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At least 91 records · Page 5

Rapid mini‐chromosome divergence among fungal isolates causing wheat blast outbreaks in Bangladesh and Zambia

Summary The fungal pathogen,Magnaporthe oryzae Triticumpathotype, causing wheat blast disease was first identified in South America and recently spread across continents to South Asia and Africa. Here, we studied the genetic relationship among isolates found on the three continents. Magnaporthe oryzaestrains closely related to a South American field isolate B71 were found to have caused the wheat blast outbreaks in South Asia and Africa. Genomic variation among isolates from the three continents was examined using an improved B71 reference genome and whole‐genome sequences. We found strong evidence to support that the outbreaks in Bangladesh and Zambia were caused by the introductions of genetically separated isolates, although they were all close to B71 and, therefore, collectively referred to as the B71 branch. In addition, B71 branch strains carried at least one supernumerary mini‐chromosome. Genome assembly of a Zambian strain revealed that its mini‐chromosome was similar to the B71 mini‐chromosome but with a high level of structural variation. Our findings show that while core genomes of the multiple introductions are highly similar, the mini‐chromosomes have undergone marked diversification. The maintenance of the mini‐chromosome and rapid genomic changes suggest the mini‐chromosomes may serve important virulence or niche adaptation roles under diverse environmental conditions.

Plant Sciences↗

High-quality Acinetobacter genomes recovered from combat wounds via metagenomic sequencing resemble cultured isolate genomes

The ability to accurately characterize wound pathogens is critical to informing clinical decisions for wound infections with complex treatment requirements. Acinetobacter baumannii is an impactful nosocomial pathogen in combat wounds and civilian hospital-acquired infections. An informed understanding of the phylogenetics and epidemiology of A. baumannii infections in military and civilian environments could guide approaches that improve antibiotic treatment regimens for both military and civilian patients. Whole-genome data for bacterial strains can be difficult to obtain due to challenges in culturing isolates from preserved military specimens. Metagenomic sequencing and assembly create opportunities for genomic analysis of pathogens directly from clinical specimens. The ability to perform comparative analyses between metagenome-derived genomes and culture-derived genomes would support a range of comparative bacterial genomic studies. Wound tissue biopsy and effluent samples from combat injuries were subjected to metagenomic sequencing and assembly. In total, 42 microbial metagenome-assembled genomes (MAGs) were obtained directly from metagenomic sequence data, 36 of which were designated “high” quality. Thirty of these genomes corresponded to Acinetobacter, with 29 mapping specifically to A. baumannii. Other observed genera included Bordetella, Citrobacter, Escherichia, and Pseudomonas. Single-copy and multi-copy orthologs were identified across Acinetobacter MAGs and publicly available isolate genomes derived from military and civilian sources. Both MAG and military isolate genomes were annotated with antimicrobial resistance data, and MAG genomes were statistically comparable to genomes obtained from isolates. Our results highlight the potential of de novo metagenome assembly for enabling high-resolution characterization directly from clinical specimens, thereby improving diagnostic precision, guiding antimicrobial stewardship, and enhancing understanding of pathogen evolution across diverse healthcare and battlefield environments.

Acinetobacter baumannii↗

Measurement of the inclusive isolated-photon production cross section in pp and Pb–Pb collisions at $\mathbf {\sqrt{\textit{s}_{NN }} = 5.02}$ TeV

The ALICE Collaboration at the CERN LHC has measured the inclusive production cross section of isolated photons at midrapidity as a function of the photon transverse momentum (p$^{γ}_{T}$), in Pb–Pb collisions in different centrality intervals, and in pp collisions, at centre-of-momentum energy per nucleon pair of $\sqrt{s_{NN}}$ = 5.02 TeV. The photon transverse momentum range is between 10–14 and 40–140 GeV/c, depending on the collision system and on the Pb–Pb centrality class. The result extends to lower p$^{γ}_{T}$ than previously published results by the ATLAS and CMS experiments at the same collision energy. The covered pseudorapidity range is |η γ | < 0.67. The isolation selection is based on a charged particle isolation momentum threshold p$^{iso, ch}_{T}$ GeV/c within a cone of radii R = 0.2 and 0.4. The nuclear modification factor is calculated and found to be consistent with unity in all centrality classes, and also consistent with the HG-PYTHIA model, which describes the event selection and geometry biases that affect the centrality determination in peripheral Pb–Pb collisions. The measurement is compared to next-to-leading order perturbative QCD calculations and to the measurements of isolated photons and Z 0 bosons from the CMS experiment, which are all found to be in agreement.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Isolated porosity: A Signature of Submarine Volcanism?

In this conference poster, we show that pumice clasts from submarine volcanoes contain more isolated pores than those from volcanoes that erupt on land. Isolated pores are void spaces that are disconnected from the clast's exterior and are unexpected because most pores coalesce in high total porosity pumice. We specifically, explore the presence of isolated pores in clasts from a 2019 eruption of Volcano F, Tonga and suggest that whole-clast cooling in water may help prevent bubble coalesce and preserve isolated pores. Poster presented at the 2025 International Association of Volcanology and Chemistry of Earth's Interior Meeting (IAVCEI).

flotation↗

Anti-idiotype isolation of a broad and potent influenza A virus-neutralizing human antibody

The VH6-1 class of antibodies includes some of the broadest and most potent antibodies that neutralize influenza A virus. Here, we elicit and isolate anti-idiotype antibodies against germline versions of VH6-1 antibodies, use these to sort human leukocytes, and isolate a new VH6-1-class member, antibody L5A7, which potently neutralized diverse group 1 and group 2 influenza A strains. While its heavy chain derived from the canonical IGHV6-1 heavy chain gene used by the class, L5A7 utilized a light chain gene, IGKV1-9, which had not been previously observed in other VH6-1-class antibodies. The cryo-EM structure of L5A7 in complex with Indonesia 2005 hemagglutinin revealed a nearly identical binding mode to other VH6-1-class members. The structure of L5A7 bound to the isolating anti-idiotype antibody, 28H6E11, revealed a shared surface for binding anti-idiotype and hemagglutinin that included two critical L5A7 regions: an FG motif in the third heavy chain-complementary determining region (CDR H3) and the CDR L1 loop. Surprisingly, the chemistries of L5A7 interactions with hemagglutinin and with anti-idiotype were substantially different. Overall, we demonstrate anti-idiotype-based isolation of a broad and potent influenza A virus-neutralizing antibody, revealing that anti-idiotypic selection of antibodies can involve features other than chemical mimicry of the target antigen.

59 BASIC BIOLOGICAL SCIENCES↗

Morphological and Genomic Features of the New Klosneuvirinae Isolate Fadolivirus IHUMI-VV54

Since the discovery of Mimivirus, viruses with large genomes encoding components of the translation machinery and other cellular processes have been described as belonging to the nucleocytoplasmic large DNA viruses. Recently, genome-resolved metagenomics led to the discovery of more than 40 viruses that have been grouped together in a proposed viral subfamily named Klosneuvirinae. Members of this group had genomes of up to 2.4Mb in size and featured an expanded array of translation system genes. Yet, despite the large diversity of the Klosneuvirinae in metagenomic data, there are currently only two isolates available. Here, we report the isolation of a novel giant virus known as Fadolivirus from an Algerian sewage site and provide morphological data throughout its replication cycle in amoeba and a detailed genomic characterization. The Fadolivirus genome, which is more than 1.5Mb in size, encodes 1,452 predicted proteins and phylogenetic analyses place this viral isolate as a near relative of the metagenome assembled Klosneuvirus and Indivirus. The genome encodes for 66 tRNAs, 23 aminoacyl-tRNA synthetases and a wide range of transcription factors, surpassing Klosneuvirus and other giant viruses. The Fadolivirus genome also encodes putative vacuolar-type proton pumps with the domains D and A, potentially constituting a virus-derived system for energy generation. The successful isolation of Fadolivirus will enable future hypothesis-driven experimental studies providing deeper insights into the biology of the Klosneuvirinae.

59 BASIC BIOLOGICAL SCIENCES↗

Genetic Complexity of CC5 Staphylococcus aureus Isolates Associated with Sternal Bursitis in Chickens: Antimicrobial Resistance, Virulence, Plasmids, and Biofilm Formation

Sternal bursitis, a common inflammatory condition in poultry, poses significant challenges to both animal welfare and public health. This study aimed to investigate the prevalence, antimicrobial resistance, and genetic characteristics of Staphylococcus aureus isolates associated with sternal bursitis in chickens. Ninety-eight samples were collected from affected chickens, and 24 S. aureus isolates were identified. Antimicrobial susceptibility testing revealed resistance to multiple agents, with a notable prevalence of aminoglycoside resistance genes. Whole genome sequencing elucidated the genetic diversity and virulence profiles of the isolates, highlighting the predominance of clonal complex 5 (CC5) strains. Additionally, biofilm formation assays demonstrated moderate biofilm production capacity among the isolates. These findings underscore the importance of vigilant monitoring and targeted interventions to mitigate the impact of sternal bursitis in poultry production systems.

Silva, Vanessa (ORCID:0000000194068433)↗

A High-Frequency Planar Transformer with Medium-Voltage Isolation: Preprint

This paper presents the design of a low-loss, high-frequency planar transformer having medium-voltage (10's of kV) isolation capability while transformer primary and secondary windings are interleaved to reduce losses. Medium-voltage isolation between adjacent printed circuit board (PCB) layers is extremely challenging using traditional PCB dielectrics. The isolation requirement is met using PCB with $7$\,kV/mil polyimide (Panasonic Felios RF775) as the dielectric, and by an appropriate layout of the windings and the inter-winding vias. The transformer is used to implement a dual active bridge (DAB) converter in a stackable dc-ac architecture where the dc port is connected to a photovoltaic (PV) string and ac outputs are connected in series to achieve direct PV string-to-medium voltage conversion without the need for low-voltage collection or a bulky line frequency transformer. Since each DAB transformer processes time-varying power, a design methodology is developed to minimize line-cycle-averaged losses. Experimental results are presented for a 1:1 planar transformer in a 7.5\,kW SiC-based dc-to-ac module operating at 200 kHz. Isolation of 26 kV between the primary and secondary layers and between the windings and the core is verified using a hipot tester.

41 EE - Solar Energy Technologies Office (EE-4S)↗

Selective solid-state isolation of NMR circuit elements using back-to-back field effect transistors

Nuclear Magnetic Resonance (NMR) electronics that employ selective solid-state isolation of circuit elements can include solid-state switches, such as back-to-back Field Effect Transistor (FET) pairs, and isolated gate drive electronics adapted to operate the solid-state switches in order to selectively decouple induction coils from receive electronics. The solid-state switches can be placed in series to achieve higher standoff voltages, and can be configured for low on resistance and short switching times. The gate drive electronics can include electrical isolation components adapted to enhance standoff voltages and reduce electrical noise at the selectively isolated receive electronics.

Walsh, David O.↗

Whole-Genome Sequencing and Bioinformatic Analysis of Environmental, Agricultural, and Human Campylobacter jejuni Isolates From East Tennessee

As a leading cause of bacterial-derived gastroenteritis worldwide, Campylobacter jejuni has a significant impact on human health in both the developed and developing worlds. Despite its prevalence as a human pathogen, the source of these infections remains poorly understood due to the mutation frequency of the organism and past limitations of whole genome analysis. Recent advances in both whole genome sequencing and computational methods have allowed for the high-resolution analysis of intraspecies diversity, leading multiple groups to postulate that these approaches may be used to identify the sources of Campylobacter jejuni infection. To address this hypothesis, our group conducted a regionally and temporally restricted sampling of agricultural and environmental Campylobacter sources and compared isolated C. jejuni genomes to those that caused human infections in the same region during the same time period. Through a network analysis comparing genomes from various sources, we found that human C. jejuni isolates clustered with those isolated from cattle and chickens, indicating these as potential sources of human infection in the region.

59 BASIC BIOLOGICAL SCIENCES↗

Earthquake-induced impact of base-isolated buildings: theory, numerical modeling, and design solutions

Earthquake shaking more intense than that used to size the horizontal clearance between a base–isolated building and near–rigid perimeter moat wall will result in hard impact, producing high–frequency, high–amplitude acceleration response in the structure and supported equipment. Herein this paper provides a design solution for the damaging effects of hard impact by installing a compliant engineered element in the load path between the base–isolated building and the moat wall, resulting in soft impact and a much smaller acceleration response. The engineered element assumed herein is a commercial–off–the–shelf marine fender with mechanical properties determined by physical testing. The attachment of a flexible engineered element, with well–defined stiffness and damping, to a near–rigid moat wall, simplifies the numerical modeling of the building–moat wall system and eliminates the need to bound the lateral stiffness of the wall for impact calculations. The simple model of the engineered element can be implemented in commercial finite element codes. Theory is developed for two–sided impact of a single–degree–of–freedom oscillator. Analytical solutions are derived for the shifted first–mode frequency of the impacted oscillator and for its free–vibration response. The shifted first–mode frequency is a function of the composite lateral stiffness of the isolator–engineered element assembly and its earthquake–induced displacement. Local peaks in the spectral response of the impacted oscillator form at odd integer multiples of the shifted first–mode frequency. The analytical solutions can be used to verify, in part, the numerical model used for impact analysis.

42 ENGINEERING↗

Controlling Reaction Pathways of Ethylene Hydroformylation Using Isolated Bimetallic Rhodium–Cobalt Sites

Designing efficient ligand-free heterogeneous catalysts for ethylene hydroformylation to produce C 3 oxygenates is of importance for both fundamental research and practical applications, but it is often hindered by insufficient catalytic activity and selectivity. Here, this work designs isolated rhodium–cobalt (Rh–Co) sites confined within a ZSM-5 zeolite to enhance ethylene hydroformylation rates and selectivity while maintaining catalyst stability. By adjusting the Co/Al ratio in Co-ZSM-5, different sizes of Co are formed; subsequent Rh introduction produces isolated Rh 1 Co x clusters with different Rh–Co coordination numbers (CNs). In-situ characterizations and density functional theory calculations reveal that a Rh–Co CN of 3, corresponding to an isolated Rh 1 Co 3 site, provides optimal bindings to reaction intermediates and thus achieves the highest hydroformylation rates among supported Rh-based catalysts. This study demonstrates the role of coordination-tuning via a secondary metal in effectively controlling the reaction pathway over single Rh atom catalysts.

03 NATURAL GAS↗

Direct reconstruction of isolated XUV or soft x-ray attosecond pulses from high-harmonic generation streaking spectra

Characterization of an isolated attosecond pulse (IAP) in the extreme ultraviolet (XUV) or soft x-ray (SXR) region is essential for its applications. Here we propose to retrieve an IAP in the time domain directly through the modulation of high-harmonic generation (HHG) spectra in the presence of a time-delayed intense few-cycle infrared or mid-infrared laser. The retrieval algorithm is derived based on the strong-field approximation and an extended quantitative rescattering model. We show that both isolated XUV pulses with a narrow spectral bandwidth and isolated SXR pulses with a broad bandwidth can be well characterized through the HHG streaking spectra. Such an all-optical method for characterizing the IAP differs from the commonly used approach based on the streaked photoelectron spectra that would require electron spectrometers. We check the robustness of the retrieval method by changing the dressing laser or by adjusting the steps of time delay. We also show that the XUV pulse can be accurately retrieved by treating the HHG streaking spectra calculated from solving the time-dependent Schrödinger equation for single atoms as the ‘experimental’ data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Fault isolation and fault-tolerant control for Takagi-Sugeno fuzzy time-varying delay stochastic distribution systems

A fault isolation, estimation, and fault-tolerant control (FTC) scheme for nonlinear time-varying delay stochastic distribution control systems was presented in this paper. The Takagi-Sugeno fuzzy model was adopted to approach the nonlinear dynamics of time-varying delay systems. According to the output equivalence principle and Laplace transformation, an augmented state vector was given to solve the time-varying delay problem. When multiple actuator faults and interference occur simultaneously, fault detection, isolation and fault estimation was designed to obtained the fault information. To decouple faults and obtain the value and location information of the fault, the system was separated into two parts through the designed multiple conversion matrices, in which one subsystem was only affected by one actuator fault. This has simplified the design of fault isolation and estimation. A adaptive observer for fault estimation was given. Then, fault information such as the time, location, and size was determined. The observer gain matrices were calculated using linear matrix inequality (LMI). When a fault was detected and diagnosed, a FTC algorithm was devised using the proportional-integral control scheme to compensate the fault as much as possible. It has been shown that even if multiple faults actuator occurred simultaneously, the FTC controller still ensured the output probability density function of the system traced the desired probability density function when a fault occurred. Finally, the expected results were obtained through the simulation example, which confirmed the effectiveness of the method.

42 ENGINEERING↗

Improbability of Post-Closure Criticality in Array of Transuranic Waste Containers after Compaction by Salt Creep at Waste Isolation Pilot Plant

Based on the rationale presented, post-closure nuclear criticality is improbable when room closure compacts containers disposing transuranic (TRU) waste emplaced at the Waste Isolation Pilot Plant (WIPP), an operating repository in bedded salt in southeastern New Mexico. As described in the original WIPP certification, a qualitative estimate of the probability of post-closure criticality in TRU waste produced from atomic energy defense activities has been low either because remote-handled TRU waste canisters are neutronically isolated by the bedded salt or because the low fissile mass in an array of contact-handled TRU waste drums cannot be compacted sufficiently by room closure from salt creep. These situations are still valid for the majority of TRU waste that is disposed at WIPP without any disposal constraints, as updated herein. This report also qualitatively evaluates the probability of criticality after disposal of TRU waste in pipe overpack containers (POC) where every POC in a shipment may have the maximum 200 fissile gram equivalent of 239Pu content. The probability of criticality for a disposal room filled with POCs is estimated during four representative phases of repository evolution: (1) a large salt block falls onto POCs in the first 20 years, (2) salt creep closes a disposal room in the first 1000 years without brine seepage and subsequent gas generation, which permits maximum compaction, (3) some brine seepage occurs into the closed room, which initiates consumption of the fiberboard (cellulose) impact absorber in the POC in the second 1000 years, and (4) full brine inundation of a room and consumption of all fiberboard thereafter. Salt-block fall in the first phase does not greatly disrupt three tiers of POCs. The compacted spacing of POCs in the later three repository conditions is calculated through high-fidelity, geomechanical modeling. Criticality evaluation of compacted 200-g 239 Pu spheres at the compacted spacing shows that neither 12-inch nor 6-inch POCs are critical after the first 1000 years, the second 1000 years, or thereafter as the sea of reflector material changes to represent the three repository conditions. Specifically, fiberboard and iron isolates 239 Pu while dry, and brine reduces the reactivity when a room is partially and fully inundated. Because POC behavior bounds behavior of other standard TRU waste containers, post-closure criticality caused by room closure compacting containers is omitted in the performance assessments for the 2019 and 2026 WIPP compliance re-certification applications to the US Environmental Protection Agency.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Five draft genome assemblies from Bacillaceae isolated from a degraded wetland environment

Abstract We isolated 5 Bacillaceae from a degraded wetland environment and sequenced their genomes using Illumina NextSeq. Here, we report draft genome sequences of Bacillus velezensus-SC119, Priestia megaterium-SC120, Bacillus zhangzhouensis-SC123, Bacillus pumilis-SC124, and Bacillus idriensis-SC127. The genomes range between 3,657,353 and 5,772,725 base pairs with %GC between 37.62% and 46.38%. Introduction Wetland environments play critical roles in the terrestrial carbon and water cycles and microbial communities are key players in healthy ecosystem function. Endospore forming bacteria in the Bacillaceae family are metabolically and genomically diverse soil heterotrophs that influence plant health, carbon and nitrogen cycling, and often produce diverse natural products that influence other bacterial and non-bacterial species in their environment (1). We collected two soil samples on January 19, 2023 from 42°43'12.7"N 73°45'01.4"W. One was highly hydrated and within a patch of invasive common reeds (Phragmites sp.) and the other was near the base of an Eastern cottonwood tree (Populus deltoides). Bacillus pumilis strain SC124 was isolated from the soil from near the cottonwood tree, while Bacillus velezensis strain SC119, Priestia megaterium strain SC120, Bacillus zhangzhouensis strain SC123, Bacillus idriensis strain SC127 and were isolated from the marshy soil.

isolate, wetlands, genome announcement↗

The survivor strain: isolation and characterization of Phormidium yuhuli AB48, a filamentous phototactic cyanobacterium with biotechnological potential

Despite their recognized potential, current applications of cyanobacteria as microbial cell factories remain in early stages of development. This is partly due to the fact that engineered strains are often difficult to grow at scale. This technical challenge contrasts with the dense and highly productive cyanobacteria populations thriving in many natural environments. It has been proposed that the selection of strains pre-adapted for growth in industrial photobioreactors could enable more productive cultivation outcomes. Here, we described the initial morphological, physiological, and genomic characterization of Phormidium yuhuli AB48 isolated from an industrial photobioreactor environment. P. yuhuli AB48 is a filamentous phototactic cyanobacterium with a growth rate comparable to Synechocystis sp . PCC 6803. The isolate forms dense biofilms under high salinity and alkaline conditions and manifests a similar nutrient profile to Arthrospira platensis ( Spirulina ). We sequenced, assembled, and analyzed the P. yuhuli AB48 genome, the first closed circular isolate reference genome for a member of the Phormidium genus. We then used cultivation experiments in combination with proteomics and metabolomics to investigate growth characteristics and phenotypes related to industrial scale cultivation, including nitrogen and carbon utilization, salinity, and pH acclimation, as well as antibiotic resistance. These analyses provide insight into the biological mechanisms behind the desirable growth properties manifested by P. yuhuli AB48 and position it as a promising microbial cell factory for industrial-scale bioproduction[221, 1631].

59 BASIC BIOLOGICAL SCIENCES↗

Influence of Mild Chronic Stress and Social Isolation on Acute Ozone-Induced Alterations in Stress Biomarkers and Brain-Region-Specific Gene Expression in Male Wistar–Kyoto Rats

Individuals with psychosocial stress often experience an exaggerated response to air pollutants. Ozone (O 3 ) exposure has been associated with the activation of the neuroendocrine stress-response system. We hypothesized that preexistent mild chronic stress plus social isolation (CS), or social isolation (SI) alone, would exacerbate the acute effects of O 3 exposure on the circulating adrenal-derived stress hormones, and the expression of the genes regulating glucocorticoid stress signaling via an altered stress adaptation in a brain-region-specific manner. Male Wistar–Kyoto rats (5 weeks old) were socially isolated, plus were subjected to either CS (noise, confinement, fear, uncomfortable living, hectic activity, and single housing), SI (single housing only, restricted handling and no enrichment) or no stress (NS; double housing, frequent handling and enrichment provided) for 8 weeks. The rats were then exposed to either air or O 3 (0.8 ppm for 4 h), and the samples were collected immediately after. The indicators of sympathetic and hypothalamic–pituitary axis (HPA) activation (i.e., epinephrine, corticosterone, and lymphopenia) increased with O 3 exposure, but there were no effects from CS or SI, except for the depletion of serum BDNF. CS and SI revealed small changes in brain-region-specific glucocorticoid-signaling-associated markers of gene expression in the air-exposed rats (hypothalamic Nr3c1, Nr3c2 Hsp90aa1, Hspa4 and Cnr1 inhibition in SI; hippocampal HSP90aa1 increase in SI; and inhibition of the bed nucleus of the stria terminalis (BNST) Cnr1 in CS). Gene expression across all brain regions was altered by O 3 , reflective of glucocorticoid signaling effects, such as Fkbp5 in NS, CS and SI. The SI effects on Fkbp5 were greatest for SI in BNST. O 3 increased Cnr2 expression in the hypothalamus and olfactory bulbs of the NS and SI groups. O 3 , in all stress conditions, generally inhibited the expression of Nr3c1 in all brain regions, Nr3c2 in the hippocampus and hypothalamus and Bdnf in the hippocampus. SI, in general, showed slightly greater O 3 -induced changes when compared to NS and CS. Serum metabolomics revealed increased sphingomyelins in the air-exposed SI and O 3 -exposed NS, with underlying SI dampening some of the O 3 -induced changes. These results suggest a potential link between preexistent SI and acute O 3 -induced increases in the circulating adrenal-derived stress hormones and brain-region-specific gene expression changes in glucocorticoid signaling, which may partly underlie the stress dynamic in those with long-term SI.

gene expression↗