pastoris central metabolism enhances recombinant protein production

The production of recombinant proteins is frequently enhanced at the levels of transcription, codon usage, protein folding and secretion. Overproduction of heterologous proteins, however, also directly affects the primary metabolism of the producing cells. By incorporation of the production of a heterologous protein into a genome scale metabolic model of the yeast Pichia pastoris, the effects of overproduction were simulated and gene targets for deletion or overexpression for enhanced productivity were predicted. Overexpression targets were localized in the pentose phosphate pathway and the TCA cycle, while knockout targets were found in several branch points of glycolysis. Five out of 9 tested targets led to an enhanced production of cytosolic human superoxide dismutase (hSOD). Expression of bacterial β-glucuronidase could be enhanced as well by most of the same genetic modifications. Beneficial mutations were mainly related to reduction of the NADP/H pool and the deletion of fermentative pathways. Overexpression of the hSOD gene itself had a strong impact on intracellular fluxes, most of which changed in the same direction as predicted by the model. In vivo fluxes changed in the same direction as predicted to improve hSOD production. Genome scale metabolic modeling is shown to predict overexpression and deletion mutants which enhance recombinant protein production with high accuracy.

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Recombinant protein production in P. pastoris affects the central metabolism.

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A genome scale metabolic model can predict these metabolic flux changes.

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Mutations in central metabolic genes enhanced recombinant protein yield up to 40%.

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These beneficial mutations were predicted by the metabolic model with high accuracy.

Study of solid-conversion gaseous detector based on GEM for high energy X-ray industrial CT

The general gaseous ionization detectors are not suitable for high energy X-ray industrial computed tomography (HEICT) because of their inherent limitations, especially low detective efficiency and large volume. The goal of this study was to investigate a new type of gaseous detector to solve these problems. The novel detector was made by a metal foil as X-ray convertor to improve the conversion efficiency, and the Gas Electron Multiplier (hereinafter "GEM") was used as electron amplifier to lessen its volume. The detective mechanism and signal formation of the detector was discussed in detail. The conversion efficiency was calculated by using EGSnrc Monte Carlo code, and the transport course of photon and secondary electron avalanche in the detector was simulated with the Maxwell and Garfield codes. The result indicated that this detector has higher conversion efficiency as well as less volume. Theoretically this kind of detector could be a perfect candidate for replacing the conventional detector in HEICT.

Carbon nanotubes for delivery of small molecule drugs

In the realm of drug delivery, carbon nanotubes (CNTs) have gained tremendous attention as promising nanocarriers, owing to their distinct characteristics, such as high surface area, enhanced cellular uptake and the possibility to be easily conjugated with many therapeutics, including both small molecules and biologics, displaying superior efficacy, enhanced specificity and diminished side effects. While most CNT-based drug delivery system (DDS) had been engineered to combat cancers, there are also emerging reports that employ CNTs as either the main carrier or adjunct material for the delivery of various non-anticancer drugs. In this review, the delivery of small molecule drugs is expounded, with special attention paid to the current progress of in vitro and in vivo research involving CNT-based DDSs, before finally concluding with some consideration on inevitable complications that hamper successful disease intervention with CNTs.

Pharmaceuticals and personal care products in the aquatic environment in China: a review

Pharmaceuticals and personal care products (PPCPs) have been detected as contaminants of emerging concern ubiquitously in the aquatic environment in China and worldwide. A clear picture of PPCP contamination in the Chinese aquatic environment is needed to gain insight for both research and regulatory needs (e.g. monitoring, control and management). The occurrence data of 112 PPCPs in waters and sediments in China has been reviewed. In most cases, the detected concentration of these PPCPs in waters and sediments were at ng/L and ng/g levels, which were lower than or comparable to those reported worldwide. A screening level risk assessment (SLERA) identified six priority PPCPs in surface waters, namely erythromycin, roxithromycin, diclofenac, ibuprofen, salicylic acid and sulfamethoxazole. The results of SLERA also revealed that the hot spots for PPCP pollution were those river waters affected by the megacities with high density of population, such as Beijing, Tianjin, Guangzhou and Shanghai. Limitations of current researches and implications for future research in China were discussed. Some regulatory issues were also addressed.

Genes alternations with exposure time of environmental factors

A theoretical model discussing the environmental factors (EFs) effect of exposure time on genes, which leads to human diseases, is presented using multi-logistic model. The advantages and limitations of this model are discussed in terms of its usefulness for simulating genetic samples. It has been shown that EFs affect genes with the same degree both at high exposure level, low exposure time and at low exposure level, high exposure time.

The impact of intravesical gemcitabine and 1/3 dose Bacillus Calmette-Guérin instillation therapy on the quality of life in patients with nonmuscle invasive bladder cancer: results of a prospective, randomized, phase II trial

PURPOSE

Bacillus Calmette-Guérin and intravesical chemotherapy represent viable adjuvant options for intermediate risk nonmuscle invasive bladder cancer. Although bacillus Calmette-Guérin is perceived as less tolerable than intravesical chemotherapy, to our knowledge no comparative studies have addressed quality of life issues. We compared the quality of life of patients with nonmuscle invasive bladder cancer who received adjuvant intravesical gemcitabine or 1/3 dose bacillus Calmette-Guérin.

MATERIALS AND METHODS

Our multicenter, prospective, randomized, phase II study included 120 patients with intermediate risk nonmuscle invasive bladder cancer. Of these patients 88 remained assessable at 1-year followup. Only 1 patient was withdrawn because of adverse events. Overall 61 patients received 2,000 mg/50 cc gemcitabine weekly for 6 weeks (maintenance monthly for 1 year) while 59 received 1/3 dose bacillus Calmette-Guérin Connaught weekly for 6 weeks (maintenance 3 weekly instillations at 3, 6 and 12 months). Quality of life was measured by the EORTC QLQ-C30 (European Organization for the Research and Treatment of Cancer Quality of Life Questionnaire Core 30 version 3.0) and QLQ-BLS24 (Quality of Life Superficial Bladder Cancer-Specific 24) questionnaires. Group differences were calculated using ANOVA (ANOVA/MANOVA).

RESULTS

Treatment was well tolerated in both groups, although local and systemic side effects were more frequently reported in the bacillus Calmette-Guérin arm. Multivariate analyses showed no significant differences between the 2 groups in all quality of life dimensions. No significant changes over time in quality of life domains were detected for patients on bacillus Calmette-Guérin and gemcitabine except for physical functioning, which decreased significantly in both groups (p = 0.002). No significant differences were detected in terms of recurrence and progression between the 2 groups at 1-year followup.

CONCLUSIONS

While a higher rate of side effects, albeit mild to moderate, was detected with 1/3 dose bacillus Calmette-Guérin compared to gemcitabine, our study failed to show significant differences between the 2 drugs in terms of quality of life.

GEM, a Novel Factor in the Coordination of Cell Division to Cell Fate Decisions in the Arabidopsis Epidermis

Cell division and cell fate decisions are highly regulated processes that need to be coordinated both spatially and temporally for correct plant growth and development. Gaining a deeper molecular and cellular understanding of these links is especially relevant for plant biology since, unlike in animals, formation of new organs is a process that takes place after embryogenesis and continues throughout the entire plant lifespan. The recent identification of a novel factor, GEM, has provided a molecular framework that coordinates cell division to cell fate in the Arabidopsis epidermis. GEM is an inhibitor of cell division through interacting with CDT1, a DNA replication protein. It also inhibits the expression of the homeobox GLABRA2 (GL2) gene that determines the hair/non-hair fate and the pavement/trichome fate in the root and leaf epidermis, respectively. GEM seems to be crucial in controlling the balance of activating/repressing histone modifications at its target promoters.