Rapid identification of inflammatory arthritis and associated adverse events following immune checkpoint therapy: a machine learning approach.

Introduction: Immune checkpoint inhibitor-induced inflammatory arthritis (ICI-IA) poses a major clinical challenge to ICI therapy for cancer, with 13% of cases halting ICI therapy and ICI-IA being difficult to identify for timely referral to a rheumatologist. The objective of this study was to rapidly identify ICI-IA patients in clinical data and assess associated immune-related adverse events (irAEs) and risk factors. Methods: We conducted a retrospective study of the electronic health records (EHRs) of 89 patients who developed ICI-IA out of 2451 cancer patients who received ICI therapy at Northwestern University between March 2011 to January 2021. Logistic regression and random forest machine learning models were trained on all EHR diagnoses, labs, medications, and procedures to identify ICI-IA patients and EHR codes indicating ICI-IA. Multivariate logistic regression was then used to test associations between ICI-IA and cancer type, ICI regimen, and comorbid irAEs. Results: Logistic regression and random forest models identified ICI-IA patients with accuracies of 0.79 and 0.80, respectively. Key EHR features from the random forest model included ICI-IA relevant features (joint pain, steroid prescription, rheumatoid factor tests) and features suggesting comorbid irAEs (thyroid function tests, pruritus, triamcinolone prescription). Compared to 871 adjudicated ICI patients who did not develop arthritis, ICI-IA patients had higher odds of developing cutaneous (odds ratio [OR]=2.66; 95% Confidence Interval [CI] 1.63-4.35), endocrine (OR=2.09; 95% CI 1.15-3.80), or gastrointestinal (OR=2.88; 95% CI 1.76-4.72) irAEs adjusting for demographics, cancer type, and ICI regimen. Melanoma (OR=1.99; 95% CI 1.08-3.65) and renal cell carcinoma (OR=2.03; 95% CI 1.06-3.84) patients were more likely to develop ICI-IA compared to lung cancer patients. Patients on nivolumab+ipilimumab were more likely to develop ICI-IA compared to patients on pembrolizumab (OR=1.86; 95% CI 1.01-3.43). Discussion: Our machine learning models rapidly identified patients with ICI-IA in EHR data and elucidated clinical features indicative of comorbid irAEs. Patients with ICI-IA were significantly more likely to also develop cutaneous, endocrine, and gastrointestinal irAEs during their clinical course compared to ICI therapy patients without ICI-IA.

Nutritional needs, resources, and barriers among unhoused adults cared for by a street medicine organization in Chicago, Illinois: a cross-sectional study.

BACKGROUND: Those experiencing houselessness rely on obtaining food from community organizers and donations. Simultaneously, the houseless face disproportionally high rates of medical conditions that may be affected by diet including diabetes, hypertension, and hyperlipidemia. There is limited literature on the resources and barriers of the houseless community regarding optimal nutrition from an actionable perspective. Further, less data is available on how street medicine organizations may best impact the nutrition of the unhoused they serve. Elucidating this information will inform how organizational efforts may best support the nutrition of the houseless community. METHODS: In partnership with the medical student-run organization, Chicago Street Medicine, at Northwestern University Feinberg School of Medicine, twenty adults experiencing houselessness in Chicago, Illinois participated in the cross-sectional study. A 10-item survey was verbally administered to characterize the participants' daily food intake, food sources, barriers, resources, and nutritional preferences and needs. All data was directly transcribed into REDCap. Descriptive statistics were generated. RESULTS: Individuals consumed a median of 2 snacks and meals per day (IQR: 1-3). No participant consumed adequate servings of every food group, with only one participant meeting the dietary intake requirements for one food group. Participants most often received their food from donations (n = 15), purchasing themselves (n = 11), food pantries (n = 4), and shelters (n = 3). Eleven of nineteen participants endorsed dental concerns as a major barrier to consuming certain foods. Twelve participants had access to a can opener and twelve could heat their meals on a stove or microwave. Seven had access to kitchen facilities where they may prepare a meal. Approximately half of participants had been counseled by a physician to maintain a particular diet, with most related to reducing sugar intake. CONCLUSION: Most houseless participants were unable to acquire a balanced diet and often relied on organizational efforts to eat. Organizations should consider the chronic health conditions, dentition needs, and physical resources and barriers to optimal nutrition when obtaining food to distribute to the unhoused.

Stimulating Effect of Trichococcus flocculiformis on a Coculture of Syntrophomonas wolfei and Methanospirillum hungatei.

Syntrophic anaerobic consortia comprised of fatty acid-degrading bacteria and hydrogen/formate-scavenging methanogenic archaea are of central importance for balanced and resilient natural and manufactured ecosystems: anoxic sediments, soils, and wastewater treatment bioreactors. Previously published studies investigated interaction between the syntrophic bi-cultures, but little information is available on the influence of fermentative bacteria on syntrophic fatty acid oxidation, even though fermentative organisms are always present together with syntrophic partners in the above-mentioned ecosystems. Here, we present experimental observations of stimulated butyrate oxidation and methane generation by a coculture of Syntrophomonas wolfei with any of the following methanogens: Methanospirillum hungatei, Methanobrevibacter arboriphilus, or Methanobacterium formicicum due to the addition of a fermentative Trichococcus flocculiformis strain ES5. The addition of T. flocculiformis ES5 to the syntrophic cocultures led to an increase in the rates of butyrate consumption (120%) and volumetric methane production (150%). Scanning electron microscopy of the most positively affected coculture (S. wolfei, M. hungatei, and T. flocculiformis ES5) revealed a tendency of T. flocculiformis ES5 to aggregate with the syntrophic partners. Analysis of coculture's proteome with or without addition of the fermentative bacterium points to a potential link with signal transducing systems of M. hungatei, as well as activation of additional butyryl coenzyme A dehydrogenase and an electron transfer flavoprotein in S. wolfei. IMPORTANCE Results from the present study open doors to fascinating research on complex microbial cultures in anaerobic environments (of biotechnological and ecological relevance). Such studies of defined mixed populations are critical to understanding the highly intertwined natural and engineered microbial systems and to developing more reliable and trustable metabolic models. By investigating the existing cultured microbial consortia, like the ones described here, we can acquire knowledge on microbial interactions that go beyond "who feeds whom" relations but yet benefit the parties involved. Transfer of signaling compounds and stimulation of gene expression are examples of indirect influence that members of mixed communities can exert on each other. Understanding such microbial relationships will enable development of new sustainable biotechnologies with mixed microbial cocultures and contribute to the general understanding of the complex natural microbial interactions.

A Model for Bioaugmented Anaerobic Granulation.

Anaerobic granular sludge comprises of highly organized microorganisms with a sophisticated metabolic network. Such aggregates can withstand storage, temperature fluctuations and changes in the substrate supplied for anaerobic digestion. However, substrate change leads to long adaptation of granular consortia, creating lags in the reactor operations. To speed up adaptation and increase digestion efficiency, bioaugmentation with a robust consortium can be performed. The computational study described here aims to elucidate the mechanisms of bioaugmenting anaerobic granules, utilizing the current body of knowledge on metabolic and biochemical interactions between bacteria in such aggregates. Using a cDynoMiCs simulation environment, an agent-based model was developed to describe bioaugmentation for adaptation of cellobiose-degrading granular consortium to a lipid-rich feed. Lipolytic bacteria were successfully incorporated in silico to the stable granular consortia after 40 days of simulation. The ratio of cellobiose and the lipid-derivative, oleate, in the feed played key role to ensure augmentation. At 0.5 g/L of both cellobiose and oleate in the feed, a homogeneous stable augmented consortium was formed and converted the given amount of substrate to 10.9 mg/L of methane as a final product of anaerobic digestion. The demonstrated model can be used as a planning tool for anaerobic digestion facilities considering transition of the inoculum to a new type of feed.

Activity of preserved anaerobic sludge.

There is a need for a broad study addressing different preservation conditions of anaerobic sludge and its activity after a prolonged storage. This study compared four different preservation methods of mesophilic anaerobic sludge for a period of up to 12 months: storage at 23 ± 2 °C, +4 °C, ‒20 °C, and freeze-dried. Anaerobic sludge was sampled from upper and bottom ports of an up flow anaerobic sludge blanket (UASB) reactor fed with microalgae and sodium acetate at organic loading rate of 5.4 gCOD/L·d. Specific methanogenic activity (SMA) tests were performed on the sludge samples after 2.5, 6, and 12 months of storage. Results demonstrated a statistically significant decrease in the SMA of the bottom port preserved sludge, but not of the upper port sludge, regardless of the method used for preservation. A varying susceptibility to the storage of the two types of the anaerobic sludge can be explained by the content of the methanogenic microorganisms, with bottom port sludge having a higher amount of the methane producing species. Interestingly, lyophilized samples were able to produce similar amounts of biogas when compared to the other three storage conditions, with the only difference of having a longer re-activation period.

Qualitative Analysis of Microbial Dynamics during Anaerobic Digestion of Microalgal Biomass in a UASB Reactor.

Anaerobic digestion (AD) is a microbiologically coordinated process with dynamic relationships between bacterial players. Current understanding of dynamic changes in the bacterial composition during the AD process is incomplete. The objective of this research was to assess changes in bacterial community composition that coordinates with anaerobic codigestion of microalgal biomass cultivated on municipal wastewater. An upflow anaerobic sludge blanket reactor was used to achieve high rates of microalgae decomposition and biogas production. Samples of the sludge were collected throughout AD and extracted DNA was subjected to next-generation sequencing using methanogen mcrA gene specific and universal bacterial primers. Analysis of the data revealed that samples taken at different stages of AD had varying bacterial composition. A group consisting of Bacteroidales, Pseudomonadales, and Enterobacteriales was identified to be putatively responsible for the hydrolysis of microalgal biomass. The methanogenesis phase was dominated by Methanosarcina mazei. Results of observed changes in the composition of microbial communities during AD can be used as a road map to stimulate key bacterial species identified at each phase of AD to increase yield of biogas and rate of substrate decomposition. This research demonstrates a successful exploitation of methane production from microalgae without any biomass pretreatment.

Food waste conversion to microbial polyhydroxyalkanoates.

Polyhydroxyalkanoates (PHAs) are biopolymers with desirable material properties similar to petrochemically derived plastics. PHAs are naturally produced by a wide range of microorganisms as a carbon storage mechanism and can accumulate to significantly high levels. PHAs are an environmentally friendly alternative to their petroleum counterparts because they can be easily degraded, potentially reducing the burden on municipal waste systems. Nevertheless, widespread use of PHAs is not currently realistic due to a variety of factors. One of the major constraints of large-scale PHA production is the cost of carbon substrate for PHA-producing microbes. The cost of production could potentially be reduced with the use of waste carbon from food-related processes. Food wastage is a global issue and therefore harbours immense potential to create valuable bioproducts. This article's main focus is to examine the state of the art of converting food-derived waste into carbon substrates for microbial metabolism and subsequent conversion into PHAs.

Modeling de novo granulation of anaerobic sludge.

BACKGROUND: A unique combination of mechanical, physiochemical and biological forces influences granulation during processes of anaerobic digestion. Understanding this process requires a systems biology approach due to the need to consider not just single-cell metabolic processes, but also the multicellular organization and development of the granule. RESULTS: In this computational experiment, we address the role that physiochemical and biological processes play in granulation and provide a literature-validated working model of anaerobic granule de novo formation. The agent-based model developed in a cDynoMiCs simulation environment successfully demonstrated a de novo granulation in a glucose fed system, with the average specific methanogenic activity of 1.11 ml C H 4/g biomass and formation of a 0.5 mm mature granule in 33 days. The simulated granules exhibit experimental observations of radial stratification: a central dead core surrounded by methanogens then encased in acidogens. Practical application of the granulation model was assessed on the anaerobic digestion of low-strength wastewater by measuring the changes in methane yield as experimental configuration parameters were systematically searched. CONCLUSIONS: In the model, the emergence of multicellular organization of anaerobic granules from randomly mixed population of methanogens and acidogens was observed and validated. The model of anaerobic de novo granulation can be used to predict the morphology of the anaerobic granules in a alternative substrates of interest and to estimate methane potential of the resulting microbial consortia. The study demonstrates a successful integration of a systems biology approach to model multicellular systems with the engineering of an efficient anaerobic digestion system.

Microbubble assisted polyhydroxybutyrate production in Escherichia coli.

BACKGROUND: One of the potential limitations of large scale aerobic Escherichia coli fermentation is the need for increased dissolved oxygen for culture growth and bioproduct generation. As culture density increases the poor solubility of oxygen in water becomes one of the limiting factors for cell growth and product formation. A potential solution is to use a microbubble dispersion (MBD) generating device to reduce the diameter and increase the surface area of sparged bubbles in the fermentor. In this study, a recombinant E. coli strain was used to produce polyhydroxybutyrate (PHB) under conventional and MBD aerobic fermentation conditions. RESULTS: In conventional fermentation operating at 350 rpm and 0.8 vvm air flow rate, an OD600 of 6.21 and PHB yield of 23 % (dry cell basis) was achieved. MBD fermentation with similar bioreactor operating parameters produced an OD600 of 8.17 and PHB yield of 43 % PHB, which was nearly double that of the conventional fermentation. CONCLUSIONS: This study demonstrated that using a MBD generator can increase oxygen mass transfer into the aqueous phase, increasing E. coli growth and bioproduct generation.

Microbial bioproducts from cheese whey through fermentation with wastewater sludge Clostridium isolates.

We demonstrated the production of hydrogen, ethanol, and a variety of acids by several Clostridium species using cheese whey as substrate. These species were isolated from the anaerobic sediments of a municipal wastewater stabilization pond. Eight isolates were obtained and all were classified taxonomically as Clostridium spp. based on 16S rRNA sequencing. Sludge isolates showed maximum bioproduct production yields and productivities after approximately 24 h of batch cultivation with 6% (m/v) cheese whey. Fermentation byproducts measured included hydrogen, ethanol, acetic acid, butyric acid, and lactic acid. The maximum yields of bioproducts were 0.59 mol H(2)/mol lactose, 0.071 g ethanol/g, 0.204 g acetic acid/g, 0.218 g butyric acid/g, and 0.144 g lactic acid/g. The production of these high value biofuels and biofuel intermediates from cheese whey could have significant implications for conversion of waste to high value bioproducts to enhance domestic energy economies.

Effects of wastewater microalgae harvesting methods on polyhydroxybutyrate production.

Microalgae have gained considerable attention recently as a sustainable means to produce biofuels and bioproducts. It has previously been demonstrated that single strain microalgae can be harvested and processed through a wet lipid extraction procedure (WLEP). After WLEP processing, acetone, butanol, ethanol, and biodiesel can be produced, and growth of recombinant Escherichia coli can be achieved from the microalgae. This study demonstrates the application of different wastewater microalgae harvesting techniques and processing through WLEP on the production of polyhydroxybutyrate (PHB) by E. coli. The harvesting techniques include: cationic potato starch (CPS), cationic corn starch (CCS), aluminum sulfate, and centrifugation. The microalgae-based media were used to grow E. coli to ∼10(13)CFU/mL and produce approximately 7.8% of dry cell weight as PHB. This study demonstrates the feasibility of harvesting wastewater algae to produce PHB and the potential for bioproduct generation.

Direct measurement and characterization of active photosynthesis zones inside wastewater remediating and biofuel producing microalgal biofilms.

Microalgal biofilm based technologies are of keen interest due to their high biomass concentrations and ability to utilize light and CO2. While photoautotrophic biofilms have long been used for wastewater remediation, biofuel production represents a relatively new and under-represented focus area. However, the direct measurement and characterization of fundamental parameters required for industrial control are challenging due to biofilm heterogeneity. This study evaluated oxygenic photosynthesis and respiration on two distinct microalgal biofilms cultured using a novel rotating algal biofilm reactor operated at field- and laboratory-scales. Clear differences in oxygenic photosynthesis and respiration were observed based on different culturing conditions, microalgal composition, light intensity and nitrogen availability. The cultures were also evaluated as potential biofuel synthesis strategies. Nitrogen depletion was not found to have the same effect on lipid accumulation compared to traditional planktonic microalgal studies. Physiological characterizations of these microalgal biofilms identify fundamental parameters needed to understand and control process optimization.

Secretion of polyhydroxybutyrate in Escherichia coli using a synthetic biological engineering approach.

BACKGROUND: Polyhydroxyalkanoates (PHAs) are a group of biodegradable plastics that are produced by a wide variety of microorganisms, mainly as a storage intermediate for energy and carbon. Polyhydroxybutyrate (PHB) is a short-chain-length PHA with interesting chemical and physical properties. Large scale production of PHB is not wide-spread mainly due to the downstream processing of bacterial cultures to extract the PHB. Secretion of PHB from Escherichia coli could reduce downstream processing costs. PHB are non-proteinaceous polymers, hence cannot be directly targeted for secretion. Phasin, PhaP1, is a low molecular weight protein that binds to PHB, reducing PHB granule size. In this study PHB is indirectly secreted with PhaP1 from E. coli via type I secretion using HlyA signal peptides. RESULTS: This study demonstrated the successful secretion of phasin and phasin bound PHB outside of the cell and into the culture medium. The secretion of PHB was initiated between 24 and 48 h after induction. After 48 h of culturing, 36% of the total PHB produced in the secreting strain was collected in the secreted fraction and 64% remained in the internal fraction. To further support the findings of this study, the PHB secretion phenomenon was observed using SEM. CONCLUSIONS: From this study, the ability to use type I secretion to: 1) secrete phasin and 2) successfully secrete PHB has been shown.

Effect of coagulant/flocculants on bioproducts from microalgae.

The potential of microalgae as a source of sustainable energy, nutritional supplements and specialized chemicals necessitates a thorough evaluation of the methods of harvesting microalgae with regards to the bioproduct(s) desired. This research assessed the effect of coagulation, flocculation, and centrifugation on the wet lipid extraction procedure, which fractionated microalgae into hydrolyzed biomass for fermentation into acetone, butanol, and ethanol, an aqueous phase as growth media for genetically engineered Escherichia coli, and a lipid fraction for the production of biodiesel. Biomass harvested by cationic starches, alum, and centrifugation produced 30, 19, and 22.5mg/g of dry wt. algae of total combined acetone, butanol, and ethanol, respectively. Higher biodiesel production was also observed for the cationic starches (9.6 mg/g of dry wt. algae) than alum (0.6 mg/g of dry wt. algae) harvested biomass. The results suggested significant effect of the harvesting methods on the yields of bioproducts.

Effect of complexing ligands on the surface adsorption, internalization, and bioresponse of copper and cadmium in a soil bacterium, Pseudomonas putida.

Environmental quality criteria for metals toxic to soil and water organisms, using the free ion activity model or the biotic ligand model, are based on the concept that the major form of the metal available to the organism is the free metal ion, yet various metal complexes are bioavailable to a variety of soil and water organisms. We test here whether neutral copper or cadmium sulfates, negatively-charged copper or cadmium citrates and positively-charged copper acetate and cadmium chloride are bioavailable to a soil bacterium, Pseudomonas putida. Adsorption onto the cell surface and uptake into the periplasm and cytoplasm of this Gram-negative root colonizing bacterium was studied by adding a single concentration of Cu or Cd and varying the concentration of the ligands to complex 10-100% of the metal. Metal association from the complexes on and within the cell was defined using selective extraction procedures and compared with free ion controls using the Langmuir isotherm. Cellular responses also were assessed using a P. putida biosensor. Both uptake and bioresponse methodologies showed that P. putida was sensitive to the metal complexes. In particular, the bioresponse to Cu and Cd supplied as a citrate complex occurred with activities of free metal ions two orders of magnitude lower than for the control. We concluded that the tested metal complexes for Cu and Cd are taken up into the cell, where they trigger a bioresponse. We also discuss the implications of these findings on interactions between soil and water organisms and nanoparticles that release metal ions.

Characterization and analysis of mycobacteria and Gram-negative bacteria and co-culture mixtures by Raman microspectroscopy, FTIR, and atomic force microscopy.

The molecular composition of mycobacteria and Gram-negative bacteria cell walls is structurally different. In this work, Raman microspectroscopy was applied to discriminate mycobacteria and Gram-negative bacteria by assessing specific characteristic spectral features. Analysis of Raman spectra indicated that mycobacteria and Gram-negative bacteria exhibit different spectral patterns under our experimental conditions due to their different biochemical components. Fourier transform infrared (FTIR) spectroscopy, as a supplementary vibrational spectroscopy, was also applied to analyze the biochemical composition of the representative bacterial strains. As for co-cultured bacterial mixtures, the distribution of individual cell types was obtained by quantitative analysis of Raman and FTIR spectral images and the spectral contribution from each cell type was distinguished by direct classical least squares analysis. Coupled atomic force microscopy (AFM) and Raman microspectroscopy realized simultaneous measurements of topography and spectral images for the same sampled surface. This work demonstrated the feasibility of utilizing a combined Raman microspectroscopy, FTIR, and AFM techniques to effectively characterize spectroscopic fingerprints from bacterial Gram types and mixtures.

Monitoring microbial diversity of bioreactors using metagenomic approaches.

With the rapid development of molecular techniques, particularly 'omics' technologies, the field of microbial ecology is growing rapidly. The applications of next generation sequencing have allowed researchers to produce massive amounts of genetic data on individual microbes, providing information about microbial communities and their interactions through in situ and in vitro measurements. The ability to identify novel microbes, functions, and enzymes, along with developing an understanding of microbial interactions and functions, is necessary for efficient production of useful and high value products in bioreactors. The ability to optimize bioreactors fully and understand microbial interactions and functions within these systems will establish highly efficient industrial processes for the production of bioproducts. This chapter will provide an overview of bioreactors and metagenomic technologies to help the reader understand microbial communities, interactions, and functions in bioreactors.

Polyhydroxyalkanoate quantification in organic wastes and pure cultures using a single-step extraction and 1H NMR analysis.

In this study, a proton nuclear magnetic resonance (1H NMR) method was developed to quantitatively analyze polyhydroxyalkanoate (PHA) content in Cupriavidus necator H16, Azotobacter vinelandii AvOP, and mixed microbial cultures from the effluent of an agricultural waste treatment anaerobic digester. In contrast to previous methods, a single-step PHA extractive method using deuterated chloroform was established, thereby facilitating direct 1H NMR analysis. The accuracy of the method was verified through comparison with well-established gas chromatography (GC) methanolysis techniques. Nile blue fluorescence staining was also carried out to serve as an independent and qualitative indicator of intracellular PHA content. The results indicate that the 1H NMR method is appropriate for rapid and non-destructive quantification of overall PHA content and determination of PHA copolymer composition in a variety of cultures. Notably, this technique was effective in measuring PHA content in full-strength waste samples where high concentrations of background impurities and organic compounds are present. The straightforward procedures minimize error-introducing steps, require less time and materials, and result in an accurate method suitable for routine analyses.

Acetone, butanol, and ethanol production from wastewater algae.

Acetone, butanol, and ethanol (ABE) fermentation by Clostridium saccharoperbutylacetonicum N1-4 using wastewater algae biomass as a carbon source was demonstrated. Algae from the Logan City Wastewater Lagoon system grow naturally at high rates providing an abundant source of renewable algal biomass. Batch fermentations were performed with 10% algae as feedstock. Fermentation of acid/base pretreated algae produced 2.74 g/L of total ABE, as compared with 7.27 g/L from pretreated algae supplemented with 1% glucose. Additionally, 9.74 g/L of total ABE was produced when xylanase and cellulase enzymes were supplemented to the pretreated algae media. The 1% glucose supplement increased total ABE production approximately 160%, while supplementing with enzymes resulted in a 250% increase in total ABE production when compared to production from pretreated algae with no supplementation of extraneous sugar and enzymes. Additionally, supplementation of enzymes produced the highest total ABE production yield of 0.311 g/g and volumetric productivity of 0.102 g/Lh. The use of non-pretreated algae produced 0.73 g/L of total ABE. The ability to engineer novel methods to produce these high value products from an abundant and renewable feedstock such as algae could have significant implications in stimulating domestic energy economies.

Effect of lactose monolaurate on pathogenic and nonpathogenic bacteria.

The antimicrobial activities of sucrose monolaurate and a novel ester, lactose monolaurate (LML), were tested. Gram-positive bacteria were more susceptible than Gram-negative bacteria to both esters. The minimal bactericidal concentrations of LML were 5 to 9.5 mM for Listeria monocytogenes isolates and 0.2 to 2 mM for Mycobacterium isolates.