Oyster aquaculture enhances sediment microbial diversity- Insights from a multi-omics study.

The global aquaculture industry has grown substantially, with consequences for coastal ecology and biogeochemistry. Oyster aquaculture can alter the availability of resources for microbes that live in sediments as oysters move large quantities of organic material to the sediments via filter feeding, possibly leading to changes in the structure and function of sediment microbial communities. Here, we use a chronosequence approach to investigate the impacts of oyster farming on sediment microbial communities over 7 years of aquaculture activity in a temperate coastal system. We detected shifts in bacterial composition (16S rRNA amplicon sequencing), changes in gene expression (meta-transcriptomics), and variations in sediment elemental concentrations (sediment geochemistry) across different durations of oyster farming. Our results indicate that both the structure and function of bacterial communities vary between control (no oysters) and farm sites, with an overall increase in diversity and a shift towards anoxic tolerance in farm sites. However, little to no variation was observed in either structure or function with respect to farming duration suggesting these sediment microbial communities are resilient to change. We also did not find any significant impact of farming on heavy metal accumulation in the sediments. The minimal influence of long-term oyster farming on sediment bacterial function and biogeochemical processes as observed here can bear important consequences for establishing best practices for sustainable farming in these areas. Importance: Sediment microbial communities drive a range of important ecosystem processes such as nutrient recycling and filtration. Oysters are well-known ecological engineers, and their presence is increasing as aquaculture expands in coastal waters globally. Determining how oyster aquaculture impacts sediment microbial processes is key to understanding current and future estuarine biogeochemical processes. Here, we use a multi-omics approach to study the effect of different durations of oyster farming on the structure and function of bacteria and elemental accumulation in the farm sediments. Our results indicate an increase in the diversity of bacterial communities in the farm sites with no such increases observed for elemental concentrations. Further, these effects persist across multiple years of farming with an increase of anoxic tolerant bacteria at farm sites. The multi-omics approach used in this study can serve as a valuable tool to facilitate understanding of the environmental impacts of oyster aquaculture.

Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2, MERS-CoV and seasonal coronaviruses

Several genome-wide CRISPR knockout screens have been conducted to identify host factors regulating SARS-CoV-2 replication, but the models used have often relied on overexpression of ACE2 receptor. Additionally, such screens have yet to identify the protease TMPRSS2, known to be important for viral entry at the plasma membrane. Here, we conducted a meta-analysis of these screens and showed a high level of cell-type specificity of the identified hits, arguing for the necessity of additional models to uncover the full landscape of SARS-CoV-2 host factors. We performed genome-wide knockout and activation CRISPR screens in Calu-3 lung epithelial cells, as well as knockout screens in Caco-2 intestinal cells. In addition to identifying ACE2 and TMPRSS2 as top hits, our study reveals a series of so far unidentified and critical host-dependency factors, including the Adaptins AP1G1 and AP1B1 and the flippase ATP8B1. Moreover, new anti-SARS-CoV-2 proteins with potent activity, including several membrane-associated Mucins, IL6R, and CD44 were identified. We further observed that these genes mostly acted at the critical step of viral entry, with the notable exception of ATP8B1, the knockout of which prevented late stages of viral replication. Exploring the pro- and anti-viral breadth of these genes using highly pathogenic MERS-CoV, seasonal HCoV-NL63 and -229E and influenza A orthomyxovirus, we reveal that some genes such as AP1G1 and ATP8B1 are general coronavirus cofactors. In contrast, Mucins recapitulated their known role as a general antiviral defense mechanism. These results demonstrate the value of considering multiple cell models and perturbational modalities for understanding SARS-CoV-2 replication and provide a list of potential new targets for therapeutic interventions.

Resurrected 'ancient' Daphnia genotypes show reduced thermal stress tolerance compared to modern descendants.

Understanding how populations adapt to rising temperatures has been a challenge in ecology. Research often evaluates multiple populations to test whether local adaptation to temperature regimes is occurring. Space-for-time substitutions are common, as temporal constraints limit our ability to observe evolutionary responses. We employed a resurrection ecology approach to understand how thermal tolerance has changed in a Daphnia pulicaria population over time. Temperatures experienced by the oldest genotypes were considerably lower than the youngest. We hypothesized clones were adapted to the thermal regimes of their respective time periods. We performed two thermal shock experiments that varied in length of heat exposure. Overall trends revealed that younger genotypes exhibited higher thermal tolerance than older genotypes; heat shock protein (hsp70) expression increased with temperature and varied among genotypes, but not across time periods. Our results indicate temperature may have been a selective factor on this population, although the observed responses may be a function of multifarious selection. Prior work found striking changes in population genetic structure, and in other traits that were strongly correlated with anthropogenic changes. Resurrection ecology approaches should help our understanding of interactive effects of anthropogenic alterations to temperature and other stressors on the evolutionary fate of natural populations.

Genotype-specific relationships among phosphorus use, growth and abundance in Daphnia pulicaria.

The framework ecological stoichiometry uses elemental composition of species to make predictions about growth and competitive ability in defined elemental supply conditions. Although intraspecific differences in stoichiometry have been observed, we have yet to understand the mechanisms generating and maintaining such variation. We used variation in phosphorus (P) content within a Daphnia species to test the extent to which %P can explain variation in growth and competition. Further, we measured 33P kinetics (acquisition, assimilation, incorporation and retention) to understand the extent to which such variables improved predictions. Genotypes showed significant variation in P content, 33P kinetics and growth rate. P content alone was a poor predictor of growth rate and competitive ability. While most genotypes exhibited the typical growth penalty under P limitation, a few varied little in growth between P diets. These observations indicate that some genotypes can maintain growth under P-limited conditions by altering P use, suggesting that decomposing P content of an individual into physiological components of P kinetics will improve stoichiometric models. More generally, attention to the interplay between nutrient content and nutrient-use is required to make inferences regarding the success of genotypes in defined conditions of nutrient supply.

Functional genomics of intraspecific variation in carbon and phosphorus kinetics in Daphnia.

Understanding how the genome interacts with the environment to produce a diversity of phenotypes is a central challenge in biology. However, we know little about how traits involved in nutrient processing interact with key ecological parameters, such as the supply of mineral nutrients, particularly in animals. The framework of ecological stoichiometry uses information on the content of key elements such as carbon (C) and phosphorus (P) in individuals to predict the success of species. Nevertheless, intraspecific variation in content and the underlying mechanisms that generate such variation has been poorly explored. We studied two genotypes (G1 and G2) of Daphnia pulex that exhibit striking genotype × environment (G × E) interaction in response to shifts in dietary stoichiometry (C:P). G1 had higher fitness under C:P ∼ 100 diet, while G2 performed better in C:P ∼ 800. Dual (14) C/(33) P radiotracer assays show that G1 was more efficient in C processing, while G2 was more efficient in P use. Microarrays revealed that after 3 days of incubation, the genotypes differentially expressed ∼ 25% (7,224) of the total genes on the array under C:P ∼ 100 diet, and ∼ 30% (8,880) of genes under C:P ∼ 800. These results indicate large differences in C and P use between two coexisting genotypes. Importantly, such physiological differences can arise via differential expression of the genome due to alterations in dietary stoichiometry. Basic frameworks such as ecological stoichiometry enable integration of physiological and transcriptomic data, and represent initial steps toward understanding the interplay between fundamental ecological parameters such as nutrient supply and important evolutionary processes such as G × E interactions.

A millennial-scale chronicle of evolutionary responses to cultural eutrophication in Daphnia.

For an accurate assessment of the anthropogenic impacts on evolutionary change in natural populations, we need long-term environmental, genetic and phenotypic data that predate human disturbances. Analysis of c. 1600 years of history chronicled in the sediments of South Center Lake, Minnesota, USA, revealed major environmental changes beginning c. 120 years ago coinciding with the initiation of industrialised agriculture in the catchment area. Population genetic structure, analysed using DNA from dormant eggs of the keystone aquatic herbivore, Daphnia pulicaria, suggested no change for c. 1500 years prior to striking shifts associated with anthropogenic environmental alterations. Furthermore, phenotypic assays on the oldest resurrected metazoan genotypes (potentially as old as c. 700 years) indicate significant shifts in phosphorus utilisation rates compared to younger genotypes. Younger genotypes show steeper reaction norms with high growth under high phosphorus (P), and low growth under low P, while 'ancient' genotypes show flat reaction norms, yet higher growth efficiency under low P. Using this resurrection ecology approach, environmental, genetic and phenotypic data spanning pre- and post-industrialised agricultural eras clearly reveal the evolutionary consequences of anthropogenic environmental change.

HPLC analysis and cell surface receptor binding activities of the crude aqueous and methanolic extract of Sesamum indicum

<p><b>OBJECTIVE</b>To identify the possible functional molecules for therapeutic uses by screening the crude aqueous and methanolic extracts derived from sesame seeds (Sesamum indicum) in vitro.</p><p><b>METHODS</b>High performance liquid chromatography was used to scan the functional molecules present in the extracts.</p><p><b>RESULTS</b>The crude aqueous extracts showed the possibilities to present caffeine and cetirizine or its derivatives like molecules. On the other hand, the crude methanolic extract may contain Loratadine or its derivatives like molecules. Both type of extracts showed hemagglutination inhibition activities in all types of human blood samples tested. However, they showed stronger binding with AB+ blood group than those of A+ and B+ blood.</p><p><b>CONCLUSIONS</b>Sesame seeds may be considered as a functional food.</p>

Cyclodextrin complexation: influence on the solubility, stability, and cytotoxicity of camptothecin, an antineoplastic agent.

The solubility of camptothecin (CPT), a highly potent antineoplastic agent, as a function of different concentrations of cyclodextrins (alpha-cyclodextrin, alpha-CD; beta-cyclodextrin, beta-CD; and gamma-cyclodextrin, gamma-CD; hydroxypropyl-beta-cyclodextrin, HP-beta-CD; and randomly substituted dimethyl-beta-cyclodextrin, RDM-beta-CD, and dimethyl-gamma-cyclodextrin, RDM-beta-CD) in 0.02 N HCl solution at 25 degrees C was investigated. The results showed a linear increase in the solubility of CPT with increasing concentration of CDs. The apparent stability constants (K(c)) for the CPT complexes with alpha-CD, beta-CD, gamma-CD, HP-beta-CD, RDM-beta-CD, and RDM-gamma-CD were 188, 266, 73, 160, 910, and 40.6 M(-1), respectively, suggesting that RDM-beta-CD afforded the most stable complex. At a 25% w/v concentration of RDM-beta-CD, the solubility of CPT was 228.45 +/- 8.45 microg/ml, about 171 times higher than that in 0.02 N HCl. The stability of CPT in pH 7.4 buffer at 25 degrees C also increased linearly with an increase in the concentration of RDM-beta-CD. The observed pseudo-first-order hydrolysis rate constants (k(obs)) for the free and complexed CPT were 11.8 x 10(-3) and 1.18 x 10(-3) min(-1), corresponding to an increase in half-life of CPT from 58.7 to 587.3 min, respectively. The preliminary cytotoxicity study against the human-derived myeloid THP-1 leukemia cell line showed RDM-beta-CD/CPT and HP-beta-CD/CPT complexes to be about two-fold more active than free CPT. In conclusion, the results showed that CDs, in general, and RDM-beta-CD, in particular, are effective complexing agents and can be used to improve the solubility and stability of CPT. The increase in cytotoxicity of CPT in the presence of CD is likely due to an increase in its stability.