Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars

Recognizing that certain biological functions can be associated with specific DNA sequences has led various fields of biology to adopt the notion of the genetic part. This concept provides a finer level of granularity than the traditional notion of the gene. However, a method of formally relating how a set of parts relates to a function has not yet emerged. Synthetic biology both demands such a formalism and provides an ideal setting for testing hypotheses about relationships between DNA sequences and phenotypes beyond the gene-centric methods used in genetics. Attribute grammars are used in computer science to translate the text of a program source code into the computational operations it represents. By associating attributes with parts, modifying the value of these attributes using rules that describe the structure of DNA sequences, and using a multi-pass compilation process, it is possible to translate DNA sequences into molecular interaction network models. These capabilities are illustrated by simple example grammars expressing how gene expression rates are dependent upon single or multiple parts. The translation process is validated by systematically generating, translating, and simulating the phenotype of all the sequences in the design space generated by a small library of genetic parts. Attribute grammars represent a flexible framework connecting parts with models of biological function. They will be instrumental for building mathematical models of libraries of genetic constructs synthesized to characterize the function of genetic parts. This formalism is also expected to provide a solid foundation for the development of computer assisted design applications for synthetic biology

5-HTTLPR Polymorphism Impacts Task-Evoked and Resting-State Activities of the Amygdala in Han Chinese

Background: Prior research has shown that the amygdala of carriers of the short allele (s) of the serotonin transporter (5-HTT) gene (5-HTTLPR) have a larger response to negative emotional stimuli and higher spontaneous activity during the resting state than non-carriers. However, recent studies have suggested that the effects of 5-HTTLPR may be specific to different ethnic groups. Few studies have been conducted to address this issue. Methodology/Principal Findings: Blood oxygenation level dependent (BOLD) functional magnetic resonance imaging (fMRI) was conducted on thirty-eight healthy Han Chinese subjects (l/l group, n = 19; s/s group, n = 19) during the resting state and during an emotional processing task. Compared with the s/s group, the l/l group showed significantly increased regional homogeneity or local synchronization in the right amygdala during the resting state (|t|.2.028, p,0.05, corrected), but no significant difference was found in the bilateral amygdala in response to negative stimuli in the emotional processing task. Conclusions/Significance: 5-HTTLPR can alter the spontaneous activity of the amygdala in Han Chinese. However, the effect of 5-HTTLPR on the amygdala both in task state and resting state in Asian population was no similar with Caucasians. The

Adding value to under-utilised Irish fish roe: a physico-chemical and sensory comparison of cured Irish pollock (Pollachius pollachius) roe with commercial mullet (Mugil cephalus) and cod (Gadus morhua) products

peer reviewedIrish marine fish roe is generally discarded at sea or processed as low value-added fishmeal and not utilised as nutritious seafood ingredients. Locally sourced pollock roes were salted, air-dried (Mediterranean-style) and compared to similar commercial mullet and cod products for: weight; moisture content; pH; instrumental texture and colour; and sensory attributes. Raw pollock roes averaged 105 g (n = 25). Roes lost on average 3.1% moisture (w/w) after a 2-h salting period and 48.8% weight reduction was observed after an average 105 h air-drying time. The moisture content of pollock was not significantly different to commercial products. Average pH for pollock, mullet and cod products was 5.9, 5.4 and 5.7, respectively (P < 0.05). Pollock and mullet had similar hardness, but cod was significantly harder than both, when measured instrumentally. Total colour difference (ΔE*) between the surface of pollock and cod, and that of pollock and mullet was 7.5 and 3.0, respectively. Sensory assessment of sliced and powdered products, using 9-point hedonic and 5-point just-about-right (JAR) scales, was conducted with 38 consumers. Pollock received the highest scores for overall liking and intention to purchase compared to commercial mullet and cod products, averaging 5.6, 5.6 and 4.9, respectively, for sliced roe products, and 6.3, 5.3 and 6.1 for powdered products. Penalty analysis of JAR showed “overall liking” was impacted by the flavour being “too fishy”. In conclusion, pollock had similar characteristics and acceptable sensory attributes compared to commercial products presenting opportunities to expand the range of value-added roe products (e.g., trout, salmon) available, while also contributing to waste reduction

BOLD fMRI detectable alterations of brain activity in children and adolescents on the autism spectrum

Abstract The dissertation consists of three peer-reviewed publications and is related to the basic research of autism spectrum disorder (ASD), especially the assessment of changes in brain function using functional magnetic resonance imaging (fMRI). The purpose was to discover possible differences in cued and spontaneous brain activity in autistic child and adolescent participants compared to typically developing controls. We used blood oxygen level dependent (BOLD) fMRI imaging of the brain, with which the participants were examined at rest and while looking at facial expressions. The resting state (RS) fMRI data artifacts were reduced, and brain networks were identified using independent component analysis. In addition, the RS was analyzed 1) over the entire measurement period using the regional homogeneity (ReHo) method, which measures local connectivity, and 2) based on the states of different brain networks grouped into shorter periods using the co-activation patterns (CAP) method. Statistically significant differences between groups were found in RS, more clearly with the CAP method. Also, significant differences in brain activity were found between the groups regarding the observation of facial expressions. The dissertation increases the understanding of changes in brain networks related to the autism spectrum, strengthening and supplementing previous research results. Based on our results, analyses of brain networks grouped into similar activation phases of shorter duration are worth further development. The new information can help develop earlier and more accurate imaging diagnostics, tentatively recognizing possible intervention target brain networks and evaluating therapeutic effects.Tiivistelmä Väitöskirja koostuu kolmesta vertaisarvioidusta julkaisusta ja liittyy autismikirjon kehityshäiriön perustutkimukseen, erityisesti aivotoiminnan muutosten arviointiin toiminnallisen magneettikuvauksen (functional MRI, fMRI) avulla. Tutkimuksen tarkoituksena oli selvittää stimuloidun ja spontaanin aivotoiminnan mahdollisia eroavaisuuksia lasten ja nuorten autismikirjossa neurotyypillisiin verrokkeihin nähden. Tutkimusmenetelmänä käytettiin veren happipitoisuudesta riippuvaista aivojen fMRI-kuvausta, jolla osallistujia tutkittiin levossa sekä heidän katsellessaan kasvojen ilmeitä. Itsenäisten komponenttien analyysilla (ICA) vähennettiin lepotilan fMRI-datan häiriöitä ja tunnistettiin aivoverkostoja. Lisäksi lepotilaa analysoitiin 1) koko mittausjakson ajalta signaalien alueellista homogeenisuutta ts. aivojen paikallista kytkennällisyyttä mittaavalla regional homogeneity (ReHo) -menetelmällä ja 2) eri aivoverkostojen tilojen perusteella lyhyemmiksi ajanjaksoiksi ns. yhtäaikaisten aktivaatioiden kuvioihin (co-activation patterns; CAP) ryhmiteltyinä. Näissä löydettiin tilastollisesti merkittäviä ryhmien välisiä eroja, selkeämmin CAP-menetelmällä. Myös kasvojen ilmeiden tarkkailuun liittyen havaittiin tilastollisesti merkittäviä aivotoiminnan eroja ryhmien välillä. Väitöskirja lisää ymmärrystä autismikirjoon liittyvistä aivoverkostojen muutoksista vahvistaen ja täydentäen aiempia tutkimustuloksia. Sen perusteella samankaltaisiin lyhempikestoisiin aktivaatiovaiheisiin ryhmiteltyjen aivoverkostojen analyyseja kannattaa kehittää. Uusi tieto voi auttaa varhaisemman ja tarkemman kuvantamisdiagnostiikan kehittämisessä, tarvittaessa oikeisiin aivoverkostoihin kohdennetuissa interventioissa ja niiden vaikutusten arvioinnissa ja seurannassa