Environmental modulation of the proteomic profiles from closely phylogenetically related populations of the red seaweed Plocamium brasiliense
The genus Plocamium encompasses seaweeds that are widely distributed throughout the world’s oceans, with Plocamium brasiliense found along the tropical and subtropical coasts of the Western Atlantic. This wide distribution can lead to structured populations due to environmental differences (e.g., light levels or temperature), restricted gene flow, and the presence of cryptic species. Abiotic variation can also affect gene expression, which consequently leads to differences in the seaweeds protein profile. This study aimed to analyze the genetic and proteomic profiles of P. brasiliense sampled in two geographically distinct sites on the coastline of Rio de Janeiro state, Brazil: Arraial do Cabo (P1) and Búzios (P2). The genetic profiles of macroalgal specimens from these two sites were indistinguishable as assessed by the markers UPA/23S, rbcL, and COI-5P; however, the protein profiles varied significantly between populations from the two sites. At both sites the ribulose-1,5-biphosphate carboxylase/oxygenase was the most abundant protein found in P. brasiliense specimens. The number of phycobiliproteins differed between both sites with the highest numbers being found at P1, possibly due to water depth. The differences in proteomic profiles of the two nearly identical populations of P. brasiliense suggest that environmental parameters such as light availability and desiccation might induce distinct protein expression, probably as a result of the phenotypic plasticity within this population of seaweed.
Calegario et al. (2019) Environmental modulation of the proteomic profiles from closely phylogenetically related populations of the red seaweed Plocamium brasiliense. PeerJ 7:e6469 https://doi.org/10.7717/peerj.6469
Reproductive biology of little tunny Euthynnus alletteratus (Rafinesque, 1810) in the southwest Gulf of Mexico
The aim of this study was to describe the reproductive dynamic of Euthynnus alletteratus in the southwest Gulf of Mexico. The annual variation of the volume fraction occupied by gametes and tissues in gonads were related with main body indexes, such as the gonadosomatic index (IG), the hepatosomatic index (IH), and the nutrition index (IN), and compared with the sea surface temperature. A total of 951 E. alletteratus individuals were sampled, where a sex ratio of 1:1 and a size interval strongly skewed towards organisms with a fork length (LF) of 36–40 cm were observed. The IG showed an increase from March to September with maximum values in April and July. Two clearly defined peaks were observed, and they were consistent with the histological analysis, where the percentage of ripe gametes predominated from April to September. The optimum thermal window for reproductive activity was from 24 to 28 °C. The size of first sex maturity was 34.35 cm of LF for males and 34.60 (LF) for females, without significant difference between sexes.
Cruz-Castán et al. (2019) Reproductive biology of little tunny Euthynnus alletteratus (Rafinesque, 1810) in the southwest Gulf of Mexico. PeerJ 7:e6558 https://doi.org/10.7717/peerj.6558
Comparison of shallow-water seston among biogenic habitats on tidal flats
Aquatic structure-formers have the potential to establish mosaics of seston in shallow water if they modify the relative amounts of deposition (or filtration) and resuspension of particles. By sampling surface water adjacent to Lagrangian drifters traveling 0.1 to 2 m above the bottom, we tested the modification of seston in water masses flowing over two biogenic marine species (native eelgrass, Zostera marina; introduced oysters, Crassostrea gigas) in comparison to unstructured tidal flats. Water properties were examined at five intertidal sites in Washington State, USA, each with 27 drifts (three drifts at different stages of the tidal cycle in each of three patches of three habitat types; drift distance 116 m (109SD), duration 24 min (15SD)). At the initiation of each drift, habitat differences in water properties were already apparent: chlorophyll-a and total suspended solid (TSS) concentrations were greater in structured habitats than bare, and TSS was also inversely related to water depth. Water flowed more slowly across eelgrass than other habitat types. As water flowed across each habitat type, TSS generally increased, especially in shallow water, but without habitat differences; chlorophyll-a in these surface-water samples showed no consistent change during drifts. At higher TSS concentrations, quality in terms of organic content declined, and this relationship was not habitat-specific. However, quality in terms of chlorophyll-a concentration increased with TSS, as well as being greater in water over eelgrass than over other habitat types. These results support widespread mobilization of seston in shallow water ebbing or flooding across Washington State’s tidal flats, especially as water passes into patches of biogenic species.
Ruesink et al. (2019) Comparison of shallow-water seston among biogenic habitats on tidal flats. PeerJ 7:e6616 https://doi.org/10.7717/peerj.6616
Prevalence of malocclusion and occlusal traits in the early mixed dentition in Shanghai, China
Background Epidemiological data on malocclusion among Chinese children are scant. The aim of this study was to provide detailed information on the prevalence of malocclusion in early mixed dentition children in Shanghai, China. Methods A cross-sectional survey was conducted from September 2016 to April 2017, and 2,810 children aged 7- to 9- years were selected from 10 primary schools by cluster random sampling. Several occlusal parameters, including Angle molar relationship, overjet, overbite, open bite, anterior and posterior crossbite, midline displacement, scissors bite, and teeth crowding and spacing, were clinically registered by five calibrated orthodontic dentists. Results We found that 79.4% children presented one or more occlusal anomalies. Angle Class I, Class II and Class III molar relationship were recorded in 42.3%, 50.9% and 5.9% of the sample, respectively. The proportion of Class III increased from 5.0% at age 7 to 7.8% at age 9. In the sagittal plane, increased overjet >3 mm was observed in 40.8% subjects, while the prevalence of severe overjet (>8 mm), anterior edge-to-edge (zero overjet) and anterior crossbite were 5.2%, 8.1% and 10.5%, respectively. Vertically, deep overbite >2/3 overlap was found in 6.2% of the children and open bite in 4.3%. Boys exhibited a higher rate of overbite than girls. For the transversal occlusal anomalies, 36.1% of the children had a midline displacement, which was followed by posterior crossbite (2.6%) and scissors bite (1.0%). Teeth space discrepancies were also common anomalies and anterior crowding (>2 mm) affecting 28.4% of the children, while anterior spacing (>4 mm) affecting 9.5%. Girls showed a higher prevalence of anterior crowding and a lower frequency of teeth spacing than boys. Conclusions Our study demonstrated that malocclusion is prevalent among children in the early mixed dentition, and more health resources should be warranted to meet the challenge of prevention or early intervention of malocclusion.
Yu et al. (2019) Prevalence of malocclusion and occlusal traits in the early mixed dentition in Shanghai, China. PeerJ 7:e6630 https://doi.org/10.7717/peerj.6630
On the half-life of thiocyanate in the plasma of the marine fish Amphiprion ocellaris: implications for cyanide detection
The illegal practice of using cyanide (CN) as a stunning agent to collect fish for both the marine aquarium and live fish food trades has been used throughout the Indo-Pacific for over 50 years. CN fishing is destructive to all life forms within the coral reef ecosystems where it is used and is certainly one of many anthropogenic activities that have led to 95% of the reefs in the Indo-Pacific being labeled at risk for degradation and loss. A field-deployable test for detecting fish caught using CN would assist in combating the use of this destructive practice, however, no reliable and robust test exists. Further, there is little toxicokinetic data available on marine fish to support the development of such a test, yet such data is critical to establishing the concentration range and time scale over which such a test would be viable. This study presents the first direct measurement of the half-life of the metabolite thiocyanate (SCN) after pulsed exposure to CN in a marine fish. SCN was measured in the plasma of Amphiprion ocellaris after exposure to 50 ppm CN for three exposure times (20, 45, and 60 s) using HPLC-UV and a C30 column pre-treated with polyethylene glycol. Plasma SCN levels observed are dose-dependent, reflecting a longer time for conversion of CN to SCN as the dose of CN increases. SCN plasma levels reached a maximum concentration (1.2–2.3 ppm) 12–20 h after exposure to CN. The half-life for the elimination of SCN was 1.01 ± 0.26 days for 45 s exposure and 0.44 ± 0.15 days for 20 s exposure. Fish were also directly exposed to SCN (100 ppm for 11 days) and the observed half-life for SCN elimination was 0.35 ± 0.07 days. Plasma SCN levels did not return to control levels, even after 41 days when exposed to CN but did return to control levels after 48 days when exposed to SCN. The similar half-lives observed for CN and SCN exposure suggests that SCN exposure can be used as a proxy for measuring the rate of SCN elimination following CN exposure. In order for plasma SCN to be used as a marker for CN exposure, these results must be extended to other species and endogenous levels of SCN in wild caught fish must be established.
Breen et al. (2019) On the half-life of thiocyanate in the plasma of the marine fish Amphiprion ocellaris: implications for cyanide detection. PeerJ 7:e6644 https://doi.org/10.7717/peerj.6644
Revision of the Late Jurassic deep-water teleosauroid crocodylomorph Teleosaurus megarhinus Hulke, 1871 and evidence of pelagic adaptations in Teleosauroidea
Teleosauroids were a successful group of semi-aquatic crocodylomorphs that were an integral part of coastal marine/lagoonal faunas during the Jurassic. Their fossil record suggests that the group declined in diversity and abundance in deep water deposits during the Late Jurassic. One of the few known teleosauroid species from the deeper water horizons of the well-known Kimmeridge Clay Formation is ‘Teleosaurus’ megarhinus Hulke, 1871, a poorly studied, gracile longirostrine form. The holotype is an incomplete snout from the Aulacostephanus autissiodorensis Sub-Boreal ammonite Zone of Kimmeridge, England. The only other referred specimen is an almost complete skull from the slightly older A. eudoxus Sub-Boreal ammonite Zone of Quercy, France. Recently, the validity of this species has been called into question. Here we re-describe the holotype as well as the referred French specimen and another incomplete teleosauroid, DORCM G.05067i-v (an anterior rostrum with three osteoderms and an isolated tooth crown), from the same horizon and locality as the holotype. We demonstrate that all specimens are referable to ‘Teleosaurus’ megarhinus and that the species is indeed a valid taxon, which we assign to a new monotypic genus, Bathysuchus. In our phylogenetic analysis, the latest iteration of the ongoing Crocodylomorph SuperMatrix Project, Bathysuchus megarhinus is found as sister taxon to Aeolodon priscus within a subclade containing Mycterosuchus nasutus and Teleosaurus cadomensis. Notably Bathysuchus has an extreme reduction in dermatocranial ornamentation and osteoderm size, thickness and ornamentation. These features are mirrored in Aeolodon priscus, a species with a well-preserved post-cranial skeleton and a similar shallow and inconspicuous dermal ornamentation. Based on these morphological features, and sedimentological evidence, we hypothesise that the Bathysuchus + Aeolodon clade is the first known teleosauroid lineage that evolved a more pelagic lifestyle.
Foffa et al. (2019) Revision of the Late Jurassic deep-water teleosauroid crocodylomorph Teleosaurus megarhinus Hulke, 1871 and evidence of pelagic adaptations in Teleosauroidea. PeerJ 7:e6646 https://doi.org/10.7717/peerj.6646
Behavioral responses around conspecific corpses in adult eastern gorillas (Gorilla beringei spp.)
Humans were once considered unique in having a concept of death but a growing number of observations of animal responses to dying and dead conspecifics suggests otherwise. Complex arrays of behaviors have been described ranging from corpse removal and burial among social insects to quiet attendance and caregiving among elephants and primates. Less frequently described, however, are behavioral responses of individuals from different age/sex classes or social position toward the death of conspecifics. We describe behavioral responses of mountain gorillas (Gorilla beringei beringei) to the deaths of a dominant silverback and a dominant adult female from the same social group in Volcanoes National Park in Rwanda and the responses of Grauer’s gorillas (Gorilla b. graueri) to the corpse of an extra-group silverback in Kahuzi-Biega National Park, Democratic Republic of Congo. In gorillas, interactions between groups or with a lone silverback often result in avoidance or aggression. We predicted that: (i) more individuals should interact with the corpses of same-group members than with the corpse of the extra-group silverback; (ii) adult females with infants should avoid the corpse of the extra-group silverback; and (iii) in the mountain gorilla cases, individuals that shared close social relationships with the dead individual should spend more time with the corpse than other individuals in the group. We used a combination of detailed qualitative reports, photos, and videos to describe all occurrences of affiliative/investigative and agonistic behaviors observed at the corpses. We observed similar responses toward the corpses of group and extra-group individuals. Animals in all three cases showed a variety of affiliative/investigative and agonistic behaviors directed to the corpses. Animals of all age/sex classes interacted with the corpses in affiliative/investigative ways but there was a notable absence of all adult females at the corpse of the extra-group silverback. In all three cases, we observed only silverbacks and blackbacks being agonistic around and/or toward the corpses. In the mountain gorilla cases, the individuals who spent the most time with the corpses were animals who shared close social relationships with the deceased. We emphasize the similarity in the behavioral responses around the corpses of group and extra-group individuals, and suggest that the behavioral responses were influenced in part by close social relationships between the deceased and certain group members and by a general curiosity about death. We further discuss the implications close interactions with corpses have for disease transmission within and between gorilla social groups.
Porter et al. (2019) Behavioral responses around conspecific corpses in adult eastern gorillas (Gorilla beringei spp.). PeerJ 7:e6655 https://doi.org/10.7717/peerj.6655
Mapping-by-sequencing using NGS-based 3′-MACE-Seq reveals a new mutant allele of the essential nodulation gene Sym33 (IPD3) in pea (Pisum sativum L.)
Large collections of pea symbiotic mutants were accumulated in the 1990s, but the causal genes for a large portion of the mutations are still not identified due to the complexity of the task. We applied a Mapping-by-Sequencing approach including Bulk Segregant Analysis and Massive Analysis of cDNA Ends (MACE-Seq) sequencing technology for genetic mapping the Sym11 gene of pea which controls the formation of symbioses with both nodule bacteria and arbuscular-mycorrhizal fungi. For mapping we developed an F2-population from the cross between pea line N24 carrying the mutant allele of sym11 and the wild type NGB1238 (=JI0073) line. Sequencing libraries were prepared from bulks of 20 plants with mutant and 12 with wild-type phenotype. MACE-Seq differential gene expression analysis between mutant-phenotype and wild-type-phenotype bulks revealed 2,235 genes, of which 514 (23%) were up-regulated and 1,721 (77%) were down-regulated in plant roots inoculated with rhizobia as a consequence of sym11 mutation. MACE-Seq also detected single nucleotide variants between bulks in 217 pea genes. Using a novel mathematical model we calculated the recombination frequency (RF) between the Sym11 gene and these 217 polymorphic genes. Six genes with the lowest RF were converted into CAPS or dCAPS markers and genetically mapped on the complete mapping population of 108 F2-plants which confirmed their tight linkage to Sym11 and to each other. The Medicago truncatula Gaertn. (Mt) homologs of these genes are located in a distinct region of Mt chromosome 5, which corresponds to linkage group I of pea. Among 94 candidate genes from this region only one was down-regulated—the pea Sym33 homolog of the Mt IPD3 gene which is essential for nodulation. Sequencing of the Sym33 allele of the N24 (sym11) mutant revealed a single nucleotide deletion (c.C319del) in its third exon resulting in a codon shift in the open reading frame and premature translation termination. Thus, we identified a novel mutant allele sym33-4 most probably responsible for the mutant phenotype of the N24 (sym11) line, thereby demonstrating that mapping by MACE-Seq can be successfully used for genetic mapping of mutations and identification of candidate genes in pea.
Zhernakov et al. (2019) Mapping-by-sequencing using NGS-based 3′-MACE-Seq reveals a new mutant allele of the essential nodulation gene Sym33 (IPD3) in pea (Pisum sativum L.). PeerJ 7:e6662 https://doi.org/10.7717/peerj.6662
Spatial variation in allometric growth of invasive lionfish has management implications
Lionfish (Pterois volitans/miles) are an invasive species in the Western Atlantic and the Caribbean. Improving management of invasive lionfish populations requires accurate total biomass estimates, which depend on accurate estimates of allometric growth; sedentary species like lionfish often exhibit high levels of spatial variation in life history characteristics. We reviewed 17 published length-weight relationships for lionfish taken throughout their invasive range and found regional differences that led to significant misestimates when calculating weight from length observations. The spatial pattern we observed is consistent with findings from other studies focused on genetics or length-at-age. Here, the use of ex situ parameter values resulted in total biomass estimates between 76.2% and 140% of true observed biomass, and up to a threefold under- or overestimation of total weight for an individual organism. These findings can have implications for management in terms of predicting effects on local ecosystems, evaluating the effectiveness of removal programs, or estimating biomass available for harvest.
Villaseñor-Derbez et al. (2019) Spatial variation in allometric growth of invasive lionfish has management implications. PeerJ 7:e6667 https://doi.org/10.7717/peerj.6667
Epizootic ulcerative syndrome causes cutaneous dysbacteriosis in hybrid snakehead (Channa maculata♀ × Channa argus♂)
Cutaneous microbiota play an important role in protecting fish against pathogens. Aphanomyces infection causes epizootic ulcerative syndrome (EUS) in fish, and by perturbing the integrity of the cutaneous microbiota, increases the potential for infection by pathogenic bacteria. However, whether the composition of the cutaneous microbiota is altered in fish with EUS, and if so, which species are changed and how this might influence infected fish, is still largely unclear. Considering the importance of cutaneous microbiota in maintaining host health, we hypothesized that Aphanomyces infection significantly enhances the presence of certain bacterial pathogens in the cutaneous microbiota and causes cutaneous dysbacteriosis. To test this hypothesis, we compared the cutaneous microbiota compositions of hybrid snakehead (Channa maculata♀ × Channa argus♂) with and without Aphanomyces infection using Illumina Miseq sequencing of the 16S rRNA gene. Our results showed that the cutaneous microbiota of hybrid snakehead were significantly altered subsequent to EUS infection and that the numbers of potentially pathogenic bacteria classified into the genera Anaerosinus, Anaerovorax, Dorea, and Clostridium were significantly enhanced in the cutaneous microbiota of hybrid snakehead with EUS, whereas bacteria classified into the genera Arthrobacter, Dysgonomonas, Anoxybacillus, Bacillus, Solibacillus, Carnobacterium, Lactococcus, Streptococcus, Achromobacter, Polynucleobacter, Vogesella, and Pseudomonas were significantly reduced. These results imply that treatment for EUS should not only take into consideration the control of Aphanomyces reproduction but should also focus on regulating the cutaneous microbiota of infected fish.
Li et al. (2019) Epizootic ulcerative syndrome causes cutaneous dysbacteriosis in hybrid snakehead (Channa maculata♀ × Channa argus♂). PeerJ 7:e6674 https://doi.org/10.7717/peerj.6674