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At least 775 records · Page 43

X-ray spectroscopic identification of strain and structure-based resonances in a series of saturated carbon-cage molecules: Adamantane, twistane, octahedrane, and cubane

Novel nanocarbons such as fullerenes, nanotubes, graphene, and nanodiamond reside at the cutting edge of nanoscience and technology. Along with chemical functionalization, geometric constraints (such as extreme curvature in nanotubes or defects within or at the surfaces of diamond nanoparticles) significantly alter the electronic states of the nanocarbon material. Understanding the effects of steric strain on the electronic structure is critical to developing nanoelectronic applications based on these materials. This paper presents a fundamental study of how strain affects the electronic structure in a benchmark series of some fundamental saturated carbon cage compounds. Adamantane, C10H16, the smallest diamondoid and arguably the smallest nanodiamond crystallite, has carbon atoms essentially commensurate with diamond lattice positions and possesses by far the least molecular strain of this series. Twistane also is a C10H16 isomer but the fixed cyclohexane twist conformation of the central ring introduces additional strain into the cage. Octahedrane [(CH)12] and cubane [(CH)8] are considerably more strained, culminating in cubane where carbon–carbon bonds lie either parallel or orthogonal to one another. Using gas-phase near-edge x-ray absorption fine structure spectroscopy to probe the unoccupied electronic states, we observe two major progressions across this series. First, a broad C–C σ* resonance in the absorption splits into two more narrow and intense resonances with increasing strain. Second, the first manifold of states previously associated with tertiary C–H σ* in the diamondoid series appears to broaden and shift to lower energy. This feature is more than twice as intense in cubane than in octahedrane, even though these two molecules have only tertiary carbons, with the chemical formula (CH)x. The spectral differences are entirely due to the shape of the molecules; in particular, in cubane, the features arise from a high degree of p-p interaction between parallel C–C bonds. In contrast to the conventional wisdom that near-edge x-ray absorption is primarily an atomically localized spectroscopy, molecular shape and associated strain lead to the dominant features in spectra acquired from this fundamental series of carbon cage structures.

36 MATERIALS SCIENCE↗

Simultaneous measurement of temperature and strain by cascaded fiber Bragg grating-silicon Fabry-Perot interferometer sensor

We report a fiber-optic sensor configuration with a cascaded fiber Bragg grating (FBG) and a silicon Fabry-Perot interferometer (FPI) for simultaneous measurement of temperature and strain. The sensor is composed of a 5 mm FBG on a single mode fiber and a 100μm thick silicon FPI attached to the tip of the optical fiber. The FBG is surface mounted on the host structure, and the FPI tip is suspended. Due to the stress-free, cantilever configuration, the silicon FPI is insensitive to strain, but sensitive to temperature with a sensitivity much higher than the FBG due to the large thermo-optic coefficient of silicon. The sensor is tested from room temperature to 100°C with varying strain up to ∼150με. The silicon FPI provides high temperature sensitivity of 89 pm/°C unaffected by strain. Since the FBG is attached to the host structure, it is affected by both thermal and mechanical strain; the sensitivity of these was experimentally obtained 32 pm/°C and 1.09 pm / με, respectively. Interrogated with a broadband light source and a high-speed spectrometer, the sensor shows temperature and strain resolutions of 1.9 × 10 −3 °C and 0.042 με, respectively. Here, due to the small size, enhanced sensitivity, and high resolution, this cascaded FBG-FPI sensor can be used in applications where accurate measurement of temperature and strain is required.

42 ENGINEERING↗

WE-EF-210-06: Ultrasound 2D Strain Measurement of Radiation-Induced Toxicity: Phantom and Ex Vivo Experiments

Purpose: Radiation-induced fibrosis is a common long-term complication affecting many patients following cancer radiotherapy. Standard clinical assessment of subcutaneous fibrosis is subjective and often limited to visual inspection and palpation. Ultrasound strain imaging describes the compressibility (elasticity) of biological tissues. This study’s purpose is to develop a quantitative ultrasound strain imaging that can consistently and accurately characterize radiation-induce fibrosis. Methods: In this study, we propose a 2D strain imaging method based on deformable image registration. A combined affine and B-spline transformation model is used to calculate the displacement of tissue between pre-stress and post-stress B-mode image sequences. The 2D displacement is estimated through a hybrid image similarity measure metric, which is a combination of the normalized mutual information (NMI) and normalized sum-of-squared-differences (NSSD). And 2D strain is obtained from the gradient of the local displacement. We conducted phantom experiments under various compressions and compared the performance of our proposed method with the standard cross-correlation (CC)- based method using the signal-to-noise (SNR) and contrast-to-noise (CNS) ratios. In addition, we conducted ex-vivo beef muscle experiment to further validate the proposed method. Results: For phantom study, the SNR and CNS values of the proposed method were significantly higher than those calculated from the CC-based method under different strains. The SNR and CNR increased by a factor of 1.9 and 2.7 comparing to the CC-based method. For the ex-vivo experiment, the CC-based method failed to work due to large deformation (6.7%), while our proposed method could accurately detect the stiffness change. Conclusion: We have developed a 2D strain imaging technique based on the deformable image registration, validated its accuracy and feasibility with phantom and ex-vivo data. This 2D ultrasound strain imaging technology may be valuable as physicians try to eliminate radiation-induce fibrosis and improve the therapeutic ratio of cancer radiotherapy. This research is supported in part by DOD PCRP Award W81XWH-13-1-0269, and National Cancer Institute (NCI) Grant CA114313.

60 APPLIED LIFE SCIENCES↗

Strain mapping of three-dimensionally structured two-dimensional materials

Strain plays a crucial role in tuning materials’ properties, influencing their optical, electrical, and chemical performances. In two-dimensional (2D) materials, applied stress often induces out-of-plane deformation, resulting in a more intricate three-dimensional (3D) topography, where mapping the strain remains a challenge due to the limitations of conventional characterization techniques. In this work, we introduce BRIGHT (Bragg-Rod Informed, Gradient-based Height-mapping Technique), an integrated method for reconstructing both the topography and planar strain profile of 3D-structured 2D materials using nanobeam four-dimensional scanning transmission electron microscopy (4D-STEM). We apply BRIGHT to a MoS2-MoSe2 transition metal dichalcogenide (TMD) lateral heterojunctions exhibiting built-in strain and out-of-plane ripples and show that varying heterojunction widths lead to distinct surface morphologies and corresponding changes in the planar strain distribution. These results establish a foundation for more effective strain engineering in 2D materials by accounting for out-of-plane structural features, thereby enabling more precise control of strain-dependent properties.

Mireles, Adan [Rice Univ., Houston, TX (United Sta↗

A Rhodopseudomonas strain with a substantially smaller genome retains the core metabolic versatility of its genus

ABSTRACT Rhodopseudomonas are a group of phototrophic microbes with a marked metabolic versatility and flexibility that underpins their potential use in the production of value-added products, bioremediation, and plant growth promotion. Members of this group have an average genome size of about 5.5 Mb, but two closely related strains have genome sizes of about 4.0 Mb. To identify the types of genes missing in a reduced genome strain, we compared strain DSM127 with other Rhodopseudomonas isolates at the genomic and phenotypic levels. We found that DSM127 can grow as well as other members of the Rhodopseudomonas genus and retains most of their metabolic versatility, but it has many fewer genes associated with high-affinity transport of nutrients, iron uptake, nitrogen metabolism, and biodegradation of aromatic compounds. This analysis indicates genes that can be deleted in genome reduction campaigns and suggests that DSM127 could be a favorable choice for biotechnology applications using Rhodopseudomonas or as a strain that can be engineered further to reside in a specialized natural environment. IMPORTANCE Rhodopseudomonas are a cohort of phototrophic bacteria with broad metabolic versatility. Members of this group are present in diverse soil and water environments, and some strains are found associated with plants and have plant growth-promoting activity. Motivated by the idea that it may be possible to design bacteria with reduced genomes that can survive well only in a specific environment or that may be more metabolically efficient, we compared Rhodopseudomonas strains with typical genome sizes of about 5.5 Mb to a strain with a reduced genome size of 4.0 Mb. From this, we concluded that metabolic versatility is part of the identity of the Rhodopseudomonas group, but high-affinity transport genes and genes of apparent redundant function can be dispensed with.

59 BASIC BIOLOGICAL SCIENCES↗

Zn 2+ -Inducible Expression Platform for Synechococcus sp. Strain PCC 7002 Based on the smtA Promoter/Operator and smtB Repressor

Synechococcus sp. strain PCC 7002 has been gaining significance as both a model system for photosynthesis research and for industrial applications. Until recently, the genetic toolbox for this model cyanobacterium was rather limited and relied primarily on tools that only allowed constitutive gene expression. This work describes a two-plasmid, Zn 2+ -inducible expression platform that is coupled with a zurA mutation, providing enhanced Zn 2+ uptake. The control elements are based on the metal homeostasis system of a class II metallothionein gene ( smtA 7942 ) and its cognate SmtB 7942 repressor from Synechococcus elongatus strain PCC 7942. Under optimal induction conditions, yellow fluorescent protein (YFP) levels were about half of those obtained with the strong, constitutive phycocyanin ( cpcBA 6803 ) promoter of Synechocystis sp. strain PCC 6803. This metal-inducible expression system in Synechococcus sp. strain PCC 7002 allowed the titratable gene expression of YFP that was up to 19-fold greater than the background level. This system was utilized successfully to control the expression of the Drosophila melanogaster β-carotene 15,15'-dioxygenase, NinaB, which is toxic when constitutively expressed from a strong promoter in Synechococcus sp. strain PCC 7002. Together, these properties establish this metal-inducible system as an additional useful tool that is capable of controlling gene expression for applications ranging from basic research to synthetic biology in Synechococcus sp. strain PCC 7002. IMPORTANCE This is the first metal-responsive expression system in cyanobacteria, to our knowledge, that does not exhibit low sensitivity for induction, which is one of the major hurdles for utilizing this class of genetic tools. In addition, high levels of expression can be generated that approximate those of established constitutive systems, with the added advantage of titratable control. Together, these properties establish this Zn 2+ -inducible system, which is based on the smtA 7942 operator/promoter and smtB 7942 repressor, as a versatile gene expression platform that expands the genetic toolbox of Synechococcus sp. strain PCC 7002.

59 BASIC BIOLOGICAL SCIENCES↗

Xenorhabdus bovienii Strain Diversity Impacts Coevolution and Symbiotic Maintenance with Steinernema spp. Nematode Hosts

Microbial symbionts provide benefits that contribute to the ecology and fitness of host plants and animals. Therefore, the evolutionary success of plants and animals fundamentally depends on long-term maintenance of beneficial associations. Most work investigating coevolution and symbiotic maintenance has focused on species-level associations, and studies are lacking that assess the impact of bacterial strain diversity on symbiotic associations within a coevolutionary framework. Here, we demonstrate that fitness in mutualism varies depending on bacterial strain identity, and this is consistent with variation shaping phylogenetic patterns and maintenance through fitness benefits. Through genome sequencing of nine bacterial symbiont strains and cophylogenetic analysis, we demonstrate diversity among Xenorhabdus bovienii bacteria. Further, we identified cocladogenesis between Steinernema feltiae nematode hosts and their corresponding X. bovienii symbiont strains, indicating potential specificity within the association. To test the specificity, we performed laboratory crosses of nematode hosts with native and nonnative symbiont strains, which revealed that combinations with the native bacterial symbiont and closely related strains performed significantly better than those with more divergent symbionts. Through genomic analyses we also defined potential factors contributing to specificity between nematode hosts and bacterial symbionts. These results suggest that strain-level diversity (e.g., subspecies-level differences) in microbial symbionts can drive variation in the success of host-microbe associations, and this suggests that these differences in symbiotic success could contribute to maintenance of the symbiosis over an evolutionary time scale.

59 BASIC BIOLOGICAL SCIENCES↗

φX216, a P2-like bacteriophage with broad Burkholderia pseudomallei and B. mallei strain infectivity

Background: Burkholderia pseudomallei and B. mallei are closely related Category B Select Agents of bioterrorism and the causative agents of the diseases melioidosis and glanders, respectively. Rapid phage-based diagnostic tools would greatly benefit early recognition and treatment of these diseases. There is extensive strain-to-strain variation in B. pseudomallei genome content due in part to the presence or absence of integrated prophages. Several phages have previously been isolated from B. pseudomallei lysogens, for example φK96243, φ1026b and φ52237. Results: We have isolated a P2-like bacteriophage, φX216, which infects 78% of all B. pseudomallei strains tested. φX216 also infects B. mallei, but not other Burkholderia species, including the closely related B. thailandensis and B. oklahomensis. The nature of the φX216 host receptor remains unclear but evidence indicates that in B. mallei φX216 uses lipopolysaccharide O-antigen but a different receptor in B. pseudomallei. The 37,637 bp genome of φX216 encodes 47 predicted open reading frames and shares 99.8% pairwise identity and an identical strain host range with bacteriophage φ52237. Closely related P2-like prophages appear to be widely distributed among B. pseudomallei strains but both φX216 and φ52237 readily infect prophage carrying strains. Conclusions: The broad strain infectivity and high specificity for B. pseudomallei and B. mallei indicate that φX216 will provide a good platform for the development of phage-based diagnostics for these bacteria.

59 BASIC BIOLOGICAL SCIENCES↗

Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction

Background: The hydrolysis of biomass to simple sugars used for the production of biofuels in biorefneries requires the action of cellulolytic enzyme mixtures. During the last 50 years, the ascomycete Trichoderma reesei, the main source of industrial cellulase and hemicellulase cocktails, has been subjected to several rounds of classical mutagenesis with the aim to obtain higher production levels. During these random genetic events, strains unable to produce cellulases were generated. Here, whole genome sequencing and transcriptomic analyses of the cellulase-negative strain QM9978 were used for the identifcation of mutations underlying this cellulase-negative phenotype. Results: Sequence comparison of the cellulase-negative strain QM9978 to the reference strain QM6a identifed a total of 43 mutations, of which 33 were located either close to or in coding regions. From those, we identifed 23 single-nucleotide variants, nine InDels, and one translocation. The translocation occurred between chromosomes V and VII, is located upstream of the putative transcription factor vib1, and abolishes its expression in QM9978 as detected during the transcriptomic analyses. Ectopic expression of vib1 under the control of its native promoter as well as overexpression of vib1 under the control of a strong constitutive promoter restored cellulase expression in QM9978, thus confrming that the translocation event is the reason for the cellulase-negative phenotype. Gene deletion of vib1 in the moderate producer strain QM9414 and in the high producer strain Rut-C30 reduced cellulase expression in both cases. Overexpression of vib1 in QM9414 and Rut-C30 had no efect on cellulase production, most likely because vib1 is already expressed at an optimal level under normal conditions. Conclusion: We were able to establish a link between a chromosomal translocation in QM9978 and the cellulasenegative phenotype of the strain. We identifed the transcription factor vib1 as a key regulator of cellulases in T. reesei whose expression is absent in QM9978. We propose that in T. reesei, as in Neurospora crassa, vib1 is involved in cellulase induction, although the exact mechanism remains to be elucidated. The data presented here show an example of a combined genome sequencing and transcriptomic approach to explain a specifc trait, in this case the QM9978 cellulase-negative phenotype, and how it helps to better understand the mechanisms during cellulase gene regulation. When focusing on mutations on the single base-pair level, changes on the chromosome level can be easily overlooked and through this work we provide an example that stresses the importance of the big picture of the genomic landscape during analysis of sequencing data.

09 BIOMASS FUELS↗

Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site

Abstract Hexavalent Chromium [Cr(VI)] is a widespread contaminant found in soil, sediment, and ground water in several DOE sites, including Hanford 100 H area. In order to stimulate microbially mediated reduction of Cr(VI) at this site, a poly-lactate hydrogen release compound was injected into the chromium contaminated aquifer. Targeted enrichment of dominant nitrate-reducing bacteria post injection resulted in the isolation of Pseudomonas stutzeri strain RCH2. P. stutzeri strain RCH2 was isolated using acetate as the electron donor and is a complete denitrifier. Experiments with anaerobic washed cell suspension of strain RCH2 revealed it could reduce Cr(VI) and Fe(III). The genome of strain RCH2 was sequenced using a combination of Illumina and 454 sequencing technologies and contained a circular chromosome of 4.6 Mb and three plasmids. Global genome comparisons of strain RCH2 with six other fully sequenced P. stutzeri strains revealed most genomic regions are conserved, however strain RCH2 has an additional 244 genes, some of which are involved in chemotaxis, Flp pilus biogenesis and pyruvate/2-oxogluturate complex formation.

59 BASIC BIOLOGICAL SCIENCES↗

A TaqMan-based multiplex qPCR assay and DNA extraction method for phylotype IIB sequevars 1&2 (select agent) strains of Ralstonia solanacearum

Ralstonia solanacearum race 3 biovar 2 strains belonging to phylotype IIB, sequevars 1 and 2 (IIB-1&2) cause brown rot of potato in temperate climates, and are quarantined pathogens in Canada and Europe. Since these strains are not established in the U.S. and because of their potential risk to the potato industry, the U.S. government has listed them as select agents. Cultivated geraniums are also a host and have the potential to spread the pathogen through trade, and its extracts strongly inhibits DNA-based detection methods. We designed four primer and probe sets for an improved qPCR method that targets stable regions of DNA. RsSA1 and RsSA2 recognize IIB-1&2 strains, RsII recognizes the current phylotype II (the newly proposed R. solanacearum species) strains (and a non-plant associated R. mannitolilytica ), and Cox1 recognizes eight plant species including major hosts of R. solanacearum such as potato, tomato and cultivated geranium as an internal plant control. We multiplexed the RsSA2 with the RsII and Cox1 sets to provide two layers of detection of a positive IIB-1&2 sample, and to validate plant extracts and qPCR reactions. The TaqMan-based uniplex and multiplex qPCR assays correctly identified 34 IIB-1&2 and 52 phylotype II strains out of 90 R. solanacearum species complex strains. Additionally, the multiplex qPCR assay was validated successfully using 169 artificially inoculated symptomatic and asymptomatic plant samples from multiple plant hosts including geranium. Moreover, we developed an extraction buffer that allowed for a quick and easy DNA extraction from infected plants including geranium for detection of R. solanacearum by qPCR. Our multiplex qPCR assay, especially when coupled with the quick extraction buffer method, allows for quick, easy and reliable detection and differentiation of the IIB-1&2 strains of R. solanacearum .

59 BASIC BIOLOGICAL SCIENCES↗

Progress Report on Alloy 617 Isochronous Stress-Strain Curves

Isochronous stress-strain curves for Alloy 617 up to a temperature of 1000°C will be required to qualify the material for elevated temperature design in Section III, Division 1, Subsection NH of the ASME Boiler and Pressure Vessel Code. Several potential methods for developing these curves are reviewed in this report. It is shown that in general power-law creep is the rate controlling deformation mechanism for a wide range of alloy heats, test temperatures and stresses. Measurement of the strain rate sensitivity of Alloy 617 indicates that the material is highly strain rate sensitive in the tensile deformation range above about 750°C. This suggests that the concept of a hot tensile curve as a bounding case on the isochronous stress-strain diagrams is problematic. The impact of strain rate on the hot tensile curves is examined and it is concluded that incorporating such a curve is only meaningful if a single tensile strain rate (typically the ASTM standard rate of 0.5%/min) is arbitrarily defined. Current experimentally determined creep data are compared to isochronous stress-strain curves proposed previously by the German programs in the 1980s and by the 1990 draft ASME Code Case. Variability in how well the experimental data are represented by the proposed design curves that suggests further analysis is necessary prior to completing a new draft Code Case.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Spontaneous Relaxation through Graphene Suggests an Alternative Strain Relaxation Mechanism in Heteroepitaxy

While conventional epitaxy produces high-quality epitaxial layers, the limited set of commercially available wafers restricts the number of material choice that can be grown through epitaxy. To extend the set of epi-materials, heteroepitaxy has been widely used although the epi-materials have severe lattice mismatch from wafers. The problem of heteroepitaxy of the lattice mismatched systems is that introducing dislocations is unavoidable because of the strain energy built up in epitaxial layers exceeds the threshold energy value to create dislocation. As the dislocations significantly reduce the materials’ properties, people have put intensive effort into finding a new way to resolve this issue. Here, we introduce a new strain relaxation approach which can efficiently engineer the lattice with minimizing dislocation formation. Remote epitaxy allows single-crystalline growths on graphene-coated substrates as atomic potential field guides atomic registry through graphene while weakening binding energy of epilayer to the substrate. We discovered that this weakened interface offers a new pathway for strain relaxation during epitaxy in the lattice mismatched systems. While conventional heteroepitaxy relaxes accumulated strain energy through involving misfit dislocations, heteroepitaxy on graphene-coated substrates spontaneously relaxes its strain minimizing dislocation density. Thus, at the same thickness and misfit strain, the epilayer grown on graphene-coated substrates shows full relaxation with substantially reduced dislocations while that by conventional heteroepitaxy exhibits slight relaxation with full of dislocations. It means that full of strain relaxation at much lower thickness is available through this approach. We strongly believe that our strategy allows broadening range of available semiconductors through epitaxy, which could lead high performance electronic and photonics.

Bae, Sang-Hoon↗

Framework for Characterizing Strain in the Vicinity of Leaky Reservoirs

The identification of leaks in the vicinity of reservoirs is critical to determining the feasibility of long-term geologic storage of CO2, methane, wastewater and other fluids. We have established a series of basic reservoir leakage scenarios and performed numerical analysis to characterize the associated pressure and strain fields created from injection into these leaky reservoir settings, as well from ambient loads, such as barometric pressure and earth tides. The end-member conceptual models evaluated include injection and ambient loads applied to: 1) a thin, horizontal layer with no leakage pathways (baseline), 2) a thin layer with a vertical conduit to the surface (e.g., a leaky fault or abandoned well) and 3) a thin layer with a conduit to an overlying aquifer. The pressure and strain fields are sensitive to the reservoir and confining unit geometry, material properties, the distribution, composition and compressibility of the pore fluid and the type of applied load (e.g., constant vs. cyclical injection, barometric pressure fluctuations, earth tides, etc.). Initial results from the numerical analyses indicate that an induced pressure change of 1 MPa in a formation at 1 km depth with a Young’s modulus of 10 GPa is sufficient to create vertical and horizontal strain signals as high as 2 με at a depth of 100 m. The signals predicted from leaky conditions compared to an intact reservoir differ by as much as 0.2 με in magnitude and evolve at different rates. We have developed instruments capable of measuring vertical and horizontal strain at a resolution of better than 5 nε and have recorded repeatable strain signals at 30 m depth in response to wastewater injection into the Avant field in Oklahoma. Based on these findings, strain signals predicted in the shallow subsurface (< 100 m) with numerical analysis are expected to be measurable, and this signal may be inverted to characterize the location and magnitude of leaks, as well as to characterize the geometry and hydromechanical properties of the formation and overlying confining units. This suggests that shallow strain measurements could be a cost effective method for characterizing and monitoring gas storage projects.

Robert, Moak↗

Strain to failure measurements of Cr coatings with different processing

Differently processed Cr coatings on Zircaloy cladding were assessed for coating strain to failure. This report includes i) quantification of Cr coating strain to failure for several coating variants, ii) incorporation of high throughput analysis developed utilizing artificial intelligence, and iii) develop a hoop direction coating strain to failure testing approach for high temperatures that doesn’t require digital image correlation strain measurements. Room temperature strain to failure measurements indicated that heat treatment had an impact on strain to failure of the coating, with increasing heat treatment temperature increasing the average strain to failure of the Cr coating.

36 MATERIALS SCIENCE↗

KBase Narrative - Complete Genome Sequence of Acidovorax temperans strain LMJ

We have isolated a new strain of Acidovorax temperans strain LMJ (hereafter called strain LMJ) from a contaminated Tris-Acetate-Phosphate (TAP) medium plate of a green micro-alga Chlamydomonas reinhardtii strain LMJ.SG0182 (a Chlamydomonas Library project (CLiP) strain). We sequenced the whole genome of the strain LMJ using the PacBio Sequel II technology and have submitted it to NCBI along with the SRA and PacBio methylation motif data. We present the whole genome sequence of this strain that offer insights into its coding and non-coding genes and its nearest taxonomic neighbors.

Mitra, Mautusi↗

Whole genome resequencing data from a collection of Clostridium Thermocellum strains

Clostridium thermocellum is an anaerobic thermophilic bacterium that natively ferments cellulose to ethanol and organic acids. This data set is a collection of whole genome resequencing data for several hundred strains of Clostridium thermocellum. It includes strains that have been engineered to increase ethanol production, strains that have been engineered to understand microbial physiology, and strains that have been adapted for desired phenotypes including increased ethanol tolerance. Resequencing data consists of paired Illumina reads, 100-150 bp on each end, with a ~500 bp insert size. One data file containing raw Illumina data (interleaved) is available for each strain. We also provide data describing the mutations identified in each strain, and distinguish between inherited and newly observed mutations. In addition to resequencing data, we also provide metadata describing the lineage of each strain, and any targeted genetic modifications.

resequencing bio energy fermentation↗

Genomic surveillance indicates clonal replacement of hypervirulent Klebsiella pneumoniae ST881 and ST29 lineage strains in vivo

The emergence of hypervirulent Klebsiella pneumoniae (hvKp) poses a significant public health threat, particularly regarding its carriage in the healthy population. However, the genomic epidemiological characteristics and population dynamics of hvKp within a single patient across distinct infection episodes remain largely unknown. This study aimed to investigate the clonal replacement of hvKp K2-ST881 and K54-ST29 lineage strains in a single patient experiencing multiple-site infections during two independent episodes. Two strains, designated EDhvKp-1 and EDhvKp-2, were obtained from blood and cerebrospinal fluid during the first admission, and the strain isolated from blood on the second admission was named EDhvKp-3. Whole-genome sequencing, utilizing both short-read Illumina and long-read Oxford Nanopore platforms, was conducted. In silico multilocus sequence typing (MLST), identification of antimicrobial resistance and virulence genes, and the phylogenetic relationship between our strains and other K. pneumoniae ST881 and ST29 genomes retrieved from the public database were performed. Virulence potentials were assessed through a mouse lethality assay. Our study indicated that the strains were highly susceptible to multiple antimicrobial agents. Plasmid sequence analysis confirmed that both virulence plasmids, pEDhvKp-1 (166,008 bp) and pEDhvKp-3 (210,948 bp), belonged to IncFIB type. Multiple virulence genes, including rmpA , rmpA2 , rmpC , rmpD , iroBCDN , iucABCD , and iutA , were identified. EDhvKp-1 and EDhvKp-2 showed the closest relationship to strain 502 (differing by 51 SNPs), while EDhvKp-3 exhibited 69 SNPs differences compared to strain TAKPN-1, which all recovered from Chinese patients in 2020. In the mouse infection experiment, both ST881 EDhvKp-1 and ST29 EDhvKp-3 displayed similar virulence traits, causing 90 and 100% of the mice to die within 72 h after intraperitoneal infection, respectively. Our study expands the spectrum of hvKp lineages and highlights genomic alterations associated with clonal switching between two distinct lineages of hvKP that successively replaced each other in vivo . The development of novel strategies for the surveillance, diagnosis, and treatment of high-risk hvKp is urgently needed.

Liu, Ning↗