Defining variant-resistant epitopes targeted by SARS-CoV-2 antibodies: A global consortium study.

Antibody-based therapeutics and vaccines are essential to combat COVID-19 morbidity and mortality after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Multiple mutations in SARS-CoV-2 that could impair antibody defenses propagated in human-to-human transmission and spillover or spillback events between humans and animals. To develop prevention and therapeutic strategies, we formed an international consortium to map the epitope landscape on the SARS-CoV-2 spike protein, defining and structurally illustrating seven receptor binding domain (RBD)­directed antibody communities with distinct footprints and competition profiles. Pseudovirion-based neutralization assays reveal spike mutations, individually and clustered together in variants, that affect antibody function among the communities. Key classes of RBD-targeted antibodies maintain neutralization activity against these emerging SARS-CoV-2 variants. These results provide a framework for selecting antibody treatment cocktails and understanding how viral variants might affect antibody therapeutic efficacy.

Functional characterization of Gram-negative bacteria from different genera as multiplex cadmium biosensors.

Widespread presence of cadmium in soil and water systems is a consequence of industrial and agricultural processes. Subsequent accumulation of cadmium in food and drinking water can result in accidental consumption of dangerous concentrations. As such, cadmium environmental contamination poses a significant threat to human health. Development of microbial biosensors, as a novel alternative method for in situ cadmium detection, may reduce human exposure by complementing traditional analytical methods. In this study, a multiplex cadmium biosensing construct was assembled by cloning a single-output cadmium biosensor element, cadRgfp, and a constitutively expressed mrfp1 onto a broad-host range vector. Incorporation of the duplex fluorescent output [green and red fluorescence proteins] allowed measurement of biosensor functionality and viability. The biosensor construct was tested in several Gram-negative bacteria including Pseudomonas, Shewanella and Enterobacter. The multiplex cadmium biosensors were responsive to cadmium concentrations ranging from 0.01 to 10µgml-1, as well as several other heavy metals, including arsenic, mercury and lead at similar concentrations. The biosensors were also responsive within 20-40min following exposure to 3µgml-1 cadmium. This study highlights the importance of testing biosensor constructs, developed using synthetic biology principles, in different bacterial genera.

Development and Application of a Synthetically-Derived Lead Biosensor Construct for Use in Gram-Negative Bacteria.

The use of lead in manufacturing has decreased significantly over the last few decades. However, previous widespread use of lead-containing products and their incorrect disposal has resulted in environmental contamination. Accumulation of harmful quantities of lead pose a threat to all living organisms, through inhalation, ingestion, or direct contact, resulting in lead poisoning. This study utilized synthetic biology principles to develop plasmid-based whole-cell bacterial biosensors for detection of lead. The genetic element of the lead biosensor construct consists of pbrR, which encodes the regulatory protein, together with its divergent promoter region and a promoterless gfp. GFP expression is controlled by PbrR in response to the presence of lead. The lead biosensor genetic element was cloned onto a low-copy number broad host range plasmid, which can stably exist in a range of laboratory and environmental isolates, including Pseudomonas, Shewanella, and Enterobacter. The biosensors constructed were found to be sensitive, rapid, and specific and could, as such, serve as monitoring tools for lead-contaminated water.

Draft Genome Sequence of Enterobacter ludwigii NCR3, a Heavy Metal-Resistant Rhizobacterium.

We report here the draft genome of Enterobacter ludwigii NCR3, a Gram-negative bacterium isolated from the Carpobrotus rossii (Haw.) Schwantes rhizosphere. The analysis of the ~4.8-Mb draft genome shows that this strain harbors several genes associated with heavy metal resistance and plant growth-promoting activity, suggesting its potential application in microbe-assisted phytoremediation.

Innovative biological approaches for monitoring and improving water quality.

Water quality is largely influenced by the abundance and diversity of indigenous microbes present within an aquatic environment. Physical, chemical and biological contaminants from anthropogenic activities can accumulate in aquatic systems causing detrimental ecological consequences. Approaches exploiting microbial processes are now being utilized for the detection, and removal or reduction of contaminants. Contaminants can be identified and quantified in situ using microbial whole-cell biosensors, negating the need for water samples to be tested off-site. Similarly, the innate biodegradative processes can be enhanced through manipulation of the composition and/or function of the indigenous microbial communities present within the contaminated environments. Biological contaminants, such as detrimental/pathogenic bacteria, can be specifically targeted and reduced in number using bacteriophages. This mini-review discusses the potential application of whole-cell microbial biosensors for the detection of contaminants, the exploitation of microbial biodegradative processes for environmental restoration and the manipulation of microbial communities using phages.

Investigating microbial activities of electrode-associated microorganisms in real-time.

Electrode-associated microbial biofilms are essential to the function of bioelectrochemical systems (BESs). These systems exist in a number of different configurations but all rely on electroactive microorganisms utilizing an electrode as either an electron acceptor or an electron donor to catalyze biological processes. Investigations of the structure and function of electrode-associated biofilms are critical to further the understanding of how microbial communities are able to reduce and oxidize electrodes. The community structure of electrode-reducing biofilms is diverse and often dominated by Geobacter spp. whereas electrode-oxidizing biofilms are often dominated by other microorganisms. The application of a wide range of tools, such as high-throughput sequencing and metagenomic data analyses, provide insight into the structure and possible function of microbial communities on electrode surfaces. However, the development and application of techniques that monitor gene expression profiles in real-time are required for a more definite spatial and temporal understanding of the diversity and biological activities of these dynamic communities. This mini review summarizes the key gene expression techniques used in BESs research, which have led to a better understanding of population dynamics, cell-cell communication and molecule-surface interactions in mixed and pure BES communities.