Maciej Pajak

Maciej Pajak


Research Interests

I'm interested in applying machine learning methods and other computational tools to real world data. I use my computational background and software engineering skills to answer research questions from various disciplines including neuroscience, cognitive science and biology.

The overarching theme of my research programme can be summarised as quantifying contribution of finely-tuned genetic regulation to emergence of complex function at the synapse using cutting edge computational tools. In the future it will also include tackling the question of the evolution of molecular etiology of neuropsychiatric disorders

Publications:
2014
  NMDA receptor-dependent regulation of miRNA expression and association with Argonaute during LTP in vivo
Pai, B, Siripornmongcolchai, T, Berentsen, B, Pakzad, A, Vieuille, C, Pallesen, S, Pajak, M, Simpson, TI, Armstrong, JD, Wibrand, K & Bramham, CR 2014, 'NMDA receptor-dependent regulation of miRNA expression and association with Argonaute during LTP in vivo' Frontiers in Cellular Neuroscience, vol 7, pp. 285. DOI: 10.3389/fncel.2013.00285
MicroRNAs (miRNAs) are major regulators of protein synthesis in the brain. A major goal is to identify changes in miRNA expression underlying protein synthesis-dependent forms of synaptic plasticity such as long-term potentiation (LTP). Previous analyses focused on changes in miRNA levels in total lysate samples. Here, we asked whether changes in total miRNA accurately reflect changes in the amount of miRNA bound to Argonaute protein within the miRNA-induced silencing complex (miRISC). Ago2 immunoprecipitation was used to isolate RISC-associated miRNAs following high-frequency stimulation (HFS)-induced LTP in the dentate gyrus of anesthetized rats. Using locked-nucleic acid-based PCR cards for high-throughput screening and independent validation by quantitative TaqMan RT-PCR, we identified differential regulation of Ago2-associated and total miRNA expression. The ratio of Ago2/total miRNA expression was regulated bidirectionally in a miRNA-specific manner and was largely dependent on N-methyl-D-aspartate receptor (NMDA) activation during LTP induction. The present results identify miRNA association with Ago2 as a potential control point in activity-dependent synaptic plasticity in the adult brain. Finally, novel computational analysis for targets of the Ago2-associated miRNAs identifies 21 pathways that are enriched and differentially targeted by the miRNAs including axon guidance, mTOR, MAPK, Ras, and LTP.

General Information
Organisations: Institute for Adaptive and Neural Computation .
Authors: Pai, Balagopal, Siripornmongcolchai, Taweeporn, Berentsen, Birgitte, Pakzad, Ashraf, Vieuille, Christel, Pallesen, Ståle, Pajak, Maciej, Simpson, T Ian, Armstrong, J Douglas, Wibrand, Karin & Bramham, Clive R.
Number of pages: 1
Pages: 285
Publication Date: 13 Jan 2014
Publication Information
Category: Article
Journal: Frontiers in Cellular Neuroscience
Volume: 7
ISSN: 1662-5102
Original Language: English
DOIs: 10.3389/fncel.2013.00285
2012
  Do we look at objects in the same way as we read words?
Pajak, M & Nuthmann, A 2012, 'Do we look at objects in the same way as we read words?' Paper presented at 2012 BPS Scottish Branch Undergraduate Student Conference, Glasgow, United Kingdom, 17/03/12 - 17/03/12, .
With regard to eye-movement control in reading, three phenomena describe the eyes’ fixation position within words: (1) the optimal viewing position (OVP), (2) the preferred viewing location (PVL), and (3) the fixation-duration Inverted-Optimal Viewing Position (IOVP) effect (e.g., Vitu et al., 2011). First, word centre is considered to be the OVP, defined as the position within a word where refixation probability is minimal. Second, fixation positions on words are normally distributed with a mean that is typically somewhat left of word centre; the mean of the distribution is the PVL. Third, the IOVP effect refers to the finding that fixations located at word centre are longer than those falling near the edges of a word. Collectively, these findings suggest that saccade targeting in reading is word based. The present study set out to investigate related phenomena for objects in naturalistic scenes. Analyses were based on a corpus of eye-tracking data collected from 72 participants looking at 135 scenes in scene memorisation and/or aesthetic judgment tasks. Based on a subset of these data, a recent study reported a PVL close to the centre of objects (Nuthmann & Henderson, 2010). The present study extended this work in several important ways. The PVL for objects in scenes was found to be modulated by both object size and centre-based launch site distance; long launch-site distances and larger object sizes both shifted within-object fixation position distributions towards the edge of an object (the edge that is closest to the launch site). In addition, an IOVP effect for objects in scenes was found: Fixations located at object centre were longer than those falling near the edges of an object. Somewhat surprisingly, there was no refixation OVP effect for objects. Taken together, these findings lend further support to the notion of object-based saccade targeting in scenes.
General Information
Organisations: Neuroinformatics DTC.
Authors: Pajak, Maciej & Nuthmann, Antje.
Publication Date: 17 Mar 2012
Publication Information
Category: Paper
Original Language: English

Projects:
Translation regulation in synaptic plasticity. Evolutionary conservation and emergence of complex function (PhD)