Macroecology in the age of Big Data – Where to go from here?

Recent years have seen an exponential increase in the amount of data available in all sciences and application domains. Macroecology is part of this “Big Data” trend, with a strong rise in the volume of data that we are using for our research. Here, we summarize the most recent developments in macroecology in the age of Big Data that were presented at the 2018 annual meeting of the Specialist Group Macroecology of the Ecological Society of Germany, Austria and Switzerland (GfÖ). Supported by computational advances, macroecology has been a rapidly developing field over recent years. Our meeting highlighted important avenues for further progress in terms of standardized data collection, data integration, method development and process integration. In particular, we focus on (a) important data gaps and new initiatives to close them, for example through space- and airborne sensors, (b) how various data sources and types can be integrated, (c) how uncertainty can be assessed in data-driven analyses and (d) how Big Data and machine learning approaches have opened new ways of investigating processes rather than simply describing patterns. We discuss how Big Data opens up new opportunities, but also poses new challenges to macroecological research. In the future, it will be essential to carefully assess data quality, the reproducibility of data compilation and analytical methods, and the communication of uncertainties. Major progress in the field will depend on the definition of data standards and workflows for macroecology, such that scientific quality and integrity are guaranteed, and collaboration in research projects is made easier.     

Cell type and differentiation dependent heterogeneity in retinoblastoma protein expression in SCID mouse fetuses.

The expression pattern of retinoblastoma (Rb) protein has been studied at the single cell level in frozen sections of 16- to 18-day-old SCID mouse fetuses by immunofluorescence staining with mouse monoclonal and rabbit polyclonal antibodies, using conventional epifluorescence and confocal laser scanning microscopy. The nuclei of megakaryocytes, hemopoietic islands of the fetal liver, osteo-, amelo-, and odontoblasts, and skeletal muscle were strongly stained. There was no detectable Rb staining in the basal cell layers of stratified squamous epithelia, but the differentiating, more superficial layers were positive. Intestinal crypts were negative, whereas the villi were positive. In the retina, Rb protein was detectable in the inner ganglion layer but not in the outer neuroblastic layer. In the central nervous system, Rb protein was present in neurons and glia cells as well. The nuclei in the collecting tubules of the kidney, the pancreas, and the adrenal cortex were Rb positive. Analysis of the differentiation dependent expression of Rb protein in relation to the prospective life cycle of the cells in which it appears may pave the way toward an understanding of the tissue specific oncogenic effect of Rb loss in families with hereditary retinoblastoma.     

Evolutionary pathway of child development

An evolutionary theory of socialization suggests that children from father-absent families will mature earlier, and form less-stable pair bonds, compared with those from father-present families. Using a sample of about 1,000 persons the recent study focuses on elements of father-absent children’s behavior that could be better explained by a Darwinian approach than by rival social science theories. As a result of their enhanced interest in male competition, father-absent boys were found to engage in rule-breaking behavior more intensively than father-present boys. Compared with father-present children, adolescents from widowed households (both boys and girls) showed a higher intensity of various kinds of noncompliant behavior, which can be linked to their earlier maturation. School attendance, age at marriage, and marital success proved to be influenced by the children’s early family experiences, governed by adapted evolutionary strategies. Father-absent daughters conceived more children than those whose fathers were present during their childhood. As evolutionary theory predicts, reproductive behavior of individuals from divorced households differed from that of individuals who grew up in widowed households. Finally, the strong correlation found between spontaneous abortion/stillbirths and family arrangement indicates that father absence has certain direct impacts on the neurohormonal processes of child development.     

The cyclic nucleotide‐gated channel AtCNGC10 transports Ca2+ and Mg2+ in Arabidopsis

The suppression of the cyclic nucleotide‐gated channel (CNGC) AtCNGC10 alters K⁺ transport in Arabidopsis plants. Other CNGCs have been shown to transport Ca²⁺, K⁺, Li⁺, Cs⁺ and Rb⁺ across the plasma membrane when expressed in heterologous systems; however, the ability of the AtCNGC10 channel to transport nutrients other than K⁺ in plants has not been previously tested. The ion fluxes along different zones of the seedling roots, as estimated by the non‐invasive ion‐specific microelectrode technique, were significantly different in two AtCNGC10 antisense lines (A2 and A3) in comparison to the wild type (WT). Most notably, the influxes of H⁺, Ca²⁺ and Mg²⁺ in the meristem and distal elongation zones of the antisense A2 and A3 lines were significantly lower than in the WT. The lower Ca²⁺ influx from the external media corresponded to a lower intracellular Ca²⁺ activity, which was estimated by fluorescence lifetime imaging measurements (FLIM). On the other hand, the intracellular pH values in the meristem zone of the roots of A2 and A3 seedlings were significantly lower (more acidic) than that of the WT, which might indicate a feedback block of H⁺ influx into meristematic cells caused by low intracellular pH. Under the control conditions, mature plants from the A2 and A3 lines contained significantly higher K⁺ and lower Ca²⁺ and Mg²⁺ content in the shoots, indicating disturbed long‐distance ion transport of these cations, possibly because of changes in xylem loading/retrieval and/or phloem loading. Exposing the plants in the flowering stage to various K⁺, Ca²⁺ and Mg²⁺ concentrations in the solution led to altered K⁺, Ca²⁺ and Mg²⁺ content in the shoots of A2 and A3 plants in comparison with the WT, suggesting a primary role of AtCNGC10 in Ca²⁺ (and probably Mg²⁺) transport in plants, which in turn regulates K⁺ transporters' activities.     

Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns

Plants feature a particularly diverse population of short (s)RNAs, the central component of all RNA silencing pathways. Next generation sequencing techniques enable deeper insights into this complex and highly conserved mechanism and allow identification and quantification of sRNAs. We employed deep sequencing to monitor the sRNAome of developing tomato fruits covering the period between closed flowers and ripened fruits by profiling sRNAs at 10 time-points. It is known that microRNAs (miRNAs) play an important role in development but very little information is available about the majority of sRNAs that are not miRNAs. Here we show distinctive patterns of sRNA expression that often coincide with stages of the developmental process such as flowering, early and late fruit maturation. Moreover, thousands of non-miRNA sRNAs are differentially expressed during fruit development and ripening. Some of these differentially expressed sRNAs derived from transposons but many derive from protein coding genes or regions that show homology to protein coding genes, several of which are known to play a role in flower and fruit development. These findings raise the possibility of a regulative role of these sRNAs during fruit onset and maturation in a crop species. We also identified six new miRNAs and experimentally validated two target mRNAs. These two mRNAs are targeted by the same miRNA but do not belong to the same gene family, which is rare for plant miRNAs. Expression pattern and putative function of these targets indicate a possible role in glutamate accumulation, which contributes to establishing the taste of the fruit.     

The crystal structure of the phosphatidylinositol 4‐kinase IIα

Phosphoinositides are a class of phospholipids generated by the action of phosphoinositide kinases with key regulatory functions in eukaryotic cells. Here, we present the atomic structure of phosphatidylinositol 4‐kinase type IIα (PI4K IIα), in complex with ATP solved by X‐ray crystallography at 2.8 Å resolution. The structure revealed a non‐typical kinase fold that could be divided into N‐ and C‐lobes with the ATP binding groove located in between. Surprisingly, a second ATP was found in a lateral hydrophobic pocket of the C‐lobe. Molecular simulations and mutagenesis analysis revealed the membrane binding mode and the putative function of the hydrophobic pocket. Taken together, our results suggest a mechanism of PI4K IIα recruitment, regulation, and function at the membrane.     

crossveinless defines a new family of Twisted-gastrulation-like modulators of bone morphogenetic protein signalling

The Twisted gastrulation (Tsg) proteins are modulators of bone morphogenetic protein (BMP) activity in both vertebrates and insects. We find that the crossveinless (cv) gene of Drosophila encodes a new tsg-like gene. Genetic experiments show that cv, similarly to tsg, interacts with short gastrulation (sog) to modulate BMP signalling. Despite this common property, Cv shows a different BMP ligand specificity as compared with Tsg, and its expression is limited to the developing wing. These findings and the presence of two types of Tsg-like protein in several insects suggest that Cv represents a subgroup of the Tsg-like BMP-modulating proteins.     

Chromosomal aberrations induced by double strand DNA breaks

It has been suggested that introduction of double strand DNA breaks (DSBs) into mammalian chromosomes can lead to gross chromosomal rearrangements through improper DNA repair. To study this phenomenon, we employed a model system in which a double strand DNA break can be produced in human cells in vivo at a predetermined location. The ensuing chromosomal changes flanking the breakage site can then be cloned and characterized. In this system, the recognition site for the I-SceI endonuclease, whose 18 bp recognition sequence is not normally found in the human genome, is placed between a strong constitutive promoter and the Herpes simplex virus thymidine kinase (HSV-tk) gene, which serves as a negative selectable marker. We found that the most common mutation following aberrant DSB repair was an interstitial deletion; these deletions typically showed features of non-homologous end joining (NHEJ), such as microhomologies and insertions of direct or inverted repeat sequences. We also detected more complex rearrangements, including large insertions from adjacent or distant genomic regions. The insertion events that involved distant genomic regions typically represented transcribed sequences, and included both L1 LINE elements and sequences known to be involved in genomic rearrangements. This type of aberrant repair could potentially lead to gene inactivation via deletion of coding or regulatory sequences, or production of oncogenic fusion genes via insertion of coding sequences.