Improving Biomanufacturing Production with Tunable Transcriptional Regulation via Elastin-like Polypeptides

The metabolism of E. coli and other microbes can be engineered to create valuable chemicals such as biofuels, medicines, etc. However, process efficiency is limited by the toxicity of intermediates in the production pathway, which induces cellular stress and killing the production in cells. By fusing elastin-like polypeptides (ELPs) with sigma factors (SF), we propose a stress feedback system can be created to recognize cues of cellular health and autoregulate expression of bioproduction pathways for improved health and production. ELPs undergo a sharp, reversible, phase transition causing an aggregation above a certain temperature (Tt) based on conditions that align with intracellular health such as intracellular pH. This behavior, along with the ability to control Tt through sequence alterations, makes ELPs ideal sensors for controlling gene expression. Fused SF, which activated gene expression, are sequestered in ELP-SF aggregates above the transition temperature, reducing their free concentration. To evaluate the potential of ELP-SF to control gene expression, we expressed green fluorescent protein (GFP) from a promoter driven by the fused SF. In vivo, this system activated the expression of GFP at levels comparable to a SF control. However, at elevated temperatures, the system reduces gene expression by 20% relative to the control demonstrating the ability of the construct to control gene expression. The dynamic performance of the system was also modeled in MATLAB to reveal key parameters that affect system behavior. These results validate our main hypothesis and suggest a new strategy to optimize the sustainable production of valuable chemicals from microbes

Computational Model for Predicting the Location of Glass Solidification in Optic Fiber Drawing

ABSTRACT This paper presents a computational model for predicting the location at which the glass fiber solidifies during a highspeed drawing process. Although modeling of the optic fiber drawing process has been of interest for the past two decades, traditional fiber drawing process uses small diameter preforms and low draw speeds, where the glass usually solidifies and turns into fiber inside the furnace. Much larger preforms drawn at higher speeds have been used in the state-of-the-art fiber drawing systems to improve production efficiency and reduce cost. Insulated post-chambers are often added below the furnace to reduce the glass cooling rate so that the optical loss in the fiber is low. To provide a basis for design optimization of the post-chamber, we have solved the conjugate problem of the glass free surface flow and the air convection to determine the location where the glass solidifies. As radiation is the dominant mode of heat transfer in the glass, the radiative transfer equation (RTE) is solved directly by discrete ordinate method (DOM). The heat flux due to the mixed convection of the air is also numerically calculated along the glass free surface, which involves the boundary layer flow around a continuously moving fiber and the buoyancy driven flow through the open-ended channel. The calculated free shapes are compared against the experimentally measured data to verify the computational model

Cost-effective Paper-based Diagnostic Using Split Proteins to Detect Yeast Infections

The common yeast infection, vulvovaginal candidiasis, affects three out of four women throughout their lifetime and can be spread to their child in the form of oral candidiasis (thrush). This disease is caused by the fungal pathogen Candida albicans, which is also a major cause of systemic candidiasis, a rarer but deadly disease with up to a 49% lethality rate. Current widely-used diagnostic methods include cell cultures, pH tests, and antibody detection, to assist effective treatment. Despite availability of various diagnostic methods, there is no inexpensive, rapid, and accurate way to detect C. albicans infection. This project aims to develop a paper-based diagnostic test for C. albicans that is, cost-effective, quick, and precise. The test detects the specific biomarkers farnesol and tyrosol produced by C. albicans by binding them to the split proteins pqsR and tyrosinase, respectively. Upon binding, a split horseradish peroxidase catalyzes and produces an amplified colorimetric signal by oxidizing the substrate tetramethylbenzidine (TMB) turning the paper blue. This test will produce a colorimetric output for a simple-to-understand diagnosis without any infrastructure. We predict that this device can give a response in under 2 minutes while costing around an estimated 10 cents per device This test may provide a way for an easy and cheap way to diagnose candidiasis worldwide, reducing the abuse of antifungals and provide an accurate way to treat vulvovaginal candidiasis and systemic candidiasis

Cost-effective Paper-based Diagnostic Using Split Proteins to Detect Yeast Infections

The common yeast infection, vulvovaginal candidiasis, affects three out of four women throughout their lifetime and can be spread to their child in the form of oral candidiasis (thrush). This disease is caused by the fungal pathogen Candida albicans, which is also a major cause of systemic candidiasis, a rarer but deadly disease with up to a 49% lethality rate. Current widely-used diagnostic methods include cell cultures, pH tests, and antibody detection, to assist effective treatment. Despite availability of various diagnostic methods, there is no inexpensive, rapid, and accurate way to detect C. albicans infection. This project aims to develop a paper-based diagnostic test for C. albicans that is, cost-effective, quick, and precise. The test detects the specific biomarkers farnesol and tyrosol produced by C. albicans by binding them to the split proteins pqsR and tyrosinase, respectively. Upon binding, a split horseradish peroxidase catalyzes and produces an amplified colorimetric signal by oxidizing the substrate tetramethylbenzidine (TMB) turning the paper blue. This test will produce a colorimetric output for a simple-to-understand diagnosis without any infrastructure. We predict that this device can give a response in under 2 minutes while costing around an estimated 10 cents per device This test may provide a way for an easy and cheap way to diagnose candidiasis worldwide, reducing the abuse of antifungals and provide an accurate way to treat vulvovaginal candidiasis and systemic candidiasis

Associations Between Maternal Distress During Early Life Periods and Offspring Respiratory Infections and Allergic Outcomes

DOI does not function. It has been reported to the journal 28.12.2022BackgroundIncreasing evidence suggests that maternal distress is a risk factor for development of respiratory infections and allergic diseases in the offspring. We aim to evaluate the link between maternal distress during critical periods in early life, namely the preconception, pregnancy and postnatal periods, and development of respiratory infections and allergic diseases in the offspring from the Singapore PREconception Study of long Term maternal and child Outcomes (S-PRESTO) cohort. MethodsMaternal perceived distress was evaluated using validated questionnaires including Beck Depression Inventory-II (BDI-II) administered during three time periods: preconception (three months apart at four timepoints), pregnancy (during each trimester) and postnatal (3 and 6 months post-delivery). Child eczema, rhinitis and wheeze outcomes were evaluated using a modified ISAAC questionnaire at ages 3, 6, 12, and 18 months. Child allergic sensitization was determined by skin prick testing at 18 months. ResultsAmong 332 mother-child pairs studied, higher maternal distress during preconception and pregnancy increased the risks of wheeze development in the first 18 months; for example, preconception and pregnancy BDI-II scores >= 20 were associated with increased risks of wheeze by 18 months [adjusted risk ratios 3.2 (95%CI 1.1-9.4) and 2.5 (1.0-5.9), respectively]. Emotional and practical support from family during preconception decreased the risks of offspring wheeze. No associations were observed between maternal distress and offspring eczema, rhinitis and allergic sensitization. ConclusionMaternal distress during critical early life periods was associated with offspring wheeze in the first 18 months of life. Supporting maternal mental health even before pregnancy could reduce the risk of offspring wheeze.Peer reviewe

Consensus guidelines for the use and interpretation of angiogenesis assays

The formation of new blood vessels, or angiogenesis, is a complex process that plays important roles in growth and development, tissue and organ regeneration, as well as numerous pathological conditions. Angiogenesis undergoes multiple discrete steps that can be individually evaluated and quantified by a large number of bioassays. These independent assessments hold advantages but also have limitations. This article describes in vivo, ex vivo, and in vitro bioassays that are available for the evaluation of angiogenesis and highlights critical aspects that are relevant for their execution and proper interpretation. As such, this collaborative work is the first edition of consensus guidelines on angiogenesis bioassays to serve for current and future reference

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Microbial Synthesis of High-Molecular-Weight, Highly Repetitive Protein Polymers

High molecular weight (MW), highly repetitive protein polymers are attractive candidates to replace petroleum-derived materials as these protein-based materials (PBMs) are renewable, biodegradable, and have outstanding mechanical properties. However, their high MW and highly repetitive sequence features make them difficult to synthesize in fast-growing microbial cells in sufficient amounts for real applications. To overcome this challenge, various methods were developed to synthesize repetitive PBMs. Here, we review recent strategies in the construction of repetitive genes, expression of repetitive proteins from circular mRNAs, and synthesis of repetitive proteins by ligation and protein polymerization. We discuss the advantages and limitations of each method and highlight future directions that will lead to scalable production of highly repetitive PBMs for a wide range of applications