High-coverage sequencing and annotated assemblies of the budgerigar genome

BACKGROUND: Parrots belong to a group of behaviorally advanced vertebrates and have an advanced ability of vocal learning relative to other vocal-learning birds. They can imitate human speech, synchronize their body movements to a rhythmic beat, and understand complex concepts of referential meaning to sounds. However, little is known about the genetics of these traits. Elucidating the genetic bases would require whole genome sequencing and a robust assembly of a parrot genome. FINDINGS: We present a genomic resource for the budgerigar, an Australian Parakeet (Melopsittacus undulatus) -- the most widely studied parrot species in neuroscience and behavior. We present genomic sequence data that includes over 300x raw read coverage from multiple sequencing technologies and chromosome optical maps from a single male animal. The reads and optical maps were used to create three hybrid assemblies representing some of the largest genomic scaffolds to date for a bird; two of which were annotated based on similarities to reference sets of non-redundant human, zebra finch and chicken proteins, and budgerigar transcriptome sequence assemblies. The sequence reads for this project were in part generated and used for both the Assemblathon 2 competition and the first de novo assembly of a giga-scale vertebrate genome utilizing PacBio single-molecule sequencing. CONCLUSIONS: Across several quality metrics, these budgerigar assemblies are comparable to or better than the chicken and zebra finch genome assemblies built from traditional Sanger sequencing reads, and are sufficient to analyze regions that are difficult to sequence and assemble, including those not yet assembled in prior bird genomes, and promoter regions of genes differentially regulated in vocal learning brain regions. This work provides valuable data and material for genome technology development and for investigating the genomics of complex behavioral traits

Expressions of Multiple Neuronal Dynamics during Sensorimotor Learning in the Motor Cortex of Behaving Monkeys

Previous studies support the notion that sensorimotor learning involves multiple processes. We investigated the neuronal basis of these processes by recording single-unit activity in motor cortex of non-human primates (Macaca fascicularis), during adaptation to force-field perturbations. Perturbed trials (reaching to one direction) were practiced along with unperturbed trials (to other directions). The number of perturbed trials relative to the unperturbed ones was either low or high, in two separate practice schedules. Unsurprisingly, practice under high-rate resulted in faster learning with more pronounced generalization, as compared to the low-rate practice. However, generalization and retention of behavioral and neuronal effects following practice in high-rate were less stable; namely, the faster learning was forgotten faster. We examined two subgroups of cells and showed that, during learning, the changes in firing-rate in one subgroup depended on the number of practiced trials, but not on time. In contrast, changes in the second subgroup depended on time and practice; the changes in firing-rate, following the same number of perturbed trials, were larger under high-rate than low-rate learning. After learning, the neuronal changes gradually decayed. In the first subgroup, the decay pace did not depend on the practice rate, whereas in the second subgroup, the decay pace was greater following high-rate practice. This group shows neuronal representation that mirrors the behavioral performance, evolving faster but also decaying faster at learning under high-rate, as compared to low-rate. The results suggest that the stability of a new learned skill and its neuronal representation are affected by the acquisition schedule.United States-Israel Binational Science FoundationIsrael Science FoundationIda Baruch FundRosetrees Trus

An Evolutionarily Conserved Enhancer Regulates Bmp4 Expression in Developing Incisor and Limb Bud

To elucidate the transcriptional regulation of Bmp4 expression during organogenesis, we used phylogenetic footprinting and transgenic reporter analyses to identify Bmp4 cis-regulatory modules (CRMs). These analyses identified a regulatory region located ∼46 kb upstream of the mouse Bmp4 transcription start site that had previously been shown to direct expression in lateral plate mesoderm. We refined this regulatory region to a 396-bp minimal enhancer, and show that it recapitulates features of endogenous Bmp4 expression in developing mandibular arch ectoderm and incisor epithelium during the initiation-stage of tooth development. In addition, this enhancer directs expression in the apical ectodermal ridge (AER) of the developing limb and in anterior and posterior limb mesenchyme. Transcript profiling of E11.5 mouse incisor dental lamina, together with protein binding microarray (PBM) analyses, allowed identification of a conserved DNA binding motif in the Bmp4 enhancer for Pitx homeoproteins, which are also expressed in the developing mandibular and incisor epithelium. In vitro electrophoretic mobility shift assays (EMSA) and in vivo transgenic reporter mutational analyses revealed that this site supports Pitx binding and that the site is necessary to recapitulate aspects of endogenous Bmp4 expression in developing craniofacial and limb tissues. Finally, Pitx2 chromatin immunoprecipitation (ChIP) demonstrated direct binding of Pitx2 to this Bmp4 enhancer site in a dental epithelial cell line. These results establish a direct molecular regulatory link between Pitx family members and Bmp4 gene expression in developing incisor epithelium

Robotic neurorehabilitation: a computational motor learning perspective

Conventional neurorehabilitation appears to have little impact on impairment over and above that of spontaneous biological recovery. Robotic neurorehabilitation has the potential for a greater impact on impairment due to easy deployment, its applicability across of a wide range of motor impairment, its high measurement reliability, and the capacity to deliver high dosage and high intensity training protocols

Ribbon: Intuitive visualization for complex genomic variation

SUMMARY: Ribbon is an alignment visualization tool that shows how alignments are positioned within both the reference and read contexts, giving an intuitive view that enables a better understanding of structural variants and the read evidence supporting them. Ribbon was born out of a need to curate complex structural variant calls and determine whether each was well supported by long-read evidence, and it uses the same intuitive visualization method to shed light on contig alignments from genome-to-genome comparisons. AVAILABILITY AND IMPLEMENTATION: Ribbon is freely available online at http://genomeribbon.com/ and is open-source at https://github.com/marianattestad/ribbon. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Exploring the factors that influence the perception of risk: The case of Volcan de Colima, Mexico

Volcan de Colima has increased its activity considerably since 1998 with four periods of effusion and since 2003, daily Vulcanian explosions. During 2005 the magnitude of the explosivity increased, producing many pyroclastic flows, two of which reached over 5 km from the volcano, making them the largest events since the last Plinian eruption in 1913. A significant risk is also presented by the lahar hazard, with various examples of damage to infrastructure during the last few years and 23 people killed in 1955. Nearly 5000 people live in small settlements within 15 km of the volcano. Since 1997 six studies have been carried out in the region in an attempt to define the relationship that exists between the population and its neighbour. Although the methodologies used were different, each study considered the results of the previous and attempted to contribute further data to define geographical variation in the perception of risk. The results of the studies highlight the minor role of increasing activity on risk perception, and distance from the volcano was shown to not directly influence risk perception. In most cases it is the combination of various socio-cultural, historical and political factors that defines the perception of volcanic risk within these villages. By studying the social representation of the risk, such complexity could be better understood. The 1997-2000 information campaign evidently improved risk perceptio

Contradicting incentives for research collaboration

This study describes the Danish publication award system (BFI), investigates whether its built-in incentives have had an effect on publication behavior at the University of Southern Denmark, and discusses the possible future implications on researcher incentives should universities wish to measure BFI on the individual level. We analyzed publication data from the university CRIS system (Pure) and from SciVal. Several studies indicate that co-authored scholarly journal articles attract more citations than single author articles. The reason for this are not clear, however, research collaboration across institutions and countries is commonly accepted in the research community and among university managements as one way of increasing the researcher’s and institution’s reputation and impact. The BFI system is designed to award scholarly publication activity at Danish universities, especially publication in international journals of high status. However, we find that the built-in incentives leave the researcher and his or her institution with a dilemma: If the researchers optimize their performance by forming author groups with external collaborators, the optimal way of doing so for the researchers is not the optimal way seen from the perspective of the university. Our analysis shows that the typical article has 6.5 authors, two of which are internal, and that this has remained stable since the introduction of the BFI. However, there is variation across the disciplines. While ‘the Arts and Humanities’ and ‘the Social Sciences’ seem to compose author groups in a way which does not optimize the performance of the institution, both ‘Health’ and ‘the Natural Sciences’ seem to optimize according to criteria other than those specified in the BFI

A novel model of human lympho-myeloid progenitor hierarchy based on single cell functional and transcriptional analysis

Human hemopoiesis produces 10 billion new, terminally mature, blood cells daily; a production that is also rapidly responsive to external change. Dysregulation of this complex process can lead to hemopoietic and immune deficiencies and blood cancers. In humans the hemopoietic progenitor hierarchy producing lymphoid and granulocytic-monocytic (myeloid) lineages is unclear. Multiple progenitor populations give rise to lymphoid and myeloid cells but they remain incompletely characterized at the immunophenotypic, transcriptional and functional level