“Follow the groove, man.” An exploration of wayfaring in the landscape of Neolithic Langdale

During the Neolithic period, the Langdale Pikes were the stage for the most prolific axe production in the British Isles, with its artefacts being distributed to all corners of the island through vast exchange networks. Their prevalence and popularity have led many archaeologists to ponder the significance of the mountainous location to Neolithic people. Like many axe production sites, Langdale has long been perceived as a liminal and even dangerous place, with the popularity of the axes attributed to their value as created by risk. In this study, we shall demonstrate that not only is this a misrepresentation of the role of mountains, but that it must be inherently false. This study will demonstrate that these were dynamic landscapes by using a combined theoretical approach to movement through least cost analysis and phenomenological fieldwork. By using both an objective and subjective approach to this landscape, the study created a path network, as defined by the various agents entangled within the landscape which were consolidated and built upon by a series of experiential walks. A methodological feedback loop was developed which overcame the limits of either approach whilst presenting the results in a credible, creative and hopefully collaborative, way through interactive story maps. Beyond the methodological developments, the results of the path network and subsequent fieldwork demonstrate a seasonal movement into this landscape wherein a variety of activities could have taken place and thus attested to the fact that this landscape could not have been liminal during the Neolithic. Successful navigation and discovery of the working sites required the traveller to be equipped with an expansive and detailed knowledge of the landscape accessed through such mnemonic movements

Imaging the developing human external and internal urogenital organs with light sheet fluorescence microscopy.

Technological advances in three-dimensional (3D) reconstruction techniques have previously enabled paradigm shifts in our understanding of human embryonic and fetal development. Light sheet fluorescence microscopy (LSFM) is a recently-developed technique that uses thin planes of light to optically section whole-mount cleared and immunolabeled biologic specimens. The advent of commercially-available light sheet microscopes has facilitated a new generation of research into protein localization and tissue dynamics at extremely high resolution. Our group has applied LSFM to study developing human fetal external genitalia, internal genitalia and kidneys. This review describes LSFM and presents our group's technique for preparing, clearing, immunostaining and imaging human fetal urogenital specimens. We then present light sheet images and videos of each element of the developing human urogenital system. To the extent of our knowledge, the work conducted by our laboratory represents the first description of a method for performing LSFM on the full human urogenital system during the embryonic and fetal periods

Oolemmal proteomics – identification of highly abundant heat shock proteins and molecular chaperones in the mature mouse egg and their localization on the plasma membrane

BACKGROUND: The mature mouse egg contains the full complement of maternal proteins required for fertilization, the transition to zygotic transcription, and the beginning stages of embryogenesis. Many of these proteins remain to be characterized, therefore in this study we have identified highly abundant egg proteins using a proteomic approach and found that several of these proteins also appear to localize to the egg surface. Characterization of such molecules will provide important insight into the cellular events of fertilization and early development. METHODS: In order to identify some of the more abundant egg proteins, whole egg extracts were resolved on coomassie-stained two-dimensional (2D) PAGE gels. Several highly abundant protein spots were cored and microsequenced by tandem mass spectrometry (TMS), and determined to be molecular chaperone proteins. Concurrent experiments were performed to identify oolemmal proteins using 2D avidin blotting. Proteins spots that appeared to be surface labeled by biotinylation were correlated with the initial coomassie-stained reference gel. Surprisingly, some of the surface labelled proteins corresponded to those abundant chaperone proteins previously identified. To confirm whether these molecules are accumulating at the oolemmal surface in eggs, we performed immunofluoresence on live, zona-free eggs using antibodies to HSP70, HSP90, GRP94, GRP78, calreticulin and calnexin. RESULTS: The putative surface-labeled proteins identified by biotinylation included the molecular chaperones HSP70 (MW 70 KDa, pI 5.5), HSP90a (MW 85 KDa, pI 4.9), GRP94 (MW 92 KDa, pI 4.7), GRP78 (MW 72 KDa, pI 5.0), Oxygen regulated protein 150 (ORP150; MW 111 KDa, pI 5.1), Calreticulin (MW 48 KDa, pI 4.3), Calnexin (MW 65 KDa, pI 4.5), and Protein disulfide isomerase (PDI; MW 57 KDa, pI 4.8). Immunofluoresence results showed that antibodies to HSP90, GRP94, GRP78 and calreticulin were reactive with oolemmal proteins. We were unable to confirm surface localization of HSP70 or calnexin by this method. CONCLUSIONS: We report here the identification of nine highly abundant molecular chaperones in the mouse egg proteome. In addition, we present preliminary data suggesting that these molecules localize to the oolemma of the mature mouse egg

Organic cation transporter 1 (OCT1) modulates multiple cardiometabolic traits through effects on hepatic thiamine content.

A constellation of metabolic disorders, including obesity, dysregulated lipids, and elevations in blood glucose levels, has been associated with cardiovascular disease and diabetes. Analysis of data from recently published genome-wide association studies (GWAS) demonstrated that reduced-function polymorphisms in the organic cation transporter, OCT1 (SLC22A1), are significantly associated with higher total cholesterol, low-density lipoprotein (LDL) cholesterol, and triglyceride (TG) levels and an increased risk for type 2 diabetes mellitus, yet the mechanism linking OCT1 to these metabolic traits remains puzzling. Here, we show that OCT1, widely characterized as a drug transporter, plays a key role in modulating hepatic glucose and lipid metabolism, potentially by mediating thiamine (vitamin B1) uptake and hence its levels in the liver. Deletion of Oct1 in mice resulted in reduced activity of thiamine-dependent enzymes, including pyruvate dehydrogenase (PDH), which disrupted the hepatic glucose-fatty acid cycle and shifted the source of energy production from glucose to fatty acids, leading to a reduction in glucose utilization, increased gluconeogenesis, and altered lipid metabolism. In turn, these effects resulted in increased total body adiposity and systemic levels of glucose and lipids. Importantly, wild-type mice on thiamine deficient diets (TDs) exhibited impaired glucose metabolism that phenocopied Oct1 deficient mice. Collectively, our study reveals a critical role of hepatic thiamine deficiency through OCT1 deficiency in promoting the metabolic inflexibility that leads to the pathogenesis of cardiometabolic disease

A single H/ACA small nucleolar RNA mediates tumor suppression downstream of oncogenic RAS.

Small nucleolar RNAs (snoRNAs) are a diverse group of non-coding RNAs that direct chemical modifications at specific residues on other RNA molecules, primarily on ribosomal RNA (rRNA). SnoRNAs are altered in several cancers; however, their role in cell homeostasis as well as in cellular transformation remains poorly explored. Here, we show that specific subsets of snoRNAs are differentially regulated during the earliest cellular response to oncogenic RASG12V expression. We describe a novel function for one H/ACA snoRNA, SNORA24, which guides two pseudouridine modifications within the small ribosomal subunit, in RAS-induced senescence in vivo. We find that in mouse models, loss of Snora24 cooperates with RASG12V to promote the development of liver cancer that closely resembles human steatohepatitic hepatocellular carcinoma (HCC). From a clinical perspective, we further show that human HCCs with low SNORA24 expression display increased lipid content and are associated with poor patient survival. We next asked whether ribosomes lacking SNORA24-guided pseudouridine modifications on 18S rRNA have alterations in their biophysical properties. Single-molecule Fluorescence Resonance Energy Transfer (FRET) analyses revealed that these ribosomes exhibit perturbations in aminoacyl-transfer RNA (aa-tRNA) selection and altered pre-translocation ribosome complex dynamics. Furthermore, we find that HCC cells lacking SNORA24-guided pseudouridine modifications have increased translational miscoding and stop codon readthrough frequencies. These findings highlight a role for specific snoRNAs in safeguarding against oncogenic insult and demonstrate a functional link between H/ACA snoRNAs regulated by RAS and the biophysical properties of ribosomes in cancer

Microstructural differences in the thalamus and thalamic radiations in the congenitally deaf

There is evidence of both crossmodal and intermodal plasticity in the deaf brain. Here, we investigated whether sub-cortical plasticity, specifically of the thalamus, contributed to this reorganisation. We contrasted diffusion weighted magnetic resonance imaging data from 13 congenitally deaf and 13 hearing participants, all of whom had learnt British Sign Language after 10 years of age. Connectivity based segmentation of the thalamus revealed changes to mean and radial diffusivity in occipital and frontal regions, which may be linked to enhanced peripheral visual acuity, and differences in how visual attention is deployed in the deaf group. Using probabilistic tractography, tracts were traced between the thalamus and its cortical targets, and microstructural measurements were extracted from these tracts. Group differences were found in microstructural measurements of occipital, frontal, somatosensory, motor and parietal thalamo-cortical tracts. Our findings suggest there is sub-cortical plasticity in the deaf brain, and that white matter alterations can be found throughout the deaf brain, rather than being restricted to, or focussed in auditory cortex

Genome-wide variation and transcriptional changes in diverse developmental processes underlie the rapid evolution of seasonal adaptation

Many organisms enter a dormant state in their life cycle to deal with predictable changes in environments over the course of a year. The timing of dormancy is therefore a key seasonal adaptation, and it evolves rapidly with changing environments. We tested the hypothesis that differences in the timing of seasonal activity are driven by differences in the rate of development during diapause in Rhagoletis pomonella, a fly specialized to feed on fruits of seasonally limited host plants. Transcriptomes from the central nervous system across a time series during diapause show consistent and progressive changes in transcripts participating in diverse developmental processes, despite a lack of gross morphological change. Moreover, population genomic analyses suggested that many genes of small effect enriched in developmental functional categories underlie variation in dormancy timing and overlap with gene sets associated with development rate in Drosophila melanogaster. Our transcriptional data also suggested that a recent evolutionary shift from a seasonally late to a seasonally early host plant drove more rapid development during diapause in the early fly population. Moreover, genetic variants that diverged during the evolutionary shift were also enriched in putative cis regulatory regions of genes differentially expressed during diapause development. Overall, our data suggest polygenic variation in the rate of developmental progression during diapause contributes to the evolution of seasonality in R. pomonella. We further discuss patterns that suggest hourglass-like developmental divergence early and late in diapause development and an important role for hub genes in the evolution of transcriptional divergence

Differential activity in Heschl's gyrus between deaf and hearing individuals is due to auditory deprivation rather than language modality

Sensory cortices undergo crossmodal reorganisation as a consequence of sensory deprivation. Congenital deafness in humans represents a particular case with respect to other types of sensory deprivation, because cortical reorganisation is not only a consequence of auditory deprivation, but also of language-driven mechanisms. Visual crossmodal plasticity has been found in secondary auditory cortices of deaf individuals, but it is still unclear if reorganisation also takes place in primary auditory areas, and how this relates to language modality and auditory deprivation.  Here, we dissociated the effects of language modality and auditory deprivation on crossmodal plasticity in Heschl's gyrus as a whole, and in cytoarchitectonic region Te1.0 (likely to contain the core auditory cortex). Using fMRI, we measured the BOLD response to viewing sign language in congenitally or early deaf individuals with and without sign language knowledge, and in hearing controls.  Results show that differences between hearing and deaf individuals are due to a reduction in activation caused by visual stimulation in the hearing group, which is more significant in Te1.0 than in Heschl's gyrus as a whole. Furthermore, differences between deaf and hearing groups are due to auditory deprivation, and there is no evidence that the modality of language used by deaf individuals contributes to crossmodal plasticity in Heschl's gyrus