Cryopreservation of threatened native Australian species—what have we learned and where to from here?

Cryogenic storage techniques have been developed and adopted for more than 100 (mainly agricultural) plant species worldwide, and within Australia, at least 30 critically endangered plants have been stored long term using cryogenic approaches. Nevertheless, there are many species that are very difficult to store using current procedures, and organizations involved in plant germplasm conservation (such as botanic gardens, agricultural institutions, etc.) that utilise cryogenic storage techniques are in some respects at a crossroads in their endeavours to cheaply and effectively store a wide selection of species and genotypes for conservation and agricultural/horticultural purposes. For taxa that are not amenable to current cryogenic approaches, new ways of developing cryogenic storage techniques need to be investigated, including research into the ways in which cell membranes interact and change when cooled to cryogenic temperatures (−196°C in liquid nitrogen) in the presence of various cryoprotective agents. This review highlights the current state of cryogenic research both within Australia and internationally, provides a case study on threatened plant species and also describes several new research initiatives that aim to provide answers to why some native species are quite amenable to widely utilised cryogenic approaches whilst others are currently non-responsive. New approaches aim to integrate laboratory and membrane modelling paradigms to provide guidelines for the development of new cryopreservation protocols and to assess the robustness of theoretical models in predicting optimum cryogenic conditions

Characterisation of the structure and oligomerisation of islet amyloid polypeptides (IAPP): A review of molecular dynamics simulation studies

Human islet amyloid polypeptide (hIAPP) is a naturally occurring, intrinsically disordered protein whose abnormal aggregation into amyloid fibrils is a pathological feature in type 2 diabetes, and its cross-aggregation with amyloid beta has been linked to an increased risk of Alzheimer’s disease. The soluble, oligomeric forms of hIAPP are the most toxic to ß-cells in the pancreas. However, the structure of these oligomeric forms is difficult to characterise because of their intrinsic disorder and their tendency to rapidly aggregate into insoluble fibrils. Experimental studies of hIAPP have generally used non-physiological conditions to prevent aggregation, and they have been unable to describe its soluble monomeric and oligomeric structure at physiological conditions. Molecular dynamics (MD) simulations offer an alternative for the detailed characterisation of the monomeric structure of hIAPP and its aggregation in aqueous solution. This paper reviews the knowledge that has been gained by the use of MD simulations, and its relationship to experimental data for both hIAPP and rat IAPP. In particular, the influence of the choice of force field and water models, the choice of initial structure, and the configurational sampling method used, are discussed in detail. Characterisation of the solution structure of hIAPP and its mechanism of oligomerisation is important to understanding its cellular toxicity and its role in disease states, and may ultimately offer new opportunities for therapeutic interventions

FUS-DDIT3 Prevents the Development of Adipocytic Precursors in Liposarcoma by Repressing PPARγ and C/EBPα and Activating eIF4E

FUS-DDIT3 is a chimeric protein generated by the most common chromosomal translocation t(12;16)(q13;p11) linked to liposarcomas, which are characterized by the accumulation of early adipocytic precursors. Current studies indicate that FUS-DDIT3- liposarcoma develops from uncommitted progenitors. However, the precise mechanism whereby FUS-DDIT3 contributes to the differentiation arrest remains to be elucidated. METHODOLOGY/PRINCIPAL FINDINGS: Here we have characterized the adipocyte regulatory protein network in liposarcomas of FUS-DITT3 transgenic mice and showed that PPARgamma2 and C/EBPalpha expression was altered. Consistent with in vivo data, FUS-DDIT3 MEFs and human liposarcoma cell lines showed a similar downregulation of both PPARgamma2 and C/EBPalpha expression. Complementation studies with PPARgamma but not C/EBPalpha rescued the differentiation block in committed adipocytic precursors expressing FUS-DDIT3. Our results further show that FUS-DDIT3 interferes with the control of initiation of translation by upregulation of the eukaryotic translation initiation factors eIF2 and eIF4E both in FUS-DDIT3 mice and human liposarcomas cell lines, explaining the shift towards the truncated p30 isoform of C/EBPalpha in liposarcomas. Suppression of the FUS-DDIT3 transgene did rescue this adipocyte differentiation block. Moreover, eIF4E was also strongly upregulated in normal adipose tissue of FUS-DDIT3 transgenic mice, suggesting that overexpression of eIF4E may be a primary event in the initiation of liposarcomas. Reporter assays showed FUS-DDIT3 is involved in the upregulation of eIF4E in liposarcomas and that both domains of the fusion protein are required for affecting eIF4E expression. CONCLUSIONS/SIGNIFICANCE: Taken together, this study provides evidence of the molecular mechanisms involve in the disruption of normal adipocyte differentiation program in liposarcoma harbouring the chimeric gene FUS-DDIT3.Research in ISG group is supported partially by FEDER and by MEC (SAF2006-03726), Junta de Castilla y León (CSI03A05), FIS (PI050087, PI050116), Fundación de Investigación MMA, Federación de Cajas de Ahorro Castilla y León (I Convocatoria de Ayudas para Proyectos de Investigación Biosanitaria con Células Madre), CDTEAM project (CENIT-Ingenio 2010) and MEC Consolider-Ingenio 2010 (Ref. CSD2007-0017).Research in ISG group is supported partially by FEDER and by MEC (SAF2006-03726 and PETRI N° 95-0913.OP), Junta de Castilla y León (CSI03A05), FIS (PI050087, PI050116), Fundación de Investigación MMA, Federación de Cajas de Ahorro Castilla y León (I Convocatoria de Ayudas para Proyectos de Investigación Biosanitaria con Células Madre), CDTEAM project (CENIT-Ingenio 2010) and MEC Consolider-Ingenio 2010 (Ref. CSD2007-0017). MSM is supported by the Ramon y Cajal Scientific Spanish Program, Fondo Investigacion Sanitaria (FIS PI04-1271), Junta de Castilla y León (SA085A06) and Fundación Manuel Solorzano, University of Salamanca.Peer reviewe

Redistribution of the Lamin B1 genomic binding profile affects rearrangement of heterochromatic domains and SAHF formation during senescence.

Senescence is a stress-responsive form of stable cell cycle exit. Senescent cells have a distinct gene expression profile, which is often accompanied by the spatial redistribution of heterochromatin into senescence-associated heterochromatic foci (SAHFs). Studying a key component of the nuclear lamina lamin B1 (LMNB1), we report dynamic alterations in its genomic profile and their implications for SAHF formation and gene regulation during senescence. Genome-wide mapping reveals that LMNB1 is depleted during senescence, preferentially from the central regions of lamina-associated domains (LADs), which are enriched for Lys9 trimethylation on histone H3 (H3K9me3). LMNB1 knockdown facilitates the spatial relocalization of perinuclear H3K9me3-positive heterochromatin, thus promoting SAHF formation, which could be inhibited by ectopic LMNB1 expression. Furthermore, despite the global reduction in LMNB1 protein levels, LMNB1 binding increases during senescence in a small subset of gene-rich regions where H3K27me3 also increases and gene expression becomes repressed. These results suggest that LMNB1 may contribute to senescence in at least two ways due to its uneven genome-wide redistribution: first, through the spatial reorganization of chromatin and, second, through gene repression

Roles of neuropeptides arginine vasotocin and isotocin in endocrine regulation of physiological process in the gilthead sea bream (Sparus aurata)

International Symposium in Marine Science (ISMS) 2012 (Cádiz, 24-26 enero de 2012). III Simposio Internacional de Ciencias del MarLos neuropéptidos arginina-vasotocina (AVT) e isotocina (IT) de teleósteos, análogos respectivamente de la arginina-vasopresina (AVP) y oxitocina (OXY) de mamíferos, participan en diversos procesos fisiológicos de los organismos.Estudio financiado por los proyectos AGL2010-14876 otorgado por el MICINN (España) a JMM y 498/N-HISZP-JPR/2009/0 (Polonia) a EK. JAM-S está financiado por una beca predoctoral (FPU, Referencia AP2008-01194) del Ministerio de Educación (España).Peer Reviewe

Analysis of cognitive performance and polymorphisms of SORL1, PVRL2, CR1, TOMM40, APOE, PICALM, GWAS_14q, CLU, and BIN1 in patients with mild cognitive impairment and cognitively healthy controls

Introduction: Alzheimer disease risk polymorphisms have been studied in patients with dementia, but have not yet been explored in mild cognitive impairment (MCI) in our population; nor have they been addressed in relation to cognitive variables, which can be predictive biomarkers of disease. Objective: To evaluate cognitive performance and presence of polymorphisms of the genes SORL1(rs11218304), PVRL2(rs6859), CR1(rs6656401), TOMM40(rs2075650), APOE (isoforms ε2, ε3, ε4), PICALM(rs3851179), GWAS_14q(rs11622883), BIN1(rs744373), and CLU(rs227959 and rs11136000) in patients with MCI and healthy individuals. Methodology: We performed a cross-sectional, exploratory, descriptive study of a prospective cohort of participants selected by non-probabilistic sampling, evaluated with neurological, neuropsychological, and genetic testing, and classified as cognitively healthy individuals and patients with MCI. Cognition was evaluated with the Neuronorma battery and analysed in relation to the polymorphic variants by means of measures of central tendency, confidence intervals, and nonparametric statistics. Results: We found differences in performance in language and memory tasks between carriers and non-carriers of BIN1, CLU, and CR1 variants and a trend towards poor cognitive performance for PICALM, GWAS_14q, SORL1, and PVRL2 variants; the APOE and TOMM40 variants were not associated with poor cognitive performance. Discussion: Differences in cognitive performance associated with these polymorphic variants may suggest that the mechanisms regulating these genes could have an effect on cognition in the absence of dementia; however, this study was exploratory and hypotheses based on these results must be explored in larger samples. Resumen: Introducción: Los polimorfismos de riesgo para el desarrollo de enfermedad de Alzheimer se han estudiado en pacientes con demencia, pero aún no se han explorado en trastorno neurocognitivo leve (TNL) en nuestra población, ni se han considerado en relación con variables cognitivas, las cuales pueden ser biomarcadores predictivos de enfermedad. Objetivo: Evaluar los desempeños cognitivos y los polimorfismos en los genes SORL1(rs11218304), PVRL2(rs6859), CR1(rs6656401), TOMM40(rs2075650), APOE(isoformas ε2, ε3, ε4), PICALM(rs3851179), GWAS_14q(rs11622883), BIN(rs744373), CLU (rs227959 y rs11136000) en pacientes con TNL y en sujetos sanos. Metodología: Estudio descriptivo, exploratorio y transversal, en una cohorte prospectiva de participantes seleccionados mediante muestreo no probabilístico, evaluados por neurología, neuropsicología y genética, y clasificados como cognitivamente sanos y pacientes con TNL, según criterios. La cognición se evaluó por medio de la batería Neuronorma y se analizó en relación con las variantes polimórficas por medio de medidas de tendencia, intervalos de confianza y estadísticos no paramétricos. Resultados: Se identificaron diferencias en los desempeños en tareas de lenguaje y memoria en relación con las variantes de BIN1, CLU y CR1, junto con tendencias en las variantes de PICALM, GWArs, SORL y PVRL2, mientras que en APOE y TOMM40 no se encontraron tendencias. Discusión: Las tendencias en los desempeños cognitivos en relación con variantes polimórficas podrían indicar que, en ausencia de demencia, los mecanismos que regulan estos genes podrían tener un efecto sobre la cognición; sin embargo, esta aproximación tiene un carácter exploratorio y sus resultados permiten generar hipótesis que requieren ser exploradas en muestras de mayor tamaño

A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes

GC-biased gene conversion (gBGC) is a recombination-associated process that favors the fixation of G/C alleles over A/T alleles. In mammals, gBGC is hypothesized to contribute to variation in GC content, rapidly evolving sequences, and the fixation of deleterious mutations, but its prevalence and general functional consequences remain poorly understood. gBGC is difficult to incorporate into models of molecular evolution and so far has primarily been studied using summary statistics from genomic comparisons. Here, we introduce a new probabilistic model that captures the joint effects of natural selection and gBGC on nucleotide substitution patterns, while allowing for correlations along the genome in these effects. We implemented our model in a computer program, called phastBias, that can accurately detect gBGC tracts about 1 kilobase or longer in simulated sequence alignments. When applied to real primate genome sequences, phastBias predicts gBGC tracts that cover roughly 0.3% of the human and chimpanzee genomes and account for 1.2% of human-chimpanzee nucleotide differences. These tracts fall in clusters, particularly in subtelomeric regions; they are enriched for recombination hotspots and fast-evolving sequences; and they display an ongoing fixation preference for G and C alleles. They are also significantly enriched for disease-associated polymorphisms, suggesting that they contribute to the fixation of deleterious alleles. The gBGC tracts provide a unique window into historical recombination processes along the human and chimpanzee lineages. They supply additional evidence of long-term conservation of megabase-scale recombination rates accompanied by rapid turnover of hotspots. Together, these findings shed new light on the evolutionary, functional, and disease implications of gBGC. The phastBias program and our predicted tracts are freely available. © 2013 Capra et al