Canopy interactions and physical stress gradients in subtidal communities

Species interactions are integral drivers of community structure and can change from competitive to facilitative with increasing environmental stress. In subtidal marine ecosystems, however, interactions along physical stress gradients have seldom been tested. We observed seaweed canopy interactions across depth and latitudinal gradients to test whether light and temperature stress structured interaction patterns. We also quantified interspecific and intraspecific interactions among nine subtidal canopy seaweed species across three continents to examine the general nature of interactions in subtidal systems under low consumer pressure. We reveal that positive and neutral interactions are widespread throughout global seaweed communities and the nature of interactions can change from competitive to facilitative with increasing light stress in shallow marine systems. These findings provide support for the stress gradient hypothesis within subtidal seaweed communities and highlight the importance of canopy interactions for the maintenance of subtidal marine habitats experiencing environmental stress.     

New Approaches for Absolute Quantification of Stable‐Isotope‐Labeled Peptide Standards for Targeted Proteomics Based on a UV Active Tag

Targeted proteomics depends on the availability of stable isotope labeled (SIL) peptide standards, which for absolute protein quantification need to be absolutely quantified. In the present study, three new approaches for absolute quantification of SIL peptides are developed. All approaches rely on a quantification tag (Qtag) with a specific UV absorption. The Qtag is attached to the peptide during synthesis and is removed by tryptic digestion under standard proteomics workflow conditions. While one quantification method (method A) is designed to allow the fast and economic production of absolutely quantified SIL peptides, two other methods (methods B and C) are developed to enable the straightforward re‐quantification of SIL peptides after reconstitution to control and monitor known problems related to peptide solubility, precipitation, and adhesion to vials. All methods yield consistent results when compared to each other and when compared to quantification by amino acid analysis. The precise quantitation methods are used to characterize the in vivo specificity of the H3 specific histone methyltransferase EZH2.     

The plant homeodomain finger protein MESR4 is essential for embryonic development in Drosophila

Misexpression Suppressor of Ras 4 (MESR4), a plant homeodomain (PHD) finger protein with nine zinc‐finger motifs has been implicated in various biological processes including the regulation of fat storage and innate immunity in Drosophila. However, the role of MESR4 in the context of development remains unclear. Here it is shown that MESR4 is a nuclear protein essential for embryonic development. Immunostaining of polytene chromosomes using anti‐MESR4 antibody revealed that MESR4 binds to numerous bands along the chromosome arms. The most intense signal was detected at the 39E‐F region, which is known to contain the histone gene cluster. P‐element insertions in the MESR4 locus, which were homozygous lethal during embryogenesis with defects in ventral ectoderm formation and head encapsulation was identified. In the mutant embryos, expression of Fasciclin 3 (Fas3), an EGFR signal target gene was greatly reduced, and the level of EGFR signal‐dependent double phosphorylated ERK (dp‐ERK) remained low. However, in the context of wing vein formation, genetic interaction experiments suggested that MESR4 is involved in the EGFR signaling as a negative regulator. These results suggested that MESR4 is a novel chromatin‐binding protein required for proper expression of genes including those regulated by the EGFR signaling pathway during development. genesis 53:701–708, 2015. © 2015 Wiley Periodicals, Inc.     

GENETIC VARIABILITY AND MOLECULAR PHYLOGENY OF DINOPHYSIS SPECIES (DINOPHYCEAE) FROM NORWEGIAN WATERS INFERRED FROM SINGLE CELL ANALYSES OF rDNA1

The objectives of this study were to determine rDNA sequences of the most common Dinophysis species in Scandinavian waters and to resolve their phylogenetic relationships within the genus and to other dinoflagellates. A third aim was to examine the intraspecific variation in D. acuminata and D. norvegica, because these two species are highly variable in both morphology and toxicity. We obtained nucleotide sequences of coding (small subunit [SSU], partial large subunit [LSU], 5.8S) and noncoding (internal transcribed spacer [ITS]1, ITS2) parts of the rRNA operon by PCR amplification of one or two Dinophysis cells isolated from natural water samples. The three photosynthetic species D. acuminata, D. acuta, and D. norvegica differed in only 5 to 8 of 1802 base pairs (bp) within the SSU rRNA gene. The nonphotosynthetic D. rotundata (synonym Phalacroma rotundatum[Claparède et Lachmann] Kofoid et Michener), however, differed in approximately 55 bp compared with the three photosynthetic species. In the D1 and D2 domains of LSU rDNA, the phototrophic species differed among themselves by 3 to 12 of 733 bp, whereas they differed from D. rotundata by more than 100 bp. This supports the distinction between Dinophysis and Phalacroma. In the phylogenetic analyses based on SSU rDNA, all Dinophysis species were grouped into a common clade in which D. rotundata diverged first. The results indicate an early divergence of Dinophysis within the Dinophyta. The LSU phylogenetic analyses, including 4 new and 11 Dinophysis sequences from EMBL, identified two major clades within the phototrophic species. Little or no intraspecific genetic variation was found in the ITS1–ITS2 region of single cells of D. norvegica and D. acuminata from Norway, but the delineation between these two species was not always clear.     

Growth characteristics of Protoheliolites norvegicus (Tabulata; Upper Ordovician; Estonia)

Protoheliolites is an early heliolitine coral characterized by closely spaced corallites separated in places by sparse coenenchyme. Growth characteristics in the type species, P. norvegicus, are revealed by detailed analysis based on serial peels and thin sections of coralla from the uppermost Katian of north‐western Estonia. Colonies of this species had a strong ability to recover from damage and partial mortality, resulting in various forms of rejuvenation, regeneration, fusion and reorganization of corallites; in some cases, this involved relatively large areas of undifferentiated soft parts. The shells of commensal cornulitids became enclosed in host coralla during colony growth. Coralla of P. norvegicus exhibit distinctive growth cycles due to responses to seasonal changes. The production of new corallites by coenenchymal increase usually occurred in low‐density bands, in which corallites generally display round to subrounded transverse outlines. In high‐density bands, the corallites became crenulated, their wall thickness increased, septal development was more pronounced, and the amount of coenenchyme increased. In addition to these cyclomorphic changes, there were significant astogenetic changes during growth. Compared with the early stage of colony development, distinctive characteristics in the late astogenetic stage include a decrease in the growth rate of the colony, better coordination among corallites, maximum development of corallite crenulations and septa in high‐density bands, more numerous coenenchymal tubules and a greater proportion of corallum area occupied by coenenchyme. In general, the role of polyps in determining morphological characteristics of individual corallites, such as tabularium area, corallite crenulations and wall thickness, was subordinate to the astogeny of the colony. Growth characteristics including colony‐wide coordination of polyp behaviour and subjugation of individuals to restore the colony following damage suggest a strong astogenetic control and high level of colony integration. Protoheliolites probably arose from a heliolitine genus rather than from a nonheliolitine group as some authors have proposed.     

Sequential Statistical Improvement of the Liquid Cultivation of Helicobacter pylori

Background: Colonization of the gastric mucosa by Helicobacter pylori is one of the most important causes of acute and chronic gastric pathologies in humans. Achieving the growth of H. pylori in liquid media is of great importance in the development of clinical studies. In this study, we developed a sequential optimization strategy based on statistical models to improve the conditions of liquid culture of H. pylori. Materials and Methods: Four statistical models were sequentially used. First, a Box‐Behnken design was used to select the best process conditions (shaking speed, inoculum concentration, and final volume of culture). Secondly, a general factorial design was used to evaluate the influence of adding gel blocks or gel beads (shape and composition). Then a D‐optimal reduce design was carried out to allow the selection of the most influential factors in increasing the cell concentration (culture media components). Finally, another Box‐Behnken design was used to optimize the concentration of the culture media components previously selected. Results: After 12 hours of liquid culture a concentration of 25 × 10⁸ cells per mL (9.4 log₁₀ cells per mL) of H. pylori was obtained, compared with a predicted 32 × 10⁸ (9.5 log₁₀ cells per mL), which means between 1 and 5 log₁₀ units higher than some previous reports. Conclusions: The sequential statistical approach increased the planktonic H. pylori cell culture. The final culture media and conditions were: Brain Heart Infusion, blood agarose (1.5% w/v), lamb’s blood (3.18% v/v), DENT (0.11% v/v), and Vitox (0.52% v/v) at 60 rpm and 37 °C with filtered CO₂ (5% v/v) bubbled directly into the culture media in a final volume of 76.22 mL.     

The first species of Hapalodectes (Mesonychia,Mammalia) from the middle Paleocene of China (Qianshan Basin,Anhui Province) sheds light on the initial radiation of hapalodectids

A lower jaw of the mesonychian Hapalodectes is reported from Nongshanian sediments (Upper Doumu Formation; middle Paleocene) of the Qianshan Basin (Anhui Province, China). The fragmentary mandible is only the third specimen of Hapalodectidae discovered in Paleocene deposits, and the first in south east China; it is moreover the oldest, the two other specimens having been found in Gashatan (late Paleocene) localities. The premolars and molars of the new fossil are morphologically similar to Hapalodectes dux (late Paleocene of Mongolia), which has been considered to be the most primitive hapalodectid, but their relative proportions recall H. paleocenus and the Eocene Hapalodectes species. As a result, the fossil described herein appears to be different from the other previously described species of Hapalodectes in being morphologically intermediate between H. dux and the other Hapalodectes species, notably the Bumbanian Hapalodectes hetangensis and H. huanghaiensis from China; it is thus identified as a new species, Hapalodectes lopatini (possibly a male individual). Its discovery is important because it sheds light on the initial radiation of hapalodectids. The presence of one primitive hapalodectid in Mongolia previously suggested the Mongolian Plateau as the centre of origination of this carnivorous family, but the discovery of H. lopatini in older sediments from south‐east China challenges this hypothesis. In the earliest Eocene, Hapalodectes dispersed from Asia to North America; this event being part of the ‘East of Eden’ dispersals. This event resulted in the geographical separation of two distinct Hapalodectes groups, in North America and south‐eastern China respectively.