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Journal of Biosciences

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https://www.readbyqxmd.com/read/30002272/fluorescence-spectroscopy-for-revealing-mechanisms-in-biology-strengths-and-pitfalls
#1
G Krishnamoorthy
This article describes the basic principles of steady-state and time-resolved fluorescence. The formal equivalence of the two methodologies is described first, followed by the extra advantages of time-resolved methods in revealing population heterogeneity in complex systems encountered in biology. Several examples from the author's work are described in support of the above contention. Finally, several misinterpretations and pitfalls in the interpretation of fluorescence data and their remedy are described.
July 2018: Journal of Biosciences
https://www.readbyqxmd.com/read/30002271/fluorescence-techniques-in-developmental-biology
#2
Sapthaswaran Veerapathiran, Thorsten Wohland
Advanced fluorescence techniques, commonly known as the F-techniques, measure the kinetics and the interactions of biomolecules with high sensitivity and spatiotemporal resolution. Applications of the F-techniques, which were initially limited to cells, were further extended to study in vivo protein organization and dynamics in whole organisms. The integration of F-techniques with multi-photon microscopy and light-sheet microscopy widened their applications in the field of developmental biology. It became possible to penetrate the thick tissues of living organisms and obtain good signal-to-noise ratio with reduced photo-induced toxicity...
July 2018: Journal of Biosciences
https://www.readbyqxmd.com/read/30002270/single-molecule-fluorescence-imaging-generating-insights-into-molecular-interactions-in-virology
#3
Sunaina Banerjee, Satyaghosh Maurya, Rahul Roy
Single-molecule fluorescence methods remain a challenging yet information-rich set of techniques that allow one to probe the dynamics, stoichiometry and conformation of biomolecules one molecule at a time. Viruses are small (nanometers) in size, can achieve cellular infections with a small number of virions and their lifecycle is inherently heterogeneous with a large number of structural and functional intermediates. Single-molecule measurements that reveal the complete distribution of properties rather than the average can hence reveal new insights into virus infections and biology that are inaccessible otherwise...
July 2018: Journal of Biosciences
https://www.readbyqxmd.com/read/30002269/dynamics-of-water-and-ions-around-dna-what-is-so-special-about-them
#4
Him Shweta, Sobhan Sen
Water around biomolecules is special for behaving strangely - both in terms of structure and dynamics, while ions are found to control various interactions in biomolecules such as DNA, proteins and lipids. The questions that how water and ions around these biomolecules behave in terms of their structure and dynamics, and how they affect the biomolecular functions have triggered tremendous research activities worldwide. Such activities not only unfolded important static and dynamic properties of water and ions around these biomolecules, but also provoked heated debate regarding their explanation and role in biological functions...
July 2018: Journal of Biosciences
https://www.readbyqxmd.com/read/30002268/ultrafast-dynamics-driven-biomolecular-recognition-where-fast-activities-dictate-slow-events
#5
Priya Singh, Damayanti Bagchi, Samir Kumar Pal
In general, biological macromolecules require significant dynamical freedom to carry out their different functions, including signal transduction, metabolism, catalysis and gene regulation. Effectors (ligands, DNA and external milieu, etc) are considered to function in a purely dynamical manner by selectively stabilizing a specific dynamical state, thereby regulating biological function. In particular, proteins in presence of these effectors can exist in several dynamical states with distinct binding or enzymatic activity...
July 2018: Journal of Biosciences
https://www.readbyqxmd.com/read/30002267/applications-of-sted-fluorescence-nanoscopy-in-unravelling-nanoscale-structure-and-dynamics-of-biological-systems
#6
C Roobala, I P Ilanila, J K Basu
Fluorescence microscopy, especially confocal microscopy, has revolutionized the field of biological imaging. Breaking the optical diffraction barrier of conventional light microscopy, through the advent of super-resolution microscopy, has ushered in the potential for a second revolution through unprecedented insight into nanoscale structure and dynamics in biological systems. Stimulated emission depletion (STED) microscopy is one such super-resolution microscopy technique which provides real-time enhanced-resolution imaging capabilities...
July 2018: Journal of Biosciences
https://www.readbyqxmd.com/read/30002266/fluorescence-based-approaches-for-monitoring-membrane-receptor-oligomerization
#7
Andrew Ha Clayton
Membrane protein structures are highly under-represented relative to water-soluble protein structures in the protein databank. This is especially the case because membrane proteins represent more than 30% of proteins encoded in the human genome yet contribute to less than 10% of currently known structures (Torres et al. in Trends Biol Sci 28:137-144, 2003). Obtaining high-resolution structures of membrane proteins by traditional methods such as NMR and x-ray crystallography is challenging, because membrane proteins are difficult to solubilise, purify and crystallize...
July 2018: Journal of Biosciences
https://www.readbyqxmd.com/read/30002265/studying-backbone-torsional-dynamics-of-intrinsically-disordered-proteins-using-fluorescence-depolarization-kinetics
#8
Debapriya DAS, Samrat Mukhopadhyay
Intrinsically disordered proteins (IDPs) do not autonomously adopt a stable unique 3D structure and exist as an ensemble of rapidly interconverting structures. They are characterized by significant conformational plasticity and are associated with several biological functions and dysfunctions. The rapid conformational fluctuation is governed by the backbone segmental dynamics arising due to the dihedral angle fluctuation on the Ramachandran φ- ψ conformational space. We discovered that the intrinsic backbone torsional mobility can be monitored by a sensitive fluorescence readout, namely fluorescence depolarization kinetics, of tryptophan in an archetypal IDP such as α-synuclein...
July 2018: Journal of Biosciences
https://www.readbyqxmd.com/read/30002264/single-molecule-photobleaching-instrumentation-and-applications
#9
Simli Dey, Sudipta Maiti
Single-molecule photobleaching (smPB) technique is a powerful tool for characterizing molecular assemblies. It can provide a direct measure of the number of monomers constituting a given oligomeric particle and generate the oligomer size distribution in a specimen. A major current application of this technique is in understanding protein aggregation, which is linked to many incurable diseases. Quantitative measurement of the size distribution of an aggregating protein in a physiological solution remains a difficult task, since techniques such as dynamic light scattering or fluorescence correlation spectroscopy (FCS) can provide an average size, but cannot accurately resolve the underlying size distribution...
July 2018: Journal of Biosciences
https://www.readbyqxmd.com/read/30002263/fluorescence-microscopy-applied-to-intracellular-transport-by-microtubule-motors
#10
Divya Pathak, Shreyasi Thakur, Roop Mallik
Long-distance transport of many organelles inside eukaryotic cells is driven by the dynein and kinesin motors on microtubule filaments. More than 30 years since the discovery of these motors, unanswered questions include motor- organelle selectivity, structural determinants of processivity, collective behaviour of motors and track selection within the complex cytoskeletal architecture, to name a few. Fluorescence microscopy has been invaluable in addressing some of these questions. Here we present a review of some efforts to understand these sub-microscopic machines using fluorescence...
July 2018: Journal of Biosciences
https://www.readbyqxmd.com/read/30002262/a-novel-fluorescence-microscopic-approach-to-quantitatively-analyse-protein-induced-membrane-remodelling
#11
Thomas J Pucadyil
Membrane remodelling or the bending and rupture of the lipid bilayer occurs during diverse cellular processes such as cell division, synaptic transmission, vesicular transport, organelle biogenesis and sporulation. These activities are brought about by the localized change in membrane curvature, which in turn causes lipid-packing stress, of a planar lipid bilayer by proteins. For instance, vesicular transport processes are typically characterized by the cooperative recruitment of proteins that induce budding of a planar membrane and catalyse fission of the necks of membrane buds to release vesicles...
July 2018: Journal of Biosciences
https://www.readbyqxmd.com/read/30002261/gfp-fluorescence-a-few-lesser-known-nuggets-that-make-it-work
#12
Parijat Sarkar, Amitabha Chattopadhyay
Use of Green Fluorescent Protein (GFP) as a marker has revolutionized biological research in the last few decades. In this brief commentary, we reflect upon the success story of GFP and highlight a few lesser-known facets about GFP that add up to its usefulness.
July 2018: Journal of Biosciences
https://www.readbyqxmd.com/read/29872028/genome-3d-architecture-its-plasticity-in-relation-to-function
#13
Kundan Sengupta
The genome of higher eukaryotes is non-randomly organized in the interphase nucleus. However, notwithstanding the absence of membrane bound sub-compartments, the nucleus coordinates a number of functions largely by organizing chromatin in a non-random but dynamic manner. The plasticity of chromatin structure and function relies on epigenetic modifications as well as its association with nuclear landmarks such as the nuclear envelope, nuclear lamina, nuclear pore complex and nuclear bodies such as the nucleolus among others...
June 2018: Journal of Biosciences
https://www.readbyqxmd.com/read/29872027/a-parasporin-from-bacillus-thuringiensis-native-to-peninsular-india-induces-apoptosis-in-cancer-cells-through-intrinsic-pathway
#14
Thomas Chubicka, Devaki Girija, Kizhakkeettil Deepa, Sasidharan Salini, Nair Meera, Achuthan Chathrattil Raghavamenon, Menon Kunnathully Divya, Thekkekara Devassy Babu
Parasporins, a class of non-insecticidal crystal proteins of Bacillus thuringiensis (Bt) are being explored as promising anticancer agents due to their specific toxicity to cancer cells. The present study has identified 25 Bt isolates harbouring parasporin genes from Western Ghats region, the hotspot of biodiversity in India. Among these, the isolate, KAU 41 (Kerala Agricultural University isolate 41) contained non-hemolytic homogenous crystals showing specific cytotoxicity towards cancer cells. SDS-PAGE analysis of this crystal, isolated by aqueous biphasic separation, revealed a 31 kDa sized peptide...
June 2018: Journal of Biosciences
https://www.readbyqxmd.com/read/29872026/spatiotemporal-oscillations-of-morphinan-alkaloids-in-opium-poppy
#15
Mahdi Rezaei, Mohammad Reza Naghavi, Abdolhadi Hosseinzadeh, Alireza Abasi, Jaber Nasiri
Here, a comprehensive endeavor is made to simultaneously scrutinize spatiotemporal oscillations of three imperative morphinan alkaloids (i.e. thebaine, codeine, and morphine) alongside dynamic transcriptional patterns of TYDC, SalAT, COR, T6ODM, and CODM genes in different tissues of Papaver somniferum (i.e. root, bottom part of stem, upper part of stem, leaf, capsule wall, and capsule content) over five distinguished ontogenic stages (i.e. rosette, bud initiation, pendulous bud, flowering, and lancing). Apart from bottom stem and leaf, the maximum thebaine content occurred in lancing stage, while its minimum content did not follow a systematic rhythm, either among six tissues or five various sampling times...
June 2018: Journal of Biosciences
https://www.readbyqxmd.com/read/29872025/spiral-waves-and-vertebrate-embryonic-handedness
#16
Antony J Durston, Joao Peres, Morrel H Cohen
During early embryonic development, the vertebrate main body axis is segmented from head-to-tail into somites. Somites emerge sequentially from the presomitic mesoderm (PSM) as a consequence of oscillatory waves of genetic activity, called somitogenesis waves. Here, we discuss the implications of the dynamic patterns of early X-Delta-2 expression in the prospective somites (somitomeres) of Xenopus laevis. We report that right somitomeres normally emerge before left to form chiral structures (i.e. structures having clockwise or counter-clockwise handedness)...
June 2018: Journal of Biosciences
https://www.readbyqxmd.com/read/29872024/inhibition-of-mir-1247-on-cell-proliferation-and-invasion-in-bladder-cancer-through-its-downstream-target-of-rab36
#17
Yudi Zhu, Shaosi Liang, Huafeng Pan, Zhongliang Cheng, Xin Rui
Recently, microRNA-1247 (miR-1247) has been reported to function as tumour suppressor in several cancer types, including pancreatic cancer, hepatocellular cancer and lung cancer. However, the biological function of miR-1247 in bladder cancer and the underlying mechanisms have remained largely uncovered. In this study, the expression of miR-1247 was significantly downregulated, while RAB36 protein was remarkably upregulated in bladder cancer tissues and cell lines compared with that in paired adjacent normal tissues or normal cell line (SU-HUC-1)...
June 2018: Journal of Biosciences
https://www.readbyqxmd.com/read/29872023/deletion-of-dictyostelium-discoideum-sir2a-impairs-cell-proliferation-and-inhibits-autophagy
#18
Rakhee Lohia, Punita Jain, Mukul Jain, Himanshu Mishra, Pradeep Kumar Burma, Anju Shrivastava, Shweta Saran
Sirtuins are a family of deacetylases (Class III histone deacetylases) with evolutionarily conserved functions in cellular metabolism and chromatin regulation. Out of the seven human Sirtuins, the function of Sirt2 is the least understood. The purpose of the present study was to investigate the role of Sir2A, a homolog of human Sirt2 in Dictyostelium discoideum (Dd), a lower eukaryote. We created both overexpressing and deletion strains of Ddsir2A to analyse its functions. We observed sir2A mRNA expression throughout development and the transcript was present in the prespore/spore region of multicellular structures developed...
June 2018: Journal of Biosciences
https://www.readbyqxmd.com/read/29872022/putative-role-of-invariant-water-molecules-in-the-x-ray-structures-of-family-g-fungal-endoxylanases
#19
Protyusha Dey, Hridoy R Bairagya, Amit Roy
Fungal endo-1,4-beta-xylanases (EC3.2.1.8), because of their widespread industrial applications have become one of the most researched industrial enzymes in recent times. Despite its significance, the role of conserved water molecules in the catalytic activities and structural stability of these enzymes from the fungi have not been studied to a great extent. Our computational structural bioinformatics and MD simulation studies have identified the existence of seven invariant water molecules (IW1- IW7) and reveals the stereo-chemical and electronic consequences of those conserved water molecules in G-xylanase enzyme from eight different fungi...
June 2018: Journal of Biosciences
https://www.readbyqxmd.com/read/29872021/gender-divergent-expression-of-lipid-and-bile-acid-metabolism-related-genes-in-adult-mice-offspring-of-dams-fed-a-high-fat-diet
#20
Yuji Tanaka, Takanori Ikeda, Kazuo Yamamoto, Shiori Masuda, Hiroshi Ogawa, Toshinori Kamisako
Maternal high-fat diet (HFD) consumption during pregnancy and lactation affects metabolic outcomes and lipid metabolism of offspring in later life in a gender-specific manner. However, it is not known whether maternal HFD alters bile acid metabolism in adult mice offspring. The purpose of this study was to elucidate the relationship between maternal HFDinduced metabolic diseases and bile acid metabolism in male and female adult mice offspring. Female mice were fed either standard chow (C) or HFD (H) for 10 weeks pre-pregnancy until lactation...
June 2018: Journal of Biosciences
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