Current Articles

Editorial
Finding your scientific story by writing backwards
David J. S. Montagnes, E. Ian Montagnes, Zhou Yang
2022, 4(1): 1-9. doi: 10.1007/s42995-021-00120-z
HTML PDF Springerlink
Abstract:
To succeed, a scientist must write well. Substantial guidance exists on writing papers that follow the classic Introduction, Methods, Results, and Discussion (IMRaD) structure. Here, we fill a critical gap in this pedagogical canon. We offer guidance on developing a good scientific story. This valuable—yet often poorly achieved—skill can increase the impact of a study and its likelihood of acceptance. A scientific story goes beyond presenting information. It is a cohesive narrative that engages the reader by presenting and solving a problem, with a beginning, middle, and end. To create this narrative structure, we urge writers to consider starting at the end of their study, starting with writing their main conclusions, which provide the basis of the Discussion, and then work backwards: Results → Methods → refine the Discussion → Introduction → Abstract → Title. In this brief and informal editorial, we offer guidance to a wide audience, ranging from upper-level undergraduates (who have just conducted their first research project) to senior scientists (who may benefit from re-thinking their approach to writing). To do so, we provide specific instruction, examples, and a guide to the literature on how to “write backwards”, linking scientific storytelling to the IMRaD structure.
Research Paper
Discrepancy in photosynthetic responses of the red alga Pyropia yezoensis to dehydration stresses under exposure to desiccation, high salinity, and high mannitol concentration
Guoying Du, Xiaojiao Li, Junhao Wang, Shuai Che, Xuefeng Zhong, Yunxiang Mao
2022, 4(1): 10-17. doi: 10.1007/s42995-021-00115-w
HTML PDF Springerlink
Abstract:
Macroalgae that inhabit intertidal zones are exposed to the air for several hours during low tide and must endure desiccation and high variations in temperature, light intensity, and salinity. Pyropia yezoensis (Rhodophyta, Bangiales), a typical intertidal red macroalga that is commercially cultivated in the northwestern Pacific Ocean, was investigated under different dehydration stresses of desiccation, high salinity, and high mannitol concentration. Using chlorophyll fluorescence imaging, photosynthetic activities of P. yezoensis thalli were analyzed using six parameters derived from quenching curves and rapid light curves. A distinct discrepancy was revealed in photosynthetic responses to different dehydration stresses. Dehydration caused by exposure to air resulted in rapid decreases in photosynthetic activities, which were always lower than two other stresses at the same water loss (WL) level. High salinity only reduced photosynthesis significantly at its maximum WL of 40% but maintained a relatively stable maximum quantum yield of photosystem Ⅱ (PSⅡ) (Fv/Fm). High mannitol concentration induced maximum WL of 20% for a longer time (60 min) than the other two treatments and caused no adverse influences on the six parameters at different WL except for a significant decrease in non-photochemical quenching (NPQ) at 20% WL. Illustrated by chlorophyll fluorescence images, severe spatial heterogeneities were induced by desiccation with lower values in the upper parts than the middle or basal parts of the thalli. The NPQ and rETRmax (maximum relative electron transport rate) demonstrated clear distinctions for evaluating photosynthetic responses, indicating their sensitivity and applicability. The findings of this study indicated that the natural dehydration of exposure to air results in stronger and more heterogeneous effects than those of high salinity or high mannitol concentration.
Evolutionary dynamics and conserved function of the Tudor domain-containing (TDRD) proteins in teleost fish
Zeyu Liu, Saisai Liu, Shiyang Guo, Wei Lu, Quanqi Zhang, Jie Cheng
2022, 4(1): 18-30. doi: 10.1007/s42995-021-00118-7
HTML PDF Springerlink
Abstract:
Tudor domain-containing (TDRD) proteins, the germline enriched protein family, play essential roles in the process of gametogenesis and genome stability through their interaction with the PIWI-interacting RNA (piRNA) pathway. Several studies have suggested the rapid evolution of the piRNA pathway in teleost lineages with striking reproductive diversity. However, there is still limited information about the function and evolution of Tdrd genes in teleost species. In this study, through genome wide screening, 13 Tdrd family genes were identified in economically important aquaculture fish, including spotted sea bass (Lateolabrax maculatus), Asian sea bass (Lates calcarifer), and tongue sole (Cynoglossus semilaevis). With copy number, structure, phylogeny, and synteny analysis, duplication of Tdrd6 and Tdrd7, as well as loss of Stk31 and Tdrd10, were characterized in teleost lineages. Codon based molecular evolution analysis indicated faster evolution of teleost Tdrd genes than that in mammals, potentially associated with the accelerated evolution of the piRNA pathway in teleost lineages. The evolutionary diversity of Tdrd genes was also detected between different teleost lineages. RNA-seq analysis showed that most teleost Tdrd genes were dominantly expressed in gonads, particularly highly expressed in testis, such as Tdrd6, Tdrd7a, Tdrd9, Ecat8, and Tdrd15. The varied expression and evolutionary pattern between the duplicated Tdrd6 and Tdrd7 in teleosts may indicate their functional diversification. All these results suggest a conserved function of teleost Tdrd family in gametogenesis and the piRNA pathway, which could lay a foundation for the evolution of Tdrd genes and be helpful for further deciphering of Tdrd functions in teleosts.
Taxonomy and systematics of a new pleurostomatid ciliate, Pseudolitonotus spirelis gen. et sp. n. (Protozoa, Ciliophora, Haptoria)
Lei Wu, Jiqiu Li, Alan Warren, Xiaofeng Lin
2022, 4(1): 31-41. doi: 10.1007/s42995-021-00123-w
HTML PDF Springerlink
Abstract:
Recent studies have revealed a high diversity of pleurostomatid ciliates in brackish habitats. Here, a novel species, Pseudolitonotus spirelis gen. et sp. n., isolated from a mangrove wetland of southern China, was investigated based on living observation, protargol staining, and molecular analyses. The new genus Pseudolitonotus gen. n. is characterized by the last left somatic kinety (LKn) being shortened and none of the right somatic kineties extending to the anterior end of the cell, thus distinguishing it from all known pleurostomatid genera. The type species, Pseudolitonotus spirelis sp. n., is characterized by the possession of two macronuclear nodules, 11–15 right and 7–9 left kineties, a single contractile vacuole subterminally located, extrusomes evenly spaced along the entire ventral margin and some forming an "apical group", two types of cortical granules, and the bottom of the oral slit invariably being twisted. Litonotus gracilis (Pan et al. Eur J Protistol 51:494–506, 2015) is believed to be another member of this new genus as its LKn and right somatic kineties are all shortened. Hence, a new combination, Pseudolitonotus gracilis (Pan et al., 2015) comb. n., is suggested and its diagnosis is improved. Molecular phylogenetic analyses based on SSU rDNA sequence data reveal that Pseudolitonotus gen. n. is monophyletic and groups with Apolitonotus (Pan et al. J Eukaryot Microbiol 67:252–262, 2020) of the family Protolitonotidae (Wu et al. Zool Scr 46:245–253, 2017). However, the familial assignment of this new genus is uncertain based on current data.
Anti-lipopolysaccharide factor D from kuruma shrimp exhibits antiviral activity
Hai-Shan Jiang, Li-Xia Lv, Jin-Xing Wang
2022, 4(1): 52-61. doi: 10.1007/s42995-021-00113-y
HTML PDF Springerlink
Abstract:
Anti-lipopolysaccharide factors (ALFs) exhibit a potent antimicrobial activity against a broad range of bacteria, filamentous fungi, and viruses. In previous reports, seven groups of ALFs (groups A–G) were identified in penaeid shrimp. Among them, group D showed negative net charges and weak antimicrobial activity. Whether this group has antiviral function is not clear. In this study, the ALF sequences of penaeid shrimp were analyzed, and eight groups of ALF family (groups A–H) were identified. The four ALFs including MjALF-C2, MjALF-D1, MjALF-D2, and MjALF-E2 from kuruma shrimp Marsupenaeus japonicus were expressed recombinantly in Escherichia coli, and the antiviral activity was screened via injection of purified recombinant ALFs into shrimp following white spot syndrome virus (WSSV) infection. Results showed that the expression of Vp28 (WSSV envelope protein) decreased significantly in the MjALF-D2-injected shrimp only. Therefore, MjALF-D2 was chosen for further study. Expression pattern analysis showed that MjAlf-D2 was upregulated in shrimp challenged by WSSV. The WSSV replication was detected in RNA, genomic DNA, and protein levels using VP28 and Ie1 (immediate-early gene of WSSV) as indicators in MjALF-D2-injected shrimp following WSSV infection. Results showed that WSSV replication was significantly inhibited compared with that in the rTRX- or PBS-injected control groups. After knockdown of MjAlf-D2 in shrimp by RNA interference, the WSSV replication increased significantly in the shrimp. All these results suggested that MjALF-D2 has an antiviral function in shrimp immunity, and the recombinant ALF-D2 has a potential application for viral disease control in shrimp aquaculture.
Design and evaluation of chitosan-amino acid thermosensitive hydrogel
Jianan Tong, Huiyun Zhou, Jingjing Zhou, Yawei Chen, Jing Shi, Jieke Zhang, Xinyu Liang, Tianyuan Du
2022, 4(1): 74-87. doi: 10.1007/s42995-021-00116-9
HTML PDF Springerlink
Abstract:
Chitosan/glycerophosphate thermosensitive hydrogel crosslinked physically was a potential drug delivery carrier; however, long gelation time limits its application. Here, chitosan-amino acid (AA) thermosensitive hydrogels were prepared from chitosan (CS), αβ-glycerophosphate (GP), and L-lysine (Lys) or L-glutamic acid (Glu). The prepared CS-Lys/GP and CS-Glu/GP hydrogel showed good thermosensitivity and could form gels in a short time. The optimal parameters of CS-Lys/GP hydrogel were that the concentration of CS-Lys was 2.5%, the ratio of CS/Lys was 3.5/1.0, the ratio of CS-Lys/GP was 4.5/1.0. The optimal parameters of CS-Glu/GP hydrogel were that the concentration of CS-Glu was 3.0%, the ratio of CS/Glu was 2.0/1.0, and the ratio of CS-Glu/GP was 4.0/1.5. Chitosan-amino acid (CS-AA) thermosensitive hydrogel had a three-dimensional network structure. The addition of model drug tinidazole (TNZ) had no obvious effect on the structure of hydrogel. The results of infrared spectroscopy showed that there were hydrogen bonds between amino acids and chitosan. In vitro release results showed that CS-Lys/GP and CS-Glu/GP thermosensitive hydrogels had sustained release effects. Thus, the chitosan-amino acid thermosensitive hydrogels hold great potential as a sustained release drug delivery system.
Structure modification, antialgal, antiplasmodial, and toxic evaluations of a series of new marine-derived 14-membered resorcylic acid lactone derivatives
Wei-Feng Xu, Na-Na Wu, Yan-Wei Wu, Yue-Xuan Qi, Mei-Yan Wei, Laura M. Pineda, Michelle G. Ng, Carmenza Spadafora, Ji-Yong Zheng, Ling Lu, Chang-Yun Wang, Yu-Cheng Gu, Chang-Lun Shao
2022, 4(1): 88-97. doi: 10.1007/s42995-021-00103-0
HTML PDF Springerlink
Abstract:
Marine natural products play critical roles in the chemical defense of many marine organisms and are essential, reputable sources of successful drug leads. Sixty-seven 14-membered resorcylic acid lactone derivatives 3-27 and 30-71 of the natural product zeaenol (1) isolated from the marine-derived fungus Cochliobolus lunatus were semisynthesized by chlorination, acylation, esterification, and acetalization in one to three steps. The structures of these new derivatives were established by HRESIMS and NMR techniques. All the compounds (1-71) were evaluated for their antialgal and antiplasmodial activities. Among them, 14 compounds displayed antifouling activities against adhesion of the fouling diatoms. In particular, 9 and 34 exhibited strong and selective inhibitory effects against the diatoms Navicula laevissima and Navicula exigua (EC50 = 6.67 and 8.55 μmol/L), respectively, which were similar in efficacy to those of the positive control SeaNine 211 (EC50 = 2.90 and 9.74 μmol/L). More importantly, 38, 39, and 69-71 showed potent antiplasmodial activities against Plasmodium falciparum with IC50 values ranging from 3.54 to 9.72 μmol/L. Very interestingly, the five antiplasmodial derivatives displayed non-toxicity in the cytotoxicity assays and the zebrafish embryos model, thus, representing potential promising antiplasmodial drug agents. The preliminary structureסctivity relationships indicated that biphenyl substituent at C-2, acetonide at positions C-5' and C-6', and tri- or tetra-substituted of acyl groups increased the antiplasmodial activity. Therefore, combining evaluation of chemical ecology with pharmacological models will be implemented as a systematic strategy, not only for environmentally friendly antifoulants but also for structurally novel drugs.
Mechanism of interactions between a-conotoxin RegIIA and carbohydrates at the human a3ߴ nicotinic acetylcholine receptor
Meiling Zheng, Han-Shen Tae, Liang Xue, Tao Jiang, Rilei Yu
2022, 4(1): 98-105. doi: 10.1007/s42995-021-00108-9
HTML PDF Springerlink
Abstract:
Conotoxins are marine peptide toxins from marine cone snails. The a-conotoxin RegIIA can selectively act on human (h) α3β4 nicotinic acetylcholine receptor (nAChR), and is an important lead for drug development. The high-resolution cryo-electron microscopy structure of the α3β4 nAChR demonstrates several carbohydrates are located near the orthosteric binding sites, which may affect a-conotoxin binding. Oligosaccharide chains can modify the physical and chemical properties of proteins by changing the conformation, hydrophobicity, quality and size of the protein. The purpose of this study is to explore the effect of oligosaccharide chains on the binding modes and activities of RegIIA and its derivatives at hα3β4 nAChRs. Through computational simulations, we designed and synthesized RegIIA mutants at position 14 to explore the importance of residue H14 to the activity of the peptide. Molecular dynamics simulations suggest that the oligosaccharide chains affect the binding of RegIIA at the hα3β4 nAChR through direct interactions with H14 and by affecting the C-loop conformation of the binding sites. Electrophysiology studies on H14 analogues suggest that in addition to forming direct interactions with the carbohydrates, the residue might play an important role in maintaining the conformation of the peptide. Overall, this study further clarifies the structureסctivity relationship of a-conotoxin RegIIA at the hα3β4 nAChR and, also provides important experimental and theoretical basis for the development of new peptide drugs.
Effects of protein oxidation, cathepsins, and various freezing temperatures on the quality of superchilled sturgeon fllets
Nana Zhao, Xianqing Yang, Yujin Li, Haohao Wu, Yiping Chen, Ruichang Gao, Feng Xiao, Fan Bai, Jinlin Wang, Zunying Liu, Xin Gao, Yuanhui Zhao
2022, 4(1): 117-126. doi: 10.1007/s42995-021-00112-z
HTML PDF Springerlink
Abstract:
Many aquatic products have been stored using superchilling technology, but rarely used for the storage of sturgeon fillets. In this study, we investigated the effects of protein oxidation, cathepsin, and various freezing temperatures on the quality of superchilled sturgeon fillets. Sensory evaluation results showed that the sensory attributes of superchilled (?3 ℃) sturgeon fillets were acceptable three times longer (18 days) than samples stored at refrigeration temperatures (4 ℃). The sarcoplasmic protein, carbonyl, myofibrillar protein, total sulfhydryl content and the surface hydrophobicity were determined using fluorescence spectrophotometry and SDS-PAGE. Results showed that superchilling might protect myofibrillar proteins from oxidation compared to refrigeration temperatures. The activity of the three cathepsins (B, L, and H) in terms of myofibrillar, mitochondria, lysosomes, and sarcoplasm demonstrated that superchilling can inhibit cathepsins activity in sturgeon and protect its muscle structure. Microscopic observations showed that as the temperature decreased, the gap area of the muscle fibers decreased, and the deformation of cross-sectional slices was gradually reduced. In addition, the freezing rate of ice crystals produced during the freezing process influenced the muscle structure, texture, and sensory attributes. Superchilled sturgeon fillets showed good hardness, chewiness, and water retention. In conclusion, superchilling technology shows promise for its ability to extend the shelf life while maintaining the texture and sensory attributes of fresh sturgeon fillets.
Community structure and activity potentials of archaeal communities in hadal sediments of the Mariana and Mussau trenches
Zixuan Wang, Li Wang, Rulong Liu, Zhenzhen Li, JiaXin Wu, Xing Wei, Wenxia Wei, Jiasong Fang, Junwei Cao, Yuli Wei, Zhe Xie
2022, 4(1): 150-161. doi: 10.1007/s42995-021-00105-y
HTML PDF Springerlink
Abstract:
Hadal trenches are the least explored marine habitat on earth. Archaea has been shown to be the dominant group in trench sediments. However, the activity potentials and detailed diversity of these communities as well as their inter-trench variations are still not known. In this study, we combined datasets from two pairs of primers to investigate at high resolution the structure and activity potentials of the archaeal communities in vertically sectioned sediment cores taken from the deepest points of the Mariana (10, 853 m) and Mussau (7011 m) trenches. The compositions of the potentially active communities revealed, via 16S ribosomal RNA gene (rDNA) and RNA (rRNA), significant differences between samples. Marine Group I (MGI), with nine identified subgroups, was the most dominant class in the active archaeal communities of the two trenches. Significantly different species composition and vertical variations were observed between the two trenches. Vertical transitions from aerobic MGI α to anaerobic MGI η and υ subgroups were observed in MST but not in MT sediments, which might be related to the faster microbial oxygen consumption in MST. These results provide a better understanding on archaeal activity and diversity in trench sediments.
Review
Neuropeptide Y and melanocortin receptors in fish: regulators of energy homeostasis
Zhi-Shuai Hou, Hai-Shen Wen
2022, 4(1): 42-51. doi: 10.1007/s42995-021-00106-x
HTML PDF Springerlink
Abstract:
Energy homeostasis, which refers to the physiological processes that the energy intake is exquisitely coordinated with energy expenditure, is critical for survival. Therefore, multiple and complex mechanisms have been involved in the regulation of energy homeostasis. The central melanocortin system plays an important role in modulating energy homeostasis. This system includes the orexigenic neurons, expressing neuropeptide Y/Agouti-related protein (NPY/AgRP), and the anorexigenic neurons expressing proopiomelanocortin (POMC). The downstream receptors of NPY, AgRP and post-translational products of POMC are G protein-coupled receptors (GPCRs). This review summarizes the compelling evidence demonstrating that NPY and melanocortin receptors are involved in energy homeostasis. Subsequently, the comparative studies on physiology and pharmacology of NPY and melanocortin receptors in humans, rodents and teleosts are summarized. Also, we provide a strategy demonstrating the potential application of the new ligands and/or specific variants of melanocortin system in aquaculture.
Structural diversity and biological activity of natural p-terphenyls
Guoliang Zhou, Tianjiao Zhu, Qian Che, Guojian Zhang, Dehai Li
2022, 4(1): 62-73. doi: 10.1007/s42995-021-00117-8
HTML PDF Springerlink
Abstract:
p-Terphenyls are aromatic compounds consisting of a central benzene ring substituted with two phenyl groups, and they are mainly isolated from terrestrial and marine organisms. The central ring of p-Terphenyls is usually modified into more oxidized forms, e.g., para quinone and phenols. In some cases, additional ring systems were observed on the terphenyl-type core structure or between two benzene moieties. p-Terphenyls have been reported to have cytotoxic, antimicrobial, antioxidant and α-glucosidase inhibitory effects. In this review, we will mainly summarize the structural diversity and biological activity of naturally occurring p-Terphenyls referring to the research works published before.
Evolving strategies for marine enzyme engineering: recent advances on the molecular modifcation of alginate lyase
Shengsheng Cao, Qian Li, Yinxiao Xu, Tiancheng Tang, Limin Ning, Benwei Zhu
2022, 4(1): 106-116. doi: 10.1007/s42995-021-00122-x
HTML PDF Springerlink
Abstract:
Alginate, an acidic polysaccharide, is formed by β-D-mannuronate (M) and α-L-guluronate (G). As a type of polysaccharide lyase, alginate lyase can efficiently degrade alginate into alginate oligosaccharides, having potential applications in the food, medicine, and agriculture fields. However, the application of alginate lyase has been limited due to its low catalytic efficiency and poor temperature stability. In recent years, various structural features of alginate lyase have been determined, resulting in modification strategies that can increase the applicability of alginate lyase, making it important to summarize and discuss the current evidence. In this review, we summarized the structural features and catalytic mechanisms of alginate lyase. Molecular modification strategies, such as rational design, directed evolution, conserved domain recombination, and non-catalytic domain truncation, are also described in detail. Lastly, the application of alginate lyase is discussed. This comprehensive summary can inform future applications of alginate lyases.
Scientific and technological progress in the microbial exploration of the hadal zone
Shen Fan, Meng Wang, Wei Ding, Yong-Xin Li, Yu-Zhong Zhang, Weipeng Zhang
2022, 4(1): 127-137. doi: 10.1007/s42995-021-00110-1
HTML PDF Springerlink
Abstract:
The hadal zone is the deepest point in the ocean with a depth that exceeds 6000 m. Exploration of the biological communities in hadal zone began in the 1950s (the first wave of hadal exploration) and substantial advances have been made since the turn of the twenty-first century (the second wave of hadal exploration), resulting in a focus on the hadal sphere as a research hotspot because of its unique physical and chemical conditions. A variety of prokaryotes are found in the hadal zone. The mechanisms used by these prokaryotes to manage the high hydrostatic pressures and acquire energy from the environment are of substantial interest. Moreover, the symbioses between microbes and hadal animals have barely been studied. In addition, equipment has been developed that can now mimic hadal environments in the laboratory and allow cultivation of microbes under simulated in situ pressure. This review provides a brief summary of recent progress in the mechanisms by which microbes adapt to high hydrostatic pressures, manage limited energy resources and coexist with animals in the hadal zone, as well as technical developments in the exploration of hadal microbial life.
Shifting chemical defence or novel weapons? A review of defence traits in Agarophyton vermiculophyllum and other invasive seaweeds
Gaoge Wang, Yifei Ren, Shasha Wang, Minglei Hou, Florian Weinberger
2022, 4(1): 138-149. doi: 10.1007/s42995-021-00109-8
HTML PDF Springerlink
Abstract:
Seaweed bioinvasions increasingly affect coastal environments around the world, which increases the need for predictive models and mitigation strategies. The biotic interactions between seaweed invaders and invaded communities are often considered a key determinant of invasion success and failure and we here revise the current evidence that the capacity of seaweed invaders to deter enemies in newly reached environments correlates with their invasion success. Particularly efficient chemical defences have been described for several of the more problematic seaweed invaders during the last decades. However, confirmed cases in which seaweed invaders confronted un-adapted enemies in newly gained environments with deterrents that were absent from these environments prior to the invasion (so-called "novel weapons") are scarce, although an increasing number of invasive and non-invasive seaweeds are screened for defence compounds. More evidence exists that seaweeds may adapt defence intensities to changing pressure by biological enemies in newly invaded habitats. However, most of this evidence of shifting defence was gathered with only one particular model seaweed, the Asia-endemic red alga Agarophyton vermiculophyllum, which is particularly accessible for direct comparisons of native and non-native populations in common garden experiments. A. vermiculophyllum interacts with consumers, epibionts and bacterial pathogens and in most of these interactions, non-native populations have rather gained than lost defensive capacity relative to native conspecifics. The increases in the few examined cases were due to an increased production of broad-spectrum deterrents and the relative scarcity of specialized deterrents perhaps reflects the circumstance that seaweed consumers and epibionts are overwhelmingly generalists.