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1. Mechanistic Insights into the Selectivity for Arsenic over Phosphate Adsorption by Fe ³⁺ -Cross-Linked Chitosan Using DFT

   https://doi.org/10.1021/acs.jpcb.3c06838  

   Nwokonkwo, Obinna; Muhich, Christopher (February 2024, The Journal of Physical Chemistry B)

   Fe3+-cross-linked chitosan exhibits the potential for selectively adsorbing arsenic (As) over competing species, such as phosphate, for water remediation. However, the effective binding mechanisms, bond nature, and controlling factor(s) of the selectivity are poorly understood. This study employs ab initio calculations to examine the competitive binding of As(V), P(V), and As(III) to neat chitosan and Fe3+-chitosan. Neat chitosan fails to selectively bind As oxyanions, as all three oxyanions bind similarly via weak hydrogen bonds with preferences of P(V) = As(V) > As(III). Conversely, Fe3+-chitosan selectively binds As(V) over As(III) and P(V) with binding energies of −1.9, −1, and −1.8 eV for As(V), As(III), and P(V), respectively. The preferences are due to varying Fe3+–oxyanion donor–acceptor characteristics, forming covalent bonds with distinct strengths (Fe–O bond ICOHP values: – 4.9 eV/bond for As(V), – 4.7 eV/bond for P(V), and −3.5 eV/bond for As(III)). Differences in pKa between As(V)/P(V) and As(III) preclude any preference for As(III) under typical environmental pH conditions. Furthermore, our calculations suggest that the binding selectivity of Fe3+-chitosan exhibits a pH dependence. These findings enhance our understanding of the Fe3+–oxyanion interaction crucial for preferential oxyanion binding using Fe3+-chitosan and provide a lens for further exploration into alternative transition-metal–chitosan combinations and coordination chemistries for applications in selective separations. 

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2. High Arsenic Levels Increase Activity Rather than Diversity or Abundance of Arsenic Metabolism Genes in Paddy Soils

   https://doi.org/10.1128/AEM.01383-21  

   Zhang, Si-Yu; Xiao, Xiao; Chen, Song-Can; Zhu, Yong-Guan; Sun, Guo-Xin; Konstantinidis, Konstantinos T. (September 2021, Applied and Environmental Microbiology)

   Cann, Isaac (Ed.)

   ABSTRACT Arsenic (As) metabolism genes are generally present in soils, but their diversity, relative abundance, and transcriptional activity in response to different As concentrations remain unclear, limiting our understanding of the microbial activities that control the fate of an important environmental pollutant. To address this issue, we applied metagenomics and metatranscriptomics to paddy soils showing a gradient of As concentrations to investigate As resistance genes ( ars ) including arsR , acr3 , arsB , arsC , arsM , arsI , arsP , and arsH as well as energy-generating As respiratory oxidation ( aioA ) and reduction ( arrA ) genes. Somewhat unexpectedly, the relative DNA abundances and diversities of ars , aioA , and arrA genes were not significantly different between low and high (∼10 versus ∼100 mg kg −1 ) As soils. Compared to available metagenomes from other soils, geographic distance rather than As levels drove the different compositions of microbial communities. Arsenic significantly increased ars gene abundance only when its concentration was higher than 410 mg kg −1 . In contrast, metatranscriptomics revealed that relative to low-As soils, high-As soils showed a significant increase in transcription of ars and aioA genes, which are induced by arsenite, the dominant As species in paddy soils, but not arrA genes, which are induced by arsenate. These patterns appeared to be community wide as opposed to taxon specific. Collectively, our findings advance understanding of how microbes respond to high As levels and the diversity of As metabolism genes in paddy soils and indicated that future studies of As metabolism in soil or other environments should include the function (transcriptome) level. IMPORTANCE Arsenic (As) is a toxic metalloid pervasively present in the environment. Microorganisms have evolved the capacity to metabolize As, and As metabolism genes are ubiquitously present in the environment even in the absence of high concentrations of As. However, these previous studies were carried out at the DNA level; thus, the activity of the As metabolism genes detected remains essentially speculative. Here, we show that the high As levels in paddy soils increased the transcriptional activity rather than the relative DNA abundance and diversity of As metabolism genes. These findings advance our understanding of how microbes respond to and cope with high As levels and have implications for better monitoring and managing an important toxic metalloid in agricultural soils and possibly other ecosystems. 

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3. Arsenite oxidation regulator AioR regulates bacterial chemotaxis towards arsenite in Agrobacterium tumefaciens GW4

   Article | OPEN | Published: 03 March 2017 Shi, K; Fan, X; Qiao, Z; Han, Y; McDermott, TR; Wang, Q; Wang, G. (March 2017, Scientific reports)

   Some arsenite [As(III)]-oxidizing bacteria exhibit positive chemotaxis towards As(III), however, the related As(III) chemoreceptor and regulatory mechanism remain unknown. The As(III)-oxidizing bacterium Agrobacterium tumefaciens GW4 displays positive chemotaxis towards 0.5–2 mM As(III). Genomic analyses revealed a putative chemoreceptor-encoding gene, mcp, located in the arsenic gene island and having a predicted promoter binding site for the As(III) oxidation regulator AioR. Expression of mcp and other chemotaxis related genes (cheA, cheY2 and fliG) was inducible by As(III), but not in the aioR mutant. Using capillary assays and intrinsic tryptophan fluorescence spectra analysis, Mcp was confirmed to be responsible for chemotaxis towards As(III) and to bind As(III) (but not As(V) nor phosphate) as part of the sensing mechanism. A bacterial one-hybrid system technique and electrophoretic mobility shift assays showed that AioR interacts with the mcp regulatory region in vivo and in vitro, and the precise AioR binding site was confirmed using DNase I foot-printing. Taken together, these results indicate that this Mcp is responsible for the chemotactic response towards As(III) and is regulated by AioR. Additionally, disrupting the mcp gene affected bacterial As(III) oxidation and growth, inferring that Mcp may exert some sort of functional connection between As(III) oxidation and As(III) chemotaxis. 

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4. Identification of differential alternative splicing events with an adjusted beta-distribution model

   https://doi.org/10.1109/EIT.2017.8053369  

   Liu, Kan; Du, Qian; Ren, Guodong; Yu, Bin; Zhang, Chi (May 2017, IEEE International Conference on Electro Information Technology (EIT))

   High-throughput next generation sequencing of cDNA, i.e. RNA-Seq, presents an unprecedented resource for characterizing the alternative splicing (AS) in complex eukaryotic transcriptomes. Accumulating evidences indicate that AS is developmentally regulated, but the precise responses of AS event to development is not well understood. Here, we describe a new method, based on an adjusted beta-distribution model, for detection of differential AS patterns from RNA-Seq data comparisons. Applying our method to two datasets of RNA-Seq for zika infection in human cells and pollen tissue in Arabidopsis thaliana, we identified 1,871 differentially AS events for 1,394 protein-coding genes in human and 496 differentially AS events for 358 protein-coding genes in Arabidopsis, respectively. The results included known AS events reported before as well as novel events, which demonstrate that the biological replicates are important in the effective identification using β-distribution. With a high accurate rate, our new method in differential AS identification will facilitate future investigation on transcriptomic annotation. 

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5. Sex Differences in Stress Response: Classical Mechanisms and Beyond

   https://doi.org/10.2174/1570159X22666231005090134  

   Hodes, Georgia E.; Bangasser, Debra; Sotiropoulos, Ioannis; Kokras, Nikolaos; Dalla, Christina (March 2024, Current Neuropharmacology)

   Abstract:Neuropsychiatric disorders, which are associated with stress hormone dysregulation, occurat different rates in men and women. Moreover, nowadays, preclinical and clinical evidence demonstratesthat sex and gender can lead to differences in stress responses that predispose males andfemales to different expressions of similar pathologies. In this curated review, we focus on what isknown about sex differences in classic mechanisms of stress response, such as glucocorticoid hormonesand corticotrophin-releasing factor (CRF), which are components of the hypothalamicpituitary-adrenal (HPA) axis. Then, we present sex differences in neurotransmitter levels, such as serotonin,dopamine, glutamate and GABA, as well as indices of neurodegeneration, such as amyloid βand Tau. Gonadal hormone effects, such as estrogens and testosterone, are also discussed throughoutthe review. We also review in detail preclinical data investigating sex differences caused by recentlyrecognizedregulators of stress and disease, such as the immune system, genetic and epigenetic mechanisms,as well neurosteroids. Finally, we discuss how understanding sex differences in stress responses,as well as in pharmacology, can be leveraged into novel, more efficacious therapeutics forall. Based on the supporting evidence, it is obvious that incorporating sex as a biological variable intopreclinical research is imperative for the understanding and treatment of stress-related neuropsychiatricdisorders, such as depression, anxiety and Alzheimer’s disease. 

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