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https://www.readbyqxmd.com/read/28315388/mechano-devo
#1
REVIEW
Olivier Hamant
In "On growth and form", D'Arcy Wentworth Thompson (1917) stresses the inevitable interactions between physics and developmental biology. With the recent progress in molecular genetics, live imaging, micromechanics and modeling, the study of morphogenesis has been rejuvenated in the present century: the activity of developmental genes can be interpreted in terms of mechanical properties to dissect the chain of events behind shape changes; in turn, patterns of shape- and growth-derived mechanical stress are calculated and shown to act as signals controlling cell effectors, in synergy with biochemical cues, thereby channeling morphogenesis...
March 15, 2017: Mechanisms of Development
https://www.readbyqxmd.com/read/28301754/bioanalytical-measurements-enabled-by-surface-enhanced-raman-scattering-sers-probes
#2
Lauren E Jamieson, Steven M Asiala, Kirsten Gracie, Karen Faulds, Duncan Graham
Since its discovery in 1974, surface-enhanced Raman scattering (SERS) has gained momentum as an important tool in analytical chemistry. SERS is used widely for analysis of biological samples, ranging from in vitro cell culture models, ex vivo tissue and blood samples, and direct in vivo application. New insights have been gained into biochemistry, with an emphasis on biomolecule detection, from small molecules such as glucose and amino acids to larger biomolecules such as DNA, proteins, and lipids. These measurements have increased our understanding of biological systems, and significantly, they have improved diagnostic capabilities...
February 23, 2017: Annual Review of Analytical Chemistry
https://www.readbyqxmd.com/read/28301747/single-cell-transcriptional-analysis
#3
Angela R Wu, Jianbin Wang, Aaron M Streets, Yanyi Huang
Despite being a relatively recent technological development, single-cell transcriptional analysis through high-throughput sequencing has already been used in hundreds of fruitful studies to make exciting new biological discoveries that would otherwise be challenging or even impossible. Consequently, this has fueled a virtuous cycle of even greater interest in the field and compelled development of further improved technical methodologies and approaches. Thanks to the combined efforts of the research community, including the fields of biochemistry and molecular biology, technology and instrumentation, data science, computational biology, and bioinformatics, the single-cell RNA-sequencing field is advancing at a pace that is both astounding and unprecedented...
March 16, 2017: Annual Review of Analytical Chemistry
https://www.readbyqxmd.com/read/28301739/systems-biology-of-metabolism
#4
Jens Nielsen
Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use mathematical models for holistic studies. The use of mathematical models in biology is referred to as systems biology. In this review, the principles of systems biology are described, and two different types of mathematical models used for studying metabolism are discussed: kinetic models and genome-scale metabolic models. The use of different omics technologies, including transcriptomics, proteomics, metabolomics, and fluxomics, for studying metabolism is presented...
March 8, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28288813/a-genomically-modified-escherichia-coli-strain-carrying-an-orthogonal-e-coli-histidyl-trna-synthetase%C3%A2-trna-his-pair
#5
Markus Englert, Oscar Vargas-Rodriguez, Noah M Reynolds, Yane-Shih Wang, Dieter Söll, Takuya Umehara
BACKGROUND: Development of new aminoacyl-tRNA synthetase (aaRS)•tRNA pairs is central for incorporation of novel non-canonical amino acids (ncAAs) into proteins via genetic code expansion (GCE). The Escherichia coli and Caulobacter crescentus histidyl-tRNA synthetases (HisRS) evolved divergent mechanisms of tRNA(His) recognition that prevent their cross-reactivity. Although the E. coli HisRS•tRNA(His) pair is a good candidate for GCE, its use in C. crescentus is limited by the lack of established genetic selection methods and by the low transformation efficiency of C...
March 10, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28287110/t-cells-and-autoimmune-kidney-disease
#6
REVIEW
Abel Suárez-Fueyo, Sean J Bradley, David Klatzmann, George C Tsokos
Glomerulonephritis is traditionally considered to result from the invasion of the kidney by autoantibodies and immune complexes from the circulation or following their formation in situ, and by cells of the innate and the adaptive immune system. The inflammatory response leads to the proliferation and dysfunction of cells of the glomerulus, and invasion of the interstitial space with immune cells, resulting in tubular cell malfunction and fibrosis. T cells are critical drivers of autoimmunity and related organ damage, by supporting B-cell differentiation and antibody production or by directly promoting inflammation and cytotoxicity against kidney resident cells...
March 13, 2017: Nature Reviews. Nephrology
https://www.readbyqxmd.com/read/28285158/catalytic-topological-insulator-bi2se3-nanoparticles-for-in-vivo-protection-against-ionizing-radiation
#7
Xiao-Dong Zhang, Yaqi Jing, Shasha Song, Jiang Yang, Jun-Ying Wang, Xuhui Xue, Yuho Min, Gyeongbae Park, Xiu Shen, Yuan-Ming Sun, Unyong Jeong
Bi2Se3 nanoparticles (NPs) have attracted wide interests in biological and medical applications. Layer-like Bi2Se3 with high active surface area is promising for free radical scavenging. Here, we extended the medical applications of Bi2Se3 NPs further to in vivo protection against ionizing radiation based on their superior antioxidant activities and electrocatalytic properties. It was found that Bi2Se3 NPs can significantly increase the surviving fraction of mice after exposure of high-energy radiation of gamma ray...
March 8, 2017: Nanomedicine: Nanotechnology, Biology, and Medicine
https://www.readbyqxmd.com/read/28277548/optimized-labeling-of-membrane-proteins-for-applications-to-super-resolution-imaging-in-confined-cellular-environments-using-monomeric-streptavidin
#8
Ingrid Chamma, Olivier Rossier, Grégory Giannone, Olivier Thoumine, Matthieu Sainlos
Recent progress in super-resolution imaging (SRI) has created a strong need to improve protein labeling with probes of small size that minimize the target-to-label distance, increase labeling density, and efficiently penetrate thick biological tissues. This protocol describes a method for labeling genetically modified proteins incorporating a small biotin acceptor peptide with a 3-nm fluorescent probe, monomeric streptavidin. We show how to express, purify, and conjugate the probe to organic dyes with different fluorescent properties, and how to label selectively biotinylated membrane proteins for SRI techniques (point accumulation in nanoscale topography (PAINT), stimulated emission depletion (STED), stochastic optical reconstruction microscopy (STORM))...
April 2017: Nature Protocols
https://www.readbyqxmd.com/read/28266535/g196-epitope-tag-system-a-novel-monoclonal-antibody-g196-recognizes-the-small-soluble-peptide-dlvpr-with-high-affinity
#9
Kasumi Tatsumi, Gyosuke Sakashita, Yuko Nariai, Kosuke Okazaki, Hiroaki Kato, Eiji Obayashi, Hisashi Yoshida, Kanako Sugiyama, Sam-Yong Park, Joji Sekine, Takeshi Urano
The recognition specificity of monoclonal antibodies (mAbs) has made mAbs among the most frequently used tools in both basic science research and in clinical diagnosis and therapies. Precise determination of the epitope allows the development of epitope tag systems to be used with recombinant proteins for various purposes. Here we describe a new family of tag derived from the epitope recognized by a highly specific mAb G196. The minimal epitope was identified as the five amino acid sequence Asp-Leu-Val-Pro-Arg...
March 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28258214/identification-of-a-feedback-loop-involving-beta-glucosidase-2-and-its-product-sphingosine-sheds-light-on-the-molecular-mechanisms-in-gaucher-disease
#10
Sophie Schonauer, Heinz G Körschen, Anke Penno, Andreas Rennhack, Bernadette Breiden, Konrad Sandhoff, Katharina Gutbrod, Peter Dörmann, Diana N Raju, Per Haberkant, Mathias J Gerl, Britta Brügger, Hila Zigdon, Ayelet Vardi, Anthony H Futerman, Christoph Thiele, Dagmar Wachten
The lysosomal acid beta-glucosidase GBA1 and the non-lysosomal beta-glucosidase GBA2 degrade glucosylceramide (GlcCer) to glucose and ceramide in different cellular compartments. Loss of GBA2 activity and the resulting accumulation of GlcCer results in male infertility, whereas mutations in the GBA1 gene and loss of GBA1 activity cause the lipid-storage disorder Gaucher disease. However, the role of GBA2 in Gaucher disease pathology and its relationship to GBA1 is not well understood. Here, we report a GBA1-dependent down-regulation of GBA2 activity in patients with Gaucher disease...
March 3, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28254242/do-mammalian-cells-really-need-to-export-and-import-heme
#11
REVIEW
Prem Ponka, Alex D Sheftel, Ann M English, D Scott Bohle, Daniel Garcia-Santos
Heme is a cofactor that is essential to almost all forms of life. The production of heme is a balancing act between the generation of the requisite levels of the end-product and protection of the cell and/or organism against any toxic substrates, intermediates and, in this case, end-product. In this review, we provide an overview of our understanding of the formation and regulation of this metallocofactor and discuss new research on the cell biology of heme homeostasis, with a focus on putative transmembrane transporters now proposed to be important regulators of heme distribution...
February 18, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28251705/selenium-supplementation-modulates-apoptotic-processes-in-thyroid-follicular-cells
#12
Immacolata C Nettore, Emma De Nisco, Silvio Desiderio, Carmela Passaro, Luigi Maione, Mariarosaria Negri, Luigi Albano, Rosario Pivonello, Claudia Pivonello, Giuseppe Portella, Paola Ungaro, Annamaria Colao, Paolo E Macchia
Selenium (Se) is an essential micronutrient modulating several physiopathological processes in the human body. The aim of the study is to characterize the molecular effects determined by Se-supplementation in thyroid follicular cells, using as model the well-differentiated rat thyroid follicular cell line FRTL5. Experiments have been performed to evaluate the effects of Se on cell growth, mortality and proliferation and on modulation of pro- and antiapoptotic pathways. The results indicate that Se-supplementation improves FRTL5 growth rate...
March 2, 2017: BioFactors
https://www.readbyqxmd.com/read/28238854/use-of-a-probabilistic-pbpk-pd-model-to-calculate-data-derived-extrapolation-factors-for-chlorpyrifos
#13
Torka S Poet, Charles Timchalk, Michael J Bartels, Jordan N Smith, Robin McDougal, Daland R Juberg, Paul S Price
A physiologically based pharmacokinetic and pharmacodynamic (PBPK/PD) model combined with Monte Carlo analysis of inter-individual variation was used to assess the effects of the insecticide, chlorpyrifos and its active metabolite, chlorpyrifos oxon in humans. The PBPK/PD model has previously been validated and used to describe physiological changes in typical individuals as they grow from birth to adulthood. This model was updated to include physiological and metabolic changes that occur with pregnancy. The model was then used to assess the impact of inter-individual variability in physiology and biochemistry on predictions of internal dose metrics and quantitatively assess the impact of major sources of parameter uncertainty and biological diversity on the pharmacodynamics of red blood cell acetylcholinesterase inhibition...
February 24, 2017: Regulatory Toxicology and Pharmacology: RTP
https://www.readbyqxmd.com/read/28238733/fragmentation-of-the-crispr-cas-type-i-b-signature-protein-cas8b
#14
Hagen Richter, Judith Rompf, Julia Wiegel, Kristina Rau, Lennart Randau
BACKGROUND: CRISPR arrays are transcribed into long precursor RNA species, which are further processed into mature CRISPR RNAs (crRNAs). Cas proteins utilize these crRNAs, which contain spacer sequences that can be derived from mobile genetic elements, to mediate immunity during a reoccurring virus infection. Type I CRISPR-Cas systems are defined by the presence of different Cascade interference complexes containing large and small subunits that play major roles during target DNA selection...
February 24, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28230335/undergraduate-medical-academic-performance-is-improved-by-scientific-training
#15
Lili Zhang, Wei Zhang, Chong Wu, Zhongming Liu, Yunfei Cai, Xingguo Cao, Yushan He, Guoxiang Liu, Hongming Miao
The effect of scientific training on course learning in undergraduates is still controversial. In this study, we investigated the academic performance of undergraduate students with and without scientific training. The results show that scientific training improves students' test scores in general medical courses, such as biochemistry and molecular biology, cell biology, physiology, and even English. We classified scientific training into four levels. We found that literature reading could significantly improve students' test scores in general courses...
February 23, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/28229590/impacts-of-cross-linkers-on-biological-effects-of-mesoporous-silica-nanoparticles
#16
Yi-Ping Chen, Si-Han Wu, I-Chih Chen, Chien-Tsu Chen
Chemically synthesized cross-linkers play decisive roles in variable cargos attached to nanoparticles (NPs). Previous studies reported that surface properties, such as the size, charge, and surface chemistry, are particularly important determinants influencing the biological fate and actions of NPs and cells. Recent studies also focused on the relationship of serum proteins with the surface properties of NPs (also called the protein corona), which is recognized as a key factor in determining the cytotoxicity and biodistribution...
March 22, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28205321/an-investigative-graduate-laboratory-course-for-teaching-modern-dna-techniques
#17
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
#18
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
#19
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
#20
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
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