Publications by authors named "A Aria Tzika"

111 Publications

Improving motor function after chronic stroke by interactive gaming with a redesigned MR-compatible hand training device.

Exp Ther Med 2021 Mar 22;21(3):245. Epub 2021 Jan 22.

Nuclear Magnetic Resonance Surgical Laboratory, Department of Surgery, Center for Surgery, Innovation and Bioengineering, Massachusetts General Hospital, Boston, MA 02114, USA.

New rehabilitation strategies enabled by technological developments are challenging the prevailing concept of there being a limited window for functional recovery after stroke. In this study, we examined the utility of a robot-assisted therapy used in combination with a serious game as a rehabilitation and motor assessment tool in patients with chronic stroke. We evaluated 928 game rounds from 386 training sessions of 8 patients who had suffered an ischemic stroke affecting middle cerebral artery territory that incurred at least 6 months prior. Motor function was assessed with clinical motor scales, including the Fugl-Meyer upper extremity (FM UE) scale, Action Research Arm Test, Modified Ashworth scale and the Box and Blocks test. Robotic device output measures (mean force, force-position correlation) and serious game score elements (collisions, rewards and total score) were calculated. A total of 2 patients exhibited a marginal improvement after a 10-week training protocol according to the FM UE scale and an additional patient exhibited a significant improvement according to Box and Blocks test. Motor scales showed strong associations of robotic device parameters and game metrics with clinical motor scale scores, with the strongest correlations observed for the mean force (0.677<Ρ<0.869), followed by the number of collisions (-0.670<Ρ<-0.585). Linear regression analysis showed that these indices were independent predictors of motor scale scores. In conclusion, a robotic device linked to a serious game can be used by patients with chronic stroke and induce at least some clinical improvements in motor performance. Robotic device output parameters and game score elements associate strongly with clinical motor scales and have the potential to be used as predictors in models of rehabilitation progress.
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http://dx.doi.org/10.3892/etm.2021.9676DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7851602PMC
March 2021

Genome mapping of a mutation in corn snakes indicates that vertebrate chromatophore vesicles are lysosome-related organelles.

Proc Natl Acad Sci U S A 2020 10 5;117(42):26307-26317. Epub 2020 Oct 5.

Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, CH-1211 Geneva, Switzerland;

Reptiles exhibit a spectacular diversity of skin colors and patterns brought about by the interactions among three chromatophore types: black melanophores with melanin-packed melanosomes, red and yellow xanthophores with pteridine- and/or carotenoid-containing vesicles, and iridophores filled with light-reflecting platelets generating structural colors. Whereas the melanosome, the only color-producing endosome in mammals and birds, has been documented as a lysosome-related organelle, the maturation paths of xanthosomes and iridosomes are unknown. Here, we first use 10x Genomics linked-reads and optical mapping to assemble and annotate a nearly chromosome-quality genome of the corn snake The assembly is 1.71 Gb long, with an N50 of 16.8 Mb and L50 of 24. Second, we perform mapping-by-sequencing analyses and identify a 3.9-Mb genomic interval where the variant resides. The lavender color morph in corn snakes is characterized by gray, rather than red, blotches on a pink, instead of orange, background. Third, our sequencing analyses reveal a single nucleotide polymorphism introducing a premature stop codon in the lysosomal trafficking regulator gene () that shortens the corresponding protein by 603 amino acids and removes evolutionary-conserved domains. Fourth, we use light and transmission electron microscopy comparative analyses of wild type versus lavender corn snakes and show that the color-producing endosomes of all chromatophores are substantially affected in the mutant. Our work provides evidence characterizing xanthosomes in xanthophores and iridosomes in iridophores as lysosome-related organelles.
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http://dx.doi.org/10.1073/pnas.2003724117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7584913PMC
October 2020

OxiOrganosolv: A novel acid free oxidative organosolv fractionation for lignocellulose fine sugar streams.

Bioresour Technol 2020 Oct 4;313:123599. Epub 2020 Jun 4.

Chemical Process and Energy Resources Institute (CPERI), CERTH, 6th Km Harilaou-Thermi Road, 57001 Thermi, Thessaloniki, Greece.

The valorization of lignocellulosic biomass towards the production of value-added products requires an efficient pretreatment/fractionation step. In this work we present a novel, acid-free, mildly oxidative organosolv delignification process -OxiOrganosolv- which employs oxygen gas to depolymerize and remove lignin. The results demonstrate that the OxiOrganosolv process achieved lignin removal as high as 97% in a single stage, with a variety of solvents; it was also efficient in delignifying both beechwood (hardwood) and pine (softwood), a task in which organosolv pretreatments have failed in the past. Minimal amounts of sugar degradation products were detected, while cellulose recovery was ~100% in the solid pulp. Enzymatic hydrolysis of pulps showed >80 wt% cellulose conversion to glucose. Overall, the OxiOrganosolv pretreatment has significant advantages, including high delignification efficiency of hardwood and softwood biomass, absence of acid homogeneous catalysis and all corresponding challenges involved, and close to zero losses of sugars to degradation products.
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http://dx.doi.org/10.1016/j.biortech.2020.123599DOI Listing
October 2020

Implementation of Physical Activity into routine Clinical pracTice in Rheumatic Musculoskeletal Disease: The IMPACT-RMD study protocol and rationale.

Mediterr J Rheumatol 2019 Dec 31;30(4):231-236. Epub 2020 Mar 31.

Department of Rheumatology, Russells Hall Hospital, Dudley Group NHS Foundation Trust, Dudley, United Kingdom.

Background: Physical activity is an important intervention for improving disease-related symptoms and systemic manifestations in rheumatic and musculoskeletal disease (RMDs). However, studies suggest that RMD patients report that the lack of individualized and consistent information about physical activity from managing doctors and healthcare professionals, acts as a barrier for engagement. On the other hand, managing doctors and healthcare professionals report lack of knowledge in this area and thus lack of confidence to educate and advise RMD patients about the beneficial effects of physical activity. The aim of the present study therefore, is to develop two e-Learning courses for RMD doctors and health professionals: a) the first one to provide consistent information about the collective benefits of physical activity in RMDs and b) the second on how to implement physical activity advice in routine clinical practice.

Methods: An international collaboration of seven countries, consisting of one academic institution and one patient organization from each country, will co-develop the two e-Learning courses. The final e-Learning courses will primarily target to improve - through physical activity advice - RMD symptoms which are important for patients.

Discussion: The main result of this study will be to co-develop two e-Learning courses that can be used by managing RMD doctors and healthcare professionals to be made aware of the overall benefits of physical activity in RMDs as well as how to implement physical activity advise within their practice.
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http://dx.doi.org/10.31138/mjr.30.4.231DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7241658PMC
December 2019

Erratum for Bandyopadhaya et al., "Pseudomonas aeruginosa Quorum Sensing Molecule Alters Skeletal Muscle Protein Homeostasis by Perturbing the Antioxidant Defense System".

mBio 2020 Feb 4;11(1). Epub 2020 Feb 4.

Department of Surgery, Center for Surgery, Innovation and Bioengineering, Massachusetts General Hospital, Harvard Medical School Boston, Boston, Massachusetts, USA

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http://dx.doi.org/10.1128/mBio.03316-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7002354PMC
February 2020

Functional MRI in Conjunction with a Novel MRI-compatible Hand-induced Robotic Device to Evaluate Rehabilitation of Individuals Recovering from Hand Grip Deficits.

J Vis Exp 2019 11 23(153). Epub 2019 Nov 23.

Harvard Medical School; NMR Surgical Laboratory, Department of Surgery, Center for Surgery, Innovation and Bioengineering, Massachusetts General Hospital, Harvard Medical School; Athinoula A. Martinos Center of Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School;

Functional magnetic resonance imaging (fMRI) is a non-invasive magnetic resonance imaging technique that images brain activation in vivo, using endogenous deoxyhemoglobin as an endogenous contrast agent to detect changes in blood-level-dependent oxygenation (BOLD effect). We combined fMRI with a novel robotic device (MR-compatible hand-induced robotic device [MR_CHIROD]) so that a person in the scanner can execute a controlled motor task, hand-squeezing, which is a very important hand movement to study in neurological motor disease. We employed parallel imaging (generalized auto-calibrating partially parallel acquisitions [GRAPPA]), which allowed higher spatial resolution resulting in increased sensitivity to BOLD. The combination of fMRI with the hand-induced robotic device allowed precise control and monitoring of the task that was executed while a participant was in the scanner; this may prove to be of utility in rehabilitation of hand motor function in patients recovering from neurological deficits (e.g., stroke). Here we outline the protocol for using the current prototype of the MR_CHIROD during an fMRI scan.
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http://dx.doi.org/10.3791/59420DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147332PMC
November 2019

Pseudomonas aeruginosa Quorum Sensing Molecule Alters Skeletal Muscle Protein Homeostasis by Perturbing the Antioxidant Defense System.

mBio 2019 10 1;10(5). Epub 2019 Oct 1.

Department of Surgery, Center for Surgery, Innovation and Bioengineering, Massachusetts General Hospital, Harvard Medical School Boston, Massachusetts, USA

Skeletal muscle function is compromised in many illnesses, including chronic infections. The quorum sensing (QS) signal, 2-amino acetophenone (2-AA), is produced during acute and chronic infections and excreted in human tissues, including the lungs of cystic fibrosis patients. We have shown that 2-AA facilitates pathogen persistence, likely via its ability to promote the formation of bacterial persister cells, and that it acts as an interkingdom immunomodulatory signal that epigenetically reprograms innate immune functions. Moreover, 2-AA compromises muscle contractility and impacts the expression of genes involved in reactive oxygen species (ROS) homeostasis in skeletal muscle and in mitochondrial functions. Here, we elucidate the molecular mechanisms of 2-AA's impairment of skeletal muscle function and ROS homeostasis. Murine and differentiated C2C12 myotube cell studies showed that 2-AA promotes ROS generation in skeletal muscle via the modulation of xanthine oxidase (XO) activity, NAD(P)H oxidase2 (NOX2) protein level, and the activity of antioxidant enzymes. ROS accumulation triggers the activity of AMP-activated protein kinase (AMPK), likely upstream of the observed locations of induction of ubiquitin ligases Muscle RING Finger 1 (MuRF1) and Muscle Atrophy F-box (MAFbx), and induces autophagy-related proteins. The protein-level perturbation in skeletal muscle of silent mating type information regulation 2 homolog 1 (SIRT1), peroxisome proliferator-activated receptor gamma coactivator 1 (PGC-1), and uncoupling protein 3 (UCP3) is rescued by the antioxidant N-acetyl-l-cysteine (NAC). Together, these results unveil a novel form of action of a QS bacterial molecule and provide molecular insights into the 2-AA-mediated skeletal muscle dysfunction caused by , a bacterium that is resistant to treatment, causes serious acute, persistent, and relapsing infections in humans. There is increasing evidence that bacterial excreted small molecules play a critical role during infection. We have shown that a quorum sensing (QS)-regulated excreted small molecule, 2-AA, which is abundantly produced by , promotes persistent infections, dampens host inflammation, and triggers mitochondrial dysfunction in skeletal muscle. QS is a cell-to-cell communication system utilized by bacteria to promote collective behaviors. The significance of our study in identifying a mechanism that leads to skeletal muscle dysfunction, via the action of a QS molecule, is that it may open new avenues in the control of muscle loss as a result of infection and sepsis. Given that QS is a common characteristic of prokaryotes, it is possible that 2-AA-like molecules promoting similar effects may exist in other pathogens.
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http://dx.doi.org/10.1128/mBio.02211-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6775459PMC
October 2019

Repeat domain-associated O-glycans govern PMEL fibrillar sheet architecture.

Sci Rep 2019 04 15;9(1):6101. Epub 2019 Apr 15.

Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, New Haven, CT, 06519, USA.

PMEL is a pigment cell-specific protein that forms a functional amyloid matrix in melanosomes. The matrix consists of well-separated fibrillar sheets on which the pigment melanin is deposited. Using electron tomography, we demonstrate that this sheet architecture is governed by the PMEL repeat (RPT) domain, which associates with the amyloid as an accessory proteolytic fragment. Thus, the RPT domain is dispensable for amyloid formation as such but shapes the morphology of the matrix, probably in order to maximize the surface area available for pigment adsorption. Although the primary amino acid sequence of the RPT domain differs vastly among various vertebrates, we show that it is a functionally conserved, interchangeable module. RPT domains of all species are predicted to be very highly O-glycosylated, which is likely the common defining feature of this domain. O-glycosylation is indeed essential for RPT domain function and the establishment of the PMEL sheet architecture. Thus, O-glycosylation, not amino acid sequence, appears to be the major factor governing the characteristic PMEL amyloid morphology.
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http://dx.doi.org/10.1038/s41598-019-42571-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6465243PMC
April 2019

Feather arrays are patterned by interacting signalling and cell density waves.

PLoS Biol 2019 02 21;17(2):e3000132. Epub 2019 Feb 21.

Roslin Institute Chicken Embryology, Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom.

Feathers are arranged in a precise pattern in avian skin. They first arise during development in a row along the dorsal midline, with rows of new feather buds added sequentially in a spreading wave. We show that the patterning of feathers relies on coupled fibroblast growth factor (FGF) and bone morphogenetic protein (BMP) signalling together with mesenchymal cell movement, acting in a coordinated reaction-diffusion-taxis system. This periodic patterning system is partly mechanochemical, with mechanical-chemical integration occurring through a positive feedback loop centred on FGF20, which induces cell aggregation, mechanically compressing the epidermis to rapidly intensify FGF20 expression. The travelling wave of feather formation is imposed by expanding expression of Ectodysplasin A (EDA), which initiates the expression of FGF20. The EDA wave spreads across a mesenchymal cell density gradient, triggering pattern formation by lowering the threshold of mesenchymal cells required to begin to form a feather bud. These waves, and the precise arrangement of feather primordia, are lost in the flightless emu and ostrich, though via different developmental routes. The ostrich retains the tract arrangement characteristic of birds in general but lays down feather primordia without a wave, akin to the process of hair follicle formation in mammalian embryos. The embryonic emu skin lacks sufficient cells to enact feather formation, causing failure of tract formation, and instead the entire skin gains feather primordia through a later process. This work shows that a reaction-diffusion-taxis system, integrated with mechanical processes, generates the feather array. In flighted birds, the key role of the EDA/Ectodysplasin A receptor (EDAR) pathway in vertebrate skin patterning has been recast to activate this process in a quasi-1-dimensional manner, imposing highly ordered pattern formation.
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http://dx.doi.org/10.1371/journal.pbio.3000132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6383868PMC
February 2019

Ontogeny and phylogeny of the mammalian chondrocranium: the cupula nasi anterior and associated structures of the anterior head region.

Zoological Lett 2018 24;4:29. Epub 2018 Nov 24.

3Senckenberg Center for Human Evolution and Palaeoenvironment (HEP) at Eberhard Karls Universität, Sigwartstraße 10, 72076 Tübingen, Germany.

Background: The study of chondrocrania has a long tradition with a focus on single specimens and stages. It revealed great interspecific diversity and a notion of intraspecific variation. As an embryonic structure, the chondrocranium is subject to major changes in ontogeny with resorption and ossification of different cartilaginous structures. The cupula nasi anterior is the anteriormost portion of the cartilaginous nasal capsule and is expected to mirror much of the animal's life history and lifestyle. Its diversity in mammals is reflected in the external nasal anatomy of newborns. Marsupials and placentals show marked differences, likely related to breathing and suckling behavior.

Results: We examined histological sections of five marsupial and three placentals species and traced the development of the cupula nasi anterior and the anterior nasal capsule. We found ontogenetic variation for nearly 50% of the 43 characters defined herein. By comparing to the literature and considering ontogenetic variation, we performed an analysis of character evolution in 70 mammalian species and reconstructed the nasal anatomy of the therian ancestor.

Conclusions: At birth, marsupials have a complete but simple cupula nasi anterior, whereas placentals display a more diverse morphology due to reductions and variations of chondrocranial elements. The more compact nasal capsule in marsupials is related to a long and strong fixation to the mother's teat after birth. Within marsupials and placentals, several derived characters distinguish major taxa, probably related to developmental and functional constraints. The reconstructed ancestral anatomy of the cupula nasi anterior supports the hypothesis that the therian ancestor was placental-like and that the marsupial lifestyle is more derived.
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http://dx.doi.org/10.1186/s40851-018-0112-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6260904PMC
November 2018

Magnetization transfer contrast MRI in GFP‑tagged live bacteria.

Mol Med Rep 2019 Jan 19;19(1):617-621. Epub 2018 Nov 19.

NMR Surgical Laboratory, Department of Surgery, Massachusetts General Hospital and Shriners Burns Hospital, Harvard Medical School, Boston, MA 02114, USA.

Green fluorescent protein (GFP) is a widely utilized molecular reporter of gene expression. However, its use in in vivo imaging has been restricted to transparent tissue mainly due to the tissue penetrance limitation of optical imaging. Magnetization transfer contrast (MTC) is a magnetic resonance imaging (MRI) methodology currently utilized to detect macromolecule changes such as decrease in myelin and increase in collagen content. MTC MRI imaging was performed to detect GFP in both in vitro cells and in an in vivo mouse model to determine if MTC imaging could be used to detect infection from Pseudomonas aeruginosa in murine tissues. It was demonstrated that the approach produces values that are protein specific and concentration dependent. This method provides a valuable, non‑invasive imaging tool to study the impact of novel antibacterial therapeutics on bacterial proliferation and perhaps viability within the host system, and could potentially suggest the modulation of bacterial gene expression within the host when exposed to such compounds.
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http://dx.doi.org/10.3892/mmr.2018.9669DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297796PMC
January 2019

Effects of a small, volatile bacterial molecule on Pseudomonas aeruginosa bacteria using whole cell high-resolution magic angle spinning nuclear magnetic resonance spectroscopy and genomics.

Int J Mol Med 2018 Oct 6;42(4):2129-2136. Epub 2018 Jul 6.

NMR Surgical Laboratory, Center for Surgery, Innovation and Bioengineering, Department of Surgery, Massachusetts General and Shriners Burns Hospitals, Harvard Medical School, Boston, MA 02114, USA.

In the present study, high-resolution magic-angle spinning (HRMAS) nuclear magnetic resonance (NMR) spectroscopy was applied to live Pseudomonas aeruginosa (PA) bacterial cells to determine the metabolome of this opportunistic Gram-negative human pathogen, and in particular, its response to the volatile aromatic low molecular weight signaling molecule, 2-aminoacetophenone (2-AA). Multi-dimensional HRMAS NMR is a promising method which may be used to determine the in vivo metabolome of live intact bacterial cells; 2-AA is produced by PA and triggers the emergence of phenotypes that promote chronic infection phenotypes in in vitro and in vivo (animal) models. In the present study, we applied one-dimensional and two-dimensional proton (1H) HRMAS NMR to PA cells which were grown with or without 2-AA in order to examine the associations between metabolites and cellular processes in response to 2-AA. We also compared whole-genome transcriptome profiles of PA cells grown with or without 2-AA and found that 2-AA promoted profound metabolic changes in the PA cells. By comparing the whole-genome transcriptome profiles and metabolomic analysis, we demonstrated that 2-AA profoundly reprogramed the gene expression and metabolic profiles of the cells. Our in vivo 1H HRMAS NMR spectroscopy may prove to be a helpful tool in the validation of gene functions, the study of pathogenic mechanisms, the classification of microbial strains into functional/clinical groups and the testing of anti-bacterial agents.
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http://dx.doi.org/10.3892/ijmm.2018.3760DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6108874PMC
October 2018

Evolution of Cortical Neurogenesis in Amniotes Controlled by Robo Signaling Levels.

Cell 2018 07 28;174(3):590-606.e21. Epub 2018 Jun 28.

Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, 03550 Alacant, Spain. Electronic address:

Cerebral cortex size differs dramatically between reptiles, birds, and mammals, owing to developmental differences in neuron production. In mammals, signaling pathways regulating neurogenesis have been identified, but genetic differences behind their evolution across amniotes remain unknown. We show that direct neurogenesis from radial glia cells, with limited neuron production, dominates the avian, reptilian, and mammalian paleocortex, whereas in the evolutionarily recent mammalian neocortex, most neurogenesis is indirect via basal progenitors. Gain- and loss-of-function experiments in mouse, chick, and snake embryos and in human cerebral organoids demonstrate that high Slit/Robo and low Dll1 signaling, via Jag1 and Jag2, are necessary and sufficient to drive direct neurogenesis. Attenuating Robo signaling and enhancing Dll1 in snakes and birds recapitulates the formation of basal progenitors and promotes indirect neurogenesis. Our study identifies modulation in activity levels of conserved signaling pathways as a primary mechanism driving the expansion and increased complexity of the mammalian neocortex during amniote evolution.
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http://dx.doi.org/10.1016/j.cell.2018.06.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6063992PMC
July 2018

A Step-by-Step Guide to Assemble a Reptilian Genome.

Methods Mol Biol 2017 ;1650:47-67

Laboratory of Artificial and Natural Evolution (LANE), Department of Genetics and Evolution, University of Geneva, Sciences III, 30, Quai Ernest-Ansermet, 1211, Geneva, Switzerland.

Multiple technologies and software are now available facilitating the de novo sequencing and assembly of any vertebrate genome. Yet the quality of most available sequenced genomes is substantially poorer than that of the golden standard in the field: the human genome. Here, we present a step-by-step protocol for the successful sequencing and assembly of a high-quality snake genome that can be applied to any other reptilian or avian species. We combine the great sequencing depth and accuracy of short reads with the use of different insert size libraries for extended scaffolding followed by optical mapping. We show that this procedure improved the corn snake scaffold N50 from 3.7 kbp to 1.4 Mbp, currently making it one of the snake genomes with the longest scaffolds. Short guidelines are also given on the extraction of long DNA molecules from reptilian blood and the necessary modifications in DNA extraction protocols. This chapter is accompanied by a website ( www.reptilomics.org/stepbystep.html ), where we provide links to the suggested software, examples of input and output files, and running parameters.
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http://dx.doi.org/10.1007/978-1-4939-7216-6_3DOI Listing
June 2018

panelcn.MOPS: Copy-number detection in targeted NGS panel data for clinical diagnostics.

Hum Mutat 2017 07 16;38(7):889-897. Epub 2017 May 16.

Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria.

Targeted next-generation-sequencing (NGS) panels have largely replaced Sanger sequencing in clinical diagnostics. They allow for the detection of copy-number variations (CNVs) in addition to single-nucleotide variants and small insertions/deletions. However, existing computational CNV detection methods have shortcomings regarding accuracy, quality control (QC), incidental findings, and user-friendliness. We developed panelcn.MOPS, a novel pipeline for detecting CNVs in targeted NGS panel data. Using data from 180 samples, we compared panelcn.MOPS with five state-of-the-art methods. With panelcn.MOPS leading the field, most methods achieved comparably high accuracy. panelcn.MOPS reliably detected CNVs ranging in size from part of a region of interest (ROI), to whole genes, which may comprise all ROIs investigated in a given sample. The latter is enabled by analyzing reads from all ROIs of the panel, but presenting results exclusively for user-selected genes, thus avoiding incidental findings. Additionally, panelcn.MOPS offers QC criteria not only for samples, but also for individual ROIs within a sample, which increases the confidence in called CNVs. panelcn.MOPS is freely available both as R package and standalone software with graphical user interface that is easy to use for clinical geneticists without any programming experience. panelcn.MOPS combines high sensitivity and specificity with user-friendliness rendering it highly suitable for routine clinical diagnostics.
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http://dx.doi.org/10.1002/humu.23237DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5518446PMC
July 2017

Revascularization and muscle adaptation to limb demand ischemia in diet-induced obese mice.

J Surg Res 2016 09 8;205(1):49-58. Epub 2016 Jun 8.

Division of Vascular and Endovascular Surgery, Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts.

Background: Obesity and type 2 diabetes are major risk factors for peripheral arterial disease in humans, which can result in lower limb demand ischemia and exercise intolerance. Exercise triggers skeletal muscle adaptation including increased vasculogenesis. The goal of this study was to determine whether demand ischemia modulates revascularization, fiber size, and signaling pathways in the ischemic hind limb muscles of mice with diet-induced obesity (DIO).

Materials And Methods: DIO mice (n = 7) underwent unilateral femoral artery ligation and recovered for 2 wks followed by 4 wks with daily treadmill exercise to induce demand ischemia. A parallel sedentary ischemia (SI) group (n = 7) had femoral artery ligation without exercise. The contralateral limb muscles of SI served as control. Muscles were examined for capillary density, myofiber cross-sectional area, cytokine levels, and phosphorylation of STAT3 and ERK1/2.

Results: Exercise significantly enhanced capillary density (P < 0.01) and markedly lowered cross-sectional area (P < 0.001) in demand ischemia compared with SI. These findings coincided with a significant increase in granulocyte colony-stimulating factor (P < 0.001) and interleukin-7 (P < 0.01) levels. In addition, phosphorylation levels of STAT3 and ERK1/2 (P < 0.01) were increased, whereas UCP1 and monocyte chemoattractant protein-1 protein levels were lower (P < 0.05) without altering vascular endothelial growth factor and tumor necrosis factor alpha protein levels. Demand ischemia increased the PGC1α messenger RNA (P < 0.001) without augmenting PGC1α protein levels.

Conclusions: Exercise-induced limb demand ischemia in the setting of DIO causes myofiber atrophy despite an increase in muscle capillary density. The combination of persistent increase in tumor necrosis factor alpha, lower vascular endothelial growth factor, and failure to increase PGC1α protein may reflect a deficient adaption to demand ischemia in DIO.
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http://dx.doi.org/10.1016/j.jss.2016.06.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5021992PMC
September 2016

Proton MRS imaging in pediatric brain tumors.

Pediatr Radiol 2016 Jun 27;46(7):952-62. Epub 2016 May 27.

Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.

Magnetic resonance (MR) techniques offer a noninvasive, non-irradiating yet sensitive approach to diagnosing and monitoring pediatric brain tumors. Proton MR spectroscopy (MRS), as an adjunct to MRI, is being more widely applied to monitor the metabolic aspects of brain cancer. In vivo MRS biomarkers represent a promising advance and may influence treatment choice at both initial diagnosis and follow-up, given the inherent difficulties of sequential biopsies to monitor therapeutic response. When combined with anatomical or other types of imaging, MRS provides unique information regarding biochemistry in inoperable brain tumors and can complement neuropathological data, guide biopsies and enhance insight into therapeutic options. The combination of noninvasively acquired prognostic information and the high-resolution anatomical imaging provided by conventional MRI is expected to surpass molecular analysis and DNA microarray gene profiling, both of which, although promising, depend on invasive biopsy. This review focuses on recent data in the field of MRS in children with brain tumors.
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http://dx.doi.org/10.1007/s00247-016-3547-5DOI Listing
June 2016

Bacterial-excreted small volatile molecule 2-aminoacetophenone induces oxidative stress and apoptosis in murine skeletal muscle.

Int J Mol Med 2016 Apr 12;37(4):867-78. Epub 2016 Feb 12.

NMR Surgical Laboratory, Center for Surgery, Innovation and Bioengineering, Department of Surgery, Massachusetts General and Shriners Burns Hospitals, Harvard Medical School, Boston, MA 02114, USA.

Oxidative stress induces mitochondrial dysfunction and facilitates apoptosis, tissue damage or metabolic alterations following infection. We have previously discovered that the Pseudomonas aeruginosa (PA) quorum sensing (QS)-excreted small volatile molecule, 2-aminoacetophenone (2-AA), which is produced in infected human tissue, promotes bacterial phenotypes that favor chronic infection, while also dampening the pathogen‑induced innate immune response, thus compromising muscle function and promoting host tolerance to infection. In this study, murine whole-genome expression data have demonstrated that 2-AA affects the expression of genes involved in reactive oxygen species (ROS) homeostasis, thus producing an oxidative stress signature in skeletal muscle. The results of the present study demonstrated that the expression levels of genes involved in apoptosis signaling pathways were upregulated in the skeletal muscle of 2-AA-treated mice. To confirm the results of our transcriptome analysis, we used a novel high-resolution magic-angle-spinning (HRMAS), proton (1H) nuclear magnetic resonance (NMR) method and observed increased levels of bisallylic methylene fatty acyl protons and vinyl protons, suggesting that 2-AA induces skeletal muscle cell apoptosis. This effect was corroborated by our results demonstrating the downregulation of mitochondrial membrane potential in vivo in response to 2-AA. The findings of the present study indicate that the bacterial infochemical, 2-AA, disrupts mitochondrial functions by inducing oxidative stress and apoptosis signaling and likely promotes skeletal muscle dysfunction, which may favor chronic/persistent infection.
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http://dx.doi.org/10.3892/ijmm.2016.2487DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4790710PMC
April 2016

In vivo high-resolution magic angle spinning magnetic and electron paramagnetic resonance spectroscopic analysis of mitochondria-targeted peptide in Drosophila melanogaster with trauma-induced thoracic injury.

Int J Mol Med 2016 Feb 8;37(2):299-308. Epub 2015 Dec 8.

NMR Surgical Laboratory, Department of Surgery, Massachusetts General Hospital and Shriners Burns Institute, Harvard Medical School, Boston, MA, USA.

Trauma is the most common cause of mortality among individuals aged between 1 and 44 years and the third leading cause of mortality overall in the US. In this study, we examined the effects of trauma on the expression of genes in Drosophila melanogaster, a useful model for investigating genetics and physiology. After trauma was induced by a non-lethal needle puncture of the thorax, we observed the differential expression of genes encoding for mitochondrial uncoupling proteins, as well as those encoding for apoptosis-related and insulin signaling-related proteins, thus indicating muscle functional dysregulation. These results prompted us to examine the link between insulin signaling and mitochondrial dysfunction using in vivo nuclear magnetic resonance (NMR) with complementary electron paramagnetic resonance (EPR) spectroscopy. Trauma significantly increased insulin resistance biomarkers, and the NMR spectral profile of the aged flies with trauma-induced thoracic injury resembled that of insulin-resistant chico mutant flies. In addition, the mitochondrial redox status, as measured by EPR, was significantly altered following trauma, indicating mitochondrial uncoupling. A mitochondria-targeted compound, Szeto-Schiller (SS)-31 that promotes adenosine triphosphate (ATP) synthesis normalized the NMR spectral profile, as well as the mitochondrial redox status of the flies with trauma-induced thoracic injury, as assessed by EPR. Based on these findings, we propose a molecular mechanism responsible for trauma-related mortality and also propose that trauma sequelae in aging are linked to insulin signaling and mitochondrial dysfunction. Our findings further suggest that SS-31 attenuates trauma-associated pathological changes.
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http://dx.doi.org/10.3892/ijmm.2015.2426DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4716799PMC
February 2016

Reptilian Transcriptomes v2.0: An Extensive Resource for Sauropsida Genomics and Transcriptomics.

Genome Biol Evol 2015 Jul 1;7(6):1827-41. Epub 2015 Jul 1.

Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, Switzerland SIB Swiss Institute of Bioinformatics, Switzerland Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Switzerland

Despite the availability of deep-sequencing techniques, genomic and transcriptomic data remain unevenly distributed across phylogenetic groups. For example, reptiles are poorly represented in sequence databases, hindering functional evolutionary and developmental studies in these lineages substantially more diverse than mammals. In addition, different studies use different assembly and annotation protocols, inhibiting meaningful comparisons. Here, we present the "Reptilian Transcriptomes Database 2.0," which provides extensive annotation of transcriptomes and genomes from species covering the major reptilian lineages. To this end, we sequenced normalized complementary DNA libraries of multiple adult tissues and various embryonic stages of the leopard gecko and the corn snake and gathered published reptilian sequence data sets from representatives of the four extant orders of reptiles: Squamata (snakes and lizards), the tuatara, crocodiles, and turtles. The LANE runner 2.0 software was implemented to annotate all assemblies within a single integrated pipeline. We show that this approach increases the annotation completeness of the assembled transcriptomes/genomes. We then built large concatenated protein alignments of single-copy genes and inferred phylogenetic trees that support the positions of turtles and the tuatara as sister groups of Archosauria and Squamata, respectively. The Reptilian Transcriptomes Database 2.0 resource will be updated to include selected new data sets as they become available, thus making it a reference for differential expression studies, comparative genomics and transcriptomics, linkage mapping, molecular ecology, and phylogenomic analyses involving reptiles. The database is available at www.reptilian-transcriptomes.org and can be enquired using a wwwblast server installed at the University of Geneva.
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http://dx.doi.org/10.1093/gbe/evv106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4494049PMC
July 2015

Two waves of anisotropic growth generate enlarged follicles in the spiny mouse.

Evodevo 2014 25;5:33. Epub 2014 Sep 25.

Department of Genetics & Evolution, Laboratory of Artificial & Natural Evolution (LANE), University of Geneva, Sciences III, 30, Quai Ernest-Ansermet, Geneva 4 1211, Switzerland.

Background: Mammals exhibit a remarkable variety of phenotypes and comparative studies using novel model species are needed to uncover the evolutionary developmental mechanisms generating this diversity. Here, we undertake a developmental biology and numerical modeling approach to investigate the development of skin appendages in the spiny mouse, Acomys dimidiatus.

Results: We demonstrate that Acomys spines, possibly involved in display and protection, are enlarged awl hairs with a concave morphology. The Acomys spines originate from enlarged placodes that are characterized by a rapid downwards growth which results in voluminous follicles. The dermal condensation (dermal papilla) at the core of the follicle is very large and exhibits a curved geometry. Given its off-centered position, the dermal papilla generates two waves of anisotropic proliferation, first of the posterior matrix, then of the anterior inner root sheath (IRS). Higher in the follicle, the posterior and anterior cortex cross-section areas substantially decrease due to cortex cell elongation and accumulation of keratin intermediate filaments. Milder keratinization in the medulla gives rise to a foamy material that eventually collapses under the combined compression of the anterior IRS and elongation of the cortex cells. Simulations, using linear elasticity theory and the finite-element method, indicate that these processes are sufficient to replicate the time evolution of the Acomys spine layers and the final shape of the emerging spine shaft.

Conclusions: Our analyses reveal how hair follicle morphogenesis has been altered during the evolution of the Acomys lineage, resulting in a shift from ancestral awl follicles to enlarged asymmetrical spines. This study contributes to a better understanding of the evolutionary developmental mechanisms that generated the great diversity of skin appendage phenotypes observed in mammals.
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http://dx.doi.org/10.1186/2041-9139-5-33DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4335386PMC
February 2015

Diagnosis of fetal submicroscopic chromosomal abnormalities in failed array CGH samples: copy number by sequencing as an alternative to microarrays for invasive fetal testing.

Ultrasound Obstet Gynecol 2015 Apr;45(4):394-401

Department of Fetal Medicine, Leeds General Infirmary, Leeds, UK; Leeds Institute of Cancer and Pathology, Leeds, UK.

Objectives: Array comparative genomic hybridization (CGH) has become the technology of choice for high-resolution prenatal whole genome analysis. Limitations of microarrays are mainly related to the analog nature of the analysis, and poor-quality DNA can result in failed quality metrics with these platforms. We examined a cohort of abnormal fetuses with failed array CGH results using a next-generation sequencing algorithm, CNV-Seq. We assessed the ability of the platform to handle suboptimal prenatal samples and generate interpretable molecular karyotypes.

Methods: Nine samples obtained from abnormal fetuses and one from a normal control fetus were sequenced using an Illumina GAIIx. A segmentation algorithm for sequencing data was used to determine regional copy number data on the sequencing datasets.

Results: Phred quality scores were satisfactory for analysis of all samples. CNV-Seq identified both large- and small-scale abnormalities in the cohort, and normal results were obtained for fetuses for which microarray data were previously uninterpretable. No variants of uncertain significance were detected. Analysis of the digital sequencing datasets offered some advantages over array CGH output.

Conclusions: Using next-generation sequencing for the detection of genomic copy number variants may be advantageous for poor-quality, invasively-acquired prenatal samples. CNV-Seq could become a potential alternative to array CGH in this setting.
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http://dx.doi.org/10.1002/uog.14767DOI Listing
April 2015

Retroviral envelope syncytin capture in an ancestrally diverged mammalian clade for placentation in the primitive Afrotherian tenrecs.

Proc Natl Acad Sci U S A 2014 Oct 29;111(41):E4332-41. Epub 2014 Sep 29.

Unité des Rétrovirus Endogènes et Eléments Rétroïdes des Eucaryotes Supérieurs, Centre National de la Recherche Scientifique Unité Mixte de Recherche 8122, Institut Gustave Roussy, 94805 Villejuif, France; Université Paris-Sud, 91405 Orsay, France;

Syncytins are fusogenic envelope (env) genes of retroviral origin that have been captured for a function in placentation. Syncytins have been identified in Euarchontoglires (primates, rodents, Leporidae) and Laurasiatheria (Carnivora, ruminants) placental mammals. Here, we searched for similar genes in species that retained characteristic features of primitive mammals, namely the Malagasy and mainland African Tenrecidae. They belong to the superorder Afrotheria, an early lineage that diverged from Euarchotonglires and Laurasiatheria 100 Mya, during the Cretaceous terrestrial revolution. An in silico search for env genes with full coding capacity within a Tenrecidae genome identified several candidates, with one displaying placenta-specific expression as revealed by RT-PCR analysis of a large panel of Setifer setosus tissues. Cloning of this endogenous retroviral env gene demonstrated fusogenicity in an ex vivo cell-cell fusion assay on a panel of mammalian cells. Refined analysis of placental architecture and ultrastructure combined with in situ hybridization demonstrated specific expression of the gene in multinucleate cellular masses and layers at the materno-fetal interface, consistent with a role in syncytium formation. This gene, which we named "syncytin-Ten1," is conserved among Tenrecidae, with evidence of purifying selection and conservation of fusogenic activity. To our knowledge, it is the first syncytin identified to date within the ancestrally diverged Afrotheria superorder.
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http://dx.doi.org/10.1073/pnas.1412268111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4205661PMC
October 2014

Identification of anti-virulence compounds that disrupt quorum-sensing regulated acute and persistent pathogenicity.

PLoS Pathog 2014 Aug 21;10(8):e1004321. Epub 2014 Aug 21.

Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts, United States of America; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America; Shriners Hospitals for Children Boston, Boston, Massachusetts, United States of America.

Etiological agents of acute, persistent, or relapsing clinical infections are often refractory to antibiotics due to multidrug resistance and/or antibiotic tolerance. Pseudomonas aeruginosa is an opportunistic Gram-negative bacterial pathogen that causes recalcitrant and severe acute chronic and persistent human infections. Here, we target the MvfR-regulated P. aeruginosa quorum sensing (QS) virulence pathway to isolate robust molecules that specifically inhibit infection without affecting bacterial growth or viability to mitigate selective resistance. Using a whole-cell high-throughput screen (HTS) and structure-activity relationship (SAR) analysis, we identify compounds that block the synthesis of both pro-persistence and pro-acute MvfR-dependent signaling molecules. These compounds, which share a benzamide-benzimidazole backbone and are unrelated to previous MvfR-regulon inhibitors, bind the global virulence QS transcriptional regulator, MvfR (PqsR); inhibit the MvfR regulon in multi-drug resistant isolates; are active against P. aeruginosa acute and persistent murine infections; and do not perturb bacterial growth. In addition, they are the first compounds identified to reduce the formation of antibiotic-tolerant persister cells. As such, these molecules provide for the development of next-generation clinical therapeutics to more effectively treat refractory and deleterious bacterial-human infections.
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http://dx.doi.org/10.1371/journal.ppat.1004321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4140854PMC
August 2014

Diagnostic whole genome sequencing and split-read mapping for nucleotide resolution breakpoint identification in CNTNAP2 deficiency syndrome.

Am J Med Genet A 2014 Oct 16;164A(10):2649-55. Epub 2014 Jul 16.

Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, United Kingdom; School of Medicine, University of Leeds, St. James's University Hospital, Leeds, United Kingdom.

Whole genome sequencing (WGS) has the potential to report on all types of genetic abnormality, thus converging diagnostic testing on a single methodology. Although WGS at sufficient depth for robust detection of point mutations is still some way from being affordable for diagnostic purposes, low-coverage WGS is already an excellent method for detecting copy number variants ("CNVseq"). We report on a family in which individuals presented with a presumed autosomal recessive syndrome of severe intellectual disability and epilepsy. Array comparative genomic hybridization (CGH) analysis had revealed a homozygous deletion apparently lying within intron 3 of CNTNAP2. Since this was too small for confirmation by FISH, CNVseq was used, refining the extent of this mutation to approximately 76.8 kb, encompassing CNTNAP2 exon 3 (an out-of-frame deletion). To characterize the precise breakpoints and provide a rapid molecular diagnostic test, we resequenced the CNVseq library at medium coverage and performed split read mapping. This yielded information for a multiplex polymerase chain reaction (PCR) assay, used for cascade screening and/or prenatal diagnosis in this family. This example demonstrates a rapid, low-cost approach to converting molecular cytogenetic findings into robust PCR-based tests.
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http://dx.doi.org/10.1002/ajmg.a.36679DOI Listing
October 2014

In vivo high-resolution magic angle spinning proton NMR spectroscopy of Drosophila melanogaster flies as a model system to investigate mitochondrial dysfunction in Drosophila GST2 mutants.

Int J Mol Med 2014 Jul 24;34(1):327-33. Epub 2014 Apr 24.

NMR Surgical Laboratory, Department of Surgery, Massachusetts General Hospital and Shriners Burn Institute, Harvard Medical School, Boston, MA 02114, USA.

In vivo nuclear magnetic resonance spectroscopy (NMR), a non-destructive biochemical tool used for investigating live organisms, has recently been performed in studies of the fruit fly Drosophila melanogaster, a useful model organism for investigating genetics and physiology. We used a novel high-resolution magic angle-spinning (HRMAS) NMR method to investigate live Drosophila GST2 mutants using a conventional 14.1-T NMR spectrometer equipped with an HRMAS probe. The results showed that, compared to wild-type (wt) controls, the GST2 mutants had a 48% greater (CH(2))n lipid signal at 1.33 ppm, which is an insulin resistance biomarker in Drosophila skeletal muscle (P=0.0444). The mutants also had a 57% greater CH(2)C= lipid signal at 2.02 ppm (P=0.0276) and a 100% greater -CH=CH- signal at 5.33 ppm (P=0.0251). Since the -CH=CH- signal encompasses protons from ceramide, this latter difference is consistent with the hypothesis that the GST2 mutation is associated with insulin resistance and apoptosis. The findings of this study corroborate our previous results, support the hypothesis that the GST2 mutation is associated with insulin signaling and suggest that the IMCL level may be a biomarker of insulin resistance. Furthermore, direct links between GST2 mutation (the Drosophila ortholog of the GSTA4 gene in mammals) and insulin resistance, as suggested in this study, have not been made previously. These findings may thus be directly relevant to a wide range of metabolically disruptive conditions, such as trauma, aging and immune system deficiencies, that lead to increased susceptibility to infection.
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http://dx.doi.org/10.3892/ijmm.2014.1757DOI Listing
July 2014

Live-cell high resolution magic angle spinning magnetic resonance spectroscopy for analysis of metabolomics.

Biomed Rep 2013 Sep 22;1(5):707-712. Epub 2013 Jul 22.

Nuclear Magnetic Resonance Surgical Laboratory, Department of Surgery, Division of Burns, Massachusetts General Hospital and Shriners Burns Institute, Harvard Medical School, Boston, MA 02114, USA ; Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.

(PA) is a pathogenic gram-negative bacterium that is widespread in nature, inhabiting soil, water, plants and animals. PA is a prevalent cause of deleterious human infections, particularly in patients whose host defense mechanisms have been compromised. Metabolomics is an important tool used to study host-pathogen interactions and to identify novel therapeutic targets and corresponding compounds. The aim of the present study was to report the metabolic profile of live PA bacteria using high-resolution magic angle spinning (HRMAS) nuclear magnetic resonance spectroscopy (NMR), in combination with 1- and 2-dimensional HRMAS NMR. This methodology provides a new and powerful technique to rapidly interrogate the metabolome of intact bacterial cells and has several advantages over traditional techniques that identify metabolome components from disrupted cells. Furthermore, application of multidimensional HRMAS NMR, in combination with the novel technique total through-Bond correlation Spectroscopy (TOBSY), is a promising approach that may be used to obtain metabolomics information from intact live bacterial cells and can mediate such analyses in a short period of time. Moreover, HRMAS H NMR enables the investigation of the associations between metabolites and cell processes. In the present study, we detected and quantified several informative metabolic molecules in live PA cells, including N-acetyl, betaine, citrulline, alanine and glycine, which are important in peptidoglycan synthesis. The results provided a complete metabolic profile of PA for future studies of PA clinical isolates and mutants. In addition, this NMR biomedical approach might have clinical utility and should prove useful in gene function validation, the study of pathogenetic mechanisms, the classification of microbial strains into functional/clinical groups, the testing of anti-bacterial agents and the determination of metabolic profiles of bacterial mutants.
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http://dx.doi.org/10.3892/br.2013.148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3917020PMC
September 2013

The genome sequence of the corn snake (Pantherophis guttatus), a valuable resource for EvoDevo studies in squamates.

Int J Dev Biol 2014 ;58(10-12):881-8

Laboratory of Artificial and Natural Evolution (LANE), Dept. of Genetics and Evolution, University of Geneva, Geneva, Switzerland.

Squamates (snakes and lizards) exhibit a striking variety of phenotypes, with little known on their generative mechanisms. Studies aiming to understand the genetic basis of this wide diversity in morphology, physiology and ecology will greatly benefit from whole genome sequencing initiatives, as they provide the foundation for comparative analyses and improve our understanding of the evolution, development and diversification of traits. Here, we present the first draft genome of the corn snake Pantherophis guttatus, an oviparous snake that we promote as a particularly appropriate model species for evolutionary developmental studies in squamates. We sequenced 100-base paired-end reads from multiple individuals of a single family (parents and offspring) that produced a genome assembly of 1.53 gigabases (Gb), roughly covering 75% of the expected total genome size, and 297,768 scaffolds >1 Kb. We were able to fully retrieve 86, and partially another 106, of the 248 CEGMA core genes, indicating that a high genome completeness was achieved, even though the assembly is fragmented. Using MAKER2, we annotated 10,917 genes with high confidence (Annotation Edit Distance (AED)<1) and an additional 5,263 predicted genes matched with the species' transcriptome. Numerous colour and colour pattern morphs exist in P. guttatus, making it an ideal model to study the genetic determinism, development, and evolution of adaptive colour traits in reptiles. Using our draft genome and a Single-Nucleotide Polymorphism (SNP) calling approach, we confirmed the interval with the causative mutation for the amelanistic phenotype, a result supported by a parallel exome-based study.
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http://dx.doi.org/10.1387/ijdb.150060atDOI Listing
April 2016

A small volatile bacterial molecule triggers mitochondrial dysfunction in murine skeletal muscle.

PLoS One 2013 30;8(9):e74528. Epub 2013 Sep 30.

Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts, United States of America ; Athinoula A. Martinos Center of Biomedical Imaging, Massachusetts General Hospital, Boston, Massachusetts, United States of America ; Shriners Hospitals for Children Boston, Boston, Massachusetts, United States of America.

Mitochondria integrate distinct signals that reflect specific threats to the host, including infection, tissue damage, and metabolic dysfunction; and play a key role in insulin resistance. We have found that the Pseudomonas aeruginosa quorum sensing infochemical, 2-amino acetophenone (2-AA), produced during acute and chronic infection in human tissues, including in the lungs of cystic fibrosis (CF) patients, acts as an interkingdom immunomodulatory signal that facilitates pathogen persistence, and host tolerance to infection. Transcriptome results have led to the hypothesis that 2-AA causes further harm to the host by triggering mitochondrial dysfunction in skeletal muscle. As normal skeletal muscle function is essential to survival, and is compromised in many chronic illnesses, including infections and CF-associated muscle wasting, we here determine the global effects of 2-AA on skeletal muscle using high-resolution magic-angle-spinning (HRMAS), proton ((1)H) nuclear magnetic resonance (NMR) metabolomics, in vivo (31)P NMR, whole-genome expression analysis and functional studies. Our results show that 2-AA when injected into mice, induced a biological signature of insulin resistance as determined by (1)H NMR analysis-, and dramatically altered insulin signaling, glucose transport, and mitochondrial function. Genes including Glut4, IRS1, PPAR-γ, PGC1 and Sirt1 were downregulated, whereas uncoupling protein UCP3 was up-regulated, in accordance with mitochondrial dysfunction. Although 2-AA did not alter high-energy phosphates or pH by in vivo (31)P NMR analysis, it significantly reduced the rate of ATP synthesis. This affect was corroborated by results demonstrating down-regulation of the expression of genes involved in energy production and muscle function, and was further validated by muscle function studies. Together, these results further demonstrate that 2-AA, acts as a mediator of interkingdom modulation, and likely effects insulin resistance associated with a molecular signature of mitochondrial dysfunction in skeletal muscle. Reduced energy production and mitochondrial dysfunctional may further favor infection, and be an important step in the establishment of chronic and persistent infections.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0074528PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3787027PMC
May 2014

Multiple enhancers regulate Hoxd genes and the Hotdog LncRNA during cecum budding.

Cell Rep 2013 Oct 26;5(1):137-50. Epub 2013 Sep 26.

School of Life Sciences, Ecole Polytechnique Fédérale, Lausanne CH-1015, Switzerland.

Hox genes are required for the development of the intestinal cecum, a major organ of plant-eating species. We have analyzed the transcriptional regulation of Hoxd genes in cecal buds and show that they are controlled by a series of enhancers located in a gene desert flanking the HoxD cluster. The start site of two opposite long noncoding RNAs (lncRNAs), Hotdog and Twin of Hotdog, selectively contacts the expressed Hoxd genes in the framework of a topological domain, coinciding with robust transcription of these genes during cecum budding. Both lncRNAs are specifically transcribed in the cecum, albeit bearing no detectable function in trans. Hedgehogs have kept this regulatory potential despite the absence of the cecum, suggesting that these mechanisms are used in other developmental situations. In this context, we discuss the implementation of a common "budding toolkit" between the cecum and the limbs.
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http://dx.doi.org/10.1016/j.celrep.2013.09.002DOI Listing
October 2013