Sex-specific covariance between metabolic rate, behaviour and morphology in the ground beetle Carabus hortensis
Background Individuals within the same species often differ in their metabolic rates, which may covary with behavioural traits (such as exploration), that are consistent across time and/or contexts, and morphological traits. Yet, despite the frequent occurrence of sexual dimorphisms in morphology and behaviour, few studies have assessed whether and how sexes differ in metabolic trait covariances. Methods We investigated sex-specific relationships among resting or active metabolic rate (RMR and AMR, respectively) with exploratory behaviour, measured independently of metabolic rate in a novel environment, body size and body mass, in Carabus hortensis ground beetles. Results RMR, AMR and exploratory behaviour were repeatable among individuals across time, except for male RMR which was unrepeatable. Female RMR neither correlated with exploratory behaviour nor body size/body mass. In contrast, AMR was correlated with both body size and exploratory behaviour. Males with larger body sizes had higher AMR, whereas females with larger body sizes had lower AMR. Both male and female AMR were significantly related to exploratory behaviour, though the relationships between AMR and exploration were body mass-dependent in males and temperature-dependent in females. Discussion Differences between sexes exist in the covariances between metabolic rate, body size and exploratory behaviour. This suggests that selection acts differently on males and females to produce these trait covariances with potentially important consequences for individual fitness.
Yarwood et al. (2021) Sex-specific covariance between metabolic rate, behaviour and morphology in the ground beetle Carabus hortensis. PeerJ 9:e12455 https://doi.org/10.7717/peerj.12455
Foreflipper and hindflipper muscle reconstructions of Cryptoclidus eurymerus in comparison to functional analogues: introduction of a myological mechanism for flipper twisting
Background Plesiosaurs, diapsid crown-group Sauropterygia, inhabited the oceans from the Late Triassic to the Late Cretaceous. Their most exceptional characteristic are four hydrofoil-like flippers. The question whether plesiosaurs employed their four flippers in underwater flight, rowing flight, or rowing has not been settled yet. Plesiosaur locomotory muscles have been reconstructed in the past, but neither the pelvic muscles nor the distal fore- and hindflipper musculature have been reconstructed entirely. Methods All plesiosaur locomotory muscles were reconstructed in order to find out whether it is possible to identify muscles that are necessary for underwater flight including those that enable flipper rotation and twisting. Flipper twisting has been proven by hydrodynamic studies to be necessary for efficient underwater flight. So, Cryptoclidus eurymerus fore- and hindflipper muscles and ligaments were reconstructed using the extant phylogenetic bracket (Testudines, Crocodylia, and Lepidosauria) and correlated with osteological features and checked for their functionality. Muscle functions were geometrically derived in relation to the glenoid and acetabulum position. Additionally, myology of functionally analogous Chelonioidea, Spheniscidae, Otariinae, and Cetacea is used to extract general myological adaptations of secondary aquatic tetrapods to inform the phylogenetically inferred muscle reconstructions. Results A total of 52 plesiosaur fore- and hindflipper muscles were reconstructed. Amongst these are flipper depressors, elevators, retractors, protractors, and rotators. These muscles enable a fore- and hindflipper downstroke and upstroke, the two sequences that represent an underwater flight flipper beat cycle. Additionally, other muscles were capable of twisting fore- and hindflippers along their length axis during down- and upstroke accordingly. A combination of these muscles that actively aid in flipper twisting and intermetacarpal/intermetatarsal and metacarpodigital/metatarsodigital ligament systems, that passively engage the successive digits, could have accomplished fore-and hindflipper length axis twisting in plesiosaurs that is essential for underwater flight. Furthermore, five muscles that could possibly actively adjust the flipper profiles for efficient underwater flight were found, too.
Krahl et al. (2021) Foreflipper and hindflipper muscle reconstructions of Cryptoclidus eurymerus in comparison to functional analogues: introduction of a myological mechanism for flipper twisting. PeerJ 9:e12537 https://doi.org/10.7717/peerj.12537
Marine soundscape and fish biophony of a Mediterranean marine protected area
Background Marine soundscape is the aggregation of sound sources known as geophony, biophony, and anthrophony. The soundscape analysis, in terms of collection and analysis of acoustic signals, has been proposed as a tool to evaluate the specific features of ecological assemblages and to estimate their acoustic variability over space and time. This study aimed to characterise the Capo Caccia-Isola Piana Marine Protected Area (Italy, Western Mediterranean Sea) soundscape over short temporal (few days) and spatial scales (few km) and to quantify the main anthropogenic and biological components, with a focus on fish biophonies. Methods Within the MPA, three sites were chosen each in a different protection zone (A for the integral protection, B as the partial protection, and C as the general protection). In each site, two underwater autonomous acoustic recorders were deployed in July 2020 at a depth of about 10 m on rocky bottoms. To characterise the contribution of both biophonies and anthrophonies, sea ambient noise (SAN) levels were measured as sound pressure level (SPL dB re: 1 μ Pa-rms) at eight 1/3 octave bands, centred from 125 Hz to 16 kHz, and biological and anthropogenic sounds were noted. Fish sounds were classified and counted following a catalogue of known fish sounds from the Mediterranean Sea based on the acoustic characteristic of sound types. A contemporary fish visual census had been carried out at the test sites. Results SPL were different by site, time (day vs. night), and hour. SPLs bands centred at 125, 250, and 500 Hz were significantly higher in the daytime, due to the high number of boats per minute whose noise dominated the soundscapes. The loudest man-made noise was found in the A zone, followed by the B and the C zone, confirming that MPA current regulations do not provide protection from acoustic pollution. The dominant biological components of the MPA soundscape were the impulsive sounds generated by some invertebrates, snapping shrimps and fish. The vast majority of fish sounds were recorded at the MPA site characterized by the highest sound richness, abundance, and Shannon-Wiener index, coherently with the results of a fish visual census. Moreover, the acoustic monitoring detected a sound associated with a cryptic species (Ophidion spp.) never reported in the study area before, further demonstrating the usefulness of passive acoustic monitoring as a complementary technique to species census. This study provides baseline data to detect future changes of the marine soundscapes and some suggestions to reduce the impact of noise on marine biodiversity.
La Manna et al. (2021) Marine soundscape and fish biophony of a Mediterranean marine protected area. PeerJ 9:e12551 https://doi.org/10.7717/peerj.12551
ANXA9 as a novel prognostic biomarker associated with immune infiltrates in gastric cancer
Background Gastric cancer (GC) is the most prevalent malignancy among the digestive system tumors. Increasing evidence has revealed that lower mRNA expression of ANXA9 is associated with a poor prognosis in colorectal cancer. However, the role of ANXA9 in GC remains largely unknown. Material and Methods The Gene Expression Profiling Interactive Analysis (GEPIA) and Human Protein Atlas databases were used to investigate the expression of ANXA9 in GC, which was then validated in the four Gene Expression Omnibus (GEO) datasets. The diagnostic value of ANXA9 for GC patients was demonstrated using a receiver operating characteristic (ROC) curve. The correlation between ANXA9 expression and clinicopathological parameters was analyzed in The Cancer Genome Atlas (TCGA) and UALCAN databases. The Kaplan-Meier (K-M) survival curve was used to elucidate the relationship between ANXA9 expression and the survival time of GC patients. We then performed a gene set enrichment analysis (GSEA) to explore the biological functions of ANXA9. The relationship of ANXA9 expression and cancer immune infiltrates was analyzed using the Tumor Immune Estimation Resource (TIMER). In addition, the potential mechanism of ANXA9 in GC was investigated by analyzing its related genes. Results ANXA9 was significantly up-regulated in GC tissues and showed obvious diagnostic value. The expression of ANXA9 was related to the age, gender, grade, TP53 mutation, and histological subtype of GC patients. We also found that ANXA9 expression was associated with immune-related biological function. ANXA9 expression was also correlated with the infiltration level of CD8+ T cells, neutrophils, and dendritic cells in GC. Additionally, copy number variation (VNV) of ANXA9 occurred in GC patients. Function enrichment analyses revealed that ANXA9 plays a role in the GC progression by interacting with its related genes. Conclusions Our results provide strong evidence of ANXA9 expression as a prognostic indicator related to immune responses in GC.
Zhang et al. (2021) ANXA9 as a novel prognostic biomarker associated with immune infiltrates in gastric cancer. PeerJ 9:e12605 https://doi.org/10.7717/peerj.12605
The cnidarian parasite Ceratonova shasta utilizes inherited and recruited venom-like compounds during infection
Background Cnidarians are the most ancient venomous organisms. They store a cocktail of venom proteins inside unique stinging organelles called nematocysts. When a cnidarian encounters chemical and physical cues from a potential threat or prey animal, the nematocyst is triggered and fires a harpoon-like tubule to penetrate and inject venom into the prey. Nematocysts are present in all Cnidaria, including the morphologically simple Myxozoa, which are a speciose group of microscopic, spore-forming, obligate parasites of fish and invertebrates. Rather than predation or defense, myxozoans use nematocysts for adhesion to hosts, but the involvement of venom in this process is poorly understood. Recent work shows some myxozoans have a reduced repertoire of venom-like compounds (VLCs) relative to free-living cnidarians, however the function of these proteins is not known. Methods We searched for VLCs in the nematocyst proteome and a time-series infection transcriptome of Ceratonova shasta, a myxozoan parasite of salmonid fish. We used four parallel approaches to detect VLCs: BLAST and HMMER searches to preexisting cnidarian venom datasets, the machine learning tool ToxClassifier, and structural modeling of nematocyst proteomes. Sequences that scored positive by at least three methods were considered VLCs. We then mapped their time-series expressions in the fish host and analyzed their phylogenetic relatedness to sequences from other venomous animals. Results We identified eight VLCs, all of which have closely related sequences in other myxozoan datasets, suggesting a conserved venom profile across Myxozoa, and an overall reduction in venom diversity relative to free-living cnidarians. Expression of the VLCs over the 3-week fish infection varied considerably: three sequences were most expressed at one day post-exposure in the fish’s gills; whereas expression of the other five VLCs peaked at 21 days post-exposure in the intestines, coinciding with the formation of mature parasite spores with nematocysts. Expression of VLC genes early in infection, prior to the development of nematocysts, suggests venoms in C. shasta have been repurposed to facilitate parasite invasion and proliferation within the host. Molecular phylogenetics suggested some VLCs were inherited from a cnidarian ancestor, whereas others were more closely related to sequences from venomous non-Cnidarian organisms and thus may have gained qualities of venom components via convergent evolution. The presence of VLCs and their differential expression during parasite infection enrich the concept of what functions a “venom” can have and represent targets for designing therapeutics against myxozoan infections.
Americus et al. (2021) The cnidarian parasite Ceratonova shasta utilizes inherited and recruited venom-like compounds during infection. PeerJ 9:e12606 https://doi.org/10.7717/peerj.12606
Morpho-physiological effects of environmental stress on yield and quality of sweet corn varieties (Zea mays L.)
Sweet corn is cultivated in different climatic regions of the world, and consumed either fresh or processed. Morpho-physiological effects of environmental stress on yield, yield components and quality of some sweet corn varieties were investigated in field experiments conducted at Southeastern Anatolia Region of Turkey during 2019 and 2020 growing seasons. The experimental lay out was randomized blocks with three replicates. Eight candidates and two control sweet corn varieties classified as moderate maturity (FAO 650–700) were used in field experiment. Mean values of pollen fertility rate (PFR, %), total soluble solids (TSS, °Brix), abscisic acid (ABA, nmol/g DW), ear length (EL, cm), plant height (PH, cm), number of grains per cob (CGN, grain) and fresh cob yield (FCY, t ha−1) were significantly different between years and sweet corn varieties. The PFR, TSS, ABA, EL, PH, CGN and FCY ranged from 40.29–67.65%, 13.24–20.09 °brix, 7.74–21.04 nmol/g DW, 9.69–15.98 cm, 97.80–171.34 cm, 289.15–420.33 grain and 4.15–10.23 t ha−1 respectively. The FCY, yield components and PFR values in the second year that had a higher temperature and lower relative humidity were lower compared to the first year, while ABA and TSS values were higher in the second year. Statistically significant correlations were recorded between the parameters investigated except FCY and TSS. The FCY and other parameters of sweet corn varieties, which produced high ABA phytohormone, were high, and the ABA hormone significantly contributed to plant growth under stress conditions. The results revealed that the PFR physiological parameter and ABA hormone in the plants provide important information about stress level and stress tolerance level of the cultivars, respectively. Despite adverse environmental stress conditions, the FCY of ŞADA-18.7 variety, one of the candidate varieties, was higher than that of the control and the mean value of the experiment.
Tas et al. (2021) Morpho-physiological effects of environmental stress on yield and quality of sweet corn varieties (Zea mays L.). PeerJ 9:e12613 https://doi.org/10.7717/peerj.12613
Genome-wide identification, evolution, and expression analysis of the NPR1-like gene family in pears
The NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) plays a master regulatory role in the salicylic acid (SA) signal transduction pathway and plant systemic acquired resistance (SAR). Members of the NPR1-like gene family have been reported to the associated with biotic/abiotic stress in many plants, however the genome-wide characterization of NPR1-like genes has not been carried out in Chinese pear (Pyrus bretschneideri Reld). In this study, a systematic analysis was conducted on the characteristics of the NPR1-like genes in P. bretschneideri Reld at the whole-genome level. A total nine NPR1-like genes were detected which eight genes were located on six chromosomes and one gene was mapped to scaffold. Based on the phylogenetic analysis, the nine PbrNPR1-like proteins were divided into three clades (Clades I–III) had similar gene structure, domain and conserved motifs. We sorted the cis-acting elements into three clades, including plant growth and development, stress responses, and hormone responses in the promoter regions of PbrNPR1-like genes. The result of qPCR analysis showed that expression diversity of PbrNPR1-like genes in various tissues. All the genes were up-regulated after SA treatment in leaves except for Pbrgene8896. PbrNPR1-like genes showed circadian rhythm and significantly different expression levels after inoculation with Alternaria alternata. These findings provide a solid insight for understanding the functions and evolution of PbrNPR1-like genes in Chinese pear.
Wei et al. (2021) Genome-wide identification, evolution, and expression analysis of the NPR1-like gene family in pears. PeerJ 9:e12617 https://doi.org/10.7717/peerj.12617
Variation in global distribution, population structures, and demographic history for four Trichiurus cutlassfishes
Background Species-specific information on distribution and demographic patterns provides important implications for conservation and fisheries management. However, such information is often lacking for morphologically-similar species, which may lead to biases in the assessments of these species and even decrease effort towards sustainable management. Here, we aimed to uncover the distribution range, population structure and demographic history for four exploited Trichiurus cutlassfishes using genetics. These cutlassfishes contribute substantial global fisheries catch, with a high proportion of catch harvested from the NW Pacific. Methods We chose the widely available mitochondrial 16S ribosomal RNA (16S) as the genetic marker for cutlassfishes. We compiled the 16S sequence data from both the GenBank and a survey of trawler catch samples along the NW Pacific coasts 22–39°N. Genealogical relationships within each species was visualized with haplotype networks and potential population differentiations were further evaluated with AMOVA. Demographic histories were estimated using neutrality test, mismatch analysis, and the Bayesian skyline plot. The reconstructed phylogenetic trees were used to delimit and estimate the divergence time of species and included populations. Results In each of two cosmopolitan species, T. lepturus and T. nanhaiensis, we observed distinct populations along the coasts of warm oceans; such population differentiation might result from historical geographic barriers in the Pleistocene. In the NW Pacific, four Trichiurus species vary in their distribution habitats, which reflect differential ecological niches among these species. The small-sized T. brevis are primarily found in nearshore habitats; the warm-affiliated T. nanhaiensis are present along the path of the Kuroshio Current; the cold-affiliated T. japonicus spatially diverged from the widely-distributed T. lepturus, with the latter mainly occupy in warmer regions. Despite these differences, a single well-mixing fish stock, thus one management unit, was identified in each of the four species, presumably due to expansion of their population sizes predated the Last Glacial Maximum and a lack of distribution barrier. The most dominant T. japonicus, which have at least one magnitude higher effective population size than the others, show a unique abrupt size expansion event at 75 to 50-kilo years ago when the low sea level occurred during the ice age. Main conclusions The demographic history revealed by our genetic analyses advances understanding of the current distribution and population structure for these congeneric species. Moreover, the uncovered population structure provides insight into the assessment and management of these species. Such information complements contemporary knowledge about these species and enables us to forecast their ability to resist future environmental and anthropogenic disturbances.
Lin et al. (2021) Variation in global distribution, population structures, and demographic history for four Trichiurus cutlassfishes. PeerJ 9:e12639 https://doi.org/10.7717/peerj.12639
Microbial associations of shallow-water Mediterranean marine cave Solenogastres (Mollusca)
The first cave-dwelling Solenogastres—marine shell-less worm-like mollusks—were sampled from Mediterranean marine caves floor silt in the Marseille area. The mollusks were 1.5 mm in length, had a transparent body with shiny spicules and appear to represent a new Tegulaherpia species. Electron microscopy revealed a high number of microbial cells, located on the surface of the spicules as well as in the cuticle of Tegulaherpia sp. The observed microbial cells varied in morphology and were unequally distributed through the cuticle, reaching a highest density on the dorsal and lateral sides and being practically absent on the ventral side. Next Generation Sequencing (NGS) of V4 region of 16S rRNA gene amplicons, obtained from the DNA samples of whole bodies of Tegulaherpia sp. revealed three dominating microorganisms, two of which were bacteria of Bacteroidetes and Nitrospirae phyla, while the third one represented archaea of Thaumarchaeota phylum. The Operational Taxonomic Unit (OTU), affiliated with Bacteroidetes was an uncultured bacteria of the family Saprospiraceae (93–95% of Bacteroidetes and 25–44% of the total community, depending on sample), OTU, affiliated with Nitrospirae belonged to the genus Nitrospira (8–30% of the community), while the thaumarchaeal OTU was classified as Candidatus Nitrosopumilus (11–15% of the community). Members of these three microbial taxa are known to form associations with various marine animals such as sponges or snails where they contribute to nitrogen metabolism or the decomposition of biopolymers. A similar role is assumed to be played by the microorganisms associated with Tegulaherpia sp.
Vortsepneva et al. (2021) Microbial associations of shallow-water Mediterranean marine cave Solenogastres (Mollusca). PeerJ 9:e12655 https://doi.org/10.7717/peerj.12655
The characteristics and roles of antimicrobial peptides as potential treatment for antibiotic-resistant pathogens: a review
The emergence of antibiotic-resistant bacteria has become a significant and ever-increasing threat to global public health, increasing both morbidity and mortality rates, and the financial burden on health services. Infection by drug-resistant bacteria is anticipated to contribute to the demise of almost 10 million people by the year 2050 unless a competent and effective response is devised to engage with this issue. The emergence and spread of resistance are commonly caused by the excessive or inappropriate use of antibiotics and substandard pharmaceuticals. It arises when pathogens adapt to different conditions and develop self-defence mechanisms. Currently, novel antimicrobial peptides (AMPs) have been reported to be the sole cure for some clinical cases of infectious diseases such as sepsis and skin infections, although these agents may, on occasion, require administration together with an adjunctive low-dose antibiotic. Although AMPs are a promising alternative form of anti-microbial therapy and easily applied in the medical sector, they still have limitations that should not be taken lightly. Hence, this review explores the characteristics, advantages and disadvantages of AMPs for their potential in treating antibiotic-resistant pathogens.
Zainal Baharin et al. (2021) The characteristics and roles of antimicrobial peptides as potential treatment for antibiotic-resistant pathogens: a review. PeerJ 9:e12193 https://doi.org/10.7717/peerj.12193