Kssdtree: an interactive Python package for phylogenetic analysis based on sketching technique.

SUMMARY: Sketching technologies have recently emerged as a promising solution for real-time, large-scale phylogenetic analysis. However, existing sketching-based phylogenetic tools exhibit drawbacks, including platform restrictions, deficiencies in tree visualization, and inherent distance estimation bias. These limitations collectively impede the overall convenience and efficiency of the analysis. In this study, we introduce Kssdtree, an interactive Python package designed to address these challenges. Kssdtree surpasses other sketching-based tools by demonstrating superior performance in terms of both accuracy and time efficiency on comprehensive benchmarking datasets. Notably, Kssdtree offers key advantages such as intra-species phylogenomic analysis and GTDB-based phylogenetic placement analysis, significantly enhancing the scope and depth of phylogenetic investigations. Through extensive evaluations and comparisons, Kssdtree stands out as an efficient and versatile method for real-time, large-scale phylogenetic analysis. AVAILABILITY AND IMPLEMENTATION: The Kssdtree Python package is freely accessible at https://pypi.org/project/kssdtree and source code is available at https://github.com/yhlink/kssdtree. The documentation and instantiation for the software is available at https://kssdtree.readthedocs.io/en/latest. The video tutorial is available at https://youtu.be/_6hg59Yn-Ws.

Systematic Investigation of Novel, Controlled Low-Temperature Sintering Processes for Inkjet Printed Silver Nanoparticle Ink.

Functional inks enable manufacturing of flexible electronic devices by means of printing technology. Silver nanoparticle (Ag NP) ink is widely used for printing conductive components. A sintering process is required to obtain sufficient conductivity. Thermal sintering is the most commonly used method, but the heat must be carefully applied to avoid damaging low-temperature substrates such as polymer films. In this work, two alternative sintering methods, damp heat sintering and water sintering are systematically investigated for inkjet-printed Ag tracks on polymer substrates. Both methods allow sintering polyvinyl pyrrolidone (PVP) capped Ag NPs at 85°C. In this way, the resistance is significantly reduced to only 1.7 times that of the samples on polyimide sintered in an oven at 250°C. The microstructure of sintered Ag NPs is analyzed. Taking the states of the capping layer under different conditions into account, the explanation of the sintering mechanism of Ag NPs at low temperatures is presented. Overall, both damp heat sintering and water sintering are viable options for achieving high conductivity of printed Ag tracks. They can broaden the range of substrates available for flexible electronic device fabrication while mitigating substrate damage risks. The choice between them depends on the specific application and the substrate used.

Development of a machine learning finite-range nonlocal density functional.

Kohn-Sham density functional theory has been the most popular method in electronic structure calculations. To fulfill the increasing accuracy requirements, new approximate functionals are needed to address key issues in existing approximations. It is well known that nonlocal components are crucial. Current nonlocal functionals mostly require orbital dependence such as in Hartree-Fock exchange and many-body perturbation correlation energy, which, however, leads to higher computational costs. Deviating from this pathway, we describe functional nonlocality in a new approach. By partitioning the total density to atom-centered local densities, a many-body expansion is proposed. This many-body expansion can be truncated at one-body contributions, if a base functional is used and an energy correction is approximated. The contribution from each atom-centered local density is a single finite-range nonlocal functional that is universal for all atoms. We then use machine learning to develop this universal atom-centered functional. Parameters in this functional are determined by fitting to data that are produced by high-level theories. Extensive tests on several different test sets, which include reaction energies, reaction barrier heights, and non-covalent interaction energies, show that the new functional, with only the density as the basic variable, can produce results comparable to the best-performing double-hybrid functionals, (for example, for the thermochemistry test set selected from the GMTKN55 database, BLYP based machine learning functional gives a weighted total mean absolute deviations of 3.33 kcal/mol, while DSD-BLYP-D3(BJ) gives 3.28 kcal/mol) with a lower computational cost. This opens a new pathway to nonlocal functional development and applications.

Where is the hidden intramolecular H-bonding vibrational signal in the proline matrix IR spectrum?

The assignment of the hydrogen bonded O-H stretch vibration in the proline matrix IR spectrum has sparked controversy. Employing constrained nuclear electronic orbital methods, we provide a clear assignment that the vibrational frequency drops to near 3000 cm-1 as a result of the interplay between electronic effects, nuclear quantum effects, and matrix effects.

Comparison of the coverage and rotation of asymmetrical and symmetrical tibial components: a systematic review and meta-analysis.

BACKGROUND: An optimized fit of the tibial component to the resection platform and correct rotational alignment are critical for successful total knee arthroplasty (TKA). However, there remains controversy regarding the superiority of symmetric tibial component versus asymmetric tibial component. The objective of this systematic review and meta-analysis was to evaluate the current evidence for comparing the coverage and rotation of asymmetrical and symmetrical tibial component. METHODS: We searched potentially relevant studies form PubMed, Web of science, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), and China National Knowledge Infrastructure (CNKI), up to 1 March 2023. Data extraction and quality assessment were performed by two independent reviewers. Meta-analysis was conducted using Review Manager 5.4. RESULTS: Sixteen articles were identified. Compared to symmetric tibial component, asymmetric tibial component increased the coverage of the proximal tibial cut surface (MD, -2.87; 95%CI, -3.45 to -2.28; P < 0.00001), improved the prevalence of tibial baseplate underhang (OR, 0.16; 95%CI, 0.07 to 0.33; P < 0.00001) and malrotation (OR, 0.13; 95%CI, 0.02 to 0.90; P = 0.04), and reduced the degree of tibial component rotation (MD, -3.11; 95%CI, -5.76 to -0.47; P = 0.02). But there was no statistical significance for improving tibial baseplate overhang (OR, 0.58; 95%CI, 0.08 to 3.97; P = 0.58). Additionally, no revision had occurred for the two tibial components in the included studies. CONCLUSION: The current evidence shows asymmetric tibial component offer advantages in terms of coverage and rotation compared with symmetric tibial component in TKA.

Enhancing Urban Mobility with Self-Tuning Fuzzy Logic Controllers for Power-Assisted Bicycles in Smart Cities.

In smart cities, bicycle-sharing systems have become an essential component of the transportation services available in major urban centers around the globe. Due to environmental sustainability, research on the power-assisted control of electric bikes has attracted much attention. Recently, fuzzy logic controllers (FLCs) have been successfully applied to such systems. However, most existing FLC approaches have a fixed fuzzy rule base and cannot adapt to environmental changes, such as different riders and roads. In this paper, a modified FLC, named self-tuning FLC (STFLC), is proposed for power-assisted bicycles. In addition to a typical FLC, the presented scheme adds a rule-tuning module to dynamically adjust the rule base during fuzzy inference processes. Simulation and experimental results indicate that the presented self-tuning module leads to comfortable and safe riding as compared with other approaches. The technique established in this paper is thought to have the potential for broader application in public bicycle-sharing systems utilized by a diverse range of riders.

Strategy for Fluorescence/Photoacoustic Signal Maximization Using Dual-Wavelength-Independent Excitation.

Dual-mode imaging of fluorescence-photoacoustics has emerged as a promising technique for biomedical applications. However, conventional dual-mode imaging is based on single-wavelength excitation, which often results in opposing fluorescence and photoacoustic signals due to competing photophysical processes in one agent, rendering the maximization of both signals infeasible. To meet this challenge, we herein propose a new strategy by using the dual-excitation approach, where one excitation wavelength generates a fluorescence signal and the other produces a photoacoustic signal, thus achieving simultaneous maximization of both signals in one fluorescence-photoacoustic molecule. Based on this strategy, three dye molecules were employed for comparison, and it was surprising to find that QHD dye with two types of excitation wavelengths could generate fluorescence and photoacoustic signals, respectively. Furthermore, this strategy was successfully implemented in dual-mode imaging of rheumatoid arthritis mice. Importantly, this study emphasizes a new design guideline for the maximization of fluorescence-photoacoustic signals by using dual-wavelength-independent excitation.

Phase-insensitive amplifier gain estimation at Cramér-Rao bound for two-mode squeezed state of light.

Phase-insensitive amplifiers (PIAs), as a class of important quantum devices, have found significant applications in the subtle manipulation of multiple quantum correlation and multipartite quantum entanglement. Gain is a very important parameter for quantifying the performance of a PIA. Its absolute value can be defined as the ratio of the output light beam power to the input light beam power, while its estimation precision has not been extensively investigated yet. Therefore, in this work, we theoretically study the estimation precision from the vacuum two-mode squeezed state (TMSS), the estimation precision of the coherent state, and the bright TMSS scenario, which has the following two advantages: it has more probe photons than the vacuum TMSS and higher estimation precision than the coherent state. The advantage in terms of estimation precision of the bright TMSS compared with the coherent state is researched. We first simulate the effect of noise from another PIA with gain M on the estimation precision of the bright TMSS, and we find that a scheme in which the PIA is placed in the auxiliary light beam path is more robust than two other schemes. Then, a fictitious beam splitter with transmission T is used to simulate the noise effects of propagation loss and imperfect detection, and the results show that a scheme in which the fictitious beam splitter is placed before the original PIA in the probe light beam path is the most robust. Finally, optimal intensity difference measurement is confirmed to be an accessible experimental technique to saturate estimation precision of the bright TMSS. Therefore, our present study opens a new avenue for quantum metrology based on PIAs.

Calculating Vibrational Excited State Absorptions with Excited State Constrained Minimized Energy Surfaces.

The modeling and interpretation of vibrational spectra are crucial for studying reaction dynamics using vibrational spectroscopy. Most prior theoretical developments focused on describing fundamental vibrational transitions while fewer developments focused on vibrational excited state absorptions. In this study, we present a new method that uses excited state constrained minimized energy surfaces (CMESs) to describe vibrational excited state absorptions. The excited state CMESs are obtained similarly to the previous ground state CMES development in our group but with additional wave function orthogonality constraints. Using a series of model systems, including the harmonic oscillator, Morse potential, double-well potential, quartic potential, and two-dimensional anharmonic potential, we demonstrate that this new procedure provides good estimations of the transition frequencies for vibrational excited state absorptions. These results are significantly better than those obtained from harmonic approximations using conventional potential energy surfaces, demonstrating the promise of excited state CMES-based methods for calculating vibrational excited state absorptions in real systems.

Linear Scaling Calculations of Excitation Energies with Active-Space Particle-Particle Random-Phase Approximation.

We developed an efficient active-space particle-particle random-phase approximation (ppRPA) approach to calculate accurate charge-neutral excitation energies of molecular systems. The active-space ppRPA approach constrains both indexes in particle and hole pairs in the ppRPA matrix, which only selects frontier orbitals with dominant contributions to low-lying excitation energies. It employs the truncation in both orbital indexes in the particle-particle and the hole-hole spaces. The resulting matrix, whose eigenvalues are excitation energies, has a dimension that is independent of the size of the systems. The computational effort for the excitation energy calculation, therefore, scales linearly with system size and is negligible compared with the ground-state calculation of the (N - 2)-electron system, where N is the electron number of the molecule. With the active space consisting of 30 occupied and 30 virtual orbitals, the active-space ppRPA approach predicts the excitation energies of valence, charge-transfer, Rydberg, double, and diradical excitations with the mean absolute errors (MAEs) smaller than 0.03 eV compared with the full-space ppRPA results. As a side product, we also applied the active-space ppRPA approach in the renormalized singles (RS) T-matrix approach. Combining the non-interacting pair approximation that approximates the contribution to the self-energy outside the active space, the active-space GRSTRS@PBE approach predicts accurate absolute and relative core-level binding energies with the MAEs around 1.58 and 0.3 eV, respectively. The developed linear scaling calculation of excitation energies is promising for applications to large and complex systems.

FGF-dependent metabolic control of vascular development.

Blood and lymphatic vasculatures are intimately involved in tissue oxygenation and fluid homeostasis maintenance. Assembly of these vascular networks involves sprouting, migration and proliferation of endothelial cells. Recent studies have suggested that changes in cellular metabolism are important to these processes. Although much is known about vascular endothelial growth factor (VEGF)-dependent regulation of vascular development and metabolism, little is understood about the role of fibroblast growth factors (FGFs) in this context. Here we identify FGF receptor (FGFR) signalling as a critical regulator of vascular development. This is achieved by FGF-dependent control of c-MYC (MYC) expression that, in turn, regulates expression of the glycolytic enzyme hexokinase 2 (HK2). A decrease in HK2 levels in the absence of FGF signalling inputs results in decreased glycolysis, leading to impaired endothelial cell proliferation and migration. Pan-endothelial- and lymphatic-specific Hk2 knockouts phenocopy blood and/or lymphatic vascular defects seen in Fgfr1/Fgfr3 double mutant mice, while HK2 overexpression partly rescues the defects caused by suppression of FGF signalling. Thus, FGF-dependent regulation of endothelial glycolysis is a pivotal process in developmental and adult vascular growth and development.

Describing proton transfer modes in shared proton systems with constrained nuclear-electronic orbital methods.

Proton transfer is crucial in various chemical and biological processes. Because of significant nuclear quantum effects, accurate and efficient description of proton transfer remains a great challenge. In this Communication, we apply constrained nuclear-electronic orbital density functional theory (CNEO-DFT) and constrained nuclear-electronic orbital molecular dynamics (CNEO-MD) to three prototypical shared proton systems and investigate their proton transfer modes. We find that with a good description of nuclear quantum effects, CNEO-DFT and CNEO-MD can well describe the geometries and vibrational spectra of the shared proton systems. Such a good performance is in significant contrast to DFT and DFT-based ab initio molecular dynamics, which often fail for shared proton systems. As an efficient method based on classical simulations, CNEO-MD is promising for future investigations of larger and more complex proton transfer systems.

New Role of D-Cycloserine: Shorten Adaptation Process and Extend Maintenance Time of Motion Sickness.

INTRODUCTION: The aim of the study was to investigate the role of D-cycloserine (DCS) in the adaptation process and maintenance of motion sickness (MS). METHODS: In experiment 1, 120 SD rats were used to study the promoting effect of DCS on the adaptation process of MS in rats. They were randomly divided into four groups, DCS-rotation (DCS-Rot), DCS-static, saline-rotation (Sal-Rot), and saline-static, and further divided into three subgroups according to the adaptation time (4 days, 7 days, and 10 days) in each group. After being given DCS (0.5 mg/kg) or 0.9% saline, they were rotated or kept static according to the group. Their fecal granules, total distance, and total activity of spontaneous activity were recorded and analyzed. In experiment 2, other 120 rats were used. The experimental grouping and specific experimental method were the same as experiment 1. According to the grouping of the adaptive maintenance duration, the animals of 14 days, 17 days, and 21 days groups were measured on the corresponding date of the changes in the animals' exploratory behavior. RESULTS: In experiment 1, the fecal granules, total distance, and total activity of spontaneous activity of Sal-Rot returned to the control level on 9 days, and the DCS-Rot group returned to the control level on 6 days, indicating that DCS could shorten the adaptation time of MS rats from 9 days to 6 days. In experiment 2, the Sal-Rot could not maintain the adaptive state after 14 days' absence from the seasickness environment. The fecal granules of DCS-Rot increased significantly, and total distance and total activity of spontaneous activity of DCS-Rot decreased significantly from 17 days. These illustrate that DCS can prolong the adaptive maintenance time from within 14 days to 17 days in MS rats. CONCLUSION: 0.5 mg/kg DCS injected intraperitoneally can shorten the MS adaptation process and extend the maintenance time of adaptation of SD rats.

Molecular Dynamics with Constrained Nuclear Electronic Orbital Density Functional Theory: Accurate Vibrational Spectra from Efficient Incorporation of Nuclear Quantum Effects.

Nuclear quantum effects play a crucial role in many chemical and biological systems involving hydrogen atoms yet are difficult to include in practical molecular simulations. In this paper, we combine our recently developed methods of constrained nuclear-electronic orbital density functional theory (cNEO-DFT) and constrained minimized energy surface molecular dynamics (CMES-MD) to create a new method for accurately and efficiently describing nuclear quantum effects in molecular simulations. By use of this new method, dubbed cNEO-MD, the vibrational spectra of a set of small molecules are calculated and compared with those from conventional ab initio molecular dynamics (AIMD) as well as from experiments. With the same formal scaling, cNEO-MD greatly outperforms AIMD in describing the vibrational modes with significant hydrogen motion characters, demonstrating the promise of cNEO-MD for simulating chemical and biological systems with significant nuclear quantum effects.

Morpho-cultural, physiological and molecular characterisation of Colletotrichum nymphaeae causing anthracnose disease of walnut in China.

Anthracnose disease has harmed walnut in recent years, resulting in yield losses in China. As a results, both morphological and molecular techniques must be used to confirm the etiology of anthracnose on walnut. In May 2020, walnut branches with indications of anthracnose were gathered in Ganquan, China (N33°56'/E105°44'). A strain named JT20 was isolated and morphologically characterized as a Colletotrichum specie. Pathogenicity tests further confirmed that the strain caused apparent anthracnose symptoms on walnut which were consistent with those seen in the field. On PDA, colonies were gray, cotton wool-like on the surface and pale gray to pale orange on the dorsal side. Conidia were aseptate, hyaline, fusiform to cylindrical with rounded to pointy ends and a length of 5.52-9.30 × 2.18-4.61 µm. PDA, lactose, yeast extract, pH 6-8, temperature of 25 °C and complete darkness were shown to be the optimum culture conditions for surface mycelium growth while PSA, lactose, urea, pH 9, temperature of 30 °C and complete darkness were found to be the best conditions for pathogen sporulation. The isolate was deduced as based on phylogenetic analysis with 3 genes (ribosomal DNA-ITS, ACT and GAPDH) as well as morphological characteristics and cultural features, the isolate was identified C. nymphaeae. This is the first report of C. nymphaeae causing walnut anthracnose in China.

Adsorption of CO and H2S on pristine and metal (Ni, Pd, Pt, Cu, Ag, and Au)-mediated SnS monolayers: a first-principles study.

A SnS monolayer is a new two-dimensional material with a black phosphorous structure, with high carrier mobility and a large surface-to-volume ratio, and is an ideal candidate material for gas sensors. The adsorption and sensing behaviors between the SnS monolayer and gas molecules are enhanced under the action of TM atoms with high catalytic performance. The adsorption behavior of CO and H2S on intrinsic and transition metal atom modified SnS monolayers is investigated based on the first principles calculations. The adsorption structure, adsorption energy, electron transfer, density of states, electron local density, work function, and desorption properties are discussed to evaluate the potential applications of SnS monolayers as scavengers and gas sensors for CO and H2S molecules. The results show that Ni, Pd, Pt and Cu atoms tend to be adsorbed on TH sites, while Ag and Au atoms are more easily captured by TS sites. Further studies have shown that all TM atoms can significantly enhance the sensing behavior between the SnS monolayer and the gas molecules. The adsorption performance of the CO molecule on the TM-mediated SnS (TM-SnS) monolayer is obviously better than that of the H2S molecule. Furthermore, the effects of electric field and biaxial strain on the sensing properties of gas molecules on Ni-SnS monolayers are also investigated. Finally, the desorption time of gas molecules from the TM-SnS monolayer is estimated. This will provide experimenters with theoretical guidance for the application of SnS-based sensing materials, and our work is of great significance for predicting new monochalcogenide sensing materials.

A label-free electrochemical immunosensor based on a gold-vertical graphene/TiO2 nanotube electrode for CA125 detection in oxidation/reduction dual channels.

A label-free immunosensor was constructed in oxidation and reduction dual channel mode for the trace detection of cancer antigen 125 (CA125) in serum. The gold-vertical graphene/titanium dioxide (Au-VG/TiO2) electrode was used as the signal-amplification platform, and cytosine and dopamine were used as probes in the oxidation and reduction channels, respectively. VG nanosheets were synthesized on a TiO2 nanotube array via chemical vapor deposition (CVD), and Au nanoparticles were deeply embedded on the surface and in the root of the VG nanosheets via electrodeposition. The CA125 antibody was then directly immobilized onto the electrode surface, benefitting from its natural affinity for Au nanoparticles. In the oxidation and reduction channels the CA125 antibody-Au-VG/TiO2 immune electrode had the same response concentration range (0.01-1000 mU∙mL-1) for the determination of the CA125 antigen. However, the oxidation channel had a higher sensitivity (14.82 µA•(log(mU•mL-1))-1 at a working potential of ~ 1.25 V vs. SCE), lower detection limit (0.0001 mU∙mL-1), higher stability, and lower performance deviation than the reduction channel. This immunosensor was successfully used for CA125 detection in human serum. The recoveries of spiked serum samples ranged from 99.8 ± 0.5 to 100 ± 0.4%. The study on the difference in the sensing performance between oxidation and reduction channels provides a preliminary experimental reference for exploring dual-channel synchronous detection immunosensors and verifying the accuracy of the assay based on dual-channel data, which will promote the development of reliable electrochemical immunosensor technology.

Identification of Chicken CD74 as a Novel Cellular Attachment Receptor for Infectious Bursal Disease Virus in Bursa B Lymphocytes.

Infectious bursal disease virus (IBDV) is an important member of the Birnaviridae family, causing severe immunosuppressive disease in chickens. The major capsid protein VP2 is responsible for the binding of IBDV to the host cell and its cellular tropism. In order to find proteins that potentially interact with IBDV VP2, a liquid chromatography-mass spectrometry (LC-MS) assay was conducted, and the host chicken CD74 protein was identified. Here, we investigate the role of chicken CD74 in IBDV attachment. Coimmunoprecipitation assays indicated that the extracellular domain of CD74 interacted with the VP2 proteins of multiple IBDV strains. Knockdown and overexpression experiments showed that CD74 promotes viral infectivity. Confocal assays showed that CD74 overexpression allows the attachment of IBDV and subvirus-like particles (SVPs) to the cell surface of nonpermissive cells, and quantitative PCR (qPCR) analysis further confirmed the attachment function of CD74. Anti-CD74 antibody, soluble CD74, depletion of CD74 by small interfering RNA (siRNA), and CD74 knockdown in the IBDV-susceptible DT40 cell line significantly inhibited IBDV binding, suggesting a pivotal role of this protein in virus attachment. These findings demonstrate that CD74 is a novel important receptor for IBDV attachment to the chicken B lymphocyte cell line DT40.IMPORTANCE CD74 plays a pivotal role in the correct folding and functional stability of major histocompatibility complex class II (MHC-II) molecules and in the presentation of antigenic peptides, acting as a regulatory factor in the antigen presentation process. In our study, we demonstrate a novel role of CD74 during IBDV infection, showing that chicken CD74 plays a significant role in IBDV binding to target B cells by interacting with the viral VP2 protein. This is the first report demonstrating that CD74 is involved as a novel attachment receptor in the IBDV life cycle in target B cells, thus contributing new insight into host-pathogen interactions.

Introductory lecture: when the density of the noninteracting reference system is not the density of the physical system in density functional theory.

A major challenge in density functional theory (DFT) is the development of density functional approximations (DFAs) to overcome errors in existing DFAs, leading to more complex functionals. For such functionals, we consider roles of the noninteracting reference systems. The electron density of the Kohn-Sham (KS) reference with a local potential has been traditionally defined as being equal to the electron density of the physical system. This key idea has been applied in two ways: the inverse calculation of such a local KS potential for the reference from a given density and the direct calculation of density and energy based on given DFAs. By construction, the inverse calculation can yield a KS reference with the density equal to the input density of the physical system. In application of DFT, however, it is the direct calculation of density and energy from a DFA that plays a central role. For direct calculations, we find that the self-consistent density of the KS reference defined by the optimized effective potential (OEP), is not the density of the physical system, when the DFA is dependent on the external potential. This inequality holds also for the density of generalized KS (GKS) or generalized OEP reference, which allows a nonlocal potential, when the DFA is dependent on the external potential. Instead, the density of the physical system, consistent with a given DFA, is given by the linear response of the total energy with respect to the variation of the external potential. This is a paradigm shift in DFT on the use of noninteracting references: the noninteracting KS or GKS references represent the explicit computational variables for energy minimization, but not the density of the physical system for external potential-dependent DFAs. We develop the expressions for the electron density so defined through the linear response for general DFAs, demonstrate the results for orbital functionals and for many-body perturbation theory within the second-order and the random-phase approximation, and explore the connections to developments in DFT.

The Dynamic Genome and Transcriptome of the Human Fungal Pathogen Blastomyces and Close Relative Emmonsia.

Three closely related thermally dimorphic pathogens are causal agents of major fungal diseases affecting humans in the Americas: blastomycosis, histoplasmosis and paracoccidioidomycosis. Here we report the genome sequence and analysis of four strains of the etiological agent of blastomycosis, Blastomyces, and two species of the related genus Emmonsia, typically pathogens of small mammals. Compared to related species, Blastomyces genomes are highly expanded, with long, often sharply demarcated tracts of low GC-content sequence. These GC-poor isochore-like regions are enriched for gypsy elements, are variable in total size between isolates, and are least expanded in the avirulent B. dermatitidis strain ER-3 as compared with the virulent B. gilchristii strain SLH14081. The lack of similar regions in related species suggests these isochore-like regions originated recently in the ancestor of the Blastomyces lineage. While gene content is highly conserved between Blastomyces and related fungi, we identified changes in copy number of genes potentially involved in host interaction, including proteases and characterized antigens. In addition, we studied gene expression changes of B. dermatitidis during the interaction of the infectious yeast form with macrophages and in a mouse model. Both experiments highlight a strong antioxidant defense response in Blastomyces, and upregulation of dioxygenases in vivo suggests that dioxide produced by antioxidants may be further utilized for amino acid metabolism. We identify a number of functional categories upregulated exclusively in vivo, such as secreted proteins, zinc acquisition proteins, and cysteine and tryptophan metabolism, which may include critical virulence factors missed before in in vitro studies. Across the dimorphic fungi, loss of certain zinc acquisition genes and differences in amino acid metabolism suggest unique adaptations of Blastomyces to its host environment. These results reveal the dynamics of genome evolution and of factors contributing to virulence in Blastomyces.