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Warming and nutrient enrichment are key pervasive drivers of ecological shifts in both aquatic and terrestrial ecosystems, impairing the physiology and survival of a wide range of foundation species. But the underlying mechanisms often remain unclear, and experiments have overlooked the potential effects mediated by changes in the microbial communities. We experimentally tested in the field orthogonal stress combinations from simulated air warming and nutrient enrichment on the intertidal foundation seaweed Cystoseira compressa, and its associated bacterial communities. A total of 523 Amplicon Sequence Variance (ASVs) formed the bacterial community on C. compressa, with 222 ASVs assigned to 69 taxa at the genus level. Most bacteria taxa experienced changes in abundance as a result of additive (65 %) and antagonistic (30 %) interactions between the two stressors, with synergies (5 %) occurring less frequently. The analysis of the predicted bacterial functional profile identified 160 metabolic pathways, and showed that these were mostly affected by additive interactions (74 %) between air warming and nutrient enrichment, while antagonisms (20 %) and synergisms (6 %) were less frequent. Overall, the two stressors combined increased functions associated with seaweed disease or degradation of major cell-wall polymers and other algicidal processes, and decreased functions associated with Quorum Quenching and photosynthetic response. We conclude that warming and nutrient enrichment can dysregulate the microbiome of seaweeds, providing a plausible mechanism for their ongoing loss, and encourage more research into the effects of human impacts on crucial but yet largely unstudied host-microbiome relationships in different aquatic and terrestrial species., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Algal-associated bacteria are fundamental to the ecological success of marine green macroalgae such as Caulerpa . The resistance and resilience of algal-associated microbiota to environmental stress can promote algal health and genetic adaptation to changing environments. The composition of bacterial communities has been shown to be unique to algal morphological niches. Therefore, the level of response to various environmental perturbations may in fact be different for each niche-specific community. Factorial in situ experiments were set up to investigate the effect of nutrient enrichment and temperature stress on the bacterial communities associated with Caulerpa cylindracea . Bacteria were characterized using the 16S rRNA gene, and the community compositions were compared between different parts of the algal thallus (endo-, epi-, and rhizomicrobiome). Resistance and resilience were calculated to further understand the changes of microbial composition in response to perturbations. The results of this study provide evidence that nutrient enrichment has a significant influence on the taxonomic and functional structure of the epimicrobiota, with a low community resistance index observed for both. Temperature and nutrient stress had a significant effect on the rhizomicrobiota taxonomic composition, exhibiting the lowest overall resistance to change. The functional performance of the rhizomicrobiota had low resilience to the combination of stressors, indicating potential additive effects. Interestingly, the endomicrobiota had the highest overall resistance, yet the lowest overall resilience to environmental stress. This further contributes to our understanding of algal microbiome dynamics in response to environmental changes., Competing Interests: The authors declare no conflict of interests., (© 2021 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

A genome-inspired route to aptamer discovery that expands the sequence space beyond that available in traditional, combinatorial selection approaches is investigated for discovery of DNA-protein interactions in cancer. These interactions could then serve as the basis for new DNA aptamers to cancer-related proteins. The genome-inspired approach uses specific DNA sequences from the human genome to capture proteins from biological protein pools. The use of naturally occurring DNA sequences takes advantage of biological evolution of DNA sequences that bind to specific proteins to perform biological functions. Linking aptamer discovery to nature increa`ses the chances of uncovering protein-DNA affinity binding interactions that have biological significance as well as analytical utility. Here, the focus is on genomic, G-rich sequences that can form G-quadruplex (G4) structures. These structures are underrepresented in combinatorial libraries used for conventional aptamer selection. Additionally, G4-forming sequences are prone to inefficient PCR amplification, further biasing aptamer selection away from these structures. Nature provides a large diversity of G4-forming sequences throughout the human genome. They are prevalent in gene promoter regions, especially in oncogene promoters, and are therefore promising candidates for aptamers to regulatory proteins in cancer. The present work investigates protein capture from nuclear and cytoplasmic extracts of the breast cancer cell line MDA-MB-468 by G4-forming sequences from the CMYC, RB, and VEGF gene promoters. The studies included the effects of modifications of the VEGF sequence on the selectivity of protein capture, from which we identified promising aptamer candidates, subject to further refinement, to the proteins nucleolin and RPL19, both of which play important regulatory functions related to cancer.

Bacteria have been shown to be involved in different species-specific interactions with eukaryotic algae such as diatoms, impacting important ecosystem processes. Recently, a strain assigned to Dyadobacter, named 'species 32', has been shown to be involved in a number of ecologically relevant diatom processes, such as biofilm formation or growth enhancement, depending on the diatom species. This bacterium was originally isolated from a culture of freshwater benthic diatoms that originated from an epilithic biofilm, in which both bacteria and diatoms coexist. A single complete circular chromosome of Dyadobacter sp. 32 was assembled with a length of 7,101,228 bp, containing 6062 protein coding genes and 3 rRNA operons. A number of interesting genetic features were found, such as a putative zeaxanthin biosynthetic gene cluster. A large number of polysaccharide utilizing gene clusters were also detected, along with genes potentially acquired from other bacteria through horizontal gene transfer, and genes previously identified in other algae-bacteria interactions. These data serve to increase our understanding of specific interactions within freshwater biofilms, and identify a number of gene targets with which to study the molecular basis of diatom-bacteria interactions., Competing Interests: Declaration of Competing Interest None., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Hypothesis: Flocculation performance using polyelectrolytes is influenced by critical design parameters including molecular weight, amount and sign of the ionic charge, and polymer architecture. It is expected that systematic variation of these characteristics will impact not only flocculation efficiency (FE) achieved but that charge density and architecture, specifically, can alter the flocculation mechanism. Therefore, it should be possible to tune these design parameters for a desired flocculation application., Experiments: Cationic-neutral and polyampholytic copolymers, exhibiting a range of molecular weights (10 3 -10 6 g/mol), varying charge levels (0-100% cationic, neutral and anionic), and random or block copolymer architecture, were applied to dilute suspensions of silica microparticles (control) and Chlorella vulgaris. FE and zeta potential values were determined over a range of flocculant doses to evaluate effectiveness and mechanism achieved., Findings: These different classes of copolymers provide specific benefits for flocculation, with many achieving >95% flocculation. Block copolymer flocculants exhibit a proposed, dominant bridging mechanism, therefore reducing flocculant dosage required for effective flocculation when compared to analogous random copolymer flocculants. Polyampholytic copolymers applied to C. vulgaris generally exhibited a bridging mechanism and increased FE compared to equivalent cationic-neutral copolymers, indicating a benefit of the anionic component on a more, complex, diversely charged suspension., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Siphonous green seaweeds, such as Caulerpa , are among the most morphologically complex algae with differentiated algal structures (morphological niches). Caulerpa is also host to a rich diversity of bacterial endo- and epibionts. The degree to which these bacterial communities are species-, or even niche-specific remains largely unknown. To address this, we investigated the diversity of bacteria associated to different morphological niches of both native and invasive species of Caulerpa from different geographic locations along the Turkish coastline of the Aegean sea. Associated bacteria were identified using the 16S rDNA marker gene for three morphological niches, such as the endobiome, epibiome, and rhizobiome. Bacterial community structure was explored and deterministic factors behind bacterial variation were investigated. Of the total variation, only 21.5% could be explained. Pronounced differences in bacterial community composition were observed and variation was partly explained by a combination of host species, biogeography and nutrient levels. The majority of the explained bacterial variation within the algal holobiont was attributed to the micro-environments established by distinct morphological niches. This study further supports the hypothesis that the bacterial assembly is largely stochastic in nature and bacterial community structure is most likely linked to functional genes rather than taxonomy.

Objective: We assessed the sensitivity and specificity of 8 electronic health record (EHR)-based phenotypes for diabetes mellitus against gold-standard American Diabetes Association (ADA) diagnostic criteria via chart review by clinical experts., Materials and Methods: We identified EHR-based diabetes phenotype definitions that were developed for various purposes by a variety of users, including academic medical centers, Medicare, the New York City Health Department, and pharmacy benefit managers. We applied these definitions to a sample of 173 503 patients with records in the Duke Health System Enterprise Data Warehouse and at least 1 visit over a 5-year period (2007-2011). Of these patients, 22 679 (13%) met the criteria of 1 or more of the selected diabetes phenotype definitions. A statistically balanced sample of these patients was selected for chart review by clinical experts to determine the presence or absence of type 2 diabetes in the sample., Results: The sensitivity (62-94%) and specificity (95-99%) of EHR-based type 2 diabetes phenotypes (compared with the gold standard ADA criteria via chart review) varied depending on the component criteria and timing of observations and measurements., Discussion and Conclusions: Researchers using EHR-based phenotype definitions should clearly specify the characteristics that comprise the definition, variations of ADA criteria, and how different phenotype definitions and components impact the patient populations retrieved and the intended application. Careful attention to phenotype definitions is critical if the promise of leveraging EHR data to improve individual and population health is to be fulfilled., (© The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com)

Unlabelled: The efficient concentration and separation of microorganisms from dilute culture suspensions is crucial to the success and productivity of many biotechnological processes. This article presents the design and characterization of polyamphoteric flocculants with a tunable, zwitterionic character for the enhanced separation of biocolloidal suspensions of yeast, wastewater, microalgae, and potentially other cellular systems. The polyamphoteric flocculants have overall molecular charges dependent upon the system pH, thereby providing a strong electrostatic attraction to the diverse but predominantly negatively-charged cellular surfaces of the biological suspensions. The polyamphoteric flocculants with tailored charge character are shown to have higher flocculation efficiencies than comparable cationic polyelectrolytes, and have an enhanced ability to 1) adsorb to the diverse range of charge character in cellular suspensions, 2) operate over an extended range of suspension pHs, and 3) operate at lower flocculant concentrations. These enhanced flocculation properties are shown to arise, perhaps counterintuitively, due to interactions between the negatively-charged functionality on the flocculant and the predominantly negatively-charged biocolloids., Statement of Significance: This article presents the design and characterization of polyamphoteric flocculants for the separations of biocolloidal suspensions of importance in the production of biopharmaceuticals, microalgal cultures for nutraceuticals and biofuels, and wastewater treatment. The polyamphoteric flocculants consist of tunable, mixed charges dependent upon system pH, thereby providing strong electrostatic attraction to the diversely-charged surfaces of cellular suspensions. Enhanced flocculation efficiencies are achieved, as compared to cationic polyelectrolyte flocculants, and result from the ability of polyampholytes to adsorb to a diverse range of charge character and operate over an extended range of pH conditions., (Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.)

Commercial laying hens are prone to injurious pecking (IP), a common multifactorial problem. A 2 × 2 × 2 factorial design assessed the effects of breed (Lohmann Brown Classic (L) or Hyline Brown (H)), beak treatment (infra-red treated (T) or not (NT)), and environment (extra enrichment (EE) or no extra enrichment (NE)) on mortality, behaviour, feather cover, and beak shape. Hens were allocated to treatments at 16 weeks of age and data were collected every four weeks from age 19 to 71 weeks. Data were analysed in Genstat using mixed models. L hens had higher all and IP-related mortality than H hens (p < 0.003), whilst NT hens had higher mortality than T hens but only due to culling of whole cages (p < 0.001). Feather cover for L hens deteriorated more quickly with age at most body sites than H hens (age × breed × body site p < 0.001). For NT hens, feather cover was worse at most body sites (beak treatment × body site p < 0.001), and worsened more quickly with age (age × beak treatment p = 0.014) than T hens. L and NE hens performed more bird-to-bird pecking than H and EE hens, respectively (breed p = 0.015, enrichment p = 0.032). More damage to mats and ropes was caused by L and NT hens than by H and T hens, respectively (age × breed p < 0.005, beak treatment p < 0.001). Though H hens had fewer mortalities and better feather cover, breed effects may have been influenced by farm management practices, as they may have been better suited to H than L hens. Though EE hens performed less bird-to-bird pecking, the enrichments were less effective at reducing feather cover damage and mortality than expected.

Microalgae-derived biofuels have potential advantages over other renewable, crop-based resources; however, large-scale production is not currently economical due, in part, to challenges in the harvesting step. In this article, we present a novel approach for the dewatering and harvesting of microalgae using flocculants that can be recovered and recycled. Polyampholytes with molecular charges dependent upon pH (ranging from net positively- to net negatively-charged) are used as a model flocculant system and provide reversible electrostatic interactions with the negatively-charged algal cells. These pH-dependent properties allow the polyampholytic flocculants to efficiently desorb from concentrated biomass and, unlike most commercial flocculants that have permanently charged functionalities, be recovered and recycled for further dewatering processes. The behavior of the model polyampholytic flocculants is characterized for the dewatering of Chlorella vulgaris (UTEX 395). The reversible and recyclable flocculants achieve >99% flocculation efficiencies, are recovered at more than 98 wt% yields after biomass dewatering, and can be recycled over five times for flocculation., (© 2014 Wiley Periodicals, Inc.)

In commercial production, broiler breeders are severely feed restricted to maintain healthy BW. This restriction can induce stereotypic behavior, including feather pecking, which has negative welfare implications for both the victim and performer. It has been suggested that the problem may be symptomatic of chronic hunger or the frustration of feeding motivation. In this study, we determined whether feather condition, as an indirect measure of feather pecking, could be improved via dietary manipulation. Six dietary treatments were tested, each with 5 replicate pens of 9 to 12 birds. Control diets (C) were fed on a daily or skip-a-day (SAD) basis. Alternative diets included soybean hulls as a bulking ingredient and calcium propionate (CaP) as an appetite suppressant of either a feed grade (F) or purified (P) quality. Both alternative diets were fed on either a daily or SAD basis. Five or 6 birds were randomly chosen from each pen and feather scored at 10, 14, 20, 26, and 36 wk of age. Six body parts (neck, back, wings, legs, vent area, tail) were given a score from 0 to 5 (0 = no feather damage, and 5 ≥ 50% feather loss with tissue damage). Scores were summed for each bird and averaged for each pen. Data were analyzed with room and feeding frequency as main factors and diet as the subfactor with repeated measures. There was an interaction between diet and time (P < 0.01) with the feather condition of the C birds worsening more quickly in comparison with the F and P birds. There was an interaction between feeding frequency and time (P = 0.015), with SAD-fed birds scoring better than daily-fed birds at 20, 26, and 36 wk. This interaction could indicate that SAD feeding increased satiety after the birds became accustomed to the schedule. Because feather condition was better with the alternative diets, this may indicate a reduction in stereotyped feather pecking with these diets. This suggests that the alternative diets increase satiety compared with the control diets., (© 2014 Poultry Science Association Inc.)

Parent stocks of meat birds are severely feed restricted to avoid obesity-related health and fertility problems. This restriction often leads to chronic hunger, accompanied by stereotypic behavior. Research based in the United Kingdom has shown that using diets containing fiber and appetite suppressants may relieve some of the symptoms of hunger. However, few data are available regarding North American-sourced ingredients or nondaily feeding regimens. This study investigated the effects of 2 alternative diets, in combination with 2 feeding frequencies on growth, productivity, and behavior in broiler breeders. Six dietary treatments were tested, each with 5 replicate pens of 12 or 13 birds. Control diets consisted of a commercial crumble, fed on a daily or skip-a-day (SAD) basis. Alternative diets included soybean hulls as a fiber source, and calcium propionate as an appetite suppressant of either a feed-grade or purified quality, fed on either a daily or SAD basis. Birds were weighed weekly and egg production was recorded daily. Video cameras were used to record behavior during and following the morning feeding bout every 2 wk from 11 to 28 wk. Data were analyzed with a mixed model ANOVA, with repeated measures. Diet, feeding frequency, time, or an interaction of the 3 had significant effects on all observed behavior during rearing. These differences appeared to diminish during lay, with most stereotypic behavior no longer present. Very little object pecking and aggression was observed during and immediately following feeding bouts; however, daily-fed control birds still displayed this behavior more often, especially during rearing (P = 0.015). During feeding bouts, SAD birds feather pecked (P = 0.003) and rested more (P = 0.0002) than daily-fed birds. Control birds feather pecked most often (P = 0.033) after feeding bouts. Overall, the feed-grade diet appeared most effective at reducing hunger-related behavior, and the control diet appeared the least effective. There was little conclusive evidence to show that daily feeding was more effective at reducing hunger.

Triggering of defences by microbes has mainly been investigated using single elicitors or microbe-associated molecular patterns (MAMPs), but MAMPs are released in planta as complex mixtures together with endogenous oligogalacturonan (OGA) elicitor. We investigated the early responses in Arabidopsis of calcium influx and oxidative burst induced by non-saturating concentrations of bacterial MAMPs, used singly and in combination: flagellin peptide (flg22), elongation factor peptide (elf18), peptidoglycan (PGN) and component muropeptides, lipo-oligosaccharide (LOS) and core oligosaccharides. This revealed that some MAMPs have additive (e.g. flg22 with elf18) and even synergistic (flg22 and LOS) effects, whereas others mutually interfere (flg22 with OGA). OGA suppression of flg22-induced defences was not a result of the interference with the binding of flg22 to its receptor flagellin-sensitive 2 (FLS2). MAMPs induce different calcium influx signatures, but these are concentration dependent and unlikely to explain the differential induction of defence genes [pathogenesis-related gene 1 (PR1), plant defensin gene 1.2 (PDF1.2) and phenylalanine ammonia lyase gene 1 (PAL1)] by flg22, elf18 and OGA. The peptide MAMPs are potent elicitors at subnanomolar levels, whereas PGN and LOS at high concentrations induce low and late host responses. This difference might be a result of the restricted access by plant cell walls of MAMPs to their putative cellular receptors. flg22 is restricted by ionic effects, yet rapidly permeates a cell wall matrix, whereas LOS, which forms supramolecular aggregates, is severely constrained, presumably by molecular sieving. Thus, MAMPs can interact with each other, whether directly or indirectly, and with the host wall matrix. These phenomena, which have not been considered in detail previously, are likely to influence the speed, magnitude, versatility and composition of plant defences.

Bacterial pathogens and symbionts must suppress or negate host innate immunity. However, pathogens release conserved oligomeric and polymeric molecules or MAMPs (Microbial Associated Molecular Patterns), which elicit host defenses [1], [2] and [3]. Extracellular polysaccharides (EPSs) are key virulence factors in plant and animal pathogenesis, but their precise function in establishing basic compatibility remains unclear [4], [5], [6] and [7]. Here, we show that EPSs suppress MAMP-induced signaling in plants through their polyanionic nature [4] and consequent ability to chelate divalent calcium ions [8]. In plants, Ca2+ ion influx to the cytosol from the apoplast (where bacteria multiply [4], [5] and [9]) is a prerequisite for activation of myriad defenses by MAMPs [10]. We show that EPSs from diverse plant and animal pathogens and symbionts bind calcium. EPS-defective mutants or pure MAMPs, such as the flagellin peptide flg22, elicit calcium influx, expression of host defense genes, and downstream resistance. Furthermore, EPSs, produced by wild-type strains or purified, suppress induced responses but do not block flg22-receptor binding in Arabidopsis cells. EPS production was confirmed in planta, and the amounts in bacterial biofilms greatly exceed those required for binding of apoplastic calcium. These data reveal a novel, fundamental role for bacterial EPS in disease establishment, encouraging novel control strategies.