Biology subjects

Chandran, K.

Publications and source records attributed to Chandran, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Phosphatidylserine receptors are critical for lethal infection by Crimean-Congo hemorrhagic fever virus

The tick-borne Crimean-Congo hemorrhagic fever virus (CCHFV) causes severe and often fatal hemorrhagic disease for which no approved countermeasures are available. Herein, we identify the phosphatidylserine receptors (PSRs) AXL, TIM-1, and TIM-4 as critical entry host factors for CCHFV in cell lines and liver-derived primary cell cultures. Small-molecule and antibody-based PSR inhibitors greatly reduced viral infection in cell culture. Germline knockout of individual PSR genes afforded partial protection against CCHFV infection, disease, and death in a murine model of lethal viral challenge. Mice engineered to lack two PSRs were completely protected from challenge, with viremia and viral replication, pathology, and inflammation in the liver and spleen reduced to baseline. Therefore, PSRs are collectively indispensable for CCHFV infection and pathogenesis. We conclude that PSRs are not just cell entry factors but bona fide determinants of infection, dissemination, and disease by CCHFV and legitimate targets for the development of new antiviral countermeasures.

microbiology↗

bioRxiv2026

Expanded protocadherin-1 usage reveals a broader hantavirus entry landscape

Mammalian hantaviruses are RNA viruses that cause hantavirus cardiopulmonary syndrome in the Americas and hemorrhagic fever with renal syndrome in Eurasia. The cellular entry mechanisms of most hantaviruses remain poorly defined. To examine entry by phylogenetically distinct hantaviruses, we generated replication-competent recombinant vesicular stomatitis viruses (rVSVs) bearing Gn/Gc proteins from Necocli, Sangassou, Thottapalayam, Kenkeme, Nova, Oxbow, and Tula viruses. All these Gn/Gc proteins except Kenkeme supported infection of primary human endothelial cells, indicating that endothelial cell entry is permissive for a broader range of hantaviruses than previously appreciated. Except for rVSV-Kenkeme, these rVSVs did not acquire additional mutations beyond pre-engineered rescue-enhancing changes during rescue and passaging. Genetic studies in human cells lacking protocadherin-1 (PCDH1) showed that Necocli, Tula, and Nova viruses use PCDH1 for efficient infection, although the Nova phenotype was weaker. These three Gn/Gc proteins bound soluble PCDH1 with different apparent avidities, and infection by the corresponding rVSVs was inhibited by soluble PCDH1; Necocli and Tula, but not Nova, were also blocked by a PCDH1-targeting monoclonal antibody. Authentic Tula virus infection was similarly reduced in PCDH1 knockout endothelial cells. Finally, the broadly reactive anti-Gn/Gc human monoclonal antibody ADI-42898 efficiently neutralized Necocli, Nova, Sangassou, and Kenkeme rVSVs but showed weak or undetectable activity against Oxbow, Tula, and Thottapalayam rVSVs. Together, these findings expand the range of hantavirus glycoproteins capable of mediating infection of human endothelial cells, broaden the phylogenetic scope of PCDH1-dependent entry, and identify receptor-targeted and viral glycoprotein-targeted strategies with differential activity. ImportanceMany newly discovered hantaviruses are known only from sequence data, leaving their ability to enter human cells and their receptor usage unresolved. Using a BSL2-compatible rVSV system, we show that glycoproteins from several divergent hantaviruses can mediate infection of primary human endothelial cells, indicating that endothelial cell entry is permissive for a broader range of hantaviruses than previously appreciated. We also show that protocadherin-1 (PCDH1), previously linked mainly to New World hantaviruses, is used by Necocli, Tula, and Nova viruses but not universally across the panel, revealing broader but heterogeneous receptor usage. An authentic Tula virus experiment supports this conclusion beyond the surrogate system. Finally, a broadly reactive anti-Gn/Gc antibody neutralizes several, but not all, of these viruses, highlighting both the promise and the limits of broadly protective countermeasures and the utility of these rVSVs for evaluating entry inhibitors.

microbiology↗

bioRxiv2026

Female-specific m6A remodeling in the liver correlates with post-transcriptional metabolic adaptation to high fat diet

Sex differences strongly influence susceptibility to metabolic dysfunction-associated steatotic liver disease (MASLD), yet the regulatory mechanisms underlying these differences remain incompletely understood. To examine sex-specific hepatic adaptation to a high-fat (HF) diet mouse model of MASLD, we integrated proteomics, transcriptomics, and Oxford Nanopore direct RNA sequencing for transcriptome-wide m6A profiling in male and female mouse livers. Female mice were relatively protected from HF diet-induced hepatic steatosis and exhibited distinct proteome remodeling enriched for peroxisomal pathways. In contrast, transcriptomic responses in females were dominated by inflammatory signatures and did not recapitulate the metabolic adaptations observed at the protein level, revealing extensive RNA-protein discordance and post-transcriptional remodeling. Integrated RNA-protein analyses identified female-specific amplification of peroxisomal proteins despite modest transcript-level changes. HF diet also induced sex-specific remodeling of m6A RNA methylation and altered regulation of the m6A methylation system. Notably, reduced 3' UTR m6A methylation of peroxisomal transcripts inversely correlated with increased protein abundance relative to RNA expression in female mice. Together, these findings implicate m6A-associated post-transcriptional regulation in sex-specific hepatic adaptation to HF diet exposure and the basis for discordance between many of the mRNAs and proteins in the liver.

systems biology↗

bioRxiv2026

Finding the Goldilocks zone: Modulating glycoprotein cleavage and fusogenicity optimizes the efficacy of a candidate Crimean-Congo hemorrhagic fever virus vaccine

Crimean-Congo hemorrhagic fever virus (CCHFV) is the etiologic agent of a lethal hemorrhagic disease spread by ticks throughout Europe, the Middle East, Africa and Asia. The lack of approved medical countermeasures and fundamental understanding of molecular mechanisms of viral assembly and egress have thus far curtailed disease prevention. Here, we identify and characterize key residues within the viral glycoprotein through forward and reverse genetics for vesicular stomatitis virus (VSV)-based vaccine candidates that are highly protective in animal models. These residues are broadly applicable across divergent CCHFV strains and lead to greater protection in vivo against heterologous challenge. We further characterize the essential role of proteolytic processing in the maintenance of a stable fusogenic state required for effective VSV-based CCHFV vaccines. This study establishes a toolkit for better understanding orthonairovirus glycoprotein processing and vaccine development.

microbiology↗

bioRxiv2026

From receptor binding to biogeography: Multi-scale prediction of filovirus hosts in bats

Forecasting zoonotic risk requires identifying which host species are biologically susceptible to infection, yet susceptibility is rarely predicted using frameworks that integrate molecular mechanisms with macroecology. Filoviruses, a diverse group of bat-associated viruses that include Ebola and Marburg viruses, illustrate this challenge: viral entry depends on interactions between viral glycoproteins and the host receptor NPC1, and host ecology and distribution determine opportunity of viral entry. Additionally, receptor sequence data used for informing viral entry are available for only a small fraction of bat species. Here, we extend virus-specific susceptibility prediction across the global diversity of bats by integrating experimentally measured and physicochemically inferred virus-receptor binding strengths with phylogenetic, ecological, and environmental data. Using boosted regression models trained on binding assay labels, we generate predictions of NPC1-mediated binding strength for more than 1,300 bat species. Predicted susceptibility is strongly structured by evolutionary relationships, with high binding concentrated in particular bat lineages, but is further differentiated within clades by morphology, life-history strategy, and environmental context. Strikingly, macroevolutionary structure alone recovers interaction patterns originally derived from amino acid-level physicochemistry, indicating that information about receptor-mediated compatibility is recoverable from host evolutionary history and ecological traits. Predicted high binding strength extends well beyond historically recognized outbreak regions, suggesting that the fundamental host range of filoviruses may be substantially broader than their currently realized distribution. By scaling receptor biology to global host diversity, this multi-scale framework expands mechanistic susceptibility forecasting beyond species with available molecular data and provides a generalizable approach for integrating molecular and ecological information in zoonotic prediction.

ecology↗

bioRxiv2025

Structural Dynamics and Allosteric Communication of a SARS-Like Bat Coronavirus Spike Glycoprotein

SARS-like bat coronaviruses (CoVs) pose ongoing public health risks due to their zoonotic potential, making it important to understand the molecular pathways driving their evolution. We recently showed that SHC014-CoV can infect human cell lines in an ACE2-dependent manner after acquiring two spike ectodomain mutations (F294L and A835D). However, how the wild-type (WT) SHC014 spike differs dynamically from these mutants remains unclear. Here, we built fully glycosylated ectodomain models of WT and three mutants (F294L, A835D, and the double mutant, DM) and performed triplicate 1-s all-atom molecular dynamics (MD) simulations for each variant. The two mutations exhibit epistasis, altering structural rearrangements relative to WT. Notably, the DM receptor binding domain (RBD) begins sampling the open conformation in our conventional MD. At the atomic level, the DM spike mitigates the dense negative packing introduced by A835D through a salt-bridge network, while F294L disrupts {pi}-mediated interactions, together enhancing RBD opening propensity--critical for viral entry. Increased flexibility of the subdomain-2 "620-loop" further modulates DM RBD openness. Dynamical network analysis identified three allosteric communication pathways. In WT and F294L, "Pathway 1" forms the baseline route linking the 620-loop to the RBD, whereas in A835D and DM it extends to the FPPR, reshaping long-range communication. "Pathway 2" is conserved across variants but is most prominent in WT and F294L. "Pathway 3" appears only in A835D and DM, compensating for reduced communication along Pathway 2. Overall, this work provides an atomistic perspective on SHC014 molecular adaptation during host-to-host transmission and highlights mechanistic features that may inform future therapeutic and pandemic-preparedness efforts. Statement of SignificanceBat coronaviruses are an important source of future pandemic threats, but we still know little about how small genetic changes help them infect humans. In this study, we used detailed computer simulations to watch how tiny mutations in a bat coronavirus spike protein change its motion and shape. We found that two specific mutations work together to make the spike more likely to open--a step required for the virus to enter human cells. By revealing how these molecular changes increase infection potential, our work helps improve understanding of coronavirus evolution and may guide strategies to prepare for future outbreaks.

biophysics↗

bioRxiv2025

Unraveling operational drivers of nitrous oxide emissions in biological wastewater treatment systems through machine learning analysis of multi-decadal datasets

This study focused on the development of machine-learning- (ML-) based strategies for mitigating nitrous oxide (N2O) emissions from various wastewater treatment systems in the United States measured using a benchmark USEPA-endorsed protocol. Results revealed that in general, poor process performance correlated with higher N2O emissions. Among the models evaluated, the Extreme Gradient Boosting (XGBoost) model demonstrated strong predictive performance for aerobic (R2=0.97), and anoxic (R2=0.87) zone process data. Specifically, the unsupervised principal component analysis (PCA), along with the trained ML models, demonstrated that local variables including zone-specific dissolved oxygen (DO), ammonia (NH3), and nitrite (NO2-) concentrations and global variables including effluent nitrite and nitrate as key contributors towards N2O emissions from both aerobic and anoxic zones of the process bioreactors. The operating regions associated with lower predicted N2O emissions included operations of aerobic and anoxic zones at DO < 4 mg O2 L-1 and < 1 mg O2L-1 respectively, coupled with appropriate solids retention times (SRTs) that maximize process performance. The scenario analysis using the trained ML model predicted 7.8-fold (95% CI: 2.2 to 52.8-fold) and 8.8-fold (95% CI: 3.83 to 21.24-fold) higher N2O flux at low DO/high NH3 and high DO/high NO2- conditions in aerobic and anoxic zones, respectively. This model predicted responses were consistent with the established nitrifier denitrification and N2O reductase inhibition pathways. Accordingly, our results underscore the utility of ML models interpreted in conjunction with bioprocess fundamentals for predicting and mitigating N2O emissions, while concomitantly improving wastewater treatment operations.

bioengineering↗

bioRxiv2025

The multiplier benefits of integrating non-sewered and sewered wastewater treatment and sanitation processes

This study showcases the beneficial integration of non-sewered sanitation systems (NSSS) with sewered wastewater treatment plants (WWTPs). Treating increasing fractions of influent wastewater loads via six different types of NSSS offered correspondingly increasing savings in operating energy costs at five WWTPs, employing a broad range of typically employed treatment processes. Two NSSS that treat both greywater and blackwater (gb-HRT) and blackwater alone (b-HRT) yielded the highest savings in annual operating energy costs across most WWTPs. Distinctly, NSSS involving urine-separation with and without internal recirculation promoted energy-positive operations, by enhancing anaerobic digestion in selected WWTPs. At the highest NSSS coverage tested (treating 50% of the influent sewage), savings in annual sewered WWTPs operating energy costs ranged from $76k to $800k and increased further to the range $301k to $1.1M annually with process optimization. Therefore, integration of NSSS with sewered WWTPs can improve overall treatment efficiency, while facilitating resilient sanitation practices.

bioengineering↗

bioRxiv2025

High-resolution in situ structures of hantavirus glycoprotein tetramers

SUMMARY/ABSTRACTNew World hantaviruses cause severe infections in humans, with case fatality rates approaching 40%. Previous structural studies have advanced our understanding of hantavirus glycoprotein architecture and function, however, the lack of high-resolution in situ structures of the glycoprotein tetramer and its lattice organization has limited mechanistic insights into viral assembly, entry, and antigenicity. Here, we leveraged a virus-like particle (VLP) system to establish a cryo-electron microscopy workflow for lattice-forming viral glycoproteins. This enabled the determination of a 2.35 [A] resolution structure of the membrane-embedded Andes virus (ANDV) glycoprotein tetramer, as well as structures of dimers of tetramers and a complex with antibody ADI-65534. These structures reveal previously uncharacterized features of glycoprotein organization, stability, and pH-sensing. Immunization of mice with self-amplifying replicon RNA (repRNA) encoding ANDV-VLPs elicited high levels of glycoprotein-binding antibodies but equivalent titers of neutralizing antibodies compared to repRNA-encoded native ANDV glycoprotein complex. Collectively, these findings advance our understanding of hantavirus glycoprotein assemblies and their function, laying a foundation for structure-based vaccine design efforts.

microbiology↗

bioRxiv2025

Bat sarbecovirus WIV1-CoV bears an adaptive mutation that alters spike dynamics and enhances ACE2 binding

SARS-like betacoronaviruses (sarbecoviruses) endemic in bats pose a significant zoonotic threat to humans. Genetic pathways associated with spillover of bat sarbecoviruses into humans are incompletely understood. We previously showed that the WT spike of the rhinolophid bat coronavirus SHC014-CoV has poor entry activity and uncovered two distinct genetic pathways outside the receptor-binding domain (RBD) that increased spike opening, ACE2 binding, and cell entry. Herein, we show that the widely studied bat sarbecovirus WIV1-CoV is likely a cell culture-adapted variant of Rs3367-CoV, which was sequenced from the same population of rhinolophid bats as SHC014-CoV. We demonstrate that the acquisition of a single amino-acid substitution in the 630 loop of the S1 subunit was the key spike adaptation event during the successful isolation of WIV1-CoV, and that it enhances spike opening, virus-receptor recognition, and cell entry in much the same manner as the substitutions we previously identified in SHC014-CoV using a pseudotype system. The conformational constraints on both the SHC014-CoV and Rs3367-CoV spikes could be alleviated by pre-cleaving them with trypsin, suggesting that the spike-opening substitutions arose to circumvent the lack of S1-S2 cleavage. We propose that the locked-down nature of these spikes and their requirement for S1-S2 cleavage to engage ACE2 represent viral optimizations for a fecal-oral lifestyle and immune evasion in their natural hosts. These adaptations may be a broader property of bat sarbecoviruses than currently recognized. The acquisition of a polybasic furin cleavage site at the S1-S2 boundary is accepted as a key viral adaptation for SARS-CoV-2 emergence that overcame a host protease barrier to viral entry in the mammalian respiratory tract. Our results suggest alternative spillover scenarios in which spike-opening substitutions that promote virus-receptor binding and entry could precede, or even initially replace, substitutions that enhance spike cleavage in the zoonotic host. Author SummaryRecent epidemic-causing coronaviruses, including SARS-CoV-2, originated in bats. Large numbers of such viruses circulate in bats and pose clear and present risks to humans. However, our incomplete understanding of the variables that influence viral spillover into new hosts challenges attempts to stratify viruses by threat level. We showed previously that the entry spike of the bat coronavirus SHC014-CoV, closely related to SARS-CoV-1 and SARS-CoV-2, exists largely in a closed conformation that is incompatible with its binding to the viral receptor, ACE2, and that genetic changes in key control sequences open the spike and unlock its entry activity. Here, we extend these findings to a second bat coronavirus. We demonstrate that WIV1-CoV, a highly studied virus that was previously isolated from the same population of Chinese horseshoe bats, is in fact a variant of the bat coronavirus Rs3367-CoV that acquired a genetic change in the same hotspot region of the spike during its propagation in cell culture. Our findings support the idea that the closed spikes of at least some (and likely, many) bat coronaviruses, while exquisitely adapted to their natural milieu in the bat digestive system, suffer poor functional activity outside this milieu, imposing a barrier to viral spillover that must be overcome through viral adaptation. Further, we identify spike genetic changes that overcome this deficit and may have value as prognostic markers of zoonotic risk.

microbiology↗

bioRxiv2024

Epistasis between N-terminal and receptor-binding domains drives cell entry in a bat coronavirus spike

Understanding the zoonotic risks posed by bat coronaviruses (CoVs) is critical for pandemic preparedness. Herein, we generated recombinant vesicular stomatitis viruses (rVSVs) bearing spikes from divergent bat CoVs to investigate their cell entry mechanisms. Unexpectedly, the successful recovery of rVSVs bearing the spike from SHC014, a SARS-like bat CoV, was associated with the acquisition of a novel substitution in the S2 fusion peptide-proximal region (FPPR). This substitution enhanced viral entry in both VSV and coronavirus contexts by increasing the availability of the spike receptor-binding domain to recognize its cellular receptor, ACE2. A second substitution in the spike N-terminal domain, uncovered through forward-genetic selection, interacted epistatically with the FPPR substitution to synergistically enhance spike:ACE2 interaction and viral entry. Our findings identify genetic pathways for adaptation by bat CoVs during spillover and host-to-host transmission, fitness trade-offs inherent to these pathways, and potential Achilles heels that could be targeted with countermeasures.

microbiology↗

bioRxiv2024

A viral vaccine design harnessing prior BCG immunization confers protection against Ebola virus

Previous studies have demonstrated the efficacy and feasibility of an anti-viral vaccine strategy that takes advantage of pre-existing CD4+ helper T (Th) cells induced by Mycobacterium bovis bacille Calmette-Guerin (BCG) vaccination. This strategy uses immunization with recombinant fusion proteins comprised of a cell surface expressed viral antigen, such as a viral envelope glycoprotein, engineered to contain well-defined BCG Th cell epitopes, thus rapidly recruiting Th cells induced by prior BCG vaccination to provide intrastructural help to virus-specific B cells. In the current study, we show that Th cells induced by BCG were localized predominantly outside of germinal centers and promoted antibody class switching to isotypes characterized by strong Fc receptor interactions and effector functions. Furthermore, BCG vaccination also upregulated Fc{gamma}R expression to potentially maximize antibody-dependent effector activities. Using a mouse model of Ebola virus (EBOV) infection, this vaccine strategy provided sustained antibody levels with strong IgG2c bias and protection against lethal challenge. This general approach can be easily adapted to other viruses, and may be a rapid and effective method of immunization against emerging pandemics in populations that routinely receive BCG vaccination.

immunology↗

bioRxiv2024

Antibodies targeting Crimean-Congo hemorrhagic fever virus GP38 limit vascular leak and viral spread

Crimean-Congo hemorrhagic fever virus (CCHFV) is a priority pathogen transmitted by tick bites, with no vaccines or specific therapeutics approved to date. Severe disease manifestations include hemorrhage, endothelial dysfunction, and multiorgan failure. Infected cells secrete the viral glycoprotein GP38, whose extracellular function is presently unknown. GP38 is considered an important target for vaccine and therapeutic design as GP38-specific antibodies can protect against severe disease in animal models, albeit through a currently unknown mechanism of action. Here, we show that GP38 induces endothelial barrier dysfunction in vitro, and that CCHFV infection, and GP38 alone, can trigger vascular leak in a mouse model. Protective antibodies that recognize specific antigenic sites on GP38, but not a protective neutralizing antibody binding the structural protein Gc, potently inhibit endothelial hyperpermeability in vitro and vascular leak in vivo during CCHFV infection. This work uncovers a function of the secreted viral protein GP38 as a viral toxin in CCHFV pathogenesis and elucidates the mode of action of non-neutralizing GP38-specific antibodies.

microbiology↗

bioRxiv2024

Engineering, structure, and immunogenicity of a Crimean-Congo hemorrhagic fever virus pre-fusion heterotrimeric glycoprotein complex

Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne virus that can cause severe disease in humans with case fatality rates of 10-40%. Although structures of CCHFV glycoproteins GP38 and Gc have provided insights into viral entry and defined epitopes of neutralizing and protective antibodies, the structure of glycoprotein Gn and its interactions with GP38 and Gc have remained elusive. Here, we used structure-guided protein engineering to produce a stabilized GP38-Gn-Gc heterotrimeric glycoprotein complex (GP38-GnH-DS-Gc). A cryo-EM structure of this complex provides the molecular basis for GP38s association on the viral surface, reveals the structure of Gn, and demonstrates that GP38-Gn restrains the Gc fusion loops in the prefusion conformation, facilitated by an N-linked glycan attached to Gn. Immunization with GP38-GnH-DS-Gc conferred 40% protection against lethal IbAr10200 challenge in mice. These data define the architecture of a GP38-Gn-Gc protomer and provide a template for structure-guided vaccine antigen development.

microbiology↗

bioRxiv2024

Crimean-Congo Hemorrhagic Fever Survivors Elicit Protective Non-Neutralizing Antibodies that Target 11 Overlapping Regions on Viral Glycoprotein GP38

Crimean-Congo hemorrhagic fever virus can cause lethal disease in humans yet there are no approved medical countermeasures. Viral glycoprotein GP38, unique to Nairoviridae, is a target of protective antibodies, but extensive mapping of the human antibody response to GP38 has not been previously performed. Here, we isolated 188 GP38-specific antibodies from human survivors of infection. Competition experiments showed that these antibodies bind across five distinct antigenic sites, encompassing eleven overlapping regions. Additionally, we reveal structures of GP38 bound with nine of these antibodies targeting different antigenic sites. Although GP38-specific antibodies were non-neutralizing, several antibodies were found to have protection equal to or better than murine antibody 13G8 in two highly stringent rodent models of infection. Together, these data expand our understanding regarding this important viral protein and inform the development of broadly effective CCHFV antibody therapeutics.

immunology↗

bioRxiv2023

Simulation-Driven Design of Stabilized SARS-CoV-2 Spike S2 Immunogens

The full-length prefusion-stabilized SARS-CoV-2 spike (S) is the principal antigen of COVID-19 vaccines. Vaccine efficacy has been impacted by emerging variants of concern that accumulate most of the sequence modifications in the immunodominant S1 subunit. S2, in contrast, is the most evolutionarily conserved region of the spike and can elicit broadly neutralizing and protective antibodies. Yet, S2s usage as an alternative vaccine strategy is hampered by its general instability. Here, we use a simulation-driven approach to design S2-only immunogens stabilized in a closed prefusion conformation. Molecular simulations provide a mechanistic characterization of the S2 trimers opening, informing the design of tryptophan substitutions that impart kinetic and thermodynamic stabilization. Structural characterization via cryo-EM shows the molecular basis of S2 stabilization in the closed prefusion conformation. Informed by molecular simulations and corroborated by experiments, we report an engineered S2 immunogen that exhibits increased protein expression, superior thermostability, and preserved immunogenicity against sarbecoviruses.

biophysics↗

bioRxiv2023

Meta-omics analysis revealed structural and metabolic shifts of acidification communities after feeding with thermal hydrolysis pretreated food waste

Engineering environmental microbiomes enables carbon upcycling from organic solid waste into valuable products, such as volatile fatty acids (VFAs). This approach leverages the broad metabolic potential of natural communities to process highly heterogeneous substrates. However, solid waste conversion is often constrained by microbial hydrolysis, which limits the breakdown of particulate substrates into soluble compounds available for fermentation. Top-down engineering enhancements, such as thermal hydrolysis pretreatment (THP), can improve feedstock solubility but do not consistently increase total acid yields and may instead shift acid profiles. This highlights our limited understanding of microbiome responses to feedstock-level engineering controls. In this study, we applied genome-resolved multi-omics analysis to link VFA production performance with molecular mechanisms in a top-down engineered microbiome fed with thermally hydrolysed food waste. THP reduced total VFA yield (p = 0.003), accompanied by decreased Shannon diversity (p = 0.03), acid-production potential (DNA; log2FC = -1.3), and acid-production activity (mRNA; log2FC = -0.2). Propionate remained the dominant product with and without THP, consistent with the predominance of the Prevotella genus; however, THP selectively enriched two Prevotella species with elevated expression of ATP-generating steps in propionate production. THP also increased butyrate and valerate fractions (p < 0.001), together with upregulated reverse {beta}-oxidation for chain elongation driven by CAG-791 sp900320025 and Megasphaera sp000417505. Overall, our results provide performance- and molecular-level evidence that THP applied to complex feedstocks didnt increase total VFA yields, but reshaped microbiome structure and function, maintained propionate dominance, and promoted chain elongation.

molecular biology↗

bioRxiv2023

Fine-tuning spatial-temporal dynamics and surface receptor expression support plasma cell-intrinsic longevity

Durable serological memory following vaccination is critically dependent on the production and survival of long-lived plasma cells (LLPCs). Yet, the factors that control LLPC specification and survival remain poorly resolved. Using intra-vital two-photon imaging, we find that in contrast to most plasma cells in the bone marrow (BM), LLPCs are uniquely sessile and organized into clusters that are dependent on APRIL, an important survival factor. Using deep, bulk RNA sequencing, and surface protein flow-based phenotyping, we find that LLPCs express a unique transcriptome and phenotype compared to bulk PCs, fine tuning expression of key cell surface molecules, CD93, CD81, CXCR4, CD326, CD44 and CD48, important for adhesion and homing. Conditional deletion of Cxcr4 in PCs following immunization leads to rapid mobilization from the BM, reduced survival of antigen-specific PCs, and ultimately accelerated decay of antibody titer. In naive mice, the endogenous LLPCs BCR repertoire exhibits reduced diversity, reduced somatic mutations, and increased public clones and IgM isotypes, particularly in young mice, suggesting LLPC specification is non-random. As mice age, the BM PC compartment becomes enriched in LLPCs, which may outcompete and limit entry of new PCs into the LLPC niche and pool. HIGHLIGHTSO_LILLPCs have reduced motility and increased clustering in the BM C_LIO_LILLPCs accumulate in the BM PC pool, with mouse age C_LIO_LILLPCs have unique surfaceome, transcriptome, and BCR clonality C_LIO_LICXCR4 controls maintenance of PCs and antibody titers C_LI

immunology↗