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Biophysics
Pre-mRNA modifications and their role in nuclear processing.
Dec 11, 2018   Quantitative Biology (Beijing, China)
Martinez NM, Gilbert WV
Pre-mRNA modifications and their role in nuclear processing.
Dec 11, 2018
Quantitative Biology (Beijing, China)
Background: Cellular non-coding RNAs are extensively modified post-transcriptionally, with more than 100 chemically distinct nucleotides identified to date. In the past five years, new sequencing based methods have revealed widespread decoration of eukaryotic messenger RNA with diverse RNA modifications whose functions in mRNA metabolism are only beginning to be known. Results: Since most of the identified mRNA modifying enzymes are present in the nucleus, these modifications have the potential to function in nuclear pre-mRNA processing including alternative splicing. Here we review recent progress towards illuminating the role of pre-mRNA modifications in splicing and highlight key areas for future investigation in this rapidly growing field. Conclusions: Future studies to identify which modifications are added to nascent pre-mRNA and to interrogate the direct effects of individual modifications are likely to reveal new mechanisms by which nuclear pre-mRNA processing is regulated.
Metastasis-related methyltransferase 1 (Merm1) represses the methyltransferase activity of Dnmt3a and facilitates RNA polymerase I transcriptional elongation.
Dec 11, 2018   Journal Of Molecular Cell Biology
Lyu G, Zong L, Zhang C, Huang X, Xie W, Fang J, Guan Y, Zhang L, Ni T, Gu J, Tao W
Metastasis-related methyltransferase 1 (Merm1) represses the methyltransferase activity of Dnmt3a and facilitates RNA polymerase I transcriptional elongation.
Dec 11, 2018
Journal Of Molecular Cell Biology
Stimulatory regulators for DNA methyltransferase activity, such as Dnmt3L and some Dnmt3b isoforms, affect DNA methylation patterns, thereby maintaining gene body methylation and maternal methylation imprinting, as well as the methylation landscape of pluripotent cells. Here we show that metastasis-related methyltransferase 1 (Merm1), a protein deleted in individuals with Williams-Beuren syndrome, acts as a repressive regulator of Dnmt3a. Merm1 interacts with Dnmt3a and represses its methyltransferase activity with the requirement of the binding motif for S-adenosyl-L-methionine. Functional analysis of gene regulation revealed that Merm1 is capable of maintaining hypomethylated rRNA gene bodies and co-localizes with RNA polymerase I in the nucleolus. Dnmt3a recruits Merm1, and in return, Merm1 ensures the binding of Dnmt3a to hypomethylated gene bodies. Such interplay between Dnmt3a and Merm1 facilitates transcriptional elongation by RNA polymerase I. Our findings reveal a repressive factor for Dnmt3a and uncover a molecular mechanism underlying transcriptional elongation of rRNA genes.
Separating Normosmic and Anosmic Patients Based on Entropy Evaluation of Olfactory Event-Related Potentials.
Dec 11, 2018   Brain Research
Guducu C, Olcay BO, Donner L, Aziz M, Schriever VA, Ozgoren M, Hummel T
Separating Normosmic and Anosmic Patients Based on Entropy Evaluation of Olfactory Event-Related Potentials.
Dec 11, 2018
Brain Research
OBJECTIVE: Methods based on electroencephalography (EEG) are used to evaluate brain responses to odors which is challenging due to the relatively low signal-to-noise ratio. This is especially difficult in patients with olfactory loss. In the present study, we aim to establish a method to separate functionally anosmic and normosmic individuals by means of recordings of olfactory event-related potentials (OERP) using an automated tool. Therefore, Shannon entropy was adopted to examine the complexity of the averaged electrophysiological responses. METHODS: A total of 102 participants received 60 rose-like odorous stimuli at an inter-stimulus interval of 10s. Olfactory-related brain activity was investigated within three time-windows of equal length; pre-, during-, and post-stimulus. RESULTS: Based on entropy analysis, patients were correctly diagnosed for anosmia with a 75% success rate. CONCLUSION: This novel approach can be expected to help clinicians to identify patients with anosmia or patients with early symptoms of neurodegenerative disorders. SIGNIFICANCE: There is no automated diagnostic tool for anosmic and normosmic patients using OERP. However, detectability of OERP in patients with functional anosmia has been reported to be in the range of 50%.
Molecular Evolution of Early-Onset Prostate Cancer Identifies Molecular Risk Markers and Clinical Trajectories.
Dec 11, 2018   Cancer Cell
Gerhauser C, Favero F, Risch T, Simon R, Feuerbach L,   . . . . . .   , Plass C, Yaspo ML, Korbel JO, Schlomm T, Weischenfeldt J
Molecular Evolution of Early-Onset Prostate Cancer Identifies Molecular Risk Markers and Clinical Trajectories.
Dec 11, 2018
Cancer Cell
Identifying the earliest somatic changes in prostate cancer can give important insights into tumor evolution and aids in stratifying high- from low-risk disease. We integrated whole genome, transcriptome and methylome analysis of early-onset prostate cancers (diagnosis ≤55 years). Characterization across 292 prostate cancer genomes revealed age-related genomic alterations and a clock-like enzymatic-driven mutational process contributing to the earliest mutations in prostate cancer patients. Our integrative analysis identified four molecular subgroups, including a particularly aggressive subgroup with recurrent duplications associated with increased expression of ESRP1, which we validate in 12,000 tissue microarray tumors. Finally, we combined the patterns of molecular co-occurrence and risk-based subgroup information to deconvolve the molecular and clinical trajectories of prostate cancer from single patient samples.
Hyperactivation of Nrf2 increases stress tolerance at the cost of aging acceleration due to metabolic deregulation.
Dec 11, 2018   Aging Cell
Tsakiri EN, Gumeni S, Iliaki KK, Benaki D, Vougas K, Sykiotis GP, Gorgoulis VG, Mikros E, Scorrano L, Trougakos IP
Hyperactivation of Nrf2 increases stress tolerance at the cost of aging acceleration due to metabolic deregulation.
Dec 11, 2018
Aging Cell
Metazoans viability depends on their ability to regulate metabolic processes and also to respond to harmful challenges by mounting anti-stress responses; these adaptations were fundamental forces during evolution. Central to anti-stress responses are a number of short-lived transcription factors that by functioning as stress sensors mobilize genomic responses aiming to eliminate stressors. We show here that increased expression of nuclear factor erythroid 2-related factor (Nrf2) in Drosophila activated cytoprotective modules and enhanced stress tolerance. However, while mild Nrf2 activation extended lifespan, high Nrf2 expression levels resulted in developmental lethality or, after inducible activation in adult flies, in altered mitochondrial bioenergetics, the appearance of Diabetes Type 1 hallmarks and aging acceleration. Genetic or dietary suppression of Insulin/IGF-like signaling (IIS) titrated Nrf2 activity to lower levels, largely normalized metabolic pathways signaling, and extended flies' lifespan. Thus, prolonged stress signaling by otherwise cytoprotective short-lived stress sensors perturbs IIS resulting in re-allocation of resources from growth and longevity to somatic preservation and stress tolerance. These findings provide a reasonable explanation of why most (if not all) cytoprotective stress sensors are short-lived proteins, and it also explains the build-in negative feedback loops (shown here for Nrf2); the low basal levels of these proteins, and why their suppressors were favored by evolution.
Single tube liquid biopsy for advanced non-small cell lung cancer.
Dec 11, 2018   International Journal Of Cancer
de Wit S, Rossi E, Weber S, Tamminga M, Manicone M,   . . . . . .   , Hiltermann TJN, Speicher MR, Heitzer E, Terstappen LWMM, Groen HJM
Identification of Two Mutations in PCDHGA4 and SLFN14 Genes in an Atrial Septal Defect Family.
Dec 11, 2018   Current Medical Science
Su W, Wang RC, Lohano MK, Wang L, Zhu P, Luo Y, Guo LJ, Lv Q, Jiang H, Wang JH, Mei L, Weng J, Su L, Dong NG
Identification of Two Mutations in PCDHGA4 and SLFN14 Genes in an Atrial Septal Defect Family.
Dec 11, 2018
Current Medical Science
Atrial septal defect (ASD) is a common acyanotic congenital cardiac disorder associated with genetic mutations. The objective of this study was to identify the genetic factors in a Chinese family with ASD patients by a whole exome sequencing approach. Causative ASD gene mutations were examined in 16 members from a three-generation family, among which 6 individuals were diagnosed as having ASD. One hundred and eighty-three unrelated healthy Chinese were recruited as a normal control group. Peripheral venous blood was collected from every subject for genetic analysis. Exome sequencing was performed in the ASD patients. Potential causal mutations were detected in non-ASD family members and normal controls by polymerase chain reaction and sequencing analysis. The results showed that all affected family members carried two novel compound mutations, c.1187delT of PCDHGA4 and c.2557insC of SLFN14, and these two mutations were considered to have synergetic function on ASD. In conclusion, the mutations of c.1187delT of PCDHGA4 and c.2557insC of SLFN14 may be pathogenic factors contributing to the development of ASD.
CW EPR and DEER Methods to Determine BCL-2 Family Protein Structure and Interactions: Application of Site-Directed Spin Labeling to BAK Apoptotic Pores.
Dec 11, 2018   Methods In Molecular Biology (Clifton, N.J.)
Mandal T, Hustedt EJ, Song L, Oh KJ
CW EPR and DEER Methods to Determine BCL-2 Family Protein Structure and Interactions: Application of Site-Directed Spin Labeling to BAK Apoptotic Pores.
Dec 11, 2018
Methods In Molecular Biology (Clifton, N.J.)
The continuous wave (CW) and pulse electron paramagnetic resonance (EPR) methods enable the measurement of distances between spin-labeled residues in biopolymers including proteins, providing structural information. Here we describe the CW EPR deconvolution/convolution method and the four-pulse double electron-electron resonance (DEER) approach for distance determination, which were applied to elucidate the organization of the BAK apoptotic pores formed in the lipid bilayers.
Sequential backbone resonance assignment of AT-rich interaction domain of human BAF200.
Dec 11, 2018   Biomolecular NMR Assignments
Bastiray A, Giri M, Singh M
Sequential backbone resonance assignment of AT-rich interaction domain of human BAF200.
Dec 11, 2018
Biomolecular NMR Assignments
BAF200 is a subunit of PBAF chromatin remodeling complex that contains an N-terminal AT-rich interaction domain (ARID). ARID domain in general has been shown to bind to the AT-rich DNA sequences. The human BAF200 ARID (~ 110 residues) has the potential to bind the DNA sequences with high affinity, however, the structure and the exact contribution of hBAF200 ARID in PBAF functions as well its DNA binding specificities have not been established. In this study, we have expressed and purified the hBAF200 ARID for NMR studies. We report the complete backbone 1H, 13C, and 15N chemical shift assignment and secondary structure of hBAF200 ARID domain.
Early Excitatory Activity-Dependent Maturation of Somatostatin Interneurons in Cortical Layer 2/3 of Mice.
Dec 11, 2018   Cerebral Cortex (New York, N.Y. : 1991)
Pan NC, Fang A, Shen C, Sun L, Wu Q, Wang X
Early Excitatory Activity-Dependent Maturation of Somatostatin Interneurons in Cortical Layer 2/3 of Mice.
Dec 11, 2018
Cerebral Cortex (New York, N.Y. : 1991)
GABAergic interneurons perform distinct functions during cortical development in the mouse brain. Among the diverse GABAergic neurons present in the brain, early-born somatostatin (SST)-expressing inhibitory interneurons, which are innervated by other interneurons and local pyramidal cells (PCs), act in a neural computational role in circuitry regulation. The synapses between the SST+ interneurons and other cells form gradually during development. Here, we traced the developmental course of the electrophysiological properties of SST+ interneurons at layer 2/3 of the neocortical secondary motor area (M2) in mouse, and the synaptic connectivity between SST+ interneurons and PCs. Also, we used toxin-mediated and genetic method to suppress the activities of PCs, and demonstrate that decreasing excitatory input at early stage (before P1) rather than late stage (after P8) would delay the functional maturation of SST+ interneurons. In conclusion, our results indicate that early functional activity of PCs is crucial for the intrinsic maturation of SST+ interneurons, following which these interneurons participate in local circuitry.
Identification of Abnormal Fucosylated-Glycans Recognized by LTL in Saliva of HBV-Induced Chronic Hepatitis, Cirrhosis, and Hepatocellular Carcinoma.
Dec 11, 2018   Glycobiology
Zhang J, Zhong Y, Zhang P, Du H, Shu J, Liu X, Zhang H, Guo Y, Jia Z, Niu L, Yang F, Li Z
Identification of Abnormal Fucosylated-Glycans Recognized by LTL in Saliva of HBV-Induced Chronic Hepatitis, Cirrhosis, and Hepatocellular Carcinoma.
Dec 11, 2018
Glycobiology
The hepatitis B virus (HBV)-induced chronic liver diseases are serious health threats worldwide. There is evidence to display the alterations of salivary N-linked glycans related to the development of HBV-infected liver diseases. Here, we further investigated the alterations of fucosylated N/O-glycans recognized by LTL in saliva from 120 subjects (30 healthy volunteers (HV), 30 patients with hepatitis B (HB), 30 patients with hepatic cirrhosis (HC), and 30 patients with hepatocellular carcinoma (HCC)) using salivary microarrys and MALDI-TOF/TOF-MS. The results showed that the expression level of fucosylated glycans recognized by LTL was significantly increased in HCC compared with other subjects (p
Detection of Cryptococcus DNA by metagenomic next-generation sequencing in symptomatic cryptococcal antigenemia.
Dec 11, 2018   Clinical Infectious Diseases : An Official Publication Of The Infectious Diseases Society Of America
Ramachandran PS, Cresswell FV, Meya DB, Crawford ED, DeRisi JL, Boulware DR, Wilson MR
Persistent upregulation of the β-tubulin tubb6, linked to muscle regeneration, is a source of microtubule disorganization in dystrophic muscle.
Dec 11, 2018   Human Molecular Genetics
Randazzo D, Khalique U, Belanto JJ, Kenea A, Talsness DM, Olthoff JT, Tran MD, Zaal KJ, Pak K, Pinal-Fernandez I, Mammen AL, Sackett D, Ervasti JM, Ralston E
Persistent upregulation of the β-tubulin tubb6, linked to muscle regeneration, is a source of microtubule disorganization in dystrophic muscle.
Dec 11, 2018
Human Molecular Genetics
In healthy adult skeletal muscle fibers microtubules form a three-dimensional grid-like network. In the mdx mouse, a model of Duchenne muscular dystrophy (DMD), microtubules are mostly disordered, without periodicity. These microtubule defects have been linked to the mdx mouse pathology. We now report that increased expression of the beta 6 class V β-tubulin (tubb6) contributes to the microtubule changes of mdx muscles. Wild-type muscle fibers overexpressing GFP-tubb6 (but not GFP-tubb5) have disorganized microtubules whereas mdx muscle fibers depleted of tubb6 (but not of tubb5) normalize their microtubules, suggesting that increasing tubb6 is toxic. However, tubb6 increases spontaneously during differentiation of mouse and human muscle cultures. Furthermore, endogenous tubb6 is not uniformly expressed in mdx muscles but is selectively increased in fiber clusters, which we identify as regenerating. Similarly, mdx-based rescued transgenic mice that retain a higher than expected tubb6 level show focal expression of tubb6 in subsets of fibers. Tubb6 is also upregulated in cardiotoxin-induced mouse muscle regeneration, in human myositis and DMD biopsies, and the tubb6 level correlates with that of embryonic myosin heavy chain, a regeneration marker. In conclusion, modulation of a β-tubulin isotype plays a role in muscle differentiation and regeneration. Increased tubb6 expression and microtubule reorganization are not pathological per se but reflect a return to an earlier developmental stage. However, chronic elevation of tubb6, as occurs in the mdx mouse, may contribute to the repeated cycles of regeneration and to the pathology of the disease.
Animal protein toxins: origins and therapeutic applications.
Dec 11, 2018   Biophysics Reports
Chen N, Xu S, Zhang Y, Wang F
Animal protein toxins: origins and therapeutic applications.
Dec 11, 2018
Biophysics Reports
Venomous animals on the earth have been found to be valuable resources for the development of therapeutics. Enzymatic and non-enzymatic proteins and peptides are the major components of animal venoms, many of which can target various ion channels, receptors, and membrane transporters. Compared to traditional small molecule drugs, natural proteins and peptides exhibit higher specificity and potency to their targets. In this review, we summarize the varieties and characteristics of toxins from a few representative venomous animals, and describe the components and applications of animal toxins as potential drug candidates in the treatment of human diseases, including cancer, neurodegenerative diseases, cardiovascular diseases, neuropathic pain, as well as autoimmune diseases. In the meantime, there are many obstacles to translate new toxin discovery to their clinical applications. The challenges, strategies, and perspectives in the development of the protein toxin-based drugs are discussed as well.
The sickle cell trait affects contact dynamics and endothelial cell activation in Plasmodium falciparum-infected erythrocytes.
Dec 11, 2018   Communications Biology
Lansche C, Dasanna AK, Quadt K, Fröhlich B, Missirlis D, Tétard M, Gamain B, Buchholz B, Sanchez CP, Tanaka M, Schwarz US, Lanzer M
The sickle cell trait affects contact dynamics and endothelial cell activation in Plasmodium falciparum-infected erythrocytes.
Dec 11, 2018
Communications Biology
Sickle cell trait, a common hereditary blood disorder, protects carriers from severe disease in infections with the human malaria parasite Plasmodium falciparum. Protection is associated with a reduced capacity of parasitized erythrocytes to cytoadhere to the microvascular endothelium and cause vaso-occlusive events. However, the underpinning cellular and biomechanical processes are only partly understood and the impact on endothelial cell activation is unclear. Here, we show, by combining quantitative flow chamber experiments with multiscale computer simulations of deformable cells in hydrodynamic flow, that parasitized erythrocytes containing the sickle cell haemoglobin displayed altered adhesion dynamics, resulting in restricted contact footprints on the endothelium. Main determinants were cell shape, knob density and membrane bending. As a consequence, the extent of endothelial cell activation was decreased. Our findings provide a quantitative understanding of how the sickle cell trait affects the dynamic cytoadhesion behavior of parasitized erythrocytes and, in turn, endothelial cell activation.
Single-cell analysis reveals individual spore responses to simulated space vacuum.
Dec 11, 2018   NPJ Microgravity
He L, Wang S, Cortesão M, Wu M, Moeller R, Setlow P, Li YQ
Single-cell analysis reveals individual spore responses to simulated space vacuum.
Dec 11, 2018
NPJ Microgravity
Outer space is a challenging environment for all forms of life, and dormant spores of bacteria have been frequently used to study the survival of terrestrial life in a space journey. Previous work showed that outer space vacuum alone can kill bacterial spores. However, the responses and mechanisms of resistance of individual spores to space vacuum are unclear. Here, we examined spores' molecular changes under simulated space vacuum (~10-5 Pa) using micro-Raman spectroscopy and found that this vacuum did not cause significant denaturation of spore protein. Then, live-cell microscopy was developed to investigate the temporal events during germination, outgrowth, and growth of individual Bacillus spores. The results showed that after exposure to simulated space vacuum for 10 days, viability of spores of two Bacillus species was reduced up to 35%, but all spores retained their large Ca2+-dipicolinic acid depot. Some of the killed spores did not germinate, and the remaining germinated but did not proceed to vegetative growth. The vacuum treatment slowed spore germination, and changed average times of all major germination events. In addition, viable vacuum-treated spores exhibited much greater sensitivity than untreated spores to dry heat and hyperosmotic stress. Among spores' resistance mechanisms to high vacuum, DNA-protective α/β-type small acid-soluble proteins, and non-homologous end joining and base excision repair of DNA played the most important roles, especially against multiple cycles of vacuum treatment. Overall, these results give new insight into individual spore's responses to space vacuum and provide new techniques for microorganism analysis at the single-cell level.
Sharpening emitter localization in front of a tuned mirror.
Dec 11, 2018   Light, Science & Applications
Heil HS, Schreiber B, Götz R, Emmerling M, Dabauvalle MC, Krohne G, Höfling S, Kamp M, Sauer M, Heinze KG
Sharpening emitter localization in front of a tuned mirror.
Dec 11, 2018
Light, Science & Applications
Single-molecule localization microscopy (SMLM) aims for maximized precision and a high signal-to-noise ratio1. Both features can be provided by placing the emitter in front of a metal-dielectric nanocoating that acts as a tuned mirror2-4. Here, we demonstrate that a higher photon yield at a lower background on biocompatible metal-dielectric nanocoatings substantially improves SMLM performance and increases the localization precision by up to a factor of two. The resolution improvement relies solely on easy-to-fabricate nanocoatings on standard glass coverslips and is spectrally and spatially tunable by the layer design and wavelength, as experimentally demonstrated for dual-color SMLM in cells.
Genome Sequences of Zika Virus Strains Recovered from Amniotic Fluid, Placenta, and Fetal Brain of a Microcephaly Patient in Thailand, 2017.
Dec 11, 2018   Microbiology Resource Announcements
Wongsurawat T, Jenjaroenpun P, Athipanyasilp N, Kaewnapan B, Leelahakorn N, Angkasekwinai N, Kantakamalakul W, Sutthent R, Ussery DW, Horthongkham N, Nookaew I
Genome Sequences of Zika Virus Strains Recovered from Amniotic Fluid, Placenta, and Fetal Brain of a Microcephaly Patient in Thailand, 2017.
Dec 11, 2018
Microbiology Resource Announcements
We present here the complete genome sequences of Zika virus strains isolated from aborted fetal tissue (brain and placenta) and amniotic fluid of a microcephaly patient in Thailand in 2017. The virus genomes that were sequenced have an average length of 10,807 nucleotides.
Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations [Article v1.0].
Dec 11, 2018   Living Journal Of Computational Molecular Science
Grossfield A, Patrone PN, Roe DR, Schultz AJ, Siderius DW, Zuckerman DM
Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations [Article v1.0].
Dec 11, 2018
Living Journal Of Computational Molecular Science
The quantitative assessment of uncertainty and sampling quality is essential in molecular simulation. Many systems of interest are highly complex, often at the edge of current computational capabilities. Modelers must therefore analyze and communicate statistical uncertainties so that "consumers" of simulated data understand its significance and limitations. This article covers key analyses appropriate for trajectory data generated by conventional simulation methods such as molecular dynamics and (single Markov chain) Monte Carlo. It also provides guidance for analyzing some 'enhanced' sampling approaches. We do not discuss systematic errors arising, e.g., from inaccuracy in the chosen model or force field.
Neuroprotective Activities of Heparin, Heparinase III, and Hyaluronic Acid on the Aβ42-Treated Forebrain Spheroids Derived from Human Stem Cells.
Dec 13, 2018   ACS Biomaterials Science & Engineering
Bejoy J, Song L, Wang Z, Sang QX, Zhou Y, Li Y
Neuroprotective Activities of Heparin, Heparinase III, and Hyaluronic Acid on the Aβ42-Treated Forebrain Spheroids Derived from Human Stem Cells.
Dec 13, 2018
ACS Biomaterials Science & Engineering
Extracellular matrix (ECM) components of the brain play complex roles in neurodegenerative diseases. The study of microenvironment of brain tissues with Alzheimer's disease revealed colocalized expression of different ECM molecules such as heparan sulfate proteoglycans (HSPGs), chondroitin sulfate proteoglycans (CSPGs), matrix metal-loproteinases (MMPs), and hyaluronic acid. In this study, both cortical and hippocampal populations were generated from human-induced pluripotent stem cell-derived neural spheroids. The cultures were then treated with heparin (competes for Aβ affinity with HSPG), heparinase III (digests HSPGs), chondroitinase (digests CSPGs), hyaluronic acid, and an MMP-2/9 inhibitor (SB-3CT) together with amyloid β (Aβ42) oligomers. The results indicate that inhibition of HSPG binding to Aβ42 using either heparinase III or heparin reduces Aβ42 expression and increases the population of β-tubulin III+ neurons, whereas the inhibition of MMP2/9 induces more neurotoxicity. The results should enhance our understanding of the contribution of ECMs to the Aβ-related neural cell death.
Significant expansion and red-shifting of fluorescent protein chromophore determined through computational design and genetic code expansion.
Dec 11, 2018   Biophysics Reports
Wang L, Chen X, Guo X, Li J, Liu Q, Kang F, Wang X, Hu C, Liu H, Gong W, Zhuang W, Liu X, Wang J
Significant expansion and red-shifting of fluorescent protein chromophore determined through computational design and genetic code expansion.
Dec 11, 2018
Biophysics Reports
Abstract: Fluorescent proteins (FPs) with emission wavelengths in the far-red and infrared regions of the spectrum provide powerful tools for deep-tissue and super-resolution imaging. The development of red-shifted FPs has evoked widespread interest and continuous engineering efforts. In this article, based on a computational design and genetic code expansion, we report a rational approach to significantly expand and red-shift the chromophore of green fluorescent protein (GFP). We applied computational calculations to predict the excitation and emission wavelengths of a FP chromophore harboring unnatural amino acids (UAA) and identify in silico an appropriate UAA, 2-amino-3-(6-hydroxynaphthalen-2-yl)propanoic acid (naphthol-Ala). Our methodology allowed us to formulate a GFP variant (cpsfGFP-66-Naphthol-Ala) with red-shifted absorbance and emission spectral maxima exceeding 60 and 130 nm, respectively, compared to those of GFP. The GFP chromophore is formed through autocatalytic post-translational modification to generate a planar 4-(p-hydroxybenzylidene)-5-imidazolinone chromophore. We solved the crystal structure of cpsfGFP-66-naphthol-Ala at 1.3 Å resolution and demonstrated the formation of a much larger conjugated π-system when the phenol group is replaced by naphthol. These results explain the significant red-shifting of the excitation and emission spectra of cpsfGFP-66-naphthol-Ala. Graphical abstract:
Raman spectra of the GFP-like fluorescent proteins.
Dec 11, 2018   Biophysics Reports
Yuan Y, Wang D, Zhang J, Liu J, Chen J, Zhang XE
Raman spectra of the GFP-like fluorescent proteins.
Dec 11, 2018
Biophysics Reports
The objective of the study was to elucidate optical characteristics of the chromophore structures of fluorescent proteins. Raman spectra of commonly used GFP-like fluorescent proteins (FPs) with diverse emission wavelengths (green, yellow, cyan and red), including the enhanced homogenous FPs EGFP, EYFP, and ECFP (from jellyfish) as well as mNeptune (from sea anemone) were measured. High-quality Raman spectra were obtained and many marker bands for the chromophore of the FPs were identified via assignment of Raman spectra bands. We report the presence of a positive linear correlation between the Raman band shift of C5=C6 and the excitation energy of FPs, demonstrated by plotting absorption maxima (cm-1) against the position of the Raman band C5=C6 in EGFP, ECFP, EYFP, the anionic chromophore and the neutral chromophore. This study revealed new Raman features in the chromophores of the observed FPs, and may contribute to a deeper understanding of the optical properties of FPs.
Small-animal SPECT/CT imaging of cancer xenografts and pulmonary fibrosis using a 99mTc-labeled integrin αvβ6-targeting cyclic peptide with improved in vivo stability.
Dec 11, 2018   Biophysics Reports
Liu H, Gao L, Yu X, Zhong L, Shi J, Jia B, Li N, Liu Z, Wang F
Small-animal SPECT/CT imaging of cancer xenografts and pulmonary fibrosis using a 99mTc-labeled integrin αvβ6-targeting cyclic peptide with improved in vivo stability.
Dec 11, 2018
Biophysics Reports
Abstract: Integrin αvβ6 is expressed at an undetectable level in normal tissues, but is remarkably upregulated during many pathological processes, especially in cancer and fibrosis. Noninvasive imaging of integrin αvβ6 expression using a radiotracer with favorable in vivo pharmacokinetics would facilitate disease diagnosis and therapy monitoring. Through disulfide-cyclized method, we synthesized in this study, a new integrin αvβ6-targeted cyclic peptide (denoted as cHK), and radiolabeled it with 99mTc. The ability of the resulting radiotracer 99mTc-HYNIC-cHK to detect integrin αvβ6 expression in pancreatic cancer xenografts and idiopathic pulmonary fibrosis was evaluated using small-animal single-photon emission computed tomography (SPECT)/computed tomography (CT). 99mTc-HYNIC-cHK showed significantly improved in vivo metabolic stability compared to the linear peptide-based radiotracer 99mTc-HYNIC-HK. 99mTc-HYNIC-cHK exhibited similar biodistribution properties to 99mTc-HYNIC-HK, but the tumor-to-muscle ratio was significantly increased (2.99 ± 0.87 vs. 1.82 ± 0.27, P < 0.05). High-contrast images of integrin αvβ6-positive tumors and bleomycin-induced fibrotic lungs were obtained by SPECT/CT imaging using 99mTc-HYNIC-cHK. Overall, our studies demonstrate that 99mTc-HYNIC-cHK is a promising SPECT radiotracer for the noninvasive imaging of integrin αvβ6 in living subjects. Graphical Abstract:
Targeting tumor cells with antibodies enhances anti-tumor immunity.
Dec 11, 2018   Biophysics Reports
Sun Z, Fu YX, Peng H
Targeting tumor cells with antibodies enhances anti-tumor immunity.
Dec 11, 2018
Biophysics Reports
Tumor-targeting antibodies were initially defined as a group of therapeutic monoclonal antibodies (mAb) that recognize tumor-specific membrane proteins, block cell signaling, and induce tumor-killing through Fc-driven innate immune responses. However, in the past decade, ample evidence has shown that tumor-targeting mAb (TTmAb) eradicates tumor cells via activation of cytotoxic T cells (CTLs). In this review, we specifically focus on how TTmAbs induce adaptive anti-tumor immunity and its potential in combination therapy with immune cytokines, checkpoint blockade, radiation, and enzyme-targeted small molecule drugs. Exploring the mechanisms of these preclinical studies and retrospective clinical data will significantly benefit the development of highly efficient and specific TTmAb-oriented anti-tumor remedies.
Fluid and PET biomarkers for amyloid pathology in Alzheimer's disease.
Dec 11, 2018   Molecular And Cellular Neurosciences
Cohen AD, Landau SM, Snitz BE, Klunk WE, Blennow K, Zetterberg H
Fluid and PET biomarkers for amyloid pathology in Alzheimer's disease.
Dec 11, 2018
Molecular And Cellular Neurosciences
Alzheimer's disease (AD) is characterized by amyloid plaques and tau pathology (neurofibrillary tangles and neuropil threads). Amyloid plaques are primarily composed of aggregated and oligomeric β-amyloid (Aβ) peptides ending at position 42 (Aβ42). The development of fluid and PET biomarkers for Alzheimer's disease (AD), has allowed for detection of Aβ pathology in vivo and marks a major advancement in understanding the role of Aβ in Alzheimer's disease (AD). In the recent National Institute on Aging and Alzheimer's Association (NIA-AA) Research Framework, AD is defined by the underlying pathology as measured in patients during life by biomarkers (Jack et al., 2018), while clinical symptoms are used for staging of the disease. Therefore, sensitive, specific and robust biomarkers to identify brain amyloidosis are central in AD research. Here, we discuss fluid and PET biomarkers for Aβ and their application.

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