The biological regulation of sea urchin larval skeletogenesis – From genes to biomineralized tissue

Biomineralization is the process in which soft organic tissues use minerals to produce shells, skeletons and teeth for various functions such as protection and physical support. The ability of the cells to control the time and place of crystal nucleation as well as crystal orientation and stiffness is far beyond the state-of-the art of human technologies. Thus, understanding the biological control of biomineralization will promote our understanding of embryo development as well as provide novel approaches for material engineering. Sea urchin larval skeletogenesis offers an excellent platform for functional analyses of both the molecular control system and mineral uptake and deposition. Here we describe the current understanding of the genetic, molecular and cellular processes that underlie sea urchin larval skeletogenesis. We portray the regulatory genes that define the specification of the skeletogenic cells and drive the various morphogenetic processes that occur in the skeletogenic lineage, including: epithelial to mesenchymal transition, cell migration, spicule cavity formation and mineral deposition into the spicule cavity. We describe recent characterizations of the size, motion and mineral concentration of the calcium-bearing vesicles in the skeletogenic cells. We review the distinct specification states within the skeletogenic lineage that drive localized skeletal growth at the tips of the spicules. Finally, we discuss the surprising similarity between the regulatory network and cellular processes that drive sea urchin skeletogenesis and those that control vertebrate vascularization. Overall, we illustrate the novel insights on the biological regulation and evolution of biomineralization, gained from studies of the sea urchin larval skeletogenesis.     

Why did the invasive walking catfish cross the road? Terrestrial chemoreception described for the first time in a fish

Clarias batrachus (walking catfish) is an invasive species in Florida, renowned for its air-breathing and terrestrial locomotor capabilities. However, it is unknown how this species orients in terrestrial environments. Furthermore, while anecdotal life history information is widespread for this species in its nonnative range, little of this information exists in the literature. The goals of this study were to identify sensory modalities that C. batrachus use to orient on land, and to describe the natural history of this species in its nonnative range. Fish (n = 150) were collected from around Ruskin, FL, and housed in a greenhouse, where experiments took place. Individual catfish were placed in the center of a terrestrial arena and were exposed to nine treatments: two controls, L-alanine, quinine, allyl isothiocynate, sucrose, volatile hydrogen sulphide, pond water and aluminium foil. These fish exhibited significantly positive chemotaxis toward alanine and pond water, and negative chemotaxis away from volatile hydrogen sulphide, suggesting chemoreception – both through direct contact and through the air – is important to their terrestrial orientation. Additionally, 88 people from Florida wildlife-related Facebook groups who have personal observations of C. batrachus on land were interviewed for information regarding their terrestrial natural history. These data were combined with observations from 38 YouTube videos. C. batrachus appear to emerge most frequently during or just after heavy summer rains, particularly from stormwater drains in urban areas, where they may feed on terrestrial invertebrates. By better understanding the full life history of C. batrachus, we can improve management of this species.     

The Scontrone turtles – A new insular testudinoid fauna from the late Miocene of the Central Mediterranean

We here describe a small turtle assemblage originating from the early Tortonian (late Miocene) palaeoisland of Scontrone, central Italy, a locality previously known mostly for its endemic mammals and giant birds, which were otherwise shared only with the Gargano localities, another fossiliferous area belonging to the same palaeobioprovince. The fossil turtle remains from Scontrone are referred to the geoemydid Mauremys sp. and a so far unidentified large-sized testudinid. The biogeographic origins of the Scontrone insular chelonians are discussed. The Scontrone geoemydid adds to the known occurrences of Mauremys in the late Miocene of the Mediterranean. The Scontrone large tortoise represents the oldest known Mediterranean insular testudinid, predating significantly the well-known Quaternary endemic island tortoises of the area.     

Is there a role for the Ca influx during fertilization of the sea urchin egg?

Both isotopic and microelectrode studies reveal a significant Ca²⁺ influx at fertilization which if freely distributed in the cytoplasm would equal 1–2 × 10⁻⁵ M. The role, if any, of this influx is disputed. We have attempted to reevaluate contradictory findings by others on this role. Our results with Strongylocentrotus purpuratus and Lytechinus pictus eggs, assessing fertilization with acrosome-reacted sperm in EGTA-buffered media (free [Ca²⁺], 4.4 × 10⁻⁸ M) indicate that exogenous Ca²⁺ is not required for fertilization and subsequent cleavage. The contradictory findings by others may have resulted from reduced fertilizability in Ca²⁺-free seawater, which can be circumvented by higher sperm concentration and by a sensitivity to temperature in Ca²⁺-free medium, which can be bypassed by carrying out fertilization at lower temperature. Also consistent with the absence of a requirement for this Ca²⁺ influx, we found that Ca²⁺ uptake can be induced in eggs by depolarizing the membrane with high [K⁺], but there is no resultant activation of egg metabolism. Under our conditions for fertilization in Ca²⁺-free media, there is no effect on the block to polyspermy but the initiation of the cortical reaction may be delayed. The data support the hypothesis that sperm induce release of Ca²⁺ from intracellular stores, perhaps by affecting an equilibrium between Ca²⁺ sequestration and Ca²⁺ release.     

The glomerulus – a view from the outside – the podocyte

In the past decade, podocyte research has been greatly aided by the development of powerful new molecular, cellular and animal tools, leading to elucidation of an increasing number of proteins involved in podocyte function and identification of mutated genes in hereditary glomerulopathies. Accumulating evidence indicates that podocyte disorders may not only underlie these hereditary glomerulopathies but also play crucial role in a broad spectrum of acquired glomerular diseases. Genetic susceptibility, environmental influence and systemic responses are all involved in the mediation of the pathogenesis of podocytopathies. Injured podocytes may predisopose to further injury of other podocytes and other adjacent/distant renal cells in a vicious cycle, leading to inexorable progression of glomerular injury. The classic view is that podocytes have a limited ability to proliferate in the normal mature kidney. However, recent research in rodents has provided suggestive evidence for podocyte regeneration resulting from differentiation of progenitor cells within Bowman's capsule.     

Adaptation to sea level rise: does local adaptation influence the demography of coastal fish populations?

This study compared the growth of two western mosquitofish Gambusia affinis populations that were previously demonstrated to have genetic adaptations that increased survival under lethal salinity exposures. The objective was to evaluate how genetic adaptations to lethal salinity stress affect population demography when exposed to sublethal salinity stress. Results indicate that chronic salinity exposure had a generally negative impact on population size, but fish originating from one of the two populations established with fish from a brackish site exhibited an increase in population size. Saltwater intrusion seems to result in reduced population size for most populations. Some populations inhabiting more saline sites, however, may develop localized adaptations, mitigating the consequences of increased salinity on population productivity.     

The glomerulus – a view from the inside – the endothelial cell

The glomerular endothelial cells are unique both in location and anatomy compared to most other endothelial cells throughout the body. The absence of a diaphragm with retention of a basement membrane and fenestrations enable these uniquely situated cells to have a key role in filtration performed by the kidney. Interaction with other glomerular cells such as the podocytes and mesangial cells, as well as with circulating and infiltrating inflammatory cells, contribute to the final impact of the glomerular endothelial cells on maintenance of body fluid homeostasis and modulation of disease. Thus, endothelial cells contribute to hemodynamic function, reactive oxygen stress, regulate the balance between pro-thrombotic and anti-thrombotic forces, and importantly, contribute to fibrosis, the key injury of progressive chronic kidney disease. Repair of endothelial cell damage and restoration of segmentally sclerosed glomeruli are key areas considered for intervention in chronic kidney disease. This review will focus on the structure, function, and interplay of endothelial cells with other glomerular cells and systemic factors, their impact on renal disease and give rationale for possible intervention that may forestall progressive injuries.     

The exogastrula-inducing peptides in embryos of the sea urchin,Anthocidaris crassispina — isolation and determination of the primary structure

Four exogastrula-inducing peptides, A, B, C, and D have been isolated from the homogenates of embryos of the sea urchin, Anthocidaris crassispina, with successive chromatographic fractionations. The complete amino acid sequences of the peptides A and D were determined by analysis of the peptides generated by their digestion with lysyl endopeptidase. They were composed of 52 and 53 amino acid residues, and their molecular weights were calculated to be 5754 and 5737, respectively. The sequences of peptides A and D were DSVYQCNRDTNSCDGFGKCEKSTFGRTTGQYICNCDDGYRNNAYGGCSPRTE, and DTVARCERDTKNCDGHGTCQLSTFGRRTGQYICFCDAGYRKPNSYGGCSPSSA, respectively. The biological significance of the exogastrula-inducing peptides was discussed.     

Cumacean assemblages on the Levantine shelf (Mediterranean Sea) – spatiotemporal trends between 2005 and 2012

Cumacea (Crustacea, Peracarida) are an important component of soft-bottom macrofauna. Their assemblages are influenced by environmental parameters, including the presence of alien species. Cumacean assemblages from 443 samples collected between 2005 and 2012, at 148 sites along the Israeli Mediterranean coast were analysed. In all, the 31,508 cumaceans were identified to 18 species. Three of the species, Eocuma rosae, E. sarsii and Scherocumella gurneyi, are considered alien for the Mediterranean Sea. Pseudocuma longicorne, S. gurneyi and Cumopsis goodsir were the most abundant species in our samples. Cumacean densities were significantly higher in spring than in autumn, except on the shelf, where the opposite was observed. At the deeper sites (55–63?m) species composition changed between seasons, suggesting a migration of some shallow-bottom dwellers (P. longicorne, Iphinoe spp.) into deeper waters in wintertime. Comparison among years revealed great differences in density, especially in P. longicorne, which experienced an outbreak in 2009. Although seasonal changes may be explained by the natural dynamics of the species' life cycles, inter-annual variability is more difficult to explain. It may be related to environmental changes and especially to the infralittoral hypernutrification along the southern Israeli coast, causing an increase in food availability. Cumacean alien species occurred only in Haifa Bay.     

Asexual reproduction in bad times? The case of Cladocora caespitosa in the eastern Mediterranean Sea

We analysed the patterns of genetic variability of eastern Mediterranean populations of the scleractinian coral Cladocora caespitosa, from the Aegean and Levantine seas, using 19 polymorphic microsatellite loci, 11 of which were newly characterized. The observed genetic pattern reflects a scenario of isolation by environment: F_ST comparisons showed a higher degree of genetic differentiation between the two Cypriot populations that are separated by only 11 km than between these two Levantine populations and the Aegean population in Greece, which are separated by 1300 km. We hypothesize that local-scale oceanographic factors influenced the dispersal of planulae between the geographically close populations, playing a crucial role in the genetic structure of this coastal coral. Yet, despite being characterized as a species with limited dispersal and high self-recruitment, large-scale migration does eventually occur as first-generation migrants were identified between the most distant populations. In line with previous findings of reproductive plasticity in C. caespitosa, we also found localized differences in reproduction mode (sexual vs. asexual) within a geographically limited context. Several individuals were identified as clones, indicating the predominance of asexual reproduction in one of the Cypriot populations. We interpret this predominance either as a direct response to or as an indirect consequence of perturbations suffered by this C. caespitosa population. These perturbations are caused by unfavourable environmental conditions that threatened local survival, in particular water temperature changes and windstorm swells. Asexual reproduction may be a mechanism used by C. caespitosa to counteract mortality events and recolonize devastated areas, and likely accounts for the occasional high levels of clonality and low levels of genetic diversity. Local adaptations such as these should therefore be considered in conservation and management strategies to maintain and preserve the gene pool of this endangered species.

     

The sea-skater Halobates (Heteroptera: Gerridae) – probable cause for extinction in the Mediterranean and potential for re-colonisation following climate change

Sea-skaters in the genus Halobates Eschscholtz 1822 include some of the most specialised water striders and are found in tropical and subtropical seas around the world. Even though species of Halobates occur in both the Atlantic Ocean and the Red Sea, no extant sea-skater has been reported from the Mediterranean Sea. A fossil, Halobates ruffoi Andersen et al., 1994, described from Middle–Upper Eocene (45 Ma) Italy indicates that sea skaters were present in this part of the world in the past. Other geological evidence points to dramatic changes in the Mediterranean Sea during the Tertiary and Quaternary that may have led to their later extinction. In this paper we review briefly the distribution, systematics, evolution and ecology of Halobates, and discuss the potential for the Mediterranean to be recolonised following expected environmental changes due to global warming.     

INDIGO – INtegrated Data Warehouse of MIcrobial GenOmes with Examples from the Red Sea Extremophiles

Background

The next generation sequencing technologies substantially increased the throughput of microbial genome sequencing. To functionally annotate newly sequenced microbial genomes, a variety of experimental and computational methods are used. Integration of information from different sources is a powerful approach to enhance such annotation. Functional analysis of microbial genomes, necessary for downstream experiments, crucially depends on this annotation but it is hampered by the current lack of suitable information integration and exploration systems for microbial genomes.

Results

We developed a data warehouse system (INDIGO) that enables the integration of annotations for exploration and analysis of newly sequenced microbial genomes. INDIGO offers an opportunity to construct complex queries and combine annotations from multiple sources starting from genomic sequence to protein domain, gene ontology and pathway levels. This data warehouse is aimed at being populated with information from genomes of pure cultures and uncultured single cells of Red Sea bacteria and Archaea. Currently, INDIGO contains information from Salinisphaera shabanensis, Haloplasma contractile, and Halorhabdus tiamatea - extremophiles isolated from deep-sea anoxic brine lakes of the Red Sea. We provide examples of utilizing the system to gain new insights into specific aspects on the unique lifestyle and adaptations of these organisms to extreme environments.

Conclusions

We developed a data warehouse system, INDIGO, which enables comprehensive integration of information from various resources to be used for annotation, exploration and analysis of microbial genomes. It will be regularly updated and extended with new genomes. It is aimed to serve as a resource dedicated to the Red Sea microbes. In addition, through INDIGO, we provide our Automatic Annotation of Microbial Genomes (AAMG) pipeline. The INDIGO web server is freely available at http://www.cbrc.kaust.edu.sa/indigo.     

The first record of anguine lizards (Anguimorpha,Anguidae) from the early Miocene locality Ulm – Westtangente in Germany

Abstract

The first fossil anguine material from the lower Miocene (MN 2) locality Ulm – Westtangente in Germany is described. The parietal and compound bone of the lower jaw can be attributed to Ophisaurus holeci, previously known only from younger age (MN 3–MN 7). Moreover, the parietal represents the largest parietal of this species. In other disarticulated material, such as frontal, maxilla, dentary and osteoderms, alpha taxonomy is not possible and these elements cannot be allocated at the species level. Despite a limited data source, a phylogenetic analysis was done (16 taxa, 36 characters) producing four equally parsimonious trees. The analysis shows a close relationship of O. holeci and the Eocene Ophisauriscus quadrupes. These two taxa form a monophyletic clade, a sister-clade to Ophisaurus + Anguis. However, more complete skeletal material of O. holeci is needed to support such a statement. We used our phylogenetic analysis to analyze trace character history for one frontal and three parietal characters. The palaeoenvironmental conditions of the locality Ulm – Westtangente bring further support of the previous hypothesis that O. holeci was adapted to environments with high ground water levels – environments around lakes or rivers.     

Creation and maintenance of habitat downstream from a weir for the greenside darter, Etheostoma blennioides – a rare fish in Canada

The biology, microhabitat use and migratory behaviour of the greenside darter, Etheostoma blennioides, was studied at the Mannheim Weir on the Grand River, Ontario during the summer of 1995 and 1996. Officially listed as vulnerable in Canada, greenside darters reached maturity at age 1 and lived up to 4 years. They were found in riffle habitats that consisted of cobble and loose boulders, with large mats of Cladophora. This type of unembedded substrate is uncommon in the Grand River watershed. However, local abundance of greenside darters immediately downstream from the Mannheim Weir was likely due to high water velocities from weir discharge, freshets and ice scour which help maintain unembedded riffle areas. Trap data indicated that greenside darters temporally partition this habitat with the stonecat, Noturus flavus. Other darter species were not commonly found in areas with greenside darters, whose depth selection and habitat choices were influenced by predators and morphology. Denil fishways at the Mannheim Weir rarely passed greenside darters due to prohibitively high water velocities and exclusion by larger fish. This revised version was published online in August 2006 with corrections to the Cover Date.     

The development of policy approaches for reducing nitro-gen pollution to coastal waters of the USA

Two-thirds of the coastal rivers and bays in the United States are degraded from nutrient pollution, and nitrogen inputs these waters continue to increase. The nitrogen comes from a variety of sources, including runoff from agricultural fields, concentrated animal feeding operations, atmospheric deposition from fossil fuel combustion, and sewage and septic wastes. Technical solutions for nitrogen pollution exist at reasonable cost. That most of these solutions have not yet been implemented to any significant extent across the United States suggests that new policy approaches are necessary. The best solution may involve a combination of voluntary and mandatory approaches, applying different approaches to different sources of nitrogen pollution. A watershed-based approach that relies heavily on voluntary mechanisms (such as crop-yield insurance to reduce over-fertilization) is likely to be the most effective for some sources of nitrogen (such as runoff from agricultural fields), while a uniform national regulatory approach may be better for others (such as NOx emissions from fossil fuel combustion). Implementation of management strategies should be carefully coupled to monitoring programs to assess the effectiveness of these strategies. While both nitrogen and phosphorus are important to control, the focus should be on nitrogen management, in part because nitrogen is more generally the causal agent of coastal eutrophication. Also, while nitrogen-control practices tend to also reduce phosphorus pollution, phosphorus-control practices often have little effect on nitrogen. Although current scientific and technical knowledge is sufficient to begin to make substantial progress toward solving coastal nitrogen pollution, progress will be made more quickly and more cost effectively with increased investment in appropriate scientific research.     

The first pollen diagram from the Hoher Fläming, Brandenburg (Germany)

A 72 cm peat core from a spring mire reveals 3300 years of vegetation history in the Hoher Fläming, a landscape formed by the penultimate glaciation in southeastern Brandenburg. Primeval beech-oak forest dominated from a.d. 550 to 1200, prior to local forest clearance. Existing maps showing the natural and potential natural vegetation as pine and oak need to be revised. Local woodland cutting in the 12th century and grassland use since the 15th century affected the development of the helokrene (spring-fed) mire deposits from alder carr to mesotrophic fen vegetation and then to the present-day Sphagnum fallax-Juncus acutiflorus wet meadows. Vegetation and mire history link together the Hoher Fläming and adjacent landscapes on a northwest-southeast gradient of suboceanic to subcontinental climate. Moreover it represents a geographical and altitudinal transition of lowland and hill vegetation from 30 to 200 m a.s.l. to the montane belts of the palynologically well investigated Harz mountains. However, regarding some trees and herbs, the Hoher Fläming does not belong to the Hercynian region and type of vegetation.     

Decreased Silica Land–sea Fluxes through Damming in the Baltic Sea Catchment – Significance of Particle Trapping and Hydrological Alterations

We tested the hypothesis that reservoirs with low water residence time and autochthonous production influence river biogeochemistry in eutrophied river systems draining cultivated watersheds. The effect of a single artificial water reservoir and consecutive reservoirs on silica (Si) river fluxes is exemplified by the moderately dammed Vistula River and the heavily regulated Daugava River that are compared with the practically undammed Oder River. The sum of the discharge weighted annual mean biogenic silica (BSi) and dissolved silicate (DSi) concentrations in the rivers Oder, Vistula and Daugava were about 160 μ M (40 + 120 μ M), 150 μ M (20 + 130 μ M) and 88 μ M (6 + 82 μ M), respectively. Assuming BSi and DSi concentrations as observed in the Oder River as typical for eutrophied but undammed rivers, complete trapping of this BSi could have lowered Si fluxes to the Baltic Sea from rivers with cultivated watersheds by 25%. The superimposed effect of hydrological alterations on reduced Si land–sea fluxes is demonstrated by studies in the boreal/subarctic and oligotrophic rivers Kalixälven and Lueälven. The DSi yield of the heavily dammed Luleälven (793 kg km^?2 yr^?1) constituted only 63% of that was found in the unregulated Kalixälven (1261 kg km^?2 yr^?1), despite the specific runoff of the Luleälven (672 mm m^?2 yr^?1) being 19% higher than that of theKalixälven (563 mm m^?2 yr^?1); runoff normalized DSi yield of the former, regulated watershed, was only half the DSi yield of the latter, unperturbed watershed. Based on these findings, it is hypothesized here that perturbed surface water–groundwater interactions are the major reasons for the reduced annual fluctuations in DSi concentrations as also seen in the heavily dammed and eutrophic river systems such as the Daugava and Danube.     

The Elimination of Lymphatic Filariasis: A Strategy for Poverty Alleviation and Sustainable Development – Perspectives from the Philippines

BACKGROUND: Hygiene and skin care are effective and important interventions in the management of lymphoedema secondary to lymphatic filariasis. We analyzed the impact on the quality of life that education and introduction of a designated nurse had on lymphoedema patients in a community that was endemic for lymphatic filariasis. METHODS: Patients' life quality was assessed using a Dermatology Life Quality Index (DLQI) questionnaire. At the same time they received education on appropriate hygiene, skin care techniques and simple exercises that encourage lymph drainage. A designated nurse was provided with educational materials and treatments. The DLQI life quality measure was repeated one year later. RESULTS: The DLQI improved for all patients and reported acute attacks were reduced. A paired t-test showed the improvement in DLQI to be highly significant (P = < 0.0001). CONCLUSIONS: A nurse-led service combined with patient education in communities endemic for lymphatic filariasis is an effective intervention in improving the quality of life of patients with lymphoedema.