A Cybernetics Update for Competitive Deep Learning System

A number of recent reports in the peer-reviewed literature have discussed irreproducibility of results in biomedical research. Some of these articles suggest that the inability of independent research laboratories to replicate published results has a negative impact on the development of, and confidence in, the biomedical research enterprise. To get more resilient data and to achieve higher reproducible result, we present an adaptive and learning system reference architecture for smart learning system interface. To get deeper inspiration, we focus our attention on mammalian brain neurophysiology. In fact, from a neurophysiological point of view, neuroscientist LeDoux finds two preferential amygdala pathways in the brain of the laboratory mouse. The low road is a pathway which is able to transmit a signal from a stimulus to the thalamus, and then to the amygdala, which then activates a fast-response in the body. The high road is activated simultaneously. This is a slower road which also includes the cortical parts of the brain, thus creating a conscious impression of what the stimulus is (to develop a rational mechanism of defense for instance). To mimic this biological reality, our main idea is to use a new input node able to bind known information to the unknown one coherently. Then, unknown "environmental noise" or/and local "signal input" information can be aggregated to known "system internal control status" information, to provide a landscape of attractor points, which either fast or slow and deeper system response can computed from. In this way, ideal cybernetics system interaction levels can be matched exactly to practical system modeling interaction styles, with no paradigmatic operational ambiguity and minimal information loss. The present paper is a relevant contribute to classic cybernetics updating towards a new General Theory of Systems, a post-Bertalanffy Systemics

Regulatory post-translational modifications and protein-protein interactions involved in function and proteostasis of aromatic amino acid hydroxylases

The non-heme iron and (6R)-L-erythro-5,6,7,8-tetrahydrobiopterin (BH4) dependent aromatic amino acid hydroxylases (AAAHs) family of enzymes include phenylalanine hydroxylase (PAH), tyrosine hydroxylase (TH), and tryptophan hydroxylase 1 and 2 (TPH1 and TPH2). PAH catalyses the rate-limiting step in the catabolism of phenylalanine (L-Phe) that mainly takes place in the liver. TH catalyses the first and rate-limiting step in the biosynthesis of catecholamine neurotransmitters and hormones dopamine, norepinephrine and epinephrine in the brain and periphery. TPHs catalyse the first and rate-limiting step in the biosynthesis of serotonin in the peripheral (TPH1) and the central (TPH2) nervous systems. The AAAHs are of physiological and clinical importance. Dysfunctional PAH results in phenylketonuria (PKU), characterised by elevated levels of L-Phe in the blood, which can lead to brain damage. Catecholamine deficiency, due to dysfunctional TH, leads to motor dysfunction and neuropsychiatric disorders, such as TH deficiency (THD) and Parkinson’s disease. Reduced level of serotonin has been linked to anxiety disorder, depression, posttraumatic stress disorder and attention deficit hyperactivity disorder. Hence, the reactions catalysed by the AAAHs are important and tightly regulated. The aim of this thesis was to study the regulation of the AAAHs PAH and TH both in physiological and pathological states. We focused on regulatory mechanisms by selected post-translational modifications and protein-protein interactions and phosphorylation, investigating their role in the function, localisation and proteostasis of these enzymes using cellular and animal models. We investigated the role of DNAJC12, a type III member of the HSP40/DNAJ family, in the folding and degradation of wild-type (Wt) and mutant PAH. We observed a positive correlation between DNAJC12 and Wt and mutant PAH protein levels in the soluble cellular fractions. Detailed characterisations in liver lysates of the hyperphenylalaninemic Enu1 mouse (p.V106A-PAH mutation) revealed increased ubiquitination, instability, and aggregation of mutant PAH compared with Wt PAH. Furthermore, we showed that in the liver lysates, DNAJC12 interacts with both Wt and mono-ubiquitinated PAH; also, PAH mutation did not alter mRNA expression of DNAJC12. Our results support the role of DNAJC12 not only in proper folding but also in the processing of misfolded ubiquitinated PAH. We characterised a new custom-made Pah-R261Q knock-in mouse carrying mutation c.782G>A in the Pah gene. The homozygous Pah-R261Q mice exhibited reduced PAH activity and BH4 responsive hyperphenylalaninemia. Moreover, the mutant mice presented a reduced BH4 content in the liver, altered lipid metabolism, and increased oxidative stress, including increased mRNA expression of DNAJC12. Furthermore, the Pah-R261Q mice displayed large amyloid-like ubiquitinated PAH aggregates. The colocalisation of mutant PAH with selective autophagy markers indicated the involvement of the autophagic pathway in the clearance of mutant aggregates. These findings indicate a paradigm shift from a loss-of-function disorder to a toxic gain-of-function in PKU pathology. We next investigated the functional role of Ser31 phosphorylation in the regulation of TH in the cellular models. We observed that the perinuclear distribution of THpSer31 was concomitant with Golgi complex and synaptic vesicle marker in rat and human dopaminergic cells. The co-distribution of THpSer31 with vesicular monoamine transporter 2 (VMAT2) and α-synuclein (α-syn) in cells and their detection as co-immunoprecipitant in mouse brain lysate indicated an association of TH with vesicles. Furthermore, disruption of the microtubules caused accumulation of TH in the cell soma. Our study revealed that Ser31 phosphorylation regulates the subcellular localisation of TH by facilitating protein-protein interaction with VMAT2 and α-syn and enabling its transport toward axon terminals along microtubules. Finally, using SH-SY5Y cells, we sought to investigate the relationship between phosphorylation at different phosphosites and the nuclear distribution of TH, which was earlier proposed to be associated with Ser19 phosphorylation. We indeed observed that THpSer19 was predominantly nuclear, yet the phospho-null mutant of Ser19 (V5-TH-S19A) surprisingly accumulated significantly higher in the nuclear fraction when compared to Wt. Moreover, other phosphosites (Ser31 and Ser40) did not seem to influence the nuclear distribution of TH. When the phospho-null mutant of Thr8 (V5-TH-T8A) was expressed in SH-SY5Y cells, recombinant TH in the nuclear fraction was significantly reduced compared to Wt and the phospho-mimicking mutant V5-THT8E, indicating the potential role of Thr8 phosphorylation in the nuclear distribution of TH. In addition, inhibition of importin-β also reduced the amount of recombinant TH in the nucleus suggesting the involvement of the importin-β/RanGTP system in the nuclear localisation of TH in SH-SY5Y cells. To conclude, this study has brought new insights on the short-term regulation of AAAHs (PAH and TH) in physiological and pathological conditions by interacting with partners and by post-translational modifications, such as ubiquitination and phosphorylation (for TH), which ultimately affect their abundance, function and availability in different compartments of cells. Thus, this study has shed light on some of the molecular mechanisms involved in the proteostasis of AAAHs. Together, these findings open new research avenues to better understand disorders associated with the AAAHs.Doktorgradsavhandlin