Microbiome and Human Health: Current Understanding, Engineering, and Enabling Technologies.

The human microbiome is composed of a collection of dynamic microbial communities that inhabit various anatomical locations in the body. Accordingly, the coevolution of the microbiome with the host has resulted in these communities playing a profound role in promoting human health. Consequently, perturbations in the human microbiome can cause or exacerbate several diseases. In this Review, we present our current understanding of the relationship between human health and disease development, focusing on the microbiomes found across the digestive, respiratory, urinary, and reproductive systems as well as the skin. We further discuss various strategies by which the composition and function of the human microbiome can be modulated to exert a therapeutic effect on the host. Finally, we examine technologies such as multiomics approaches and cellular reprogramming of microbes that can enable significant advancements in microbiome research and engineering.

Systematic review and meta-analysis of tumour microsatellite-instability status as a predictor of response to fluorouracil-based adjuvant chemotherapy in colorectal cancer.

PURPOSE: Colorectal cancer (CRC) can be classified according to the chromosomal-instability pathway (a microsatellite-stable (MSS) pathway) and the microsatellite-instability (MSI) pathway. Adjuvant therapy after surgery in advanced CRC is usually based on fluoropyrimidine 5-fluorouracil (5-FU) alone or combined with other agents. Controversy however remains on the use of 5-FU-based regimens in treating MSI-related tumours. AIMS: To systematically investigate the relationship between tumour microsatellite profile and 5-year overall survival in patients with CRC treated with 5-FU. METHODS: A systematic literature review of PubMed and Embase databases was conducted. Pre-specified criteria determined study inclusion/exclusion. The PRISMA and QUADAS-2 criteria were used to assess study suitability and quality respectively. Patients were categorised as having either MSI or MSS CRC. Overall 5-year survival was estimated from Kaplan-Meier curves. Publication bias was assessed using funnel-plots and Egger's test. RESULTS: 1807 studies were identified, with meta-analysis performed using nine studies. 5-FU treated individuals with CRC who died at 5 years were found to be 0.31 times less likely to have MSI than those who were alive, although this was not statistically significant. There was an insufficient number of studies to enable subgroup analysis by stage. CONCLUSIONS: In this meta-analysis, MSI status does not alter 5-year survival of patients with CRC patients treated with adjuvant 5-FU, however there is significant heterogeneity in the design of individual studies in the data synthesis. More studies are necessary to clarify whether CRC patients with MSI CRC, in particular early stage, should be offered 5-FU based adjuvant chemotherapy.

Carbon Nanosheets by Morphology-Retained Carbonization of Two-Dimensional Assembled Anisotropic Carbon Nanorings.

Two-dimensional (2D) carbon nanomaterials possessing promising physical and chemical properties find applications in high-performance energy storage devices and catalysts. However, large-scale fabrication of 2D carbon nanostructures is based on a few specific carbon templates or precursors and poses a formidable challenge. Now a new bottom-up method for carbon nanosheet fabrication using a newly designed anisotropic carbon nanoring molecule, CPPhen, is presented. CPPhen was self-assembled at a dynamic air-water interface with a vortex motion to afford molecular nanosheets, which were then carbonized under inert gas flow. Their nanosheet morphologies were retained after carbonization, which has never been seen for low-molecular weight compounds. Furthermore, adding pyridine as a nitrogen dopant in the self-assembly step successfully afforded nitrogen-doped carbon nanosheets containing mainly pyridinic nitrogen species.

Structural and Functional Analysis of the Escherichia coli Acid-Sensing Histidine Kinase EvgS.

The EvgS/EvgA two-component system of Escherichia coli is activated in response to low pH and alkali metals and regulates many genes, including those for the glutamate-dependent acid resistance system and a number of efflux pumps. EvgS, the sensor kinase, is one of five unconventional histidine kinases (HKs) in E. coli and has a large periplasmic domain and a cytoplasmic PAS domain in addition to phospho-acceptor, HK and dimerization, internal receiver, and phosphotransfer domains. Mutations that constitutively activate the protein at pH 7 map to the PAS domain. Here, we built a homology model of the periplasmic region of EvgS, based on the structure of the equivalent region of the BvgS homologue, to guide mutagenesis of potential key residues in this region. We show that histidine 226 is required for induction and that it is structurally colocated with a proline residue (P522) at the top of the predicted transmembrane helix that is expected to play a key role in passing information to the cytoplasmic domains. We also show that the constitutive mutations in the PAS domain can be further activated by low external pH. Expression of the cytoplasmic part of the protein alone also gives constitutive activation, which is lost if the constitutive PAS mutations are present. These findings are consistent with a model in which EvgS senses both external and internal pH and is activated by a shift from a tight inactive to a weak active dimer, and we present an analysis of the purified cytoplasmic portion of EvgS that supports this.IMPORTANCE One of the ways bacteria sense their environment is through two-component systems, which have one membrane-bound protein to do the sensing and another inside the cell to turn genes on or off in response to what the membrane-bound protein has detected. The membrane-bound protein must thus be able to detect the stress and signal this detection event to the protein inside the cell. To understand this process, we studied a protein that helps E. coli to survive exposure to low pH, which it must do before taking up residence in the gastrointestinal tract. We describe a predicted structure for the main sensing part of the protein and identify some key residues within it that are involved in the sensing and signaling processes. We propose a mechanism for how the protein may become activated and present some evidence to support our proposal.

A New Class of Nitroanilinic Dimer, the PNA O-Dimer: Electronic Structure and Emission Characteristics of O-Dimeric Aggregates.

p-Nitroaniline (PNA) has been reported as a "J" aggregate species. In retrospect, this communication confirms a radically different "oblique" orientation of the PNA units in all three solid, liquid, and gas phases of the dimer, the O-dimer. The nonvanishing transition dipole moments (TDM) associated with the allowed electronic excitations of the O-dimer, computed using electron-hole pair density distribution (EDD and HDD) analyses ascertained the two monomers to be inclined at slippage (θ) and polarization (α) angles of 18.5° and 55.4°, respectively. A detailed structure-property relationship of the PNA O-dimeric aggregate was carried out using UV-vis absorption and matrix scan emission spectroscopy, supported by electronic structure calculations at DFT-M062X/6-31G+(d,p) level using integral equation formalism polarizable continuum model (IEFPCM). The computed potential energy surface (PES) implied the global minimum of the PNA O-dimer stabilized by 4.8 kcal.mol(-1), owing to bifurcated intermolecular hydrogen bonding. In the excited PNA O-dimeric aggregate, an exchange of excitation energy between the monomeric units resulted in two distinct electronic states separated by an interaction energy of -1644 cm(-1). The TD-DFT computed excited state equilibrium structures of the PNA O-dimer corroborated the experimentally observed pronounced Stoke's shift to internal conversion following vibrational relaxation of the allowed electronic excited states. On the basis of the detailed structural analysis of PNA O-dimer, the observed energy shifts in optical absorption spectroscopy were evident within the framework of exciton coupling model.

Immunotherapy-Induced Overlap Syndrome: Myositis, Myasthenia Gravis, and Myocarditis-A Case Series.

Immune checkpoint inhibitors (ICI) are monoclonal antibodies that target immune checkpoint inhibitory receptors. They have revolutionised cancer treatment but can be associated with a wide range of adverse side effects. Rarely, they can be associated with the triad of myositis, myasthenia gravis, and myocarditis or overlap syndrome. Prompt recognition and early intervention are needed to treat these potentially life-threatening conditions. We report a case series of patients with ICI-related overlap syndrome, including the first with avelumab, and discuss the current management guidelines.

Future Implications of Artificial Intelligence in Medical Education.

Artificial intelligence has experienced explosive growth in the past year that will have implications in all aspects of our lives, including medicine. In order to train a physician workforce that understands these new advancements, medical educators must take steps now to ensure that physicians are adequately trained in medical school, residency, and fellowship programs to become proficient in the usage of artificial intelligence in medical practice. This manuscript discusses the various considerations that leadership within medical training programs should be mindful of when deciding how to best integrate artificial intelligence into their curricula.

Prodrug-conjugated tumor-seeking commensals for targeted cancer therapy.

Prodrugs have been explored as an alternative to conventional chemotherapy; however, their target specificity remains limited. The tumor microenvironment harbors a range of microorganisms that potentially serve as tumor-targeting vectors for delivering prodrugs. In this study, we harness bacteria-cancer interactions native to the tumor microbiome to achieve high target specificity for prodrug delivery. We identify an oral commensal strain of Lactobacillus plantarum with an intrinsic cancer-binding mechanism and engineer the strain to enable the surface loading of anticancer prodrugs, with nasopharyngeal carcinoma (NPC) as a model cancer. The engineered commensals show specific binding to NPC via OppA-mediated recognition of surface heparan sulfate, and the loaded prodrugs are activated by tumor-associated biosignals to release SN-38, a chemotherapy compound, near NPC. In vitro experiments demonstrate that the prodrug-loaded microbes significantly increase the potency of SN-38 against NPC cell lines, up to 10-fold. In a mouse xenograft model, intravenous injection of the engineered L. plantarum leads to bacterial colonization in NPC tumors and a 67% inhibition in tumor growth, enhancing the efficacy of SN-38 by 54%.

FELICX: A robust nucleic acid detection method using flap endonuclease and CRISPR-Cas12.

Nucleic acid detection is crucial for monitoring diseases for which rapid, sensitive, and easy-to-deploy diagnostic tools are needed. CRISPR-based technologies can potentially fulfill this need for nucleic acid detection. However, their widespread use has been restricted by the requirement of a protospacer adjacent motif in the target and extensive guide RNA optimization. In this study, we developed FELICX, a technique that can overcome these limitations and provide a useful alternative to existing technologies. FELICX comprises flap endonuclease, Taq ligase and CRISPR-Cas for diagnostics (X) and can be used for detecting nucleic acids and single-nucleotide polymorphisms. This method can be deployed as a point-of-care test, as only two temperatures are needed without thermocycling for its functionality, with the result generated on lateral flow strips. As a proof-of-concept, we showed that up to 0.6 copies/µL of DNA and RNA could be detected by FELICX in 60 min and 90 min, respectively, using simulated samples. Additionally, FELICX could be used to probe any base pair, unlike other CRISPR-based technologies. Finally, we demonstrated the versatility of FELICX by employing it for virus detection in infected human cells, the identification of antibiotic-resistant bacteria, and cancer diagnostics using simulated samples. Based on its unique advantages, we envision the use of FELICX as a next-generation CRISPR-based technology in nucleic acid diagnostics.

Engineered microbial systems for advanced drug delivery.

The human body is a natural habitat for a multitude of microorganisms, with bacteria being the major constituent of the microbiota. These bacteria colonize discrete anatomical locations that provide suitable conditions for their survival. Many bacterial species, both symbiotic and pathogenic, interact with the host via biochemical signaling. Based on these attributes, commensal and attenuated pathogenic bacteria have been engineered to deliver therapeutic molecules to target specific diseases. Recent advances in synthetic biology have enabled us to perform complex genetic modifications in live bacteria and bacteria-derived particles, which simulate micron or submicron lipid-based vectors, for the targeted delivery of therapeutic agents. In this review, we highlight various examples of engineered bacteria or bacteria-derived particles that encapsulate, secrete, or surface-display therapeutic molecules for the treatment or prevention of various diseases. The review highlights recent studies on (i) the production of therapeutics by microbial cell factories, (ii) disease-triggered release of therapeutics by sense and respond systems, (iii) bacteria targeting tumor hypoxia, and (iv) bacteria-derived particles as chassis for drug delivery. In addition, we discuss the potential of such drug delivery systems to be translated into clinical therapies.

3D Media Stabilizes Membrane and Prolongs Lifespan of Defolliculated Xenopus laevis Oocytes.

Xenopus laevis oocytes are commonly used in many fundamental biological studies. One of the major limitations of X. laevis oocytes is their short storage lifespan with most defolliculated oocytes physically deteriorating in 10 days or less. Herein, we identified a 3D Cultrex-based storage media that incorporates extracellular membrane-based hydrogels to maintain oocyte integrity. Under these treatments, the lifespan of the oocytes increased to more than 20 days compared to standard conditions. The treatment preserved the oocytes membrane integrity and did not interfere with mRNA- or cDNA-derived protein expression.

Future trends in synthetic biology in Asia.

Synthetic biology research and technology translation has garnered increasing interest from the governments and private investors in Asia, where the technology has great potential in driving a sustainable bio-based economy. This Perspective reviews the latest developments in the key enabling technologies of synthetic biology and its application in bio-manufacturing, medicine, food and agriculture in Asia. Asia-centric strengths in synthetic biology to grow the bio-based economy, such as advances in genome editing and the presence of biofoundries combined with the availability of natural resources and vast markets, are also highlighted. The potential barriers to the sustainable development of the field, including inadequate infrastructure and policies, with suggestions to overcome these by building public-private partnerships, more effective multi-lateral collaborations and well-developed governance framework, are presented. Finally, the roles of technology, education and regulation in mitigating potential biosecurity risks are examined. Through these discussions, stakeholders from different groups, including academia, industry and government, are expectantly better positioned to contribute towards the establishment of innovation and bio-economy hubs in Asia.

Engineering probiotics for therapeutic applications: recent examples and translational outlook.

Engineered probiotics are the next generation of live biotherapeutics that have been genetically modified to target specific diseases. With the advancements in synthetic biology, the engineering of probiotics has become increasingly sophisticated which has led to the development of therapies for treating cancer, infection, metabolic disorders and inflammation, as well as for diagnosing and preventing them. Herein, we review some of the recent examples of probiotics which have been engineered to target such diseases. Although there are numerous examples of engineered probiotics showing efficacy in animal models, there are no approved products on the market with very few in clinical trials. Therefore, we also discuss a set of features that may be incorporated into engineered probiotics to aid in clinical translation and ultimately, realizing the potential of these biotherapeutics.

Appendiceal mucocele secondary to torsion in an asymptomatic patient.

Torsion of the appendix associated with an appendiceal mucocele is extremely rare with just a few published cases. To our knowledge, we report the first case of appendiceal mucocele secondary to torsion in an asymptomatic patient. In this case, numerous adhesions were found attaching the tip of the appendix mucocele to the peritoneum contributing to torsion as well as a lack of evidence for appendiceal neoplasm. Complications of appendiceal mucocele include obstruction, intussusception and pseudomyxoma peritonei, which has a particularly poor prognosis. Clinicians should, therefore, consider prompt surgical resection for definitive histopathological diagnosis and management.