Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

<p>Abstract</p> <p>Background</p> <p>Alfalfa, [<it>Medicago sativa </it>(L.) sativa], a widely-grown perennial forage has potential for development as a cellulosic ethanol feedstock. However, the genomics of alfalfa, a non-model species, is still in its infancy. The recent advent of RNA-Seq, a massively parallel sequencing method for transcriptome analysis, provides an opportunity to expand the identification of alfalfa genes and polymorphisms, and conduct in-depth transcript profiling.</p> <p>Results</p> <p>Cell walls in stems of alfalfa genotype 708 have higher cellulose and lower lignin concentrations compared to cell walls in stems of genotype 773. Using the Illumina GA-II platform, a total of 198,861,304 expression sequence tags (ESTs, 76 bp in length) were generated from cDNA libraries derived from elongating stem (ES) and post-elongation stem (PES) internodes of 708 and 773. In addition, 341,984 ESTs were generated from ES and PES internodes of genotype 773 using the GS FLX Titanium platform. The first alfalfa (<it>Medicago sativa</it>) gene index (MSGI 1.0) was assembled using the Sanger ESTs available from GenBank, the GS FLX Titanium EST sequences, and the <it>de novo </it>assembled Illumina sequences. MSGI 1.0 contains 124,025 unique sequences including 22,729 tentative consensus sequences (TCs), 22,315 singletons and 78,981 pseudo-singletons. We identified a total of 1,294 simple sequence repeats (SSR) among the sequences in MSGI 1.0. In addition, a total of 10,826 single nucleotide polymorphisms (SNPs) were predicted between the two genotypes. Out of 55 SNPs randomly selected for experimental validation, 47 (85%) were polymorphic between the two genotypes. We also identified numerous allelic variations within each genotype. Digital gene expression analysis identified numerous candidate genes that may play a role in stem development as well as candidate genes that may contribute to the differences in cell wall composition in stems of the two genotypes.</p> <p>Conclusions</p> <p>Our results demonstrate that RNA-Seq can be successfully used for gene identification, polymorphism detection and transcript profiling in alfalfa, a non-model, allogamous, autotetraploid species. The alfalfa gene index assembled in this study, and the SNPs, SSRs and candidate genes identified can be used to improve alfalfa as a forage crop and cellulosic feedstock.</p

Southern Bound A Gulf Coast Journalist on Books, Writers, and Literary Pilgrimages of the Heart

Engaging and spirited, Southern Bound represents the critical art at its most accessible and will prove entertaining fare for anyone who loves the written word.Cover -- Title -- Copyright -- Contents -- List of Illustrations -- Foreword -- Acknowledgments -- Introduction: For the Love of Books -- The South -- Essence of the South Remains Hard to Define -- Slaves in the Family -- Ball's Book Strikes Personal Chord with Historian -- Rivers of History -- Bumper Crop of Poems Celebrates Life on the Land -- Faulkner's "Blood and Thunder" Novel Endures -- Oprah Makes Brave, Bold Choice with Faulkner -- Liuzzo Biographer Brings a Sense of Justice to Topic -- South Carolina's Charms Preserved in Encyclopedia -- Young Woman's Diaries Basis of Wonderful Book -- Painter Mary Whyte Shows Keen Eye for Laborers in Working South -- The Civil War -- Slaves' Memories Offer Harrowing Accounts of War -- LSU Press Revives Story of Army of Tennessee -- Lee's True Legacy beyond Latest Biographer -- Pelham's Valor Shines in Maxwell's Perfect Lion -- Eye of the Storm: Union Soldier's Illustrated Memoir Confirms Civil War Was Tragedy for All -- Co. Aytch a Direct Link to Army in Gray -- Chance Discovery Reveals Details of Mobile Campaign -- Chaffin Cuts Through to Clear View of Hunley -- Poetry Collection from out of the Blue and Gray -- Rosen Invigorates Civil War Setting -- The Gulf Coast Renaissance -- Year in Greece Yields Book for Native Mobilian -- Our Voice of Reason -- Author Finds Inspiration in Writer Eugene Walter -- Store Specializes in Antique Volumes -- Hollon's The God File Deserves National Attention -- Black Belt Chronicles Richly Deserve Recognition -- Mobile Native Knight a Fast-Rising Literary Star -- Breech a Violent, Dark Tale from Franklin -- Scully's In the Hope of Rising Again a Gem -- Chicken Dreaming Corn: Family Tales Spur Captivating Novel of Mobile -- Emotional Exploration of a Deplorable Event -- Groom Takes Big Step with Vicksburg -- Architecture -- How Did Our Gardens Grow? Famously, It SeemsMississippi's Victorian Treasures Get Their Due -- Alabama's Architecture Gets Some Overdue Respect -- William Faulkner and the Tangible Past: The Architecture of Yoknapatawpha -- Matrana Shows Pride and Ruin of Plantations -- Historian Upends Ideas on American Architecture -- Scholar-Town Houses Have Many Tales to Tell -- Legacy Presents a Detailed Look at Rayfield's Work -- Fallingwater Study Cuts Myths, Affirms Merits -- The Architect of America -- New Orleans Takes Shape in an Architect's Memoir -- Literary Pilgrimages -- Stumbling on a Fossil of a Southern Dinosaur -- McMurtry's Hometown a Paradise for Collectors -- Drama of Story Comes Alive in Monroeville -- A Night in the Library -- Finding Cahaba: New Book Rekindles Fascination with Alabama's First Capital -- Looking Past Midnight -- A Literary Ramble through Old New Orleans -- Oxford, Mississippi: A Literary Profile -- A Small City of Literary Giants: Greenville, Mississippi -- Visit to Library Is a Return to Childhood -- Images from the Literary Side of Paris, with a Personal Touch -- Walter-Inspired Dream an Affirmation of Creativity -- Classics and Old Favorites Revisited -- A Tale Worthy of the Centuries: Looking into Chapman's Iliad -- Plato's Ancient Words Inspire the Modern Mind -- Old Story, New Life: Heaney Makes Epic Worth the Wait -- Decline and Fall Stands Test of Time -- Last of the Mohicans Was First of Its Kind -- Omoo a Showcase for Melville's Lighter Side -- Slowly, Beautifully: That's How the Cookie Crumbles -- Revisiting a Classic at the Water's Edge -- Joseph Conrad's Typhoon Shows Power of Storm -- One Man's Trash Is Another Man's Pleasure -- Pride and Prejudice Run Deep in Memoir -- Old Soldier Sahib a Rare Chronicle of Bygone Empire -- Cather's Look Westward Broke New Literary Ground -- Shane Stands as Classic of Western GenreBook behind Classic Wayne Film Still Holds Up -- Pacific Battleground Is More Than a Memory -- The International Scene -- A Shadowed Friendship: Book Looks Back on Broken Bond between Two Powerful Writers -- Quirky Italian Novel Shines in Recent Reissue -- Just an adventurer": An Aid Worker's Strange Path -- Cuba in Mind Brings Island Near Enough to Touch -- Events Make Brick Lane a Timely Volume -- Long Way Gone a Tribute to Human Spirit -- My Forbidden Face Drives Home Sufferings of Women under Taliban -- Márquez Classic Still Rewards Reader's Effort -- Istanbul, Not Constantinople, Gets the Works from a Nobel-Winning Native Son -- Iconic AK47 Assault Rifle Subject of Far-Ranging Biography -- Controversy and Censorship -- Plagiarism Charges Pull Prize-Winner from Shelves -- Alexandria's Library Rises from the Ashes-but Fires Still Burn -- George and Lennie Feeling the Squeeze -- Proposed Book Ban Deserves Firm Rebuttal -- America Flap Puts Mississippi in Spotlight -- Writer Takes Clear-Eyed Look at Battle Flag's Past and Present -- Without Sanctuary Confronts an Ugly Past -- Poe Folks Perturbed by Graveyard Guest -- Breach of Faith Offers Incisive Critiques -- An Open Letter to Louisiana's Governor -- School's Switch Alarms Book Lovers -- Old Writings Preserve Sense of Beaches' Beauty -- Reading and Writing Life -- My First Gun Became a Boy's Rite of Passage -- The Reader: A Quieter Side of Michael Jackson -- Politics Aside, Spanish Opens Rich Literary Terrain -- In Changing Times, It's Hard to Turn the Page -- Southern Writers Save the Style for the Page -- Oscar Wilde: One Fine Figure of a Writer -- Everybody Has a Story, but Who Wants to Read It? -- Odd Fantasy Reveals Deep-Seated Desire -- Coleridge Tome More Than Equal to Georges -- Favorite Reading Spots Make Good Books Better -- Elysium -- Mentor's Passing Time for ReflectionMississippian's Deep Roots Yielded a Towering Legacy -- In Memoriam: Eudora Welty -- George Plimpton's Wit, Grace Will Be Missed -- Foote Takes His Place among Heavenly Host -- Norman Mailer Leaves Larger-Than-Life Legacy -- A Chess Board Warrior's Influence Remembered -- A Father's Reading List Holds Share of TreasuresEngaging and spirited, Southern Bound represents the critical art at its most accessible and will prove entertaining fare for anyone who loves the written word.Description based on publisher supplied metadata and other sources.Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, YYYY. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries

A Novel Application of Deep Learning (Convolutional Neural Network) for Traumatic Spinal Cord Injury Classification Using Automatically Learned Features of EMG Signal

In this study, a traumatic spinal cord injury (TSCI) classification system is proposed using a convolutional neural network (CNN) technique with automatically learned features from electromyography (EMG) signals for a non-human primate (NHP) model. A comparison between the proposed classification system and a classical classification method (k-nearest neighbors, kNN) is also presented. Developing such an NHP model with a suitable assessment tool (i.e., classifier) is a crucial step in detecting the effect of TSCI using EMG, which is expected to be essential in the evaluation of the efficacy of new TSCI treatments. Intramuscular EMG data were collected from an agonist/antagonist tail muscle pair for the pre- and post-spinal cord lesion from five Macaca fasicularis monkeys. The proposed classifier is based on a CNN using filtered segmented EMG signals from the pre- and post-lesion periods as inputs, while the kNN is designed using four hand-crafted EMG features. The results suggest that the CNN provides a promising classification technique for TSCI, compared to conventional machine learning classification. The kNN with hand-crafted EMG features classified the pre- and post-lesion EMG data with an F-measure of 89.7% and 92.7% for the left- and right-side muscles, respectively, while the CNN with the EMG segments classified the data with an F-measure of 89.8% and 96.9% for the left- and right-side muscles, respectively. Finally, the proposed deep learning classification model (CNN), with its learning ability of high-level features using EMG segments as inputs, shows high potential and promising results for use as a TSCI classification system. Future studies can confirm this finding by considering more subjects

Detection of cartilage matrix degradation by autofluorescence lifetime

Cartilage is a vital organ to maintain joint function. Upon arthritis, proteolytic enzymes initiate degradation of cartilage extracellular matrix (ECM) resulting in eventual loss of joint function. However, there are only limited ways of non-invasively monitoring early chemical changes in cartilage matrix. Here we report that the autofluorescence decay profiles of cartilage tissue are significantly affected by proteolytic degradation of cartilage ECM and can be characterised by measurements of the autofluorescence lifetime (AFL). A compact multidimensional fluorometer coupled to a fibre-optic probe was developed for single point measurements of AFL and applied to cartilage that was treated with different proteinases. Upon treating cartilage with bacterial collagenase, trypsin or matrix metalloproteinase 1, a significant dose and time dependent decrease of AFL was observed. Our data suggest that AFL of cartilage tissue is a potential non-invasive readout to monitor cartilage matrix integrity that may contribute to future diagnosis of cartilage defects as well as monitoring the efficacy of anti-joint therapeutic agents