Predicting drug activity against cancer through genomic profiles and SMILES

Due to the constant increase in cancer rates, the disease has become a leading cause of death worldwide, enhancing the need for its detection and treatment. In the era of personalized medicine, the main goal is to incorporate individual variability in order to choose more precisely which therapy and prevention strategies suit each person. However, predicting the sensitivity of tumors to anticancer treatments remains a challenge. In this work, we propose two deep neural network models to predict the impact of anticancer drugs in tumors through the half-maximal inhibitory concentration (IC50). These models join biological and chemical data to apprehend relevant features of the genetic profile and the drug compounds, respectively. In order to predict the drug response in cancer cell lines, this study employed different DL methods, resorting to Recurrent Neural Networks (RNNs) and Convolutional Neural Networks (CNNs). In the first stage, two autoencoders were pre-trained with high-dimensional gene expression and mutation data of tumors. Afterward, this genetic background is transferred to the prediction models that return the IC50 value that portrays the potency of a substance in inhibiting a cancer cell line. When comparing RSEM Expected counts and TPM as methods for displaying gene expression data, RSEM has been shown to perform better in deep models and CNNs model can obtain better insight in these types of data. Moreover, the obtained results reflect the effectiveness of the extracted deep representations in the prediction of the IC50 value that portrays the potency of a substance in inhibiting a tumor, achieving a performance of a mean squared error of 1.06 and surpassing previous state-of-the-art models.

Research Advances in the Role of the Tropomyosin Family in Cancer

Cancer is one of the most difficult diseases for human beings to overcome. Its development is closely related to a variety of factors, and its specific mechanisms have been a hot research topic in the field of scientific research. The tropomyosin family (Tpm) is a group of proteins closely related to the cytoskeleton and actin, and recent studies have shown that they play an important role in various cancers, participating in a variety of biological activities, including cell proliferation, invasion, and migration, and have been used as biomarkers for various cancers. The purpose of this review is to explore the research progress of the Tpm family in tumorigenesis development, focusing on the molecular pathways associated with them and their relevant activities involved in tumors. PubMed and Web of Science databases were searched for relevant studies on the role of Tpms in tumorigenesis and development and the activities of Tpms involved in tumors. Data from the literature suggest that the Tpm family is involved in tumor cell proliferation and growth, tumor cell invasion and migration, tumor angiogenesis, tumor cell apoptosis, and immune infiltration of the tumor microenvironment, among other correlations. It can be used as a potential biomarker for early diagnosis, follow-up, and therapeutic response of some tumors. The Tpm family is involved in cancer in a close relationship with miRNAs and LncRNAs. Tpms are involved in tumor tissue invasion and migration as a key link. On this basis, TPM is frequently used as a biomarker for various cancers. However, the specific molecular mechanism of its involvement in cancer progression has not been explained clearly, which remains an important direction for future research.

Relationship between lean manufacturing tools and their sustainable economic benefits

Traditionally, the isolated relationship of total preventive maintenance (TPM), quick setup (QS), overall equipment effectiveness (OEE), and one-piece flow (OPF) with economic sustainability (ESU) has been investigated; however, these lean manufacturing (LM) tools are implemented together into production systems, and traditional research does not report their relationships and interactions. To contribute to this gap, this paper integrates all those variables in a structural equation model (SEM), which are related by seven hypotheses that are validated using the partial least squares (PLS) technique using information from 176 responses to a questionnaire applied to the Mexican maquiladora industry. Additionally, a sensitivity analysis has been carried out to determine the probability of occurrence at high and low implementation levels for all variables when they occur in isolation, jointly and conditionally. Findings indicate that TPM is a precursor of QS and OEE, while QS is a precursor of OEE and OPF, OEE is a precursor of OPF and ESU, but also OPF is a precursor of ESU. The sensitivity analysis indicates that low levels of TPM are a risk for reaching adequate levels of OEE and QC, while low levels in OEE and OPF are a risk for reaching adequate ESU levels.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s00170-022-10208-0.

Annotation depth confounds direct comparison of gene expression across species

BACKGROUND

Comparisons of the molecular framework among organisms can be done on both structural and functional levels. One of the most common top-down approaches for functional comparisons is RNA sequencing. This estimation of organismal transcriptional responses is of interest for understanding evolution of molecular activity, which is used for answering a diversity of questions ranging from basic biology to pre-clinical species selection and translation. However, direct comparison between species is often hindered by evolutionary divergence in structure of molecular framework, as well as large difference in the depth of our understanding of the genetic background between humans and other species. Here, we focus on the latter. We attempt to understand how differences in transcriptome annotation affect direct gene abundance comparisons between species.

RESULTS

We examine and suggest some straightforward approaches for direct comparison given the current available tools and using a sample dataset from human, cynomolgus monkey, dog, rat and mouse with a common quantitation and normalization approach. In addition, we examine how variation in genome annotation depth and quality across species may affect these direct comparisons.

CONCLUSIONS

Our findings suggest that further efforts for better genome annotation or computational normalization tools may be of strong interest.

TPM, FPKM, or Normalized Counts? A Comparative Study of Quantification Measures for the Analysis of RNA-seq Data from the NCI Patient-Derived Models Repository

Background

In order to correctly decode phenotypic information from RNA-sequencing (RNA-seq) data, careful selection of the RNA-seq quantification measure is critical for inter-sample comparisons and for downstream analyses, such as differential gene expression between two or more conditions. Several methods have been proposed and continue to be used. However, a consensus has not been reached regarding the best gene expression quantification method for RNA-seq data analysis.

Methods

In the present study, we used replicate samples from each of 20 patient-derived xenograft (PDX) models spanning 15 tumor types, for a total of 61 human tumor xenograft samples available through the NCI patient-derived model repository (PDMR). We compared the reproducibility across replicate samples based on TPM (transcripts per million), FPKM (fragments per kilobase of transcript per million fragments mapped), and normalized counts using coefficient of variation, intraclass correlation coefficient, and cluster analysis.

Results

Our results revealed that hierarchical clustering on normalized count data tended to group replicate samples from the same PDX model together more accurately than TPM and FPKM data. Furthermore, normalized count data were observed to have the lowest median coefficient of variation (CV), and highest intraclass correlation (ICC) values across all replicate samples from the same model and for the same gene across all PDX models compared to TPM and FPKM data.

Conclusion

We provided compelling evidence for a preferred quantification measure to conduct downstream analyses of PDX RNA-seq data. To our knowledge, this is the first comparative study of RNA-seq data quantification measures conducted on PDX models, which are known to be inherently more variable than cell line models. Our findings are consistent with what others have shown for human tumors and cell lines and add further support to the thesis that normalized counts are the best choice for the analysis of RNA-seq data across samples.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12967-021-02936-w.

Complexity of gene paralogues resolved in biosynthetic pathway of hepatoprotective iridoid glycosides in a medicinal herb, Picrorhiza kurroa through differential NGS transcriptomes

Picrorhiza kurroa is a medicinal herb with diverse pharmacological applications due to the presence of iridoid glycosides, picroside-I (P-I), and picroside-II (P-II), among others. Any genetic improvement in this medicinal herb can only be undertaken if the biosynthetic pathway genes are correctly identified. Our previous studies have deciphered biosynthetic pathways for P-I and P-II, however, the occurrence of multiple copies of genes has been a stumbling block in their usage. Therefore, a methodological strategy was designed to identify and prioritize paralogues of pathway genes associated with contents of P-I and P-II. We used differential transcriptomes varying for P-I and P-II contents in different tissues of P. kurroa. All transcripts for a particular pathway gene were identified, clustered based on multiple sequence alignment to notify as a representative of the same gene (≥ 99% sequence identity) or a paralogue of the same gene. Further, individual paralogues were tested for their expression level via qRT-PCR in tissue-specific manner. In total 44 paralogues in 14 key genes have been identified out of which 19 gene paralogues showed the highest expression pattern via qRT-PCR. Overall analysis shortlisted 6 gene paralogues, PKHMGR3, PKPAL2, PKDXPS1, PK4CL2, PKG10H2 and PKIS2 that might be playing role in the biosynthesis of P-I and P-II, however, their functional analysis need to be further validated either through gene silencing or over-expression. The usefulness of this approach can be expanded to other non-model plant species for which transcriptome resources have been generated.

Effect of Different Crowding Agents on the Architectural Properties of the Bacterial Nucleoid-Associated Protein HU

HU is a nucleoid-associated protein expressed in most eubacteria at a high amount of copies (tens of thousands). The protein is believed to bind across the genome to organize and compact the DNA. Most of the studies on HU have been carried out in a simple in vitro system, and to what extent these observations can be extrapolated to a living cell is unclear. In this study, we investigate the DNA binding properties of HU under conditions approximating physiological ones. We report that these properties are influenced by both macromolecular crowding and salt conditions. We use three different crowding agents (blotting grade blocker (BGB), bovine serum albumin (BSA), and polyethylene glycol 8000 (PEG8000)) as well as two different MgCl₂ conditions to mimic the intracellular environment. Using tethered particle motion (TPM), we show that the transition between two binding regimes, compaction and extension of the HU protein, is strongly affected by crowding agents. Our observations suggest that magnesium ions enhance the compaction of HU–DNA and suppress filamentation, while BGB and BSA increase the local concentration of the HU protein by more than 4-fold. Moreover, BGB and BSA seem to suppress filament formation. On the other hand, PEG8000 is not a good crowding agent for concentrations above 9% (w/v), because it might interact with DNA, the protein, and/or surfaces. Together, these results reveal a complex interplay between the HU protein and the various crowding agents that should be taken into consideration when using crowding agents to mimic an in vivo system.

Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols

In recent years, RNA-sequencing (RNA-seq) has emerged as a powerful technology for transcriptome profiling. For a given gene, the number of mapped reads is not only dependent on its expression level and gene length, but also the sequencing depth. To normalize these dependencies, RPKM (reads per kilobase of transcript per million reads mapped) and TPM (transcripts per million) are used to measure gene or transcript expression levels. A common misconception is that RPKM and TPM values are already normalized, and thus should be comparable across samples or RNA-seq projects. However, RPKM and TPM represent the relative abundance of a transcript among a population of sequenced transcripts, and therefore depend on the composition of the RNA population in a sample. Quite often, it is reasonable to assume that total RNA concentration and distributions are very close across compared samples. Nevertheless, the sequenced RNA repertoires may differ significantly under different experimental conditions and/or across sequencing protocols; thus, the proportion of gene expression is not directly comparable in such cases. In this review, we illustrate typical scenarios in which RPKM and TPM are misused, unintentionally, and hope to raise scientists' awareness of this issue when comparing them across samples or different sequencing protocols.

Cryptographic Considerations for Automation and SCADA Systems Using Trusted Platform Modules

The increased number of cyber threats against the Supervisory Control and Data Acquisition (SCADA) and automation systems in the Industrial-Internet-of-Things (IIoT) and Industry 4.0 era has raised concerns in respect to the importance of securing critical infrastructures and manufacturing plants. The evolution towards interconnection and interoperability has expanded the vulnerabilities of these systems, especially in the context of the widely spread legacy standard protocols, by exposing the data to the outside network. After gaining access to the system data by launching a variety of attacks, an intruder can cause severe damage to the industrial process in place. Hence, this paper attempts to respond to the security issue caused by legacy structures using insecure communication protocols (e.g., Modbus TCP, DNP3, S7), presenting a different perspective focused on the capabilities of a trusted platform module (TPM). Furthermore, the intent is to assure the authenticity of the data transmitted between two entities on the same (horizontal interoperation) or different (vertical interoperation) hierarchical levels communicating through Modbus TCP protocol based on functionalities obtained by integrating trusted platform modules. From the experimental results perspective, the paper aims to show the advantages of integrating TPMs in automation/SCADA systems in terms of security. Two methods are proposed in order to assure the authenticity of the messages which are transmitted, respectively the study presents the measurements related to the increased time latency introduced due to the proposed concept.

Differential Effects of TPM, A Phosphorylated Tocopherol Mixture, and Other Tocopherol Derivatives as Excipients for Enhancing the Solubilization of Co-Enzyme Q10 as a Lipophilic Drug During Digestion of Lipid- Based Formulations

BACKGROUND

The tocopherol-based excipient, TPM, when incorporated into a medium-chain triglyceride (MCT)-based lipid formulation, has been previously shown to improve the solubilization of Coenzyme Q10 (CoQ10) during in vitro digestion which is strongly correlated with enhanced exposure in vivo.

METHODS

The current study aimed to gain further understanding of the MCT + TPM co-formulation, by assessing the formulation performance under fasted and fed in vitro digestion conditions, with different drug and excipient loading levels. Natural and synthetic-derived TPM were equivalent, and with d-α- tocopherol polyethylene glycol 1000 succinate (TPGS) outperformed other derivatives in enhancing the solubilisation of CoQ10 during digestion.

RESULT

Fed conditions significantly improved the solubility of CoQ10 during in vitro digestion of the formulation in comparison with fasted conditions. The addition of TPM at 10% (w/w) of the total MCT + TPM provided optimal performance in terms of CoQ10 solubilization during digestion.

CONCLUSION

The results further highlights the potential of TPM as an additive in lipid formulations to improve the solubilization and oral bioavailability of poorly water-soluble compounds.

Genotoxicity evaluation of tobacco and nicotine delivery products: Part One. Mouse lymphoma assay

Conduct of the mouse lymphoma assay (MLA) is underpinned by Organisation for Economic Co-operation and Development (OECD) Test Guideline 490 and International Conference on Harmonisation S2(R1) guidance and is a recognised in vitro genotoxicity test battery assay. It has been used on a limited number of occasions for the assessment of some tobacco and nicotine products, such as e-cigarettes and tobacco heating products (THP). The aim of this study was to assess the suitability of the MLA for genotoxicity testing with a variety of tobacco and nicotine products. Total particulate matter (TPM) from a 3R4F cigarette was compared against a commercial electronic cigarette liquid (e-liquid), electronic cigarette (e-cigarette) aerosol matter captured from the same e-liquid, and TPM from a commercial THP. Treatment conditions included 3 h exposures with and without metabolic activation and a longer 24 h exposure without metabolic activation (-S9) at concentrations up to 500 μg/mL. Under all treatment conditions, 3R4F produced a clear positive response with regard to induction of mutation. In contrast, no marked induction of mutation was observed for the e-liquid, e-cigarette aerosol or THP. Additionally, data are presented as a function of nicotine equivalents for comparisons between these different tobacco products and test matrices.

Genotoxicity evaluation of tobacco and nicotine delivery products: Part Two. In vitro micronucleus assay

In this study, a variety of test matrices from tobacco and nicotine delivery products were assessed against a 3R4F Kentucky reference cigarette using the in vitro micronucleus assay. Testing was conducted using two Chinese hamster cell lines (CHO and V79), and a human lymphoblastoid cell line (TK6), in accordance with established guidelines. Total particulate matter (TPM) from a 3R4F Reference cigarette was compared to an electronic cigarette e-liquid, electronic cigarette TPM and TPM from a commercial tobacco heating product using a standard and an extended treatment condition with recovery period. Cells were assessed with 3R4F TPM prior to assessment of the other tobacco and nicotine product test matrices. These cell lines gave varied responses to 3R4F TPM with the most robust response using V79 cells. The use of an extended exposure/recovery period was seen to increase assay sensitivity for CHO and V79 cell lines but was less clear for TK6 cells. Negative responses were observed for all products except 3R4F across all treatment conditions in V79 cells. The most potent response to cigarette smoke was following extended treatment with recovery, suggesting this may be a more appropriate treatment for the future assessment of tobacco and nicotine product test matrices.

Topical Topiramate Improves Wound Healing in an Animal Model of Hyperglycemia

Wound healing is severely affected in hyperglycemia and other metabolic conditions. Finding new therapeutic approaches that accelerate wound healing and improve the quality of the scar may reduce the morbidity commonly associated with skin lesions in diabetes. This study evaluated the effect of topical topiramate (TPM) on wound healing in C57 mice. Streptozotocin-induced hyperglycemic mice were subjected to a wound on the back and randomly allocated for treatment with either vehicle or topical TPM cream (2%) once a day for 14 days. Polymerase chain reaction, Western blotting, and microscopy were performed for the analysis. TPM improved wound healing (complete resolution at Day 10, 98% ± 5 for TPM vs. 81% ± 28 for vehicle), increased organization and deposition of collagen Type I, and enhanced the quality of the scars as determined by microscopy. In addition, TPM modulated the expression of cytokines and proteins of the insulin-signaling pathway: In early wound-healing stages, expression of interleukin-10, an anti-inflammatory marker, increased, whereas at the late phase, the pro-inflammatory markers tumor necrosis factor-α and monocyte chemoattractant protein-1 increased and there was increased expression of a vascular endothelial growth factor. Proteins of the insulin-signaling pathway were stimulated in the late wound-healing phase. Topical TPM improves the quality of wound healing in an animal model of hyperglycemia. The effect of TPM is accompanied by modulation of inflammatory and growth factors and proteins of the insulin-signaling pathway. Therefore, topical TPM presents as a potential therapeutic agent in skin wounds in patients with hyperglycemia.

Tropomyosins: Potential Biomarkers for Urothelial Bladder Cancer

Despite the incidence and prevalence of urothelial bladder cancer (UBC), few advances in treatment and diagnosis have been made in recent years. In this review, we discuss potential biomarker candidates: the tropomyosin family of genes, encoded by four loci in the human genome. The expression of these genes is tissue-specific. Tropomyosins are responsible for diverse cellular roles, most notably based upon their interplay with actin to maintain cellular processes, integrity and structure. Tropomyosins exhibit a large variety of splice forms, and altered isoform expression levels have been associated with cancer, including UBC. Notably, tropomyosin isoforms are detectable in urine, offering the potential for non-invasive diagnosis and risk-stratification. This review collates the basic knowledge on tropomyosin and its isoforms, and discusses their relationships with cancer-related phenomena, most specifically in UBC.

Suppression of Neutrophil Antimicrobial Functions by Total Particulate Matter From Cigarette Smoke

Chronic cigarette smoking is widely known to alter immune functions and compromise host defense against microbial infection. Neutrophils play an essential role in the immune defense against microbial pathogens and also participate in the development of the inflammatory responses. However, there is limited information about the effects of cigarette smoking on neutrophil response. In this study, cultured bone marrow neutrophils were exposed to total particulate matter (TPM) from cigarette smoke. We found that TPM not only reduced LPS-induced TNFα production, but also suppressed neutrophil bactericidal activity. We also observed that TPM priming reduced the expression of NADPH oxidase component gp91 and iNOS, molecules important for bacterial killing. Mechanistically, we documented that TPM-primed neutrophils have reduced STAT1 activation following subsequent LPS challenge. STAT1 is a key transcription factor responsible for the expression of inflammatory genes as well as gp91 and iNOS. Collectively, reduced STAT1 activation and reduced NADPH oxidase/iNOS may potentially explain the compromised anti-microbial function of TPM-programmed neutrophils. Taken together, our findings reveal that the key innate immune neutrophil is subject to reprogramming by smoking to adopt an immune-suppressed state, potentially responsible for chronic smoking-mediated immunosuppression.

Evaluation of flavourings potentially used in a heated tobacco product: Chemical analysis, in vitro mutagenicity, genotoxicity, cytotoxicity and in vitro tumour promoting activity

We designed a novel tobacco-heating product (THP) that heats tobacco to release nicotine and aerosolised components, such as glycerol and tobacco volatiles from a tobacco rod (Neostik). Heating tobacco significantly reduces levels of combustion-derived toxicants in the aerosol compared to cigarette smoke. This study was conducted to determine whether the inclusion of potential flavourings in the THP would add to the levels of toxicants in the emissions or alter in vitro responses. Levels of measured toxicants were similar in the flavoured and unflavoured Neostik emissions and significantly less than emissions from the reference cigarette, 3R4F. No mutagenicity was observed with the Neostiks in the Ames test or in the mouse lymphoma assay. There was evidence of a weak genotoxic response in the in vitro micronucleus test using V79 cells from both Neostiks and these responses were less than 3R4F. They did not show tumour-promoting potential in the Bhas 42 cell transformation assay and were not cytotoxic in the Neutral Red uptake assay. 3R4F elicited toxic responses in all assays at significantly lower concentrations. The addition of flavourings to the Neostik tested did not alter the chemical profile of THP emissions or change in vitro responses relative to the unflavoured Neostik.

Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

BACKGROUND

Current normalization methods for RNA-sequencing data allow either for intersample comparison to identify differentially expressed (DE) genes or for intrasample comparison for the discovery and validation of gene signatures. Most studies on optimization of normalization methods typically use simulated data to validate methodologies. We describe a new method, GeTMM, which allows for both inter- and intrasample analyses with the same normalized data set. We used actual (i.e. not simulated) RNA-seq data from 263 colon cancers (no biological replicates) and used the same read count data to compare GeTMM with the most commonly used normalization methods (i.e. TMM (used by edgeR), RLE (used by DESeq2) and TPM) with respect to distributions, effect of RNA quality, subtype-classification, recurrence score, recall of DE genes and correlation to RT-qPCR data.

RESULTS

We observed a clear benefit for GeTMM and TPM with regard to intrasample comparison while GeTMM performed similar to TMM and RLE normalized data in intersample comparisons. Regarding DE genes, recall was found comparable among the normalization methods, while GeTMM showed the lowest number of false-positive DE genes. Remarkably, we observed limited detrimental effects in samples with low RNA quality.

CONCLUSIONS

We show that GeTMM outperforms established methods with regard to intrasample comparison while performing equivalent with regard to intersample normalization using the same normalized data. These combined properties enhance the general usefulness of RNA-seq but also the comparability to the many array-based gene expression data in the public domain.

A new lipid excipient, phosphorylated tocopherol mixture, TPM enhances the solubilisation and oral bioavailability of poorly water soluble CoQ10 in a lipid formulation

Phosphorylated tocopherols are a new class of lipid excipients that have demonstrated potential in pharmaceutical applications. Their ability to solubilise poorly water soluble drugs indicates their potential utility in improving bioavailability of drugs where solubility limits their bioavailability. In this study a commercial mixture of phosphorylated tocopherols, TPM was combined with medium chain triglyceride (MCT) as a formulation for CoQ₁₀, and in vitro and in vivo performance compared to the effect of addition of alternative tocopherol-based excipients. In in vitro digestion experiments, CoQ₁₀ was poorly solubilised in the digesting MCT as anticipated. Addition of TPM facilitated the enhanced solubilisation of CoQ₁₀ as did vitamin E TPGS (TPGS). Other tocopherol derivatives (tocopherol acetate, tocopherol) were less effective at solubilising the active during the digestion process. The trends in in vitro solubilisation were conserved in the in vivo bioavailability of CoQ₁₀ after oral administration to rats, with TPM and TPGS formulations providing approximately double the exposure of MCT alone, while the addition of the other tocopherol derivatives reduced the overall exposure. Collectively, the results indicate potential of TPM as a new solubilising excipient for use in oral drug delivery for poorly water soluble drugs.

Tocopheryl phosphate mixture (TPM) as a novel lipid-based transdermal drug delivery carrier: formulation and evaluation

Transdermal drug delivery is a useful route of administration that avoids first-pass metabolism and more invasive delivery options. However, many drugs require enhancers to enable sufficient drug absorption to reach therapeutic effect. Alpha-tocopheryl phosphate (TP) and di-alpha-tocopheryl phosphate (T2P) are two phosphorylated forms of vitamin E which form tocopheryl phosphate mixture (TPM) when combined, and have been proposed to enhance the dermal and transdermal delivery of actives of interest. Here, we report the physicochemical characteristics and morphological properties of TPM formulations, including particle size, deformability and morphology, and its ability to facilitate the transport of carnosine, vitamin D3, CoEnzyme Q10 and caffeine into, and across, the skin. Results demonstrate that TPM self-assembles to form vesicular structures in hydroethanolic solutions ranging in mean size from 101 to 162 nM depending on the amount of TPM and ethanol present in the formulation. The ratio of TP to T2P in TPM formulations altered vesicle size and elasticity, with vesicles high in TP found to be more deformable than those rich in T2P. TPM produced a significant (p < 0.05) 2.4-3.4-fold increase in the absorption of carnosine, vitamin D3, CoEnzyme Q10 and caffeine into, or through, the skin. The TPM delivery platform was able to deliver a diverse range of actives with differing size and solubility profiles and therefore has significant potential to expand the number and types of drugs available for topical application and transdermal delivery.

The mechanics of DNA loops bridged by proteins unveiled by single-molecule experiments

Protein-induced DNA bridging and looping is a common mechanism for various and essential processes in bacterial chromosomes. This mechanism is preserved despite the very different bacterial conditions and their expected influence on the thermodynamic and kinetic characteristics of the bridge formation and stability. Over the last two decades, single-molecule techniques carried out on in vitro DNA systems have yielded valuable results which, in combination with theoretical works, have clarified the effects of different parameters of nucleoprotein complexes on the protein-induced DNA bridging and looping process. In this review, I will outline the features that can be measured for such processes with various single-molecule techniques in use in the field. I will then describe both the experimental results and the theoretical models that illuminate the contribution of the DNA molecule itself as well as that of the bridging proteins in the DNA looping mechanism at play in the nucleoid of E. coli.

Expression of various sarcomeric tropomyosin isoforms in equine striated muscles

In order to better understand the training and athletic activity of horses, we must have complete understanding of the isoform diversity of various myofibrillar protein genes like tropomyosin. Tropomyosin (TPM), a coiled-coil dimeric protein, is a component of thin filament in striated muscles. In mammals, four TPM genes (TPM1, TPM2, TPM3, and TPM4) generate a multitude of TPM isoforms via alternate splicing and/or using different promoters. Unfortunately, our knowledge of TPM isoform diversity in the horse is very limited. Hence, we undertook a comprehensive exploratory study of various TPM isoforms from horse heart and skeletal muscle. We have cloned and sequenced two sarcomeric isoforms of the TPM1 gene called TPM1α and TPM1κ, one sarcomeric isoform of the TPM2 and one of the TPM3 gene, TPM2α and TPM3α respectively. By qRT-PCR using both relative expression and copy number, we have shown that TPM1α expression compared to TPM1κ is very high in heart. On the other hand, the expression of TPM1α is higher in skeletal muscle compared to heart. Further, the expression of TPM2α and TPM3α are higher in skeletal muscle compared to heart. Using western blot analyses with CH1 monoclonal antibody we have shown the high expression levels of sarcomeric TPM proteins in cardiac and skeletal muscle. Due to the paucity of isoform specific antibodies we cannot specifically detect the expression of TPM1κ in horse striated muscle. To the best of our knowledge this is the very first report on the characterization of sarcmeric TPMs in horse striated muscle.

The mutagenic assessment of an electronic-cigarette and reference cigarette smoke using the Ames assay in strains TA98 and TA100

Salmonella typhimurium strains TA98 and TA100 were used to assess the mutagenic potential of the aerosol from a commercially available, rechargeable, closed system electronic-cigarette. Results obtained were compared to those for the mainstream smoke from a Kentucky reference (3R4F) cigarette. Two different test matrices were assessed. Aerosol generated from the e-cigarette was trapped on a Cambridge filter pad, eluted in DMSO and compared to cigarette smoke total particulate matter (TPM), which was generated in the same manner for mutagenicity assessment in the Salmonella assay. Fresh e-cigarette and cigarette smoke aerosols were generated on the Vitrocell® VC 10 smoking robot and compared using a modified scaled-down 35mm air agar interface (AAI) methodology. E-cigarette aerosol collected matter (ACM) was found to be non-mutagenic in the 85mm plate incorporation Ames assay in strains TA98 and TA100 conducted in accordance with OECD 471, when tested up to 2400μg/plate. Freshly generated e-cigarette aerosol was also found to be negative in both strains after an AAI aerosol exposure, when tested up to a 1L/min dilution for up to 3h. Positive control responses were observed in both strains, using benzo[a]pyrene, 2-nitrofluorene, sodium azide and 2-aminoanthracene in TA98 and TA100 in the presence and absence of metabolic activation respectively. In contrast, cigarette smoke TPM and aerosol from 3R4F reference cigarettes were found to be mutagenic in both tester strains, under comparable test conditions to that of e-cigarette exposure. Limited information exists on the mutagenic activity of captured e-cigarette particulates and whole aerosol AAI approaches. With the lower toxicant burden of e-cigarette aerosols compared to cigarette smoke, it is clear that a more comprehensive Ames package of data should be generated when assessing e-cigarettes, consisting of the standard OECD-five, TA98, TA100, TA1535, TA1537 (or TA97) and E. coli (or TA102). In addition, TA104 which is more sensitive to the carbonyl based compounds found in e-cigarette aerosols under dry-wicking conditions may also prove a useful addition in a testing battery. Regulatory standard product testing approaches as used in this study will become important when determining whether e-cigarette aerosols are in fact less biologically active than cigarette smoke, as this study suggests. Future studies should be supported by in vitro dosimetry approaches to draw more accurate comparisons between cigarette smoke, e-cigarette aerosol exposure and human use.

Protective effect of topiramate on hypoxic-ischemic brain injury in neonatal rat

OBJECTIVE

To explore protective effect of topiramate (TPM) on hypoxic-ischemic brain injury.

METHODS

A total of 360 neonatal rats were selected then randomly divided into sham operation group, ischemia and hypoxia group, conventional treatment group and degradation therapy group (n=90). After surgical treatment, sham and ischemic hypoxia group were treat with normal saline; conventional treatment group was received TPM solution 100 mg/kg, 2 times/d; degradation therapy group received TPM solution 150 mg/kg, 2 times/d, per 3 d treatment each dosage was reduced 50 mg/kg, the lowest reduced to 50 mg/kg. Four groups received continuous treatment for 10 d. After treatment for 1 d, 4 d, 7 d, 10 d the cerebral edema, neuron-specific enolase (NSE) and γ-aminobutyric acid (GABA) levels and cognitive abilities of four groups were observed.

RESULTS

After 1 d, 4 d of treatment, the brain water content and NSE levels in ischemia and hypoxia group, the conventional treatment group and the degradation therapy group were significantly higher than that in sham group (P<0.05), the brain water content and NSE levels of the conventional treatment group and the degradation therapy group were significantly lower than that in the ischemic hypoxia group (P<0.05). GABA levels and learning ability of the ischemia and hypoxia group, the conventional treatment group and degradation therapy group were significantly lower than the sham group (P<0.05), the GABA levels and learning ability of the conventional treatment group and degradation therapy group were significantly higher than the ischemia and hypoxia group (P<0.05). After 7 d, 10 d of treatment, the brain water content and NSE levels in the sham operation group, the conventional treatment group and degradation therapy group were significantly lower than the ischemia and hypoxia group (P<0.05), while the GABA levels and learning ability of these three groups were significantly higher than that in the ischemia and hypoxia group (P<0.05), the GABA levels in the conventional treatment group were significantly higher than degradation therapy group (P<0.05); After 10 d of treatment, the GABA levels of the conventional treatment group were significantly higher than the sham group, the learning ability of the degradation therapy group and sham operation group were significantly higher than the conventional treatment group (P<0.05).

CONCLUSIONS

The correct amount of short-term TPM has protective effect on hypoxic-ischemic brain injury, but long-term or excessive use may cause new damage to the brain and reduce the cognitive ability.

The adverse effects of phoxim exposure in the midgut of silkworm, Bombyx mori

The silkworm is an important economic insect. Poisoning of silkworms by organophosphate pesticides causes tremendous loss to the sericulture. In this study, Solexa sequencing technology was performed to profile the gene expression changes in the midgut of silkworms in response to 24h of phoxim exposure and the impact on detoxification, apoptosis and immune defense were addressed. The results showed that 254 genes displayed at least 2.0-fold changes in expression levels, with 148 genes up-regulated and 106 genes down-regulated. Cytochrome P450 played an important role in detoxification. Histopathology examination and transmission electron microscope revealed swollen mitochondria and disappearance of the cristae of mitochondria, which are the important features in insect apoptotic cells. Cytochrome C release from mitochondria into the cytoplasm was confirmed. In addition, the Toll and immune deficiency (IMD) signal pathways were all inhibited using qRT-PCR. Our results could help better understand the impact of phoxim exposure on silkworm.

Quantitation of the DNA tethering effect in long-range DNA looping in vivo and in vitro using the Lac and λ repressors

Efficient and specific interactions between proteins bound to the same DNA molecule can be dependent on the length of the DNA tether that connects them. Measurement of the strength of this DNA tethering effect has been largely confined to short separations between sites, and it is not clear how it contributes to long-range DNA looping interactions, such as occur over separations of tens to hundreds of kilobase pairs in vivo. Here, gene regulation experiments using the LacI and λ CI repressors, combined with mathematical modeling, were used to quantitate DNA tethering inside Escherichia coli cells over the 250- to 10,000-bp range. Although LacI and CI loop DNA in distinct ways, measurements of the tethering effect were very similar for both proteins. Tethering strength decreased with increasing separation, but even at 5- to 10-kb distances, was able to increase contact probability 10- to 20-fold and drive efficient looping. Tethering in vitro with the Lac repressor was measured for the same 600-to 3,200-bp DNAs using tethered particle motion, a single molecule technique, and was 5- to 45-fold weaker than in vivo over this range. Thus, the enhancement of looping seen previously in vivo at separations below 500 bp extends to large separations, underlining the need to understand how in vivo factors aid DNA looping. Our analysis also suggests how efficient and specific looping could be achieved over very long DNA separations, such as what occurs between enhancers and promoters in eukaryotic cells.

Effect of sildenafil, a selective phosphodiesterase 5 inhibitor, on the anticonvulsant action of some antiepileptic drugs in the mouse 6-Hz psychomotor seizure model

Sildenafil, a selective phosphodiesterase 5 inhibitor (PDE5), has been recently reported to have both pro- and anticonvulsant action in various experimental models of seizures and epilepsy. Furthermore, it affects anticonvulsant action of some antiepileptic drugs (AEDs) in mice seizure tests and both pharmacodynamic and pharmacokinetic interactions were noted. The present study was carried out to investigate influence of sildenafil on the threshold for 6 Hz-induced psychomotor seizures in mice. Effect of sildenafil on activity of some AEDs, i.e., phenobarbital (PB), clonazepam (CZP), ethosuximide (ETS), valproic acid (VPA), tiagabine (TGB), oxcarbazepine (OXC) and levetiracetam (LEV), in 6 Hz test was also examined. Moreover, combination of sildenafil with LEV was investigated in terms of influence on motor coordination (determined by the chimney test), muscular strength (evaluated in the grip-strength test) and long-term memory (assessed in the passive avoidance task) in mice. To determine the type of pharmacological interaction between sildenafil and LEV, free plasma and total brain concentrations of this AED were determined by LC-MS/MS method. Sildenafil at a dose ranging from 10 to 40 mg/kg statistically increased psychomotor seizure threshold in mice. Moreover, sildenafil enhanced the anticonvulsant action of all the studied AEDs in this test. Interactions between this PDE5 inhibitor and PB, CZP, ETS, TGB and OXC seem to be pharmacodynamic. Since sildenafil increased free plasma and total brain concentration of LEV, interactions between these drugs have pharmacokinetic nature. This kind of interaction was also noted between sildenafil and VPA. Neither LEV (2.32 mg/kg) nor its co-administration with sildenafil (40 mg/kg) produced any significant changes in motor coordination, muscular strength and long-term memory in mice.

The PICTURE study -- prostate imaging (multi-parametric MRI and Prostate HistoScanning™) compared to transperineal ultrasound guided biopsy for significant prostate cancer risk evaluation

OBJECTIVE

The primary objective of the PICTURE study is to assess the negative predictive value of multi-parametric MRI (mp-MRI) and Prostate HistoScanning™ (PHS) in ruling-out clinically significant prostate cancer.

PATIENTS AND METHODS

PICTURE is a prospective diagnostic validating cohort study conforming to level 1 evidence. PICTURE will assess the diagnostic performance of multi-parametric Magnetic Resonance Imaging (mp-MRI) and Prostate HistoScanning™ (PHS) ultrasound. PICTURE will involve validating both index tests against a reference test, transperineal Template Prostate Mapping (TPM) biopsies, which can be applied in all men under evaluation. Men will be blinded to the index test results and both index tests will be reported prospectively prior to the biopsies being taken to ensure reporter blinding. Paired analysis of each of the index tests to the reference test will be done at patient level. Those men with an imaging lesion will undergo targeted biopsies to assess the clinical utility of sampling only suspicious areas. The study is powered to assess the negative predictive value of these imaging modalities in ruling-out clinically significant prostate cancer.

DISCUSSION

The PICTURE study aims to assess the performance characteristics of two imaging modalities (mp-MRI and Prostate HistoScanning) for their utility in the prostate cancer pathway. PICTURE aims to identify if either imaging test may be useful for ruling out clinically significant disease in men under investigation, and also to examine if either imaging modality is useful for the detection of disease. Recruitment is underway and expected to complete in 2014.

Aspects of the design protocol and the statistical methods for analysis of tar, nicotine and carbon monoxide yields in cigarette smoke that can affect the measurement variability within collaborative studies

Statistical principles described in ISO 5725-1 (1994) are a robust basis for evaluating cigarette smoke data from collaborative studies under the ISO 3308 machine smoking and for specifying the criteria for the removal of outlier data and determination of mean yields and their variability. However, the standard only provides recommendations on outlier removal that should be taken into account by experts who undertake data interpretation. The potential for over-interpretation of data from small numbers of laboratories is highlighted and recommendations made to deal with this possibility. Key variables to the statistical analysis, the number of cigarettes per replicate and replicates performed in each laboratory, the number of participating laboratories and the use of linear and rotary smoking machines in smoke collection, are identified and their relevance to obtaining robust data are considered. The statistical methods routinely used for data analysis from the ISO regime, are re-assessed for their suitability to analyse data obtained under the Canadian intense (CI) regime, where yield differences between linear and rotary smoking machines are found. This machine effect can lead to more outliers being detected and difficulties in outlier detection which may affect the provision of robust estimates of mean yields, repeatability and reproducibility.

Antiepileptic drug clearance and seizure frequency during pregnancy in women with epilepsy

The aims of the study were to characterize the magnitude of clearance changes during pregnancy for multiple antiepileptic drugs (AEDs) and to assess seizure frequency and factors increasing seizure risk in pregnant women with epilepsy. A retrospective analysis was performed for 115 pregnancies in 95 women with epilepsy followed at the Emory Epilepsy Center between 1999 and 2012. Antiepileptic drug blood levels (ABLs) obtained during routine clinical practice were used to calculate AED clearance at multiple points during pregnancy. Antiepileptic drug doses and seizure activity were also recorded. The data were analyzed for changes in clearance and dose across pregnancy and for an association between ABL and changes in seizure frequency. Significant changes in clearance during pregnancy were observed for lamotrigine (p<0.001) and levetiracetam (p<0.006). Average peak clearance increased by 191% for lamotrigine and 207% for levetiracetam from nonpregnant baseline. Marked variance was present across individual women and also across repeat pregnancies in individual women. Despite increased AED dose across most AEDs, seizures increased in 38.4% of patients during pregnancy. Seizure deterioration was significantly more likely in patients with seizures in the 12 months prior to conception (p<0.001) and those with localization-related epilepsy (p=0.005). When ABL fell >35% from preconception baseline, seizures worsened significantly during the second trimester when controlling for seizure occurrence in the year prior to conception. Substantial pharmacokinetic changes during pregnancy occur with multiple AEDs and may increase seizure risk. Monitoring of AED serum concentrations with dose adjustment is recommended in pregnant women with epilepsy. Further studies are needed for many AEDs.

Differentially expressed genes in the ovary of the sixth day of pupal "Ming" lethal egg mutant of silkworm, Bombyx mori

The "Ming" lethal egg mutant (l-em) is a vitelline membrane mutant in silkworm, Bombyx mori. The eggs laid by the l-em mutant lose water, ultimately causing death within an hour. Previous studies have shown that the deletion of BmEP80 is responsible for the l-em mutation in silkworm, B. mori. In the current study, digital gene expression (DGE) was performed to investigate the difference of gene expression in ovaries between wild type and l-em mutant on the sixth day of the pupal stage to obtain a global view of gene expression profiles using the ovaries of three l-em mutants and three wild types. The results showed a total of 3,463,495 and 3,607,936 clean tags in the wild type and the l-em mutant libraries, respectively. Compared with those of wild type, 239 differentially expressed genes were detected in the l-em mutant, wherein 181 genes are up-regulated and 58 genes are down-regulated in the mutant strain. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis results showed that no pathway was significantly enriched and three pathways are tightly related to protein synthesis among the five leading pathways. Moreover, the expression profiles of eight important differentially expressed genes related to oogenesis changed. These results provide a comprehensive gene expression analysis of oogenesis and vitellogenesis in B. mori which facilitates understanding of both the specific molecular mechanism of the 1-em mutant and Lepidopteran oogenesis in general.

In vitro micronucleus assay for the analysis of total particulate matter in cigarette smoke: comparison of flow cytometry and laser scanning cytometry with microscopy

The possible genotoxicity of the total particulate matter (TPM) in cigarette smoke has typically been evaluated using the in vitro micronucleus assay. In recent years, automated scoring techniques have been developed to replace the manual counting process in this assay. However, these automated scoring techniques have not been applied in routine genotoxicity assays for the analysis of TPM to improve the assay efficiency. Chinese hamster ovary (CHO) cells were treated with TPM produced from 14 types of cigarettes at five concentrations (25-200μg/ml) without exogenous metabolic activation. The three following methods were used to score the micronucleus (MN) frequency: (a) flow cytometry with SYTOX and EMA dyes, which differentially stain micronuclei and apoptotic/necrotic chromatin to enhance assay reliability; (b) laser scanning cytometry with FITC and PI dyes, which is a system that combines the analytical capabilities of flow and image cytometry; and (c) visual microcopy with Giemsa dye. The test results obtained using the three methods were compared using correlation analysis. The key findings for this set of compounds include the following: (a) both flow cytometry- and laser scanning cytometry-based methods were effective for MN identification, (b) the three scoring methods could detect dose-dependent micronucleus formation for the 14 types of TPM, and (c) the MN frequencies that were measured in the same samples by flow cytometry, laser scanning cytometry, and visual microscopy were highly correlated, and there were no significant differences (p>0.05). In conclusion, both flow cytometry and laser scanning cytometry can be used to evaluate the MN frequency induced by TPM without exogenous metabolic activation. The simpler and faster processing and the high correlation of the results make these two automatic methods appropriate tools for use in in vitro micronucleus assays for the analysis of TPM using CHO cells.

Identification and expression analysis of a new glycoside hydrolase family 55 exo-β-1,3-glucanase-encoding gene in Volvariella volvacea suggests a role in fruiting body development

The edible straw mushroom Volvariella volvacea is an important crop in South East Asia and is predominantly harvested in the egg stage. Rapid stipe elongation and cap expansion result in a swift transition from the egg to elongation and maturation stage, which are subjected to fast senescence and deterioration. In other mushrooms, β-1,3-glucanases have been associated with degradation (softening) of the cell wall during stipe elongation and senescence. We present a new glycoside hydrolase family 55 (GH55) exo-β-1,3-glucanase gene, exg2, and highly conserved deduced EXG2 protein. The 3D model and presumed catalytic residues of V. volvacea EXG2 are identical to Lentinula edodes EXG2 and Phanerochaete chrysosporium Lam55A, supporting similar enzymatic functions. In addition to previous association to stipe elongation and senescence, our data clearly indicates a role for cap (pileus) expansion. Digital gene expression, quantitative PCR and isobaric tags for relative and absolute quantification analysis showed low exg2 and EXG2 levels in primordia, button, egg and elongation stages and significantly increased levels in the maturation stage. Subsequent relative quantitative PCR analysis designated expression of exg2 to the stipe in the elongation stage and to the pileus and stipe in the maturation stage. EXG2 cell wall softening activity, close correlation of exg2 expression with the principal expanding mushroom tissues and a strong conservation of expression patterns and protein sequences in other mushrooms, make V. volvacea exg2 an important candidate for future studies on mechanisms of fruiting body expansion and senescence causing commodity value loss.