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Saccharina ( Laminaria) is an important economic seaweed. Simple sequence repeat (SSR) markers were developed for S. japonica from an SSR-enriched genomic library using a modified magnetic-bead enrichment protocol. Sequence analysis of 2,853 randomly picked recombinant colonies indicated that 1,092 of the colonies contained microsatellites. After filtration, the remaining 593 unique sequences were examined for their suitability and 266 primer pairs were ultimately designed. Among them, 179 could be used for genetic study by practicability tests. Then, 23 pairs of core primers with good representativeness were selected to analyze 13 Saccharina ( Laminaria) gametophyte lines, which are widely used in breeding and economic cultivation in China. A total of 72 alleles were detected with an average of 3.13 alleles per locus. The Nei's (1973) gene diversity ( H) of these markers ranged from 0.1420 to 0.7222. Cluster analysis was generated from genetic distance by the Unweighted Pair-Group Method with Arithmetic Mean (UPGMA) which resolved the 13 lines into two main groups in accord with their geographic distribution. These results indicated that the SSR markers developed in this study were informative and would be useful for genetic analysis and germplasm management in Saccharina ( Laminaria). [ABSTRACT FROM AUTHOR] more...

Both Calvin-Benson-Bassham (C3) and Hatch-Slack (C4) cycles are most important autotrophic CO2 fixation pathways on today’s Earth. C3 cycle is believed to be originated from cyanobacterial endosymbiosis. However, studies on evolution of different biochemical variants of C4 photosynthesis are limited to tracheophytes and origins of C4-cycle genes are not clear till now. Our comprehensive analyses on bioinformatics and phylogenetics of novel transcriptomic sequencing data of 21 rhodophytes and 19 Phaeophyceae marine species and public genomic data of more algae, tracheophytes, cyanobacteria, proteobacteria and archaea revealed the origin and evolution of C4 cycle-related genes. Almost all of C4-related genes were annotated in extensive algal lineages with proteobacterial or archaeal origins, except for phosphoenolpyruvate carboxykinase (PCK) and aspartate aminotransferase (AST) with both cyanobacterial and archaeal/proteobacterial origin. Notably, cyanobacteria may not possess complete C4 pathway because of the flawed annotation of pyruvate orthophosphate dikinase (PPDK) genes in public data. Most C4 cycle-related genes endured duplication and gave rise to functional differentiation and adaptation in different algal lineages. C4-related genes of NAD-ME (NAD-malic enzyme) and PCK subtypes exist in most algae and may be primitive ones, while NADP-ME (NADP-malic enzyme) subtype genes might evolve from NAD-ME subtype by gene duplication in chlorophytes and tracheophytes. [ABSTRACT FROM AUTHOR] more...

In the past two decades, many studies have focused on the classification within genus Laminaria, ultimately trying to divide it into two subgroups or genera: Laminaria and Saccharina. A significant debate still surrounds the question of its division, as the conflicting phylogenetic hypotheses that have resulted from the classification studies are based on different taxon sampling, molecular markers, or analysis methods. It is aimed at elucidate the molecular phylogeny within Laminaria and Saccharina. The nine species of Laminariales are sampled from northern Asia and Europe, and 23 new sequences in the nuclear, plastid, and mitochondrial genomes are determined to identify their taxonomic status. The phylogenetic analyses of 71 species are performed, including representatives from six of the seven families of the order Laminariales, based on three separate data sets. An evidence is provided to strongly support a clear split that maintains the two recognized genera, Laminaria and Saccharina, with Laminaria appearing to be the ancestor group. Further, analyses indicate that all taxa in Saccharina and Laminaria did not form a monophyletic lineage, instead Laminariaceae and Lessoniaceae grouped together interlacedly, and Costariaceae appeared as the sister taxon of the Lessoniaceae-Laminariaceae clade. In the phylogenetic analysis, mitochondrial c oxidase I (COI) sequences appeared to be the most credible molecular marker which was more befitting than nuclear encoded internal transcribed spacer (ITS) and plastid encoded rbcL for establishment of Laminariales systematics. It is the most comprehensive phylogeny of the order Laminariales, and contributes to an enhanced understanding and estimation of the phylogenetic relationships for the economically important seaweeds, Laminaria and Saccharina. [ABSTRACT FROM AUTHOR] more...

An organ unique to mammals, the mammary gland develops 90% of its mass after birth and experiences the pregnancylactation-involution cycle (PL cycle) during reproduction. To understand mammogenesis at the transcriptomic level and using a ribo-minus RNA-seq protocol, we acquired greater than 50 million reads each for the mouse mammary gland during pregnancy (day 12 of pregnancy), lactation (day 14 of lactation), and involution (day 7 of involution). The pregnancy-, lactation- and involution-related sequencing reads were assembled into 17344, 10160, and 13739 protein-coding transcripts and 1803, 828, and 1288 non-coding RNAs (ncRNAs), respectively. Differentially expressed genes (DEGs) were defined in the three samples, which comprised 4843 DEGs (749 up-regulated and 4094 down-regulated) from pregnancy to lactation and 4926 DEGs (4706 up-regulated and 220 down-regulated) from lactation to involution. Besides the obvious and substantive up- and down-regulation of the DEGs, we observe that lysosomal enzymes were highly expressed and that their expression coincided with milk secretion. Further analysis of transcription factors such as Trps1, Gtf2i, Tcf7l2, Nupr1, Vdr, Rb1, and Aebp1, and ncRNAs such as mir-125b, Let7, mir-146a, and mir-15 has enabled us to identify key regulators in mammary gland development and the PL cycle. [ABSTRACT FROM AUTHOR] more...

Ishige okamurae, with leathery branched narrow fronds consisting of cylindrical hairs, is the typical species of the genus Ishige, which is considered as one of the most basal genera in the phylogeny of the Phaeophyceae. Apart from great public interest from the evolutionary respect, more attention has been brought on the abundant bioactive compounds in I. okamurae for therapeutic or economic considerations, such as diphlorethohydroxycarmalol and ishigoside. Yet little is known about related key genes or metabolic pathways involved in I. okamurae, which calls upon us to carry out global analyses of transcriptome by next generation sequencing. Altogether, we obtained 78 583 assembled scaffolds with N50 of 1 709 nucleotides, and 25 357 unigenes with significant BLAST matches (E-value cutoff of 10). In terms of characterization of the transcriptome of I. okamurae, we focused on anti-stress metabolic pathways and synthetic routes of bioactive compounds in an attempt to obtain a better understanding of the interactive organism-environment regulatory networks. Pathway-based analysis helped us to deepen our comprehension of the interaction between I. okamurae and its surroundings, with MAPK signal pathway as an example. Furthermore, we discovered a wide range of novel putative functional proteins that could be of wide application, such as Rab family, using sequence-based transcriptome. In conclusion, transcriptome characterization of I. okamurae (Phaeophyceae) shows strong environmental acclimation. [ABSTRACT FROM AUTHOR] more...

Brown algae (Chromista, Ochrophyta, Phaeophyceae) are a large group of multicellular algae that play important roles in the ocean's ecosystem and biodiversity. However, poor molecular bases for studying their phylogenetic evolutions and novel metabolic characteristics have hampered progress in the field. In this study, we sequenced the de novo transcriptome of 18 major species of brown algae in China, covering six orders and seven families, using the high-throughput sequencing platform Illumina HiSeq 2000. From the transcriptome data of these 18 species and publicly available genome data of Ectocarpus siliculosus and Phaeodactylum tricornutum, we identified 108 nuclear-generated orthologous genes and clarified the phylogenetic relationships among these brown algae based on a multigene method. These brown algae could be separated into two clades: Clade Ishigeales-Dictyotales and Clade Ectocarpales-Laminariales-Desmarestiale-Fucales. The former was at the base of the phylogenetic tree, indicating its early divergence, while the latter was divided into two branches, with Order Fucales diverging from Orders Ectocarpales, Laminariales, and Desmarestiale. In our analysis of taxonomy-contentious species, Sargassum fusiforme and Saccharina sculpera were found to be closely related to genera Sargassum and Saccharina, respectively, while Petalonia fascia showed possible relation to genus Scytosiphon. The study provided molecular evidence for the phylogenetic taxonomy of brown algae. [ABSTRACT FROM AUTHOR] more...

Saccharina is one of the most important cold-water living marine brown algal genera. In this study we analyzed the transcriptome of S. japonica, which belongs to the 1 000 Plants (OneKP) Project, by using a next-generation high-throughput DNA sequencing technique. About 5.16 GB of raw data were generated, and 65 536 scaffolds with an average length of 454 bp were assembled with SOAP de novo assembly method. In total, 19 040 unigenes were identified by BLAST; 25 734 scaffolds were clustered into 37 Gene ontology functional groups; 6 760 scaffolds were classified into 25 COG categories, as well as 2 665 scaffolds that were assigned to 306 KEGG pathways. Majority of the unigenes exhibited more similarities to algae including brown algae and diatom than other cyanobacteria, marine diatom, and plant. Saccharina japonica has the outstanding capability to accumulate halogen such as Br and I via halogenation processes from seawater. We acquired 42 different vanadium-dependent haloperoxidases (vHPO) in S. japonica transcriptome data, including 5 segments of vanadium-dependent iodoperoxidase (vIPO) and 37 segments of vanadium-dependent bromoperoxidase (vBPO). Complicated analyses of identified fulllength S. japonica vBPO1 and S. japonica vBPO2 revealed the importance of vBPO among species of brown algae and the strong relationship between marine algal vBPOs and vIPOs. This study will enhance our understanding of the biological characteristics and economic values of S. japonica species. [ABSTRACT FROM AUTHOR] more...

Species of Sargassum are distributed worldwide, and are of great ecological and economic importance in marine ecosystems and bioresources. In this study, transcriptome sequencings of six Sargassum species were performed for the first time using an Illumina platform. For each sample, a total of 2.1-2.5 Gb of nucleotides are collected and assembled into 69 871-116 790 scaffolds, with an average length of 410-550 bp and N50 length of 756-1 462 bp. A total of 20 512-28 684 unigenes of each sample were annotated and compared well with known gene sequences from nr database. Clusters of Orthologous Groups (COG), gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were also performed for further understanding of gene functions and regulation pathways. Gene expression levels were calculated based on RPKM values and compared among these species, especially for those genes related to carbohydrate metabolism. Cluster analyses indicated that the differences of global gene expression between S. fusiforme, which was nominated as Hizikia fusiformis before, and other five species were not significant. Further phylogenetic analysis of 108 orthologous genes confirmed that S. fusiforme had closer relationship with S. hemiphyllum rather than S. horneri. These transcriptome data provided valuable information for better understanding of genome and gene characteristics of Sargassum algae and benefiting comparative and phylogenetic studies of Phaeophyceae species in future studies. [ABSTRACT FROM AUTHOR] more...

Betaphycus gelatinus, Kappaphycus alvarezii and Eucheuma denticulatum of Family Solieriaceae, Order Gigartinales, Class Rhodophyceae are three important carrageenan-producing red algal species, which produce different types of carrageenans, beta (β)-carrageenan, kappa (κ)-carrageenan and iota (ι)-carrageenan. So far the carrageenan biosynthesis pathway is not fully understood and few information is about the Solieriaceae genome and transcriptome sequence. Here, we performed the de novo transcriptome sequencing, assembly, functional annotation and comparative analysis of these three commercial-valuable species using an Illumina short-sequencing platform Hiseq 2000 and bioinformatic software. Furthermore, we compared the different expression of some unigenes involved in some pathways relevant to carrageenan biosynthesis. We finally found 861 different expressed KEGG orthologs which contained a glycolysis/gluconeogenesis pathway (21 orthologs), carbon fixation in photosynthetic organisms (16 orthologs), galactose metabolism (5 orthologs), and fructose and mannose metabolism (9 orthologs) which are parts of the carbohydrate metabolism. We also found 8 different expressed KEGG orthologs for sulfur metabolism which might be importantly related to biosynthesis of different types of carrageenans. The results presented in this study provided valuable resources for functional genomics annotation and investigation of mechanisms underlying the biosynthesis of carrageenan in Family Solieriaceae. [ABSTRACT FROM AUTHOR] more...

The chloroplast and mitochondrion of red algae (Phylum Rhodophyta) may have originated from different endosymbiosis. In this study, we carried out phylogenomic analysis to distinguish their evolutionary lineages by using red algal RNA-seq datasets of the 1 000 Plants (1KP) Project and publicly available complete genomes of mitochondria and chloroplasts of Rhodophyta. We have found that red algae were divided into three clades of orders, Florideophyceae, Bangiophyceae and Cyanidiophyceae. Taxonomy resolution for Class Florideophyceae showed that Order Gigartinales was close to Order Halymeniales, while Order Gracilariales was in a clade of Order Ceramials. We confirmed Prionitis divaricata (Family Halymeniaceae) was closely related to the clade of Order Gracilariales, rather than to genus Grateloupia of Order Halymeniales as reported before. Furthermore, we found both mitochondrial and chloroplastic genes in Rhodophyta under negative selection (Ka/Ks < 1), suggesting that red algae, as one primitive group of eukaryotic algae, might share joint evolutionary history with these two organelles for a long time, although we identified some differences in their phylogenetic trees. Our analysis provided the basic phylogenetic relationships of red algae, and demonstrated their potential ability to study endosymbiotic events. [ABSTRACT FROM AUTHOR] more...

Endogenous viral elements (EVEs) are host-genomic fragments originated from viral genomes. They have been found universally in animal and plant genomes. Here we carried out a systematic screening and analysis of EVEs in algal genomes and found that EVEs commonly exist in algal genomes. We classified the EVE fragments into three categories according to the length of EVE fragments. Due to the probability of sequence similarity by chance, we ignored the potential function of medium-length EVE fragments. However, longlength EVE fragments probably had capability to encode protein domains or even entire proteins, and some short-length EVE fragments had high similarity with host's siRNA sequences and possibly served functions of small RNAs. Therefore, short and long EVE fragments might provide regulomic and proteomic novelty to the host's metabolism and adaptation. We also found several EVE fragments shared by more than 3 algal genomes. By phylogenetic analysis of the shared EVEs and their corresponding species, we found that the integration of viral fragments into host genomes was an ancient event, possibly before the divergence of Chlorophytes and Ochrophytes. Our findings show that there is a frequent genetic flow from viruses to algal genomes. Moreover, study on algal EVEs shed light on the virus-host interaction in large timescale and could also help us understand the balance of marine ecosystems. [ABSTRACT FROM AUTHOR] more...

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Considering its high theoretical energy density and high safety, the all-solid-state lithium-sulfur battery (ASSLSB) has become a promising candidate for the next-generation energy storage system. However, the low reactivity of sulfur and high interfacial resistances between the cathodes and solid electrolytes seriously hinder the practical application of high performance ASSLSBs. Sulfurized polyacrylonitrile (S@pPAN), which can effectively alleviate the volume expansion of sulfur, is a suitable choice for the sulfur cathode, but shows limited performance in ASSLSB. Here, we demonstrate a tellurium-doped S@pPAN (Te 0.05 S 0.95 @pPAN) cathode coated with solid electrolyte (Li 7 P 3 S 11) for an ASSLSB with high reactivity and significant cycling stability. Benefiting from the thin layer coating of Li 7 P 3 S 11 and the effect of Te-doping, the Te 0.05 S 0.95 @pPAN@Li 7 P 3 S 11 composite delivers significantly enhanced reaction kinetics and excellent interfacial compatibility with the solid electrolyte. At room temperature, the assembled ASSLSB exhibits excellent rate and long cycling performance, with a reversible capacity over 1173.1 mAh g−1 and stable cycling over 500 cycles. The strategy of Te-doping and surface coating not only is facile and promising, but also provides guidance for constructing applicable ASSLSBs. A facile strategy involving Te-doping and surface coating is demonstrated in modifying sulfurized polyacrylonitrile (S@pPAN) cathode for all-solid-state lithium-sulfur battery (ASSLSB). Benefiting from the thin layer coating of Li 7 P 3 S 11 and the effect of Te-doping, the Te 0.05 S 0.95 @pPAN@Li 7 P 3 S 11 composite exhibits elevated reactivity and cycling stability, resulting in a high performance ASSLSB. Image 1 ● A facile strategy using Te-doping and surface coating is shown to modify the cathode for a high performance all-solid-state lithium-sulfur battery. ● Through an in situ liquid-phase approach, a thin solid electrolyte (Li 7 P 3 S 11) is coated on the surface of Te-doped sulfurized polyacrylonitrile. ● The combination of Te-doping and surface coating leads to enhanced reactivity and cycling stability in the all-solid-state battery. [ABSTRACT FROM AUTHOR] more...

Simple Summary: The present study aimed to characterize the complete mitochondrial genome of Streptopelia decaocto (Frivaldszky, 1838) and investigated the evolutionary relationships among species within the Columbidae family. The mtDNA full sequence length of S. decaocto was 17,160 bp. The mitogenome of S. decaocto comprised 13 PCGs, 22 tRNA genes, 2 rRNA genes, non-coding regions, and a control region. Analysis of the entire mtDNA of S. decaocto revealed consistently positive AT-skew values, except for nad3, nad6, and the D-loop. Conversely the GC-skew values were consistently negative, except for nad6. These findings suggest that S. decaocto belongs to the Columbinae subfamily. In this research, the mitochondrial genome of the Streptopelia decaocto was sequenced and examined for the first time to enhance the comprehension of the phylogenetic relationships within the Columbidae. The complete mitochondrial genome of Streptopelia decaocto (17,160 bp) was structurally similar to the recognized members of the Columbidae family, but with minor differences in gene size and arrangement. The structural AT content was 54.12%. Additionally, 150 mitochondrial datasets, representing valid species, were amassed in this investigation. Maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees and evolutionary time relationships of species were reconstructed based on cytb gene sequences. The findings from the phylogenetic evaluations suggest that the S. decaocto was classified under the Columbinae subfamily, diverging from the Miocene approximately 8.1 million years ago, indicating intricate evolutionary connections with its close relatives, implying a history of species divergence and geographic isolation. The diversification of the Columbidae commenced during the Late Oligocene and extended into the Miocene. This exploration offers crucial molecular data for the S. decaocto, facilitating the systematic taxonomic examination of the Columbidae and Columbiformes, and establishing a scientific foundation for species preservation and genetic resource management. [ABSTRACT FROM AUTHOR] more...

Simple Summary: The water environment in Laizhou Bay has experienced mild eutrophication in recent years, impacting the interactions between environmental factors, microorganisms, and aquatic species. The metagenomic analysis of 142 samples from various water layers revealed that Oplegnathus punctatus mariculture significantly increases microbial abundance and complexity in the culture area. These alterations were more noticeable in sediments compared to seawater. Cyanobacteria and Candidatus Micrarchaeota in seawater, and Actinobacteria and Thaumarchaeota in sediments show notably higher abundances in the mariculture area, indicating shifts in microbial community structure due to aquaculture practices. Antibiotic resistance genes (ARGs) in sediments are highly sensitive to environmental variables, particularly oxygen solubility and salinity. This indicates that Oplegnathus punctatus mariculture can impact the occurrence and spread of antibiotic resistance in marine ecosystems. The study underscores the intricate and dynamic relationships between microorganisms, environmental conditions, and ARGs, highlighting the need for region-specific strategies in managing marine resources sustainably. (1) Background: Laizhou Bay is an important aquaculture area in the north of China. Oplegnathus punctatus is one of the species with high economic benefits. In recent years, the water environment of Laizhou Bay has reached a mild eutrophication level, while microorganisms are an important group between the environment and species. In this study, we evaluated alterations in environmental elements, microbial populations, and antibiotic resistance genes (ARGs) along with their interconnections during Oplegnathus punctatus net culture. (2) Methods: A total of 142 samples from various water layers were gathered for metagenome assembly analysis. Mariculture increases the abundance of microorganisms in this culture area and makes the microbial community structure more complex. The change had more significant effects on sediment than on seawater. (3) Results: Certain populations of cyanobacteria and Candidatus Micrarchaecta in seawater, and Actinobacteria and Thaumarchaeota in sediments showed high abundance in the mariculture area. Antibiotic resistance genes in sediments were more sensitive to various environmental factors, especially oxygen solubility and salinity. (4) Conclusions: These findings highlight the complex and dynamic nature of microorganism–environment–ARG interactions, characterized by regional specificity and providing insights for a more rational use of marine resources. [ABSTRACT FROM AUTHOR] more...

Betaphycus Doty, Eucheuma J. Agardh, and Kappaphycus Doty (Solieriaceae, Gigartinales) are the three most commercially important seaweed genera that produce carrageenan. In the present study we provide mitogenomes of Betaphycus gelatinus, Eucheuma denticulatum and Kappaphycus alvarezii. The mitogenomes of these three species contain a set of 50 genes, including 24 protein-coding genes, 2 rRNA genes, and 24 tRNA genes. The mitogenome length ranges from 25,198 bp (Kappaphycus alvarezii) to 25,327 bp (Eucheuma denticulatum). As compared with the previous published mitogenomes of Florideophyceae species, only the species in Gelidiaceae and Pterocladiaceae have smaller mitochondrial genome size than these reported here. At the junction of two transcription units, we identified a stem-loop structure in six representative Gigartinales species, which is presumed to play an important role in the replication and transcription of mitochondrial genes. In Gigartinales the difference in gene order among the four Solieriaceae (B. gelatinus, E. denticulatum, K. alvarezii, K. striatus) and other two Gigartinales species (Chondrus crispus and Mastocarpus papillatus) can be explained by inversion of two tRNA genes. Collinearity analysis of the 12 mitochondrial genomes of Florideophyceae showed considerable sequence synteny across all the species compared, with the exception of a highly variable region between atp6 and rpl20 genes. Phylogenetic analyses based on 21 shared mitochondrial genes showed that the four Solieriaceae species form one clade (Solieriaceae clade). Within this clade, B. gelatinae is basal relative to the other three species. The genus Kappaphycus is more closely related to Eucheuma than Betaphycus. [ABSTRACT FROM AUTHOR] more...

Tubulin is the target for very widely used anti-tumor drugs, including Vinca alkaloids, taxanes, and epothilones, which are an important component of chemotherapy in breast cancer and other malignancies. Paclitaxel and other tubulin-targeting drugs bind to the β subunit of tubulin, which is a heterodimer of α and β subunits. β-Tubulin exists in the form of multiple isotypes, which are differentially expressed in normal and neoplastic cells and differ in their ability to bind to drugs. Among them, the βIII isotype is overexpressed in many aggressive and metastatic cancers and may serve as a prognostic marker in certain types of cancer. The underpinning mechanisms accounting for the overexpression of this isotype in cancer cells are unclear. To better understand the role of β-tubulin isotypes in cancer, we analyzed over 1000 clones from 90 breast cancer patients, sequencing their β-tubulin isotypes, in search of novel mutations. We have elucidated two putative emerging molecular subgroups of invasive breast cancer, each of which involve mutations in the βI-, βIIA-, or βIVB isotypes of tubulin that increase their structural, and possibly functional, resemblance to the βIII isotype. A unifying feature of the first of the two subgroups is the mutation of the highly reactive C239 residue of βI- or βIVB-tubulin to L239, R239, Y239, or P239, culminating in probable conversion of these isotypes from ROS-sensitive to ROS-resistant species. In the second subgroup, βI, βIIA, and βIVB have up to seven mutations to the corresponding residues in βIII-tubulin. Given that βIII-tubulin has emerged as a pro-survival factor, overexpression of this isotype may confer survival advantages to certain cancer cell types. In this mini-review, we bring attention to a novel mechanism by which cancer cells may undergo adaptive mutational changes involving alternate β-tubulin isotypes to make them acquire some of the pro-survival properties of βIII-tubulin. These 'hybrid' tubulins, combining the sequences and/or properties of two wild-type tubulins (βIII and either βI, βIIA, or βIVB), are novel isotypes expressed solely in cancer cells and may contribute to the molecular understanding and stratification of invasive breast cancer and provide novel molecular targets for rational drug development. [ABSTRACT FROM AUTHOR] more...

Marine organisms are threatened by various environmental contaminants, and nanoplastics (NPs) is one of the most concerned. Studied have shown that NPs has a certain impact on marine organisms, but the specific molecular mechanism is still unclear. At present, researches on the effect of NPs on marine life mostly focus on crustaceans, gastropods, and bivalves. In this study, cephalopod Sepia esculenta larvae were first used to investigate the potential immune response molecular mechanisms caused by PS-NPs (50 nm, 50 mg/L) short-term exposure (4 and 24 h). Through S. esculenta larvae transcriptome profile of gene expression analysis, 548 and 1990 genes showed differential expression at 4 and 24 h after NPs exposure, respectively. GO and KEGG enrichment analysis were performed to find immune related DEGs. Then, the interaction relationship between the immune related DEGs after NPs exposure was known through the constructed protein-protein interaction network. 20 hub genes were found on the base of KEGG pathway numbers involved and protein-protein interaction numbers. This research supply valuable genes for the study of cephalopod immune response caused by NPs, which can help us further uncover the molecular mechanisms of organism against NPs. • This study is the first transcriptome analysis in cephalopod larvae exposed to NPs. • The effect of NPs on S. esculenta larvae is time-dependent. • Twenty speculated immune-related hub genes are helpful to reveal the immune response mechanisms of S. esculenta against NPs. [ABSTRACT FROM AUTHOR] more...

Understanding the response of soil aggregates and soil carbon pools to different tillage practices is an important way to illustrate the role of conservation tillage in climate change mitigation. Therefore, a long-term tillage experiment was conducted from 2007 to 2020 with four tillage practices: 1) The rotational tillage practice consisting of no-tillage in the first year, conventional tillage in the second year, subsoiling in the third year and a cycle of three years (NCS); 2) no-tillage (NT); 3) subsoiling (ST); and 4) conventional tillage (CT) to explore the relationship among soil aggregates, soil carbon pools, soil carbon sequestration and emissions. After long-term experiment, NCS and NT improved the soil total organic carbon (TOC) stock by 14.4% and 9.0% compared with CT in the 0–40 cm soil depth. Meanwhile, NCS, NT, ST decreased carbon emissions by 18.6∼36.6% during the observation period, when compared with CT. Partial least squares path model revealed that soil aggregates structures and soil carbon pools stability were the main causes of soil carbon sequestration and emissions affected by conservation tillage. NCS, NT and ST increased soil aggregates proportion, mean weight diameter, geometric mean diameter and aggregates associated carbon compared with CT. Meanwhile, NCS and NT improved the carbon pools management index (CPMI) by 11.1% and 16.5%, respectively. The increased stability of soil aggregates and the improvement of soil carbon pools reduced soil carbon emissions and increased soil carbon sequestration. However, NT and ST significantly increased the TOC stratification ratios (SR) by 38.8% and 30.1% in the 0–10 and 10–20 cm soil depth compared with NCS, which was not conducive to the vertical distribution of TOC. In additional, NCS, NT and ST increased yield by 16.7∼22.6% compared with CT. Collectively, based on the combined effects of environmental protection, production, and soil physicochemical property improvement, we recommend NCS (with highest comprehensive index: 6.76) as a sustainable tillage practice that can improve yield with ecological effects. • Rotational tillage improves the vertical distribution characteristic of soil carbon. • Soil aggregate structure directly promote soil carbon sequestration. • The protective effect of aggregates on organic carbon reduces CO 2 emissions. • Rotational tillage has a combined yield and ecological effect. [ABSTRACT FROM AUTHOR] more...

The first order Hardy–Trudinger–Moser type inequalities were only known in two dimensional hyperbolic space B 2 in the literature (Wang and Ye, 2012; Mancini et al., 2013; Lu and Yang, 2016). In this paper, we establish the Hardy–Trudinger–Moser inequalities in any N -dimensional hyperbolic spaces B N for N ≥ 2. Namely, for any N ≥ 2 there exists a constant C = C (N) > 0 such that for all u ∈ W 0 1 , N (B N) with ∫ B N | ∇ H u | N d V − N − 1 N N ∫ B N | u | N d V ≤ 1 , there holds ∫ B N Φ N (β N | u | N N − 1 ) d V ≤ C and ∫ B N e β N | u | N N − 1 d x ≤ C , where d V = 2 1 − | x | 2 N d x is the hyperbolic volume, ∇ H u is the hyperbolic gradient, β N = N N π N 2 Γ (N 2 + 1) 1 N − 1 and Φ N (t) = e t − ∑ k = 0 N − 1 t k k !. In the two dimensional case N = 2 , we further establish that if and only if λ < 1 4 there exists a constant C ′ = C ′ (λ) > 0 such that for all u ∈ W 0 1 , 2 (B 2) with ∫ B 2 | ∇ H u | 2 d V − 1 4 ∫ B 2 | u | 2 d V − λ ∫ B 2 (1 − | x | 2) | u | 2 d V ≤ 1 , there holds ∫ B 2 e 4 π u 2 − 1 − 4 π u 2 (1 − | x | 2) 2 d x ≤ C ′ and ∫ B 2 e 4 π u 2 d x ≤ C ′. In fact, 1 4 is the sharp constant on the right hand side of the following inequality ∫ B 2 | ∇ H u | 2 d V − 1 4 ∫ B 2 | u | 2 d V ≥ 1 4 ∫ B 2 (1 − | x | 2) | u | 2 d V. These improve the known results in dimension two in the literature. [ABSTRACT FROM AUTHOR] more...

Betaphycus, Eucheuma and Kappaphycus (Gigartinales, Florideophyceae) are the most commercially important genera of the family Solieriaceae that produce carrageenan. Here, three complete plastid genomes of Betaphycus gelatinus, Eucheuma denticulatum and Kappaphycus striatus were fully sequenced using next-generation sequencing technology. Genome organizations and gene contents of the three plastid genomes were highly alike. They all had circular mapping organizations and the sizes were 178,394 bp (B. gelatinus), 177,003 bp (E. denticulatum), and 176,763 bp (K. striatus). They encoded almost the same set of plastid genes (238–240), including 202 to 204 protein-encoding genes, 30 transfer RNA genes (tRNAs), 3 ribosomal RNA genes (rRNAs), 2 misc_RNAs (ffs, rnpB), and 1 transfer-messenger RNA gene (tmRNA). One group II intron interrupting the trnMe gene was identified in each of these three plastid genomes. Other three plastid genomes from species of the order Gigartinales including Kappaphycus alvarezii, Chondrus crispus and Mastocarpus papillatus have been reported. The plastid genome organization at the level of the order Gigartinales was highly conserved. Co-linear analysis among the six plastid genomes of the Gigartinales showed the considerable sequence synteny with the exception of one remarkable gene rearrangement. The approximately 12.5-kb gene fragment from gene psaM to ycf21 in plastid genomes of the four species of the Solieriaceae was completely reversed compared to that of M. papillatus and C. crispus. It might be used as the potential phylogenetic markers uniting the species of the Solieriaceae. In addition, phylogenetic analysis based on 138 shared protein-encoding genes from 53 Florideophyceae plastid genomes indicated all species were clearly divided into five clades corresponding to their subclasses. The results suggested there was a non-monophyletic relationship of the order Gigartinales. Four species of the family Solieriaceae formed one clade and E. denticulatum was basal relative to the other three species. The novel plastid genomes expand the available plastid pool for red algae which would facilitate the phylogenetic study in algae. [ABSTRACT FROM AUTHOR] more...