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https://www.readbyqxmd.com/read/28205321/an-investigative-graduate-laboratory-course-for-teaching-modern-dna-techniques
#1
Alexandre de Lencastre, A Thomas Torello, Lani C Keller
This graduate-level DNA methods laboratory course is designed to model a discovery-based research project and engages students in both traditional DNA analysis methods and modern recombinant DNA cloning techniques. In the first part of the course, students clone the Drosophila ortholog of a human disease gene of their choosing using Gateway(®) cloning. In the second part of the course, students examine the expression of their gene of interest in human cell lines by reverse transcription PCR and learn how to analyze data from quantitative reverse transcription PCR (qRT-PCR) experiments...
February 16, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/28202539/parps-and-adp-ribosylation-recent-advances-linking-molecular-functions-to-biological-outcomes
#2
REVIEW
Rebecca Gupte, Ziying Liu, W Lee Kraus
The discovery of poly(ADP-ribose) >50 years ago opened a new field, leading the way for the discovery of the poly(ADP-ribose) polymerase (PARP) family of enzymes and the ADP-ribosylation reactions that they catalyze. Although the field was initially focused primarily on the biochemistry and molecular biology of PARP-1 in DNA damage detection and repair, the mechanistic and functional understanding of the role of PARPs in different biological processes has grown considerably of late. This has been accompanied by a shift of focus from enzymology to a search for substrates as well as the first attempts to determine the functional consequences of site-specific ADP-ribosylation on those substrates...
January 15, 2017: Genes & Development
https://www.readbyqxmd.com/read/28195249/building-blocks-of-the-gipu-italian-group-of-ultrastructural-pathology
#3
V Papa, R Costa, G Cenacchi
The Italian Group of Ultrastructural Pathology, GIPU, is a scientific organization committed to promote the art and science of Electron Microscopy (EM) in the pathology field in Italy, sharing its professional work with a public audience. The history of the GIPU goes back to 1990s when a founder group set up the Italian Group of Ultrastructural Diagnostic (GIDU) in Milan. The central focus of annual meetings was on EM, transmission and scanning one, about interesting cases in which it was instrumental in diagnosis...
June 2016: Pathologica
https://www.readbyqxmd.com/read/28188860/genetic-incorporation-of-n-%C3%AE%C2%B5-acetyllysine-reveals-a-novel-acetylation-sumoylation-switch-in-yeast
#4
Sang-Woo Kim, Kyung Jin Lee, Sinil Kim, Jihyo Kim, Kyukwang Cho, Hyeon-Su Ro, Hee-Sung Park
The lysine acetylation of proteins plays a key role in regulating protein functions, thereby controlling a wide range of cellular processes. Despite the prevalence and significance of lysine acetylation in eukaryotes, however, its systematic study has been challenged by the technical limitations of conventional approaches for selective lysine acetylation in vivo. Here, we report the in vivo study of lysine acetylation via the genetic incorporation of N(ε)-acetyllysine in yeast. We demonstrate that a newly discovered acetylation-sumoylation switch precisely controls the localization and cellular function of the yeast septin protein, Cdc11, during the cell cycle...
February 7, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28174720/netrin-1-protects-hepatocytes-against-cell-death-through-sustained-translation-during-the-unfolded-protein-response
#5
Thomas Lahlali, Marie-Laure Plissonnier, Cristina Romero-López, Maud Michelet, Benjamin Ducarouge, Alfredo Berzal-Herranz, Fabien Zoulim, Patrick Mehlen, Romain Parent
BACKGROUND & AIMS: Netrin-1, a multifunctional secreted protein, is up-regulated in cancer and inflammation. Netrin-1 blocks apoptosis induced by the prototypical dependence receptors deleted in colorectal carcinoma and uncoordinated phenotype-5. Although the unfolded protein response (UPR) triggers apoptosis on exposure to stress, it first attempts to restore endoplasmic reticulum homeostasis to foster cell survival. Importantly, UPR is implicated in chronic liver conditions including hepatic oncogenesis...
May 2016: Cellular and Molecular Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28162022/proteomic-analysis-of-red-blood-cells-and-the-potential-for-the-clinic-what-have-we-learned-so-far
#6
Angelo D'Alessandro, Lello Zolla
Red blood cells (RBC) are the most abundant host cells in the human body. Mature erythrocytes are devoid of nuclei and organelles and have always been regarded as circulating "bags of hemoglobin". The advent of proteomics has challenged this assumption, revealing unanticipated complexity and novel roles for RBCs not just in gas transport, but also in systemic metabolic homeostasis in health and disease. Areas covered: In this review we will summarize the main advancements in the field of discovery mode and redox/quantitative proteomics with respect to RBC biology...
February 4, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28153753/mistranslation-from-adaptations-to-applications
#7
REVIEW
Kyle S Hoffman, Patrick O'Donoghue, Christopher J Brandl
BACKGROUND: The conservation of the genetic code indicates that there was a single origin, but like all genetic material, the cell's interpretation of the code is subject to evolutionary pressure. Single nucleotide variations in tRNA sequences can modulate codon assignments by altering codon-anticodon pairing or tRNA charging. Either can increase translation errors and even change the code. The frozen accident hypothesis argued that changes to the code would destabilize the proteome and reduce fitness...
January 30, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28132906/adenylyl-cyclase-signalling-complexes-pharmacological-challenges-and-opportunities
#8
REVIEW
Michelle L Halls, Dermot M F Cooper
Signalling pathways involving the vital second messanger, cAMP, impact on most significant physiological processes. Unsurprisingly therefore, the activation and regulation of cAMP signalling is tightly controlled within the cell by processes including phosphorylation, the scaffolding of protein signalling complexes and sub-cellular compartmentalisation. This inherent complexity, along with the highly conserved structure of the catalytic sites among the nine membrane-bound adenylyl cyclases, presents significant challenges for efficient inhibition of cAMP signalling...
January 26, 2017: Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/28128334/protein-kinase-c-%C3%AE-a-new-target-therapy-to-prevent-the-long-term-atypical-antipsychotics-induced-weight-gain
#9
Alessandro Rimessi, Chiara Pavan, Elli Ioannidi, Federica Nigro, Claudia Morganti, Alberto Brugnoli, Francesco Longo, Chiara Gardin, Letizia Ferroni, Michele Morari, Vincenzo Vindigni, Barbara Zavan, Paolo Pinton
Antipsychotic drugs are currently used in clinical practice for a variety of mental disorders. Among them, clozapine is the most effective medication for treatment-resistant schizophrenia and is most helpful in controlling aggression and the suicidal behavior in schizophrenia and schizoaffective disorder. Although clozapine is associated with a low likelihood of extrapyramidal symptoms and other neurological side effects, it is well-known for the weight gain and metabolic side effects, which expose the patient to a greater risk of cardiovascular disorders, premature death, as well as psychosocial issues leading to non-adherence to therapy...
January 27, 2017: Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/28063488/analyses-of-calcium-independent-phospholipase-a2beta-ipla2%C3%AE-in-biological-systems
#10
S E Barbour, S Ramanadham
The Ca(2+)-independent phospholipases A2 (iPLA2s) are part of a diverse family of PLA2s, manifest activity in the absence of Ca(2+), are ubiquitous, and participate in a variety of biological processes. Among the iPLA2s, the cytosolic iPLA2β has received considerable attention and ongoing studies from various laboratories suggest that dysregulation of iPLA2β can have a profound impact on the onset and/or progression of many diseases (e.g., cardiovascular, neurological, metabolic, autoimmune). Therefore, appropriate approaches are warranted to gain a better understanding of the role of iPLA2β in vivo and its contribution to pathophysiology...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28062838/enzymes-as-modular-catalysts-for-redox-half-reactions-in-h2-powered-chemical-synthesis-from-biology-to-technology
#11
REVIEW
Holly A Reeve, Philip A Ash, HyunSeo Park, Ailun Huang, Michalis Posidias, Chloe Tomlinson, Oliver Lenz, Kylie A Vincent
The present study considers the ways in which redox enzyme modules are coupled in living cells for linking reductive and oxidative half-reactions, and then reviews examples in which this concept can be exploited technologically in applications of coupled enzyme pairs. We discuss many examples in which enzymes are interfaced with electronically conductive particles to build up heterogeneous catalytic systems in an approach which could be termed synthetic biochemistry We focus on reactions involving the H(+)/H2 redox couple catalysed by NiFe hydrogenase moieties in conjunction with other biocatalysed reactions to assemble systems directed towards synthesis of specialised chemicals, chemical building blocks or bio-derived fuel molecules...
January 15, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28052921/the-circadian-oscillator-of-the-cerebral-cortex-molecular-biochemical-and-behavioral-effects-of-deleting-the-arntl-clock-gene-in-cortical-neurons
#12
Tenna Bering, Mikkel Bloss Carstensen, Gitta Wörtwein, Pia Weikop, Martin Fredensborg Rath
A molecular circadian oscillator resides in neurons of the cerebral cortex, but its role is unknown. Using the Cre-LoxP method, we have here abolished the core clock gene Arntl in those neurons. This mouse represents the first model carrying a deletion of a circadian clock component specifically in an extrahypothalamic cell type of the brain. Molecular analyses of clock gene expression in the cerebral cortex of the Arntl conditional knockout mouse revealed disrupted circadian expression profiles, whereas clock gene expression in the suprachiasmatic nucleus was still rhythmic, thus showing that Arntl is required for normal function of the cortical circadian oscillator...
January 3, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/28043965/cell-scientist-to-watch-madeline-lancaster
#13
(no author information available yet)
Madeline Lancaster received her first degree in biochemistry from the Occidental College in Los Angeles, California, and continued to follow her interests by pursuing a PhD in biomedical sciences in the laboratory of Joseph Gleeson at University of California, San Diego. She then left the USA to train as a postdoctoral fellow with Jürgen Knoblich at the Institute of Molecular Biotechnology of the Austrian Academy of Sciences in Vienna. Madeline was a recipient of the EMBO, Helen Hay Whitney and Marie Curie Incoming Fellowships, and in 2014 her work was recognised when she was awarded the Eppendorf Award for Young Investigators...
January 1, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28043964/interview-with-the-guest-editor-andrew-ewald
#14
(no author information available yet)
Andrew Ewald is an Associate Professor of Cell Biology, Oncology and Biomedical Engineering at the Johns Hopkins University School of Medicine, Baltimore, MD. He joined the Johns Hopkins faculty in 2008, after postdoctoral work with Zena Werb in mammary biology and cancer at the University of California, San Francisco. Andrew earned his PhD in 2003 in biochemistry and molecular biophysics from the California Institute of Technology, studying with Scott Fraser. Andrew studies how organs form and how breast cancer progresses to metastasis...
January 1, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28040509/integration-of-proteomics-and-metabolomics-to-elucidate-metabolic-adaptation-in-leishmania
#15
Snezhana Akpunarlieva, Stefan Weidt, Dhilia Lamasudin, Christina Naula, David Henderson, Michael Barrett, Karl Burgess, Richard Burchmore
: Leishmania parasites multiply and develop in the gut of a sand fly vector in order to be transmitted to a vertebrate host. During this process they encounter and exploit various nutrients, including sugars, and amino and fatty acids. We have previously generated a mutant Leishmania line that is deficient in glucose transport and which displays some biologically important phenotypic changes such as reduced growth in axenic culture, reduced biosynthesis of hexose-containing virulence factors, increased sensitivity to oxidative stress, and dramatically reduced parasite burden in both insect vector and macrophage host cells...
December 29, 2016: Journal of Proteomics
https://www.readbyqxmd.com/read/28032413/variation-in-external-representations-as-part-of-the-classroom-lecture-an-investigation-of-virtual-cell-animations-in-introductory-photosynthesis-instruction
#16
Eric E Goff, Katie M Reindl, Christina Johnson, Phillip McClean, Erika G Offerdahl, Noah L Schroeder, Alan R White
The use of external representations (ERs) to introduce concepts in undergraduate biology has become increasingly common. Two of the most prevalent are static images and dynamic animations. While previous studies comparing static images and dynamic animations have resulted in somewhat conflicting findings in regards to learning outcomes, the benefits of each have been shown individually. Using ERs developed by the Virtual Cell Animation project, we aim to further investigate student learning using different ERs as part of an introductory biology lecture...
December 28, 2016: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/28027953/neurophysiological-assessment-of-neural-network-plasticity-and-connectivity-progress-towards-early-functional-biomarkers-for-disease-interception-therapies-in-alzheimer-s-disease
#17
REVIEW
C Walsh, W H I M Drinkenburg, A Ahnaou
Despite a great deal of research into Alzheimer's disease (AD) over the last 20 years, an effective treatment to halt or slow its progression has yet to be developed. With many aspects of the disease progression still to be elucidated, focus has shifted from reducing levels of amyloid β (Aβ) in the brains of AD patients towards tau, another pathology, which initiates much earlier in deeper brainstem networks and is thought to propagate via cell-to-cell processes prior to the onset of amyloid pathology and cognitive impairments...
February 2017: Neuroscience and Biobehavioral Reviews
https://www.readbyqxmd.com/read/28009974/dissonance-strikes-a-chord-in-stilbene-synthesizers
#18
Cynthia K Holland, Barbara Cascella, Joseph M Jez
In this issue of Cell Chemical Biology, Mori et al. (2016) combine X-ray crystallography and biochemistry to discover a new mechanism for stilbene synthesis in bacteria. The dialkyl-condensing enzyme StlD catalyzes formation of cyclohexanediones using a non-canonical β-ketosynthase active site. Aromatization by StlC completes production of the stilbene product.
December 22, 2016: Cell Chemical Biology
https://www.readbyqxmd.com/read/28007610/structure-biochemistry-and-biology-of-pak-kinases
#19
REVIEW
Rakesh Kumar, Rahul Sanawar, Xiaodong Li, Feng Li
PAKs, p21-activated kinases, play central roles and act as converging junctions for discrete signals elicited on the cell surface and for a number of intracellular signaling cascades. PAKs phosphorylate a vast number of substrates and act by remodeling cytoskeleton, employing scaffolding, and relocating to distinct subcellular compartments. PAKs affect wide range of processes that are crucial to the cell from regulation of cell motility, survival, redox, metabolism, cell cycle, proliferation, transformation, stress, inflammation, to gene expression...
March 20, 2017: Gene
https://www.readbyqxmd.com/read/28005420/exposure-memory-and-lung-regeneration
#20
Young-Mi Go, Dean P Jones
Many acute and chronic lung diseases could benefit from improved regeneration therapy. In development and throughout life, genetically encoded exposure memory systems allow environmental exposures, diet, and infectious agents to direct subsequent phenotypic adaptation and responses. The impact of such memory systems on lung regeneration is currently unknown. This article provides a brief overview of advances in redox biology and medicine as a framework for elucidating exposure memory and delineating spatiotemporal responses in lung regeneration...
December 2016: Annals of the American Thoracic Society
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