Low Nucleic Acid Research Articles

Abundant and rare bacteria in anthropogenic estuary: Community co-occurrence and assembly patterns

In estuary, bacteria are critically vital to ecosystem function and sustainability. However, the effect of geographic distance and its related factors (i.e., salinity and nutrients) on bacterial diversity, co-occurrence, as well as community assembly on the abundant and rare species scale remained to be discussed. In this study, we deciphered the bacterial dynamics and ecological processes in the anthropogenic estuary of the Haihe River, in China. The results revealed that salinity was the major abiotic factor to shape bacterial community composition, diversity, and network complexity, and the role of biotic cytometric characteristics was considerable as well. Furthermore, the salinity gradient tended to select bacteria with low nucleic acid (LNA) such as Candidatus Pelagibacter and Longivirga, and abundant bacteria were more sensitive to the salinity gradient in comparison with rare ones. The similar keystone number and network topology values indicated that both abundant and rare bacteria played important ecological functions in degrading pollutants, developing co-occurrence networks, and maintaining compositional stability and complexity. In addition, drift and dispersion limitation dominated the ecological processes in the community assembly, suggesting that although salinity caused the migration of species, its ecological role was still weaker than that of stochastic processes. Further, niche differentiation contributed to different stochastic components of abundant and rare species. In high-salinity areas, rare bacteria with small population sizes but high diversity were enriched, which made the bacterial community more affected by ecological drift. Our study illustrated the different responses of abundant and rare bacteria to salinity and the assembly process of bacterial communities in anthropogenic estuary, deepening the understanding of their ecological processes in the estuarine ecosystem.

Trophic and Microbial Patterns in the Ross Sea Area (Antarctica): Spatial Variability during the Summer Season

In open regions of the Ross Sea, the role of the microbial community in the turnover of organic matter has scarcely been investigated; indeed, very little is known on how microbial distribution and functional diversity respond to environmental conditions and hydrographic structures. During the austral summer of 2017, two pelagic areas of the Ross Sea [the Drygalski Ice Tongue and the nearby Terra Nova Bay polynya (A area), and the continental Shelf Break area near Cape Adare (C area)] were studied at selected depths [surface, Deep Chlorophyll Maximum (DCM), Circumpolar Deep Water (CDW), deep waters]. Trophic properties [nutrient concentrations, particulate (POC), dissolved organic carbon (DOC) and its optically significant fraction (CDOM) were measured, together with the main hydrological variables. Microbial community abundance [total prokaryotes, living, dead, and actively respiring fraction, high- and low nucleic acid cells (HNA and LNA), pico- and nano-eukaryotes, culturable heterotrophic bacteria], composition, and metabolism (as whole community and as isolated bacteria) were also assessed. Through a multidisciplinary dataset, this study highlighted the variable response of microbial abundance, diversity, and metabolism of the microbial community to the changing local environmental conditions of the Ross Sea. Different forces, such as organic matter inputs (mostly of detrital nature) released from the Drygalski glacier in the A area, and a coastal-to-offshore gradient in the C area, coexisted within this extreme ecosystem. This resulted in a significant spatial segregation of the edaphic parameters, and of the microbial community distribution and metabolic activity patterns.

Nucleic acid amplification with specific signal filtration and magnification for ultrasensitive colorimetric detection

Recently, sensitive, fast and low cost nucleic acid isothermal amplification technologies (such as loop-mediated isothermal amplification, LAMP) have attracted great attention in the urgent needs of point-of-care testing (POCT) and regular epidemic prevention and control. However, unlike PCR which usually employs TaqMan probe to report specific signals, specific-signal-output strategies in isothermal amplification are immature and visual detection even rare, which limits their popularity in POCT. We hypothesize to address this issue by designing a visual-signal-report system to both filtrate and magnify the target information in isothermal amplification. In this work, we developed a specific signal filtration and magnification colorimetric isothermal sensing platform (SFMC for short) for ultrasensitive detection of DNA and RNA. SFMC consists of two processes: an isothermal amplification with specific signal filtration and a self-replication catalyzed hairpin assembly (SRCHA) for rapid target-specific signal magnification and outputting. With these unique properties, this biosensing platform could detect target DNA as low as 5 copies per reaction and target RNA as low as 10 copies per reaction by naked eyes. Benefited from the excellent colorimetric detection performance, this biosensing platform has been successfully used for African swine fever virus (ASFV) and SARS-CoV-2 detection.

Contrasting sensitivity among oligotrophic marine microbial communities to priority PAHs

Oligotrophic areas represent a large proportion of the oceans, wherein microbial food webs largely determine carbon flux dynamics and biogeochemical cycles. However, little is known regarding the sensitivity of microbial planktonic communities to pollutants in such areas. Organic pollutants such as polycyclic aromatic hydrocarbons (PAH/s) are toxic oil derivatives that occur as complex mixtures and reach marine environments through different sources. Therefore, our study analyzed the PAH tolerance of natural photosynthetic and heterotrophic bacteria and eukaryotes from the oligotrophic Red Sea, which is uniquely susceptible to high oil contamination. Natural communities sampled from the surface layer were exposed to a concentration gradient of a mixture of 16 priority PAHs at in situ conditions for 48 h. The populations of the dominant picocyanobacteria Synechococcus sp., picophytoeukaryotes, and low nucleic acid (LNA) bacteria decreased upon exposure to PAHs in a strong dose-dependent manner. Chlorophyll-a, which was measured as an indicator of the total autotrophic community response, also decreased substantially. High nucleic acid (HNA) bacteria, however, exhibited lower growth inhibition (<50%). The lethal concentration (LC10) thresholds to the 16-PAH mixture demonstrated contrasting sensitivities among the microbial communities studied increasing from picoeukaryotes (5.98 ± 2.08 μg L−1) < chlorophyll-a (19.51 ± 8.11 μg L−1) < LNA bacteria (23.63 ± 10.64 μg L−1) < Synechococcus sp. (26.77 ± 13.34 μg L−1) < HNA bacteria (97.13 ± 17.28 μg L−1). The sensitivity of Red Sea Synechococcus and picophytoeukaryotes to the 16-PAH mixture was between 2 and 6.5 times higher compared to single PAH compounds tested previously. However, some populations of HNA bacteria and Synechococcus sp., were highly tolerant, suggesting an adaptation to chronic pollution. Concerningly, the LC10 toxicity thresholds approached the ambient PAH concentrations in the Red Sea, suggesting that environmental oil pollution actively shapes the microbial community structures in the region.

Abstract B012: Visualization of EWSR1’s colocalization with phosphorylated RNA-Polymerase II reveals its concentration at a subset of active regions of transcription in ewing sarcoma cells

Abstract EWSR1, a member of the FET protein family, contains low complexity and nucleic acid binding domains and functions in transcription regulation and RNA metabolism. Recent biochemical and EWSR1-depletion studies demonstrated that EWSR1 regulates critical phosphorylation events that control basal transcription. In Ewing sarcoma (EWS) cells, the interaction of EWSR1 and the fusion oncoprotein EWS-FLI1 results in EWSR1 no longer functioning as an effective regulator of transcription, which following DNA damage, enhances R-loop formation. To further elucidate EWSR1’s function in EWS and its contribution to EWS-FLI1’s deregulation of gene expression, we have generated reporter systems to visualize and quantify its endogenous expression within EWS cells. We used CRISPR-Cas9 and sgRNAs targeting sequences at the 5’ end of the first exon of EWSR1 to insert a fluorescent mNeonGreen (mNG) reporter gene into the EWSR1 loci of A673 or TC-32 EWS cell lines. We employed sequencing and RNAi-based analysis to identify and validate successfully modified clones. All modified clones harbored insertions into the unrearranged EWSR1 allele. We then employed super-resolution confocal microscopy to assess EWSR1’s localization in EWS cells. Analysis of modified EWS-cells showed mNG-EWSR1 forms puncta, restricted to the nucleoplasm, consistent with a nuclear protein in an active state. A subset of puncta exhibits a high density (HD) mNG-EWSR1 signal, defined by fluorescence at least twice the background signal. Our results show minimal colocalization of mNG-EWSR1 (total or HD) and a marker of chromatin accessibility, H3K27Ac. A small percentage (~5%) of total Ser5-phosphorylated RNA-pol II (pS5-RP-II), a marker of transcription initiation, colocalizes with total mNG-EWSR1, but critically the HD mNG-EWSR1 puncta all colocalize with pS5-RP-II. About 20% of total Ser2-phosphorylated RNA-pol II (pS2-RP-II), a marker of transcription elongation colocalizes with total mNG-EWSR1. As observed for pS5-RP-II, 100% of HD-mNG-EWSR1 puncta colocalize with pS2-RP-II. Finally, when we examined nuclear speckle structures (SC35/SRSF2 &amp;gt;200 µm), we observed a 20% overlap in their signals. We have seen comparable results using the mNG-EWSR1 expressing A673 cells. These findings demonstrate image-based quantification of endogenous EWSR1’s colocalization with RNA-polymerase II within EWS cells. Overall, EWSR1 colocalizes with about 20% of RNA-pol II in a state consistent with active transcription, and over 90% of high-density EWSR1 colocalizes with phosphorylated RNA pol II. Ongoing studies will assess changes in the distribution of EWSR1’s interactions with different proteins following inhibition of RNA-pol II phosphorylation, alterations in EWS-FLI1 expression, or the disruption of low complexity domain interactions. We anticipate findings from these studies will offer critical insights into the functional interactions that EWSR1 contributes to regulating gene expression in EWS cells. Citation Format: Natasha J. Caplen, Soumya Sundara Rajan, Vernon Ebegboni, Tamara L. Jones, Michael J. Kruhlak, Jan Wisniewski, Patricio Pichling, Katelyn R. Ludwig, Javed Khan, Raj Chari. Visualization of EWSR1’s colocalization with phosphorylated RNA-Polymerase II reveals its concentration at a subset of active regions of transcription in ewing sarcoma cells [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr B012.

Combining real-time fluorescence spectroscopy and flow cytometry to reveal new insights in DOC and cell characterization of drinking water

Sudden changes in drinking water quality can cause harmful consequences for end users. Thus, real-time monitoring of drinking water quality can allow early warning and provide crucial gains for securing safe water distribution. This study investigated the advantages of simultaneous real-time measuring of flow cytometry and fluorescence spectroscopy. A contamination event was investigated in a laboratory-scale analysis by spiking drinking water samples with organic nutrients. Flow cytometric data were analyzed by creating fingerprints based on differentiation into high and low nucleic acid cells (HNA/LNA). The detailed characterization of these data showed that an increase in HNA cells indicated an increase in the bacterial growth potential even before actual TCC increases. The fluorescence data was decomposed via the PARAFAC method to reveal seven fluorescent components. Three aromatic protein-like components were associated with the microbiological condition of the drinking water cells; namely, Components 4 (λEx = 279 nm, λEm = 351 nm), 6 (λEx = 279 nm, λEm = 332 nm), and 7 (λEx = 276 nm, λEm = 302 nm). Component 6 was identified as a possible organic variable for appropriate monitoring of TCC, whereas Components 4 and 7 were identified as organic compounds representing nutrients for organisms present in drinking water. Overall, combining both methods for real-time monitoring can be a powerful tool to guarantee drinking water quality.

Stagnation trigger changes to tap water quality in winter season: Novel insights into bacterial community activity and composition

The drinking water distribution system is important for water supply and it affects the quality of the drinking water. Indoor pipeline water quality is regulated by physical, hydraulic and biological elements, such as indoor temperature and stagnation. In this work, the effects of indoor heating and overnight stagnation on the variation in bacterial community structure and the total cell count were assessed by full-length 16S rRNA gene sequencing and flow cytometry, respectively. The results exhibited that the average intact cell count was 6.99 × 104 cells/mL and the low nucleic acid (LNA) bacteria was 4.48 × 104 cells/mL after stagnation. The average concentration of total and intracellular adenosine triphosphate (ATP) was 3.64 × 10−12 gATP/mL and 3.13 × 10−17 gATP/cell in stagnant water, respectively. The growth of LNA cells played a crucial role in increasing ATP. The dominant phylum observed was Proteobacteria (87.21 %), followed by Actinobacteria (8.25 %). Opportunistic pathogens increased the risk of disease in stagnant water (up to 1.2-fold for Pseudomonas sp. and 5.8-fold for Mycobacterium sp.). Meanwhile, structural equation model (SEM) and redundancy analysis (RDA) also illustrated that water temperature, residual chlorine and Fe significantly affected the abundance and composition of bacterial community. Taking together, these results show response of tap water quality to overnight stagnation and indoor heating, and provide scientific basis for drinking water security management in winter season.

Characteristics, Biodiversity, and Cultivation Strategy of Low Nucleic Acid Content Bacteria.

Low nucleic acid content (LNA) bacteria are ubiquitous and estimated to constitute 20%–90% of the total bacterial community in marine and freshwater environment. LNA bacteria with unique physiological characteristics, including small cell size and small genomes, can pass through 0.45-μm filtration. The researchers came up with different terminologies for low nucleic acid content bacteria based on different research backgrounds, such as: filterable bacteria, oligotrophic bacteria, and low-DNA bacteria. LNA bacteria have an extremely high level of genetic diversity and play an important role in material circulation in oligotrophic environment. However, the majority of LNA bacteria in the environment remain uncultivated. Thus, an important challenge now is to isolate more LNA bacteria from oligotrophic environments and gain insights into their unique metabolic mechanisms and ecological functions. Here, we reviewed LNA bacteria in aquatic environments, focusing on their characteristics, community structure and diversity, functions, and cultivation strategies. Exciting future prospects for LNA bacteria are also discussed.

Investigation of the effect of sustainable magnetic treatment on the microbiological communities in drinking water

The drinking water scarcity is posing a threat to mankind, hence better water quality management methods are required. Magnetic water treatment, which has been reported to improve aesthetic water quality and reduce scaling problems, can be an important addition to the traditional disinfectant dependent treatment. Despite the extensive market application opportunities, the effect of magnetic fields on (microbial) drinking water communities and subsequently the biostability is still largely unexplored, although the first patent was registered already 1945.Here flow cytometry was applied to assess the effect of weak magnetic fields (≤10 G) with strong gradients (≈800 G/m) on drinking water microbial communities. Drinking water was collected from the tap and placed inside the magnetic field (treated) and 5 m away from the magnet to avoid any background interferences (control) using both a static set-up and a shaking set-up. Samples were collected during a seven-day period for flow cytometry examination. Additionally, the effects of magnetic fields on the growth of Pseudomonas aeruginosa in autoclaved tap water were examined. Based on the fluorescent intensity of the stained nucleic acid content, the microbial cells were grouped into low nucleic acid content (LNA) and high nucleic acid content (HNA). Our results show that the LNA was dominant under nutrient limited condition while the HNA dominates when nutrient is more available. Such behavior of LNA and HNA matches well with the long discussed r/K selection model where r-strategists adapted to eutrophic conditions and K-strategists adapted to oligotrophic conditions. The applied magnetic fields selectively promote the growth of LNA under nutrient rich environment, which indicates a beneficial effect on biostability enhancement. Inhibition on an HNA representative Pseudomonas aeruginosa has also been observed. Based on our laboratory observations, we conclude that magnetic field treatment can be a sustainable method for microbial community management with great potential.

Pulsed export of carbon in the north-western Mediterranean Sea

The short term (hourly scale) variability of heterotrophic prokaryote (HP) vertical distribution and respiratory activity, was investigated in the north-western (NW) Mediterranean Sea. HP vertical distribution was determined on board by flow cytometry analysis of seawater samples collected by series of CTD casts. Cell counts and viability were determined for all samples. HP respiratory rates were determined later in the laboratory from filtered seawater samples (23 dm3) from 300–1 150-m depth. The average cell viability was 94.8%±2.2% (n=240). There was no accumulation of dead cells, due to quick decay of damaged cells. In the epipelagic layer, three HP groups were distinguished, two (HNA1, HNA2) whose cells exhibited a high nucleic acid content and one (LNA) with low nucleic acid content cells. HNA2 was most populated at 50 m but not detected at 90 m and below, presumably aerobic anoxygenic photoheterotrophic bacteria (AAPs). The variability in HP abundance was mainly confined in the upper 80 m. A few secondary peaks of HP abundance were observed (80–150 m) in connection with abundance troughs in the surface layer. HP cells were continuously present in a wide layer around 500 m (mean 191×103 cells/cm3). Below this layer, HP abundance randomly exhibited peaks, coupled to respiratory rate peaks. The HP abundance and variability in the water column was suppressed during a strong wind event. The observed sporadic variability was tentatively interpreted through a pulsed carbon-export mechanism induced by the microorganism production of dissolved polysaccharides, followed by flocculation and rapid sinking. This mechanism would thus contribute to (i) preventing organic matter accumulation in the epipelagic layer, (ii) seeding the water column with live HP cells, and (iii) supplying the aphotic water column with fresh and labile organic matter. This important vertical flux mechanism needs further observations and modelling.

High-Selectivity Single-Nucleotide Variant Capture Technology Based on the DNA Reaction Network.

The extremely low abundance of circulating tumor DNA in blood samples has limited the development of liquid biopsy techniques for the early diagnosis of major diseases. In this study, we demonstrate a DRN-based screening technique, SCREEN, which achieves the specific capture and enrichment of low abundance SNV nucleic acid samples without selective amplification. The SCREEN technique achieved a 108-fold increase in the abundance of single-nucleotide variant (SNV) nucleic acids from highly homologous mixtures (from 0.01% to 1.08%) and has been shown to significantly increase the abundance of SNV nucleic acids from 0.1% to 51% further through two rounds of capture. As a highly effective pre-enrichment technique, SCREEN has demonstrated the ability to enhance NGS in detecting an ultralow abundance SNV nucleic acid powerfully and has high compatibility with existing molecular diagnostic methods.

Modeling polar marine ecosystem functions guided by bacterial physiological and taxonomic traits

Abstract. Heterotrophic marine bacteria utilize organic carbon for growth and biomass synthesis. Thus, their physiological variability is key to the balance between the production and consumption of organic matter and ultimately particle export in the ocean. Here we investigate a potential link between bacterial traits and ecosystem functions in the rapidly warming West Antarctic Peninsula (WAP) region based on a bacteria-oriented ecosystem model. Using a data assimilation scheme, we utilize the observations of bacterial groups with different physiological traits to constrain the group-specific bacterial ecosystem functions in the model. We then examine the association of the modeled bacterial and other key ecosystem functions with eight recurrent modes representative of different bacterial taxonomic traits. Both taxonomic and physiological traits reflect the variability in bacterial carbon demand, net primary production, and particle sinking flux. Numerical experiments under perturbed climate conditions demonstrate a potential shift from low nucleic acid bacteria to high nucleic acid bacteria-dominated communities in the coastal WAP. Our study suggests that bacterial diversity via different taxonomic and physiological traits can guide the modeling of the polar marine ecosystem functions under climate change.

An invasive and native plant differ in their effects on the soil food-web and plant-soil phosphorus cycle

Although invasive species threaten the functional integrity of ecosystems significantly, their impacts on essential ecosystem processes such as soil phosphorus (P) cycling are not well understood. In a field experiment, we used a randomized complete block design to study how an invasive plant species may disrupt soil functioning, particularly P cycling compared to a native plant species. After three years of experiments, we compared soil P properties and soil micro food-webs (microorganisms and nematodes) induced by these two species. We also compared plant biomass and P allocation in the different tissues for these plants. A second microcosm experiment was performed to check whether the interactions of nematode and microorganisms affected the ecological processes of soil organic P mineralization. Compared to native species, invasive species had higher alkaline phosphomonoesterase (ALP)-producing bacteria, bacterivorous nematodes, and ALP activity and induced a stronger acceleration of soil organic P decomposition through the more interactions between ALP-producing bacteria and bacterivores. Moreover, the mycorrhizal colonization rate of the invasive species was higher than the native species, allowing it to absorb more P and allocate more to above-ground biomass, and thus maintaining its faster expansion. The invasive species had lower nucleic acid P, structural P, and residual P in foliar than the native species because invasive species allocate more P to metabolic P for photosynthesis. Our study suggests that invasive plants can enhance the organic P decomposition through microbial-microfaunal interactions. In addition, invasive plants might have higher P utilization efficiency than native ones. Although these findings need to be generalized with more native and invasive plant species, they still provide novel mechanistic explanations into how invasive species can expand quickly in P-poor lower latitudes.

Microbial Growth and Organic Matter Cycling in the Pacific Ocean Along a Latitudinal Transect Between Subarctic and Subantarctic Waters

The Pacific Ocean constitutes about half of the global oceans and thus microbial processes in this ocean have a large impact on global elemental cycles. Despite several intensely studied regions large areas are still greatly understudied regarding microbial activities, organic matter cycling and biogeography. Refined information about these features is most important to better understand the significance of this ocean for global biogeochemical and elemental cycles. Therefore we investigated a suite of microbial and geochemical variables along a transect from the subantarctic to the subarctic Pacific in the upper 200 m of the water column. The aim was to quantify rates of organic matter processing, identify potential controlling factors and prokaryotic key players. The assessed variables included abundance of heterotrophic prokaryotes and cyanobacteria, heterotrophic prokaryotic production (HPP), turnover rate constants of amino acids, glucose, and acetate, leucine aminopeptidase and β-glucosidase activities, and the composition of the bacterial community by fluorescence in situ hybridization (FISH). The additional quantification of nitrate, dissolved amino acids and carbohydrates, chlorophyll a, particulate organic carbon and nitrogen (POC, PON) provided a rich environmental context. The oligotrophic gyres exhibited the lowest prokaryotic abundances, rates of HPP and substrate turnover. Low nucleic acid prokaryotes dominated in these gyres, whereas in temperate and subpolar regions further north and south, high nucleic acid prokaryotes dominated. Turnover rate constants of glucose and acetate, as well as leucine aminopeptidase activity, increased from (sub)tropical toward the subpolar regions. In contrast, HPP and bulk growth rates were highest near the equatorial upwelling and lowest in the central gyres and subpolar regions. The SAR11 clade, the Roseobacter group and Flavobacteria constituted the majority of the prokaryotic communities. Vertical profiles of the biogeochemical and microbial variables markedly differed among the different regions and showed close covariations of the microbial variables and chlorophyll a, POC and PON. The results show that hydrographic, microbial, and biogeochemical properties exhibited distinct patterns reflecting the biogeographic provinces along the transect. The microbial variables assessed contribute to a better and refined understanding of the scales of microbial organic matter processing in large areas of the epipelagic Pacific beyond its well-studied regions.

Viral Production in Seawater Filtered Through 0.2-μm Pore-Size Filters: A Hidden Biogeochemical Cycle in a Neglected Realm

Viral production is a key parameter for assessing virus-mediated biogeochemical cycles. One widely used method for the determination of viral production, called the virus reduction assay, reduces viral abundance, while maintaining bacterial abundance, using 0.2-μm pore-size filters. Viral production is estimated from the increase of viral abundance during incubation. We hypothesized that small-cell-sized bacterial communities can pass through 0.2-μm filters and drive viral production, representing a missing fraction of viral production that is missed by the virus reduction assay. Coastal seawater was filtered through 0.2-μm filters and diluted with virus-free seawater. Viral production in the <0.2-μm filtrate was estimated from changes in viral abundance determined through flow cytometry. We found that viruses were produced in the <0.2-μm communities, which were strongly enriched with low nucleic acid content bacteria. Estimated viral production in the <0.2-μm filtrates accounted for up to 43% of total viral production and 10% of dissolved organic carbon production mediated by viral lysis of bacterial cells. By not considering viral production in these <0.2-μm communities, the virus reduction assay may underestimate viral production. Virus–bacteria interactions in <0.2-μm communities may represent a significant and overlooked role of viruses in marine food webs and carbon fluxes.

Zero-Emission of Palm Oil Mill Effluent Final Discharge Promoted Bacterial Biodiversity Rebound in the Receiving Water System

Zero-emission technology for palm oil mill effluent (POME) has led to a breakthrough in the palm oil industry in relation to the goal of sustainable development. However, there are limited resources on how this technology has affected the bacterial community in the receiving river that has previously been polluted with POME final discharge. Thus, the current study assessed the recoverability of the unexplored bacterial community in the receiving water of a constructed river water system post-zero emission of POME final discharge. An artificial river water system was constructed in this study, where the viability status and the composition of the bacterial community were assessed for 15 days using a flow cytometry-based assay and high-throughput sequencing by Illumina MiSeq, respectively. The zero-emission of POME final discharge reduced not only the physicochemical properties and nutrient contents of the receiving water, but also the bacterial cells’ viability from 40.3% to 24.5% and shifted the high nucleic acid (HNA) to low nucleic acid (LNA) content (38.7% to 34.5%). The proposed POME bacterial indicators, Alcaligenaceae and Chromatiaceae were not detectable in the rainwater (control) but were detected in the artificial river water system after the introduction of POME final discharge at the compositions of 1.0–1.3% and 2.2–5.1%, respectively. The implementation of a zero-emission system decreased the composition of Chromatiaceae from 2.2% on day 8 until it was undetectable on day 15, while Alcaligenaceae was continuously reduced from 1.2% to 0.9% within that similar time frame. As indicated by principal coordinate (PCO) analysis, the reductions in biological oxygen demand (BOD5) would further diminish the compositions of these bioindicators. The zero-emission of POME final discharge has demonstrated its efficacy, not only in reducing the polluting properties, but also in the bacterial biodiversity rebound in the affected water system.

Picoplankton Diel Variability and Estimated Growth Rates in Epipelagic and Mesopelagic Waters of the Central Red Sea

The diel variability of the abundance and cell size of picoplanktonic groups in the central Red Sea was monitored every 2 h in situ on 4 occasions (once per season) from 2015 to 2016. We distinguished Prochlorococcus, low (LF-Syn) and high (HF-Syn) fluorescence Synechococcus, small (Speuk) and large (Lpeuk) picoeukaryotes and two groups of heterotrophic prokaryotes of low (LNA) and high (HNA) nucleic acid content. The diel variability in abundance was less marked than in cell size and more apparent in autotrophs than heterotrophs. Specific growth rates were estimated by an empirical relationship from measurements obtained in bottle incubations of surface and deep samples collected in the winter compared with in situ variations in cell size over 24 h. Autotrophic picoplankton groups generally grew faster (0.23–0.77 d–1) than heterotrophic prokaryotes (0.12–0.50 d–1). Surface to 100 m depth-weighted specific growth rates displayed a clear seasonal pattern for Prochlorococcus, with maxima in winter (0.77 ± 0.07 d–1) and minima in fall (0.52 ± 0.07 d–1). The two groups of Synechococcus peaked in spring, with slightly higher growth rates of LF-Syn (0.57 ± 0.04 d–1) than HF-Syn (0.43 ± 0.04 d–1). Speuk and Lpeuk showed different seasonal patterns, with lower values of the former (0.27 ± 0.02 and 0.37 ± 0.04 d–1, respectively). HNA consistently outgrew LNA heterotrophic prokaryotes, with a higher growth in the epipelagic (0–200 m, 0.36 ± 0.03 d–1) than in the mesopelagic (200–700 m, 0.26 ± 0.03 d–1), while no differences were found for LNA cells (0.19 ± 0.03 d–1 and 0.17 ± 0.02 d–1, respectively). With all data pooled, the mean diel abundances of autotrophic picoplankton in the upper epipelagic and of HNA cells in the epipelagic and mesopelagic layers were significantly correlated with the specific growth rates estimated from cell size variations. Our high-resolution sampling dataset suggests that changes in growth rates underlie the noticeable seasonality of picoplankton recently described in these tropical waters.

Biosensors Designed for Clinical Applications

Emerging and validated biomarkers promise to revolutionize clinical practice, shifting the emphasis away from the management of chronic disease towards prevention, early diagnosis and early intervention. The challenge of detecting these low abundance protein and nucleic acid biomarkers within the clinical context demands the development of highly sensitive, even single molecule, assays that are also capable of selectively measuring a small number of defined analytes in complex samples such as whole blood, interstitial fluid, saliva or urine. Success relies on significant innovations in nanomaterials, bioreceptor engineering, transduction strategies and microfluidics. Primarily using examples from our work, this article discusses some recent advance in the selective and sensitive detection of disease biomarkers, highlights key innovations in sensor materials and identifies issues and challenges that need to be carefully considered especially for researchers entering the field.

Ontogeny versus environmental forcing off the Southwest Atlantic Ocean: Nutritional condition of Fuegian sprat (Sprattus fuegensis) early stages

AbstractThe Fuegian sprat, Sprattus fuegensis, plays a key trophic role in the Southwest Atlantic Ocean. Growth and survival of small pelagic fishes like sprat are strongly affected by environmental variability and can determine recruitment success. We estimated the nucleic acid composition and assessed with a standardized RNA/DNA index (sRD) the nutritional condition of 273 larvae, metamorphosing, and juvenile Fuegian sprat from two environmentally distinct habitats: the waters off Tierra del Fuego (TDF) and the Marine Protected Area Namuncurá/Burdwood Bank (MPAN/BB). A similar ontogenetic pattern, in which nucleic acid concentrations decreased and sRD increased with increasing standard length (SL) among larval stages was observed in both habitats. A higher percentage of preflexion larvae were under the sRD threshold for growth and optimal growth performance, with sRD values being significantly higher in TDF. Postflexion larvae in both habitats showed maximum sRD values, suggesting that both habitats are suitable nursery grounds. In contrast, metamorphosing and juvenile sprat (only captured in TDF) had consistently low nucleic acid concentrations and sRD values despite increasing SL. Environmental forcing (temperature, salinity, and station depth) was assessed over size‐corrected larval sRD. The best model included a negative response to station depth, and the effect of processes associated with this factor are discussed. Although further analyses are needed to reveal underlying dynamics determining early development, these results comprise a baseline for future monitoring approaches on Fuegian sprat life traits and factors affecting their recruitment in this region.

Naphthalimide‐modified dendrimers as efficient and low cytotoxic nucleic acid delivery vectors

AbstractPoly(amidoamine) (PAMAM) dendrimers have been widely used as nucleic acid delivery vectors. To improve the transfection efficacy, ligands such as amino acid, peptide and lipid are conjugated to the periphery of dendrimers. However, the structures of these ligands are generally flexible, and few reports about rigid‐ligand‐modified dendrimers are reported. In this work, three novel PAMAM dendrimers (G5‐1, G5‐2 and G5‐3) modified with rigid naphthalimide were synthesized as nucleic acid delivery vectors. Magnetic resonance spectroscopy showed that the average numbers of naphthalimide molecules conjugated on the PAMAM periphery in compounds G5‐1, G5‐2 and G5‐3 are 8, 30 and 50, respectively. The 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide (MTT) assay revealed good cytocompatibility of these vectors in multiple cell lines, including MG63, HeLa, HEK293 and MC3T3‐E1 cells, with a cell survival rate of more than 90% in most cases. Among the three dendrimers, G5‐1 with fewer naphthalimide molecules showed stronger RNA binding ability than G5‐2 and G5‐3. G5‐1 also exhibited the best gene silencing efficacy at a dendrimer to miRNA weight ratio of 1:2 in MC3T3‐E1 cells, which is much higher than the commercial transfection agent Lipofectamine 2000 tested under the same conditions. In addition, G5‐1 showed high transfection efficacy in plasmid DNA‐mediated luciferase expression experiments. These results suggest that rigid ligand modification can be developed as a new strategy to design safe and highly efficient nucleic acid delivery vectors. © 2021 Society of Industrial Chemistry.