Identification of candidate anti-cancer molecular mechanisms of compound kushen injection using functional genomics

Compound Kushen Injection (CKI) has been clinically used in China for over 15 years to treat various types of solid tumours. However, because such Traditional Chinese Medicine (TCM) preparations are complex mixtures of plant secondary metabolites, it is essential to explore their underlying molecular mechanisms in a systematic fashion. We have used the MCF-7 human breast cancer cell line as an initial in vitro model to identify CKI induced changes in gene expression. Cells were treated with CKI for 24 and 48 hours at two concentrations (1 and 2 mg/mL total alkaloids), and the effect of CKI on cell proliferation and apoptosis were measured using XTT and Annexin V/Propidium Iodide staining assays respectively. Transcriptome data of cells treated with CKI or 5-Fluorouracil (5-FU) for 24 and 48 hours were subsequently acquired using high-throughput Illumina RNA-seq technology. In this report we show that CKI inhibited MCF-7 cell proliferation and induced apoptosis in a dose-dependent fashion. We integrated and applied a series of transcriptome analysis methods, including gene differential expression analysis, pathway over-representation analysis, de novo identification of long non-coding RNAs (lncRNA) as well as co-expression network reconstruction, to identify candidate anti-cancer molecular mechanisms of CKI. Multiple pathways were perturbed and the cell cycle was identified as the potential primary target pathway of CKI in MCF-7 cells. CKI may also induce apoptosis in MCF-7 cells via a p53 independent mechanism. In addition, we identified novel lncRNAs and showed that many of them might be expressed as a response to CKI treatment.Zhipeng Qu, Jian Cui, Yuka Harata-Lee, Thazin Nwe Aung, Qianjin Feng, Joy M. Raison, Robert Daniel Kortschak, David L. Adelso

bíogo: a simple high-performance bioinformatics toolkit for the Go language

biogo is a framework designed to ease development and maintenance of computationally intensive bioinformatics applications (Kortschak and Adelson 2014). The library is written in the Go programming language, a garbage-collected, strictly typed compiled language with built in support for concurrent processing, and performance comparable to C and Java. It provides a variety of data types and utility functions to facilitate manipulation and analysis of large scale genomic and other biological data. biogo uses a concise and expressive syntax, lowering the barriers to entry for researchers needing to process large data sets with custom analyses while retaining computational safety and ease of code review. We believe biogo provides an excellent environment for training and research in computational biology because of its combination of strict typing, simple and expressive syntax, and high performance.R. Daniel Kortschak, Josh Bleecher Snyder, Manolis Maragkakis, and David L. Adelso

Does Perceptual Belongingness Affect Lightness Constancy?

Scientists have shown that two equal grey patches may differ in lightness when belonging to different reflecting surfaces. We extend this investigation to the constancy domain. In a CRT simulation of a bipartite field of illumination, we manipulated the arrangement of twelve patches: six squares and six diamonds. Patches of the same shape could be placed: (i) all within the same illumination field; or (ii) forming a row across the illumination fields. Furthermore, we manipulated proximity between the innermost patches and the illumination edge. The patches could be (i) touching (forming an X-junction); or (ii) not touching (not forming an X-junction). Observers were asked to perform a lightness match between two additional patches, one illuminated and the other in shadow. We found better lightness constancy when the patches of the same shape formed a row across the fields, with no effect of X-junctions

Long read reference genome-free reconstruction of a full-length transcriptome from Astragalus membranaceus reveals transcript variants involved in bioactive compound biosynthesis

Astragalus membranaceus, also known as Huangqi in China, is one of the most widely used medicinal herbs in Traditional Chinese Medicine. Traditional Chinese Medicine formulations from Astragalus membranaceus have been used to treat a wide range of illnesses, such as cardiovascular disease, type 2 diabetes, nephritis and cancers. Pharmacological studies have shown that immunomodulating, anti-hyperglycemic, anti-inflammatory, antioxidant and antiviral activities exist in the extract of Astragalus membranaceus. Therefore, characterising the biosynthesis of bioactive compounds in Astragalus membranaceus, such as Astragalosides, Calycosin and Calycosin-7-O-beta-D-glucoside, is of particular importance for further genetic studies of Astragalus membranaceus. In this study, we reconstructed the Astragalus membranaceus full-length transcriptomes from leaf and root tissues using PacBio Iso-Seq long reads. We identified 27 975 and 22 343 full-length unique transcript models in each tissue respectively. Compared with previous studies that used short read sequencing, our reconstructed transcripts are longer, and are more likely to be full-length and include numerous transcript variants. Moreover, we also re-characterised and identified potential transcript variants of genes involved in Astragalosides, Calycosin and Calycosin-7-O-beta-D-glucoside biosynthesis. In conclusion, our study provides a practical pipeline to characterise the full-length transcriptome for species without a reference genome and a useful genomic resource for exploring the biosynthesis of active compounds in Astragalus membranaceus.Jun Li, Yuka Harata-Lee, Matthew D Denton, Qianjin Feng, Judith R Rathjen, Zhipeng Qu, David L Adelso

In depth analysis of the Sox4 gene locus that consists of sense and natural antisense transcripts

Available online 17 February 2016SRY (Sex Determining Region Y)-Box 4 or Sox4 is an important regulator of the pan-neuronal gene expression during post-mitotic cell differentiation within the mammalian brain. Sox4 gene locus has been previously characterized with multiple sense and overlapping natural antisense transcripts [1], [2]. Here we provide accompanying data on various analyses performed and described in Ling et al. [2]. The data include a detail description of various features found at Sox4 gene locus, additional experimental data derived from RNA-Fluorescence in situ Hybridization (RNA-FISH), Western blotting, strand-specific reverse-transcription quantitative polymerase chain reaction (RT-qPCR), gain-of-function and in situ hybridization (ISH) experiments. All the additional data provided here support the existence of an endogenous small interfering- or PIWI interacting-like small RNA known as Sox4_sir3, which origin was found within the overlapping region consisting of a sense and a natural antisense transcript known as Sox4ot1.King-Hwa Ling, Peter J. Brautigan, Sarah Moore, Rachel Fraser, Melody Pui-Yee Leong, Jia-Wen Leong, Shahidee Zainal Abidin, Han-Chung Lee, Pike-See Cheah, Joy M. Raison, Milena Babic, Young Kyung Lee, Tasman Daish, Deidre M. Mattiske, Jeffrey R. Mann, David L. Adelson, Paul Q. Thomas, Christopher N. Hahn, Hamish S.Scot

Action Recognition with a Bio--Inspired Feedforward Motion Processing Model: The Richness of Center-Surround Interactions

International audienceHere we show that reproducing the functional properties of MT cells with various center--surround interactions enriches motion representation and improves the action recognition performance. To do so, we propose a simplified bio--inspired model of the motion pathway in primates: It is a feedforward model restricted to V1-MT cortical layers, cortical cells cover the visual space with a foveated structure, and more importantly, we reproduce some of the richness of center-surround interactions of MT cells. Interestingly, as observed in neurophysiology, our MT cells not only behave like simple velocity detectors, but also respond to several kinds of motion contrasts. Results show that this diversity of motion representation at the MT level is a major advantage for an action recognition task. Defining motion maps as our feature vectors, we used a standard classification method on the Weizmann database: We obtained an average recognition rate of 98.9%, which is superior to the recent results by Jhuang et al. (2007). These promising results encourage us to further develop bio--inspired models incorporating other brain mechanisms and cortical layers in order to deal with more complex videos

Microgeometry capture using an elastomeric sensor

We describe a system for capturing microscopic surface geometry. The system extends the retrographic sensor [Johnson and Adelson 2009] to the microscopic domain, demonstrating spatial resolution as small as 2 microns. In contrast to existing microgeometry capture techniques, the system is not affected by the optical characteristics of the surface being measured---it captures the same geometry whether the object is matte, glossy, or transparent. In addition, the hardware design allows for a variety of form factors, including a hand-held device that can be used to capture high-resolution surface geometry in the field. We achieve these results with a combination of improved sensor materials, illumination design, and reconstruction algorithm, as compared to the original sensor of Johnson and Adelson [2009].National Science Foundation (U.S.) (Grant 0739255)National Institutes of Health (U.S.) (Contract 1-R01-EY019292-01

Toward stronger theory in critical public health: Insights from debates surrounding posthumanism

The “posthumanist turn” in critical theory comprises efforts to recognize and analyze the interdependence of human existence with non-human entities, including other animals, spaces, and technologies. Scholarship aligned to and debating posthumanism pertains to public health, but has yet to be clearly articulated for a public health audience. This commentary and an appended glossary illustrate the relevance of these ideas for enhancing critical theory in public health. Keywords: Social Sciences, Humanities, Technology, Animals, Public HealthCanadian Institutes of Health Researc

IND-Enabling Studies for a Clinical Trial to Genetically Program a Persistent Cancer-Targeted Immune System

PURPOSE: To improve persistence of adoptively transferred T-cell receptor (TCR)-engineered T cells and durable clinical responses, we designed a clinical trial to transplant genetically-modified hematopoietic stem cells (HSCs) together with adoptive cell transfer of T cells both engineered to express an NY-ESO-1 TCR. Here, we report the preclinical studies performed to enable an investigational new drug (IND) application. EXPERIMENTAL DESIGN: HSCs transduced with a lentiviral vector expressing NY-ESO-1 TCR and the PET reporter/suicide gene HSV1-sr39TK and T cells transduced with a retroviral vector expressing NY-ESO-1 TCR were coadministered to myelodepleted HLA-A2/Kb mice within a formal Good Laboratory Practice (GLP)-compliant study to demonstrate safety, persistence, and HSC differentiation into all blood lineages. Non-GLP experiments included assessment of transgene immunogenicity and in vitro viral insertion safety studies. Furthermore, Good Manufacturing Practice (GMP)-compliant cell production qualification runs were performed to establish the manufacturing protocols for clinical use. RESULTS: TCR genetically modified and ex vivo-cultured HSCs differentiated into all blood subsets in vivo after HSC transplantation, and coadministration of TCR-transduced T cells did not result in increased toxicity. The expression of NY-ESO-1 TCR and sr39TK transgenes did not have a detrimental effect on gene-modified HSC's differentiation to all blood cell lineages. There was no evidence of genotoxicity induced by the lentiviral vector. GMP batches of clinical-grade transgenic cells produced during qualification runs had adequate stability and functionality. CONCLUSIONS: Coadministration of HSCs and T cells expressing an NY-ESO-1 TCR is safe in preclinical models. The results presented in this article led to the FDA approval of IND 17471

Challenges Enrolling Children Into Traumatic Brain Injury Trials: An Observational Study

ObjectivesIn preparation for a clinical trial of therapeutic agents for children with moderate‐to‐severe blunt traumatic brain injuries (TBIs) in emergency departments (EDs), we conducted this feasibility study to (1) determine the number and clinical characteristics of eligible children, (2) determine the timing of patient and guardian arrival to the ED, and (3) describe the heterogeneity of TBIs on computed tomography (CT) scans.MethodsWe conducted a prospective observational study at 16 EDs of children ≤ 18 years of age presenting with blunt head trauma and Glasgow Coma Scale scores of 3–12. We documented the number of potentially eligible patients, timing of patient and guardian arrival, patient demographics and clinical characteristics, severity of injuries, and cranial CT findings.ResultsWe enrolled 295 eligible children at the 16 sites over 6 consecutive months. Cardiac arrest and nonsurvivable injuries were the most common characteristics that would exclude patients from a future trial. Most children arrived within 2 hours of injury, but most guardians did not arrive until 2–3 hours after the injury. There was a substantial range in types of TBIs, with subdural hemorrhages being the most common.ConclusionEnrolling children with moderate‐to‐severe TBI into time‐sensitive clinical trials will require large numbers of sites and meticulous preparation and coordination and will prove challenging to obtain informed consent given the timing of patient and guardian arrival. The Federal Exception from Informed Consent for Emergency Research will be an important consideration for enrolling these children.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/135996/1/acem13085_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/135996/2/acem13085.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/135996/3/acem13085-sup-0001-DataSupplementS1.pd