Age related and hypothyroidism related changes on the stoichiometry of neurofilament subunits in the developing rat brain

Neurofilament Biophysics: From Structure to Biomechanics

Neurofilaments (NFs) are multisubunit, neuron-specific intermediate filaments consisting of a 10-nm diameter filament "core" surrounded by a layer of long intrinsically disordered protein (IDP) "tails." NFs are thought to regulate axonal caliber during development and then stabilize the mature axon, with NF subunit misregulation, mutation, and aggregation featuring prominently in multiple neurological diseases. The field's understanding of NF structure, mechanics, and function has been deeply informed by a rich variety of biochemical, cell biological, and mouse genetic studies spanning more than four decades. These studies have contributed much to our collective understanding of NF function in axonal physiology and disease. In recent years, however, there has been a resurgence of interest in NF subunit proteins in two new contexts: as potential blood- and cerebrospinal fluid-based biomarkers of neuronal damage, and as model IDPs with intriguing properties. Here, we review established principles and more recent discoveries in NF structure and function. Where possible, we place these findings in the context of biophysics of NF assembly, interaction, and contributions to axonal mechanics.

Expression of Neurofilament Subunits at Neocortical Glutamatergic and GABAergic Synapses

Neurofilaments (NFs) are neuron-specific heteropolymers that have long been considered as structural proteins. However, it has recently been documented that they may play a functional role at synapses. Indeed, the four NF subunits—NFL, NFM, NFH and α-internexin—are integral components of synapses in the striatum and hippocampus, since their elimination disrupts synaptic plasticity and impairs social memory, an observation that might have important implications for some neuropsychiatric diseases. Here, we studied NFs localization in VGLUT1-, VGLUT2-, VGAT-, PSD-95- and gephyrin-positive (+) puncta, and in glutamatergic and GABAergic synapses in the cerebral cortex of adult rats. Synapses were identified by pre- and postsynaptic markers: glutamatergic synapses by VGLUT1+ or VGLUT2+ puncta contacting PSD-95+ puncta; and GABAergic synapses by VGAT+ puncta contacting gephyrin+ puncta. In VGLUT1 glutamatergic synapses NF showed a greater expression in the compartment labeled by postsynaptic markers (20%–30%) than in those labeled by presynaptic markers (10%–20%), whereas in GABAergic synapses a similar expression was detected in both compartments (20%–30%). Moreover, NF expression was higher in the GABAergic (20%–30%) than in the glutamatergic (10%–15%) compartments labeled by presynaptic markers. Finally, a higher colocalization of VGLUT1+, VGLUT2+ and VGAT+ puncta with NFs was seen when presynaptic puncta contacted elements labeled by postsynaptic markers. These findings show that the four NF subunits are expressed at some neocortical synapses, and contribute to glutamatergic and GABAergic synapse heterogeneity.

An automated framework for hypotheses generation using literature

Background

In bio-medicine, exploratory studies and hypothesis generation often begin with researching existing literature to identify a set of factors and their association with diseases, phenotypes, or biological processes. Many scientists are overwhelmed by the sheer volume of literature on a disease when they plan to generate a new hypothesis or study a biological phenomenon. The situation is even worse for junior investigators who often find it difficult to formulate new hypotheses or, more importantly, corroborate if their hypothesis is consistent with existing literature. It is a daunting task to be abreast with so much being published and also remember all combinations of direct and indirect associations. Fortunately there is a growing trend of using literature mining and knowledge discovery tools in biomedical research. However, there is still a large gap between the huge amount of effort and resources invested in disease research and the little effort in harvesting the published knowledge. The proposed hypothesis generation framework (HGF) finds “crisp semantic associations” among entities of interest - that is a step towards bridging such gaps.

Methodology

The proposed HGF shares similar end goals like the SWAN but are more holistic in nature and was designed and implemented using scalable and efficient computational models of disease-disease interaction. The integration of mapping ontologies with latent semantic analysis is critical in capturing domain specific direct and indirect “crisp” associations, and making assertions about entities (such as disease X is associated with a set of factors Z).

Results

Pilot studies were performed using two diseases. A comparative analysis of the computed “associations” and “assertions” with curated expert knowledge was performed to validate the results. It was observed that the HGF is able to capture “crisp” direct and indirect associations, and provide knowledge discovery on demand.

Conclusions

The proposed framework is fast, efficient, and robust in generating new hypotheses to identify factors associated with a disease. A full integrated Web service application is being developed for wide dissemination of the HGF. A large-scale study by the domain experts and associated researchers is underway to validate the associations and assertions computed by the HGF.

Immunolocalization of steroidogenic acute regulatory protein-related lipid transfer (START) domain-containing proteins in the developing cerebellum of normal and hypothyroid rats

Cholesterol transport proteins are a prerequisite for neurosteroidogenesis. Steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domain-containing proteins, such as StAR and START domain-containing 6 (StarD6), are known to be distributed in the brain. Since perinatal hypothyroidism affects cerebellar development, we examined postnatal changes in StAR and StarD6 immunolocalization in the developing cerebellum of control and hypothyroid rats. Pregnant Sprague-Dawley rats were given 0.05% 6-propyl-2-thiouracil (PTU) or water from gestation day 11 until postnatal day (P) 28, and were then killed together with age-matched control rats. As shown by calbindin D-28k immunostaining, the developing cerebellar cytoarchitecture and Purkinje cells were affected by PTU-induced hypothyroidism as compared to control rats. The immunolocalization of StAR and StarD6 generally followed the maturation pattern of Purkinje cells from the vermis to the cerebellar hemisphere. StAR immunostaining first appeared in the Purkinje cells of the vermis at P7 in both control and hypothyroid rats. In control rats, a few StarD6 immunoreactive cells were seen at birth and a nuclear localization of StarD6 in Purkinje cells was obvious at P14. PTU-induced hypothyroidism delayed the appearance of StarD6 immunopositive cells until P7. Moreover, the nuclear localization of StarD6 in PTU-treated rats was not obvious at P14. An adult-like distribution of StAR and StarD6 was achieved by P21 in control and hypothyroid rats. These results suggest that StarD6 may affect the development of Purkinje cells during the first and second postnatal weeks, a known period of thyroid hormone action.

ALS genetic modifiers that increase survival of SOD1 mice and are suitable for therapeutic development

Amyotrophic lateral sclerosis (ALS) is a frequently fatal motor neuron disease without any cure. To find molecular therapeutic targets, several studies crossed transgenic ALS murine models with animals transgenic for some ALS target genes. We aimed to revise the new discoveries and new works in this field. We selected the 10 most promising genes, according to their capability when down-regulated or up-regulated in ALS animal models, for increasing life span and mitigating disease progression: XBP-1, NogoA and NogoB, dynein, heavy and medium neurofilament, NOX1 and NOX2, MLC-mIGF-1, NSE-VEGF, and MMP-9. Interestingly, some crucial modifier genes have been described as being involved in common pathways, the most significant of which are inflammation and cytoskeletal activities. The endoplasmic reticulum also seems to play an important role in ALS pathogenesis, as it is involved in different selected gene pathways. In addition, these genes have evident links to each other, introducing the hypothesis of a single unknown, common pathway involving all of these identified genes and others to be discovered.