Use of Methylation Markers for Age Estimation of an unknown Individual based ...QIAGEN
Biological samples and traces collected at crime scenes have potential to be used for predicting
the age of the individuals from whom the samples originated. In no-suspect cases and cases with
no DNA profile match against a database, such information could be critical for providing additional intelligence for criminal investigations. Read more.
Use of Methylation Markers for Age Estimation of an unknown Individual based ...QIAGEN
Biological samples and traces collected at crime scenes have potential to be used for predicting
the age of the individuals from whom the samples originated. In no-suspect cases and cases with
no DNA profile match against a database, such information could be critical for providing additional intelligence for criminal investigations. Read more.
Austin Neurology & Neurosciences is an open access, peer reviewed, scholarly journal dedicated to publish articles covering all areas of Neurology & Neurological Sciences.
The journal aims to promote research communications and provide a forum for doctors, researchers, physicians and healthcare professionals to find most recent advances in all areas of Neurology & Neurological Sciences. Austin Neurology & Neurosciences accepts original research articles, reviews, mini reviews, case reports and rapid communication covering all aspects of neurology & neurosciences.
Austin Neurology & Neurosciences strongly supports the scientific up gradation and fortification in related scientific research community by enhancing access to peer reviewed scientific literary works. Austin Publishing Group also brings universally peer reviewed journals under one roof thereby promoting knowledge sharing, mutual promotion of multidisciplinary science.
Tumor Mutational Load assessment of FFPE samples using an NGS based assayThermo Fisher Scientific
Understanding the molecular determinants of response to immune checkpoint blockade inhibitors is a critical unmet need for translational oncology research. Research tools to characterize the mutational landscape of cancers may potentially help identify predictive biomarkers for immuno-therapy that can be tested in future studies. Herein, we describe a targeted Ion AmpliSeq assay to determine the mutational load and signature of cancer research samples.
The Effects of Octanol on Gap Junctions and Actin of Neoblasts during Smed Pl...Marianne Gadiano
An independent project for Developmental Biology Lab (BIOL340), testing the effects of octanol exposure on the regeneration of Schmidtea mediterranea planaria. We tested to see whether or not actin was involved in the gap junction communication of migrating neoblasts during regeneration. We performed RT-PCR and Western Blot assays to detect any changes in actin levels from RNA and protein. Our results show that there seems to be little correlation between actin and gap junctions. We would like to conduct future studies on myosin, F-actin, and G-actin. The poster for this project was presented as part of the Spring 2016 Investigative Biology Labs Poster Session at the University of Maryland, Baltimore County (UMBC). Including BIOL340L, the session also features research projects from students in the Molecular and General Genetics Lab, and the Phage Hunters: Genome Analysis Lab. The session serves to inform the public about the upper-level laboratories offered by the Biological Sciences department at UMBC.
Lecture from whole-cell modeling summer school March 3-9, 2015 at the University of Rostock. See http://sites.google.com/site/vwwholecellsummerschool/ for more information.
A Next-Generation Sequencing Assay to Estimate Tumor Mutation Load at > 5% Al...Thermo Fisher Scientific
Immunotherapies have shown anti-cancer effects in melanoma, NSCLC, and bladder cancer. High tumor mutation load is associated with positive responses from immune checkpoint inhibitors. However, current methods to estimate tumor mutation load often have high infrastructure needs, and require large amounts of DNA.
Creating custom gene panels for next-generation sequencing: optimization of 5...Thermo Fisher Scientific
Next-generation sequencing gene panels enable the examination of multiple genes, identifying previously described variants and discovering novel variants, to elucidate genetic disease. The challenges are substantial, including: identification of all genes of interest; assay optimization to create robust, reproducible, multiplex panels; and developing accurate, comprehensive, reproducible analysis pipelines.
A computational framework for large-scale analysis of TCRβ immune repertoire ...Thermo Fisher Scientific
TCRβ immune repertoire analysis by next-generation sequencing is emerging as a valuable tool for research studies of the tumor microenvironment and potential immune responses to cancer immunotherapy. Generation of insight from immune repertoire profiling often requires comparative analysis of immune repertoires across research sample cohorts representing immune responses to defined antigens or immunomodulatory agents. Here we describe the development of a computational framework enabling large-scale comparative analysis of immune repertoire data on cloud-based infrastructure.
Widespread human T cell receptor beta variable gene polymorphism: implication...Thermo Fisher Scientific
Polymorphism within the TCRB variable gene (TRBV) has been linked to chronic autoimmune diseases such as Type 1 Diabetes, Rheumatoid Arthritis, Psoriatic Arthritis, Multiple Sclerosis and Asthma (1-8), and may also be mechanistically linked to immune mediated adverse events (IMAEs) during immunotherapy (9-11). Here we use the Ion-AmpliSeq™ Immune Repertoire Plus TCRB assay to evaluate TRBV gene polymorphism in a group of 85 Caucasians with melanoma. The assay provides coverage of all three CDR domains to enable detection of TRBV polymorphism. We find evidence of extensive genetic diversity within the TRBV gene, including 15 nonsynonymous variants that are absent from the IMGT database (12). TRBV gene allele typing may provide rich biomarker information for the prediction of IMAEs and chronic autoimmune disease.
Paper memo: Optimal-Transport Analysis of Single-Cell Gene Expression Identif...Ryohei Suzuki
Journal club slide for the following paper:
Schiebinger et al., 2016, Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming, Cell 176, 928--943.
Austin Neurology & Neurosciences is an open access, peer reviewed, scholarly journal dedicated to publish articles covering all areas of Neurology & Neurological Sciences.
The journal aims to promote research communications and provide a forum for doctors, researchers, physicians and healthcare professionals to find most recent advances in all areas of Neurology & Neurological Sciences. Austin Neurology & Neurosciences accepts original research articles, reviews, mini reviews, case reports and rapid communication covering all aspects of neurology & neurosciences.
Austin Neurology & Neurosciences strongly supports the scientific up gradation and fortification in related scientific research community by enhancing access to peer reviewed scientific literary works. Austin Publishing Group also brings universally peer reviewed journals under one roof thereby promoting knowledge sharing, mutual promotion of multidisciplinary science.
Tumor Mutational Load assessment of FFPE samples using an NGS based assayThermo Fisher Scientific
Understanding the molecular determinants of response to immune checkpoint blockade inhibitors is a critical unmet need for translational oncology research. Research tools to characterize the mutational landscape of cancers may potentially help identify predictive biomarkers for immuno-therapy that can be tested in future studies. Herein, we describe a targeted Ion AmpliSeq assay to determine the mutational load and signature of cancer research samples.
The Effects of Octanol on Gap Junctions and Actin of Neoblasts during Smed Pl...Marianne Gadiano
An independent project for Developmental Biology Lab (BIOL340), testing the effects of octanol exposure on the regeneration of Schmidtea mediterranea planaria. We tested to see whether or not actin was involved in the gap junction communication of migrating neoblasts during regeneration. We performed RT-PCR and Western Blot assays to detect any changes in actin levels from RNA and protein. Our results show that there seems to be little correlation between actin and gap junctions. We would like to conduct future studies on myosin, F-actin, and G-actin. The poster for this project was presented as part of the Spring 2016 Investigative Biology Labs Poster Session at the University of Maryland, Baltimore County (UMBC). Including BIOL340L, the session also features research projects from students in the Molecular and General Genetics Lab, and the Phage Hunters: Genome Analysis Lab. The session serves to inform the public about the upper-level laboratories offered by the Biological Sciences department at UMBC.
Lecture from whole-cell modeling summer school March 3-9, 2015 at the University of Rostock. See http://sites.google.com/site/vwwholecellsummerschool/ for more information.
A Next-Generation Sequencing Assay to Estimate Tumor Mutation Load at > 5% Al...Thermo Fisher Scientific
Immunotherapies have shown anti-cancer effects in melanoma, NSCLC, and bladder cancer. High tumor mutation load is associated with positive responses from immune checkpoint inhibitors. However, current methods to estimate tumor mutation load often have high infrastructure needs, and require large amounts of DNA.
Creating custom gene panels for next-generation sequencing: optimization of 5...Thermo Fisher Scientific
Next-generation sequencing gene panels enable the examination of multiple genes, identifying previously described variants and discovering novel variants, to elucidate genetic disease. The challenges are substantial, including: identification of all genes of interest; assay optimization to create robust, reproducible, multiplex panels; and developing accurate, comprehensive, reproducible analysis pipelines.
A computational framework for large-scale analysis of TCRβ immune repertoire ...Thermo Fisher Scientific
TCRβ immune repertoire analysis by next-generation sequencing is emerging as a valuable tool for research studies of the tumor microenvironment and potential immune responses to cancer immunotherapy. Generation of insight from immune repertoire profiling often requires comparative analysis of immune repertoires across research sample cohorts representing immune responses to defined antigens or immunomodulatory agents. Here we describe the development of a computational framework enabling large-scale comparative analysis of immune repertoire data on cloud-based infrastructure.
Widespread human T cell receptor beta variable gene polymorphism: implication...Thermo Fisher Scientific
Polymorphism within the TCRB variable gene (TRBV) has been linked to chronic autoimmune diseases such as Type 1 Diabetes, Rheumatoid Arthritis, Psoriatic Arthritis, Multiple Sclerosis and Asthma (1-8), and may also be mechanistically linked to immune mediated adverse events (IMAEs) during immunotherapy (9-11). Here we use the Ion-AmpliSeq™ Immune Repertoire Plus TCRB assay to evaluate TRBV gene polymorphism in a group of 85 Caucasians with melanoma. The assay provides coverage of all three CDR domains to enable detection of TRBV polymorphism. We find evidence of extensive genetic diversity within the TRBV gene, including 15 nonsynonymous variants that are absent from the IMGT database (12). TRBV gene allele typing may provide rich biomarker information for the prediction of IMAEs and chronic autoimmune disease.
Paper memo: Optimal-Transport Analysis of Single-Cell Gene Expression Identif...Ryohei Suzuki
Journal club slide for the following paper:
Schiebinger et al., 2016, Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming, Cell 176, 928--943.
Notch signaling is essential to maintain skeletal muscle stem cells in quiescence. However, the
precise roles of different Notch receptors are incompletely defined. Here, we demonstrate a
role for Notch3 (N3) in the self-renewal of muscle stem cells. We found that N3 is active in quiescent C2C12 reserve cells (RCs), and N3 over-expression and knockdown studies in C2C12 and
primary satellite cells reveal a role in self-renewal.
Activity-dependent transcriptional dynamics in mouse primary cortical and hum...Darya Vanichkina
Poster I presented at Lorne Genome 2012. Subsequently formed part of the paper
Barry G, Briggs JA, Vanichkina DP, Poth EM, Beveridge NJ, Ratnu VS, Nayler SP, Nones K, Hu J, Bredy TW, Nakagawa S, Rigo F, Taft RJ, Cairns MJ, Blackshaw S, Wolvetang EJ, Mattick JS (2013). The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing. Molecular psychiatry doi: 10.1038/mp.2013.45
Duplicate of http://figshare.com/articles/Activity_dependent_transcriptional_dynamics_in_mouse_primary_cortical_and_human_iPS_derived_neurons/978468
Apoptosis Post Microwave Ablation of the Liver: Does it Change with Power?asclepiuspdfs
Summary: Apoptosis is a type of the delayed or indirect cellular responses that happen after microwave ablation. It helps eradicate the few cancer cells that might survive the applied heat during cancer ablation. The extent of its expression is yet to be defined. Aims: We investigated whether the ablation power made any difference to the expression of apoptosis in the ablated and normal areas. Methods: Ablations with 50W, 70W, and 90W powers were created in three ex vivo perfused porcine livers. Biopsies were collected from the lesions and were assessed with Hematoxylin-Eosin and immunohistochemistry (Caspase 3 and M30) looking for apoptosis in each zone (central necrotic zone [CNZ], transitional zone [TZ], and normal surrounding zone [NZ]). Statistical analysis was performed using ANOVA and t-test.
Kupffer Cells Mediate Leptin-Induced Liver Fibrosis.
GASTROENTEROLOGY 2009;137:713–723
JIANHUA WANG,* ISABELLE LECLERCQ,‡ JOANNE M. BRYMORA,* NING XU,* MEHDI RAMEZANI–MOGHADAM,* ROSLYN M. LONDON,* DAVID BRIGSTOCK,§ and JACOB GEORGE*
*Storr Liver Unit, Westmead Millennium Institute, University of Sydney and Westmead Hospital, Westmead, Australia; ‡Laboratory of Gastroenterology, Faculty of
Medicine, Université Catholique de Louvain, Brussels, Belgium; and §Center for Cell and Vascular Biology, Children’s Research Institute, Columbus, Ohio
瘦素(Leptin)是一由脂肪細胞(Adipocyte)所分泌之荷爾蒙,是調控體重及新陳代謝之重要因子。過去研究發現病態肥胖(Obese)、脂肪肝(Nonalcoholic steatohepatitis)及酒精性肝炎(Alcoholic liver disease)等病患之血液循環中,Leptin量有明顯增加。而近期研究報告指出leptin具有促進肝臟纖維化(Liver fibrosis)之能力,當中分子機理並未明確。
在肝纖維化過程中,肝臟星狀細胞(HSC)會被活化增生及促進胞外基質(ECM)產生,而鄰近之Kupffer細胞(KC)則已知可透過促發炎因子(Proinflammatory factor)和促纖維化因子(Profibrogenic factors)例如TGF-β1和ROS影響HSC表現。雖然HSC是肝纖維化過程中重要角色,前人研究卻發現leptin似對HSC無任何調控作用。故本篇作者針對Leptin是否透過間接作用於HSC鄰近之KC,刺激其產生促纖維化因子,以活化HSC。
為探討leptin直接或間接影響HSC之分子機理,本篇作者透過RT-PCR、Immunoblot等分子生物學方法,分別測定leptin刺激後HSC及KC中Collagen I、TIMP1等促纖維化因子基因及蛋白表現,發現leptin雖可促使HSC增生,但對其纖維化能力之影響甚微。而leptin可刺激KC中TGF-β1及CTGF/CCN2等肝纖維化中重要之cytokines表現。另發現Leptin-treated KC-conditioned培養液可刺激HSC增生及增加其中Collagen I、TIMP1等表現,得出了leptin是透過刺激KC來活化HSC之推論。作者亦於後續實驗中,透過磷酸化測定、EMSA等方法探討leptin訊號傳遞作用,發現leptin可活化KC中STAT3、ERK1/2、AKT等路徑,及下游因子AP-1、NF-κB,而此兩種蛋白具有增強TGF-β1及CTGF/CCN2基因表現之能力。
CELLULAR REPROGRAMMING: Current Technology, Perspectives and Generation of iP...Munna Yadav
Reprogramming refers to erasure and remodelling of epigenetic marks, such as DNA methylation, during mammalian development. Exposure of a differentiated cell nucleus to the cytoplasm of less differentiated cell leads to erasure of the stable epigenetic code that maintains the differentiated cell’s phenotype. Gradually, the nucleus acquires a new epigenetic code that is characteristic of the dedifferentiated cell donating the cytoplasm, a process termed cellular reprogramming.
LncRNA WARS2-IT1 Functions as an Oncogene and is Associated with Poor Outcome...semualkaira
Glioblastoma multiforme (GBM) is one of the most common malignant brain tumors in adults and has high mortality and relapse rates. Over the past few years, great advances have been made in the diagnosis and treatment of GBM, but unfortunately, the five-year overall survival rate of GBM patients is approximately 5.1%. Our study aimed to investigate the new mechanism of Long noncoding RNAs (lncRNAs) WARS2-IT1 regulate the malignant progression of Glioblastoma.
LncRNA WARS2-IT1 Functions as an Oncogene and is Associated with Poor Outcome...semualkaira
Glioblastoma multiforme (GBM) is one of the most common malignant brain tumors in adults and has high mortality and relapse rates. Over the past few years, great advances have been made in the diagnosis and treatment of GBM, but unfortunately, the five-year overall survival rate of GBM patients is approximately 5.1%. Our study aimed to investigate the new mechanism of Long noncoding RNAs (lncRNAs) WARS2-IT1 regulate the malignant progression of Glioblastoma.
LncRNA WARS2-IT1 Functions as an Oncogene and is Associated with Poor Outcome...semualkaira
Glioblastoma multiforme (GBM) is one of the most common malignant brain tumors in adults and has high mortality and relapse rates. Over the past few years, great advances have been made in the diagnosis and treatment of GBM, but unfortunately, the five-year overall survival rate of GBM patients is approximately 5.1%. Our study aimed to investigate the new mechanism of Long noncoding RNAs (lncRNAs) WARS2-IT1 regulate the malignant progression of Glioblastoma.
Similar to BrandeisBiologyREUResearchPoster_final_final (20)
LncRNA WARS2-IT1 Functions as an Oncogene and is Associated with Poor Outcome...
BrandeisBiologyREUResearchPoster_final_final
1. Quantitative Comparison of Nuclear and Somatic
CaMKIV Expression in PyramidalVisual Cortex Neurons
Victor M. Suarez1, Anne Joseph2, Nathaniel Miska2, and Dr. Gina Turrigiano2*
1New Jersey Center for Science, Technology, and Mathematics Department, Kean University
2Department of Biology, Brandeis University
Abstract
Experimental Design
ConclusionData
Introduction
Future Works
Acknowledgements
Homeostatic plasticity is vital for neuron networks to maintain equilibrium in the face of
perturbations. This is accomplished through a series of mechanisms that allow neurons
to regulate their firing rates around a stable firing rate set point (FRSP). While this
phenomenon is observed both in vivo and in vitro, the process of maintaining a FRSP
is not very well understood. Calcium-calmodulin kinase IV (CaMKIV) is suspected to
play a critical role in the structure of FRSPs. We hypothesize that a drastic shift in
activity beyond the current FRSP results in CaMKIV activation leading to translocation
to the nucleus to regulate transcription. To test this, immunocytochemistry was utilized
to assess nuclear versus somatic CaMKIV expression and obtain a ratio of the two in
vitro in visual cortical pyramidal neurons treated with tetrodoxin (TTX) or bicuculline
(BCC). Preliminary data indicates that TTX treated cells exhibit significantly higher
nuclear/somatic CaMKIV localization when compared to control cells; however, BCC
data indicates no significant difference. Results suggest an inverse relationship
between CaMKIV and activity to moderate neuron homeostasis.
CaMKIV is a member of the Ca2+/calmodulin-
dependent protein kinase family which is
activated by an influx of intracellular calcium
ions causing translocation from the soma to
the nucleus of the cell. Once in the nucleus,
CaMKIV is known to be involved in the
phosphorylation of transcription factors and
regulation of genes critically involved in
synaptic and intrinsic excitability. TTX, a
potent neurotoxin that causes drastic
depression in cell firing rate activity, and
BCC, a competitive antagonist of GABA
receptors that induces an epileptic increase
of firing rate activity, were used to observe
cytoplasmic vs nuclear CaMKIV expression
under two extreme perturbations to attempt
to elucidate what role CaMKIV plays in
homeostatic regulation.
• I would like to extend my thanks to Dr. Gina Turrigiano for
allowing me to work in her lab, to my mentors Anne Joseph
and Nathaniel Miska for providing guidance, and to Darred
Surin and Kamil Moroz for their support.
• This project was made possible through the generous funding
and support of the Cell and Molecular Visualization REU
Grant REU DBI 1359172.
• Additional funding provided by the Garden State Louise
Stokes Alliance for Minority Participation (GS-LSAMP) Kean
University Chapter.
References
• Joseph, A. & Turrigiano G.G.
• Ibata, K., Sun, Q., & Turrigiano, G. G. (2008). Rapid synaptic scaling induced by
changes in postsynaptic firing. Neuron, 57(6), 819-826.
• Soderling, T. R. (1999). The Ca 2+–calmodulin-dependent protein kinase cascade.
Trends in biochemical sciences, 24(6), 232-236.
• Turrigiano, G. G. (2008). The self-tuning neuron: synaptic scaling of excitatory
synapses. Cell, 135(3), 422-435.
• Wayman, G. A., Lee, Y. S., Tokumitsu, H., Silva, A., & Soderling, T. R. (2008).
Calmodulin-kinases: modulators of neuronal development and plasticity. Neuron, 59(6),
914-931.
• Immunofluorescence Background [Online image]. (2016).Retrieved July 16, 2016 from
http://www.di.uq.edu.au/sparqcbeifbackground
A
Figure 1A: CaMKIV pathway cascade
resulting in scaling due to unknown scaling
factor. (Turrigiano et al 2008)
Figure 1B: Simplified CaMKIV pathway
depicting translocation from the soma to the
nucleus activating transcription (Joseph et
al, adapted from Wayman et al 2008.
A B
B
C
Quantification of Fluorescence Intensity
Figure 2A: Experimental workflow where each arrow represents an individual step preformed. Experiments typical ran 5 to 6 days per dissociation.
Figure 2B: Neurons were transfected with GFP, treated with BCC/TTX for six hours, and then mounted with nuclear DAPI stain (DIV8).
Figure 3B: Neurons imaged and average fluorescence intensity was measured and quantified using MetaMorph software. Data suggests that
nuclear CaMKIV expression increases in the TTX condition implying that transcription factors have been activated in response to the decrease of cell
activity. In contrast, nuclear CaMKIV expression in BCC treated cells resulted in highly variable data.
A
B
C
Figure 2: Representative images of selected neurons using LAS imaging software. GFP (green) was utilized to identify neurons on classical pyramidal morphology. CaMKIV (red) expression was measured and DAPI (blue) was used to
identify nuclear CaMKIV. Figure 2A: Stained control cells demonstrated a high variability in CaMKIV expression in transfect vs non-transfected neurons. Figure 2B: TTX treated cells expressed higher levels of CaMKIV in the nucleus
implying that transcription factors have been activated in response to the decrease of cell activity. Figure 2C: BCC treated cells expressed no clear trend in CaMKIV expression resulting in highly variable data.
Figure 3A: BCC treated cells produced results that were opposite of the original hypothesis. Nuclear
CaMKIV expression appears more intense when compared to somatic expression implying that
CaMKIV is still being activated. While a trend of nuclear CaMKIV expression is seen when compared
to control cells, no significant conclusions can be drawn at this time.
Figure 3B: TTX treated cell data supported the original hypothesis that when cells respond to a decrease in
activity by increasing CaMKIV in attempt to scale up activity to a new set point through transcription factor
activation. The average nuclear CaMKIV (*) expression (p=0.0644) is close to being significant.
Figure 3C: Non-transfected pyramidal cells were
imaged to investigate the high variability in CaMKIV
expression when compared to transfected cells. The
average nuclear to somatic CaMKIV (**) expression
ratio (p=0.0065) showed approximately a two-fold
increase. Nuclear CaMKIV (***) expression
(p=0.0494) showed an approximate four-fold
increase when compared to control cells.
There is no clear reason as to why the fluorescence
intensity increases so dramatically in the non-
transfected cells. It is unknown if BCC treated, non-
transfected cells would express a similar trend.
• Non-transfected cells treated with TTX showed a
significant increase in nuclear CaMKIV relative to
somatic CaMKIV.
• Cells transfected with GFP showed a nonsignificant
trend toward increased nuclear/somatic CaMKIV when
treated with either TTX or BCC.
• Non-transfected neurons appear to express more
CaMKIV when compared to transfected neurons.
• TTX-treated cells demonstrate an inverse ratio of
CaMKIV to activity (i.e. low activity, higher CaMKIV and
vice versa).
• BCC-treated cells elicit nuclear CaMKIV localization
similar to TTX-treated cells, paradoxically.
• Investigate why non-transfected cells express such a
significant increase in CaMKIV expression when
compared to transfected cells in the TTX condition.
• Determine if non-transfected cells treated with BCC
demonstrate similar changes in expression when
compared to transfected cells.
• Implement a more reliable method of pyramidal cell
identification than only morphology such as NeuN stain.
• Run treatments for 2, 4, and 6 hour intervals to
determine is there is ceiling/floor level of activity.
A
*
B
**
***
C