m6A methyltransferase AflIme4 orchestrates mycelial growth, development and aflatoxin B1 biosynthesis in Aspergillus flavus

Aflatoxin B1 (AFB1), a highly toxic secondary metabolite produced by Aspergillus flavus, poses a severe threat to agricultural production, food safety and human health. The methylation of mRNA m6A has been identified as a regulator of both the growth and AFB1 production of A. flavus. However, its intracellular occurrence and function needs to be elucidated. Here, we identified and characterized a m6A methyltransferase, AflIme4, in A. flavus. The enzyme was localized in the cytoplasm, and knockout of AflIme4 significantly reduced the methylation modification level of mRNA. Compared with the control strains, ΔAflIme4 exhibited diminished growth, conidial formation, mycelial hydrophobicity, sclerotium yield, pathogenicity and increased sensitivity to CR, SDS, NaCl and H2O2. Notably, AFB1 production was markedly inhibited in the A. flavus ΔAflIme4 strain. RNA-Seq coupled with RT-qPCR validation showed that the transcriptional levels of genes involved in the AFB1 biosynthesis pathway including aflA, aflG, aflH, aflK, aflL, aflO, aflS, aflV and aflY were significantly upregulated. Methylated RNA immunoprecipitation-qPCR (MeRIP-qPCR) analysis demonstrated a significant increase in m6A methylation modification levels of these pathway-specific genes, concomitant with a decrease in mRNA stability. These results suggest that AflIme4 attenuates the mRNA stability of genes in AFB1 biosynthesis by enhancing their mRNA m6A methylation modification, leading to impaired AFB1 biosynthesis. Our study identifies a novel m6A methyltransferase AflIme4 and highlights it as a potential target to control A. flavus growth, development and aflatoxin pollution.

Fast Emulation of Fermionic Circuits with Matrix Product States

We describe a matrix product state (MPS) extension for the Fermionic Quantum Emulator (FQE) software library. We discuss the theory behind symmetry-adapted MPSs for approximating many-body wave functions of spin-1/2 Fermions, and we present an open-source, MPS-enabled implementation of the FQE interface (MPS-FQE). The software uses the open-source pyblock3 and block2 libraries for most elementary tensor operations, and it can largely be used as a drop-in replacement for FQE that allows for more efficient but approximate emulation of larger Fermionic circuits. Finally, we show several applications relevant to both near-term and fault-tolerant quantum algorithms where approximate emulation of larger systems is expected to be useful: characterization of state preparation strategies for quantum phase estimation, the testing of different variational quantum eigensolver ansätze, the numerical evaluation of Trotter errors, and the simulation of general quantum dynamics problems. In all these examples, approximate emulation with MPS-FQE allows us to treat systems that are significantly larger than those accessible with a full statevector emulator.

Mechanisms of methyl 2-methylbutyrate suppression on Aspergillus flavus growth and aflatoxin B1 biosynthesis

Aspergillus flavus and subsequently produced carcinogenic aflatoxins frequently contaminate postharvest food crops, resulting in a threat to global food safety. Chemical preservatives are currently the main antifungal agents. However, fungal resistance effect, biological toxicity, and environmental contamination limit their practical applications. The application of natural volatile organic compounds has great potential for controlling fungal and mycotoxin contamination of postharvest food crops. This study therefore investigated the antifungal and anti-aflatoxigenic activities of the volatile compound, methyl 2-methylbutyrate (M2M), against Aspergillus flavus and its potential mechanisms. M2M effectively inhibited A. flavus mycelia growth, with a minimum inhibitory concentration of 2.0 μL/mL. Moreover, M2M also suppressed aflatoxin production, sclerotia production, and the pathogenicity on peanut and corn flour. RNA-Seq results showed that 2899 differentially expressed genes (DEGs), and DEGs involved in ergosterol synthesis, cell wall structure, glycolysis, citric acid cycle, mitogen activated protein kinase signaling pathway, DNA replication, and aflatoxin biosynthesis, were down-regulated in A. flavus. Further studies showed that M2M strongly damaged the cell membrane and cell wall integrity, reduced ATP levels, and induced reactive oxygen species (ROS) accumulation and DNA damage. Notably, a GATA type zinc finger transcription factor, AfSreA (AFLA_132440), which is essential for A. flavus growth and aflatoxin production, was identified. The growth and aflatoxin yield in the ΔAfSreA strain decreased by 94.94 % and 71.82 %, respectively. Additionally, deletion of AfSreA destroyed cell wall integrity and decreased expressions of genes involved in aflatoxin biosynthesis. Taken together, our results identified the antifungal and anti-aflatoxigenic mechanisms of M2M against A. flavus, and confirmed the potential of M2M in protecting peanut and corn from fungal contamination.

Comprehensive analysis of aflatoxin B1 biosynthesis in Aspergillus flavus via transcriptome-wide m6A methylome response to cycloleucine

Aspergillus flavus and its toxic aflatoxins secondary metabolites contaminate food and grains, posing a severe threat to human health and leading to liver cancer. Here, we demonstrated that cycloleucine blocked aflatoxin B1 synthesis by inhibiting N6-methyladenosine (m6A) methylation modification of messenger RNA (mRNA). m6A Methylation Immunoprecipitation Sequencing (m6A MeRIP-Seq)-based comprehensive transcriptome-wide m6A profiling identified 102 differentially expressed genes that underwent m6A modification, of which 22 hypermethylated genes were downregulated and 49 hypomethylated genes were upregulated, suggesting a negative correlation between m6A methylation and gene expression. Notably, cycloleucine inhibited aflatoxin B1 production via multiple targets. The m6A sites of several key genes involved in the aflatoxin B1 biosynthesis pathway were significantly enriched in the coding sequence and around the stop codon, resulting in their downregulation. Furthermore, m6A methylation on genes related to the aflatoxin B1 biosynthesis pathway led to reduced mRNA stability. Cycloleucine inhibition of aflatoxin B1 production highlights its potential as an agent for removing mycotoxins in environmental pollution. ENVIRONMENTAL IMPLICATION: Aflatoxins, highly carcinogenic secondary metabolites produced by Aspergillus flavus, frequently contaminate crops such as peanut, corn, wheat and sesame leading to irreversible loss in the quality and yield of agricultural products and posing serious threats to food safety. Aflatoxins has also been linked to developmental delays and liver cancer in humans. In our study, 'monitoring aflatoxin concentrations and its bioaccumulation in organisms' has been conducted. The results demonstrated that aflatoxin production in A. flavus was completely blocked after cycloleucine treatment. Additionally, we demonstrated that inhibition of aflatoxin was linked to N6-methyladenosine methylation of multiple genes in aflatoxin biosynthesis pathway.

Block2: A comprehensive open source framework to develop and apply state-of-the-art DMRG algorithms in electronic structure and beyond

block2 is an open source framework to implement and perform density matrix renormalization group and matrix product state algorithms. Out-of-the-box it supports the eigenstate, time-dependent, response, and finite-temperature algorithms. In addition, it carries special optimizations for ab initio electronic structure Hamiltonians and implements many quantum chemistry extensions to the density matrix renormalization group, such as dynamical correlation theories. The code is designed with an emphasis on flexibility, extensibility, and efficiency and to support integration with external numerical packages. Here, we explain the design principles and currently supported features and present numerical examples in a range of applications.

Multireference Protonation Energetics of a Dimeric Model of Nitrogenase Iron-Sulfur Clusters

Characterizing the electronic structure of the iron-sulfur clusters in nitrogenase is necessary to understand their role in the nitrogen fixation process. One challenging task is to determine the protonation state of the intermediates in the nitrogen fixing cycle. Here, we use a dimeric iron-sulfur model to study relative energies of protonation at C, S, or Fe. Using a composite method based on coupled cluster and density matrix renormalization group energetics, we converge the relative energies of four protonated configurations with respect to basis set and correlation level. We find that accurate relative energies require large basis sets as well as a proper treatment of multireference and relativistic effects. We have also tested ten density functional approximations for these systems. Most of them give large errors in their relative energies. The best performing functional in this system is B3LYP, which gives mean absolute and maximum deviations of only 10 and 13 kJ/mol with respect to our correlated wave function estimates, respectively, comparable to the uncertainty in our correlated estimates. Our work provides benchmark results for the calibration of new approximate electronic structure methods and density functionals for these problems.

Functional Characterization of Aldehyde Dehydrogenase in Fusarium graminearum

Aldehyde dehydrogenase (ALDH), a common oxidoreductase in organisms, is an aldehyde scavenger involved in various metabolic processes. However, its function in different pathogenic fungi remains unknown. Fusarium graminearum causes Fusarium head blight in cereals, which reduces grain yield and quality and is an important global food security problem. To elucidate the pathogenic mechanism of F. graminearum, seven genes encoding ALDH were knocked out and then studied for their function. Single deletions of seven ALDH genes caused a decrease in spore production and weakened the pathogenicity. Furthermore, these deletions altered susceptibility to various abiotic stresses. FGSG_04194 is associated with a number of functions, including mycelial growth and development, stress sensitivity, pathogenicity, toxin production, and energy metabolism. FGSG_00139 and FGSG_11482 are involved in sporulation, pathogenicity, and SDH activity, while the other five genes are multifunctional. Notably, we found that FGSG_04194 has an inhibitory impact on ALDH activity, whereas FGSG_00979 has a positive impact. RNA sequencing and subcellular location analysis revealed that FGSG_04194 is responsible for biological process regulation, including glucose and lipid metabolism. Our results suggest that ALDH contributes to growth, stress responses, pathogenicity, deoxynivalenol synthesis, and mitochondrial energy metabolism in F. graminearum. Finally, ALDH presents a potential target and theoretical basis for fungicide development.

An Ab Initio Correction Vector Restricted Active Space Approach to the L-Edge XAS and 2p3d RIXS Spectra of Transition Metal Complexes

We describe an ab initio approach to simulate L-edge X-ray absorption (XAS) and 2p3d resonant inelastic X-ray scattering (RIXS) spectroscopies. We model the strongly correlated electronic structure within a restricted active space and employ a correction vector formulation instead of sum-over-state expressions for the spectra, thus eliminating the need to calculate a large number of intermediate and final electronic states. We present benchmark simulations of the XAS and RIXS spectra of the iron complexes [FeCl4]1-/2- and [Fe(SCH3)4]1-/2- and interpret the spectra by deconvolving the correction vectors. Our approach represents a step toward simulating the X-ray spectroscopies of larger metal cluster systems that play a pivotal role in biology.

[Analysis of respiratory syncytial virus nonstructural protein 1 amino acid variation and clinical characteristics]

Objective: To investigate the relationship between amino acid variations of respiratory syncytial virus (RSV) nonstructural protein (NS) 1 and the clinical characteristics. Method: A retrospective case review was conducted. From December 2018 to January 2020, a total of 81 cases of hospitalized children who were tested only positive for RSV by RT-PCR or PCR at the Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University were included in the study. The NS1 genes of RSV subtype A and subtype B were amplified by PCR and sequenced. The amino acid sequences were analyzed. The Chi-square test and Mann-Whitney rank sum test were used to compare the clinical characteristics and type Ⅰ interferon levels of children with or without NS1 variation in the variation and non-variation groups. Results: Among 81 cases, there were 58 males and 23 females. There were 11 cases in the variation group, the age of onset was 2.0 (1.0, 11.0) months, included 4 cases of subtype A (variant sites were: 2 cases for Lys33Gln, one case for Gly2Asp, Pro67Ser, Leu137Phe, respectively) and 7 cases of subtype B (variant sites were: two cases for Val121Ile, one case for Tyr30Cys, Val65Met, Asn85Ser, Ser118Asn, Asp124Asn, respectively). These variant sites all appeared at a very low frequency 0.08 (0.04, 0.29) % in the NCBI PROTEIN database. There were 70 cases in non-variation group, the onset age was 3.5 (1.0, 7.0) months. The proportion of dyspnea in the variation group was higher than that in the non-variation group (10/11 vs. 47% (33/70), χ²=7.31, P<0.01). Conclusions: There are some variant sites in nonstructural protein NS1 of RSV. Children may be prone to have dyspnea with NS1 variations.

Assessment of DFT functionals for a minimal nitrogenase [Fe(SH)4H]- model employing state-of-the-art ab initio methods

We have designed a [Fe(SH)4H]- model with the fifth proton binding either to Fe or S. We show that the energy difference between these two isomers (∆E) is hard to estimate with quantum-mechanical (QM) methods. For example, different density functional theory (DFT) methods give ∆E estimates that vary by almost 140 kJ/mol, mainly depending on the amount of exact Hartree-Fock included (0%-54%). The model is so small that it can be treated by many high-level QM methods, including coupled-cluster (CC) and multiconfigurational perturbation theory approaches. With extrapolated CC series (up to fully connected coupled-cluster calculations with singles, doubles, and triples) and semistochastic heat-bath configuration interaction methods, we obtain results that seem to be converged to full configuration interaction results within 5 kJ/mol. Our best result for ∆E is 101 kJ/mol. With this reference, we show that M06 and B3LYP-D3 give the best results among 35 DFT methods tested for this system. Brueckner doubles coupled cluster with perturbaitve triples seems to be the most accurate coupled-cluster approach with approximate triples. CCSD(T) with Kohn-Sham orbitals gives results within 4-11 kJ/mol of the extrapolated CC results, depending on the DFT method. Single-reference CC calculations seem to be reasonably accurate (giving an error of ∼5 kJ/mol compared to multireference methods), even if the D1 diagnostic is quite high (0.25) for one of the two isomers.

Hierarchical Clifford Transformations to Reduce Entanglement in Quantum Chemistry Wave Functions

The performance of computational methods for many-body physics and chemistry is strongly dependent on the choice of the basis used to formulate the problem. Hence, the search for similarity transformations that yield better bases is important for progress in the field. So far, tools from theoretical quantum information have not been thoroughly explored for this task. Here we take a step in this direction by presenting efficiently computable Clifford similarity transformations for the molecular electronic structure Hamiltonian, which expose bases with reduced entanglement in the corresponding molecular ground states. These transformations are constructed via block-diagonalization of a hierarchy of truncated molecular Hamiltonians, preserving the full spectrum of the original problem. We show that the bases introduced here allow for more efficient classical and quantum computations of ground-state properties. First, we find a systematic reduction of bipartite entanglement in molecular ground states as compared to standard problem representations. This entanglement reduction has implications in classical numerical methods, such as those based on the density matrix renormalization group. Then, we develop variational quantum algorithms that exploit the structure in the new bases, showing again improved results when the hierarchical Clifford transformations are used.

Evaluating the evidence for exponential quantum advantage in ground-state quantum chemistry

Due to intense interest in the potential applications of quantum computing, it is critical to understand the basis for potential exponential quantum advantage in quantum chemistry. Here we gather the evidence for this case in the most common task in quantum chemistry, namely, ground-state energy estimation, for generic chemical problems where heuristic quantum state preparation might be assumed to be efficient. The availability of exponential quantum advantage then centers on whether features of the physical problem that enable efficient heuristic quantum state preparation also enable efficient solution by classical heuristics. Through numerical studies of quantum state preparation and empirical complexity analysis (including the error scaling) of classical heuristics, in both ab initio and model Hamiltonian settings, we conclude that evidence for such an exponential advantage across chemical space has yet to be found. While quantum computers may still prove useful for ground-state quantum chemistry through polynomial speedups, it may be prudent to assume exponential speedups are not generically available for this problem.

AnAzf1 acts as a positive regulator of ochratoxin A biosynthesis in Aspergillus niger

Aspergillus niger produces genotoxic and carcinogenic ochratoxin A (OTA) that severely threatens human and animal health. Transcription factor Azf1 is essential in regulating fungal cell development and primary metabolism. However, its effect and mechanism on secondary metabolism are unclear. Here, we characterized and deleted a Azf1 homolog gene, An15g00120 (AnAzf1), in A. niger, which completely blocked OTA production, and repressed the OTA cluster genes, p450, nrps, hal, and bzip at the transcriptional level. The results indicated that AnAzf1 was a positive regulator of OTA biosynthesis. Transcriptome sequencing results showed that the AnAzf1 deletion significantly upregulated antioxidant genes and downregulated oxidative phosphorylation genes. Enzymes involved in reactive oxygen species (ROS) scavenging, including catalase (CAT) and peroxidase (POD) were increased, and the corresponding ROS levels were decreased. Upregulation of genes (cat, catA, hog1, and gfd) in the MAPK pathway and downregulation of genes in iron homeostasis were associated with decreased ROS levels, linking the altered MAPK pathway and iron homeostasis to lower ROS levels caused by AnAzf1 deletion. Additionally, enzymes including complex I (NADH-ubiquinone oxidoreductase), and complex V (ATP synthase), as well as ATP levels, were significantly decreased, indicating impaired oxidative phosphorylation caused by the AnAzf1-deletion. During lower ROS levels and impaired oxidative phosphorylation, OTA was not produced in ∆AnAzf1. Together, these results strongly suggested that AnAzf1 deletion blocked OTA production in A. niger by a synergistic interference of ROS accumulation and oxidative phosphorylation. KEY POINTS: • AnAzf1 positively regulated OTA biosynthesis in A. niger. • Deletion of AnAzf1 decreased ROS levels and impaired oxidative phosphorylation. • An altered MAPK pathway and iron homeostasis were associated with lower ROS levels.

Density Matrix Renormalization Group for Transcorrelated Hamiltonians: Ground and Excited States in Molecules

We present the theory of a density matrix renormalization group (DMRG) algorithm which can solve for both the ground and excited states of non-Hermitian transcorrelated Hamiltonians and show applications in molecular systems. Transcorrelation (TC) accelerates the basis set convergence rate by including known physics (such as, but not limited to, the electron-electron cusp) in the Jastrow factor used for the similarity transformation. It also improves the accuracy of approximate methods such as coupled cluster singles and doubles (CCSD) as shown by recent studies. However, the non-Hermiticity of the TC Hamiltonians poses challenges for variational methods like DMRG. Imaginary-time evolution on the matrix product state (MPS) in the DMRG framework has been proposed to circumvent this problem, but this is currently limited to treating the ground state and has lower efficiency than the time-independent DMRG (TI-DMRG) due to the need to eliminate Trotter errors. In this work, we show that with minimal changes to the existing TI-DMRG algorithm, namely, replacing the original Davidson solver with the general Davidson solver to solve the non-Hermitian effective Hamiltonians at each site for a few low-lying right eigenstates, and following the rest of the original DMRG recipe, one can find the ground and excited states with improved efficiency compared to the original DMRG when extrapolating to the infinite bond dimension limit in the same basis set. An accelerated basis set convergence rate is also observed, as expected, within the TC framework.

[Metagenomic sequencing for diagnosis of sparganosis mansoni: a case report]

The patient was found to develop a migrating mass in the lower abdomen without any known cause in 2000, and the cause had not been identified following multiple diagnoses since then. The mass was found to migrate to the left anterior axillary regions on August 11, 2020. Then, three segments of incomplete white worms were resected through minimally invasive surgery, and metagenomic sequencing revealed sparganosis mansoni. After surgical resection of complete worms was performed on October 21, 2021, the case was cured and discharged from the hospital. Follow-up revealed satisfactory outcomes and no new mass was found throughout the body.

A comparison between the one- and two-step spin-orbit coupling approaches based on the ab initio Density Matrix Renormalization Group

The efficient and reliable treatment of both spin-orbit coupling (SOC) and electron correlation is essential for understanding f-element chemistry. We analyze two approaches to the problem, the one-step approach where both effects are treated simultaneously, and the two-step state interaction approach. We report an implementation of the ab initio density matrix renormalization group(DMRG) with a one-step treatment of the SOC effect which can be compared to prior two-step treatments on an equal footing. Using a dysprosium octahedral complex and bridged dimer as benchmark systems, we identify characteristics of problems where the one-step approach is beneficial for obtaining the low-energy spectrum.

Afper1 contributes to cell development and aflatoxin biosynthesis in Aspergillus flavus

Aspergillus flavus contaminates crops and produces carcinogenic aflatoxins that pose severe threat to food safety and human health. To identify potential targets to control aflatoxin contamination, we characterized a novel Afper1 protein, which regulates cell development and secondary metabolite biosynthesis in A. flavus. Afper1 is localized in the nucleus and is required for hyphal growth, conidial and sclerotial production, and responses to osmotic stress and essential oils such as cinnamaldehyde and thymol. More importantly, aflatoxin production was impaired in the Afper1 deletion mutant. Proteomics analysis revealed that extracellular hydrolases and proteins involved in conidial development, endoplasmic reticulum (ER) homeostasis, and aflatoxin biosynthesis were differentially regulated in ΔAfper1. Unexpectedly, enzymes participated in reactive oxygen species (ROS) scavenging, including catalase (catA, catB) and superoxide dismutase (sodM) were significantly downregulated, and the ROS accumulation and sensitivity to hydrogen peroxide were confirmed experimentally. Additionally, Afper1 deletion significantly upregulated heterochromatin protein HepA and downregulated acetyltransferases involved in heterochromatin formation. Accompanying ROS accumulation and chromatin remodeling, proteins related to aflatoxins, ustiloxin B and gliotoxin were downregulated. These results implied that Afper1 deletion affected chromatin remodeling and disturbed ER homeostasis, leading to ROS accumulation, and ultimately resulting in defective growth and impaired secondary metabolite biosynthesis.

Systematic electronic structure in the cuprate parent state from quantum many-body simulations

The quantitative description of correlated electron materials remains a modern computational challenge. We demonstrate a numerical strategy to simulate correlated materials at the fully ab initio level beyond the solution of effective low-energy models and apply it to gain a detailed microscopic understanding across a family of cuprate superconducting materials in their parent undoped states. We uncover microscopic trends in the electron correlations and reveal the link between the material composition and magnetic energy scales through a many-body picture of excitation processes involving the buffer layers. Our work illustrates a path toward a quantitative and reliable understanding of more complex states of correlated materials at the ab initio many-body level.

The Chromium Dimer: Closing a Chapter of Quantum Chemistry

The complex electronic structure and unusual potential energy curve of the chromium dimer have fascinated scientists for decades, with agreement between theory and experiment so far elusive. Here, we present a new ab initio simulation of the potential energy curve and vibrational spectrum that significantly improves on all earlier estimates. Our data support a shift in earlier experimental assignments of a cluster of vibrational frequencies by one quantum number. The new vibrational assignment yields an experimentally derived potential energy curve in quantitative agreement with theory across all bond lengths and across all measured frequencies. By solving this long-standing problem, our results raise the possibility of quantitative quantum chemical modeling of transition metal clusters with spectroscopic accuracy.

Insights into the Underlying Mechanism of Ochratoxin A Production in Aspergillus niger CBS 513.88 Using Different Carbon Sources

Aspergillus niger produces carcinogenic ochratoxin A (OTA), a serious food safety and human health concern. Here, the ability of A. niger CBS 513.88 to produce OTA using different carbon sources was investigated and the underlying regulatory mechanism was elucidated. The results indicated that 6% sucrose, glucose, and arabinose could trigger OTA biosynthesis and that 1586 differentially expressed genes (DEGs) overlapped compared to a non-inducing nutritional source, peptone. The genes that participated in OTA and its precursor phenylalanine biosynthesis, including pks, p450, nrps, hal, and bzip, were up-regulated, while the genes involved in oxidant detoxification, such as cat and pod, were down-regulated. Correspondingly, the activities of catalase and peroxidase were also decreased. Notably, the novel Gal4-like transcription factor An12g00840 (AnGal4), which is vital in regulating OTA biosynthesis, was identified. Deletion of AnGal4 elevated the OTA yields by 47.65%, 54.60%, and 309.23% using sucrose, glucose, and arabinose as carbon sources, respectively. Additionally, deletion of AnGal4 increased the superoxide anion and H₂O₂ contents, as well as the sensitivity to H₂O₂, using the three carbon sources. These results suggest that these three carbon sources repressed AnGal4, leading to the up-regulation of the OTA biosynthetic genes and alteration of cellular redox homeostasis, ultimately triggering OTA biosynthesis in A. niger.

Lysine 2-hydroxyisobutyrylation orchestrates cell development and aflatoxin biosynthesis in Aspergillus flavus

Lysine 2-hydroxyisobutyrylation (K_hib ) is a recently identified post-translational modifications (PTM) that regulates numerous cellular metabolic processes. In pathogenic microorganism, although glycolysis and fungal virulence are regulated by K_hib , its potential roles in fungi remains to be elusive. Our preliminary results showed that levels of K_hib fluctuate over time in Aspergillus flavus, which frequently contaminates crops and produces carcinogenic aflatoxins. However, the perception of K_hib function in A. flavus is limited, especially in mycotoxin-producing strains. Here, we performed a comprehensive analysis of K_hib in A. flavus, and 7156 K_hib sites were identified in 1473 proteins. Notably, we demonstrated that K_hib of AflM, a key enzyme in aflatoxin biosynthesis, affected conidia production and sclerotia formation. Furthermore, aflM deletion impaired aflatoxin biosynthesis, and more importantly, strains in which K_hib was mimicked by K to T mutation at K49, K179 and K180 sites showed reduced aflatoxin production compared with wild type and ΔaflM complementation strains. These results indicate that K_hib at these sites of AflM negatively regulates aflatoxin biosynthesis in A. flavus. In summary, our study revealed the potential roles of K_hib in A. flavus, and particularly shed light on a new way to regulate aflatoxin production via K_hib . This article is protected by copyright. All rights reserved.

Conservation laws in coupled cluster dynamics at finite temperature

We extend the finite-temperature Keldysh non-equilibrium coupled cluster theory (Keldysh-CC) [A. F. White and G. K.-L. Chan, J. Chem. Theory Comput. 15, 6137-6253 (2019)] to include a time-dependent orbital basis. When chosen to minimize the action, such a basis restores local and global conservation laws (Ehrenfest's theorem) for all one-particle properties while remaining energy conserving for time-independent Hamiltonians. We present the time-dependent Keldysh orbital-optimized coupled cluster doubles method in analogy with the formalism for zero-temperature dynamics, extended to finite temperatures through the time-dependent action on the Keldysh contour. To demonstrate the conservation property and understand the numerical performance of the method, we apply it to several problems of non-equilibrium finite-temperature dynamics: a 1D Hubbard model with a time-dependent Peierls phase, laser driving of molecular H₂, driven dynamics in warm-dense silicon, and transport in the single impurity Anderson model.

Externally Corrected CCSD with Renormalized Perturbative Triples (R-ecCCSD(T)) and the Density Matrix Renormalization Group and Selected Configuration Interaction External Sources

We investigate the renormalized perturbative triples correction together with the externally corrected coupled-cluster singles and doubles (ecCCSD) method. We use the density matrix renormalization group (DMRG) and heat-bath CI (HCI) as external sources for the ecCCSD equations. The accuracy is assessed for the potential energy surfaces of H₂O, N₂, and F₂. We find that the triples correction significantly improves upon ecCCSD, and we do not see any instability of the renormalized triples with respect to dissociation. We explore how to balance the cost of computing the external source amplitudes against the accuracy of the subsequent CC calculation. In this context, we find that very approximate wave functions (and their large amplitudes) serve as an efficient and accurate external source. Finally, we characterize the domain of correlation treatable using the ecCCSD and renormalized triples combination studied in this work via a well-known wave function diagnostic.

Hsa_circ_0011946 promotes the migration and invasion of hepatocellular carcinoma by inducing EMT process

OBJECTIVE

Recently, the vital role of circular RNAs is discovered in many diseases including tumor progression and metastasis. Hepatocellular carcinoma (HCC) is one of the most ordinary malignant tumors. The purpose of our study is to detect the potential function of hsa_circ_0011946 in HCC to offer new biomarkers and targets.

PATIENTS AND METHODS

The level of hsa_circ_0011946 in HCC tissues and cell lines was monitored by Real Time Quantitative Polymerase Chain Reaction (RT-qPCR). Pearson's Chi-square test was used to determine the association between hsa_circ_0011946 expression and several clinicopathological factors. Then, hsa_circ_0011946 was knocked down in HCC cells to uncover its function in metastasis of HCC. Cell migrated and invaded ability was measured through transwell assay, Matrigel assay and wound healing assay. Western blot assay was performed to analyze the effect of hsa_circ_0011946 on the epithelial-to-mesenchymal transition (EMT) process.

RESULTS

In this research, the expression level of hsa_circ_0011946 was significantly increased in HCC tissues compared to that in adjacent samples. The expression of hsa_circ_0011946 was also increased in HCC cell lines. The hsa_circ_0011946 expression was associated with lymphatic metastasis in HCC patients. Knockdown of hsa_circ_0011946 led to the inhibition of cell migration and invasion in HCC. In addition, results of further experiments revealed that the EMT-related proteins were regulated via the knockdown of hsa_circ_0011946 in HCC.

CONCLUSIONS

The hsa_circ_0011946 could enhance cell migration and invasion of HCC by inducing the EMT process.

Is lower low-density lipoprotein cholesterol associated with lower androgen and erectile dysfunction in men?

BACKGROUND AND AIMS

Therapeutic possibilities now exist to lower low-density lipoprotein cholesterol (LDL-C) to very low levels. However, substantial controversy remains in clinical practice with regard to its safety, and the question of whether low LDL-C levels per se may provoke adverse effects in humans arises. We aimed to explore the association of LDL-C with androgen and erectile dysfunction (ED) in a general population of men.

METHODS AND RESULTS

A total of 4203 men without hormone replacement therapy were enrolled from 22 sites in East China. Total testosterone (T) and Free T were assessed. Free androgen index (FAI) was calculated. The IIEF-5 questionnaire was used to assess ED. We found that free T and FAI gradually and markedly increased with increasing LDL-C levels. Using linear regression, after adjusting for age, educational level, economic status, smoking status, drinking status, BMI, diabetes, and use of lipid-lowering medication, LDL-C was positively associated with free T (B = 0.175, 95% CI: 0.084, 0.266) and FAI (B = 0.064, 95% CI: 0.016, 0.112). Meanwhile, there was a U-shaped curvilinear relationship between LDL-C and prevalence of ED. In the logistic regression analysis, compared to those with LDL-C among the 10th-90th percentile, the ORs of ED in men in the lowest and highest deciles were 1.938 (95% CI: 1.121, 3.349) and 1.804 (95% CI: 1.117, 2.916), respectively.

CONCLUSION

Lower LDL-C levels were significantly associated with lower free T and lower FAI in a general population of men. Moreover, both low and high levels of LDL-C might be risk factors for ED.

Local Fluxionality of Surface-Deposited Cluster Catalysts: The Case of Pt7 on Al2O3

Subnano surface-supported catalytic clusters can be generally characterized by many low-energy isomers accessible at elevated temperatures of catalysis. The most stable isomer may not be the most catalytically active. Additionally, isomers may interconvert across barriers, i.e., exhibit fluxionality, during catalysis. To study the big picture of the cluster fluxional behavior, we model such a process as isomerization graph using bipartite matching algorithm, harmonic transition state theory, and paralleled nudged elastic band method. All the minimal energy paths form a minimum spanning tree (MST) of the original graph. Detailed inspection shows that, at temperatures typical for catalysis, the cluster geometry changes frequently within several regions in the MST, while transition across regions is less likely. As a further confirmation, the structural similarity analysis was additionally performed based on molecular dynamics trajectories. This local fluxionality picture provides a new perspective on understanding finite-temperate catalytic processes.

Abstract P1-03-10: HER2 expression in clinical breast cancer samples: A novel detection methodology for HER2 protein quantitation using fluorescent nanoparticles

Background: The human epidermal growth factor receptor-2 (HER2) is a member of a family of transmembrane tyrosine kinase receptors that play an important role in regulated normal cell growth and differentiation. The over-expression of HER2 in a subset of 15-20% of invasive breast cancers has an important bearing on prognosis, as HER2-positive tumors are associated with an aggressive clinical course and poor outcome. Targeting HER2-overexpression has been shown to be a remarkably effective therapeutic modality; however testing of tumor samples to assess the HER2 status of the patient's breast cancer is required. Clinical assays to assess the HER2 status in patients being considered for targeted therapy include immunohistochemistry (IHC), which detects protein over-expression, or fluorescence in situ hybridization (FISH), which detects gene amplification. Both the IHC and FISH methodologies have limitations. Given that the target of the currently approved drugs is the receptor protein, novel detections systems that could more accurately and quantitatively detect HER2 protein in clinical samples over a broad dynamic range would be advantageous and may be clinically helpful.

Material and Methods: A novel detection technology using streptavidin-coated Phosphor Integrated Dot fluorescent nanoparticles (PID) has been developed that can be visualized by fluorescence microscopy and used for quantitative immunofluorescence detection of protein in clinical samples using computer assisted image analysis. In the current study, PID- nanoparticles were used to analyze HER2 protein expression in breast cancer cell lines and 120 well characterized breast cancer samples. These results have been compared with HER2 IHC and HER2 FISH analysis.

Results: The expression levels of HER2 protein from 8 breast cancer cell lines was evaluated by antibody-binding capacity with FACS analysis. Formalin fixed paraffin embedded cell pellets for these cell lines were prepared and used for quantitative HER2 analysis by PID. The PID score/cell for each of these cell lines showed a strong linear correlation with antibody-binding capacity sites/cell by FACS analysis (R2 = 0.94). For the 120 breast cancer samples, PID score/cell was measured and compared against HER2 IHC membrane intensity measure by image analysis (Aperio) and HER2 FISH results. The HER2 PID score/cell showed a correlation coefficient of R2=0.72 versus the average HER2 copy number per cell by FISH, compared with a correlation coefficient of R2=0.41 for HER2 IHC membrane intensity measured by Aperio. For the HER2/CEP17 ratio, the correlation coefficient for the PID score/cell was R2=0.79 compared with a correlation coefficient of R2=0.32 for the HER2 IHC membrane intensity.

Conclusions: PID-nanoparticles demonstrate great potential for the quantitative measurement of protein of clinical interest in routine clinical samples with morphologic confirmation of the tissue being studied. Further studies looking for PID-score thresholds for HER2 gene amplification and correlations with clinical outcome data are warranted and ongoing.

Citation Format: Hicks DG, Goda H, Zhai H, Okada H, McMahon L, Sullivan N, Tang P, Nakano Y. HER2 expression in clinical breast cancer samples: A novel detection methodology for HER2 protein quantitation using fluorescent nanoparticles [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-03-10.

Identification of Chromosome Segment Substitution Lines of Gossypium barbadense Introgressed in G. hirsutum and Quantitative Trait Locus Mapping for Fiber Quality and Yield Traits

Chromosome segment substitution lines MBI9804, MBI9855, MBI9752, and MBI9134, which were obtained by advanced backcrossing and continuously inbreeding from an interspecific cross between CCRI36, a cultivar of upland cotton (Gossypium hirsutum) as the recurrent parent, and Hai1, a cultivar of sea island cotton (G. barbadense) as the donor parent, were used to construct a multiple parent population of (MBI9804×MBI9855)×(MBI9752×MBI9134). The segregating generations of double-crossed F1 and F2 and F2:3 were used to map the quantitative trait locus (QTL) for fiber quality and yield-related traits. The recovery rate of the recurrent parent CCRI36 in the four parental lines was from 94.3%-96.9%. Each of the parental lines harbored 12-20 introgressed segments from Hai1across 21 chromosomes. The number of introgressed segments ranged from 1 to 27 for the individuals in the three generations, mostly from 9 to 18, which represented a genetic length of between 126 cM and 246 cM. A total of 24 QTLs controlling fiber quality and 11 QTLs controlling yield traits were detected using the three segregating generations. These QTLs were distributed across 11 chromosomes and could collectively explain 1.78%-20.27% of the observed phenotypic variations. Sixteen QTLs were consistently detected in two or more generations, four of them were for fiber yield traits and 12 were for fiber quality traits. One introgressed segment could significantly reduce both lint percentage and fiber micronaire. This study provides useful information for gene cloning and marker-assisted breeding for excellent fiber quality.

True digestible phosphorus requirement for forty- to eighty-kilogram pigs

The objective of this study was to determine the true digestible P requirement of 40- to 60-kg (Exp. 1) and 60- to 80-kg (Exp. 2) pigs by broken-line analysis of growth performance data using 6 levels of true digestible P. In each 3-wk experiment, 108 barrows and gilts were used, and 6 levels of monocalcium phosphate were added to a corn-soybean meal-based diet to establish 6 graded levels of true total tract digestible P ranging from 1.26 to 3.98 g/kg of diet in Exp. 1 or from 1.21 to 3.31 g/kg in Exp. 2. The true digestible P content was calculated using true total tract digestibility of 40.53%, 35.96%, and 84.31% for P in corn, soybean meal, and monocalcium phosphate, respectively. Limestone was added accordingly to maintain a constant Ca level across all diets of each experiment. The results of Exp. 1 showed that with graded supplementation of monocalcium phosphate, ADG linearly increased ( < 0.001) in wk 1 and both linearly and quadratically increased ( < 0.01) in wk 2, wk 3, and wk 0 to 3, and G:F linearly improved ( < 0.001) in wk 1, quadratically improved ( < 0.05) in wk 3, and both linearly and quadratically improved ( < 0.05) in wk 2 and wk 0 to 3 ( < 0.05). In Exp. 2, ADG linearly increased ( < 0.001) in wk 1 and both linearly and quadratically increased ( < 0.05) in wk 2, wk 3, and wk 0 to 3, with the graded supplementation of monocalcium phosphate, and G:F linearly improved ( < 0.01) in wk 1 and wk 3 and both linearly and quadratically improved ( < 0.001) in wk 2 and wk 0 to 3. In Exp. 1, the true digestible P requirement was estimated to be 2.66, 2.79, and 2.51 g/kg of diet (884 g DM/kg) for pigs of mixed sex, barrows, and gilts, respectively, on the basis of broken-line regression of ADG data for wk 0 to 3 against 6 true digestible P levels. Using G:F, the P requirement estimate was correspondingly 2.67, 2.51, and 2.93 g/kg of diet. In Exp. 2, the true digestible P requirement was estimated to be 2.29, 2.20, and 2.39 g/kg of diet (884 g DM/kg) using ADG data for wk 0 to 3 as the response variable and to be 2.33, 2.19, and 2.47 g/kg using wk 0 to 3 G:F data for pigs of mixed sex, barrows, and gilts, respectively. In conclusion, the mean TTTD-based P requirement was 2.66 and 2.31 g/kg of diet (884 g DM/kg) for 40- to 60-kg and 60- to 80-kg pigs, respectively.

Development of secondary mutations in wild-type and mutant EZH2 alleles cooperates to confer resistance to EZH2 inhibitors

The histone methyltransferase Enhancer of Zeste Homolog 2 (EZH2) is frequently dysregulated in cancers, and gain-of-function (GOF) EZH2 mutations have been identified in non-Hodgkin lymphomas. Small-molecule inhibitors against EZH2 demonstrated anti-tumor activity in EZH2-mutated lymphomas and entered clinical trials. Here, we developed models of acquired resistance to EZH2 inhibitor EI1 with EZH2-mutated lymphoma cells. Resistance was generated by secondary mutations in both wild-type (WT) and GOF Y641N EZH2 alleles. These EZH2 mutants retained the substrate specificity of their predecessor complexes but became refractory to biochemical inhibition by EZH2 inhibitors. Resistant cells were able to maintain a high level of H3K27Me3 in the presence of inhibitors. Interestingly, mutation of EZH2 WT alone generated an intermediate resistance phenotype, which is consistent with a previously proposed model of cooperation between EZH2 WT and Y641N mutants to promote tumorigenesis. In addition, the findings presented here have implications for the clinical translation of EZH2 inhibitors and underscore the need to develop novel EZH2 inhibitors to target potential resistance emerging in clinical settings.