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Additional file 1: Supplemental figures S1-S9. Figure S1. Nlgn3−/y rats display reduced classic freezing behaviour in a contextual fear conditioning paradigm. Figure S2. Freezing analysed as “paw immobility response” (all four paws unmoving but allowing for movement of head and neck). Figure S3. WT and Nlgn3−/y rats show similar activity in an open field, rotational platform & marble interaction tasks. Figure S4. Effect of repeated footshocks & thermal stimulus on WT and Nlgn3−/y rats. Figure S5. Intrinsic properties of PAG cells recorded from WT and Nlgn3−/y rats. Figure S6. Hyperexcitability of dorsal, but not ventral PAG neurons in 8-10 week old Nlgn3−/y rats. Figure S7. PAG LFPs during fear recall are significantly shorter duration in Nlgn3−/y rats. Figure S8. Defensive reactions were not elicited by electrical stimulation of primary somatosensory cortex in WT or Nlgn3−/y rats. Figure S9. Western blots showing lack expression of NLGN3 in Nlgn3−/y rats both in sensory cortex and periaqueductal grey.

Additional file 2: Supplemental table 1. Summary of statistics for main figures 2–7. Supplemental table 2. Summary of statistics for supplemental figures 1–7.

Summary Differences in the growth and maturation of diverse forebrain tissues depend on region-specific transcriptional regulation. Individual transcription factors act simultaneously in multiple regions that develop very differently, raising questions about the extent to which their actions vary regionally. We found that the transcription factor Pax6 affects the transcriptomes and the balance between proliferation and differentiation in opposite directions in the diencephalon versus cerebral cortex. We tested several possible mechanisms to explain Pax6's tissue-specific actions and found that the presence of the transcription factor Foxg1 in the cortex but not in the diencephalon was most influential. We found that Foxg1 is responsible for many of the differences in cell cycle gene expression between the diencephalon and cortex and, in cortex lacking Foxg1, Pax6's action on the balance of proliferation versus differentiation becomes diencephalon like. Our findings reveal a mechanism for generating regional forebrain diversity in which one transcription factor completely reverses the actions of another., Graphical Abstract, Highlights • Pax6 loss affects transcriptome profiles oppositely in cortex versus diencephalon • Pax6 promotes neuron differentiation in cortex, whereas proliferation in the diencephalon • Foxg1-null cortex develops a diencephalon-like profile of cell cycle gene expression • Foxg1 presence in cortex but not in diencephalon explains Pax6 tissue-specific actions, Neuroscience; Molecular Neuroscience; Developmental Neuroscience

Rani, predimplantacijski, period razvoja sisavaca obuhvaća razdoblje od oplodnje jajne stanice do implantacije blastociste u stijenku maternice. U tom su periodu aktivni razni oblici genske regulacije i ona se, osim na transkripcijskoj, odvija na više razina. Regulacija genske ekspresije kroz razvojne stadije je vrlo dinamična i poznato je nekoliko događaja genskih aktivacija i inaktivacija. Istraživanja regulacije genske ekspresije tijekom razvoja provode se pomoću analize ekspresije u vremenskom slijedu. Metoda sekvenciranja stanične mRNA (RNA-seq) omogućuje nepristranu analizu transkriptoma i kvantifikaciju ekspresije. Analizirao sam rezultate RNA-seq eksperimenata koristeći stanice miša u uzastopnim stadijima razvoja od primarne oocite do blastule. Nakon kvantifikacije ekspresije, identificirao sam diferencijalno eksprimirane gene koje sam metodama nenadgledanog strojnog učenja grupirao u ekspresijske profile. Nad profilima sam proveo funkcionalnu anotaciju i analizu obogaćenja motiva prepoznatih od transkripcijskih faktora. Rezultati pokazuju da se na ovaj način mogu grupirati geni s promjenama u ekspresiji u određenim stadijima te su profilima pridodani funkcionalni elementi koji mogu biti povezani uz regulaciju ekspresije. Također sam identificirao transkripcijske faktore koji utječu na ekspresiju pojedinih profila. Mammalian preimplantation development is a period starting with the fertilization of the oocyte and ending with the implantation of blastocyst into the wall of the uterus. This is a period where dynamic changes in gene expression are regulated through various mechanisms, which act on both transcriptional and non-transcriptional levels. High-throughput research of genetic regulation during development is done in form of time-course expression analysis. RNA-seq is a method of sequencing the total cellular mRNA and provides a capability of unbiased transcriptome analysis and expression quantification. Mouse cells in early developmental stages were analysed using RNA-seq in order to quantify the expression through the time-course. I identified differentially expressed genes and clustered them into expression profiles using unsupervised machine learning methods. I searched the profiles for enrichment of functional elements and sequence motifs recognized by DNA binding transcription factors. Results show that genes can be clustered by their expression patterns into distinct groups, thus enabling the observation of significant changes in expression. Functional elements related to gene expression were assigned to profiles. Finally, I identified the transcription factors that may influence the regulation of expression.

Cilj proteomskih istraživanja je identifikacija svih proteinskih molekula u stanicama i tkivima pojedinih organizama, a s vremenom su se istraživanja proširila i na određivanje funkcije tih proteina. U početku se smatralo da su preko centralne dogme molekularne biologije genom i proteom u direktnoj vezi, no otkrićem PTM se pokazalo da takav pristup u istraživanjima i ne mora biti sasvim točan. PTM na različite načine utječu na funkciju proteina, bilo da se radi o regulaciji enzimatske aktivnosti, lokalizaciji unutar stanice ili staničnih membrana, usmjeravanja u različite biokemijske ili sekretorne puteve ili označavanjem za degradaciju. Bolje razumijevanje PTM omogućio je razvoj tehnologije, posebice na području MS metoda. Daljnjim razvojem tih metoda i primjenom bioinformatičke analize moći ćemo saznati više o PTM proteina, komponentama modifikacija i mjestima na kojima se one događaju. Konačan cilj bio bi dostignut kada bismo pomoću tih podataka i bez eksperimentalnih dokaza mogli identificirati proteine koji će proći kroz PTM, predvidjeti na kojim mjestima će se one dogoditi i u konačnici odrediti njihovu funkciju. The goal of proteomic research is the identification of all protein species in all cells and tissues of certain organisms and lately these research projects include identification of protein functions. In early stages of proteome research it was considered that genome and proteome are in a direct relation. However, the discovery of PTM of proteins has shown us that the central dogma of molecular biology may not be so correct after all. PTM can have different effects on their target proteins and such may include changes in regulation of their enzymatic activity, their localization in cell compartments or membranes, inclusion in metabolic or biochemical pathways, or they can serve as markers for targeting proteins bound to degradation. Technological breakthroughs have allowed us to gain better understanding in PTM, especially by development of MS methods. Further development of research options with application of bioinformatics analysis would allow us to gain better knowledge of PTM, their components and localization. The final goal would be achieved when it would be simple to determine which proteins would undergo PTM, foresee the site of the modification and finally, to determine their function.

Sa razvojem tehnologije smanjila se potreba za fizičkim radom i tjelesnom aktivnošću općenito, dok je istovremeno hrana postala dostupnija, što je rezultiralo povećanim brojem pretilih osoba. Cilj ovog istraživanja bio je utvrditi temeljne prehrambene navike zagrebačkih srednjoškolaca i analizirati u kojoj mjeri takova prehrana zadovoljava njihove potrebe. U ovom periodu razvoja navike stečene u roditeljskom domu dopunjuju se i mijenjaju pod utjecajem društva i snažne propagandne aktivnosti javnih medija, da bi se kao stečeni obrazac ponašanja ponijele u zrelu dob. Navike stečene u ovoj dobi teško je mijenjati, što pojačava značaj edukacije i praćenja ove populacije kako bi se pravovremeno spriječilo negativne posljedice.