A coral colony is composed of physiologically integrated polyps. In stony corals, coloniality adopts a wide diversity of forms and involves complex ontogenetic dynamics. However, molecular mechanisms ...underlying coloniality have been little studied. To understand the genetic basis of coloniality and its contribution to coral ecology, we induced polyp bail-out in a colonial coral, Pocillopora acuta, and compared transcription profiles of bailed-out polyps and polyps in normal colonies, and their responses to heat shock and hyposalinity. Consistent with morphological formation of a gastrovascular system and its neural transmission and molecular transport functions, we found genetic activation of neurogenesis and development of tube-like structures in normal colonies that is absent in bailed-out polyps. Moreover, relative to bailed-out polyps, colonies showed significant overexpression of genes for angiotensin-converting enzymes and endothelin-converting enzymes. In response to hyperthermal and hyposaline treatments, a high proportion of genetic regulation proved specific to either bailed-out polyps or colonies. Elevated temperatures even activated NF-κB signaling in colonies. On the other hand, colonies showed no discernible advantage over bailed-out polyps in regard to hyposalinity. The present study provides a first look at the genetic basis of coloniality and documents different responses to environmental stimuli in P. acuta colonies versus those in bailed-out polyps. Overexpression of angiotensin-converting enzymes and endothelin-converting enzymes in colonies suggests possible involvement of these genes in development of the gastrovascular system in P. acuta. Functional characterization of these coral genes and further investigation of other forms of the transition to coloniality in stony corals should be fruitful areas for future research.
A massive coral bleaching event occurred in 2016 in the interior of Japan's largest coral lagoon, the Sekisei Lagoon, located in the Kuroshio upstream region in southwestern Japan. Recovery of the ...coral lagoon will require the influx of coral spawn and larvae; therefore, it is important to identify and conserve source sites. A surface-particle-tracking simulation of coral spawn and larvae was used to identify source areas of coral spawn outside of the Sekisei Lagoon for potential recovery of the interior lagoon. The northern coastal zone of Iriomote Island, including Hatoma Island, was identified as a major source area. Hatoma Island was also identified as a key source for the Kuroshio downstream region and for aiding the poleward migration of coral habitat under ongoing global climate change, making it one of the most important source areas in the Nansei Archipelago.
Feeding by zooplanktivorous fish depends on their foraging movements and the flux of prey to which they are exposed. While prey flux is a linear function of zooplankton density and flow speed, those ...two factors are expected to contribute differently to fish movements. Our objective was to determine the effects of these factors for garden eels, stationary fish that feed while anchored to the sandy bottom by keeping the posterior parts of their bodies inside a burrow. Using a custom-made flume with a sandy bottom, we quantified the effects of prey density and flow speed on feeding rates by spotted garden eels (Heteroconger hassi). Feeding rates increased linearly with prey density. However, feeding rates did not show a linear relationship with flow speed and decreased at 0.25 m s-1. Using label-free tracking of body points and 3D movement analysis, we found that the reduction in feeding rates was related to modulation of the eel's movements, whereby the expected increase in energy expenditure was avoided by reducing exposure and drag. No effects of flow speed on strike speed, reactive distance or vectorial dynamic body acceleration (VeDBA) were found. A foraging model based on the body length extended from the burrow showed correspondence with observations. These findings suggest that as a result of their unique foraging mode, garden eels can occupy self-made burrows in exposed shelter-free sandy bottoms where they can effectively feed on drifting zooplankton.
Polyp bail-out is a stress response exhibited by some pocilloporid corals, with mechanisms and consequences distinct from those of bleaching. Although induction of polyp bail-out has been ...demonstrated in the laboratory, molecular mechanisms underlying this response have rarely been discussed. We conducted genetic analyses of
Pocillopora acuta
during initiation of hyperosmosis-induced polyp bail-out, using both transcriptomic and qPCR techniques. Beyond upregulation of apoptosis and proteolysis, corals showed significant activation of tumor necrosis factor and fibroblast growth factor (FGF) signaling pathways during induction of polyp bail-out. In our qPCR analysis, a common upregulation profile, peaking at 43.0‰ salinity, was found in the FAS and CASP8 genes, whereas a different profile, showing significant upregulation up to 45.0‰, was displayed by matrix metalloproteinases and genes in the FGF signaling pathway. These results suggest parallel involvement of an extrinsic apoptotic signaling pathway and FGF-mediated extracellular matrix degradation in polyp bail-out. Furthermore, in the XIAP, JNK, and NFKB1 genes, we detected a third expression profile showing linear upregulation that becomes maximal at the endpoint salinity level of the experiment (46.0‰), indicating activation of anti-apoptotic and cell survival signals during polyp bail-out. Our results provide new insights into signaling pathways responsible for polyp bail-out and suggest the feasibility of inducing bail-out by specifically triggering these pathways without exerting lethal stresses on the corals, which in turn will facilitate acquisition of viable polyps for possible use in coral reef restoration.
The epidemiology of nontuberculous mycobacterial pulmonary disease (NTM-PD) remains unclear in the majority of countries, including Japan.
To estimate the nationwide incidence and prevalence of ...NTM-PD in Japan and to describe case characteristics and geographical variation.
In this cross-sectional study, we analyzed data from all health insurance claims made for NTM-PD collected from the National Database in Japan between 2009 and 2014. A patient with NTM-PD was identified on the basis of at least one claim submitted with International Classification of Diseases Version 10 codes associated with NTM-PD and at least one claim for combinations of antimycobacterial medications. We calculated the incidence and prevalence rates for 2011 by sex, age group, and geographical region and evaluated comorbidities.
The numbers of incident and prevalent NTM-PD cases in 2011 were 11,034 (8.6 per 100,000 person-years; 95% confidence interval CI, 8.5-8.8) and 37,063 (29.0 per 100,000 persons; 95% CI, 28.7-29.3), respectively. Among incident cases, the mean ± standard deviation age was 69.3 ± 12.3 years, and 69.6% were women. The incidence rate sharply increased after 50 years of age in both sexes and was higher among women in all age groups, except for those aged 80 years and above. Among men, the incidence rate was highest among older adults, with a sharp increase in comorbidities with age. The most prevalent comorbidities were bronchiectasis for women and chronic obstructive pulmonary disease for men. Most southwestern regions showed high incidence rates, except for Okinawa, which is the southernmost island in Japan.
Our results revealed that the incidence and prevalence rates of NTM-PD were among the highest worldwide, despite the conservative treatment-based case definition of NTM-PD used in this study. Prolonged disease duration accompanied by comorbidities probably affected this high prevalence rate. Older adults and women had an especially high risk of NTM-PD, but older men with comorbidities also require more attention. Further studies are required to investigate the factors underlying this geographical variation.
While interactions between regular wave driven flooding and reefs have been widely studied due to climate change pressure, the effects of reefs on tsunami flooding have less been investigated. From ...studies of historical events, reefs can behave as buffers or as amplifiers of inundation, depending upon the location. Interactions between reefs and tsunamis have generally been analyzed with idealized models, and there have been only few studies of specific reefs and their characteristics. Using numerical NonLinear Shallow Water models, this study characterizes the influence of the Southeast Ishigaki Island reef during the 1771 tsunami that hit the Yaeyama Islands. In this work, we modified reef topography in silico and then, measured the impact of these changes using a new parameter, the Reef Impact Factor (RIF). First, a reference model was built, simulating the real event with an accurate reef representation and using run-up data to calibrate bottom friction. This calibration highlights the difficulty of representing reef friction with a homogeneous coefficient. Second, a model without a reef was compared to the reference model. The impact of reef removal varies considerably along the coastline and maximum wave heights at the shore were strongly affected, with a 12.5% increase on average. Overall, this suggests a protective role of the reef along most of the coast. However, at local scale, channels that break the continuity of the front reef, increased wave heights by up to 40% on the proximate coast, revealing their strong focusing influence. Finally, changes in tide level, which regulates reef depth, were investigated, showing a global positive correlation between sea level and maximum wave height at the coast. However, the impact of the reef depth appeared weak compared to the impact of incident wave parameters. This study contributes to a global effort to understand tsunami-reef interactions in a non-idealized framework, suggesting a Reef Impact Factor for inter-reef/study comparisons. Moreover, vulnerable and exposed coasts were identified at Ishigaki Island, which may help to improve inundation forecasting, resulting in more appropriate management of these vulnerable sections of the coast.
•A numerical study of the impact of the reef during the 1771 extreme tsunami event at Ishigaki Island (Japan) is presented.•Nonlinear Shallow Water models are build for this study of this event.•A new parameter quantifying the amplification or dumping of the tsunami inundation depending of the reef parameters is defined.•While globally the reef acted as a buffer, locally channels were shown to be more dangerous than the absence of reef.
Abstract Phaeocystis is a cosmopolitan, bloom-forming phytoplankton genus that contributes significantly to global carbon and sulfur cycles. During blooms, Phaeocystis species produce large ...carbon-rich colonies, creating a unique interface for bacterial interactions. While bacteria are known to interact with phytoplankton—e.g., they promote growth by producing phytohormones and vitamins—such interactions have not been shown for Phaeocystis. Therefore, we investigated the composition and function of P. globosa microbiomes. Specifically, we tested whether microbiome compositions are consistent across individual colonies from four P. globosa strains, whether similar microbiomes are re-recruited after antibiotic treatment, and how microbiomes affect P. globosa growth under limiting conditions. Results illuminated a core colonial P. globosa microbiome—including bacteria from the orders Alteromonadales, Burkholderiales, and Rhizobiales—that was re-recruited after microbiome disruption. Consistent microbiome composition and recruitment is indicative that P. globosa microbiomes are stable-state systems undergoing deterministic community assembly and suggests there are specific, beneficial interactions between Phaeocystis and bacteria. Growth experiments with axenic and nonaxenic cultures demonstrated that microbiomes allowed continued growth when B-vitamins were withheld, but that microbiomes accelerated culture collapse when nitrogen was withheld. In sum, this study reveals symbiotic and opportunistic interactions between Phaeocystis colonies and microbiome bacteria that could influence large-scale phytoplankton bloom dynamics and biogeochemical cycles.
Phaeocystis globosa forms dense, monospecific blooms in temperate, northern waters. Blooms are usually dominated by the colonial morphotype—nonflagellated cells embedded in a secreted mucilaginous ...mass. Colonial Phaeocystis blooms significantly affect food‐web structure and function and negatively impact fisheries and aquaculture, but factors regulating colony formation remain enigmatic. Destructive P. globosa blooms have been reported in tropical and subtropical regions more recently and warm‐water blooms could become more common with continued climate change and coastal eutrophication. We therefore assessed genetic pathways associated with colony formation by investigating differential gene expression between colonial and solitary cells of a warm‐water P. globosa strain. Our results illustrate a transcriptional shift in colonial cells with most of the differentially expressed genes downregulated, supporting a reallocation of resources associated with forming and maintaining colonies. Dimethylsulfide and acrylate production and pathogen interaction pathways were upregulated in colonial cells, suggesting a defensive role for producing colonies. We identify several protein kinase signaling pathways that may influence the transition between morphotypes, providing targets for future research into factors affecting colony formation. This study provides novel insights into genetic mechanisms involved in Phaeocystis colony formation and provides new evidence supporting a defensive role for Phaeocystis colonies.
Whole-genome sequencing (WGS) with next-generation DNA sequencing (NGS) is an increasingly accessible and affordable method for genotyping hundreds of Mycobacterium tuberculosis (Mtb) isolates, ...leading to more effective epidemiological studies involving single nucleotide variations (SNVs) in core genomic sequences based on molecular evolution. We developed an all-in-one web-based tool for genotyping Mtb, referred to as the Total Genotyping Solution for TB (TGS-TB), to facilitate multiple genotyping platforms using NGS for spoligotyping and the detection of phylogenies with core genomic SNVs, IS6110 insertion sites, and 43 customized loci for variable number tandem repeat (VNTR) through a user-friendly, simple click interface. This methodology is implemented with a KvarQ script to predict MTBC lineages/sublineages and potential antimicrobial resistance. Seven Mtb isolates (JP01 to JP07) in this study showing the same VNTR profile were accurately discriminated through median-joining network analysis using SNVs unique to those isolates. An additional IS6110 insertion was detected in one of those isolates as supportive genetic information in addition to core genomic SNVs. The results of in silico analyses using TGS-TB are consistent with those obtained using conventional molecular genotyping methods, suggesting that NGS short reads could provide multiple genotypes to discriminate multiple strains of Mtb, although longer NGS reads (≥ 300-mer) will be required for full genotyping on the TGS-TB web site. Most available short reads (~100-mer) can be utilized to discriminate the isolates based on the core genome phylogeny. TGS-TB provides a more accurate and discriminative strain typing for clinical and epidemiological investigations; NGS strain typing offers a total genotyping solution for Mtb outbreak and surveillance. TGS-TB web site: https://gph.niid.go.jp/tgs-tb/.
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