Biomolecular Tools Research Articles

Use of Biomolecular Tools to Control the Labels of Ethnic Food Coming from Eastern Europe.

In recent years, due to the large Romanian community present in Italy, the retail of foods coming from Eastern Europe has increased. The most common type of violation detected in these foods consists of incorrect labeling and species-replacement frauds. In this paper, the compliance of labels of 43 ethnic processed food coming from Eastern Europe and commercialized in Italy was evaluated by means of PCR and Sanger sequencing. Our data revealed 33% of non-compliant labels in samples containing swine, ruminants, and avian ingredients. These results demonstrate that PCR can be easily used for the identification of species in highly processed products, proving to be a rapid, effective, and economic method. On the other hand, samples reporting fish as ingredients highlighted the ineffectiveness of the applied sequencing protocol, due to the low informative property of targeted fragments or to the lack of consensus sequences in the case of uncommon species.

Temperature regulates sex determination and growth in the paralichthid flatfishCalifornia halibut.

California halibut (Paralichthys californicus) is a candidate species for aquaculture and stock enhancement. These applications rely on sex control, either to maximize the production of faster growing females or to match sex ratios in the wild. Other paralichthids exhibit temperature-dependent sex determination (TSD), but the presence and pattern of TSD is not well defined in California halibut. Juvenile California halibut were cultured at three distinct temperatures (15°C, 19°C, and 23°C) through the developmental period presumed to be thermosensitive based on findings from congeners. Sex ratios were quantified in each treatment using phenotypic sex identification techniques applied early (molecular biomarkers; 51-100 mm total length [TL]) and late (visual examination of the gonads; ≥100 mm TL) in the juvenile phase. Both techniques indicated similar sex determination trends at each temperature, with overall sex ratios assessed as 49.9% maleat 15°C, 74.5% maleat 19°C, and 98.2% maleat 23°C. Growth rates were highest at 23°C and lowest at 15°C, with intrinsically fast- and slow-growing individuals at all temperatures. At 15°C and 19°C, females comprised a higher proportion among the fast growers than they did among the slow growers. These data show that California halibut exhibit TSD, with temperatures of 19°C and 23°C masculinizing fish while 15°C appears to produce a 1:1 sex ratio. This study will help optimize sex ratios and growth in hatcheries through thermal manipulation. Furthermore, the developed biomolecular tools and identified temperature thresholds will be important in future work to understand the influence of global warming on wild population demographics.

Uncovering the Holocene roots of contemporary disease-scapes: bringing archaeology into One Health.

The accelerating pace of emerging zoonotic diseases in the twenty-first century has motivated cross-disciplinary collaboration on One Health approaches, combining microbiology, veterinary and environmental sciences, and epidemiology for outbreak prevention and mitigation. Such outbreaks are often caused by spillovers attributed to human activities that encroach on wildlife habitats and ecosystems, such as land use change, industrialized food production, urbanization and animal trade. While the origin of anthropogenic effects on animal ecology and biogeography can be traced to the Late Pleistocene, the archaeological record-a long-term archive of human-animal-environmental interactions-has largely been untapped in these One Health approaches, thus limiting our understanding of these dynamics over time. In this review, we examine how humans, as niche constructors, have facilitated new host species and 'disease-scapes' from the Late Pleistocene to the Anthropocene, by viewing zooarchaeological, bioarchaeological and palaeoecological data with a One Health perspective. We also highlight how new biomolecular tools and advances in the '-omics' can be holistically coupled with archaeological and palaeoecological reconstructions in the service of studying zoonotic disease emergence and re-emergence.

High-resolution crystal structure of the Mu8.1 conotoxin from Conus mucronatus.

Marine cone snails produce a wealth of peptide toxins (conotoxins) that bind their molecular targets with high selectivity and potency. Therefore, conotoxins constitute valuable biomolecular tools with a variety of biomedical purposes. The Mu8.1 conotoxin from Conus mucronatus is the founding member of the newly identified saposin-like conotoxin class of conotoxins and has been shown to target Cav2.3, a voltage-gated calcium channel. Two crystal structures have recently been determined of Mu8.1 at 2.3 and 2.1 Å resolution. Here, a high-resolution crystal structure of Mu8.1 was determined at 1.67 Å resolution in the high-symmetry space group I4122. The asymmetric unit contained one molecule, with a symmetry-related molecule generating a dimer equivalent to that observed in the two previously determined structures. The high resolution allows a detailed atomic analysis of a water-filled cavity buried at the dimer interface, revealing a tightly coordinated network of waters that shield a lysine residue (Lys55) with a predicted unusually low side-chain pKa value. These findings are discussed in terms of a potential functional role of Lys55 in target interaction.

Survey of bed bug infestations in homeless shelters in southern France

Bed bug has become a major public health pest worldwide. Infestation may result in numerous negative health effects. Homeless shelters are one of the most habitats that can be infested with bed bugs, a few studies have focused on bed bug infestations in these settings. We conducted a survey of infestations of bed bugs in a homeless shelter in southern France, using an innovative seven-level scale (0–6) to assess the degree of infestation, MALDI TOF-MS to identify bed bugs, and a biomolecular tool to detect bacteria. Bed bug infestations were documented in 13% (9/68) of investigated rooms. A total of 184 bed bugs were collected and morphologically identified as Cimex lectularius. MALDI TOF–MS analysis allowed us to obtain high-quality MS spectra for all 184 specimens, to correctly identify all specimens, and included 178/184 (97%) Log Score Values higher than 1.8. Among the bacteria tested, Wolbachia sp. DNA was found in 149/184 (81%) of the bed bugs, and one sample was positive for Coxiella burnetii, the agent of Q fever. Our study is the first of its kind that offers new perspectives for increasing public awareness of the conditions in homeless shelters.

Functional imaging-guided cell selection for evolving genetically encoded fluorescent indicators

Genetically encoded fluorescent indicators are powerful tools for tracking cellular dynamic processes. Engineering these indicators requires balancing screening dimensions with screening throughput. Herein, we present a functional imaging-guided photoactivatable cell selection platform, Faculae (functional imaging-activated molecular evolution), for linking microscopic phenotype with the underlying genotype in a pooled mutant library. Faculae is capable of assessing tens of thousands of variants in mammalian cells simultaneously while achieving photoactivation with single-cell resolution in seconds. To demonstrate the feasibility of this approach, we applied Faculae to perform multidimensional directed evolution for far-red genetically encoded calcium indicators (FR-GECIs) with improved brightness (Nier1b) and signal-to-baseline ratio (Nier1s). We anticipate that this image-based pooled screening method will facilitate the development of a wide variety of biomolecular tools.

The Emerging Role of Engineering Immune Cells in Cancer Treatments

Cell-based immunotherapy has become one of the forefronts of cancer treatments and led to significant clinical success in multiple refractory/recurrent hematological malignancies. Compared with other conventional treatment approaches, engineered immune cells are considered “living factories” that are able to continually produce anti-tumor factors and have the potential to mediate long-lasting therapeutic benefits following a single application. The intrinsic ability to expand and respond in portion to needs encompasses this technology a greater and more transformative potential to enable a more effective anti-tumor response with less off-target toxicity. Nevertheless, there are still some significant barriers to successfully applying cell-based therapy to treat solid tumors. Five main challenges include restricted trafficking and infiltration, antigen escape and heterogeneity, suboptimal persistence, immunosuppressive tumor microenvironment (TME), and potentially severe side effects and immune-related toxicities. The technological advancement of various biomolecular tools and genetic engineering strategies provides exciting opportunities to address these limitations. In addition, combination therapy that incorporates other treatment modalities within the treatment regimen of cell-based strategy also creates therapeutic synergies that can greatly improve the clinical success of the therapy. This review introduces current observed challenges in treating cancers, with an emphasis on solid malignancies, and discusses some potential engineering solutions that have shown promising results in recent preclinical studies.

Biopanning of specific peptide for SARS-CoV-2 nucleocapsid protein and enzyme-linked immunosorbent assay-based antigen assay

The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread worldwide which triggered serious public health issues. The search for rapid and accurate diagnosis, effective prevention, and treatment is urgent. The nucleocapsid protein (NP) of SARS-CoV-2 is one of the main structural proteins expressed and most abundant in the virus, and is considered a diagnostic marker for the accurate and sensitive detection of SARS-CoV-2. Herein, we report the screening of specific peptides from the pIII phage library that bind to SARS-CoV-2 NP. The phage monoclone expressing cyclic peptide N1 (peptide sequence, ACGTKPTKFC, with C&C bridged by disulfide bonding) specifically recognizes SARS-CoV-2 NP. Molecular docking studies reveal that the identified peptide is bound to the “pocket” region on the SARS-CoV-2 NP N-terminal domain mainly by forming a hydrogen bonding network and through hydrophobic interaction. Peptide N1 with the C-terminal linker was synthesized as the capture probe for SARS-CoV-2 NP in ELISA. The peptide-based ELISA was capable of assaying SARS-CoV-2 NP at concentrations as low as 61 pg/mL (∼1.2 pM). Furthermore, the as-proposed method could detect the SARS-CoV-2 virus at limits as low as 50 TCID50 (median tissue culture infective dose)/mL. This study demonstrates that selected peptides are powerful biomolecular tools for SARS-CoV-2 detection, providing a new and inexpensive method of rapidly screening infections as well as rapidly diagnosing coronavirus disease 2019 patients.

Technique of flat-mount immunostaining for mapping the olfactory epithelium and counting the olfactory sensory neurons.

The pathophysiology underlying olfactory dysfunction is still poorly understood, and more efficient biomolecular tools are necessary to explore this aspect. Immunohistochemistry (IHC) on cross sections is one of the major tools to study the olfactory epithelium (OE), but does not allow reliable counting of olfactory sensory neurons (OSNs) or cartography of the OE. In this study, we want to present an easy immunostaining technique to compensate for these defects of IHC. Using the rat model, we first validated and pre-screened the key OSN markers by IHC on cross sections of the OE. Tuj-1, OMP, DCX, PGP9.5, and N-cadherin were selected for immunostaining on flat-mounted OE because of their staining of OSN dendrites. A simple technique for immunostaining on flat-mounted septal OE was developed: fixation of the isolated septum mucosa in 0.5% paraformaldehyde (PFA) preceded by pretreatment of the rat head in 1% PFA for 1 hour. This technique allowed us to correctly reveal the olfactory areas using all the 5 selected markers on septum mucosa. By combining the mature OSN marker (OMP) and an immature OSN marker (Tuj-1), we quantified the mature (OMP+, Tuj-1-), immature (OMP-, Tuj-1+), transitory (OMP+, Tuj-1+) and total OSN density on septal OE. They were respectively 42080 ± 11820, 49384 ± 7134, 14448 ± 5865 and 105912 ± 13899 cells per mm2 (mean ± SD). Finally, the same immunostaining technique described above was performed with Tuj-1 for OE cartography on ethmoid turbinates without flat-mount.

REVAMP: Rapid Exploration and Visualization through an Automated Metabarcoding Pipeline

The revolution and acceleration in DNA sequencing over the past three decades has driven the development of new biomolecular tools like environmental DNA (eDNA) metabarcoding for characterizing marine biodiversity. In order to operationalize eDNA approaches for routine NOAA observatories, new bioinformatic programs and improved organismal reference barcodes are needed to serve accurate and reliable biological data in a timely manner. To address these needs, we present Rapid Exploration and Visualization through an Automated Metabarcoding Pipeline (REVAMP), which provides streamlined end-to-end data processing from raw reads to data exploration, visualization, and hypothesis generation. One benefit of REVAMP is the ability to iteratively assess marker gene and reference database performance. Here, we used a filtered reference database that only included sequences uploaded prior to specified date cutoffs from 1995 to 2022 to analyze changes in eDNA metabarcoding taxonomic assignments, revealing patterns of uneven improvement in taxonomic assignment depth and accuracy across time, region, and marker sets. This work highlights the need for targeted reference sequencing efforts for key regional taxa and the importance of such efforts for improving eDNA biomonitoring approaches in the future.

Aptamers 101: aptamer discovery and in vitro applications in biosensors and separations.

Aptamers are single-stranded nucleic acids that bind and recognize targets much like antibodies. Recently, aptamers have garnered increased interest due to their unique properties, including inexpensive production, simple chemical modification, and long-term stability. At the same time, aptamers possess similar binding affinity and specificity as their protein counterpart. In this review, we discuss the aptamer discovery process as well as aptamer applications to biosensors and separations. In the discovery section, we describe the major steps of the library selection process for aptamers, called systematic evolution of ligands by exponential enrichment (SELEX). We highlight common approaches and emerging strategies in SELEX, from starting library selection to aptamer-target binding characterization. In the applications section, we first evaluate recently developed aptamer biosensors for SARS-CoV-2 virus detection, including electrochemical aptamer-based sensors and lateral flow assays. Then we discuss aptamer-based separations for partitioning different molecules or cell types, especially for purifying T cell subsets for therapeutic applications. Overall, aptamers are promising biomolecular tools and the aptamer field is primed for expansion in biosensing and cell separation.

(Invited) Biomolecular Engineering for Electrochemical Applications in Fuel Cells/Electrolyzers and Beyond

Control of ionomer thin film structures on metal surfaces is pivotal for efficient performance in electrochemical devices such as fuel cells and electrolyzers. Unfortunately, the assembly of these thin film structures is difficult to control using conventional methods and ideal arrangements remain unknown. Engineered polypeptides have emerged as powerful biomolecular tools in electrode assembly because binding sites and polypeptide structures can be easily modulated by changing the amino acid sequence. However, no studies have been conducted showing polypeptides can be engineered to interact with ionomers, attach them to metal surfaces, and control their arrangement. Our lab has recently developed this technology, using an elastin-like polypeptide to bind to metals, and bind to acidic and basic ionomer via ionic interactions. We use a quartz crystal microbalance with dissipation to provide detailed information about the loading, thickness, and binding behavior of the polypeptide and ionomer layers. We also use atomic force microscopy and grazing-incidence small-angle X-ray scattering to understand the impact of the biomolecules on ionomer phase separation. Finally, we have analyzed the performance (ionic conductivity) of the assembled films using interdigitated electrodes and electrochemical impedance spectroscopy. Through these techniques, we show that 1) our biomolecular system is highly flexible, easily adapting to different materials, 2) the polypeptide sequence can dictate ionomer phase separated structures, and 3) this system can be used to improve the performance of ionomer thin films and gain structure-function understanding. Generally, our results demonstrate that engineered polypeptides are promising tools for ionomer control in electrode engineering for fuel cells/electrolyzers and beyond. Furthermore, this work demonstrates that the creative combination of applied electrochemistry and biomolecular engineering supported and encouraged by leaders in each field can lead to unique research pathways that benefit heath, energy and the environment.

(Invited) Engineering Polypeptides for Controlled Assembly of Ionomer Thin Films: Expanding Beyond Typical Assembly Tools

Control of ionomer thin film structures on metal surfaces is pivotal for efficient performance in electrochemical devices such as fuel cells and electrolyzers. Unfortunately, the assembly of these thin film structures is difficult to control using conventional methods and ideal arrangements remain unknown. Engineered polypeptides have emerged as powerful biomolecular tools in electrode assembly because binding sites and polypeptide structures can be easily modulated by changing the amino acid sequence. However, no studies have been conducted showing polypeptides can be engineered to interact with ionomers, attach them to metal surfaces, and control their arrangement. Our lab has recently developed this technology, using an elastin-like polypeptide to bind to metals, and bind to acidic and basic ionomer via ionic interactions. We use a quartz crystal microbalance with dissipation to provide detailed information about the loading, thickness, and binding behavior of the polypeptide and ionomer layers. We also use atomic force microscopy and grazing-incidence small-angle X-ray scattering to understand the impact of the biomolecules on ionomer phase separation. Finally, we have analyzed the performance (ionic conductivity) of the assembled films using interdigitated electrodes and electrochemical impedance spectroscopy. Through these techniques, we show that 1) our biomolecular system is highly flexible, easily adapting to different materials, 2) the polypeptide sequence can dictate ionomer phase separated structures, and 3) this system can be used to improve the performance of ionomer thin films and gain structure-function understanding. Finally, alternative ionomer assembly techniques are discussed for future exploration. Generally, our results demonstrate that engineered polypeptides are promising tools for ionomer control in electrode engineering.

The Landscape of Genome-Wide and Gender-Specific Microsatellites in Indo-Pacific Humpback Dolphin and Potential Applications in Cetacean Resource Investigation

Microsatellites are one of the important genome characterizations that can be a valuable resource for variety identification, genetic diversity, phylogenetic analysis, as well as comparative and conservation genomics research. Here, we developed comprehensive microsatellites through genome-wide mining for the threatened cetacean Indo-Pacific humpback dolphin (Sousa chinensis). We found 87,757 microsatellites with 2–6 bp nucleotide motifs, showing that about 32.5 microsatellites per megabase comprises microsatellites sequences. Approximately 97.8% of the markers developed in this study were consistent with the published identified markers. About 75.3% microsatellites were with dinucleotide motifs, followed by tetranucleotide motifs (17.4%), sharing the same composition pattern as other cetaceans. The microsatellites were not evenly distributed in the S. chinensis genome, mainly in non-coding regions, with only about 0.5% of the markers located in coding regions. The microsatellite-containing genes were mainly functionally enriched in the methylation process, probably demonstrating the potential impacts of microsatellites on biological functions. Polymorphic microsatellites were developed between different genders of S. chinensis, which was expected to lay the foundation for genetic diversity investigation in cetaceans. The specific markers for a male Indo-Pacific humpback dolphin will provide comprehensive and representative male candidate markers for sex identification, providing a potential biomolecular tool for further analysis of population structure and social behavior of wild populations, population trend evaluation, and species conservation management.

High Prevalence of Tick-Borne Zoonotic Rickettsia slovaca in Ticks from Wild Boars, Northeastern Italy.

Simple SummaryTick-borne rickettsioses are emerging diseases that have become widespread in many European countries, particularly in those facing the Mediterranean basin. Although Rickettsia conorii was traditionally thought to be the most threatening species, in recent decades, thanks to the improvements in biomolecular tools, other zoonotic species have been identified, such as Rickettsia slovaca, the etiological agent of scalp eschar and neck lymphadenopathy after tick bite (SENLAT), as well as other neglected species. These pathogens are present in Italy, but few data are available. This research aimed to improve the epidemiological knowledge of rickettsial infections in tick and wild boar populations in the Euganean Hills Regional Park, an enclosed area in northeastern Italy. Both tick and wild boar blood samples were tested using biomolecular methods to detect and identify Rickettsia species. Only ticks tested positive, and Rickettsia slovaca was the most frequently detected species, showing a high prevalence, followed by Rickettsia monacensis and Rickettsia helvetica. These data highlight a non-negligible presence of these pathogens in northern Italy and outline that rickettsial infections deserve further investigation.Tick-borne rickettsiae are emerging pathogens that are becoming widespread in Europe. Rickettsiae are endemic in Italy, but epidemiological data are currently scarce. This study aimed to improve our knowledge about rickettsial infections in tick and wild boar populations. Blood and ticks were collected from 102 wild boars in 2010 and 2018. Ticks were also collected from the vegetation in the area. All of the samples were examined using real-time PCR targeting the gltA gene to detect Rickettsia DNA. Positivity was confirmed by PCR amplifying the gltA and/or ompB genes. A total of 254 ticks and 89 blood samples were analyzed. Zoonotic rickettsiae were detected in the ticks but not in the blood samples. Rickettsia slovaca (R. slovaca) was the most prevalent in ticks and was found in 23.7% of Dermacentor marginatus (D. marginatus) and in 3.4% of Ixodes ricinus (I. ricinus). Other zoonotic species were identified, such as Rickettsia monacensis, which was detected in 12% of I. ricinus ticks, and Rickettsia helvetica which was found in 3.4% of questing I. ricinus ticks and in 1.1% of D. marginatus collected from wild boars. This study highlights a high prevalence of zoonotic rickettsiae, particularly that of R. slovaca, in northeastern Italy. As rickettsioses are underreported and underdiagnosed in human medicine, both clinicians and researchers should pay more attention to this topic.

Development of a Real-Time Pectic Oligosaccharide-Detecting Biosensor Using the Rapid and Flexible Computational Identification of Non-Disruptive Conjugation Sites (CINC) Biosensor Design Platform.

Fluorescently labeled, solute-binding proteins that change their fluorescent output in response to ligand binding are frequently used as biosensors for a wide range of applications. We have previously developed a “Computational Identification of Non-disruptive Conjugation sites” (CINC) approach, an in silico pipeline utilizing molecular dynamics simulations for the rapid design and construction of novel protein–fluorophore conjugate-type biosensors. Here, we report an improved in silico scoring algorithm for use in CINC and its use in the construction of an oligogalacturonide-detecting biosensor set. Using both 4,5-unsaturated and saturated oligogalacturonides, we demonstrate that signal transmission from the ligand-binding pocket of the starting protein scaffold to the CINC-selected reporter positions is effective for multiple different ligands. The utility of an oligogalacturonide-detecting biosensor is shown in Carbohydrate Active Enzyme (CAZyme) activity assays, where the biosensor is used to follow product release upon polygalacturonic acid (PGA) depolymerization in real time. The oligogalacturonide-detecting biosensor set represents a novel enabling tool integral to our rapidly expanding platform for biosensor-based carbohydrate detection, and moving forward, the CINC pipeline will continue to enable the rational design of biomolecular tools to detect additional chemically distinct oligosaccharides and other solutes.

Triggered Reversible Disassembly of an Engineered Protein Nanocage*.

Protein nanocages play crucial roles in sub-cellular compartmentalization and spatial control in all domains of life and have been used as biomolecular tools for applications in biocatalysis, drug delivery, and bionanotechnology. The ability to control their assembly state under physiological conditions would further expand their practical utility. To gain such control, we introduced a peptide capable of triggering conformational change at a key structural position in the largest known encapsulin nanocompartment. We report the structure of the resulting engineered nanocage and demonstrate its ability to disassemble and reassemble on demand under physiological conditions. We demonstrate its capacity for in vivo encapsulation of proteins of choice while also demonstrating in vitro cargo loading capabilities. Our results represent a functionally robust addition to the nanocage toolbox and a novel approach for controlling protein nanocage disassembly and reassembly under mild conditions.

Triggered Reversible Disassembly of an Engineered Protein Nanocage**

AbstractProtein nanocages play crucial roles in sub‐cellular compartmentalization and spatial control in all domains of life and have been used as biomolecular tools for applications in biocatalysis, drug delivery, and bionanotechnology. The ability to control their assembly state under physiological conditions would further expand their practical utility. To gain such control, we introduced a peptide capable of triggering conformational change at a key structural position in the largest known encapsulin nanocompartment. We report the structure of the resulting engineered nanocage and demonstrate its ability to disassemble and reassemble on demand under physiological conditions. We demonstrate its capacity for in vivo encapsulation of proteins of choice while also demonstrating in vitro cargo loading capabilities. Our results represent a functionally robust addition to the nanocage toolbox and a novel approach for controlling protein nanocage disassembly and reassembly under mild conditions.

Fungal-fungal and fungal-bacterial interactions in aquatic decomposer communities: bacteria promote fungal diversity.

Fungi produce a variety of extracellular enzymes, making recalcitrant substrates bioavailable. Thus, fungi are central for the decomposition of dead organic matter such as leaf litter. Despite their ecological importance, our understanding of relationships between fungal species diversity and ecosystem functioning is limited, especially with regard to aquatic habitats. Moreover, fungal interactions with other groups of microorganisms such as bacteria are rarely investigated. This lack of information may be attributed to methodological limitations in tracking the biomass of individual fungal species in communities, impeding a detailed assessment of deviations from the overall performance expected from the sum of individual species' performances, so-called net diversity effects (NDEs). We used fungal species-specific biomolecular tools to target fungal-fungal and fungal-bacterial interactions on submerged leaves using four cosmopolitan aquatic fungal species and a stream microbial community dominated by bacteria. In microcosms, we experimentally manipulated fungal diversity and bacterial absence/presence and assessed functional performances and fungal community composition after 14d of incubation. Fungal community data were used to evaluate NDEs on leaf colonization. The individual fungal species were functionally distinct and fungal cultures were on average more efficient than the bacterial culture. In absence of bacteria, NDEs correlated with growth rate (negatively) and genetic divergence (positively), but were predominantly negative, suggesting that higher fungal diversity led to a lower colonization success (niche overlap). In both absence and presence of bacteria, the overall functional performances of the communities were largely defined by their composition (i.e., no interactions at the functional level). In the presence of bacteria, NDEs correlated with genetic divergence (positively) and were largely positive, suggesting higher fungal diversity stimulated colonization (niche complementarity). This stimulation may be driven by a bacteria-induced inhibition of fungal growth, alleviating competition among fungi. Resulting feedback loops eventually promote fungal coexistence and synergistic interactions. Nonetheless, overall functional performances are reduced compared to bacteria-free cultures. These findings highlight the necessity to conduct future studies, investigating biodiversity-ecosystem functioning relationships using artificial systems, without exclusion of key organisms naturally co-occurring in the compartment of interest. Otherwise, study outcomes might not reflect true ecological relationships and ultimately misguide conservation strategies.

Noble metal nanomaterial-based aptasensors for microbial toxin detection.

Microbial toxins generated by bacteria, fungi and algae cause serious food-safety problems due to the frequent contamination of foodstuffs and their poisonous nature. Becoming acquainted with the contamination condition of foodstuffs is highly dependent on developing sensitive, specific, and accurate methods for targeting microbial toxins. Aptamers, obtained from systematic evolution of ligands by exponential enrichment (SELEX), have significant advantages for microbial toxin analysis, such as small size, reproducible chemical synthesis, and modification, as well as high binding affinity, specificity, and stability. Besides, aptamers have a predictable structure and can be tailored using biomolecular tools (e.g., ligase, endonuclease, exonuclease, polymerase, and so on), which is conducive to the development of flexible and variable amplification methods. Recent studies revealed that the combination of aptamers and noble metal nanomaterials offers unprecedented opportunities for microbial toxin detection. Noble metal nanomaterials with outstanding physical and chemical properties facilitate the detection process and improve the sensitivity and specificity. In this review, we discuss current progress in the development of various noble metal nanomaterial-based aptasensors for microbial toxin detection. These noble metal nanomaterials include gold nanoparticles, gold nanorods, gold nanoclusters, silver nanoparticles, silver nanoclusters, and bimetallic nanomaterials. Aptasensors based on noble metal nanomaterials exhibiting high selectivity and sensitivity represent a promising tool for microbial toxin detection.