bluuebunny/crossref_metadata_2025 huggingface dataset:
Soil carbon in the boreal region under climate and land use change
Authors: Vallotton Jeremiah D. , Unc Adrian
Published: September 2024

Carbon cycling in boreal regions is controlled naturally by fire disturbance, climate, hydrology, snowmelt, soil heterogeneity, acidity, low nitrogen and phosphorus availability, mycorrhizal distribution, plant cover, and cryoturbation/permafrost at the northern edge. It is primarily altered by human management via and following land clearance. Each factor interacts with others in complex ways, creating a system characterized by high carbon storage and shaped by natural and anthropogenic disturbance. This paper examines boreal research to answer the question: ‘what are the primary factors controlling boreal carbon cycling?’ Though climate change threatens boreal systems, they may yet be resilient given many natural feedback loops that resist massive carbon loss. Perhaps the greatest danger is land conversion, which causes permanent losses and drastic alteration of certain carbon pools. Accordingly, it might be argued that it would be overall better to implement policies that keep these lands as forests, including managed forests, rather than convert to agriculture. Conversely, farming of marginal boreal soils might be managed to enhance carbon storage while satisfying local food security needs. However, the impact of agriculture on soil carbon storage is yet to be effectively quantified and initial results offer inconsistent assessments, reflected in the as‐yet natural sciences data‐scarce policy development. Research targeting long‐term carbon cycling, land conversion practices, agroforestry, and communication between boreal scientists and other groups (climate scientists, policymakers, public, and farmers) must be addressed through creation of long‐term experiments.
Pre‐ and post‐attachment resistance response of popular western Kenya maize hybrids to parasitism by witchweed (Striga)
Authors: Odero Calvins Okoth , Kibet Willy , Oduor Richard Okoth , Dida Mathews Mito , Runo Steven
Published: September 2024

Striga hermonthica (Delile) Benth is a root parasitic weed that causes significant crop losses in cereals in the sub‐Saharan Africa. Host resistance is a sustainable management approach; however, Striga resistance in maize is rare. Furthermore, hybrids, preferred for high yield and other agronomic traits are more susceptible than local landraces. We sought to determine the responses of popular maize hybrids against Striga infection using in vitro germination and rhizotron assays. We screened 16 maize hybrids commonly cultivated in Kenya against two common Striga ecotypes (Kibos and Alupe) by measuring their (i) ability to induce the germination of S. hermonthica seeds in an in vitro system (pre‐attachment resistance) and (ii) ability to resist the attachment and establishment of effective parasitism (post‐attachment resistance). Results showed that two maize hybrids H614D and H629 exhibit both pre‐ and post‐attachment resistance comparable to a Striga resistant landrace KSTP'94 used in this study as a resistant check. Other hybrids displayed moderate Striga resistance; DK8031 (pre‐attachment resistance) and Duma43, phb30G19 and WH507 (post‐attachment resistance). Striga virulence, defined as aggressiveness of the parasite—measured by response to germination and host colonisation, was higher for the Kibos ecotype compared to the Alupe ecotype. However, the resistance pattern of maize genotypes remained consistent across the different Striga ecotypes. These results provide a basis for informed decisions on cultivation of various maize hybrids under Striga infestation in western Kenya.
Heat Transfer Rate Analysis of Hydrogen-Enriched Internal Combustion Engine Under Different Load Conditions
Authors: Shahid Muhammad Ihsan , Rao Anas , Farhan Muhammad , Liu Yongzheng , Fanhua Ma
Published: September 2024

A series of experiments were conducted on a compressed natural gas internal combustion engine across varying load conditions with 1200rpm, 20% hydrogen, different exhaust gas recirculation (EGR) and spark timing to capture in-cylinder pressure data and heat transfer rate. The authors compared six distinct models for heat transfer. These models systematically incorporated into a quasi-dimensional combustion model (QDCM) for hydrogen-compressed natural gas engine, accounting for diverse load conditions by using MATLAB code. Convective heat transfer models, including Woschni, Nusselt, Hohenberg, Han, Eichelberg, and Assanis correlations, were employed. Comparative analyses were undertaken to identify the most precise correlation for predicting engine in-cylinder pressure and heat transfer rates with experimental results across a broad spectrum of operational conditions. The Woschni model, as presented, is most suitable for the QDCM of the hydrogen-compressed natural gas fuel blend, particularly when exhaust gas recirculation is used in, as indicated by the proximity of Taylor length and turbulent intensity coefficients to 1, and the minimal absolute percentage error for indicated mean effective pressure. It’s also observed that the heat transfer rate increases by 13.29% by increasing from 75% to 100% load conditions. Heat transfer rate is increased by increasing the engine load 25%, 50%, 75% and 100% as 49.57 J/deg, 129.26 J/deg, 245.35 J/deg and 250.62 J/deg respectively with woschni model as depicted in figure 13. Heat transfer rate is different for different models with 100% load as 250.62 J/deg, 36.85 J/deg, 16.11 J/deg, 29.46 J/deg, 27.71 J/deg and 15.52 J/deg with Woschni, Nusselt, Hohenberg, han, Eichelberg and Assanis respectively.
Determining the Thermal Properties of Insulating Material Intended for Steering Plasma Beams
Authors: McMasters Robert L. , Keyser Ethan E. , Dinwiddie Ralph B.
Published: September 2024

In order to determine the thermal properties of three different types of insulating material intended for use in steering plasma beams in nuclear fusion reactors, flash diffusivity tests were conducted at the Oak Ridge National Laboratory. Using a thermal camera, the temperatures on the non-heated side of the samples were measured over time. Because of the irregular shape of the samples, the traditional flash diffusivity analysis would not yield accurate results. Therefore, three-dimensional numerical models were generated for each sample. The temperature histories that resulted from the flash diffusivity tests were then fitted by employing the three-dimensional models generated using ANSYS. Various models involving convective and radiative heat losses from the sample surfaces were compared, including a model accounting for penetration of the flash beyond the surface of the semi-porous materials. A significant improvement in the standard deviation of the residuals resulted from the application of the models which accounted for convection and flash penetration. The differences in the resulting thermal diffusivity values ranged from 17 percent to 46 percent from the values obtained using the traditional Parker analysis method for the three types of materials. Plots of the residuals are included to show the improvements gained by the use of the higher-order models.
Modeling and Simulation of Aerodynamic Nosecone Ablation
Authors: Mehmedagic Igbal , Thangam Siva
Published: September 2024

This work deals with the modeling and simulation of ablation in aerodynamic heating of a highspeed projectile. Generic projectiles with plastic hollow nosecones (for housing the radar system) in supersonic flight are considered for the purpose of developing efficient designs for high-speed projectiles. Computations are performed using the shear-stress transport (SST) k-omega model that is widely used for many aerodynamic applications. The time-averaged equations of motion and energy are solved using the modeled form of transport equations for the turbulence kinetic energy and specific turbulent dissipation rate with an efficient finite-volume algorithm. The possible melting and phase change during flight conditions are modeled in the context projectile design. Modeling liquidized material flow by ablation along the solid surface of the supersonic projectile uses a multiphase treatment of the plastic nosecone melt material under influence of the high velocity gas. The model considers stratified/free-surface flow in which two immiscible fluids are separated by a clearly defined interface. Computational findings show that a commonly used plastic nosecone material would ablate during high-speed flights. The magnitude of ablation, changes to the shape and resultant aerodynamic penalty for the projectile are quantified and discussed.
Gas Species Separation of the Vortex Tube With Six Nozzle-Driven Vortex
Authors: Trinh Ngoc Van , Nghiem Quan Thien Phan , Kim Younghyeon , Pae Wansung , Yu Sangseok
Published: September 2024

Emissions of greenhouse gases are rising due to resource depletion caused by fossil fuel usage. While these novel and renewable technologies are being investigated, Carbon capture and storage (CCS) technology is being created to lower carbon dioxide. CCS technology allows for capturing, transporting, and storing greenhouse gases produced by burning fossil fuels. Vortex tubes are a contender for CO2 separation via cryogenics with flow vortex. This study is designed to investigate the basic features of vortex tubes for gas separation by flow characteristics.

The key factors considered were the CO2 mass fraction and mixed gas pressure. Using a six-nozzle generator, these metrics verified the temperature and CO2 separation in the vortex tube. When the pressure of the mixture gas was at 3 bar at the horizontal arrangement for the six-nozzle generator, the temperature separation also increased simultaneously. With a cold flow ratio at 3 pressure, the temperature and CO2 concentration peaked. Additionally, when the system was running at 3 bar, there was a peak CO2 separation at the cold outlet. As a result, the separation of various pressures was evaluated at 20% of the CO2 mass fraction. For the six-nozzle generator with a 3-bar inlet pressure, the CO2 separation performed best at the cold outlet at a cold mass flow ratio of 0.3.
Development of the Temperature Profile Optimization Method for Thermal Conditioning of Large Bodies
Authors: Sezmen Ramazan Aykut
Published: September 2024

The performance of various systems, such as electronic cards, avionics, and propulsion systems, is highly depend on thermal effects and the system’s temperature. As the operational temperatures of these systems undergo changes throughout their life cycles, the characterization of temperature-dependent performances necessitates different tests, including performance tests under controlled temperature conditions. Obtaining desired temperature distribution for smaller components, such as avionics or electronic components can be achieved within several hours or even minutes inside the industrial furnaces. Conversely, temperature conditioning for larger structures, such as propulsion systems, may require several days or even weeks. The process of temperature conditioning, conducted under a constant furnace temperature is a time-consuming operation when it is considered in terms of project workflow. In an effort to decrease the duration of these last long and inefficient constant furnace temperature processes, a time optimization study is proposed which is aiming to obtain varying furnace temperature profile to acquired needed temperature distribution throughout these large structures. Three-dimensional, two-dimensional, and axisymmetric finite element models are established for a comprehensive examination of a large-scale system by considering the nature of the problem. Outcomes from these distinct finite element models leads to the determination that the axisymmetric model is most suited for the ensuing optimization study. The constraints and the objective of the optimization are clearly defined. An iterative procedure is conducted between the optimization tool and heat transfer analysis solver. As a result of the study, required time for the temperature conditioning is decreased by almost 50% by using the obtained varying furnace temperature profiles instead of using constant furnace temperature. It is noteworthy that diverse constraints and objectives may be implemented within the developed model to accommodate case-specific exigencies.
Enhancing Thermal Performance in a PCM Heatsink Assembly By Incorporating Fins and Copper Oxide Nanoparticles
Authors: Jones Austin , Darabi Jeff
Published: September 2024

Phase Change Materials (PCMs) have become a common addition to heatsinks to help control the temperature of electronic components during operation. PCM heatsinks utilize the latent heat of materials like paraffin wax to mitigate the rising temperature of electronic components as the PCM undergoes melting. This allows electronics to operate for extended periods without needing to shut down before they reach their maximum operating temperature. However, these materials typically exhibit low thermal conductivity. To enhance the overall thermal conductivity of the system, fins can be added to the assembly. Another approach involves incorporating metallic nanoparticles into the pure wax. Both methods aim to strike a balance between effective thermal conductivity and available latent heat. This paper presents experimental and numerical results from a heatsink assembly with two different fin geometries. A constant heat flux is applied to the bottom of the assembly. The thermal effectiveness of this assembly was examined both with and without the addition of pure paraffin wax. Additionally, copper oxide (CuO) nanoparticles were introduced to the wax and their effects were studied. The experimental data collected from the wax with added CuO nanoparticles were used to validate a finite element model created using ANSYS Fluent. The study also investigates the impact of removing the fins and adding copper oxide nanoparticles on the thermal effectiveness of the heat sink assembly. The heat source interface temperature was lowered by 8°C when fins were added, but this resulted in a reduction in latent heat storage of the assembly. The addition of CuO nanoparticles without the use of fins was found to reduce the operating temperature of the heat source interface by 5°C.
Convergent and Divergent Shell and Tube TES Partially Filled With PCM and Metal Foam
Authors: Buonomo Bernardo , Golia Maria Rita , Manca Oronzio , Nardini Sergio , Plomitallo Renato Elpidio
Published: September 2024

The ongoing European energy crisis and the imperative to reduce carbon emissions have driven the exploration of energy storage systems. This research focuses on latent heat thermal energy storage systems (LTES). LTESs, utilizing phase change materials (PCMs) combined with metal foams, offer advantages over sensible thermal energy storage systems. Metal foams enhance the thermal conductivity of PCMs, creating a system with a fast-absorbing energy zone defined by low thermal resistance. The study investigates a vertical shell and tube geometry with a non-constant internal tube section, filled by a combination of PCM embedded in a metal foam and PCM alone. A variable is introduced to define the partial filling ratio. The Brinkman-Forchheimer-extended Darcy model and enthalpy-porosity theory are employed to analyze heat transfer and phase change processes. Ansys-Fluent provides numerical solutions. Examining natural convection impact on heat transfer, the study explores the effects of the inclination angle variation inside the shell and tube. Numerical simulations report melting time, average temperature, and specific energy storage rate. Results demonstrate enhanced heat transfer in LTES with metal foam and PCM especially in converging tube cases. The findings demonstrate that the convergent configuration with s = 1/2, in the case with an inclination angle of 10°, achieves maximum stored energy 50% faster than the identical configuration without a section variation.
Design of Test Bench for the Analysis of Efficiency and Effectiveness of Extended Surfaces for Educational Purpose
Authors: Jervis Freddy X. , Cando Gabriela , Moreira Daniel , Moreira Cesar , Zabala Gonzalo
Published: September 2024

Hands-on experience such as laboratory practices can be beneficial as students gain a better perspective of the theory presented in class. However, acquisition of these types of equipment can be expensive for institutions in developing countries. The heat transfer phenomena are an imperative topic to understand for undergraduate engineering students in the Mechanical Engineering curriculum as well as other engineering disciplines. For these reasons, a test bench design and experimentation project for heat transfer phenomena is being carried out. In this study, the design of a test bench for the analysis of extended surfaces under varying convection conditions is proposed. The test bench proposed uses locally available materials as well as an open-source interface (Arduino-based). The test bench offers the ability to easily mount and dismount different fin models and arrays. An experimental procedure is developed over three types of fins: straight rectangular fins, rectangular pin fins, and rectangular fin array under natural and forced convection. The design also contemplates a flow velocity controller that will allow the study of forced convection under steady state and transient conditions. The test bench follows national safety standards so that students can freely manipulate the different arrays under laboratory technician supervision. A cost analysis between importing the equipment to the assembly with local suppliers was also conducted. The design is expected to contribute to engineering programs providing a cost-effective solution for a hands-on laboratory experience.
Exergy Analysis on an Innovative Vapor-Compression Ejector Heat Pump Water Heater
Authors: Spitzenberger Jeremy , Ma Hongbin
Published: September 2024

Ejector-driven systems are thermally operated and capable of utilizing excess thermal energy to aid in boosting the overall efficiency of the system. Traditionally, ejectors have been implemented into systems for cooling purposes, however, recent studies have demonstrated their potential to increase the efficiency in heat pump systems. In this study a theoretical model is developed, its performance is modeled, and an exergy analysis is performed on an innovative vapor compression ejector heat pump (VCEHP) for the purposes of water heating. The analysis is performed assuming the evaporator temperature of 6.5 °C, and a low temperature evaporator (LTE) temperature of 20 °C, for condenser outlet temperature range of 40–60 °C, with R134a acting as the working fluid. The ejector model incorporated was compared to previous experimental studies utilizing R134a, and the predicted coefficient of performance (COP) and back pressures to within 4.01%. The results of the VCEHP are compared to that of a traditional vapor compression heat pump (VCHP) water heater. The theoretical results have shown that the incorporation of the ejector can lead to a 22.78% increase in the system heating COP.
Pyrolysis and Heat Release Rate Predictions of Heated Solid Specimens in the OSU Apparatus
Authors: Farouk Bakhtier , Cappello Garrett , Burns Michael
Published: September 2024

A mathematical model is being developed to describe the pyrolysis (degradation of solid materials exposed to external heat) and heat release rate of aircraft cabin materials in the OSU (Ohio State University) apparatus. The OSU apparatus is used to expose aircraft interior cabin materials to an incident radiant heat flux of 35 kW/m2. This test determines if the material complies with FAR 25.853 requirements. The OSU heat release rate apparatus is a Federal Aviation Administration (FAA) designated combustion test instrument for testing the heat release rate of aircraft cabin materials. The results of the research completed include transient solutions of the flow-field variables (velocity, temperature, and pressure) within the fluid domain of the OSU apparatus using ANSYS FLUENT. A model of the basic overall geometry with a surface-to-surface radiation model was also developed. For the ongoing pyrolysis simulations of the specimens, a reduced computational domain has been considered that will include the effect of the radiant heaters (along a boundary of the proposed domain (Figure 6), the specimen holder within the OSU apparatus bounding walls.
Transport and Flow Characteristics of Graphene-Doped Nanofluids at Moderate Temperatures in Double-Pipe Heat Exchangers
Authors: Gaudio Philip J. , Skelly Jerome M. , Yavuzturk Cy C. , Chiasson Andrew D. , Johnson Drew W.
Published: September 2024

The objective of this study is to assess the thermal and hydraulic characteristics of water-based graphene-doped nanofluids experimentally as well as analytically in counter-flow concentric tube heat exchangers for the purpose of evaluating their viability as compared to pure water and other water-based solutions such as methanol and propylene glycol. A concentric pipe system (copper-PVC) was configured such that graphene-doped primary fluid flowed in the inner tube (copper), while a secondary flow of de-ionized water was introduced in the annulus. The nanofluids in volume fractions of 0.001, 0.005, 0.01, and 0.015 of graphene nanoplatelets were tested using a base fluid of deionized water at varying temperatures of 30°C, 45°C, 60°C, and 75°C, with the secondary fluid set to a constant temperature of 4°C lower. The increase in the volume fraction of the graphene nanoplatelets showed an appreciable corresponding increase in the thermal conductivity of the nanofluid. However, the flow regime was adversely affected as it transitioned from turbulent to laminar owing to increased viscosity of the nanofluid. This flow transition resulted in a corresponding decrease in the convective heat transfer coefficient. The research results have implications on the assessment and understanding of heat transfer characteristics of graphene based nanofluids in various heat transfer processes. The results show that in the turbulent flow regime the incremental improvements in the thermal conductivity of the nanofluid are far outweighed by disproportionally large increases in pumping power requirements. However, it is observed that appropriately doped graphene nanofluids appear to have advantages over propylene glycol in the laminar flow regime and may be considered as a replacement.
Speech intelligibility prediction based on a physiological model of the human ear and a hierarchical spiking neural network
Authors: Kou Yinxin , Liu Houguang , Wang Jie , Guo Weiwei , Yang Jianhua , Yang Shanguo
Published: September 2024

A speech intelligibility (SI) prediction model is proposed that includes an auditory preprocessing component based on the physiological anatomy and activity of the human ear, a hierarchical spiking neural network, and a decision back-end processing based on correlation analysis. The auditory preprocessing component effectively captures advanced physiological details of the auditory system, such as retrograde traveling waves, longitudinal coupling, and cochlear nonlinearity. The ability of the model to predict data from normal-hearing listeners under various additive noise conditions was considered. The predictions closely matched the experimental test data under all conditions. Furthermore, we developed a lumped mass model of a McGee stainless-steel piston with the middle-ear to study the recovery of individuals with otosclerosis. We show that the proposed SI model accurately simulates the effect of middle-ear intervention on SI. Consequently, the model establishes a model-based relationship between objective measures of human ear damage, like distortion product otoacoustic emissions, and speech perception. Moreover, the SI model can serve as a robust tool for optimizing parameters and for preoperative assessment of artificial stimuli, providing a valuable reference for clinical treatments of conductive hearing loss.
Novel cellular functions of Cys
2
-His
2
zinc finger proteins in anthracnose development and dissemination on pepper fruits by
Colletotrichum scovillei
Authors: Fu Teng , Song Yong-Won , Gao Guoyang , Kim Kyoung Su
Published: September 2024

Colletotrichum
species are notorious for causing anthracnose on many fruits, leading to significant economic losses worldwide. As a model, we functionally characterized cys2-his2 (C
2
H
2
) zinc finger proteins (CsCZFs) in
Colletotrichum scovillei
, a major causal agent of pepper fruit anthracnose in many countries. In all, 62 CsCZFs were identified by
in silico
genomic analysis. Twelve were selected based on their expression profiles to generate targeted deletion mutants for functional investigation.
ΔCsczf1
markedly reduced conidiation and constitutive expression of
CsCZF1
partially recovered conidiation in an asexual reproduction-defective mutant,
ΔCshox2
. Deletion of
CsCZF12
, orthologous to the calcineurin-responsive transcription factor
Crz1
, impaired autophagy in
C. scovillei. ΔCsczf9
was defective in surface recognition, appressorium formation, and suppression of host defenses.
CsCZF9
was identified as an essential and novel regulator under the control of the mitogen-activated protein kinase (CsPMK1) in an early step of appressorium development in
C. scovillei
. This study provides novel insights into
CsCZF
-mediated regulation of differentiation and pathogenicity in
C. scovillei
, contributing to understanding the regulatory mechanisms governing fruit anthracnose epidemics.

IMPORTANCE

The phytopathogenic fungus
Colletotrichum scovillei
is known to cause serious anthracnose on chili pepper. However, the molecular mechanism underlying anthracnose caused by this fungus remains largely unknown. Here, we systematically analyzed the functional roles of cys2-his2 zinc finger proteins (CsCZFs) in the dissemination and pathogenic development of this fungus. Our results showed that CsCZF1 plays an important role in conidiation and constitutive expression of CsCZF1 restored conidiation in an asexual reproduction-defective mutant,
ΔCshox2
. The CsCZF9, a novel target of the mitogen-activated protein kinase (CsPMK1), is essential for surface recognition to allow appressorium formation and suppression of host defenses in
C. scovillei
. The CsCZF12, orthologous to the calcineurin-responsive transcription factor Crz1, is involved in the autophagy of
C. scovillei
. Our findings reveal a comprehensive mechanism underlying CsCZF-mediated regulation of differentiation and pathogenicity of
C. scovillei
, which contributes to the understanding of fruit anthracnose epidemics and the development of novel strategies for disease management.
Phage-antibiotic synergy suppresses resistance emergence of
Klebsiella pneumoniae
by altering the evolutionary fitness
Authors: Qin Kunhao , Shi Xing , Yang Kai , Xu Qiuqing , Wang Fuxing , Chen Senxiong , Xu Tingting , Liu Jinquan , Wen Wangrong , Chen Rongchang , Liu Zheng , Cui Li , Zhou Kai
Published: September 2024

Phage-antibiotic synergy (PAS) represents a superior treatment strategy for pathogen infections with less probability of resistance development. Here, we aim to understand the molecular mechanism by which PAS suppresses resistance in terms of population evolution. A novel hypervirulent
Klebsiella pneumoniae
(KP) phage H5 was genetically and structurally characterized. The combination of H5 and ceftazidime (CAZ) showed a robust synergistic effect in suppressing resistance emergence. Single-cell Raman analysis showed that the phage-CAZ combination suppressed bacterial metabolic activities, contrasting with the upregulation observed with phage alone. The altered population evolutionary trajectory was found to be responsible for the contrasting metabolic activities under different selective pressures, resulting in pleiotropic effects. A pre-existing
wcaJ
point mutation (

wcaJ
G949A

) was exclusively selected by H5, conferring a fitness advantage and up-regulated activity of carbohydrate metabolism, but also causing a trade-off between phage resistance and collateral sensitivity to CAZ. The
wcaJ
point mutation was counter-selected by H5-CAZ, inducing various mutations in
galU
that imposed evolutionary disadvantages with higher fitness costs, and suppressed carbohydrate metabolic activity. H5 and H5-CAZ treatments resulted in opposite effects on the transcriptional activity of the phosphotransferase system and the ascorbate and aldarate metabolism pathway, suggesting potential targets for phage resistance suppression. Our study reveals a novel mechanism of resistance suppression by PAS, highlighting how the complexity of bacterial adaptation to selective pressures drives treatment outcomes.

IMPORTANCE

Phage-antibiotic synergy (PAS) has been recently proposed as a superior strategy for the treatment of multidrug-resistant pathogens to effectively reduce bacterial load and slow down both phage and antibiotic resistance. However, the underlying mechanisms of resistance suppression by PAS have been poorly and rarely been studied. In this study, we tried to understand how PAS suppresses the emergence of resistance using a hypervirulent
Klebsiella pneumoniae
(KP) strain and a novel phage H5 in combination with ceftazidime (CAZ) as a model. Our study reveals a novel mechanism by which PAS drives altered evolutionary trajectory of bacterial populations, leading to suppressed emergence of resistance. The findings advance our understanding of how PAS suppresses the emergence of resistance, and are imperative for optimizing the efficacy of phage-antibiotic therapy to further improve clinical outcomes.
Diverse BCR usage and T cell activation induced by different COVID-19 sequential vaccinations
Authors: Wang Junxiang , Li Kaiyi , Wang Yuan , Lin Zhengfang , Li Weidong , Cao Jinpeng , Mei Xinyue , Wei Rui , Yang Jinglu , Zhai Xiaobing , Huang Deyi , Zhou Kaiwen , Liang Xinyue , Wang Zhongfang
Published: September 2024

Limited knowledge is available on the differences in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) specific antibody breadth and T cell differentiation among different COVID-19 sequential vaccination strategies. In this study, we compared the immunogenicity of the third different dose of COVID-19 vaccines, such as mRNA (I-I-M), adenoviral vector (I-I-A), and recombinant protein (I-I-R) vaccines, in terms of the magnitude and breadth of antibody response and differentiation of SARS-CoV-2-specific T and B cells. These studies were performed in the same clinical trial, and the samples were assessed in the same laboratory. IGHV1-69, IGHV3-9, and IGHV4-34 were the dominant B cell receptor (BCR) usages of the I-I-M, I-I-A, and I-I-R groups, respectively; the RBD
+
B cell activation capacities were comparable. Additionally, the I-I-R group was characterized by higher numbers of regulatory T cells, circulating T follicular helper cells (cTFH) – cTFH1 (CXRC3
+
CCR6
-
), cTFH1-17 (CXRC3
+
CCR6
+
), cTFH17 (CXRC3
-
CCR6
+
), and cTFH-CM (CD45RA
-
CCR7
+
), and lower SMNE
+
T cell proliferative capacity than the other two groups, whereas I-I-A showed a higher proportion and number of virus-specific CD4
+
T cells than I-I-R, as determined in ex vivo experiments. Our data confirmed different SARS-CoV-2-specific antibody profiles among the three different vaccination strategies and also provided insights regarding BCR usage and T/B cell activation and differentiation, which will guide a better selection of vaccination strategies in the future.

IMPORTANCE

Using the same laboratory test to avoid unnecessary interference due to cohort ethnicity, and experimental and statistical errors, we have compared the T/B cell immune response in the same cohort sequential vaccinated by different types of COVID-19 vaccine. We found that different sequential vaccinations can induce different dominant BCR usage with no significant neutralizing titers and RBD
+
B-cell phenotype. Recombinant protein vaccine can induce higher numbers of regulatory T cells, circulating TFH (CTFH)1, CTFH17, and CTFH-CM, and lower SMNE
+
T-cell proliferative capacity than the other two groups, whereas I-I-A showed higher proportion and number of virus-specific CD4
+
T cells than I-I-R. Overall, our study provides a deep insight about the source of differences in immune protection of different types of COVID-19 vaccines, which further improves our understanding of the mechanisms underlying the immune response to SARS-CoV-2.
Cell shape and division septa positioning in filamentous
Streptomyces
require a functional cell wall glycopolymer ligase CglA
Authors: Bhowmick Sukanya , Viveros Ruth P. , Latoscha Andreas , Commichau Fabian M. , Wrede Christoph , Al-Bassam Mahmoud M. , Tschowri Natalia
Published: September 2024

The cell wall of monoderm bacteria consists of peptidoglycan and glycopolymers in roughly equal proportions and is crucial for cellular integrity, cell shape, and bacterial vitality. Despite the immense value of
Streptomyces
in biotechnology and medicine as antibiotic producers, we know very little about their cell wall biogenesis, composition, and functions. Here, we have identified the LCP-LytR_C domain protein CglA (Vnz_13690) as a key glycopolymer ligase
,
which specifically localizes in zones of cell wall biosynthesis in
S. venezuelae
. Reduced amount of glycopolymers in the
cglA
mutant results in enlarged vegetative hyphae and failures in FtsZ-rings formation and positioning. Consequently, division septa are misplaced leading to the formation of aberrant cell compartments, misshaped spores, and reduced cell vitality. In addition, we report our discovery that c-di-AMP signaling and decoration of the cell wall with glycopolymers are physiologically linked in
Streptomyces
since the deletion of
cglA
restores growth of the
S. venezuelae disA
mutant at high salt. Altogether, we have identified and characterized CglA as a novel component of cell wall biogenesis in
Streptomyces
, which is required for cell shape maintenance and cellular vitality in filamentous, multicellular bacteria.

IMPORTANCE

Streptomyces
are our key producers of antibitiotics and other bioactive molecules and are, therefore, of high value for medicine and biotechnology. They proliferate by apical extension and branching of hyphae and undergo complex cell differentiation from filaments to spores during their life cycle. For both, growth and sporulation, coordinated cell wall biogenesis is crucial. However, our knowledge about cell wall biosynthesis, functions, and architecture in
Streptomyces
and in other Actinomycetota is still very limited. Here, we identify CglA as the key enzyme needed for the attachment of glycopolymers to the cell wall of
S. venezuelae
. We demonstrate that defects in the cell wall glycopolymer content result in loss of cell shape in these filamentous bacteria and show that division-competent FtsZ-rings cannot assemble properly and fail to be positioned correctly. As a consequence, cell septa placement is disturbed leading to the formation of misshaped spores with reduced viability.
Vaccine-induced NA immunity decreases viral shedding, but does not disrupt chains of airborne transmission for the 2009 pandemic H1N1 virus in ferrets
Authors: Septer K. M. , Heinly T. A. , Sim D. G. , Patel D. R. , Roder A. E. , Wang W. , Chung M. , Johnson K. E. E. , Ghedin E. , Sutton T. C.
Published: September 2024

Split-virion-inactivated influenza vaccines are formulated based on viral hemagglutinin content. These vaccines also contain the viral neuraminidase (NA) protein, but NA content is not standardized and varies between manufacturers. In clinical studies and animal models, antibodies directed toward NA reduced disease severity and viral load; however, the impact of vaccine-induced NA immunity on airborne transmission of influenza A viruses is not well characterized. Therefore, we evaluated if vaccination against NA could disrupt chains of airborne transmission for the 2009 pandemic H1N1 virus in ferrets. Immunologically naïve donor ferrets were infected with the 2009 pandemic H1N1 virus and then paired in transmission cages with mock- or NA-vaccinated respiratory contacts. The mock- and NA-vaccinated animals were then monitored daily for infection, and once infected, these animals were paired with a naive secondary respiratory contact. In these studies, all mock- and NA-vaccinated animals became infected; however, NA-vaccinated animals shed significantly less virus for fewer days relative to mock-vaccinated animals. For the secondary contacts, 6/6 and 5/6 animals became infected after exposure to mock- and NA-vaccinated animals, respectively. To determine if vaccine-induced immune pressure selected for escape variants, we sequenced viruses recovered from ferrets. No mutations in NA became enriched during transmission. These findings indicate that despite reducing viral load, vaccine-induced NA immunity does not prevent infection during continuous airborne exposure and subsequent onward airborne transmission of the 2009 pandemic H1N1 virus.

IMPORTANCE

In humans and animal models, immunity against neuraminidase (NA) reduces disease severity and viral replication during influenza infection. However, we have a limited understanding of the impact of NA immunity on viral transmission. Using chains of airborne transmission in ferrets as a strategy to simulate a more natural route of infection, we assessed if vaccine-induced NA immunity could disrupt transmission of the 2009 pandemic H1N1 virus. The 2009 pandemic H1N1 virus transmitted efficiently through chains of transmission in the presence of NA immunity, but NA-vaccinated animals shed significantly less virus and had accelerated viral clearance. To determine if immune pressure led to the generation of escape variants, viruses in ferret nasal wash samples were sequenced, and no mutations in NA were identified. These findings demonstrate that vaccine-induced NA immunity is not sufficient to prevent infection via airborne exposure and onward airborne transmission of the 2009 pandemic H1N1 virus.
A plasmid-mediated type III secretion system associated with invasiveness and diarrheagenicity of
Providencia rustigianii
Authors: Hassan Jayedul , Hinenoya Atsushi , Hatanaka Noritoshi , Awasthi Sharda Prasad , Manjunath Goutham Belagula , Rahman Nahid , Yamate Jyoji , Nakamura Shota , Motooka Daisuke , Nagita Akira , Faruque Shah M. , Yamasaki Shinji
Published: September 2024

We have recently described a clinical isolate of
Providencia rustigianii
strain JH-1 carrying the genes for cytolethal distending toxin (CDT) in a conjugative plasmid. A
cdtB
mutant of strain JH-1, which lost CDT activity, was still found to retain invasiveness and diarrheagenicity. The strain was subjected to phenotypic and genetic analyses including whole genome sequencing (WGS) to explore the genetic determinants of the observed invasiveness and diarrheagenic properties. Analysis and annotation of WGS data revealed the presence of two distinct type III secretion systems (T3SS) in strain JH-1, one of which was located on the chromosome designated as cT3SS (3,992,833 bp) and the other on a mega-plasmid designated as pT3SS (168,819 bp). Comparative genomic analysis revealed that cT3SS is generally conserved in
Providencia
spp. but pT3SS was limited to a subset of
Providencia
spp., carrying
cdt
genes. Strain JH-1 was found to invade HeLa cells and induce fluid accumulation with characteristic pathological lesions in rabbit ileal loops. Remarkably, these phenomena were associated with the pT3SS but not cT3SS. The plasmid could be transferred by conjugation from strain JH-1 to other strains of
P. rustigianii
,
Providencia rettgeri
, and
Escherichia coli
with concomitant transfer of these virulence properties. This is the first report of a functional and mobile T3SS in
P. rustigianii
and its association with invasiveness and diarrheagenicity of this bacterium. These data suggest that
P. rustigianii
and other CDT-producing
Providencia
strains might carry T3SS and exert their diarrheagenic effect by exploiting the T3SS nano-machinery.

IMPORTANCE

The precise mechanism of virulence of
Providencia rustigianii
is unclear, although some strains produce cytolethal distending toxin as a putative virulence factor. We have detected the presence of a type III secretion system (T3SS) for the first time on a plasmid in a
P. rustigianii
strain. Plasmid-mediated T3SS seems to be directly involved in virulence of
P. rustigianii
and may serve as a means of horizontal transfer of T3SS genes. Our results may have implication in understanding the mechanism of emergence of new pathogenic strains of
P. rustigianii
.
Draft genome sequence of
Taiwanofungus gaoligongensis
strain YAF008 isolated from Gaoligong Mountain
Authors: Bao Yuanduo , Yuan Xiaolong , Chen Zihong , Yang Yuming , Zheng Yuan , Wang Yi
Published: September 2024

The draft genome sequence of
Taiwanofungus gaoligongensis
YAF008 was reported. The genome size of
T. gaoligongensis
YAF008 was 34.7M bp with 50.72% GC content. The genome resource will support future research into potential secondary metabolite diversity of this fungus.
Draft genome sequence of a
spa
non-typeable
Staphylococcus aureus
USA300 isolate causing complicated bacteremia
Authors: Felton Emily A. , Diaz Vera Jesus , Katzman Ju Hee , Daniels Sara , Lima Amorce , Becker Deanna , Silbert Suzane , Kim Kami , Shaw Lindsey N.
Published: September 2024

Spa-typing is a major genetic tool used to distinguish between
Staphylococcus aureus
strains. Interestingly, although rare, ~1%–2 of isolates are considered Spa-non-typeable . Herein, we present the draft genome sequence of just such a strain,
S. aureus
TGH1097, a USA300 isolate from a complex bacteremia infection.
Complete genome sequence of
Bacillus pumilus
LBUM494, a plant-beneficial strain isolated from the rhizosphere of a strawberry plant
Authors: Biessy Adrien , Filion Martin
Published: September 2024

Here, we present the complete genome sequence of
Bacillus pumilus
LBUM494, a plant-beneficial bacterial strain isolated from the rhizosphere of a strawberry plant grown in an agricultural field located in Bouctouche, New Brunswick, Canada. The genome size is 3,699,913 bp with a GC content of 41.7%.
Potential of training of anti-
Staphylococcus aureus
therapeutic phages against
Staphylococcus epidermidis
multidrug-resistant isolates is restricted by inter- and intra-sequence type specificity
Authors: Kolenda Camille , Bonhomme Mélanie , Medina Mathieu , Pouilly Mateo , Rousseau Clara , Troesch Emma , Martins-Simoes Patricia , Stegger Marc , Verhoeven Paul O. , Laumay Floriane , Laurent Frédéric
Published: September 2024

Phage therapy appears to be a promising approach to tackle multidrug-resistant bacteria, including staphylococci. However, most anti-staphylococcal phages have been characterized in
Staphylococcus aureus
, while a limited number of studies investigated phage activity against
S. epidermidis
. We studied the potential of phage training to extend the host range of two types of anti-
S
.
aureus
phages against
S. epidermidis
isolates. The Appelmans protocol was applied to a mixture of
Kayvirus
and a mixture of
Silviavirus
phages repeatedly exposed to seven
S
.
epidermidis
strains representative of nosocomial-associated sequence types (ST), including the world-wide disseminated ST2. We observed increased activity only for the
Kayvirus
mixture against two of these strains (ST2 or ST35). Phage subpopulations isolated from the training mixture using these two strains (five/strain) exhibited different evolved phenotypes, active only against their isolation strain or strains of the same ST. Of note, 16/47 ST2 strains were susceptible to one of the groups of trained phages. A comparative genomic analysis of ancestral and trained phage genomes, conducted to identify potential bacterial determinants of such specific activity, found numerous recombination events between two of the three ancestors. However, a small number of trained phage genes had nucleotide sequence modifications impacting the corresponding protein compared to ancestral phages, two to four of them per phage genome being specific of each group of phage subpopulations exhibiting different host range. The results suggest that anti-
S
.
aureus
phages can be adapted to
S. epidermidis
isolates but with inter- and intra-ST specificity.

Importance

S. epidermidis
is increasingly recognized as a threat for public health. Its clinical importance is notably related to multidrug resistance. Phage therapy is one of the most promising alternative therapeutic strategies to antibiotics. Nonetheless, only very few phages active against this bacterial species have been described. In the present study, we showed that phage training can be used to extend the host range of polyvalent
Kayvirus
phages within the
Staphylococcus
genera to include
S. epidermidis
species. In the context of rapid development of phage therapy,
in vitro
forced adaptation of previously characterized phages could be an appealing alternative to fastidious repeated isolation of new phages to improve the therapeutic potential of a phage collection.
Flagellum-deficient
Pseudomonas aeruginosa
is more virulent than non-motile but flagellated mutants in a cystic fibrosis mouse model
Authors: Moustafa Dina A. , Fantone Kayla M. , Tucker Samantha L. , McCarty Nael A. , Stecenko Arlene A. , Goldberg Joanna B. , Rada Balázs
Published: September 2024

Loss of the flagellum marks the pathoadaptation of
Pseudomonas aeruginosa
to the cystic fibrosis (CF) airway environment during lung disease. Losing the flagellum is advantageous to the bacterium as the flagellum can be recognized by immune cells. The primary purpose of the flagellum is, however, to provide motility to the bacterium. Our goal was to determine whether the loss of flagellar motility or the loss of flagellum expression contributes to
P. aeruginosa
lung infection in CF. To address this, wild-type and gut-corrected FABP-human cystic fibrosis transmembrane conductance regulator (hCFTR) mice deficient in the murine
Cftr
gene were infected intratracheally with lethal doses of wild-type or flagellum-deficient
P. aeruginosa
. While there was no significant difference in the survival of wild-type mice after infection with either of the bacterial strains, a significantly higher mortality was observed in FABP-hCFTR mice infected with flagellum-deficient
P. aeruginosa
, compared to mice infected with their flagellated counterparts. When FABP-hCFTR mice were infected with isogenic, motility-deficient flagellated mutants, animal survival and lung bacterial titers were similar to those observed in mice infected with the wild-type bacterium. Airway levels of neutrophils and the amount neutrophil elastase were similar in mice infected with either the wild-type bacteria or the flagellum-deficient
P. aeruginosa
. Our results show that FABP-hCFTR mice have a different response to flagellum loss in
P. aeruginosa
compared to wild-type animals. The loss of flagellum expression, rather than the loss of motility, is the main driver behind the increased virulence of flagellum-deficient
P. aeruginosa
in CF. These observations provide new insight into
P. aeruginosa
virulence in CF.

IMPORTANCE

Pseudomonas aeruginosa
, a major respiratory pathogen in cystic fibrosis, is known to lose its flagellum during the course of infection in the airways. Here, we show that the loss of flagellum leads to a more enhanced virulence in Cftr-deficient cystic fibrosis mice than in control animals. Loss of flagellum expression, rather than the loss of flagellar swimming motility, represents the main driver behind this increased virulence suggesting that this appendage plays a specific role in
P. aeruginosa
virulence in cystic fibrosis airways.