The Zebrafish equivalent of Alzheimer's disease-associated PRESENILIN Isoform PS2V regulates inflammatory and other responses to hypoxic stress

Dominant mutations in the PRESENILIN genes PSEN1 and PSEN2 cause familial Alzheimer's disease (fAD) that usually shows onset before 65 years of age. In contrast, genetic variation at the PSEN1 and PSEN2 loci does not appear to contribute to risk for the sporadic, late onset form of the disease (sAD), leading to doubts that these genes play a role in the majority of AD cases. However, a truncated isoform of PSEN2, PS2V, is upregulated in sAD brains and is induced by hypoxia and high cholesterol intake. PS2V can increase γ-secretase activity and suppress the unfolded protein response (UPR), but detailed analysis of its function has been hindered by lack of a suitable, genetically manipulable animal model since mice and rats lack this PRESENILIN isoform. We recently showed that zebrafish possess an isoform, PS1IV, that is cognate to human PS2V. Using an antisense morpholino oligonucleotide, we can block specifically the induction of PS1IV that normally occurs under hypoxia. Here, we exploit this ability to identify gene regulatory networks that are modulated by PS1IV. When PS1IV is absent under hypoxia-like conditions, we observe changes in expression of genes controlling inflammation (particularly sAD-associated IL1B and CCR5), vascular development, the UPR, protein synthesis, calcium homeostasis, catecholamine biosynthesis, TOR signaling, and cell proliferation. Our results imply an important role for PS2V in sAD as a component of a pathological mechanism that includes hypoxia/oxidative stress and support investigation of the role of PS2V in other diseases, including schizophrenia, when these are implicated in the pathology.Esmaeil Ebrahimie, Seyyed Hani Moussavi Nik, Morgan Newman, Mark Van Der Hoek and Michael Lardell

Lithium Phthalocyanine: A Probe for Electron Paramagnetic Resonance Oximetry in Viable Biological Systems.

Lithium phthalocyanine (LiPc) is a prototype of another generation of synthetic, metallic-organic, paramagnetic crystallites that appear very useful for in vitro and in vivo electron paramagnetic resonance oximetry. The peak-to-peak line width of the electron paramagnetic resonance spectrum of LiPc is a linear function of the partial pressure of oxygen (pO2); this linear relation is independent of the medium surrounding the LiPc. It has an extremely exchange-narrowed spectrum (peak-to-peak line width = 14 mG in the absence of O2). Physicochemically LiPc is very stable; its response to pO2 does not change with conditions and environments (e.g., pH, temperature, redox conditions) likely to occur in viable biological systems. These characteristics provide the sensitivity, accuracy, and range to measure physiologically and pathologically pertinent O2 tensions (0.1-50 mmHg; 1 mmHg = 133 Pa). The application of LiPc in biological systems is demonstrated in measurements of pO2 in vivo in the heart, brain, and kidney of rats

Improving Productive and Reproductive Performance of Holstein Dairy Cows through Dry Period Management

To determine the effects of dry period (DP) length on milk yield, milk composition, some blood metabolites, complete blood count (CBC), body weight and score and follicular status, twenty five primiparous and multiparous Holstein cows were assigned to a completely randomized design with DP-60 (n = 13) and DP-20 (n = 12) dry period lengths. Cows in the DP-60 produced more milk, protein, SNF, serum non-esterified fatty acids (NEFA) and beta hydroxyl butyrate acid (BHBA) compared with cows in DP-20 (p≤0.05). Serum glucose, blood urea nitrogen (BUN), urea, and glutamic oxaloacetic transaminase (GOT) were all similar among the treatments. Body Condition Score (BCS), body weight (BW), complete blood count (CBC) and health problems were similar between the treatments. Diameter of the first dominant follicle and diameter of the dominant follicle on d 14 were different among the treatments. Thus, results of this study showed that reducing the dry period length to DP-20 had a negative effect on milk production, milk composition and reproductive performance in Holstein dairy cows

Identification and expression analysis of the zebrafish orthologues of the mammalian MAP1LC3 gene family

Autophagy is the principle pathway within cells involved in clearing damaged proteins and organelles. Therefore autophagy is necessary to maintain the turnover balance of peptides and homoeostasis. Autophagy occurs at basal levels under normal conditions but can be upregulated by chemical inducers or stress conditions. The zebrafish (Danio rerio) serves as a versatile tool to understand the functions of genes implicated in autophagy. We report the identification of the zebrafish orthologues of mammalian genes MAP1LC3A (map1lc3a) and MAP1LC3B (map1lc3b) by phylogenetic and conserved synteny analysis and we examine their expression during embryonic development. The zebrafish map1lc3a and map1lc3b genes both show maternally contributed transcripts in early embryogenesis. However, levels of map1lc3a transcript steadily increase until at least 120h post-fertilisation while the levels of map1lc3b show a more variable pattern across developmental time. We have also validated the LC3I ratio/LC3I immunoblot autophagy assay in the presence of chloroquine (a lysosomal proteolysis inhibitor). We found that the LC3II/LC3I ratio is significantly increased in the presence of sodium azide with chloroquine supporting that hypoxia induces autophagy in zebrafish. This was supported by our qPCR assay that showed increased map1lc3a transcript levels in the presence of sodium azide. In contrast, levels of map1lc3b transcripts were reduced in the presence of rapamycin but the decrease in the presence of sodium azide did not reach statistical significance. Our study supports the use of zebrafish for analysing the interplay between hypoxia, development and autophagy.Swamynathan Ganesan, Seyyed Hani Moussavi Nik, Morgan Newman, Michael Lardell

Antarctic Supraglacial Lake Identification Using Landsat-8 Image Classification

Surface meltwater generated on ice shelves fringing the Antarctic Ice Sheet can drive ice-shelf collapse, leading to ice sheet mass loss and contributing to global sea level rise. A quantitative assessment of supraglacial lake evolution is required to understand the influence of Antarctic surface meltwater on ice-sheet and ice-shelf stability. Cloud computing platforms have made the required remote sensing analysis computationally trivial, yet a careful evaluation of image processing techniques for pan-Antarctic lake mapping has yet to be performed. This work paves the way for automating lake identification at a continental scale throughout the satellite observational record via a thorough methodological analysis. We deploy a suite of different trained supervised classifiers to map and quantify supraglacial lake areas from multispectral Landsat-8 scenes, using training data generated via manual interpretation of the results from k-means clustering. Best results are obtained using training datasets that comprise spectrally diverse unsupervised clusters from multiple regions and that include rock and cloud shadow classes. We successfully apply our trained supervised classifiers across two ice shelves with different supraglacial lake characteristics above a threshold sun elevation of 20°, achieving classification accuracies of over 90% when compared to manually generated validation datasets. The application of our trained classifiers produces a seasonal pattern of lake evolution. Cloud shadowed areas hinder large-scale application of our classifiers, as in previous work. Our results show that caution is required before deploying ‘off the shelf’ algorithms for lake mapping in Antarctica, and suggest that careful scrutiny of training data and desired output classes is essential for accurate results. Our supervised classification technique provides an alternative and independent method of lake identification to inform the development of a continent-wide supraglacial lake mapping product

Gene Ontology-based analysis of zebrafish’ omics data using the web tool Comparative Gene Ontology

Gene Ontology (GO) analysis is a powerful tool in systems biology, which uses a defined nomenclature to annotate genes/proteins within three categories: ‘‘Molecular Function,’’ ‘‘Biological Process,’’ and ‘‘Cellular Component.’’ GOanalysis can assist in revealing functionalmechanisms underlying observed patterns in transcriptomic, genomic, and proteomic data. The already extensive and increasing use of zebrafish for modeling genetic and other diseases highlights the need to develop a GO analytical tool for this organism. The web tool Comparative GO was originally developed for GO analysis of bacterial data in 2013 (www.comparativego.com). We have now upgraded and elaborated this web tool for analysis of zebrafish genetic data using GOs and annotations from the Gene Ontology Consortium.Esmaeil Ebrahimie, Mario Fruzangohar, Seyyed Hani Moussavi-Nik, and Morgan Newma