In this study, we addressed whether a single 454 Life Science GS20 sequencing run provides new gene discovery from a normalized cDNA library, and whether the short reads produced via this technology ...are of value in gene structure annotation.
A single 454 GS20 sequencing run on adapter-ligated cDNA, from a normalized cDNA library, generated 292,465 reads that were reduced to 252,384 reads with an average read length of 92 nucleotides after cleaning. After clustering and assembly, a total of 184,599 unique sequences were generated containing over 400 SSRs. The 454 sequences generated hits to more genes than a comparable amount of sequence from MtGI. Although short, the 454 reads are of sufficient length to map to a unique genome location as effectively as longer ESTs produced by conventional sequencing. Functional interpretation of the sequences was carried out by Gene Ontology assignments from matches to Arabidopsis and was shown to cover a broad range of GO categories. 53,796 assemblies and singletons (29%) had no match in the existing MtGI. Within the previously unobserved Medicago transcripts, thousands had matches in a comprehensive protein database and one or more of the TIGR Plant Gene Indices. Approximately 20% of these novel sequences could be found in the Medicago genome sequence. A total of 70,026 reads generated by the 454 technology were mapped to 785 Medicago finished BACs using PASA and over 1,000 gene models required modification. In parallel to 454 sequencing, 4,445 5'-prime reads were generated by conventional sequencing using the same library and from the assembled sequences it was shown to contain about 52% full length cDNAs encoding proteins from 50 to over 500 amino acids in length.
Due to the large number of reads afforded by the 454 DNA sequencing technology, it is effective in revealing the expression of transcripts from a broad range of GO categories and contains many rare transcripts in normalized cDNA libraries, although only a limited portion of their sequence is uncovered. As with longer ESTs, 454 reads can be mapped uniquely onto genomic sequence to provide support for, and modifications of, gene predictions.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Listeria monocytogenes, a foodborne bacterial pathogen, is comprised of four phylogenetic lineages that vary with regard to their serotypes and distribution among sources. In order to characterize ...lineage-specific genomic diversity within L. monocytogenes, we sequenced the genomes of eight strains from several lineages and serotypes, and characterized the accessory genome, which was hypothesized to contribute to phenotypic differences across lineages. The eight L. monocytogenes genomes sequenced range in size from 2.85-3.14 Mb, encode 2,822-3,187 genes, and include the first publicly available sequenced representatives of serotypes 1/2c, 3a and 4c. Mapping of the distribution of accessory genes revealed two distinct regions of the L. monocytogenes chromosome: an accessory-rich region in the first 65° adjacent to the origin of replication and a more stable region in the remaining 295°. This pattern of genome organization is distinct from that of related bacteria Staphylococcus aureus and Bacillus cereus. The accessory genome of all lineages is enriched for cell surface-related genes and phosphotransferase systems, and transcriptional regulators, highlighting the selective pressures faced by contemporary strains from their hosts, other microbes, and their environment. Phylogenetic analysis of O-antigen genes and gene clusters predicts that serotype 4 was ancestral in L. monocytogenes and serotype 1/2 associated gene clusters were putatively introduced through horizontal gene transfer in the ancestral population of L. monocytogenes lineage I and II.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Epigenetic modification of OXT and human sociability Haas, Brian W.; Filkowski, Megan M.; Cochran, R. Nick ...
Proceedings of the National Academy of Sciences - PNAS,
07/2016, Letnik:
113, Številka:
27
Journal Article
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Across many mammalian species there exist genetic and biological systems that facilitate the tendency to be social. Oxytocin is a neuropeptide involved in social-approach behaviors in humans and ...others mammals. Although there exists a large, mounting body of evidence showing that oxytocin signaling genes are associated with human sociability, very little is currently known regarding the way the structural gene for oxytocin (OXT) confers individual differences in human sociability. In this study, we undertook a comprehensive approach to investigate the association between epigenetic modification of OXT via DNA methylation, and overt measures of social processing, including self-report, behavior, and brain function and structure. Genetic data were collected via saliva samples and analyzed to target and quantify DNA methylation across the promoter region of OXT. We observed a consistent pattern of results across sociability measures. People that exhibit lower OXT DNA methylation (presumably linked to higher OXT expression) display more secure attachment styles, improved ability to recognize emotional facial expressions, greater superior temporal sulcus activity during two social-cognitive functional MRI tasks, and larger fusiform gyrus gray matter volume than people that exhibit higher OXT DNA methylation. These findings provide empirical evidence that epigenetic modification of OXT is linked to several overt measures of sociability in humans and serve to advance progress in translational social neuroscience research toward a better understanding of the evolutionary and genetic basis of normal and abnormal human sociability.
Psychopathic individuals are notorious for their callous disregard for others’ emotions. Prior research has linked psychopathy to deficits in affective mechanisms underlying empathy (e.g., affective ...sharing), yet research relating psychopathy to cognitive mechanisms underlying empathy (e.g., affective perspective-taking and Theory of Mind) requires further clarification. To elucidate the neurobiology of cognitive mechanisms of empathy in psychopathy, we administered an fMRI task and tested for global as well as emotion-specific deficits in affective perspective-taking. Adult male incarcerated offenders (N = 94) viewed images of two people interacting, with one individual's face obscured by a shape. Participants were cued to either identify the emotion of the obscured individual or identify the shape from one of two emotion or shape choices presented on each trial. Target emotions included anger, fear, happiness, sadness, and neutral. Contrary to predictions, psychopathy was unrelated to neural activity in the Affective Perspective-taking > Shape contrast. In line with predictions, psychopathy was negatively related to task accuracy during affective perspective-taking for fear, happiness, and sadness. Psychopathy was related to reduced hemodynamic activity exclusively during fear perspective-taking in several areas: left anterior insula extending into posterior orbitofrontal cortex, right precuneus, left superior parietal lobule, and left superior occipital cortex. Although much prior research has emphasized psychopathy-related abnormalities in affective mechanisms mediating empathy, current results add to growing evidence of psychopathy-related abnormalities in a cognitive mechanism related to empathy. These findings highlight brain regions that are hypoactive in psychopathy when explicitly processing another's fear.
Loa loa, the African eyeworm, is a major filarial pathogen of humans. Unlike most filariae, L. loa does not contain the obligate intracellular Wolbachia endosymbiont. We describe the 91.4-Mb genome ...of L. loa and that of the related filarial parasite Wuchereria bancrofti and predict 14,907 L. loa genes on the basis of microfilarial RNA sequencing. By comparing these genomes to that of another filarial parasite, Brugia malayi, and to those of several other nematodes, we demonstrate synteny among filariae but not with nonparasitic nematodes. The L. loa genome encodes many immunologically relevant genes, as well as protein kinases targeted by drugs currently approved for use in humans. Despite lacking Wolbachia, L. loa shows no new metabolic synthesis or transport capabilities compared to other filariae. These results suggest that the role of Wolbachia in filarial biology is more subtle than previously thought and reveal marked differences between parasitic and nonparasitic nematodes.
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DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
Cultural sensitivity in societal development has been advocated for since at least the 1960s but has remained understudied. Our goal is to address this gap and to investigate folk theories of ...societal development. We aimed to identify both universal and culturally specific lay beliefs about what constitutes good societal development. We collected data from 2,684 participants from Japan, Hong Kong (China), Poland, Turkey, Brazil, France, Nigeria, the USA, and Canada. We measured preferences for 28 development aims. We used multidimensional scaling, analysis of variance, and pairwise comparisons to identify universal and country‐specific preferences. Our results demonstrate that what people understand as modernization is fairly universal across countries, but specific pathways of development and preferences towards these pathways tend to vary between countries. We distinguished three facets of modernization—foundational aims (e.g., trust, economic development), welfare aims (e.g., poverty eradication, education), and inclusive aims (e.g., openness, gender equality)—and incorporated them into a folk meta‐theory of modernization. In all nine countries, the three facets of modernization were preferred more than conventional aims (e.g., military, demographic growth). We propose a method of implementing our findings into a culturally sensitive modernization index.
Emotional Conflict and Neuroticism Haas, Brian W; Omura, Kazufumi; Constable, R. Todd ...
Behavioral neuroscience,
04/2007, Letnik:
121, Številka:
2
Journal Article
Recenzirano
The amygdala and subgenual anterior cingulate (AC) have been associated with anxiety and mood disorders, for which trait neuroticism is a risk factor. Prior work has not related individual ...differences in amygdala or subgenual AC activation with neuroticism. Functional magnetic resonance imaging was used to investigate changes in blood oxygen level-dependent signal within the amygdala and subgenual AC associated with trait neuroticism in a nonclinical sample of 36 volunteers during an emotional conflict task. Neuroticism correlated positively with amygdala and subgenual AC activation during trials of high emotional conflict, compared with trials of low emotional conflict. The subscale of neuroticism that reflected the anxious form of neuroticism (N1) explained a greater proportion of variance within the observed clusters than the subscale of neuroticism that reflected the depressive form of neuroticism (N3). Using a task that is sensitive to individual differences in the detection of emotional conflict, the authors have provided a neural correlate of the link between neuroticism and anxiety and mood disorders. This effect was driven to a greater extent by the anxious relative to the depressive characteristics of neuroticism and may constitute vulnerability markers for anxiety-related disorders.
Many higher education instructions have set forth explicit objectives to improve college students’ intercultural sensitivity and communication. However, there currently exits considerable ...heterogeneity in terms of the extent and methods that higher education institutions undertake in order to achieve these important goals. This praxis essay provides a framework to understand the process of intercultural learning in college students, the core features of academic cultural psychology, and makes specific recommendations for effective and innovative ways to teach a cultural psychology course to a broad range of undergraduate students. Specific teaching techniques are offered to target specific intercultural learning areas.
Implicit theories and psychological essentialism are valuable frameworks used to model how changeable many traits are perceived to be. These frameworks, however, characterise changeability as a broad ...and generalised construct and do not fully capture the nuance and specificity involved in personality changeability. We therefore sought to deconstruct implicit theories about changeability into underlying more specific aspects of changeability. We measured how changeable people theorise personality traits to be according to three underlying specific factors: volitional control, context and age. We investigated how specific implicit theories about changeability vary across different personality traits. We show that two personality traits (agreeableness and conscientiousness) are linked to dissociable patterns of specific factors used to explain how changeable they are. These findings yield new insight into the way people explain why personality traits are changeable and demonstrate that different types of reasons are used to explain the changeability of agreeableness and conscientiousness.
Castor bean (Ricinus communis) is an oilseed crop that belongs to the spurge (Euphorbiaceae) family, which comprises approximately 6,300 species that include cassava (Manihot esculenta), rubber tree ...(Hevea brasiliensis) and physic nut (Jatropha curcas). It is primarily of economic interest as a source of castor oil, used for the production of high-quality lubricants because of its high proportion of the unusual fatty acid ricinoleic acid. However, castor bean genomics is also relevant to biosecurity as the seeds contain high levels of ricin, a highly toxic, ribosome-inactivating protein. Here we report the draft genome sequence of castor bean (4.6-fold coverage), the first for a member of the Euphorbiaceae. Whereas most of the key genes involved in oil synthesis and turnover are single copy, the number of members of the ricin gene family is larger than previously thought. Comparative genomics analysis suggests the presence of an ancient hexaploidization event that is conserved across the dicotyledonous lineage.
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