Highly-Selective Harvesting of (6,4) SWCNTs Using the Aqueous Two-Phase Extraction Method and Nonionic Surfactants.

Monochiral single-walled carbon nanotubes (SWCNTs) are indispensable for advancing the technology readiness level of nanocarbon-based concepts. In recent times, many separation techniques have been developed to obtain specific SWCNTs from raw unsorted materials to catalyze the development in this area. This work presents how the aqueous two-phase extraction (ATPE) method can be enhanced for the straightforward isolation of (6,4) SWCNTs in one step. Introducing nonionic surfactant into the typically employed mixture of anionic surfactants, which drive the partitioning, is essential to increasing the ATPE system's resolution. A thorough analysis of the parameter space by experiments and modeling reveals the underlying interactions between SWCNTs, surfactants, and phase-forming agents, which drive the partitioning. Based on new insight gained on this front, a separation mechanism is proposed. Notably, the developed method is highly robust, which is proven by isolating (6,4) SWCNTs from several raw SWCNT materials, including SWCNT waste generated over the years in the laboratory.

The Gut Microbiome Modulates Body Temperature Both in Sepsis and Health.

Rationale: Among patients with sepsis, variation in temperature trajectories predicts clinical outcomes. In healthy individuals, normal body temperature is variable and has decreased consistently since the 1860s. The biologic underpinnings of this temperature variation in disease and health are unknown. Objectives: To establish and interrogate the role of the gut microbiome in calibrating body temperature. Methods: We performed a series of translational analyses and experiments to determine whether and how variation in gut microbiota explains variation in body temperature in sepsis and in health. We studied patient temperature trajectories using electronic medical record data. We characterized gut microbiota in hospitalized patients using 16S ribosomal RNA gene sequencing. We modeled sepsis using intraperitoneal LPS in mice and modulated the microbiome using antibiotics, germ-free, and gnotobiotic animals. Measurements and Main Results: Consistent with prior work, we identified four temperature trajectories in patients hospitalized with sepsis that predicted clinical outcomes. In a separate cohort of 116 hospitalized patients, we found that the composition of patients' gut microbiota at admission predicted their temperature trajectories. Compared with conventional mice, germ-free mice had reduced temperature loss during experimental sepsis. Among conventional mice, heterogeneity of temperature response in sepsis was strongly explained by variation in gut microbiota. Healthy germ-free and antibiotic-treated mice both had lower basal body temperatures compared with control animals. The Lachnospiraceae family was consistently associated with temperature trajectories in hospitalized patients, experimental sepsis, and antibiotic-treated mice. Conclusions: The gut microbiome is a key modulator of body temperature variation in both health and critical illness and is thus a major, understudied target for modulating physiologic heterogeneity in sepsis.

In critically ill patients, anti-anaerobic antibiotics increase risk of adverse clinical outcomes.

BACKGROUND: Critically ill patients routinely receive antibiotics with activity against anaerobic gut bacteria. However, in other disease states and animal models, gut anaerobes are protective against pneumonia, organ failure and mortality. We therefore designed a translational series of analyses and experiments to determine the effects of anti-anaerobic antibiotics on the risk of adverse clinical outcomes among critically ill patients. METHODS: We conducted a retrospective single-centre cohort study of 3032 critically ill patients, comparing patients who did and did not receive early anti-anaerobic antibiotics. We compared intensive care unit outcomes (ventilator-associated pneumonia (VAP)-free survival, infection-free survival and overall survival) in all patients and changes in gut microbiota in a subcohort of 116 patients. In murine models, we studied the effects of anaerobe depletion in infectious (Klebsiella pneumoniae and Staphylococcus aureus pneumonia) and noninfectious (hyperoxia) injury models. RESULTS: Early administration of anti-anaerobic antibiotics was associated with decreased VAP-free survival (hazard ratio (HR) 1.24, 95% CI 1.06-1.45), infection-free survival (HR 1.22, 95% CI 1.09-1.38) and overall survival (HR 1.14, 95% CI 1.02-1.28). Patients who received anti-anaerobic antibiotics had decreased initial gut bacterial density (p=0.00038), increased microbiome expansion during hospitalisation (p=0.011) and domination by Enterobacteriaceae spp. (p=0.045). Enterobacteriaceae were also enriched among respiratory pathogens in anti-anaerobic-treated patients (p<2.2×10-16). In murine models, treatment with anti-anaerobic antibiotics increased susceptibility to Enterobacteriaceae pneumonia (p<0.05) and increased the lethality of hyperoxia (p=0.0002). CONCLUSIONS: In critically ill patients, early treatment with anti-anaerobic antibiotics is associated with increased mortality. Mechanisms may include enrichment of the gut with respiratory pathogens, but increased mortality is incompletely explained by infections alone. Given consistent clinical and experimental evidence of harm, the widespread use of anti-anaerobic antibiotics should be reconsidered.

AlphaFold2 models indicate that protein sequence determines both structure and dynamics.

AlphaFold 2 (AF2) has placed Molecular Biology in a new era where we can visualize, analyze and interpret the structures and functions of all proteins solely from their primary sequences. We performed AF2 structure predictions for various protein systems, including globular proteins, a multi-domain protein, an intrinsically disordered protein (IDP), a randomized protein, two larger proteins (> 1000 AA), a heterodimer and a homodimer protein complex. Our results show that along with the three dimensional (3D) structures, AF2 also decodes protein sequences into residue flexibilities via both the predicted local distance difference test (pLDDT) scores of the models, and the predicted aligned error (PAE) maps. We show that PAE maps from AF2 are correlated with the distance variation (DV) matrices from molecular dynamics (MD) simulations, which reveals that the PAE maps can predict the dynamical nature of protein residues. Here, we introduce the AF2-scores, which are simply derived from pLDDT scores and are in the range of [0, 1]. We found that for most protein models, including large proteins and protein complexes, the AF2-scores are highly correlated with the root mean square fluctuations (RMSF) calculated from MD simulations. However, for an IDP and a randomized protein, the AF2-scores do not correlate with the RMSF from MD, especially for the IDP. Our results indicate that the protein structures predicted by AF2 also convey information of the residue flexibility, i.e., protein dynamics.

Antibiotics cause metabolic changes in mice primarily through microbiome modulation rather than behavioral changes.

BACKGROUND: The microbiome is an important and increasingly-studied mediator of organismal metabolism, although how the microbiome affects metabolism remains incompletely understood. Many investigators use antibiotics to experimentally perturb the microbiome. However, antibiotics have poorly understood yet profound off-target effects on behavior and diet, including food and water aversion, that can confound experiments and limit their applicability. We thus sought to determine the relative influence of microbiome modulation and off-target antibiotic effects on the behavior and metabolic activity of mice. RESULTS: Mice treated with oral antibiotics via drinking water exhibited significant weight loss in fat, liver, and muscle tissue. These mice also exhibited a reduction in water and food consumption, with marked variability across antibiotic regimens. While administration of bitter-tasting but antimicrobially-inert compounds caused a similar reduction in water consumption, this did not cause tissue weight loss or reduced food consumption. Mice administered intraperitoneal antibiotics (bypassing the gastrointestinal tract) exhibited reduced tissue weights and oral intake, comparable to the effects of oral antibiotics. Antibiotic-treated germ-free mice did not have reduced tissue weights, providing further evidence that direct microbiome modulation (rather than behavioral effects) mediates these metabolic changes. CONCLUSIONS: While oral antibiotics cause profound effects on food and water consumption, antibiotic effects on organismal metabolism are primarily mediated by microbiome modulation. We demonstrate that tissue-specific weight loss following antibiotic administration is due primarily to microbiome effects rather than food and water aversion, and identify antibiotic regimens that effectively modulate gut microbiota while minimizing off-target behavioral effects.

Molecular dynamics simulations reveal single-stranded DNA (ssDNA) forms ordered structures upon adsorbing onto single-walled carbon nanotubes (SWCNT).

Replica exchange molecular dynamics were used to observe the adsorption of single-stranded DNA (ssDNA) onto the surface of single-walled carbon nanotubes (SWCNTs). The assembly of these systems has garnered interest as a method by which SWCNTs can be separated based on chirality. While the exact mechanism of separation is yet unknown, it is hypothesized that the structure of the ssDNA layer pays an important role. Characterization of such an adsorbed layer has been a matter of recent work with the focus being on atomic level detail or such as base-stacking and hydrogen bonding. In this manuscript, we detail a new observation of ssDNA organization and demonstrate how it can be used to infer additional information about the way in which such biopolymers wrap around the cylindrical SWCNT.

The bacterial density of clinical rectal swabs is highly variable, correlates with sequencing contamination, and predicts patient risk of extraintestinal infection.

BACKGROUND: In ecology, population density is a key feature of community analysis. Yet in studies of the gut microbiome, bacterial density is rarely reported. Studies of hospitalized patients commonly use rectal swabs for microbiome analysis, yet variation in their bacterial density-and the clinical and methodologic significance of this variation-remains undetermined. We used an ultra-sensitive quantification approach-droplet digital PCR (ddPCR)-to quantify bacterial density in rectal swabs from 118 hospitalized patients. We compared bacterial density with bacterial community composition (via 16S rRNA amplicon sequencing) and clinical data to determine if variation in bacterial density has methodological, clinical, and prognostic significance. RESULTS: Bacterial density in rectal swab specimens was highly variable, spanning five orders of magnitude (1.2 × 104-3.2 × 109 16S rRNA gene copies/sample). Low bacterial density was strongly correlated with the detection of sequencing contamination (Spearman ρ = - 0.95, p < 10-16). Low-density rectal swab communities were dominated by peri-rectal skin bacteria and sequencing contaminants (p < 0.01), suggesting that some variation in bacterial density is explained by sampling variation. Yet bacterial density was also associated with important clinical exposures, conditions, and outcomes. Bacterial density was lower among patients who had received piperacillin-tazobactam (p = 0.017) and increased among patients with multiple medical comorbidities (Charlson score, p = 0.0040) and advanced age (p = 0.043). Bacterial density at the time of hospital admission was independently associated with subsequent extraintestinal infection (p = 0.0028), even when controlled for severity of illness and comorbidities. CONCLUSIONS: The bacterial density of rectal swabs is highly variable, and this variability is of methodological, clinical, and prognostic significance. Microbiome studies using rectal swabs are vulnerable to sequencing contamination and should include appropriate negative sequencing controls. Among hospitalized patients, gut bacterial density is associated with clinical exposures (antibiotics, comorbidities) and independently predicts infection risk. Bacterial density is an important and under-studied feature of gut microbiome community analysis. Video abstract.

Interaction of DNA-Complexed Boron Nitride Nanotubes and Cosolvents Impacts Dispersion and Length Characteristics.

Processing boron nitride nanotubes (BNNTs) for applications ranging from nanomedicine to electronics generally requires dispersions of nanotubes that are stable in various compounds and solvents. We show that alcohol/water cosolvents, particularly isopropyl alcohol (IPA), are essential for the complexation of BNNTs with DNA under mild bath sonication. The resulting DNA-wrapped BNNT complexes are highly stable during purification and solvent exchange from cosolvents to water, providing potential for the versatile liquid-phase processing of BNNTs. Via molecular dynamics simulations, we demonstrate that IPA assists in the solvation of BNNTs due to its pseudosurfactant nature by verifying that water is replaced in the solvation layer as IPA is added. We quantify the solvation free energy of BNNTs in various IPA/water mixtures and observe a nonmonotonic trend, highlighting the importance of utilizing solvent-nanotube interactions in nanomaterial dispersions. Additionally, we show that nanotube lengths can be characterized by rheology measurements via determining the viscosity of dilute dispersions of DNA-BNNTs. This represents the bulk sample property in the liquid state, as compared to conventional imaging techniques that require surface deposition and drying. Our results also demonstrate that BNNT dispersions exhibit the rheological behavior of dilute Brownian rigid rods, which can be further exploited for the controlled processing and property enhancement of BNNT-enabled assemblies such as films and fibers.

Whole lung tissue is the preferred sampling method for amplicon-based characterization of murine lung microbiota.

BACKGROUND: Low-biomass microbiome studies (such as those of the lungs, placenta, and skin) are vulnerable to contamination and sequencing stochasticity, which obscure legitimate microbial signal. While human lung microbiome studies have rigorously identified sampling strategies that reliably capture microbial signal from these low-biomass microbial communities, the optimal sampling strategy for characterizing murine lung microbiota has not been empirically determined. Performing accurate, reliable characterization of murine lung microbiota and distinguishing true microbial signal from noise in these samples will be critical for further mechanistic microbiome studies in mice. RESULTS: Using an analytic approach grounded in microbial ecology, we compared bacterial DNA from the lungs of healthy adult mice collected via two common sampling approaches: homogenized whole lung tissue and bronchoalveolar lavage (BAL) fluid. We quantified bacterial DNA using droplet digital PCR, characterized bacterial communities using 16S rRNA gene sequencing, and systematically assessed the quantity and identity of bacterial DNA in both specimen types. We compared bacteria detected in lung specimens to each other and to potential source communities: negative (background) control specimens and paired oral samples. By all measures, whole lung tissue in mice contained greater bacterial signal and less evidence of contamination than did BAL fluid. Relative to BAL fluid, whole lung tissue exhibited a greater quantity of bacterial DNA, distinct community composition, decreased sample-to-sample variation, and greater biological plausibility when compared to potential source communities. In contrast, bacteria detected in BAL fluid were minimally different from those of procedural, reagent, and sequencing controls. CONCLUSIONS: An ecology-based analytical approach discriminates signal from noise in this low-biomass microbiome study and identifies whole lung tissue as the preferred specimen type for murine lung microbiome studies. Sequencing, analysis, and reporting of potential source communities, including negative control specimens and contiguous biological sites, are crucial for biological interpretation of low-biomass microbiome studies, independent of specimen type. Video abstract.

Gut Microbiota Predict Enterococcus Expansion but Not Vancomycin-Resistant Enterococcus Acquisition.

Vancomycin-resistant Enterococcus (VRE) is a leading cause of hospital-acquired infections and continues to spread despite widespread implementation of pathogen-targeted control guidelines. Commensal gut microbiota provide colonization resistance to VRE, but the role of gut microbiota in VRE acquisition in at-risk patients is unknown. To address this gap in our understanding, we performed a case-control study of gut microbiota in hospitalized patients who did (cases) and did not (controls) acquire VRE. We matched case subjects to control subjects by known risk factors and "time at risk," defined as the time elapsed between admission until positive VRE screen. We characterized gut bacterial communities using 16S rRNA gene amplicon sequencing of rectal swab specimens. We analyzed 236 samples from 59 matched case-control pairs. At baseline, case and control subjects did not differ in gut microbiota when measured by community diversity (P = 0.33) or composition (P = 0.30). After hospitalization, gut communities of cases and controls differed only in the abundance of the Enterococcus-containing operational taxonomic unit (OTU), with the gut microbiota of case subjects having more of this OTU than time-matched control subjects (P = 0.01). Otherwise, case and control communities after the time at risk did not differ in diversity (P = 0.33) or community structure (P = 0.12). Among patients who became VRE colonized, those having the Blautia-containing OTU on admission had lower Enterococcus relative abundance once colonized (P = 0.004). Our results demonstrate that the 16S profile of the gut microbiome does not predict VRE acquisition in hospitalized patients, likely due to rapid and profound microbiota change. The gut microbiome does not predict VRE acquisition, but it may be associated with Enterococcus expansion, suggesting that these should be considered two distinct processes.IMPORTANCE The Centers for Disease Control and Prevention estimates that VRE causes an estimated 54,000 infections and 539 million dollars in attributable health care costs annually. Despite improvements in hand washing, environmental cleaning, and antibiotic use, VRE is still prevalent in many hospitals. There is a pressing need to better understand the processes by which patients acquire VRE. Multiple lines of evidence suggest that intestinal microbiota may help some patients resist VRE acquisition. In this large case-control study, we compared the 16S profile of intestinal microbiota on admission in patients that did and did not subsequently acquire VRE. The 16S profile did not predict subsequent VRE acquisition, in part due to rapid and dramatic change in the gut microbiome following hospitalization. However, Blautia spp. present on admission predicted decreased Enterococcus abundance after VRE acquisition, and Lactobacillus spp. present on admission predicted Enterococcus dominance after VRE acquisition. Thus, VRE acquisition and domination may be distinct processes.

Lung and gut microbiota are altered by hyperoxia and contribute to oxygen-induced lung injury in mice.

Inhaled oxygen, although commonly administered to patients with respiratory disease, causes severe lung injury in animals and is associated with poor clinical outcomes in humans. The relationship between hyperoxia, lung and gut microbiota, and lung injury is unknown. Here, we show that hyperoxia conferred a selective relative growth advantage on oxygen-tolerant respiratory microbial species (e.g., Staphylococcus aureus) as demonstrated by an observational study of critically ill patients receiving mechanical ventilation and experiments using neonatal and adult mouse models. During exposure of mice to hyperoxia, both lung and gut bacterial communities were altered, and these communities contributed to oxygen-induced lung injury. Disruption of lung and gut microbiota preceded lung injury, and variation in microbial communities correlated with variation in lung inflammation. Germ-free mice were protected from oxygen-induced lung injury, and systemic antibiotic treatment selectively modulated the severity of oxygen-induced lung injury in conventionally housed animals. These results suggest that inhaled oxygen may alter lung and gut microbial communities and that these communities could contribute to lung injury.

Solvation Free Energy of Self-Assembled Complexes: Using Molecular Dynamics to Understand the Separation of ssDNA-Wrapped Single-Walled Carbon Nanotubes.

Molecular dynamics simulations were used to characterize the self-assembly of single-stranded DNA (ssDNA) on a (6,5) single-walled carbon nanotube (SWCNT) in aqueous solution for the purpose of gaining an improved theoretical understanding of separation strategies for SWCNTs using ssDNA as a dispersant. Four separate ssDNA sequences, ((TAT)4, TTA(TAT)2ATT, C12, (GTC)2GT), at various levels of loading, were chosen for study based on published experimental work showing selective extraction of particular SWCNT species based on the ssDNA dispersant sequence. We develop a unique workflow based on free energy perturbation (FEP) and use this to determine the relative solubility of these complexes due to the adsorption of the ssDNA on the SWCNT surface, and hence, rank the favorability of separations observed during experiments. Results qualitatively agree with experiments and indicate that the nucleobase sequence of the adsorbed ssDNA greatly affects the free energy of complex solvation which ultimately drives SWCNT separation. Further, to elucidate the underlying physics governing the ssDNA-SWCNT solubility rankings, we also present calculations for four structural characteristics of ssDNA adsorption. We demonstrate that a unique type of intra-strand hydrogen bonding is the most important factor contributing to the stability of the ssDNA-SWCNT complexes and show how these adsorption characteristics are coupled with the FEP results.

Lessons from a Minimal Genome: What Are the Essential Organizing Principles of a Cell Built from Scratch?

One of the primary challenges facing synthetic biology is reconstituting a living system from its component parts. A particularly difficult landmark is reconstituting a self-organizing system that can undergo autonomous chromosome compaction, segregation, and cell division. Here, we discuss how the syn3.0 minimal genome can inform us of the core self-organizing principles of a living cell and how these self-organizing processes can be built from the bottom up. The review underscores the importance of fundamental biology in rebuilding life from its molecular constituents.

Constitutive activation of the PI3K-AKT pathway and cardiovascular abnormalities in an individual with Kosaki overgrowth syndrome.

Kosaki overgrowth syndrome is a recently described syndrome characterized by distinctive facial features, brain white matter lesions, and developmental delay. Germline activating heterozygous PDGFRB mutations have been reported in this condition. Systemic connective tissue-type findings have been described in some individuals. We describe a 19-year-old Caucasian female with a history of hydrocephalus, Dandy-Walker malformation, cervical spine arachnoid cyst, progressive scoliosis, and overgrowth. Her physical exam included distinctive craniofacial dysmorphism, as well as soft and hyperextensible skin. Cardiovascular imaging during adolescence revealed saccular aneurysms in both coronary artery systems and subtle tortuosity of the cervical vertebral arteries. Exome sequencing trio analysis identified a de novo previously reported pathogenic variant in PDGFRB, c.1696T>C (p.[Trp566Arg]). Further functional studies included platelet-derived growth factor cellular metabolic pathway activity that confirmed the variant causes a constitutive activation of the PI3K-AKT pathway. This is the first report to characterize the activating nature of this PDGFRB variant. We also highlight the connective tissue findings seen in Kosaki overgrowth syndrome and recommend baseline echocardiographic evaluation in all individuals with this condition with particular emphasis on coronary arteries.

Postnatal Outcomes of Fetal Supraventricular Tachycardia: a Multicenter Study.

Supraventricular tachycardia (SVT), the most common fetal tachycardia, can be difficult to manage in utero. We sought to better understand predictors of the postnatal clinical course in neonates who experienced fetal SVT. We hypothesized that fetuses with hydrops or those with refractory SVT (failure of first-line SVT therapy) are more likely to experience postnatal SVT. This was a retrospective multicenter cohort study of subjects diagnosed with fetal SVT between 2006 and 2014. Fetuses with structural heart disease were excluded. Descriptive comparative statistics and univariate analysis with logistic regression were utilized to determine factors that most strongly predicted postnatal SVT and preterm delivery. The cohort consisted of 103 subjects. Refractory SVT was found in 37% (N = 38) of the cohort with this group more likely to be delivered prematurely (median = 36 vs. 37.5 weeks, p = 0.04). Refractory SVT did not increase the risk of postnatal SVT (p = 0.09). Postnatal SVT was seen in 61% (N = 63). Of those, 68% (N = 43) had postnatal SVT at ≤2 days of age. Postnatal SVT was associated with a later fetal SVT diagnosis (median = 30 vs. 27.5 weeks, p = 0.006). We found a strong correlation between postnatal SVT and later gestational age at fetal SVT diagnosis. Subjects with refractory SVT or hydrops did not have a higher risk of postnatal SVT. We propose strong consideration for term delivery in the absence of significant clinical compromise. Further studies to assess whether outcomes vary for preterm delivery versus expectant management in those with refractory SVT should be performed.

A multi-institutional study of factors affecting resource utilisation following the Fontan operation.

The few studies evaluating data on resource utilisation following the Fontan operation specifically are outdated. We sought to evaluate resource utilisation and factors associated with increased resource use after the Fontan operation in a contemporary, large, multi-institutional cohort. This retrospective cohort study of children who had the Fontan between January, 2004 and June, 2013 used the Pediatric Health Information Systems Database. Generalised linear regression analyses evaluated factors associated with resource use. Of 2187 Fontan patients included in the study, 62% were males. The median age at Fontan was 3.2 years (inter-quartile range (IQR): 2.6-3.8). The median length of stay following the Fontan was 9 days (IQR: 7-14). The median costs and charges in 2012 dollars for the Fontan operation were $93,900 (IQR: $67,800-$136,100) and $156,000 (IQR: $112,080-$225,607), respectively. Postoperative Fontan mortality (30 days) was 1% (n=21). Factors associated with increased resource utilisation included baseline and demographic factors such as region, race, and renal anomaly, factors at the bidirectional Glenn such as seizures, valvuloplasty, and surgical volume, number of admissions between the bidirectional Glenn and the Fontan, and factors at the Fontan such as surgical volume and age at Fontan. The most strongly associated factors for both increased Fontan length of stay and increased Fontan charges were number of bidirectional Glenn to Fontan admissions (p<0.001) and Fontan surgical volume per year (p<0.001). As patient characteristics and healthcare-related delivery variables accounted for most of the factors predicting increased resource utilisation, changes should target healthcare delivery factors to reduce costs in this resource-intensive population.