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Reproduction of the sea cucumber Apostichopus japonicus is critical for aquaculture production. Gonadal development is the basis of reproduction, and lipids, which are among the main nutrients required for gonadal development, directly affect reproduction. We investigated whether gonadal and intestinal lipid metabolism differed between male and female A. japonicus. Transcriptome analysis of the intestines of sexually mature male and female wild-caught individuals revealed differences in gene expression, with 27 and 39 genes being up-regulated in females and males, respectively. In particular, the expression of the fatty acid synthase gene was higher in males than in females. Metabolome analysis of the gonads identified 141 metabolites that were up-regulated and 175 metabolites that were down-regulated in the testes compared with the ovaries in the positive/negative mode of an LC-MS/MS analysis. A variety of polyunsaturated fatty acids were found at higher concentrations in the testes than in the ovaries. 16 s rDNA sequencing analysis showed that the composition and structure of the intestinal microbiota were similar between males and females. These results suggest that sex differences in intestinal metabolism of A. japonicus are not due to differences in the microbiota, and we speculate that gonadal metabolism may be related to intestinal morphology. This information might be useful in improving the reproductive efficiency of sea cucumbers in captivity.

Seafloor massive sulfide (SMS) deposits are important deep-sea mineral resources expected to occur predominantly on slow- and ultraslow-spreading mid-ocean ridges. Resource estimates are already available for some of the largest SMS deposits on slow-spreading ridges but not on ultraslow-spreading ridges. Based on geological mapping and sampling, this study investigates the distribution and content of sulfide-rich deposits in the Yuhuang-1 hydrothermal field (YHF), located on the ultraslow-spreading Southwest Indian Ridge. The sulfide-rich deposits in the YHF are composed of two areas ∼500 m apart: the southwest sulfide area (SWS) and the northeast sulfide area (NES). We calculated the volume of sulfide-rich mounds in the YHF and arrived at a total accumulation of ∼10.6 × 106 tons, including at least ∼7.5 × 105 tons of copper and zinc and ∼18 tons of gold. Furthermore, considering the coverage of layered hydrothermal sediment mixed with sulfide-rich breccias, which may have underlying massive sulfide deposits, the maximum total mass was estimated at ∼45.1 × 106 tons. This suggests that the YHF is one of the largest SMS deposits worldwide and confirm that ultraslow-spreading ridges have the greatest potential to form large-scale SMS deposits.

Hydrothermal activities on ultraslow-spreading ridges exhibit diverse characteristics, long histories with multiple participants, and might form large-scale, high-grade sulfide deposits. The Duanqiao hydrothermal field (DHF) is located at the segment with the thickest oceanic crust and a large axial magma chamber on the Southwest Indian Ridge, providing unique perspective of sulfide metallogenesis on ultraslow-spreading ridges. Previous studies revealed that DHF sulfide exhibits distinct features of enrichment of ore-forming elements in comparison with those of hydrothermal fields on sediment-starved mid-ocean ridges. However, the genesis and processes responsible for such differences remain poorly constrained. In this study, mineralogical, geochemical and S and Pb isotopic analyses were performed on relict sulfide mound samples to characterize DHF formation. The samples show clear concentric mineral zonation from the interior to the exterior wall. Assemblages of chalcopyrite, sphalerite, and pyrite are distributed mainly in the interior wall, whereas pyrite and marcasite are distributed mainly in the exterior wall. The low Cu content and Pb isotopic composition of the sulfide indicate that the metals are derived mainly from basement basalts. The δ34S values exhibit positive values distributed over a reasonably narrow range (2.42‰–7.97‰), which suggests approximately 62.1%–88.5% of S with basaltic origin. Compared with most hydrothermal fields along the sediment starved mid-ocean ridges, the DHF sulfide shows particularly high contents of Pb (263–2630 ppm), As (234–726 ppm), Sb (7.32–44.3 ppm), and Ag (35.2 to >100 ppm). The δ34S values exhibit an increasing tendency from the sample exterior to the interior. We propose that these features probably reflect the existence of a subsurface zone refining process. Our results provide new insight into the sulfide formation process and contribute to understanding the metallogenic mechanism of hydrothermal sulfides on ultraslow-spreading ridges.

Ligand peptides that have high affinity for ion channels are critical for regulating ion flux across the plasma membrane. These peptides are now being considered as potential drug candidates for many diseases, such as cardiovascular disease and cancers. In this work, we developed Multi-Branch-CNN, a CNN method with multiple input branches for identifying three types of ion channel peptide binders (sodium, potassium, and calcium) from intra- and inter-feature types. As for its real-world applications, prediction models that are able to recognize novel sequences having high or low similarities to training sequences are required. To this end, we tested our models on two test sets: a general test set including sequences spanning different similarity levels to those of the training set, and a novel-test set consisting of only sequences that bear little resemblance to sequences from the training set. Our experiments showed that the Multi-Branch-CNN method performs better than thirteen traditional ML algorithms (TML13), yielding an improvement in accuracy of 3.2%, 1.2%, and 2.3% on the test sets as well as 8.8%, 14.3%, and 14.6% on the novel-test sets for sodium, potassium, and calcium ion channels, respectively. We confirmed the effectiveness of Multi-Branch-CNN by comparing it to the standard CNN method with one input branch (Single-Branch-CNN) and an ensemble method (TML13-Stack). The data sets, script files to reproduce the experiments, and the final predictive models are freely available at https://github.com/jieluyan/Multi-Branch-CNN.

Antimicrobial resistance has become a critical global health problem due to the abuse of conventional antibiotics and the rise of multi-drug-resistant microbes. Antimicrobial peptides (AMPs) are a group of natural peptides that show promise as next-generation antibiotics due to their low toxicity to the host, broad spectrum of biological activity, including antibacterial, antifungal, antiviral, and anti-parasitic activities, and great therapeutic potential, such as anticancer, anti-inflammatory, etc. Most importantly, AMPs kill bacteria by damaging cell membranes using multiple mechanisms of action rather than targeting a single molecule or pathway, making it difficult for bacterial drug resistance to develop. However, experimental approaches used to discover and design new AMPs are very expensive and time-consuming. In recent years, there has been considerable interest in using in silico methods, including traditional machine learning (ML) and deep learning (DL) approaches, to drug discovery. While there are a few papers summarizing computational AMP prediction methods, none of them focused on DL methods. In this review, we aim to survey the latest AMP prediction methods achieved by DL approaches. First, the biology background of AMP is introduced, then various feature encoding methods used to represent the features of peptide sequences are presented. We explain the most popular DL techniques and highlight the recent works based on them to classify AMPs and design novel peptide sequences. Finally, we discuss the limitations and challenges of AMP prediction.

Anthropogenic noise of variable temporal patterns is increasing in aquatic environments, causing physiological stress and sensory impairment. However, scarce information exists on exposure effects to continuous versus intermittent disturbances, which is critical for noise sustainable management. We tested the effects of different noise regimes on the auditory system and behaviour in the zebrafish (Danio rerio). Adult zebrafish were exposed for 24 h to either white noise (150 ± 10 dB re 1 μPa) or silent control. Acoustic playbacks varied in temporal patterns—continuous, fast and slow regular intermittent, and irregular intermittent. Auditory sensitivity was assessed with Auditory Evoked Potential recordings, revealing hearing loss and increased response latency in all noise-treated groups. The highest mean threshold shifts (c. 13 dB) were registered in continuous and fast intermittent treatments, and no differences were found between regular and irregular regimes. Inner ear saccule did not reveal significant hair cell loss but showed a decrease in presynaptic Ribeye b protein especially after continuous exposure. Behavioural assessment using the standardized Novel Tank Diving assay showed that all noise-treated fish spent > 98% time in the bottom within the first minute compared to 82% in control, indicating noise-induced anxiety/stress. We provide first data on how different noise time regimes impact a reference fish model, suggesting that overall acoustic energy is more important than regularity when predicting noise effects.

Fish represent the largest group of vertebrates and display the greatest diversity of auditory structures. However, studies addressing how the form and function of the auditory system change during development to enhance perception of the acoustic environment are rather sparse in this taxon compared to other vertebrate groups. An ontogenetic perspective of the auditory system in fishes provides a readily testable framework for understanding structure–function relationships. Additionally, studying ancestral models such as fish can convey valuable comparable information across vertebrates, as early developmental events are often evolutionary conserved. This chapter reviews the literature on the morphological development of the fish auditory system, with particular focus on the inner ear structures that evolve from an otic placode during early embryonic development and then continue to undergo differentiation and maturation in the postembryonic phase. Moreover, the chapter provides a systematic overview of how auditory sensitivity develops during ontogeny. Although most studies indicate a developmental improvement in auditory sensitivity, there is considerably species-specific variation. Lastly, the paucity of information and literature concerning the development of auditory capabilities for social communication in fishes is also discussed. Further investigation on the development of structure and function of the fish auditory system is recommended in order to obtain a deeper understanding of how ontogenetic morphological changes in the auditory pathway relate to modifications in acoustic reception, auditory processing, and the capacity to communicate acoustically.

Vocal differentiation is widely documented in birds and mammals but has been poorly investigated in other vertebrates, including fish, which represent the oldest extant vertebrate group. Neural circuitry controlling vocal behaviour is thought to have evolved from conserved brain areas that originated in fish, making this taxon key to understanding the evolution and development of the vertebrate vocal-auditory systems. This study examines ontogenetic changes in the vocal repertoire and whether vocal differentiation parallels auditory development in the Lusitanian toadfish Halobatrachus didactylus (Batrachoididae). This species exhibits a complex acoustic repertoire and is vocally active during early development. Vocalisations were recorded during social interactions for four size groups (fry: <2 cm; small juveniles: 2–4 cm; large juveniles: 5–7 cm; adults >25 cm, standard length). Auditory sensitivity of juveniles and adults was determined based on evoked potentials recorded from the inner ear saccule in response to pure tones of 75–945 Hz. We show an ontogenetic increment in the vocal repertoire from simple broadband-pulsed ‘grunts’ that later differentiate into four distinct vocalisations, including low-frequency amplitude-modulated ‘boatwhistles’. Whereas fry emitted mostly single grunts, large juveniles exhibited vocalisations similar to the adult vocal repertoire. Saccular sensitivity revealed a three-fold enhancement at most frequencies tested from small to large juveniles; however, large juveniles were similar in sensitivity to adults. We provide the first clear evidence of ontogenetic vocal differentiation in fish, as previously described for higher vertebrates. Our results suggest a parallel development between the vocal motor pathway and the peripheral auditory system for acoustic social communication in fish.

Fishes show remarkably diverse aggressive behaviour. Aggression is expressed to secure resources; adjusting aggression levels according to context is key to avoid negative consequences for fitness and survival. Nonetheless, despite its importance, the physiological basis of aggression in fishes is still poorly understood. Several reports suggest hormonal modulation of aggression, particularly by androgens, but contradictory studies have been published. Studies exploring the role of chemical communication in aggressive behaviour are also scant, and the pheromones involved remain to be unequivocally characterized. This is surprising as chemical communication is the most ancient form of information exchange and plays a variety of other roles in fishes. Furthermore, the study of chemical communication and aggression is relevant at the evolutionary, ecological and economic levels. A few pioneering studies support the hypothesis that aggressive behaviour, at least in some teleosts, is modulated by “dominance pheromones” that reflect the social status of the sender, but there is little information on the identity of the compounds involved. This review aims to provide a global view of aggressive behaviour in fishes and its underlying physiological mechanisms including the involvement of chemical communication, and discusses the potential use of dominance pheromones to improve fish welfare. Methodological considerations and future research directions are also outlined.

Abstract Much controversy has occurred in the past few decades regarding the nature of the sources, the petrogenetic processes, and the tectonic regime(s) of the Jurassic magmatism within the Southeast China magmatic belt. This study aims to contribute to the discussion with mineral chemistry, and whole-rock element and Sr-Nd-Hf-Pb isotopic geochemical data from granitic rocks and microgranular mafic enclaves from Macao, where two discrete groups of I-type biotite granites have been identified (referred to as Macao Group I [MGI] and Macao Group II [MGII]). It is proposed that the granitic magmas were generated by partial melting of infracrustal medium- to high-K, basaltic Paleoproterozoic to Mesoproterozoic protoliths (Nd depleted mantle model age [TDM2] = 1.7–1.6 Ga and Hf TDM2 = 1.8–1.6 Ga), triggered by underplating of hot mantle-derived magmas in an extensional setting related to the foundering of a previously flat slab (paleo–Pacific plate) beneath the SE China continent. The main differences between the two groups of Macao granites are attributed to assimilation and fractional crystallization processes, during which upper-crustal Paleozoic metasediments were variably assimilated by MGI magmas. This is evidenced by an increase in initial 87Sr/86Sr ratios with degree of evolution, presence of metasedimentary enclaves, and high percentage of zircon xenocrysts with Paleozoic ages. In addition, other processes like late-stage fluid/melt interaction and magma mixing also left some imprints on granite compositions (rare earth element tetrad effect plus non–charge-and-radius-controlled behavior of trace elements and decoupling between different isotope systems, respectively). The distribution of isotopically distinct granites in SE China reflects the nature of the two Cathaysia crustal blocks juxtaposed along the Zhenghe-Dapu fault.

The widespread W-(Mo)-Sn-Nb-Ta polymetallic mineralization in Southeast (SE) China is genetically associated with Mesozoic highly fractionated granitic rocks. Such rocks have enigmatic mineralogical and geochemical features, making its petrogenesis an intensely debated topic. To better understand the underlying magma evolution processes, petrography, garnet chemistry and whole-rock major and trace element data are reported for Jurassic highly fractionated granitic rocks and associated microgranite and aplitepegmatite dikes from Macao and compared with coeval similar granitic rocks from nearby areas in SE China. Despite the fact that the most evolved rocks in Macao are garnet-bearing aplite-pegmatite dikes, the existence of coeval two-mica and garnet-bearing biotite and muscovite granites displaying more evolved compositions (e.g, lower Zr/Hf ratios) indicates that the differentiation sequence reached higher degrees of fractionation at a regional scale. Although crystal fractionation played an important role, late-stage fluid/melt interactions, involving F-rich fluids, imparted specific geochemical characteristics to Macao and SE China highly fractionated granitic rocks such as the non-CHARAC (CHArge-and-RAdius-Controlled) behavior of trace elements, leading, for example, to non-chondritic Zr/Hf ratios, Rare Earth Elements (REE) tetrad effects and Nb-Ta enrichment and fractionation. Such process contributed to the late-stage crystallization of accessory phases only found in these highly evolved facies. Among the latter, two populations of garnet were identified in MGI (Macao Group I) highly fractionated granitic rocks: small grossular-poor euhedral grains and large grossular-rich skeletal garnet grains with quartz inclusions. The first group was mainly formed through precipitation from highly evolved Mn-rich slightly peraluminous melts under low-pressure and relatively low temperature (∼700 °C) conditions. Assimilation of upper crust metasedimentary materials may have contributed as a source of Mn and Al to the formation of garnet. The second group has a metasomatic origin related to the interaction of magmatic fluids with previously crystallized mineral phases and, possibly, with assimilated metasedimentary enclaves or surrounding metasedimentary strata. The highly fractionated granitic rocks in Macao represent the first stage in the development of granite-related W-(Mo)-Sn-Nb-Ta mineralization associated with coeval more evolved lithotypes in SE China.