CO-DELIVERY of glutamic acid-extended peptide antigen and imidazoquinoline TLR7/8 agonist via ionizable lipid nanoparticles induces protective anti-tumor immunity.

Cancer vaccines aim at generating cytotoxic CD8+ T cells that kill cancer cells and confer durable tumor regression. Hereto, CD8+ peptide epitopes should be presented by antigen presenting cells to CD8+ T cells in lymphoid tissue. Unfortunately, in unformulated soluble form, peptide antigens are poorly taken up by antigen presenting cells and do not efficiently reach lymph nodes. Hence, the lack of efficient delivery remains a major limitation for successful clinical translation of cancer vaccination using peptide antigens. Here we propose a generic peptide nanoformulation strategy by extending the amino acid sequence of the peptide antigen epitope with 10 glutamic acid residues. The resulting overall anionic charge of the peptide allows encapsulation into lipid nanoparticles (peptide-LNP) by electrostatic interaction with an ionizable cationic lipid. We demonstrate that intravenous injection of peptide-LNP efficiently delivers the peptide to immune cells in the spleen. Peptide-LNP that co-encapsulate an imidazoquinoline TLR7/8 agonist (IMDQ) induce robust innate immune activation in a broad range of immune cell subsets in the spleen. Peptide-LNP containing the minimal CD8+ T cell epitope of the HPV type 16 E7 oncoprotein and IMDQ induces high levels of antigen-specific CD8+ T cells in the blood, and can confer protective immunity against E7-expressing tumors in both prophylactic and therapeutic settings.

Comparison of the Accuracy and Efficiency of Two Dynamic Navigation System Workflow for Fiber-Post Removal: Small versus Large Field-of-View Registration Workflows.

INTRODUCTION: This study investigates the feasibility of a dynamic navigation system (DNS) small field of view workflow (DNS-SFOVw) for fiber-post removal and compares its accuracy and efficiency to the conventional large field of view workflow (DNS-LFOVw). METHODS: Fifty-six extracted human maxillary molars were divided into DNS-SFOVw (n=28) and DNS-LFOVw (n=28). The palatal canal was restored with an intra-radicular RelyX fiber post and luted with RelyX Unicem; a core buildup was used. Teeth were mounted in a 3D-printed surgical jaw. A preoperative cone-beam-computed tomography (CBCT) scan was taken with a 40 x 40 mm FOV for the DNS-SFOVw and a single arch CBCT scan for the DNS-LFOVw. The drilling entry point, trajectory, angle, and depth were planned in the X-guide software. The DNS registration method for the DNS-SFOVw was virtual-based registration on teeth, and the marker point-based method was used for the DNS-LFOVw. The fiber posts were drilled out under DNS guidance. A postoperative CBCT scan was taken. Three-dimensional (3D) deviations, angular deflection, number of mishaps, registration, and total operation time were calculated. RESULTS: The DNS-SFOVw was as accurate as DNS-LFOVw (p>.05). The DNS-LFOVw registration time was less than DNS-SFOVw (p<.05). There was no difference in the number of mishaps (p>.05). Both DNS-SFOVw and DNS-LFOVw were time-efficient, with DNS-LFOVw taking less total operational time (p<.05). CONCLUSION: Within the limitations of this in-vitro study, the DNS-SFOVw was as accurate as the DNS-LFOVw for fiber-post removal. Both DNS-LFOVw and DNS-SFOVw were time-efficient in removing fiber-posts.

Performance of Saccharomyces cerevisiae strains against the application of adaptive laboratory evolution strategies for butanol tolerance.

Although the industrial production of butanol has been carried out for decades by bacteria of the Clostridium species, recent studies have shown the use of the yeast Saccharomyces cerevisiae as a promising alternative. While the production of n-butanol by this yeast is still very far from its tolerability (up to 2% butanol), the improvement in the tolerance can lead to an increase in butanol production. The aim of the present work was to evaluate the adaptive capacity of the laboratory strain X2180-1B and the Brazilian ethanol-producing strain CAT-1 when submitted to two strategies of adaptive laboratory Evolution (ALE) in butanol. The strains were submitted, in parallel, to ALE with successive passages or with UV irradiation, using 1% butanol as selection pressure. Despite initially showing greater tolerance to butanol, the CAT-1 strain did not show great improvements after being submitted to ALE. Already the laboratory strain X2180-1B showed an incredible increase in butanol tolerance, starting from a condition of inability to grow in 1% butanol, to the capacity to grow in this same condition. With emphasis on the X2180_n100#28 isolated colony that presented the highest maximum specific growth rate among all isolated colonies, we believe that this colony has good potential to be used as a model yeast for understanding the mechanisms that involve tolerance to alcohols and other inhibitory compounds.

Effects of Delaying the Storage of 'Hass' Avocados under a Controlled Atmosphere on Skin Color, Bioactive Compounds and Antioxidant Capacity.

During ripening, 'Hass' avocado skin changes from green to purple/black. Low-temperature storage with a controlled atmosphere (CA) is the most widely used method for avocado storage; however, few studies have simulated this technology and considered the days of regular air (RA) storage prior to CA storage. Herein, the effect of delaying the storage of 'Hass' avocado (>30% dry matter) in a CA was examined. Long-term storage conditions (5 °C for 50 days) corresponded to (i) regular air storage (RA), (ii) CA (4 kPa O2 and 6 kPa CO2) and (iii) 10 days in RA + 40 days in a CA and (iv) 20 days in RA + 30 days in a CA. Evaluations were performed during storage and at the ready-to-eat (RTE) stage. Skin color remained unchanged during storage, but at the RTE stage, more color development was observed for fruits stored under CA conditions, as these fruits were purple/black (>50%). At the RTE stage, the anthocyanin content increased, and compared to fruit under RA, fruit under a CA contained a five-fold greater content. A 20-day delay between harvest and CA storage increased the fruit softening rate and skin color development after cold storage, reducing the effectiveness of CA as a postharvest technology for extending storage life.

Epigenetic mechanisms linking early-life adversities and mental health.

Early-life adversities, whether prenatal or postnatal exposure, have been linked to adverse mental health outcomes later in life increasing the risk of several psychiatric disorders. Research on its neurobiological consequences demonstrated an association between exposure to adversities and persistent alterations in the structure, function, and connectivity of the brain. Consistent evidence supports the idea that regulation of gene expression through epigenetic mechanisms are involved in embedding the impact of early-life experiences in the genome and mediate between social environments and later behavioral phenotypes. In addition, studies from rodent models and humans suggest that these experiences and the acquired risk factors can be transmitted through epigenetic mechanisms to offspring and the following generations potentially contributing to a cycle of disease or disease risk. However, one of the important aspects of epigenetic mechanisms, unlike genetic sequences that are fixed and unchangeable, is that although the epigenetic markings are long-lasting, they are nevertheless potentially reversible. In this review, we summarize our current understanding of the epigenetic mechanisms involved in the mental health consequences derived from early-life exposure to malnutrition, maltreatment and poverty, adversities with huge and pervasive impact on mental health. We also discuss the evidence about transgenerational epigenetic inheritance in mammals and experimental data suggesting that suitable social and pharmacological interventions could reverse adverse epigenetic modifications induced by early-life negative social experiences. In this regard, these studies must be accompanied by efforts to determine the causes that promote these adversities and that result in health inequity in the population.

Contemporary educational methods in periodontology.

AIM: The 1st European Workshop on Periodontal Education in 2009 made recommendations regarding the scope of periodontal education at undergraduate (UG), postgraduate (PG) and continuing professional development (CPD) levels, defining competencies and learning outcomes that were instrumental at the time in helping to define periodontal teaching curricula. The 19th European Workshop on Periodontology and 2nd European Consensus Workshop on Education in Periodontology (Education in Periodontology in Europe) was held in 2023 to identify changes and future developments in periodontal education (including those informed by the COVID-19 pandemic) and embracing methods and formats of periodontal teaching and training. The aim of this review was to assess current knowledge regarding education methods in periodontology, including traditional face-to-face (F2F) teaching and the move to student-centred methods, virtual learning methods and use of digital technology, as well as blended teaching and learning (including teaching delivery and assessment) at UG, PG and CPD levels. MATERIALS AND METHODS: Systematic searches were conducted to identify relevant studies from the literature. Data were extracted and descriptive summaries collated. RESULTS: The pandemic was a major disruptor of traditional F2F teaching but provided opportunities for rapid implementation of alternative and supplementary teaching methods. Although online learning has become an integral part of periodontal education, teachers and learners alike favour some form of F2F teaching. Blended teaching and learning are feasible in many areas of periodontal education, both for knowledge and skills acquisition as well as in assessment. Student-centred methods and blended approaches such as the flipped classroom seem highly effective, and online/virtual classrooms with both synchronous and asynchronous lectures are highly valued. Learning with haptic methods and virtual reality (VR) enhances the educational experience, especially when VR is integrated with traditional methods. The quality of the teacher continues to be decisive for the best knowledge transfer in all its forms. CONCLUSIONS: Live F2F teaching continues to be highly trusted; however, all types of student-centred and interactive forms of knowledge transfer are embraced as enhancements. While digital methods offer innovation in education, blended approaches integrating both virtual and traditional methods appear optimal to maximize the achievement of learning outcomes. All areas of periodontal education (UG, PG and CPD) can benefit from such approaches; however, more research is needed to evaluate their benefits, both for knowledge transfer and skills development, as well as in assessment.

Relevance of controlled cooling and freezing phases in T-cell cryopreservation.

When cells are cryopreserved, they go through a freezing process with several distinct phases (i.e., cooling until nucleation, ice nucleation, ice crystal growth and cooling to a final temperature). Conventional cell freezing approaches often employ a single cooling rate to describe and optimize the entire freezing process, which neglects its complexity and does not provide insight into the effects of the different freezing phases. The aim of this work was to elucidate the impact of each freezing phase by varying different process parameters per phase. Hereto, spin freezing was used to freeze Jurkat T cells in either a Me2SO-based or Me2SO-free formulation. The cooling rates before ice nucleation and after total ice crystallization impacted cell viability, resulting in viability ranging from 26.7% to 52.8% for the Me2SO-free formulation, and 22.5%-42.6% for the Me2SO-based formulation. Interestingly, the degree of supercooling upon nucleation did not exhibit a significant effect on cell viability in this work. However, the rate of ice crystal formation emerged as a crucial factor, with viability ranging from 2.4% to 53.2% for the Me2SO-free formulation, and 0.3%-53.2% for the Me2SO-based formulation, depending on the freezing rate. A morphological study of the cells post-cryopreservation was performed using confocal microscopy, and it was found that cytoskeleton integrity and cell volume were impacted, depending on the formulation-process parameter combination. These findings underscore the importance of scrutinizing all cooling and freezing phases, as each phase impacted post-thaw viability in a distinct way, depending of the specific formulation used.

Further Examination of the Pulsed- and Steady-Pedestal Paradigms under Hypothetical Parvocellular- and Magnocellular-Biased Conditions.

The pulsed- and steady-pedestal paradigms were designed to track increment thresholds (ΔC) as a function of pedestal contrast (C) for the parvocellular (P) and magnocellular (M) systems, respectively. These paradigms produce contrasting results: linear relationships between ΔC and C are observed in the pulsed-pedestal paradigm, indicative of the P system's processing, while the steady-pedestal paradigm reveals nonlinear functions, characteristic of the M system's response. However, we recently found the P model fits better than the M model for both paradigms, using Gabor stimuli biased towards the M or P systems based on their sensitivity to color and spatial frequency. Here, we used two-square pedestals under green vs. red light in the lower-left vs. upper-right visual fields to bias processing towards the M vs. P system, respectively. Based on our previous findings, we predicted the following: (1) steeper ΔC vs. C functions with the pulsed than the steady pedestal due to different task demands; (2) lower ΔCs in the upper-right vs. lower-left quadrant due to its bias towards P-system processing there; (3) no effect of color, since both paradigms track the P-system; and, most importantly (4) contrast gain should not be higher for the steady than for the pulsed pedestal. In general, our predictions were confirmed, replicating our previous findings and providing further evidence questioning the general validity of using the pulsed- and steady-pedestal paradigms to differentiate the P and M systems.

Lipid nanoparticle composition for adjuvant formulation modulates disease after influenza virus infection in quadrivalent influenza vaccine vaccinated mice.

There are considerable avenues through which currently licensed influenza vaccines could be optimized. We tested influenza vaccination in a mouse model with two adjuvants: Sendai virus-derived defective interfering (SDI) RNA, a RIG-I agonist; and an amphiphilic imidazoquinoline (IMDQ-PEG-Chol), a TLR7/8 agonist. The negatively charged SDI RNA was formulated into lipid nanoparticles (LNPs) facilitating direct delivery of SDI RNA to the cytosol, where RIG-I sensing induces inflammatory and type I interferon responses. We previously tested SDI RNA and IMDQ-PEG-Chol as standalone and combination adjuvants for influenza and SARS-CoV-2 vaccines. Here, we tested two different ionizable lipids, K-Ac7-Dsa and S-Ac7-Dog, for LNP formulations. The LNPs were incorporated with SDI RNA to determine its potential as a combination adjuvant with IMDQ-PEG-Chol by evaluating the host immune response to vaccination and infection in immunized BALB/c mice. Adjuvanticity of IMDQ-PEG-Chol with and without empty or SDI-loaded LNPs was validated with quadrivalent inactivated influenza vaccine (QIV), showing robust induction of antibody titers and T-cell responses. Depending on the adjuvant combination and LNP formulation, humoral and cellular vaccine responses could be tailored towards type 1 or type 2 host responses with specific cytokine profiles that correlated with the protective responses to viral infection. The extent of protection conferred by different vaccine/LNP/adjuvant combinations was tested by challenging mice with a vaccine-matched strain of influenza A virus A/Singapore/gp1908/2015 IVR-180 (H1N1). Groups that received either LNP formulated with SDI or IMDQ-PEG-Chol, or both, showed very low levels of viral replication in their lungs at 5 days post-infection (DPI). These studies provide evidence that the combination of vaccines with LNPs and/or adjuvants promote antigen-specific cellular responses that can contribute to protection upon infection. Interestingly, we observed differences in humoral and cellular responses to vaccination between different groups receiving K-Ac7-Dsa or S-Ac7-Dog lipids in LNP formulations. The differences were also reflected in inflammatory responses in lungs of vaccinated animals to infection, depending on LNP formulations. Therefore, this study suggests that the composition of the LNPs, particularly the ionizable lipid, plays an important role in inducing inflammatory responses in vivo, which is important for vaccine safety and to prevent adverse effects upon viral exposure.

Comprehensive Two-Dimensional Gas Chromatography-Mass Spectrometry as a Tool for the Untargeted Study of Hop and Their Metabolites.

Since hop secondary metabolites have a direct correlation with the quality of beer and other hop-based beverages, and the volatile fraction of hop has a complex composition, requiring effective separation, here we explore the application of headspace solid-phase microextraction as a sample preparation method, coupled with comprehensive two-dimensional gas chromatography-mass spectrometry (GC×GC-MS) analysis. The methodology involved the use of a DVB/PDMS fibre with 500 mg of hop cone powder, extracted for 40 min at 50 °C, for both GC-MS and GC×GC-MS. The varieties Azacca, Cascade, Enigma, Loral, and Zappa were studied comprehensively. The results demonstrate that GC×GC-MS increases the number of peaks by over 300% compared to classical GC-MS. Overall, 137 compounds were identified or tentatively identified and categorised into 10 classes, representing between 87.6% and 96.9% of the total peak area. The composition revealed the highest concentration of sesquiterpene hydrocarbons for Enigma, whilst Zappa showed a relatively significant concentration of monoterpene hydrocarbons. Principal component analysis for all compounds and classes, along with hierarchical cluster analysis, indicated similarities between Zappa and Cascade, and Azacca and Loral. In conclusion, this method presents an optimistic advancement in hop metabolite studies with a simple and established sample preparation procedure in combination with an effective separation technique.

Thermally Triggered Triazolinedione-Tyrosine Bioconjugation with Improved Chemo- and Site-Selectivity.

A bioconjugation strategy is reported that allows the derivatization of tyrosine side chains through triazolinedione-based "Y-clicking". Blocked triazolinedione reagents were developed that, in contrast to classical triazolinedione reagents, can be purified before use, can be stored for a long time, and allow functionalization with a wider range of cargoes and labels. These reagents are bench-stable at room temperature but steadily release highly reactive triazolinediones upon heating to 40 °C in buffered media at physiological pH, showing a sharp temperature response over the 0 to 40 °C range. This conceptually interesting strategy, which is complementary to existing photo- or electrochemical bioorthogonal bond-forming methods, not only avoids the classical synthesis and handling difficulties of these highly reactive click-like reagents but also markedly improves the selectivity profile of the tyrosine conjugation reaction itself. It avoids oxidative damage and "off-target" tryptophan labeling, and it even improves site-selectivity in discriminating between different tyrosine side chains on the same protein or different polypeptide chains. In this research article, we describe the stepwise development of these reagents, from their short and modular synthesis to small-molecule model bioconjugation studies and proof-of-principle bioorthogonal chemistry on peptides and proteins.

Thermosensitive polymer prodrug nanoparticles prepared by an all-aqueous nanoprecipitation process and application to combination therapy.

Despite their great versatility and ease of functionalization, most polymer-based nanocarriers intended for use in drug delivery often face serious limitations that can prevent their clinical translation, such as uncontrolled drug release and off-target toxicity, which mainly originate from the burst release phenomenon. In addition, residual solvents from the formulation process can induce toxicity, alter the physico-chemical and biological properties and can strongly impair further pharmaceutical development. To address these issues, we report polymer prodrug nanoparticles, which are prepared without organic solvents via an all-aqueous formulation process, and provide sustained drug release. This was achieved by the "drug-initiated" synthesis of well-defined copolymer prodrugs exhibiting a lower critical solution temperature (LCST) and based on the anticancer drug gemcitabine (Gem). After screening for different structural parameters, prodrugs based on amphiphilic diblock copolymers were formulated into stable nanoparticles by all-aqueous nanoprecipitation, with rather narrow particle size distribution and average diameters in the 50-80 nm range. They exhibited sustained Gem release in human serum and acetate buffer, rapid cellular uptake and significant cytotoxicity on A549 and Mia PaCa-2 cancer cells. We also demonstrated the versatility of this approach by formulating Gem-based polymer prodrug nanoparticles loaded with doxorubicin (Dox) for combination therapy. The dual-drug nanoparticles exhibited sustained release of Gem in human serum and acidic release of Dox under accelerated pathophysiological conditions. Importantly, they also induced a synergistic effect on triple-negative breast cancer line MDA-MB-231, which is a relevant cell line to this combination.

Inducing molecular orientation in solution-processed thin films of fluorene-bithiophene-based copolymer: thermal annealing vs. solvent additive.

A deep understanding of the factors influencing the morphology of thin films based on conjugated polymers is essential to boost their performance in optoelectronic devices. Herein, we investigated the electronic structure and morphology of thin films of the copolymer poly(9,9-dioctyl-fluorenyl-co-bithiophene) (F8T2) in its pristine form as well as samples processed with the solvent additive 1,8-diiodooctane (DIO) or post-processed through thermal annealing treatment. Measurements were carried out using angle-resolved S K-edge NEXAFS (near-edge X-ray absorption fine structure) in total electron yield (TEY) and fluorescence yield (FY) detection modes. Two main transitions were observed at the S 1s NEXAFS spectra: S 1s → π* and S 1s → σ* (S-C). The observed dichroism pointed to a face-on orientation of the conjugated backbone, which was significantly increased for F8T2 films processed with DIO. Resonant Auger decay spectra were obtained and analyzed using the core-hole clock (CHC) method. An enhancement in the charge transfer process was observed for thermally annealed films, especially for samples processed with DIO, corresponding to an increase in film ordering. Furthermore, the investigated films were characterized using X-ray photoelectron spectroscopy, attesting to the presence of the thiophene unit in the samples and demonstrating that some of its sulfur atoms were positively polarized in the F8T2 films. All these experimental findings were compared with molecular dynamics (MD) simulations of film evaporation with and without DIO. The use of MD, together with mathematical modeling, was able to explain the major effects found in the experiments, including the polarization of sulfur atoms. The simultaneous use of powerful spectroscopic techniques and theoretical methods shed light on key aspects linking film morphology with fabrication procedures.

Expression and purification of active shikimate dehydrogenase from Plasmodium falciparum.

Plasmodium falciparum is known to cause severe malaria, current treatment consists in artemisinin-based combination therapy, but resistance can lead to treatment failure. Knowledge concerning P. falciparum essential proteins can be used for searching new antimalarials, among these a potential candidate is shikimate dehydrogenase (SDH), an enzyme part of the shikimate pathway which is responsible for producing endogenous aromatic amino acids. SDH from P. falciparum (PfSDH) is unexplored by the scientific community, therefore, this study aims to establish the first protocol for active PfSDH expression. Putative PfSDH nucleotide sequence was used to construct an optimized expression vector pET28a+PfSDH inserted in E. coli BL21(DE3). As a result, optimal expression conditions were acquired by varying IPTG and temperature through time. Western Blot analysis was applied to verify appropriate PfSDH expression, solubilization and purification started with lysis followed by two-steps IMAC purification. Enzyme activity was measured spectrophotometrically by NADPH oxidation, optimal PfSDH expression occur at 0.1 mM IPTG for 48 hours growing at 37 °C and shaking at 200 rpm, recombinant PfSDH obtained after purification was soluble, pure and its physiological catalysis was confirmed. Thus, this study describes the first protocol for heterologous expression of PfSDH in soluble and active form.

Soft-tissue, non-osteogenic distraction of the mandible and lower face in bilateral hemifacial microsomia-technical report.

The aim of this study is to present a sequential strategy of soft-tissue, non-osteogenic distraction with a novel device, followed by microvascular bony reconstruction for severe cases of mandibular hypoplasia. The case of a 21-year-old woman with Goldenhar syndrome is presented, whose mandible remained severely hypoplastic despite previous attempts at distraction and was not suitable for further osteogenic distraction. Soft tissue deficiency and pin track scarring prevented free fibular transfers. A personalized distractor, anchored to the cranium and the mandibular symphysis, was designed to expand the soft tissues while allowing for physiological temporomandibular joint (TMJ) movement without compression forces. Internal distractors were placed along the osteotomies to prevent condylar luxation. After completion of the soft tissue distraction, the native mandible was resected except for the condyles and reconstructed with two free fibula flaps. This report represents the proof of concept of a sequential approach to severe lower face soft-tissue and bone deficiency, which preserves TMJ function and avoids the transfer of poorly matched skin to the face.

Towards scaling up the sonochemical synthesis of Pt-nanocatalysts.

Large scale production of electrocatalysts for electrochemical energy conversion devices such as proton exchange membrane fuel cells must be developed to reduce their cost. The current chemical reduction methods used for this synthesis suffer from problems with achieving similar particle properties such as particle size and catalytic activity when scaling up the volume or the precursor concentration. The continuous production of reducing agents through the sonochemical synthesis method could help maintain the reducing conditions (and also the particle properties) upon increasing the reactor volume. In this work we demonstrate that the reducing conditions of Pt-nanoparticles are indeed maintained when the reactor volume is increased from 200 mL to 800 mL. Similar particle sizes, 2.1(0.3) nm at 200 mL and 2.3(0.4) nm at 800 mL, and catalytic activities towards the oxygen reduction reaction (ORR) are maintained as well. The reducing conditions were assessed through TiOSO4 dosimetry, sonochemiluminesence imaging, acoustic power measurements, and Pt(II) reduction rate measurements. Cyclic voltammetry, CO-stripping, hydrogen evolution measurements, ORR measurements, and electron microscopy were used to evaluate the catalytic activity and particle size. The similar particle properties displayed from the two reactor volumes suggest that the sonochemical synthesis of Pt-nanoparticles is suitable for large scale production.

Lipid nanoparticle composition for adjuvant formulation modulates disease after influenza virus infection in QIV vaccinated mice.

Adjuvants can enhance vaccine effectiveness of currently licensed influenza vaccines. We tested influenza vaccination in a mouse model with two adjuvants: Sendai virus derived defective interfering (SDI) RNA, a RIG-I agonist, and an amphiphilic imidazoquinoline (IMDQ-PEG-Chol), TLR7/8 adjuvant. The negatively charged SDI RNA was formulated into lipid nanoparticles (LNPs) facilitating the direct delivery of a RIG-I agonist to the cytosol. We have previously tested SDI and IMDQ-PEG-Chol as standalone and combination adjuvants for influenza and SARS-CoV-2 vaccines. Here we tested two different ionizable lipids, K-Ac7-Dsa and S-Ac7-Dog, for LNP formulations. The adjuvanticity of IMDQ-PEG-Chol with and without empty or SDI-loaded LNPs was validated in a licensed vaccine setting (quadrivalent influenza vaccine or QIV) against H1N1 influenza virus, showing robust induction of antibody titres and T cell responses. Depending on the adjuvant combination and LNP lipid composition (K-Ac7-Dsa or S-Ac7-Dog lipids), humoral and cellular vaccine responses could be tailored towards type 1 or type 2 host responses with specific cytokine profiles that correlated with protection during viral infection. The extent of protection conferred by different vaccine/LNP/adjuvant combinations was examined against challenge with the vaccine-matching strain of H1N1 influenza A virus. Groups that received either LNP formulated with SDI, IMDQ-PEG-Chol or both showed very low levels of viral replication in their lungs at five days post virus infection. LNP ionizable lipid composition as well as loading (empty versus SDI) also skewed host responses to infection, as reflected in the cytokine and chemokine levels in lungs of vaccinated animals upon infection. These studies show the potential of LNPs as adjuvant delivery vehicles for licensed vaccines and illustrate the importance of LNP composition for subsequent host responses to infection, an important point of consideration for vaccine safety.

Adjusting for false discoveries in constraint-based differential metabolic flux analysis.

One of the critical steps to characterize metabolic alterations in multifactorial diseases, as well as their heterogeneity across different patients, is the identification of reactions that exhibit significantly different usage (or flux) between cohorts. However, since metabolic fluxes cannot be determined directly, researchers typically use constraint-based metabolic network models, customized on post-genomics datasets. The use of random sampling within the feasible region of metabolic networks is becoming more prevalent for comparing these networks. While many algorithms have been proposed and compared for efficiently and uniformly sampling the feasible region of metabolic networks, their impact on the risk of making false discoveries when comparing different samples has not been investigated yet, and no sampling strategy has been so far specifically designed to mitigate the problem. To be able to precisely assess the False Discovery Rate (FDR), in this work we compared different samples obtained from the very same metabolic model. We compared the FDR obtained for different model scales, sample sizes, parameters of the sampling algorithm, and strategies to filter out non-significant variations. To be able to compare the largely used hit-and-run strategy with the much less investigated corner-based strategy, we first assessed the intrinsic capability of current corner-based algorithms and of a newly proposed one to visit all vertices of a constraint-based region. We show that false discoveries can occur at high rates even for large samples of small-scale networks. However, we demonstrate that a statistical test based on the empirical null distribution of Kullback-Leibler divergence can effectively correct for false discoveries. We also show that our proposed corner-based algorithm is more efficient than state-of-the-art alternatives and much less prone to false discoveries than hit-and-run strategies. We report that the differences in the marginal distributions obtained with the two strategies are related to but not fully explained by differences in sample standard deviation, as previously thought. Overall, our study provides insights into the impact of sampling strategies on FDR in metabolic network analysis and offers new guidelines for more robust and reproducible analyses.