Structural dynamics of the heme pocket and intersubunit coupling in the dimeric hemoglobin from Scapharca inaequivalvis.

Cooperativity is essential for the proper functioning of numerous proteins by allosteric interactions. Hemoglobin from Scapharca inaequivalvis (HbI) is a homodimeric protein that can serve as a minimal unit for studying cooperativity. We investigated the structural changes in HbI after carbon monoxide dissociation using time-resolved resonance Raman spectroscopy and observed structural rearrangements in the Fe-proximal histidine bond, the position of the heme in the pocket, and the hydrogen bonds between heme and interfacial water upon ligand dissociation. Some of the spectral changes were different from those observed for human adult hemoglobin due to differences in subunit assembly and quaternary changes. The structural rearrangements were similar for the singly and doubly dissociated species but occurred at different rates. The rates of the observed rearrangements indicated that they occurred synchronously with subunit rotation and are influenced by intersubunit coupling, which underlies the positive cooperativity of HbI.

Comprehensive analysis on the regulation of differentially expressed of mRNA and ncRNA in different ovarian stages of ark shell Scapharca broughtonii.

BACKGROUND: Ovarian development is an important prerequisite and basis for animal reproduction. In many vertebrates, it is regulated by multiple genes and influenced by sex steroid hormones and environmental factors. However, relative information is limited in shellfish. To explore the biological functions and molecular mechanisms of mRNA and non-coding RNA that regulate ovarian development in Scapharca broughtonii, we performed whole transcriptome sequencing analysis on ovaries at three developmental stages. Furthermore, the biological processes involved in the differential expression of mRNA and ncRNA were analyzed. RESULTS: A total of 11,342 mRNAs, 6897 lncRNAs, 135 circRNAs, and 275 miRNAs were differentially expressed. By mapping the differentially expressed RNAs from the three developmental stages of Venn diagram, multiple groups of shared mRNAs and lncRNAs were found to be associated with ovarian development, with some mRNA and ncRNA functions associated with steroid hormone. In addition, we constructed and visualized the lncRNA/circRNA-miRNA-mRNA network based on ceRNA targeting relationships. CONCLUSIONS: These findings may facilitate our further understanding the mRNA and ncRNAs roles in the regulation of shellfish reproduction.

Effect of hypersalinic stress on hemocyte morphology and hemolymph cellular composition of the ark clam (Anadarakagoshimensis).

Bivalve mollusks as typical osmoconformers are unable to maintain a constant level of internal osmolarity in conditions of salinity stress. Adaptation to fluctuations of environmental salinity is achieved through cellular osmoregulatory responses, which are accompanied with a substantial shift in functional state of cells. In the present work we investigated the effect of hypersalinity stress on hemolymph cellular composition and morphology of the ark clam (Anadara kagoshimensis) hemocytes. Ark clams were subjected to a gradual increase of environmental salinity from 18‰ to 35‰ and 45‰ and maintained at those conditions for two days. Exposure to hypersalinity 35‰ induced changes in erythrocyte morphology and led to a decrease of their diameter. At salinity 45‰ a substantial increase of hemocyte average diameter was observed, whereas the shape of cells did not change (18‰). Hyperosmotic stress was not associated with changes in hemocyte viability as well as changes in hemolymph cellular composition. The results of the present work demonstrate high tolerance of A. kagoshimensis to short-time exposure to hypersalinic conditions.

Anti-inflammatory action of ark shell (Scapharca subcrenata) protein hydrolysate in LPS-stimulated RAW264.7 murine macrophages.

Potential anti-inflammatory effects of ark shell (Scapharca subcrenata) protein hydrolysates were investigated. Ark shell protein hydrolysates were prepared using Alcalase® and pepsin and were designated ASAH and ASPH, respectively. The nitric oxide (NO) inhibitory activity of ASAH and ASPH was determined in lipopolysaccharides (LPS)-stimulated RAW264.7 murine macrophages, and the results showed that ASAH inhibited better NO inhibitory activity than ASPH. ASAH suppressed inflammatory mediator, a prostaglandin E2, secretion of pro-inflammatory cytokines (TNF-α, IL-1ß, and IL-6), and production of reactive oxygen species (ROS) dose dependently. It inhibited the protein expression of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) and simulated heme oxygenase-1 (HO-1) protein expression. However, the pharmacological approach revealed that pretreatment with zinc protoporphyrin ІX (ZnPP), an inhibitor of HO-1, reversed the anti-inflammatory effect of ASAH. Moreover, ASAH upregulated phosphorylation of mitogen-activated protein kinases (MAPKs) including ERK1/2, JNK1/2, and p38 MAPK. To find out the role of MAPKs phosphorylation, MAPKs inhibitors were used, and the results showed that ASAH-mediated HO-1 protein expression and Nrf2 nuclear translocation were abolished. Taken all together, this study revealed that ASAH has a potential anti-inflammatory activity through regulation of the MAPK-dependent HO-1/Nrf2 pathway. PRACTICAL APPLICATIONS: Food-derived marine bioactive peptides, due to their pivotal role in biological activities, are gaining much attention recently. However, the anti-inflammatory activities of ark shell protein hydrolysates still remain to be investigated. This study investigated that ASAH shows potential anti-inflammatory activities through regulation of the MAPK-dependent HO-1/Nrf2 pathway in RAW264.7 murine macrophages. These findings indicated that ASAH may be used as a dietary supplement, functional food, and medicinal drug for the management of inflammation and inflammation-associated diseases.

Structural characterization and immunoregulatory activity of a novel acidic polysaccharide from Scapharca subcrenata.

A novel acidic polysaccharide named SSPA50-1 was isolated from Scapharca subcrenata using a simulated gastric fluid extraction method. SSPA50-1 is a heteropolysaccharide with an average molecular weight of 44.7 kDa that is composed of galacturonic acid, glucose, galactose, mannose, ribose, rhamnose, fucose, xylose and arabinose at a molar ratio of 1.00:5.40:9.04:3.10:1.59:4.01:2.10:2.21:2.28. The structural characterization based on the methylation and 1D/2D NMR analyses indicated that SSPA50-1 is composed of →3)-ß-L-Rhap-(1→, →3)-ß-L-2-O-Me-Fucp-(1→, →2)-α-D-Xylp-(1→, →5)-α-L-Araf-(1→, →3)-ß-D-Galp-(1→, →6)-α-D-Glcp-(1→, →3,4)-ß-D-Manp-(1→, →3,4)-ß-D-Galp-(1→, ß-D-Ribf-(1→, α-D-Glcp-(1→, and α-D-GalAp6Me-(1→. Furthermore, SSPA50-1 possessed potent immunoregulatory activity by enhancing the phagocytosis and NO, iNOS, TNF-α and IL-6 secretion capacity of RAW264.7 cells. Otherwise, SSPA50-1 significantly promoted the proliferation of splenic lymphocytes and RAW264.7 macrophages. These results indicated that SSPA50-1 could be developed as a potential ingredient for immunostimulatory agents.

Iron Regulatory Protein 1 Inhibits Ferritin Translation Responding to OsHV-1 Infection in Ark Clams, Scapharca Broughtonii.

Elemental iron is an indispensable prosthetic group of DNA replication relative enzymes. The upregulation of ferritin translation by iron regulatory proteins (IRP1) in host cells is a nutritional immune strategy to sequester available iron to pathogens. The efficient replication of Ostreid herpesvirus 1 (OsHV-1), a lethal dsDNA virus among bivalves, depends on available iron. OsHV-1 infection was found to trigger iron limitation in ark clams; however, it is still an enigma how OsHV-1 successfully conducted rapid replication, escaping host iron limitations. In this study, we identified the IRP1 protein (designated as SbIRP-1) in the ark clam (Scapharca broughtonii) and found it could bind to the iron-responsive element (IRE) of ferritin (SbFn) mRNA based on electrophoretic mobility shift assay (EMSA). Knockdown of SbIRP-1 expression (0.24 ± 1.82-fold of that in NC group, p < 0.01) by RNA interference resulted in the accumulation of SbFn in hemocytes (1.79 ± 0.01-fold, p < 0.01) post-24 h of enhanced RNA interference injection. During OsHV-1 infection, SbFn mRNA was significantly upregulated in hemocytes from 24 h to 60 h, while its protein level was significantly reduced from 24 h to 48 h, with the lowest value at 36 h post-infection (0.11 ± 0.01-fold, p < 0.01). Further analysis by RNA immunoprecipitation assays showed that OsHV-1 could enhance the binding of SbIRP-1 with the SbFn IRE, which was significantly increased (2.17 ± 0.25-fold, p < 0.01) at 36 h post-infection. Consistently, SbIRP-1 protein expression was significantly increased in hemocytes from 12 h to 48 h post OsHV-1 infection (p < 0.01). In conclusion, the results suggest that OsHV-1 infection could suppress post-transcriptional translation of SbFn through the regulation of SbIRP-1, which likely contributes to OsHV-1 evasion of SbFn-mediating host iron limitation.

Paired miRNA and RNA sequencing provides a first insight into molecular defense mechanisms of Scapharca broughtonii during ostreid herpesvirus-1 infection.

Ostreid herpesvirus 1 (OsHV-1) infection caused mortalities with relevant economic losses in bivalve aquaculture industry worldwide. Initially described as an oyster pathogen, OsHV-1 can infect other bivalve species, like the blood clam Scapharca broughtonii. However, at present, little is known about the molecular interactions during OsHV-1 infection in the blood clam. We produced paired miRNA and total RNA-seq data to investigate the blood clam transcriptional changes from 0 to 72 h after experimental infection with OsHV-1. High-throughput miRNA sequencing of 24 libraries revealed 580 conserved and 270 new blood clam miRNAs, whereas no genuine miRNA was identified for OsHV-1. Total 88-203 differently expressed miRNAs were identified per time point, mostly up-regulated and mainly targeting metabolic pathways. Most of the blood clam mRNAs, in contrast, were down-regulated up to 60 h post-injection, with the trend analysis revealing the activation of immune genes only when comparing the early and latest stage of infection. Taken together, paired short and long RNA data suggested a miRNA-mediated down-regulation of host metabolic and energetic processes as a possible antiviral strategy during early infection stages, whereas antiviral pathways appeared upregulated only at late infection.

Chromosome-level genome assembly of Scapharca kagoshimensis reveals the expanded molecular basis of heme biosynthesis in ark shells.

Ark shells are commercially important clam species that inhabit in muddy sediments of shallow coasts in East Asia. For a long time, the lack of genome resources has hindered scientific research of ark shells. Here, we report a high-quality chromosome-level genome assembly of Scapharca kagoshimensis, with an aim to unravel the molecular basis of heme biosynthesis, and develop genomic resources for genetic breeding and population genetics in ark shells. Nineteen scaffolds corresponding to 19 chromosomes were constructed from 938 contigs (contig N50 = 2.01 Mb) to produce a final high-quality assembly with a total length of 1.11 Gb and scaffold N50 around 60.64 Mb. The genome assembly represents 93.4% completeness via matching 303 eukaryota core conserved genes. A total of 24,908 protein-coding genes were predicted and 24,551 genes (98.56%) of which were functionally annotated. The enrichment analyses suggested that genes in heme biosynthesis pathways were expanded and positive selection of the haemoglobin genes was also found in the genome of S. kagoshimensis, which gives important insights into the molecular mechanisms and evolution of the heme biosynthesis in mollusca. The valuable genome assembly of S. kagoshimensis would provide a solid foundation for investigating the molecular mechanisms that underlie the diverse biological functions and evolutionary adaptations of S. kagoshimensis.

Viral Decoys: The Only Two Herpesviruses Infecting Invertebrates Evolved Different Transcriptional Strategies to Deflect Post-Transcriptional Editing.

The highly versatile group of Herpesviruses cause disease in a wide range of hosts. In invertebrates, only two herpesviruses are known: the malacoherpesviruses HaHV-1 and OsHV-1 infecting gastropods and bivalves, respectively. To understand viral transcript architecture and diversity we first reconstructed full-length viral genomes of HaHV-1 infecting Haliotis diversicolor supertexta and OsHV-1 infecting Scapharca broughtonii by DNA-seq. We then used RNA-seq over the time-course of experimental infections to establish viral transcriptional dynamics, followed by PacBio long-read sequencing of full-length transcripts to untangle viral transcript architectures at two selected time points. Despite similarities in genome structure, in the number of genes and in the diverse transcriptomic architectures, we measured a ten-fold higher transcript variability in HaHV-1, with more extended antisense gene transcription. Transcriptional dynamics also appeared different, both in timing and expression trends. Both viruses were heavily affected by post-transcriptional modifications performed by ADAR1 affecting sense-antisense gene pairs forming dsRNAs. However, OsHV-1 concentrated these modifications in a few genomic hotspots, whereas HaHV-1 diluted ADAR1 impact by elongated and polycistronic transcripts distributed over its whole genome. These transcriptional strategies might thus provide alternative potential roles for sense-antisense transcription in viral transcriptomes to evade the host's immune response in different virus-host combinations.

Two-sided effects of prolonged hypoxia and sulfide exposure on juvenile ark shells (Anadara broughtonii).

Oxygen deficit and sulfide have been restrictive factors in mariculture zones. However, the adaptive mechanism in aquatic lives is still unclear. The commercial ark shells Anadara broughtonii were selected to test the tolerance and adaptive responses to prolonged and intermittent hypoxia with or without exogenous sulfide (mild, moderate, high) by evaluating their behavior, mortality, oxidative level, antioxidant responses, and the MAPK-mediated apoptosis in gills. The results indicated that the clams were tolerant to hypoxia and sulfide exposure but vulnerable during reoxygenation from the challenges. Even so, sulfide had remarkable effect on attenuating the accumulation of reactive oxygen species (ROS) and lipid peroxides caused by reoxygenation from prolonged hypoxia. The increase of glutathione level was probably as an early and primary protective response to prevent the expected reperfusion injury from reoxygenation. The challenges suppressed the oxidative level with a dose-dependent effect of sulfide, with an exception when exposed to mild sulfide. Synchronously, biphasic effects of exogenous sulfide on apoptotic cascade, which was induced by mild sulfide while it was inhibited by higher sulfide, were also detected in gills. The induced or inhibited apoptosis by hypoxia and sulfide kept to a typical ROS-MAPK-CASPASE cascade, desiderating further investigation.

Transcriptomic analyses provide insights into the adaptive responses to heat stress in the ark shells, Scapharca subcrenata.

The ark shell, Scapharca subcrenata, is susceptible to high temperature which may lead to mass mortality in hot summers. Herein, we conducted the transcriptomic analyses of haemocytes in ark shells under thermal stress, to reveal the underlying molecular mechanisms of heat resistance in these animals. The results showed that a total of 7773, 11,500 and 13,046 unigenes were expressed differentially at 12, 24 and 48 h post thermal stress, respectively. The expression levels of key DEGs as revealed by RNA-seq were confirmed by quantitative real-time PCR. GO and KEGG enrichment analyses showed that the DEGs were mainly associated with apoptosis, NF-kappa B signaling pathway, TNF signaling pathway and RIG-I-like receptor signaling pathway. Among the DEGs, 40 were candidate heat stress response-related genes and 169 were identified to be involved in antioxidant defense, cell detoxification, protein metabolism and endoplasmic reticulum stress responses. It seemed that ark shells may adapt to short term thermal stress through regulation of protein metabolism, DNA replication and anti-apoptotic system. However, if the stress sustains, it may cause irreparable injury gradually in the animals due to oxygen limitation and metabolic dysregulation. Noteworthily, the expression of DEGs involved in protein biosynthesis and proteolysis was significantly elevated in ark shells under heat stress. These findings may provide preliminary insights into the molecular response of ark shells to acute thermal stress and lay the groundwork for marker-assisted selection of heat-resistant strains in S. subcrenata.

Change in vibrational entropy with change in protein volume estimated with mode Grüneisen parameters.

For a small adjustment in average volume, due to a change in state of a protein or other macromolecule at constant temperature, the change in vibrational entropy is related to the mode Grüneisen parameters, which relate shifts in frequency to a small volume change. We report here values of mode Grüneisen parameters computed for two hydrated proteins, cytochrome c and myoglobin, which exhibit trends with mode frequency resembling those of glassy systems. We use the mode Grüneisen parameters to relate volumetric thermal expansion to previously computed values of the isothermal compressibility for several proteins. We also estimate changes in vibrational entropy resulting from the change in volume upon ligand bonding of myoglobin and the homodimeric hemoglobin from Scapharca inaequivalvis (HbI). We compare estimates of the change in entropy upon ligation obtained in terms of mode Grüneisen parameters with the results of normal mode analysis for myoglobin and earlier molecular dynamics simulations of HbI. The results illustrate how small changes in average volume can yield changes in entropy that contribute to ligand binding and allostery.

Locating and Navigating Energy Transport Networks in Proteins.

We review computational methods to locate energy transport networks in proteins that are based on the calculation of local energy diffusion in nanoscale systems. As an illustrative example, we discuss energy transport networks computed for the homodimeric hemoglobin from Scapharca inaequivalvis, where channels for facile energy transport, which include the cluster of water molecules at the interface of the globules, have been found to lie along pathways that experiments reveal are important in allosteric processes. We also review recent work on master equation simulations to model energy transport dynamics, including efforts to relate rate constants in the master equation to protein structural dynamics. Results for apomyoglobin involving relations between fluctuations in the length of hydrogen bonds and the energy flux between them are presented.

Transcriptomic analysis and expression of C-type lectins in response to Vibrio parahaemolyticus challenge in Scapharca subcrenata.

Little information is available on innate immune defense mechanisms of Scapharca subcrenata. C-type lectins (CTLs) are not only pattern recognition proteins that can bind pathogen-associated molecular patterns, but also crucial maternally-derived immune factors in mollusc egg. In this study, the comparative transcriptome analysis of Vibrio parahaemolyticus-infected and untreated hepatopancreas were performed to identify the key genes involved in maternal transfer of immunity. A total of 3514 and 9327 differentially expressed genes (DEGs) were identified at 6 and 48 h post challenge compared to control groups. Gene Ontology and Cluster of Orthologous Groups analysis showed that most DEGs were classified under regulation of signal transduction, regulation of the metabolic process of carbohydrates and secondary metabolites, while the processes of posttranscriptional modification and protein translation were inhibited manifestly. The DEGs were most enriched in pathways related to lysosome, phagosome and EMC-receptor interaction. Among the DEGs, 191 maternal immune-related genes that could provide developing embryos a better protection against pathogen infection were identified according to previous studies. Additionally, five CTLs (designated as SsCTL1-5) identified from the DEGs were cloned, and their expression patterns in different tissues and post immune stimulation were analyzed. These findings would be beneficial for understanding the innate immune defense mechanisms of S. subcrenata.

Ligand-Linked Association-Dissociation in Transport Proteins and Hormone Receptors.

Ligand-linked changes in the aggregation state of biological macromolecules occur and have importance in several physiological processes, e.g., the response of hormone receptors, cooperative ligand binding, and others. The mathematical formalisms that express the thermodynamics governing these processes are complex, as they are required to describe observations made under experimental conditions in which many parameters may be simultaneously varied. The description of the functional behaviour of proteins that present ligand-linked association-dissociation events must accommodate cases where both the binding stoichiometries and reaction mechanisms are variable. In this paper, we review some paradigmatic cases that cover different structural arrangements and binding modes, with special attention to the case of dissociating homodimeric transport proteins and receptors. Even though we cannot pretend to be comprehensive on the proteins presenting this behaviour, we believe that we can attempt to be comprehensive on the structural arrangements and thermodynamic properties of these systems, which fall into a limited set of possible types.

Water-mediated biomolecular dynamics and allostery.

Dynamic coupling with water contributes to regulating the functional dynamics of a biomolecule. We discuss protein-water dynamics, with emphasis on water that is partially confined, and the role of protein-confined water dynamics in allosteric regulation. These properties are illustrated with two systems, a homodimeric hemoglobin from Scapharca inaequivalvis (HbI) and an A2A adenosine receptor (A2AAR). For HbI, water-protein interactions, long known to contribute to the thermodynamics of cooperativity, are seen to influence the dynamics of the protein not only around the protein-water interface but also into the core of each globule, where dynamic and entropic changes upon ligand binding are coupled to protein-water contact dynamics. Similarly, hydration waters trapped deep inside the core region of A2AAR enable the formation of an allosteric network made of water-mediated inter-residue contacts. Extending from the ligand binding pocket to the G-protein binding site, this allosteric network plays key roles in regulating the activity of the receptor.

Purification and Characterization of a New CRISP-Related Protein from Scapharca broughtonii and Its Immunomodulatory Activity.

More and more attention has been paid to bioactive compounds isolated from marine organisms or microorganisms in recent years. At the present study, a new protein coded as HPCG2, was purified from Scapharca broughtonii by stepwise chromatography methods. The molecular weight of HPCG2 was determined to be 30.71 kDa by MALDI-TOF-MS. The complete amino acid sequence of HPCG2 was obtained by tandem mass spectrometry combined with transcriptome database analysis, and its secondary structure was analyzed using circular dichroism. HPCG2 comprised 251 amino acids and contained 28.4% α-helix, 26% ß-sheet, 18.6% ß-turn, and 29.9% random coil. HPCG2 was predicted to be a cysteine-rich secretory protein-related (CRISP-related) protein by domain prediction. Moreover, HPCG2 was proved to possess the immunomodulatory effect on the murine immune cells. MTT assay showed that HPCG2 promoted the proliferation of splenic lymphocytes and the cytotoxicity of NK cells against YAC-1 cells. Flow cytometry test revealed that HPCG2 enhanced the phagocytic function of macrophages and polarized them into M1 type in RAW264.7 cells. In particular, Western blot analysis indicated that the immunomodulatory mechanism of HPCG2 was associated with the regulation on TLR4/JNK/ERK and STAT3 signaling pathways in RAW 264.7 cells. These results suggested that HPCG2 might be developed as a potential immunomodulatory agent or new functional product from marine organisms.

Effects of a Sudden Drop in Salinity on Scapharca subcrenata Antioxidant Defenses and Metabolism Determined Using LC-MS Non-targeted Metabolomics.

In this experiment, the effects of a sudden drop in salinity on the antioxidant defense system and related gene expression of the ark shell Scapharca subcrenata were examined. The sudden drop in seawater salinity after a rainstorm was simulated, and subsequently differentially expressed metabolic markers were identified by LC-MS non-targeted metabolomics. When the salinity dropped to 14‰ (S14), the total anti-oxidant content, activity of Na+/K+-ATPase, superoxide dismutase (SOD), and catalase (CAT), content of malondialdehyde, and expression levels of Mn-SOD, CAT, and C-type lectin of S. subcrenata were significantly higher than in groups with salinity of 22‰ (S22) or 30‰ (S30) (P < 0.05). The activity of glutathione peroxidase (GPx), the content of reduced glutathione, and the expression levels of GPx were not significantly different between S14 and S22, but the values in each group were significantly higher than those in S30 (P < 0.05). Using the metabolomics technique, 361, 271, and 264 metabolites with significant differences were identified from S22 vs. S14, S30 vs. S14, and S30 vs. S22, respectively. The drop in salinity was accompanied by up-regulation of phosphatidylcholine (PC) (20:4 (5Z, 8Z, 11Z, 14Z)/P-18: 1 (11Z)), PC (16:0/22: 6 (4Z, 7Z, 10Z, 13Z, 16Z, 19Z)), phosphatidylethanolamine (PE) (18:4 (6Z, 9Z, 12Z, 15Z)/24:1 (15Z)), phosphatidylinositol (PI) (20:1 (11Z)/0:0), phalluside-1, C16 sphinganine, and LacCer (d18:0/14:0) and by significant down-regulation of PI-Cer (d18:1/14:0) and PE (14:0/16:1(9Z). The results of this study illustrate how these nine metabolites can be used as metabolic markers for the response of S. subcrenata to a sudden drop in salinity. They also provide the theoretical groundwork for selection of bottom areas with salinity that is optimal for release and proliferation of S. subcrenata, which is needed to restore the declining populations of this species.

Microbial community and interspecies interaction during grazing of ark shell bivalve (Scapharca subcrenata) in a full-scale bioremediation system of mariculture effluents.

A novel biological approach using ark shell bivalves as potential species for remediation of effluents was studied to determine the microbial community interspecies interaction and nutrient cycling in a restoration system of mariculture effluents. A field study showed that Scapharca subcrenata was the main driver of the microbial community's interspecies-interaction (PERMANOVA, R = 0.0572, P = 0.005) in the treatment zone (TZ). Analysis of co-occurrence networks based on random matrix theory (RMT) indicated that the network's complexity parameters were enhanced in the TZ and disrupted in the control zone (CZ) due to eutrophic disturbances. Concurrently, the TZ was correlated with more profound network modifications (i.e., higher modularity, total nodes (n), cohesion, and proportion of positive links), suggesting that S. subcrenata influenced microbial interspecies interactions in the system. Similarly, the co-occurring networks of generalists Proteobacteria (OTU2037) at genus Anaerospora and Actinobacteria (OTU9660) at genus Candidatus aquiluna for anaerobic ammonia-oxidation (ANAMMOX) were highly significant in the TZ. The top-down and bottom-up forces of S. subcrenata influenced the removal efficiency of nitrogenous compounds by reducing 81.51% of nitrite (NO2--N), 84.61% of total ammonium nitrogen (TAN) and 72.78% of nitrate (NO3--N). Generally, the introduction of ark shell bivalve (S. subcrenata) to the system as a biofilter provides a very low-cost bioremediation technology that could be one of the best restorations and remediation tools for mariculture effluents.

Energy Transport across Interfaces in Biomolecular Systems.

Energy transport during chemical reactions or following photoexcitation in systems of biological molecules is mediated by numerous interfaces that separate chemical groups and molecules. Describing and predicting energy transport has been complicated by the inhomogeneous environment through which it occurs, and general rules are still lacking. We discuss recent work on identification of networks for vibrational energy transport in biomolecules and their environment, with focus on the nature of energy transfer across interfaces. Energy transport is influenced both by structure of the biomolecular system as well as by equilibrium fluctuations of nonbonded contacts between chemical groups, biomolecules, and water along the network. We also discuss recent theoretical and computational work on the related topic of thermal transport through molecular interfaces, with focus on systems important in biology as well as relevant experimental studies.