ACS Chem Biol. 2023 Jun 16. doi: 10.1021/acschembio.3c00027. Online ahead of print.

ABSTRACT

The structure and mechanism of the bacterial enzyme β-lactamase have been well-studied due to its clinical role in antibiotic resistance. β-Lactamase is known to hydrolyze the β-lactam ring of the cephalosporin scaffold, allowing a spontaneous self-immolation to occur. Previously, cephalosporin-based sensors have been developed to evaluate β-lactamase expression in both mammalian cells and zebrafish embryos. Here, we present a circular caged morpholino oligonucleotide (cMO) activated by β-lactamase-mediated cleavage of a cephalosporin motif capable of silencing the expression of T-box transcription factor Ta (tbxta), also referred to as no tail a (ntla), eliciting a distinct, observable phenotype. We explore the use of β-lactamase to elicit a biological response in aquatic embryos for the first time and expand the utility of cephalosporin as a cleavable linker beyond targeting antibiotic-resistant bacteria. The addition of β-lactamase to the current suite of enzymatic triggers presents unique opportunities for robust, orthogonal control over endogenous gene expression in a spatially resolved manner.

PMID:37326511 | DOI:10.1021/acschembio.3c00027

Front Bioinform. 2023 Jun 1;3:1189723. doi: 10.3389/fbinf.2023.1189723. eCollection 2023.

ABSTRACT

Computational modeling has emerged as a critical tool in investigating the complex molecular processes involved in biological systems and diseases. In this study, we apply Boolean modeling to uncover the molecular mechanisms underlying Parkinson's disease (PD), one of the most prevalent neurodegenerative disorders. Our approach is based on the PD-map, a comprehensive molecular interaction diagram that captures the key mechanisms involved in the initiation and progression of PD. Using Boolean modeling, we aim to gain a deeper understanding of the disease dynamics, identify potential drug targets, and simulate the response to treatments. Our analysis demonstrates the effectiveness of this approach in uncovering the intricacies of PD. Our results confirm existing knowledge about the disease and provide valuable insights into the underlying mechanisms, ultimately suggesting potential targets for therapeutic intervention. Moreover, our approach allows us to parametrize the models based on omics data for further disease stratification. Our study highlights the value of computational modeling in advancing our understanding of complex biological systems and diseases, emphasizing the importance of continued research in this field. Furthermore, our findings have potential implications for the development of novel therapies for PD, which is a pressing public health concern. Overall, this study represents a significant step forward in the application of computational modeling to the investigation of neurodegenerative diseases, and underscores the power of interdisciplinary approaches in tackling challenging biomedical problems.

PMID:37325771 | PMC:PMC10267406 | DOI:10.3389/fbinf.2023.1189723

Front Immunol. 2023 May 31;14:1187554. doi: 10.3389/fimmu.2023.1187554. eCollection 2023.

NO ABSTRACT

PMID:37325654 | PMC:PMC10265110 | DOI:10.3389/fimmu.2023.1187554

Mol Biol Evol. 2023 May 22;40(6):msad121. doi: 10.1093/molbev/msad121/7175457.

ABSTRACT

When challenged by similar environmental conditions, phylogenetically distant taxa often independently evolve similar traits (convergent evolution). Meanwhile, adaptation to extreme habitats might lead to divergence between taxa that are otherwise closely related. These processes have long existed in the conceptual sphere, yet molecular evidence, especially for woody perennials, is scarce. The karst endemic Platycarya longipes, and its only congeneric species, P. strobilacea, which is widely distributed in the mountains in East Asia, provide an ideal model for examining the molecular basis of both convergent evolution and speciation. Using chromosome-level genome assemblies of both species, and whole genome resequencing data from 207 individuals spanning their entire distribution range, we demonstrate that P. longipes and P. strobilacea form two species-specific clades, which diverged around 2.09 million years ago. We find an excess of genomic regions exhibiting extreme interspecific differentiation, potentially due to long-term selection in P. longipes, likely contributing to the incipient speciation of the genus Platycarya. Interestingly, our results unveil underlying karst adaptation in both copies of the calcium influx channel gene TPC1 in P. longipes. TPC1 has previously been identified as a selective target in certain karst-endemic herbs, indicating a convergent adaptation to high calcium stress among karst-endemic species. Our study reveals the genic convergence of TPC1 among karst endemics, and the driving forces underneath the incipient speciation of the two Platycarya lineages.

PMID:37325551 | PMC:PMC10257982 | DOI:10.1093/molbev/msad121/7175457

J Multidiscip Healthc. 2023 Jun 9;16:1617-1618. doi: 10.2147/JMDH.S423363. eCollection 2023.

NO ABSTRACT

PMID:37325124 | PMC:PMC10263010 | DOI:10.2147/JMDH.S423363

Int J Biol Sci. 2023 May 11;19(9):2678-2694. doi: 10.7150/ijbs.81892. eCollection 2023.

ABSTRACT

Diabetic kidney disease (DKD) is one of the most common and severe microvascular complications of diabetes mellitus (DM), and has become the leading cause of end-stage renal disease (ESRD) worldwide. Although the exact pathogenic mechanism of DKD is still unclear, programmed cell death has been demonstrated to participate in the occurrence and development of diabetic kidney injury, including ferroptosis. Ferroptosis, an iron-dependent form of cell death driven by lipid peroxidation, has been identified to play a vital role in the development and therapeutic responses of a variety of kidney diseases, such as acute kidney injury (AKI), renal cell carcinoma and DKD. In the past two years, ferroptosis has been well investigated in DKD patients and animal models, but the specific mechanisms and therapeutic effects have not been fully revealed. Herein, we reviewed the regulatory mechanisms of ferroptosis, summarized the recent findings associated with the involvement of ferroptosis in DKD, and discussed the potential of ferroptosis as a promising target for DKD treatment, thereby providing a valuable reference for basic study and clinical therapy of DKD.

PMID:37324941 | PMC:PMC10266077 | DOI:10.7150/ijbs.81892

Front Plant Sci. 2023 May 30;14:1181035. doi: 10.3389/fpls.2023.1181035. eCollection 2023.

ABSTRACT

Switchgrass (Panicum virgatum L.) is a promising perennial bioenergy crop that achieves high yields with relatively low nutrient and energy inputs. Modification of cell wall composition for reduced recalcitrance can lower the costs of deconstructing biomass to fermentable sugars and other intermediates. We have engineered overexpression of OsAT10, encoding a rice BAHD acyltransferase and QsuB, encoding dehydroshikimate dehydratase from Corynebacterium glutamicum, to enhance saccharification efficiency in switchgrass. These engineering strategies demonstrated low lignin content, low ferulic acid esters, and increased saccharification yield during greenhouse studies in switchgrass and other plant species. In this work, transgenic switchgrass plants overexpressing either OsAT10 or QsuB were tested in the field in Davis, California, USA for three growing seasons. No significant differences in the content of lignin and cell wall-bound p-coumaric acid or ferulic acid were detected in transgenic OsAT10 lines compared with the untransformed Alamo control variety. However, the transgenic overexpressing QsuB lines had increased biomass yield and slightly increased biomass saccharification properties compared to the control plants. This work demonstrates good performance of engineered plants in the field, and also shows that the cell wall changes in the greenhouse were not replicated in the field, emphasizing the need to validate engineered plants under relevant field conditions.

PMID:37324714 | PMC:PMC10266223 | DOI:10.3389/fpls.2023.1181035

Front Plant Sci. 2023 May 30;14:1189998. doi: 10.3389/fpls.2023.1189998. eCollection 2023.

ABSTRACT

Tetraploid (AABB) and hexaploid (AABBDD) wheat have multiple sets of similar chromosomes, with successful meiosis and preservation of fertility relying on synapsis and crossover (CO) formation only taking place between homologous chromosomes. In hexaploid wheat, the major meiotic gene TaZIP4-B2 (Ph1) on chromosome 5B, promotes CO formation between homologous chromosomes, whilst suppressing COs between homeologous (related) chromosomes. In other species, ZIP4 mutations eliminate approximately 85% of COs, consistent with loss of the class I CO pathway. Tetraploid wheat has three ZIP4 copies: TtZIP4-A1 on chromosome 3A, TtZIP4-B1 on 3B and TtZIP4-B2 on 5B. Here, we have developed single, double and triple zip4 TILLING mutants and a CRISPR Ttzip4-B2 mutant, to determine the effect of ZIP4 genes on synapsis and CO formation in the tetraploid wheat cultivar 'Kronos'. We show that disruption of two ZIP4 gene copies in Ttzip4-A1B1 double mutants, results in a 76-78% reduction in COs when compared to wild-type plants. Moreover, when all three copies are disrupted in Ttzip4-A1B1B2 triple mutants, COs are reduced by over 95%, suggesting that the TtZIP4-B2 copy may also affect class II COs. If this is the case, the class I and class II CO pathways may be interlinked in wheat. When ZIP4 duplicated and diverged from chromosome 3B on wheat polyploidization, the new 5B copy, TaZIP4-B2, could have acquired an additional function to stabilize both CO pathways. In tetraploid plants deficient in all three ZIP4 copies, synapsis is delayed and does not complete, consistent with our previous studies in hexaploid wheat, when a similar delay in synapsis was observed in a 59.3 Mb deletion mutant, ph1b, encompassing the TaZIP4-B2 gene on chromosome 5B. These findings confirm the requirement of ZIP4-B2 for efficient synapsis, and suggest that TtZIP4 genes have a stronger effect on synapsis than previously described in Arabidopsis and rice. Thus, ZIP4-B2 in wheat accounts for the two major phenotypes reported for Ph1, promotion of homologous synapsis and suppression of homeologous COs.

PMID:37324713 | PMC:PMC10266424 | DOI:10.3389/fpls.2023.1189998

Front Plant Sci. 2023 May 30;14:1161245. doi: 10.3389/fpls.2023.1161245. eCollection 2023.

ABSTRACT

MicroRNA (miRNA)-target gene modules are essential components of plants' abiotic stress signalling pathways Little is known about the drought-responsive miRNA-target modules in wheat, but systems biology approaches have enabled the prediction of these regulatory modules and systematic study of their roles in responses to abiotic stresses. Using such an approach, we sought miRNA-target module(s) that may be differentially expressed under drought and non-stressed conditions by mining Expressed Sequence Tag (EST) libraries of wheat roots and identified a strong candidate (miR1119-MYC2). We then assessed molecular and physiochemical differences between two wheat genotypes with contrasting drought tolerance in a controlled drought experiment and assessed possible relationships between their tolerance and evaluated traits. We found that the miR1119-MYC2 module significantly responds to drought stress in wheat roots. It is differentially expressed between the contrasting wheat genotypes and under drought versus non-stressed conditions. We also found significant associations between the module's expression profiles and ABA hormone content, water relations, photosynthetic activities, H2O2 levels, plasma membrane damage, and antioxidant enzyme activities in wheat. Collectively, our results suggest that a regulatory module consisting of miR1119 and MYC2 may play an important role in wheat's drought tolerance.

PMID:37324698 | PMC:PMC10266357 | DOI:10.3389/fpls.2023.1161245

Front Plant Sci. 2023 May 31;14:1166511. doi: 10.3389/fpls.2023.1166511. eCollection 2023.

ABSTRACT

Roots are the hidden parts of plants, anchoring their above-ground counterparts in the soil. They are responsible for water and nutrient uptake and for interacting with biotic and abiotic factors in the soil. The root system architecture (RSA) and its plasticity are crucial for resource acquisition and consequently correlate with plant performance while being highly dependent on the surrounding environment, such as soil properties and therefore environmental conditions. Thus, especially for crop plants and regarding agricultural challenges, it is essential to perform molecular and phenotypic analyses of the root system under conditions as near as possible to nature (#asnearaspossibletonature). To prevent root illumination during experimental procedures, which would heavily affect root development, Dark-Root (D-Root) devices (DRDs) have been developed. In this article, we describe the construction and different applications of a sustainable, affordable, flexible, and easy to assemble open-hardware bench-top LEGO® DRD, the DRD-BIBLOX (Brick Black Box). The DRD-BIBLOX consists of one or more 3D-printed rhizoboxes, which can be filled with soil while still providing root visibility. The rhizoboxes sit in a scaffold of secondhand LEGO® bricks, which allows root development in the dark and non-invasive root tracking with an infrared (IR) camera and an IR light-emitting diode (LED) cluster. Proteomic analyses confirmed significant effects of root illumination on barley root and shoot proteomes. Additionally, we confirmed the significant effect of root illumination on barley root and shoot phenotypes. Our data therefore reinforces the importance of the application of field conditions in the lab and the value of our novel device, the DRD-BIBLOX. We further provide a DRD-BIBLOX application spectrum, spanning from investigating a variety of plant species and soil conditions and simulating different environmental conditions and stresses, to proteomic and phenotypic analyses, including early root tracking in the dark.

PMID:37324682 | PMC:PMC10264708 | DOI:10.3389/fpls.2023.1166511

Therap Adv Gastroenterol. 2023 Jun 6;16:17562848231174298. doi: 10.1177/17562848231174298. eCollection 2023.

ABSTRACT

BACKGROUND: In patients with inflammatory bowel disease (IBD), Crohn's disease (CD), and ulcerative colitis (UC), numerous cases of exacerbations could be observed after colonoscopy, raising the possible pathogenetic effect of colonic microbiota alterations in IBD flare.

OBJECTIVES: We aimed to investigate the changes in the fecal microbiota composition in IBD patients influenced by the bowel preparation with sodium picosulfate.

DESIGN: We enrolled patients with IBD undergoing bowel preparation for colonoscopy in the prospective cohort study. The control group (Con) comprised non-IBD patients who underwent colonoscopy. Clinical data, blood, and stool samples were collected before colonoscopy (timepoint A), 3 days later (timepoint B), and 4 weeks later (timepoint C).

METHODS: Disease activity and gut microbiota changes were assessed at each timepoint. Fecal microbiota structure - at family level - was determined by sequencing the V4 region of the 16S rRNA gene. Statistical analysis included differential abundance analysis and Mann-Whitney tests.

RESULTS: Forty-one patients (9 CD, 13 UC, and 19 Con) were included. After bowel preparation, alpha diversity was lower in the CD group than in the UC (p = 0.01) and Con (p = 0.02) groups at timepoint B. Alpha diversity was significantly higher in the UC group than in the CD and Con (p = 0.03) groups at timepoint C. Beta diversity difference differed between the IBD and Con (p = 0.001) groups. Based on the differential abundance analysis, the Clostridiales family was increased, whereas the Bifidobacteriaceae family was decreased in CD patients compared to the Con at timepoint B.

CONCLUSIONS: Bowel preparation may change the fecal microbial composition in IBD patients, which may have a potential role in disease exacerbation after bowel cleansing.

PMID:37324319 | PMC:PMC10265323 | DOI:10.1177/17562848231174298

Front Oncol. 2023 May 31;13:1217212. doi: 10.3389/fonc.2023.1217212. eCollection 2023.

NO ABSTRACT

PMID:37324018 | PMC:PMC10264770 | DOI:10.3389/fonc.2023.1217212

Front Oncol. 2023 May 31;13:1215332. doi: 10.3389/fonc.2023.1215332. eCollection 2023.

NO ABSTRACT

PMID:37324002 | PMC:PMC10265629 | DOI:10.3389/fonc.2023.1215332

Front Microbiol. 2023 May 30;14:1181562. doi: 10.3389/fmicb.2023.1181562. eCollection 2023.

ABSTRACT

The advances in high-throughput sequencing (HTS) technologies and bioinformatic tools have provided new opportunities for virus and viroid discovery and diagnostics. Hence, new sequences of viral origin are being discovered and published at a previously unseen rate. Therefore, a collective effort was undertaken to write and propose a framework for prioritizing the biological characterization steps needed after discovering a new plant virus to evaluate its impact at different levels. Even though the proposed approach was widely used, a revision of these guidelines was prepared to consider virus discovery and characterization trends and integrate novel approaches and tools recently published or under development. This updated framework is more adapted to the current rate of virus discovery and provides an improved prioritization for filling knowledge and data gaps. It consists of four distinct steps adapted to include a multi-stakeholder feedback loop. Key improvements include better prioritization and organization of the various steps, earlier data sharing among researchers and involved stakeholders, public database screening, and exploitation of genomic information to predict biological properties.

PMID:37323908 | PMC:PMC10265641 | DOI:10.3389/fmicb.2023.1181562

Front Genet. 2023 May 30;14:1223913. doi: 10.3389/fgene.2023.1223913. eCollection 2023.

NO ABSTRACT

PMID:37323675 | PMC:PMC10262209 | DOI:10.3389/fgene.2023.1223913

Bio Protoc. 2023 Jun 5;13(11):e4685. doi: 10.21769/BioProtoc.4685. eCollection 2023 Jun 5.

ABSTRACT

Gene deletion is one of the standard approaches in genetics to investigate the roles and functions of target genes. However, the influence of gene deletion on cellular phenotypes is usually analyzed sometime after the gene deletion was introduced. Such lags from gene deletion to phenotype evaluation could select only the fittest fraction of gene-deleted cells and hinder the detection of potentially diverse phenotypic consequences. Therefore, dynamic aspects of gene deletion, such as real-time propagation and compensation of deletion effects on cellular phenotypes, still need to be explored. To resolve this issue, we have recently introduced a new method that combines a photoactivatable Cre recombination system and microfluidic single-cell observation. This method enables us to induce gene deletion at desired timings in single bacterial cells and to monitor their dynamics for prolonged periods. Here, we detail the protocol for estimating the fractions of gene-deleted cells based on a batch-culture assay. The duration of blue light exposure significantly affects the fractions of gene-deleted cells. Therefore, gene-deleted and non-deleted cells can coexist in a cellular population by adjusting the duration of blue light exposure. Single-cell observations under such illumination conditions allow the comparison of temporal dynamics between gene-deleted and non-deleted cells and unravel phenotypic dynamics provoked by gene deletion.

PMID:37323637 | PMC:PMC10262074 | DOI:10.21769/BioProtoc.4685

Adv Sci (Weinh). 2023 Jun 15:e2206307. doi: 10.1002/advs.202206307. Online ahead of print.

ABSTRACT

Single cell RNA-seq (scRNA-seq) profiles conceal temporal and spatial tissue developmental information. De novo reconstruction of single cell temporal trajectory has been fairly addressed, but reverse engineering single cell 3D spatial tissue organization is hitherto landmark based, and de novo spatial reconstruction is a compelling computational open problem. Here it is shown that a proposed algorithm for de novo coalescent embedding (D-CE) of oligo/single cell transcriptomic networks can help to address this problem. Relying on the spatial information encoded in the expression patterns of genes, it is found that D-CE of cell-cell association transcriptomic networks, by preserving mesoscale network organization, captures spatial domains, identifies spatially expressed genes, reconstructs cell samples' 3D spatial distribution, and uncovers spatial domains and markers necessary for understanding the design principles on spatial organization and pattern formation. Comparison to the novoSpaRC and CSOmap (the only available de novo 3D spatial reconstruction methods) on 14 datasets and 497 reconstructions, reveals a significantly superior performance of D-CE.

PMID:37323105 | DOI:10.1002/advs.202206307

Math Biosci Eng. 2023 Apr 11;20(6):10570-10589. doi: 10.3934/mbe.2023467.

ABSTRACT

In systems biology, the analysis of complex nonlinear systems faces many methodological challenges. For the evaluation and comparison of the performances of novel and competing computational methods, one major bottleneck is the availability of realistic test problems. We present an approach for performing realistic simulation studies for analyses of time course data as they are typically measured in systems biology. Since the design of experiments in practice depends on the process of interest, our approach considers the size and the dynamics of the mathematical model which is intended to be used for the simulation study. To this end, we used 19 published systems biology models with experimental data and evaluated the relationship between model features (e.g., the size and the dynamics) and features of the measurements such as the number and type of observed quantities, the number and the selection of measurement times, and the magnitude of measurement errors. Based on these typical relationships, our novel approach enables suggestions of realistic simulation study designs in the systems biology context and the realistic generation of simulated data for any dynamic model. The approach is demonstrated on three models in detail and its performance is validated on nine models by comparing ODE integration, parameter optimization, and parameter identifiability. The presented approach enables more realistic and less biased benchmark studies and thereby constitutes an important tool for the development of novel methods for dynamic modeling.

PMID:37322949 | DOI:10.3934/mbe.2023467

ACS Synth Biol. 2023 Jun 16;12(6):1579-1582. doi: 10.1021/acssynbio.3c00238.

ABSTRACT

Synthetic biology (SynBio) has attracted like no other recent development the attention not only of Life Science researchers and engineers but also of intellectuals, technology think-tanks, and private and public investors. This is largely due to its promise to propel biotechnology beyond its traditional realms in medicine, agriculture, and environment toward new territories historically dominated by the chemical and manufacturing industries─but now claimed to be amenable to complete biologization. For this to happen, it is crucial for the field to remain true to its foundational engineering drive, which relies on mathematics and quantitative tools to construct practical solutions to real-world problems. This article highlights several SynBio themes that, in our view, come with somewhat precarious promises that need to be tackled. First, SynBio must critically examine whether enough basic information is available to enable the design or redesign of life processes and turn biology from a descriptive science into a prescriptive one. Second, unlike circuit boards, cells are built with soft matter and possess inherent abilities to mutate and evolve, even without external cues. Third, the field cannot be presented as the one technical solution to many grave world problems and so must avoid exaggerated claims and hype. Finally, SynBio should pay heed to public sensitivities and involve social science in its development and growth, and thus change the technology narrative from sheer domination of the living world to conversation and win-win partnership.

PMID:37322887 | DOI:10.1021/acssynbio.3c00238

Sci Total Environ. 2023 Jun 13:164645. doi: 10.1016/j.scitotenv.2023.164645. Online ahead of print.

ABSTRACT

Understanding the effects of environmental stressors (e.g., potential changes in climate and land use) on ecological status is essential for freshwater management. The ecological response of rivers to stressors can be evaluated by several physico-chemical, biological, and hydromorphological elements as well as computer tools. In this study, an ecohydrological model based on SWAT (Soil and Water Assessment Tool) is used to investigate climate change impact on the ecological status of Albaida Valley Rivers. The predictions of five General Circulation Models (GCMs) each with four Representative Concentration Pathways (RCPs) are employed as input to the model for simulating several chemical and biological quality indicators (nitrate, ammonium, total phosphorus, and the IBMWP (Iberian Biological Monitoring Working Party) index) in three future periods (Near Future: 2025-2049, Mid Future: 2050-2074, and Far Future: 2075-2099). Based on chemical and biological status predicted with the model, the ecological status is determined at 14 representative sites. As a result of increased temperatures and decreased precipitations from most of GCMs projections, the model predicts decreased river discharge, increased concentrations of nutrients, and decreased values of IBMWP for future compared to the baseline period (2005-2017). While most representative sites have poor ecological status (10 sites with poor ecological status and four sites with bad ecological status) in the baseline, our model projects bad ecological status for most representative sites (four sites with poor ecological status and 10 sites with bad ecological status) under most emission scenarios in the future. It should be noted that the bad ecological status is projected for all 14 sites under the most extreme scenario (i.e., RCP8.5) in the Far Future. Despite the different emission scenarios, and all possible changes in water temperature and annual precipitation, our findings emphasize the urgent need for scientifically informed decisions to manage and preserve freshwaters.

PMID:37321493 | DOI:10.1016/j.scitotenv.2023.164645