Tracing Organophosphate Ester Pollutants in Hadal Trenches─Distribution, Possible Origins, and Transport Mechanisms.

Unraveling the mysterious pathways of pollutants to the deepest oceanic realms holds critical importance for assessing the integrity of remote marine ecosystems. This study tracks the transport of pollutants into the depths of the oceans, a key step in protecting the sanctity of these least explored ecosystems. By analyzing hadal trench samples from the Mariana, Mussau, and New Britain trenches, we found the widespread distribution of organophosphate ester (OPE) flame retardants but a complex transport pattern for the OPE in these regions. In the Mariana Trench seawater column, OPE concentrations range between 17.4 and 102 ng L-1, with peaks at depths of 500 and 4000 m, which may be linked to Equatorial Undercurrent and topographic Rossby waves, respectively. Sediments, particularly in Mariana (422 ng g-1 dw), showed high OPE affinity, likely due to organic matter serving as a transport medium, influenced by "solvent switching", "solvent depletion", and "filtering processes". Amphipods in the three trenches had consistent OPE levels (29.1-215 ng g-1 lipid weight), independent of the sediment pollution patterns. The OPEs in these amphipods appeared more linked to surface-dwelling organisms, suggesting the influence of "solvent depletion". This study highlights the need for an improved understanding of deep-sea pollutant sources and transport, urging the establishment of protective measures for these remote marine habitats.

Complex economic decisions from simple neurocognitive processes: the role of interactive attention.

Neurocognitive theories of value-based choice propose that people additively accumulate choice attributes when making decisions. These theories cannot explain the emergence of complex multiplicative preferences such as those assumed by prospect theory and other economic models. We investigate an interactive attention mechanism, according to which attention to attributes (like payoffs) depends on other attributes (like probabilities) attended to previously. We formalize this mechanism using a Markov attention model combined with an accumulator decision process, and test our model on eye-tracking and mouse-tracking data in risky choice. Our tests show that interactive attention is necessary to make good choices, that most participants display interactive attention and that allowing for interactive attention in accumulation-based decision models improves their predictions. By equipping established decision models with sophisticated attentional dynamics, we extend these models to describe complex economic choice, and in the process, we unify two prominent theoretical approaches to studying value-based decision making.

Information acquisition and decision strategies in intertemporal choice.

Intertemporal decision models describe choices between outcomes with different delays. While these models mainly focus on predicting choices, they make implicit assumptions about how people acquire and process information. A link between information processing and choice model predictions is necessary for a complete mechanistic account of decision making. We establish this link by fitting 18 intertemporal choice models to experimental datasets with both choice and information acquisition data. First, we show that choice models have highly correlated fits: people that behave according to one model also behave according to other models that make similar information processing assumptions. Second, we develop and fit an attention model to information acquisition data. Critically, the attention model parameters predict which type of intertemporal choice models best describes a participant's choices. Overall, our results relate attentional processes to models of intertemporal choice, providing a stepping stone towards a complete mechanistic account of intertemporal decision making.

Cerebellum anatomy predicts individual risk-taking behavior and risk tolerance.

Human risk tolerance is highly idiosyncratic and individuals often show distinctive preferences when faced with similar risky situations. However, the neural underpinnings of individual differences in risk-taking remain unclear. Here we combined structural and perfusion MRI and examined the associations between brain anatomy and individual risk-taking behavior/risk tolerance in a sample of 115 healthy participants during the Balloon Analogue Risk Task, a well-established sequential risky decision paradigm. Both whole brain and region-of-interest analyses showed that the left cerebellum gray matter volume (GMV) has a strong association with individual risk-taking behavior and risk tolerance, outperforming the previously reported associations with the amygdala and right posterior parietal cortex (PPC) GMV. Left cerebellum GMV also accounted for risk tolerance and risk-taking behavior changes with aging. However, regional cerebral blood flow (CBF) provided no additional predictive power. These findings suggest a novel cerebellar anatomical contribution to individual differences in risk tolerance. Further studies are necessary to elucidate the underestimated important role of cerebellum in risk-taking.

Insights into the vision of the hadal snailfish Pseudoliparis swirei through proteomic analysis of the eye.

No sunlight can reach the hadal trench, but some fishes dwelling there still have apparent eye morphology. However, whether they are capable of sensing light remains unknown. In this study, the eyes of the dominant hadal endemic snailfish Pseudoliparis swirei from the Mariana Trench were analyzed using liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). A total of 2088 proteins were identified in the eye proteome, most of which had at least one hit against public databases and could be mapped to 316 metabolic pathways. Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways directly contributing to visual phototransduction were significantly enriched from the top 10% dominant proteins, implying abundant metabolic activities in the eye and it is still a functional visual organ. One rhodopsin was identified in the eye proteome, sequence analysis indicated that it might have an absorption maximum at ∼480 nm and be sensitive to dim blue light. In addition, proteins that might contribute to extreme environment adaptation, such as heat shock proteins and chaperonin-containing T-complex protein 1, were also highly expressed in the eye. Overall, these results provide insights into the molecular mechanism underlying the vision of hadal snailfish and provide a useful database for further research.

Characteristics of Two Crustins from Alvinocaris longirostris in Hydrothermal Vents.

Crustins are widely distributed among different crustacean groups. They are characterized by a whey acidic protein (WAP) domain, and most examined Crustins show activity against Gram-positive bacteria. This study reports two Crustins, Al-crus 3 and Al-crus 7, from hydrothermal vent shrimp, Alvinocaris longirostris. Al-crus 3 and Al-crus 7 belong to Crustin Type IIa, with a similarity of about 51% at amino acid level. Antibacterial assays showed that Al-crus 3 mainly displayed activity against Gram-positive bacteria with MIC50 values of 10-25 µM. However, Al-crus 7 not only displayed activity against Gram-positive bacteria but also against Gram-negative bacteria Imipenem-resistant Acinetobacter baumannii, in a sensitive manner. Notably, in the effective antibacterial spectrum, Methicillin-sensitive Staphylococcus aureus, Escherichia coli (ESBLs) and Imipenem-resistant A. baumannii were drug-resistant pathogens. Narrowing down the sequence to the WAP domain, Al-crusWAP 3 and Al-crusWAP 7 demonstrated antibacterial activities but were weak. Additionally, the effects on bacteria did not significantly change after they were maintained at room temperature for 48 h. This indicated that Al-crus 3 and Al-crus 7 were relatively stable and convenient for transportation. Altogether, this study reported two new Crustins with specific characteristics. In particular, Al-crus 7 inhibited Gram-negative imipenem-resistant A. baumannii.

Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli.

BACKGROUND: The metabolic capacity, stress response and evolution of uncultured environmental Tenericutes have remained elusive, since previous studies have been largely focused on pathogenic species. In this study, we expanded analyses on Tenericutes lineages that inhabit various environments using a collection of 840 genomes. RESULTS: Several environmental lineages were discovered inhabiting the human gut, ground water, bioreactors and hypersaline lake and spanning the Haloplasmatales and Mycoplasmatales orders. A phylogenomics analysis of Bacilli and Tenericutes genomes revealed that some uncultured Tenericutes are affiliated with novel clades in Bacilli, such as RF39, RFN20 and ML615. Erysipelotrichales and two major gut lineages, RF39 and RFN20, were found to be neighboring clades of Mycoplasmatales. We detected habitat-specific functional patterns between the pathogenic, gut and the environmental Tenericutes, where genes involved in carbohydrate storage, carbon fixation, mutation repair, environmental response and amino acid cleavage are overrepresented in the genomes of environmental lineages, perhaps as a result of environmental adaptation. We hypothesize that the two major gut lineages, namely RF39 and RFN20, are probably acetate and hydrogen producers. Furthermore, deteriorating capacity of bactoprenol synthesis for cell wall peptidoglycan precursors secretion is a potential adaptive strategy employed by these lineages in response to the gut environment. CONCLUSIONS: This study uncovers the characteristic functions of environmental Tenericutes and their relationships with Bacilli, which sheds new light onto the pathogenicity and evolutionary processes of Mycoplasmatales.

"Unicorn from Hades", a new genus of Mysidae (Malacostraca: Mysida) from the Mariana Trench, with a systematic analysis of the deep-sea mysids.

Since the 19th century, oceanic explorations have confirmed that the hadal zone (water depth > 6000 m) is not lifeless, but contains many fascinating organisms. Amongst them are the Mysida, which is a group of crustaceans found in many deep-sea trenches. Based on morphological observations and molecular phylogenetic analyses of an undescribed taxon within the subfamily Erythropinae, a new genus of deep-sea mysids, Xenomysis gen. n., is described from the Challenger Deep in the Mariana Trench. The new genus is not assigned to any of the tribes within the Erythropinae, as our analyses do not support the current classification scheme of Erythropinae. The result of a molecular-clock analysis with fossil calibration reveals that several groups of Mysida have independently colonized deep water habitats in different geological periods, from Triassic to Cretaceous. In addition, ancestral state reconstruction analyses indicate the degenerate eyes in both Mysidae and Petalophthalmidae is a result of parallel evolution, and the reduction of compound eyes to both "single fused eyeplate" and "two separate eyeplates" occurred multiple times independently in the evolution of Erythropinae.

Occurrence of Halogenated Organic Pollutants in Hadal Trenches of the Western Pacific Ocean.

The hadal trenches are the most remote and inaccessible habitats on earth and were once believed to be pristine. A recent study has reported the detection of high levels of persistent organic pollutants (POPs), including polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs), in endemic amphipods from two hadal trenches (Mariana and Kermadec) in the Western Pacific, implicating that the trenches are indeed polluted. However, a fundamental question remains unanswered, if and to what extent such the physical environment of the trenches is polluted by POPs. In this study, we sampled Mariana, Mussau, and New Britain trenches and analyzed samples of amphipods, sediment, and suspended particulate matter (SPM). Our results show that the amphipods contained elevated levels of PCBs and PBDEs, comparable to those reported in the earlier study. We also detected significantly high concentrations (up to 1343 ng g-1 lw) of chlorinated pesticides, such as dichlorodiphenyltrichloroethanes and chlordanes. Furthermore, four brominated natural products (BNPs), which structurally resembled methoxylated brominated diphenyl ethers or polybrominated biphenyls, were identified in the endemic amphipods. However, neither POPs nor BNPs were detected in sediments or SPM. Taken together, we propose that the POPs detected in endemic amphipods likely resulted from bioaccumulation by feeding on polluted large detritus (e.g., carrion) falling to the trench bottoms from the surface ocean.

Overexpression of Bone Morphogenetic Protein-1 Promotes Osteogenesis of Bone Marrow Mesenchymal Stem Cells In Vitro.

BACKGROUND Osteogenesis of bone marrow mesenchymal stem cells (BMSCs) is an important research topic in the application of bone tissue engineering. Bone morphogenetic protein-1 (BMP-1) is important in bone formation and stability, but its effects on the osteogenesis of BMSCs are unclear. This study aimed to investigate the association of BMP-1 with the osteogenic capacity of BMSCs. MATERIAL AND METHODS Primary rabbit BMSCs were cultured and divided into a BMP-1-overexpressing group, a Green Fluorescent Protein-expressing (GFP) group, and a Control group. The transfection efficiency of BMP-1 was tested by Western blotting. Cell viabilities, alkaline phosphatase (ALP) activities, Ca2+ concentrations, and gross examinations of BMSC sheets were examined at different times. The osteogenic marker collagen I was assessed by immunohistochemical analysis. RESULTS The cell viability, ALP activity, and Ca2+ content of the BMP1-overexpressed group were significantly enhanced compared with the GFP group and Control group. Immunohistochemistry staining results showed that BMP-1 promoted the expression of type I collagen in BMSCs sheets. CONCLUSIONS Our results suggest that the overexpression of BMP-1 can promote the osteogenesis of BMSCs and provides an improved method of cell-based tissue engineering.

Unique tRNA gene profile suggests paucity of nucleotide modifications in anticodons of a deep-sea symbiotic Spiroplasma.

The position 34 of a tRNA is always modified for efficient recognition of codons and accurate integration of amino acids by the translation machinery. Here, we report genomics features of a deep-sea gut symbiotic Spiroplasma, which suggests that the organism does not require tRNA(34) anticodon modifications. In the genome, there is a novel set of tRNA genes composed of 32 species for recognition of the 20 amino acids. Among the anticodons of the tRNAs, we witnessed the presence of both U34- and C34-containing tRNAs required to decode NNR (A/G) 2:2 codons as countermeasure of probable loss of anticodon modification genes. In the tRNA fragments detected in the gut transcriptome, mismatches expected to be caused by some tRNA modifications were not shown in their alignments with the corresponding genes. However, the probable paucity of modified anticodons did not fundamentally change the codon usage pattern of the Spiroplasma. The tRNA gene profile that probably resulted from the paucity of tRNA(34) modifications was not observed in other symbionts and deep-sea bacteria, indicating that this phenomenon was an evolutionary dead-end. This study provides insights on co-evolution of translation machine and tRNA genes and steric constraints of codon-anticodon interactions in deep-sea extreme environment.

Insights into the Synthesis, Secretion and Curing of Barnacle Cyprid Adhesive via Transcriptomic and Proteomic Analyses of the Cement Gland.

Barnacles represent one of the model organisms used for antifouling research, however, knowledge regarding the molecular mechanisms underlying barnacle cyprid cementation is relatively scarce. Here, RNA-seq was used to obtain the transcriptomes of the cement glands where adhesive is generated and the remaining carcasses of Megabalanus volcano cyprids. Comparative transcriptomic analysis identified 9060 differentially expressed genes, with 4383 upregulated in the cement glands. Four cement proteins, named Mvcp113k, Mvcp130k, Mvcp52k and Mvlcp1-122k, were detected in the cement glands. The salivary secretion pathway was significantly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the differentially expressed genes, implying that the secretion of cyprid adhesive might be analogous to that of saliva. Lysyl oxidase had a higher expression level in the cement glands and was speculated to function in the curing of cyprid adhesive. Furthermore, the KEGG enrichment analysis of the 352 proteins identified in the cement gland proteome partially confirmed the comparative transcriptomic results. These results present insights into the molecular mechanisms underlying the synthesis, secretion and curing of barnacle cyprid adhesive and provide potential molecular targets for the development of environmentally friendly antifouling compounds.

Mutual regulation of JAG2 and PRAF2 promotes migration and invasion of colorectal cancer cells uncoupled from epithelial-mesenchymal transition.

BACKGROUND: Our previous studies revealed that Jagged 2 (JAG2) is involved in the regulation of migration and invasion of colon cancer cells without affecting cell proliferation. This study further explored the specific mechanism by which JAG2 promotes migration and invasion of colorectal cancer cells. METHODS: JAG2 mRNA expression in different clinical stages of colorectal cancer and normal intestinal tissues was detected by quantitative PCR (QPCR). QPCR and Western Blot were used to analyze the differential expression of JAG2 mRNA and protein between normal human colon tissue cells and various colorectal cancer cells. Co-expression status of JAG2 and epithelial-mesenchymal transition (EMT) markers in colon cancer tissues and cells was analyzed. The difference between TGF-ß-induced EMT model and the JAG2 overexpression model were compared in promoting migration and invasion of HT29 cells. HT29 cells were treated with EMT pathway inhibitors (LY2157299 and Slug siRNA) to identify a cross-talk between the JAG2 effect and the Notch pathway. Co-expressed genes of JAG2 in colorectal cancer cells were identified using siRNA and transcriptome microarray technology. The mutual regulation of JAG2 and the co-expressed gene PRAF2 and the regulation of the paracrine effect of exosomes were analyzed. RESULTS: JAG2 was abnormally expressed in colorectal cancer tissues and directly related to clinical stages. Similar to the findings in tissues, the expression of both JAG2 mRNA and protein was significantly increased in the colorectal cancer cell lines compared with that of normal colorectal cell line CCD18-Co. It was shown in our cell model that JAG2 was involved in the regulation of migration and invasion independent of the canonical Notch signaling pathway. More interestingly, JAG2 also promoted the migration and invasion of colon cancer cells in a non-EMT pathway. Further analysis revealed the co-expression of JAG2 with PRAF2 in colorectal cancer cells. JAG2-rich exosomes were released from colorectal cancer cells in a PRAF2-dependent way, while these exosomes regulated the metastasis of colorectal cancer cells in a paracrine manner. CONCLUSIONS: This is the evidence supporting the biological function of JAG2 through non-canonical Notch and non-EMT-dependent pathways and also the first demonstration of the functions of PRAF2 in colorectal cancer cells. These findings also provide theoretical basis for the development of small molecules or biological agents for therapeutic intervention targeting JAG2/PRAF2.

Variable time preference.

We re-examine behavioral patterns of intertemporal choice with recognition that time preferences may be inherently variable, focusing in particular on the explanatory power of an exponential discounting model with variable discount factors - the variable exponential model. We provide analytical results showing that this model can generate systematically different choice patterns from an exponential discounting model with a fixed discount factor. The variable exponential model accounts for the common behavioral pattern of decreasing impatience, which is typically attributed to hyperbolic discounting. The variable exponential model also generates violations of strong stochastic transitivity in choices involving intertemporal dominance. We present the results of two experiments designed to evaluate the variable exponential model in terms of quantitative fit to individual-level choice data. Data from these experiments reveal that allowing for a variable discount factor significantly improves the fit of the exponential model, and that a variable exponential model provides a better account of individual-level choice probabilities than hyperbolic discounting models. In a third experiment we find evidence of strong stochastic transitivity violations when intertemporal dominance is involved, in accordance with the variable exponential model. Overall, our analytical and experimental results indicate that exponential discounting can explain intertemporal choice behavior that was supposed to be beyond its descriptive scope if the discount factor is permitted to vary at random. Our results also highlight the importance of allowing for different sources of randomness in choice modeling.

Spatial-Resolution Cell Type Proteome Profiling of Cancer Tissue by Fully Integrated Proteomics Technology.

Increasing attention has been focused on cell type proteome profiling for understanding the heterogeneous multicellular microenvironment in tissue samples. However, current cell type proteome profiling methods need large amounts of starting materials which preclude their application to clinical tumor specimens with limited access. Here, by seamlessly combining laser capture microdissection and integrated proteomics sample preparation technology SISPROT, specific cell types in tumor samples could be precisely dissected with single cell resolution and processed for high-sensitivity proteome profiling. Sample loss and contamination due to the multiple transfer steps are significantly reduced by the full integration and noncontact design. H&E staining dyes which are necessary for cell type investigation could be selectively removed by the unique two-stage design of the spintip device. This easy-to-use proteome profiling technology achieved high sensitivity with the identification of more than 500 proteins from only 0.1 mm2 and 10 µm thickness colon cancer tissue section. The first cell type proteome profiling of four cell types from one colon tumor and surrounding normal tissue, including cancer cells, enterocytes, lymphocytes, and smooth muscle cells, was obtained. 5271, 4691, 4876, and 2140 protein groups were identified, respectively, from tissue section of only 5 mm2 and 10 µm thickness. Furthermore, spatially resolved proteome distribution profiles of enterocytes, lymphocytes, and smooth muscle cells on the same tissue slices and across four consecutive sections with micrometer distance were successfully achieved. This fully integrated proteomics technology, termed LCM-SISPROT, is therefore promising for spatial-resolution cell type proteome profiling of tumor microenvironment with a minute amount of clinical starting materials.

Toward understanding barnacle cementing by characterization of one cement protein-100kDa in Amphibalanus amphitrite.

Barnacles, as major fouling organisms, have attracted more attentions. It is no doubt that the study on cement proteins is required to illustrate the mechanism of barnacle cementing. A cement protein defined as Aa-cp100k was characterized from Amphibalanus amphitrite in this study. The amino acid sequence of Aa-cp100k was shown a high similarity to other three barnacles including Megabalanus rosa (Mr-cp100k), Tetraclita japonica formosana (Tj-cp100k) and Pollicipes pollicipes (Pp-cp100k). Moreover, the localization of Aa-cp100k in the vacuoles of cyprid ß secretory cells and the adult cement gland cells by immunofluorescence microscopy, indicating that Aa-cp100k existed in both cyprid and adult barnacle. Aa-cp100k from basal plate could be dissolved in urea buffer without high concentration of dithiothreitol (DTT), different from that in Megabalanus rosa, implying diverse possible roles of cp100k in cementing.

The Enigmatic Genome of an Obligate Ancient Spiroplasma Symbiont in a Hadal Holothurian.

Protective symbiosis has been reported in many organisms, but the molecular mechanisms of the mutualistic interactions between the symbionts and their hosts are unclear. Here, we sequenced the 424-kbp genome of "Candidatus Spiroplasma holothuricola," which dominated the hindgut microbiome of a sea cucumber, a major scavenger captured in the Mariana Trench (6,140 m depth). Phylogenetic relationships indicated that the dominant bacterium in the hindgut was derived from a basal group of Spiroplasma species. In this organism, the genes responsible for the biosynthesis of amino acids, glycolysis, and sugar transporters were lost, strongly suggesting endosymbiosis. The highly decayed genome consists of two chromosomes and harbors genes coding for proteolysis, microbial toxin, restriction-methylation systems, and clustered regularly interspaced short palindromic repeats (CRISPRs), composed of three cas genes and 76 CRISPR spacers. The holothurian host is probably protected against invading viruses from sediments by the CRISPRs/Cas and restriction systems of the endosymbiotic spiroplasma. The protective endosymbiosis indicates the important ecological role of the ancient Spiroplasma symbiont in the maintenance of hadal ecosystems.IMPORTANCE Sea cucumbers are major inhabitants in hadal trenches. They collect microbes in surface sediment and remain tolerant against potential pathogenic bacteria and viruses. This study presents the genome of endosymbiotic spiroplasmas in the gut of a sea cucumber captured in the Mariana Trench. The extreme reduction of the genome and loss of essential metabolic pathways strongly support its endosymbiotic lifestyle. Moreover, a considerable part of the genome was occupied by a CRISPR/Cas system to provide immunity against viruses and antimicrobial toxin-encoding genes for the degradation of microbes. This novel species of Spiroplasma is probably an important protective symbiont for the sea cucumbers in the hadal zone.

Assessing the Quality of Life in Patients With Dentofacial Deformities Before and After Orthognathic Surgery.

PURPOSE: This study aimed to assess the effect of health-related quality of life (QoL) among patients with dentofacial deformities who underwent orthognathic surgery compared with a control group without dentofacial deformities by use of generic oral health and condition-specific approaches. PATIENTS AND METHODS: In this prospective study, 2 questionnaires were administered to 85 patients (31 male and 54 female patients) who were evaluated before undergoing orthognathic surgery. The Short Form Oral Health Impact Profile Questionnaire (OHIP-14) and the Orthognathic Quality of Life Questionnaire (OQLQ) were administered before and 5 to 7 months after orthognathic surgery. The control group comprised 96 young university student volunteers without dentofacial deformities. RESULTS: The questionnaires were collected 5 to 7 months after surgery. The preoperative scores of the patients and the control group were contrasted separately. The respondents' postoperative OHIP-14 and OQLQ scores were significantly lower (P < .001 for total scores). The preoperative OQLQ scores for all domains were significantly higher among the patients than among the controls (P < .001 for total scores), whereas the total scores and 3 subscale scores of the OHIP-14 in the functional and psychological domains were significantly higher among the patients than among the controls (P < .05 for total scores). The preoperative and postoperative OQLQ total scores were remarkably different between male and female patients (P < .05). The postoperative OQLQ total scores were considerably higher in older patients than in younger patients (P < .05). All patients in the Class III group who underwent double-jaw surgery showed remarkable changes after surgery (P < .001 for total scores). CONCLUSIONS: Patients with dentofacial deformities had a poorer QoL compared with the healthy population, especially in functional and psychological aspects. Orthognathic surgery had a significant positive impact on QoL. Patients with Class III malocclusion who underwent double-jaw surgery seemingly benefitted the most after surgery.

Molecular Characterization of a Novel N-Acetylneuraminate Lyase from a Deep-Sea Symbiotic Mycoplasma.

N-acetylneuraminic acid (Neu5Ac) based novel pharmaceutical agents and diagnostic reagents are highly required in medical fields. However, N-acetylneuraminate lyase（NAL）for Neu5Ac synthesis is not applicable for industry due to its low catalytic efficiency. In this study, we biochemically characterized a deep-sea NAL enzyme (abbreviated form: MyNal) from a symbiotic Mycoplasma inhabiting the stomach of a deep-sea isopod, Bathynomus jamesi. Enzyme kinetic studies of MyNal showed that it exhibited a very low Km for both cleavage and synthesis activities compared to previously described NALs. Though it favors the cleavage process, MyNal out-competes the known NALs with respect to the efficiency of Neu5Ac synthesis and exhibits the highest kcat/Km values. High expression levels of recombinant MyNal could be achieved (9.56 mol L-1 culture) with a stable activity in a wide pH (5.0-9.0) and temperature (40-60 °C) range. All these features indicated that the deep-sea NAL has potential in the industrial production of Neu5Ac. Furthermore, we found that the amino acid 189 of MyNal (equivalent to Phe190 in Escherichia coli NAL), located in the sugar-binding domain, GX189DE, was also involved in conferring its enzymatic features. Therefore, the results of this study improved our understanding of the NALs from different environments and provided a model for protein engineering of NAL for biosynthesis of Neu5Ac.

Molecular adaptation in the world's deepest-living animal: Insights from transcriptome sequencing of the hadal amphipod Hirondellea gigas.

The Challenger Deep in the Mariana Trench is the deepest point in the oceans of our planet. Understanding how animals adapt to this harsh environment characterized by high hydrostatic pressure, food limitation, dark and cold is of great scientific interest. Of the animals dwelling in the Challenger Deep, amphipods have been captured using baited traps. In this study, we sequenced the transcriptome of the amphipod Hirondellea gigas collected at a depth of 10,929 m from the East Pond of the Challenger Deep. Assembly of these sequences resulted in 133,041 contigs and 22,046 translated proteins. Functional annotation of these contigs was made using the go and kegg databases. Comparison of these translated proteins with those of four shallow-water amphipods revealed 10,731 gene families, of which 5659 were single-copy orthologs. Base substitution analysis on these single-copy orthologs showed that 62 genes are positively selected in H. gigas, including genes related to ß-alanine biosynthesis, energy metabolism and genetic information processing. For multiple-copy orthologous genes, gene family expansion analysis revealed that cold-inducible proteins (i.e., transcription factors II A and transcription elongation factor 1) as well as zinc finger domains are expanded in H. gigas. Overall, our results indicate that genetic adaptation to the hadal environment by H. gigas may be mediated by both gene family expansion and amino acid substitutions of specific proteins.