The origins, evolution, and functional potential of alternative splicing in vertebrates.

Alternative splicing (AS) has the potential to greatly expand the functional repertoire of mammalian transcriptomes. However, few variant transcripts have been characterized functionally, making it difficult to assess the contribution of AS to the generation of phenotypic complexity and to study the evolution of splicing patterns. We have compared the AS of 309 protein-coding genes in the human ENCODE pilot regions against their mouse orthologs in unprecedented detail, utilizing traditional transcriptomic and RNAseq data. The conservation status of every transcript has been investigated, and each functionally categorized as coding (separated into coding sequence [CDS] or nonsense-mediated decay [NMD] linked) or noncoding. In total, 36.7% of human and 19.3% of mouse coding transcripts are species specific, and we observe a 3.6 times excess of human NMD transcripts compared with mouse; in contrast to previous studies, the majority of species-specific AS is unlinked to transposable elements. We observe one conserved CDS variant and one conserved NMD variant per 2.3 and 11.4 genes, respectively. Subsequently, we identify and characterize equivalent AS patterns for 22.9% of these CDS or NMD-linked events in nonmammalian vertebrate genomes, and our data indicate that functional NMD-linked AS is more widespread and ancient than previously thought. Furthermore, although we observe an association between conserved AS and elevated sequence conservation, as previously reported, we emphasize that 30% of conserved AS exons display sequence conservation below the average score for constitutive exons. In conclusion, we demonstrate the value of detailed comparative annotation in generating a comprehensive set of AS transcripts, increasing our understanding of AS evolution in vertebrates. Our data supports a model whereby the acquisition of functional AS has occurred throughout vertebrate evolution and is considered alongside amino acid change as a key mechanism in gene evolution.

eggNOG v4.0: nested orthology inference across 3686 organisms

With the increasing availability of various 'omics data, high-quality orthology assignment is crucial for evolutionary and functional genomics studies. We here present the fourth version of the eggNOG database (available at http://eggnog.embl.de) that derives nonsupervised orthologous groups (NOGs) from complete genomes, and then applies a comprehensive characterization and analysis pipeline to the resulting gene families. Compared with the previous version, we have more than tripled the underlying species set to cover 3686 organisms, keeping track with genome project completions while prioritizing the inclusion of high-quality genomes to minimize error propagation from incomplete proteome sets. Major technological advances include (i) a robust and scalable procedure for the identification and inclusion of high-quality genomes, (ii) provision of orthologous groups for 107 different taxonomic levels compared with 41 in eggNOGv3, (iii) identification and annotation of particularly closely related orthologous groups, facilitating analysis of related gene families, (iv) improvements of the clustering and functional annotation approach, (v) adoption of a revised tree building procedure based on the multiple alignments generated during the process and (vi) implementation of quality control procedures throughout the entire pipeline. As in previous versions, eggNOGv4 provides multiple sequence alignments and maximum-likelihood trees, as well as broad functional annotation. Users can access the complete database of orthologous groups via a web interface, as well as through bulk download.

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates which provides nearly 30% of the world's annual sugar production and is a source for bioethanol and animal feed. The species belongs to the order of Caryophylalles, is diploid with 2n = 18 chromosomes, has an estimated genome size of 714-758 megabases and shares an ancient genome triplication with other eudicot plants. Leafy beets have been cultivated since Roman times, but sugar beet is one of the most recently domesticated crops. It arose in the late eighteenth century when lines accumulating sugar in the storage root were selected from crosses made with chard and fodder beet. Here we present a reference genome sequence for sugar beet as the first non-rosid, non-asterid eudicot genome, advancing comparative genomics and phylogenetic reconstructions. The genome sequence comprises 567 megabases, of which 85% could be assigned to chromosomes. The assembly covers a large proportion of the repetitive sequence content that was estimated to be 63%. We predicted 27,421 protein-coding genes supported by transcript data and annotated them on the basis of sequence homology. Phylogenetic analyses provided evidence for the separation of Caryophyllales before the split of asterids and rosids, and revealed lineage-specific gene family expansions and losses. We sequenced spinach (Spinacia oleracea), another Caryophyllales species, and validated features that separate this clade from rosids and asterids. Intraspecific genomic variation was analysed based on the genome sequences of sea beet (Beta vulgaris ssp. maritima; progenitor of all beet crops) and four additional sugar beet accessions. We identified seven million variant positions in the reference genome, and also large regions of low variability, indicating artificial selection. The sugar beet genome sequence enables the identification of genes affecting agronomically relevant traits, supports molecular breeding and maximizes the plant's potential in energy biotechnology.

Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds.

Pseudomonas knackmussii B13 was the first strain to be isolated in 1974 that could degrade chlorinated aromatic hydrocarbons. This discovery was the prologue for subsequent characterization of numerous bacterial metabolic pathways, for genetic and biochemical studies, and which spurred ideas for pollutant bioremediation. In this study, we determined the complete genome sequence of B13 using next generation sequencing technologies and optical mapping. Genome annotation indicated that B13 has a variety of metabolic pathways for degrading monoaromatic hydrocarbons including chlorobenzoate, aminophenol, anthranilate and hydroxyquinol, but not polyaromatic compounds. Comparative genome analysis revealed that B13 is closest to Pseudomonas denitrificans and Pseudomonas aeruginosa. The B13 genome contains at least eight genomic islands [prophages and integrative conjugative elements (ICEs)], which were absent in closely related pseudomonads. We confirm that two ICEs are identical copies of the 103 kb self-transmissible element ICEclc that carries the genes for chlorocatechol metabolism. Comparison of ICEclc showed that it is composed of a variable and a 'core' region, which is very conserved among proteobacterial genomes, suggesting a widely distributed family of so far uncharacterized ICE. Resequencing of two spontaneous B13 mutants revealed a number of single nucleotide substitutions, as well as excision of a large 220 kb region and a prophage that drastically change the host metabolic capacity and survivability.

Perceptual defense in anxiety disorders

RÉSUMÉ Plusieurs auteurs ont étudié la perception en fonction de la psychopathologie. Dans cette optique, Borgeat, David, Saucier et Dumont en 1994 et Borgeat, Sauvageau, David et Saucier en 1997 ont utilisé la méthode tachistoscopique afin de comparer, dans une étude prospective, la perception de stimuli émotionnels entre des femmes souffrant d'une dépression du post- partum et des femmes non atteintes. Par ailleurs, des études antérieures, notamment les travaux de MacLeod et Rutherford en 1992, avaient montré la possibilité d'un processus de perception différent entre sujets anxieux et non anxieux. L'étude actuelle pose l'hypothèse d'une interaction entre caractéristiques du stimulus et trouble anxieux du sujet. Cette hypothèse suppose donc un processus préconscient de l'information, avec analyse sémantique de cette dernière, à même d'influencer (inhiber ou faciliter) la perception de certains stimuli en fonction de leur charge affective. L'étude que nous présentons a pour but d'évaluer la perception de stimuli anxiogènes chez les patients atteints de troubles anxieux, et plus particulièrement chez des sujets souffrant d'attaque de panique et de troubles obsessionnels-compulsifs. A cette fin, nous avons choisi, contrairement à la plupart des études effectuées jusqu'à présent où la méthode Stroop avait été utilisée, la technique tachistoscopique qui, à notre avis, permet une mesure plus directe de la rapidité du processus perceptuel. Ainsi, trois groupes de sujets ont pris part à l'étude : un groupe contrôle (N = 22), un groupe de patients souffrant d'attaques de panique (N = 21) et un groupe de patients atteints de troubles obsessionnels-compulsifs (N = 20). Ces 63 sujets, âgés entre 18 et 60 ans, ont à la fois répondu au Fear Questionnaire ainsi qu'au Questionnaire Beck 13 pour la dépression et procédé à la reconnaissance de 42 mots (six groupes de sept mots) présentés aléatoirement à l'ordinateur, en cycles successifs de 15 millisecondes. Cinq parmi les six groupes de mots se référaient à un trouble anxieux spécifique, le sixième étant considéré comme un groupe de mots « neutres ». Le temps, en millisecondes, nécessaire à la reconnaissance de chaque mot a été enregistré. Les résultats montrent une lenteur de la part des patients souffrant d'attaques de panique pour la reconnaissance de tous les stimuli par rapport aux sujets contrôle, avec une performance intermédiaire entre les deux groupes pour les patients atteints de troubles obsessionnels-compulsifs. De plus, l'analyse statistique a révélé deux effets d'interaction : les patients atteints d'attaques de panique sont plus rapides à reconnaître le groupe de mots en rapport avec leur angoisse, de même que les patients soufflant de troubles obsessionnels- compulsifs ont un temps moyen de reconnaissance des mots en rapport avec leur trouble plus bas que prévu. Ces résultats amènent à une double conclusion. La première est que les patients anxieux manifestent une défense perceptuelle globale face aux stimuli anxiogènes en général, et que cette défense est plus marquée chez les patients atteints d'attaques de panique que chez les sujets souffrant de troubles obsessionnels-compulsifs. La deuxième est que ces mêmes patients, confrontés à des stimuli en rapport avec leur propre angoisse, montrent une vigilance accrue. Ainsi, ces données évoquent une double stratégie de traitement de l'information chez les patients anxieux : un évitement perceptuel général face à l'information émotionnellement chargée, et un traitement sélectif de l'information ayant un rapport direct avec l'angoisse dont ils soufflent. SUMMARY Prior research by MacLeod and Rutherford (1992) indicates that anxious subjects could have perceptual strategies different from nonanxious subjects. 42 verbal stimuli of six types (disease, social anxiety, panic, agoraphobia, obsessive-compulsive, and neutral) were tachistoscopically presented to three groups of subjects, aged 18 to 60 years: Panic Disorder group (n =21: 13 women and 8 men), and Obsessive-Compulsive Disorder group (n=20: 14 women and 6 men), recruited from an outpatient clinic, and a Control group (n=22: 14 women and 8 men), recruited among students and hospital staff. The times required for correct identification were generally longer for anxious subjects but quicker for stimuli specifically related to their disorder. The data could indicate a two-step perceptual strategy or two distinct ways of perceiving, usually, a generalized perceptual defense for a majority of anxiety-loaded stimuli, but also a selectively facilitated processing for stimuli specific to the disorder.

Aging preferentially affects molecular pathways implicated in development and disease of myelinating glial cells

The central and peripheral nervous systems are involved in multiple age-dependent neurological deficits that are often attributed to alterations in function of myelinating glial cells. However, the molecular events that underlie the age-related decline of glial cell function are unknown. We used Schwann cells as a model to study biological processes affected in glial cells by aging. We comprehensively profiled gene expression of the Schwann cellrich mouse sciatic nerve throughout life, from day of birth until senescence (840 days of age). We combined the aging data with the microarray transcriptional data obtained using nerves isolated from Schwann cell-specific neuropathy-inducing mutants MPZCre/+/Lpin1fE2−3/fE2−3 , MPZCre/+/ScapfE1/fE1 and Pmp22-null mice. The majority of age related transcripts were also affected in the analyzed mouse models of neuropathy (54.4%) and in development (59.5%) indicating a high level of overlapping in implicated molecular pathways. We observed that compared to peripheral nerve development, dynamically changing expression profiles in aging have opposite (anticorrelated) orientation while they copy the orientation of transcriptional changes observed in analyzed neuropathy models. Subsequent clustering and biological annotation of dynamically changing transcripts revealed that the processes most significantly deregulated in aging include inflammatory/immune response and lipid biosynthesis/metabolism. Importantly, the changes in these pathways were also observed in myelinated oligodendrocyte-rich optic nerves of aged mice, albeit with lower magnitude. This observation suggests that similar biological processes are affected in aging glial cells in central and peripheral nervous systems, however with different dynamics. Our data, which provide the first comprehensive comparison of molecular changes in glial cells in three distinct biological conditions comprising development, aging and disease, provide not only a new inside into the molecular alterations underlying neural system aging but also identify target pathways for potential therapeutic approaches to prevent or delay complications associated with age-related and inherited forms of neuropathies. *Current address: Department of Physiology, UCSF, San Francisco, CA, USA.

Comparative analysis of the transcriptome across distant species.

The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features. Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a 'universal model' based on a single set of organism-independent parameters.

Aging preferentially affects molecular pathways implicated in development and disease of myelinating glial cells

The central and peripheral nervous systems are involved in multiple agedependent neurological deficits that are often attributed to alterations in function of myelinating glial cells. However, the molecular events that underlie the age-related decline of glial cell function are unknown. We used Schwann cells as a model to study biological processes affected in glial cells by aging. We comprehensively profiled gene expression of the Schwann cell-rich mouse sciatic nerve throughout life, from day of birth until senescence (840 days of age). We combined the aging data with the microarray transcriptional data obtained using nerves isolated from Schwann cell-specific neuropathy-inducing mutants MPZCre/þ/Lpin1fE2-3/fE2-3, MPZCre/þ/ScapfE1/fE1 and Pmp22-null mice. A majority of age related transcripts were also affected in the analyzed mouse models of neuropathy (54.4%) and in development (59.5%) indicating a high level of overlapping in implicated molecular pathways. We observed that compared to peripheral nerve development, dynamically changing expression profiles in aging have opposite (anticorrelated) orientation while they copy the orientation of transcriptional changes observed in analyzed neuropathy models. Subsequent clustering and biological annotation of dynamically changing transcripts revealed that the processes most significantly deregulated in aging include inflammatory/ immune response and lipid biosynthesis/metabolism. Importantly, the changes in these pathways were also observed in myelinated oligodendrocyte- rich optic nerves of aged mice, albeit with lower magnitude. This observation suggests that similar biological processes are affected in aging glial cells in central and peripheral nervous systems, however with different dynamics. Our data, which provide the first comprehensive comparison of molecular changes in glial cells in three distinct biological conditions comprising development, aging and disease, provide not only a new inside into the molecular alterations underlying neural system aging but also identify target pathways for potential therapeutical approaches to prevent or delay complications associated with age-related and inherited forms of neuropathies.

What to compare and how: Comparative transcriptomics for Evo-Devo.

Evolutionary developmental biology has grown historically from the capacity to relate patterns of evolution in anatomy to patterns of evolution of expression of specific genes, whether between very distantly related species, or very closely related species or populations. Scaling up such studies by taking advantage of modern transcriptomics brings promising improvements, allowing us to estimate the overall impact and molecular mechanisms of convergence, constraint or innovation in anatomy and development. But it also presents major challenges, including the computational definitions of anatomical homology and of organ function, the criteria for the comparison of developmental stages, the annotation of transcriptomics data to proper anatomical and developmental terms, and the statistical methods to compare transcriptomic data between species to highlight significant conservation or changes. In this article, we review these challenges, and the ongoing efforts to address them, which are emerging from bioinformatics work on ontologies, evolutionary statistics, and data curation, with a focus on their implementation in the context of the development of our database Bgee (http://bgee.org). J. Exp. Zool. (Mol. Dev. Evol.) 324B: 372-382, 2015. © 2015 Wiley Periodicals, Inc.

Study on Accuracy of Judgments by Chinese Fingerprint Examiners

The interpretation of fingerprint evidence depends on the judgments of fingerprint examiners. This study assessed the accuracy of different judgments made by fingerprint examiners following the Analysis, Comparison, and Evaluation (ACE) process. Each examiner was given five marks for analysis, comparison, and evaluation. We compared the experts' judgments against the ground truth and used an annotation platform to evaluate how Chinese fingerprint examiners document their comparisons during the identification process. The results showed that different examiners demonstrated different accuracy of judgments and different mechanisms to reach them.

A survey of transposable element classification systems--a call for a fundamental update to meet the challenge of their diversity and complexity.

The increase of publicly available sequencing data has allowed for rapid progress in our understanding of genome composition. As new information becomes available we should constantly be updating and reanalyzing existing and newly acquired data. In this report we focus on transposable elements (TEs) which make up a significant portion of nearly all sequenced genomes. Our ability to accurately identify and classify these sequences is critical to understanding their impact on host genomes. At the same time, as we demonstrate in this report, problems with existing classification schemes have led to significant misunderstandings of the evolution of both TE sequences and their host genomes. In a pioneering publication Finnegan (1989) proposed classifying all TE sequences into two classes based on transposition mechanisms and structural features: the retrotransposons (class I) and the DNA transposons (class II). We have retraced how ideas regarding TE classification and annotation in both prokaryotic and eukaryotic scientific communities have changed over time. This has led us to observe that: (1) a number of TEs have convergent structural features and/or transposition mechanisms that have led to misleading conclusions regarding their classification, (2) the evolution of TEs is similar to that of viruses by having several unrelated origins, (3) there might be at least 8 classes and 12 orders of TEs including 10 novel orders. In an effort to address these classification issues we propose: (1) the outline of a universal TE classification, (2) a set of methods and classification rules that could be used by all scientific communities involved in the study of TEs, and (3) a 5-year schedule for the establishment of an International Committee for Taxonomy of Transposable Elements (ICTTE).

How environmental sounds become meaningful

The term "sound object" describes an auditory experience that is associated with an acoustic event produced by a sound source. In natural settings, a sound produced by a living being or an object provides information about the identity and the location of the sound source. Sound's identity is orocessed alono the ventral "What" pathway which consists of regions within the superior and middle temporal cortices as well as the inferior frontal gyrus. This work concerns the creation of individual auditory object representations in narrow semantic categories and their plasticity using electrical imaging. Discrimination of sounds from broad category has been shown to occur along a temporal hierarchy and in different brain regions along the ventral "What" pathway. However, sounds belonging to the same semantic category, such as faces or voices, were shown to be discriminated in specific brain areas and are thought to represent a special class of stimuli. I have investigated how cortical representations of a narrow category, here birdsongs, is modulated by training novices to recognized songs of individual bird species. Dynamic analysis of distributed source estimations revealed differential sound object representations within the auditory ventral "What" pathway as a function of the level of expertise newly acquired. Correct recognition of trained items induces a sharpening within a left-lateralized semantic network starting around 200ms, whereas untrained items' processing occurs later in lower-level and memory-related regions. With another category of sounds belonging to the same category, here heartbeats, I investigated the cortical representations of correct and incorrect recognition of sounds. Source estimations revealed differential representations partially overlapping with regions involved in the semantic network that is activated when participants became experts in the task. Incorrect recognition also induces a higher activation when compared to correct recognition in regions processing lower-level features. The discrimination of heartbeat sounds is a difficult task and requires a continuous listening. I investigated whether the repetition effects are modulated by participants' behavioral performance. Dynamic source estimations revealed repetition suppression in areas located outside of the semantic network. Therefore, individual environmental sounds become meaningful with training. Their representations mainly involve a left-lateralized network of brain regions that are tuned with expertise, as well as other brain areas, not related to semantic processing, and occurring in early stages of semantic processing. -- Le terme objet sonore" décrit une expérience auditive associée à un événement acoustique produit par une source sonore. Dans l'environnement, un son produit par un être vivant ou un objet fournit des informations concernant l'identité et la localisation de la source sonore. Les informations concernant l'identité d'un son sont traitée le long de la voie ventrale di "Quoi". Cette voie est composée de regions situées dans le cortex temporal et frontal. L'objet de ce travail est d'étudier quels sont les neuro-mecanismes impliqués dans la représentation de nouveaux objets sonores appartenant à une meme catégorie sémantique ainsi que les phénomènes de plasticité à l'aide de l'imagerie électrique. Il a été montré que la discrimination de sons appartenant à différentes catégories sémantiques survient dans différentes aires situées le long la voie «Quoi» et suit une hiérarchie temporelle II a également été montré que la discrimination de sons appartenant à la même catégorie sémantique tels que les visages ou les voix, survient dans des aires spécifiques et représenteraient des stimuli particuliers. J'ai étudié comment les représentations corticales de sons appartenant à une même catégorie sémantique, dans ce cas des chants d'oiseaux, sont modifiées suite à un entraînement Pour ce faire, des sujets novices ont été entraînés à reconnaître des chants d'oiseaux spécifiques L'analyse des estimations des sources neuronales au cours du temps a montré que les representations des objets sonores activent de manière différente des régions situées le long de la vo,e ventrale en fonction du niveau d'expertise acquis grâce à l'entraînement. La reconnaissance des chants pour lesquels les sujets ont été entraînés implique un réseau sémantique principalement situé dans l'hémisphère gauche activé autour de 200ms. Au contraire, la reconnaissance des chants pour lesquels les sujets n'ont pas été entraînés survient plus tardivement dans des régions de plus bas niveau. J'ai ensuite étudié les mécanismes impliqués dans la reconnaissance et non reconnaissance de sons appartenant à une autre catégorie, .es battements de coeur. L'analyse des sources neuronales a montre que certaines régions du réseau sémantique lié à l'expertise acquise sont recrutées de maniere différente en fonction de la reconnaissance ou non reconnaissance du son La non reconnaissance des sons recrute des régions de plus bas niveau. La discrimination des bruits cardiaques est une tâche difficile et nécessite une écoute continue du son. J'ai étudié l'influence des réponses comportementales sur les effets de répétitions. L'analyse des sources neuronales a montré que la reconnaissance ou non reconnaissance des sons induisent des effets de repétition différents dans des régions situées en dehors des aires du réseau sémantique. Ainsi, les sons acquièrent un sens grâce à l'entraînement. Leur représentation corticale implique principalement un réseau d'aires cérébrales situé dans l'hémisphère gauche, dont l'activité est optimisée avec l'acquisition d'un certain niveau d'expertise, ainsi que d'autres régions qui ne sont pas liée au traitement de l'information sémantique. L'activité de ce réseau sémantique survient plus rapidemement que la prédiction par le modèle de la hiérarchie temporelle.