A nonparametric procedure to assess the accuracy of the normality assumption for annual rainfall totals, based on the marginal statistics of daily rainfall: an application to the NOAA/NCDC rainfall database

We develop a nonparametric procedure to assess the accuracy of the normality assumption for annual rainfall totals (ART), based on the marginal statistics of daily rainfall. The procedure is addressed to practitioners and hydrologists that operate in data-poor regions. To do so we use 1) goodness-of-fit metrics to conclude on the approximate convergence of the empirical distribution of annual rainfall totals to a normal shape and classify 3007 daily rainfall time series from the NOAA/NCDC Global Historical Climatology Network database, with at least 30 years of recordings, into Gaussian (G) and non-Gaussian (NG) groups; 2) logistic regression analysis to identify the statistics of daily rainfall that are most descriptive of the G/NG classification; and 3) a random-search algorithm to conclude on a set of constraints that allows classification of ART samples on the basis of the marginal statistics of daily rain rates. The analysis shows that the Anderson–Darling (AD) test statistic is the most conservative one in determining approximate Gaussianity of ART samples (followed by Cramer–Von Mises and Lilliefors’s version of Kolmogorov–Smirnov) and that daily rainfall time series with fraction of wet days fwd < 0.1 and daily skewness coefficient of positive rain rates skwd > 5.92 deviate significantly from the normal shape. In addition, we find that continental climate (type D) exhibits the highest fraction of Gaussian distributed ART samples (i.e., 74.45%; AD test at α = 5% significance level), followed by warm temperate (type C; 72.80%), equatorial (type A; 68.83%), polar (type E; 62.96%), and arid (type B; 60.29%) climates

A synoptic study of phytoplankton in the deep lakes south of the Alps (lakes Garda, Iseo, Como, Lugano and Maggiore)

This paper presents a synoptic account of the most important results emerging from studies on the phytoplankton communities in the deep southern subalpine lakes Garda, Iseo, Como, Lugano and Maggiore (DSL) in the second half of the 1990s. At present, the trophogenic layers of these lakes are trophically different, ranging from the oligo-mesotrophy of lakes Maggiore and Garda to the meso-eutrophy of lakes Iseo and Lugano. The research confirmed the existence of a common pool of species developing in the DSL, as already suggested by early studies conducted on a seasonal basis from the end of the 1970s to the first half of the 1980s. However, multivariate analyses (Correspondence Analysis, CA, and a subsequent application of Non Metric Multidimensional Scaling) demonstrated that the species in this common pool were developing differently or exclusively along a geographic and a trophic gradient. The major differences in the geographic distribution were found between the easternmost lakes (Garda and Iseo) and those farthest to the West (Lugano and, partly, Maggiore), with intermediate characteristics in Lake Como. These differences were due mainly to changes in the dominance relationships and only secondarily to compositional changes. The detection of the ultimate causes of these differences should take into account other factors not considered in the paper (i.e. the specific analysis of the food webs, local climatic conditions, hydrology and seasonal input of nutrients). Despite the observed differences, common patterns in the sequence of seasonal assemblages in the DSL could be recognised and defined. The second gradient in the species distribution identified by CA was strongly correlated with the principal trophic descriptors (algal biomass and total phosphorus); this meant that the phytoplankton taxa could be ranked along a trophic spectrum, from oligotrophy to eutrophy. A brief examination of the main differences which have historically arisen with the progress of eutrophication in the DSL showed that the species identified in this study as being indicative of more eutrophic conditions were increasing in importance in some of the lakes

Defending the genome from the enemy within:mechanisms of retrotransposon suppression in the mouse germline

The viability of any species requires that the genome is kept stable as it is transmitted from generation to generation by the germ cells. One of the challenges to transgenerational genome stability is the potential mutagenic activity of transposable genetic elements, particularly retrotransposons. There are many different types of retrotransposon in mammalian genomes, and these target different points in germline development to amplify and integrate into new genomic locations. Germ cells, and their pluripotent developmental precursors, have evolved a variety of genome defence mechanisms that suppress retrotransposon activity and maintain genome stability across the generations. Here, we review recent advances in understanding how retrotransposon activity is suppressed in the mammalian germline, how genes involved in germline genome defence mechanisms are regulated, and the consequences of mutating these genome defence genes for the developing germline

Microarray-Based Approach Identifies Differentially Expressed MicroRNAs in Porcine Sexually Immature and Mature Testes

MicroRNAs (miRNAs) are short non-coding RNA molecules which are proved to be involved in mammalian spermatogenesis. Their expression and function in the porcine germ cells are not fully understood.We employed a miRNA microarray containing 1260 unique miRNA probes to evaluate the miRNA expression patterns between sexually immature (60-day) and mature (180-day) pig testes. One hundred and twenty nine miRNAs representing 164 reporter miRNAs were expressed differently (p<0.1). Fifty one miRNAs were significantly up-regulated and 78 miRNAs were down-regulated in mature testes. Nine of these differentially expressed miRNAs were validated using quantitative RT-PCR assay. Totally 15,919 putative miRNA-target sites were detected by using RNA22 method to align 445 NCBI pig cDNA sequences with these 129 differentially expressed miRNAs, and seven putative target genes involved in spermatogenesis including DAZL, RNF4 gene were simply confirmed by quantitative RT-PCR.Overall, the results of this study indicated specific miRNAs expression in porcine testes and suggested that miRNAs had a role in regulating spermatogenesis

ZNF280BY and ZNF280AY: autosome derived Y-chromosome gene families in Bovidae

<p>Abstract</p> <p>Background</p> <p>Recent progress in exploring the Y-chromosome gene content in humans, mice and cats have suggested that "autosome-to-Y" transposition of the male fertility genes is a recurrent theme during the mammalian Y-chromosome evolution. These transpositions are lineage-dependent. The purpose of this study is to investigate the lineage-specific Y-chromosome genes in bovid.</p> <p>Results</p> <p>We took a direct testis cDNA selection strategy and discovered two novel gene families, <it>ZNF280BY </it>and <it>ZNF280AY</it>, on the bovine (<it>Bos taurus</it>) Y-chromosome (BTAY), which originated from the transposition of a gene block on the bovine chromosome 17 (BTA17) and subsequently amplified. Approximately 130 active <it>ZNF280BY </it>loci (and ~240 pseudogenes) and ~130 pseudogenized <it>ZNF280AY </it>copies are present over the majority of the male-specific region (MSY). Phylogenetic analysis indicated that both gene families fit with the "birth-and-death" model of evolution. The active <it>ZNF280BY </it>loci share high sequence similarity and comprise three major genomic structures, resulted from insertions/deletions (indels). Assembly of a 1.2 Mb BTAY sequence in the MSY ampliconic region demonstrated that <it>ZNF280BY </it>and <it>ZNF280AY</it>, together with <it>HSFY </it>and <it>TSPY </it>families, constitute the major elements within the repeat units. The <it>ZNF280BY </it>gene family was found to express in different developmental stages of testis with sense RNA detected in all cell types of the seminiferous tubules while the antisense RNA detected only in the spermatids. Deep sequencing of the selected cDNAs revealed that different loci of <it>ZNF280BY </it>were differentially expressed up to 60-fold. Interestingly, different copies of the <it>ZNF280AY </it>pseudogenes were also found to differentially express up to 10-fold. However, expression level of the <it>ZNF280AY </it>pseudogenes was almost 6-fold lower than that of the <it>ZNF280BY </it>genes. <it>ZNF280BY </it>and <it>ZNF280AY </it>gene families are present in bovid, but absent in other mammalian lineages.</p> <p>Conclusions</p> <p><it>ZNF280BY </it>and <it>ZNF280AY </it>are lineage-specific, multi-copy Y-gene families specific to <it>Bovidae</it>, and are derived from the transposition of an autosomal gene block. The temporal and spatial expression patterns of <it>ZNF280BY</it>s in testis suggest a role in spermatogenesis. This study offers insights into the genomic organization of the bovine MSY and gene regulation in spermatogenesis, and provides a model for studying evolution of multi-copy gene families in mammals.</p

Mice Lacking Alkbh1 Display Sex-Ratio Distortion and Unilateral Eye Defects

Escherichia coli AlkB is a 2-oxoglutarate- and iron-dependent dioxygenase that reverses alkylated DNA damage by oxidative demethylation. Mouse AlkB homolog 1 (Alkbh1) is one of eight members of the newly discovered family of mammalian dioxygenases.In the present study we show non-Mendelian inheritance of the Alkbh1 targeted allele in mice. Both Alkbh1(-/-) and heterozygous Alkbh1(+/-) offspring are born at a greatly reduced frequency. Additionally, the sex-ratio is considerably skewed against female offspring, with one female born for every three to four males. Most mechanisms that cause segregation distortion, act in the male gametes and affect male fertility. The skewing of the sexes appears to be of paternal origin, and might be set in the pachythene stage of meiosis during spermatogenesis, in which Alkbh1 is upregulated more than 10-fold. In testes, apoptotic spermatids were revealed in 5-10% of the tubules in Alkbh1(-/-) adults. The deficiency of Alkbh1 also causes misexpression of Bmp2, 4 and 7 at E11.5 during embryonic development. This is consistent with the incompletely penetrant phenotypes observed, particularly recurrent unilateral eye defects and craniofacial malformations.Genetic and phenotypic assessment suggests that Alkbh1 mediates gene regulation in spermatogenesis, and that Alkbh1 is essential for normal sex-ratio distribution and embryonic development in mice

What Martian Meteorites Reveal About the Interior and Surface of Mars

Martian meteorites are the only direct samples from Mars, thus far. Currently, there are a total of 262 individual samples originating from at least 11 ejection events. Geochemical analyses, through techniques that are also used on terrestrial rocks, provide fundamental insights into the bulk composition, differentiation and evolution, mantle heterogeneity, and role of secondary processes, such as aqueous alteration and shock, on Mars. Martian meteorites display a wide range in mineralogy and chemistry, but are predominantly basaltic in composition. Over the past 6 years, the number of martian meteorites recovered has almost doubled allowing for studies that evaluate these meteorites as suites of igneous rocks. However, the martian meteorites represent a biased sampling of the surface of Mars with unknown ejection locations. The geology of Mars cannot be unraveled solely by analyzing these meteorites. Rocks analyzed by rovers on the surface of Mars are of distinct composition to the meteorites, highlighting the importance of Mars missions, especially sample return. The Mars 2020 Perseverance rover will collect and cache—for eventual return to Earth—over 30 diverse surface samples from Jezero crater. These returned samples will allow for Earth‐based state‐of‐the‐art analyses on diverse martian rocks with known field context. The complementary study of returned samples and meteorites will help to constrain the evolution of the martian interior and surface. Here, we review recent findings and advances in the study of martian meteorites and examine how returned samples would complement and enhance our knowledge of Mars