Biology Strategies Research Articles

Bioinformatic Multi-Strategy Profiling of Congenital Heart Defects for Molecular Mechanism Recognition

Congenital heart defects (CHDs) rank among the most common birth defects, presenting diverse phenotypes. Genetic and environmental factors are critical in molding the process of cardiogenesis. However, these factors’ interactions are not fully comprehended. Hence, this study aimed to identify and characterize differentially expressed genes involved in CHD development through bioinformatics pipelines. We analyzed experimental datasets available in genomic databases, using transcriptome, gene enrichment, and systems biology strategies. Network analysis based on genetic and phenotypic ontologies revealed that EP300, CALM3, and EGFR genes facilitate rapid information flow, while NOTCH1, TNNI3, and SMAD4 genes are significant mediators within the network. Differential gene expression (DGE) analysis identified 2513 genes across three study types, (1) Tetralogy of Fallot (ToF); (2) Hypoplastic Left Heart Syndrome (HLHS); and (3) Trisomy 21/CHD, with LYVE1, PLA2G2A, and SDR42E1 genes found in three of the six studies. Interaction networks between genes from ontology searches and the DGE analysis were evaluated, revealing interactions in ToF and HLHS groups, but none in Trisomy 21/CHD. Through enrichment analysis, we identified immune response and energy generation as some of the relevant ontologies. This integrative approach revealed genes not previously associated with CHD, along with their interactions and underlying biological processes.

Using the ibsr technique as a psychological intervention to alleviate student stress in biology learning: Impacts on motivation, knowledge construction, and cognitive anxiety

Learning difficulties are a common issue faced by students, with stress being a significant contributing factor. One psychological treatment that has been shown to effectively reduce stress is Inquiry-Based Stress Reduction (IBSR). The objective of this study is to integrate IBSR into a discovery learning strategy in Biology in the classroom, with the aim of increasing students' learning motivation and knowledge construction while reducing their learning difficulties and cognitive anxiety. This is quasi-experimental research that used a post-test non-equivalent control group design. The study involved 72 11th-grade science students from two different classes at one of the public high schools in Bandung City. One class, consisting of 36 students, received IBSR treatment, while the other class, also consisting of 36 students, did not. Both classes used a discovery learning framework for teaching. Data on motivation, learning difficulties, and cognitive anxiety were collected using a rating scale questionnaire with eight scales. Students' ability to construct knowledge was measured using the German Cognitive Load (GCL) instrument in the form of a written test with indicators taken from Mayer's cognitive taxonomy (2002) in the realm of understanding. The study found that incorporating IBSR techniques into learning strategies for the immune system material can reduce student stress and improve learning performance, motivation, and knowledge construction (GCL), while also decreasing learning difficulties and cognitive anxiety.

Critical role of non-coding RNA-mediated ferroptosis in urologic malignancies.

Urologic malignancies, characterized by their high aggressiveness and metastatic potential, pose a significant public health challenge globally. Ferroptosis, a novel mode of cell death, typically arises from intracellular iron ion overload and the accumulation of lipid peroxides. This process has been shown to play a crucial regulatory role in various pathological conditions, particularly in cancer, including urologic cancers. However, the comprehensive regulatory mechanisms underlying ferroptosis remain poorly understood, which somewhat limits its broader application in cancer therapy. Non-coding RNAs (ncRNAs), which encompass microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), are non-coding transcripts that play pivotal roles in various physiological processes, such as proliferation, differentiation, apoptosis, and cell cycle regulation, by modulating the expression of target genes. The biological functions and potential regulatory mechanisms of ncRNAs in the context of cancer-related ferroptosis have been partially elucidated. Research indicates that ncRNAs can influence the progression of urologic cancers by affecting cell proliferation, migration, and drug resistance through the regulation of ferroptosis. Consequently, this review aims to clarify the functions and mechanisms of the ncRNA-ferroptosis axis in urologic cancers and to evaluate the clinical significance of ferroptosis-related ncRNAs, thereby providing new insights into cancer biology and therapeutic strategies that may ultimately benefit a diverse range of cancer patients.

Biosynthesis of Natural and Unnatural Perylenequinones for Drug Development.

A wide range of perylenequinones (PQs) with diverse structures and versatile bioactivities have long been isolated, positioning them as highly promising agents for photodynamic therapy (PDT). However, the lack of an efficient and cost-effective method to obtain these compounds and to introduce structural diversity and complexity currently hinders their further research and application. In this concept, we present a comprehensive overview of the advancements in the biosynthetic pathways of natural PQs based on their structural classification, and also summarize recent progress in the biosynthesis of natural PQs and derivatives. These pioneering efforts may pave the way for structure modification and large-scale bioproduction of natural and unnatural PQs through synthetic biology strategies to promote their drug development.

Controlling Directional Liquid Transfer over a Ratchet-like Surface with Oriented Open-Wedges

Directed transfer of liquids is widely used as an important mass transfer strategy in the nature biology, industry, agriculture, and medical fields. Based on the bionic concept, researchers have constructed various forms of surface structures to realize controlled transport of liquids. However, current methods for preparing surfaces with directional liquid transport often suffer from cumbersome preparation processes, complexity of the prepared structures, and high costs. In this paper, we prepared a topological structure surface capable of precisely controlling liquid transport by a facile method. By utilizing 3D printing technology, we designed and fabricated a wedge-shaped surface with a periodic tilting scale arrangement. We accomplished the precise regulation of liquid transport on the surface of the structure, which not only realized the bi-directional transport of liquid anisotropically to the uni-directional transport on the surface but also achieved the precise regulation of the distance and speed of liquid transport through adjusting the opening angle formed by the open-wedges. We expect that the as-prepared wedge-shaped surface will provide a facile and efficient strategy for directional liquid transport.

7542 Androgen Receptor Oligomerization State Allows Cells to Exhibit Non-Linear Dose Responses to Androgens Resulting in Distinct Biological Outputs

Abstract Disclosure: R. Safi: None. S.E. Wardell: None. P. Watkinson: None. X. Qin: None. M. Lee: None. S. Park: None. T. Krebs: None. E. Dolan: None. T. Tsuji: None. S. Nayak: None. M. Khater: None. M. Newlin: None. M. Kirkland: None. Y. Xie: None. H. Long: None. E. Fink: None. S.W. Fanning: None. S. Runyon: None. M. Brown: None. S. Xu: None. K. Owzar: None. J.D. Norris: None. D.P. McDonnell: None. An unanswered fundamental question in androgen action is how cells recognize and respond in a non-linear fashion to different levels of androgens to elicit distinct biological outputs such as occurs in prostate cancer (PCa) cells. Indeed, most PCa express the androgen receptor (AR), and tumor growth and progression are facilitated by exceedingly low levels of systemic or intratumorally produced androgens. Paradoxically, high dose androgens have been used to treat patients with late-stage metastatic PCa. We have determined that androgen dose regulates the relative cellular abundance of AR monomers and dimers in cells and that the biological output of each oligomeric form of the receptor is different. Using in vitro systems that model exposure from castrate (low dose; LD) to eugonadal levels and above (high dose; HD) of androgens, we have determined that the global changes in gene expression are substantially different, with the changes induced by LD androgens (monomeric AR) being associated with cell proliferation, and HD androgens (dimeric AR) inducing a differentiated phenotype. A similar distinction in response to androgen levels was observed in vivo. Using a chemical biology strategy, we identified ligands which freeze AR in a monomeric form and demonstrate that these compounds faithfully recapitulate the LD biology exhibited by physiological AR agonists. Mechanistically, we determined that monomeric AR facilitates a non-genomic activation of the mTOR signaling pathway to drive proliferation, while the dimer suppresses c-MYC expression, inhibit proliferation, and drive a transcriptional program associated with a differentiated phenotype. These findings highlight the inherent liabilities in current approaches used to inhibit AR-action in prostate cancer and are instructive as to strategies that can be used to develop new therapeutics for this disease and other androgenopathies. Presentation: 6/3/2024

Exploring potential biomarkers and lead molecules in gastric cancer by network biology, drug repurposing and virtual screening strategies.

Gastric cancer poses a significant global health challenge, necessitating innovative approaches for biomarker discovery and therapeutic intervention. This study employs a multifaceted strategy integrating network biology, drug repurposing, and virtual screening to elucidate and expand the molecular landscape of gastric cancer. We identified and prioritized key genes implicated in gastric cancer by utilizing data from diverse databases and text-mining techniques. Network analysis underscored intricate gene interactions, emphasizing potential therapeutic targets such as CTNNB1, BCL2, TP53, etc, and highlighted ACTB among the top hub genes crucial in disease progression. Drug repurposing on 626 FDA-approved drugs for digestive system-related cancers revealed Norgestimate and Nimesulide as likely top candidates for gastric cancer, validated by molecular docking and dynamics simulations. Further, combinatorial synthesis of scaffold libraries derived from known chemotypes generated 56,160 virtual compounds, of which 76 new compounds were prioritized based on promising binding affinities and interactions at critical residues. Hotspot residue analysis identified GLU 214 and others as essential for ligand binding stability, enhancing compound efficacy and specificity. These findings support the therapeutic potential of targeting beta-actin protein in gastric cancer treatment, suggesting a future for further experimental validation and clinical translation. In conclusion, this study highlights the potential of repurposable drugs and virtual screening which can be used in combination with existing anti-gastric cancer drugs for gastric cancer therapy, emphasizing the role of computational methodologies in drug discovery.

Treatment of neurologic pathology and inflammation in Machado-Joseph disease through in vivo self-assembled siRNA.

Machado-Joseph disease, also known as Spinocerebellar ataxia type 3 (MJD/SCA3), is a fatal autosomal dominant hereditary ataxia characterized by cerebellar ataxia resulting from the abnormal expansion of CAG repeats in exon 10 of the ATXN3 gene. Presently, there is no effective treatment for SCA3. Small interfering RNAs (siRNAs) are emerging as potential therapeutic strategies to specifically target the disease-causing mutant ATXN3 (mATXN3) protein. However, the delivery efficiency of siRNAs remains a major obstacle for clinical application, particularly in brain disorders. This study aimed to develop a synthetic biology strategy to reprogram the host liver as a tissue chassis to induce and deliver in vivo self-assembled siRNAs (IVSA-siRNAs) to target the ATXN3 gene. A synthetic construct directed by a cytomegalovirus promoter was designed to encode a neuron-targeting rabies virus glycoprotein tag and mATXN3-siRNA. After intravenous injection, the synthetic construct was taken up by mouse livers, which were then reprogrammed to enable the self-assembly, production, and secretion of small extracellular vesicles (sEVs) encapsulating mATXN3-siRNA. The sEV-encapsulated mATXN3-siRNA was further transported through the endogenous circulating system of sEVs, crossing the blood-brain barrier and reaching the cerebellar cortex and spinal cerebellar tract, where they silenced the ATXN3 gene. Treatment with the synthetic construct for 8 or 12 weeks led to significant improvements in motor balance ability and reduction of cerebellar atrophy in YACMJD84.2 transgenic mice. The number of Purkinje cells in the cerebellar cortex was significantly increased, and the loss of myelin basic protein was reduced. Moreover, the quantity of neurotoxic nuclear inclusion bodies and the expression of glial fibrillary acidic protein, which promotes neuroinflammation in activated astrocytes, were decreased significantly. The synthetic construct facilitated the generation and delivery of IVSA-siRNA to the cerebellar cortex and spinal cerebellar tract, thereby inhibiting the expression of mATXN3 protein. This treatment successfully addressed motor impairments, alleviated neuropathological phenotypes, and mitigated neuroinflammation in YACMJD84.2 transgenic mice. Our strategy effectively overcomes the primary challenges associated with siRNA therapy for cerebellar ataxia, offering a promising avenue for future clinical treatments.

Eriophyid mites in fruit crops: Biology, ecology, molecular aspects, and innovative control strategies

Eriophyid mites, minute arachnids within the family Eriophyidae, pose significant threats to fruit crops globally, leading to substantial economic losses in agriculture. This comprehensive review aims to elucidate the intricate biology, ecology, molecular aspects, and innovative control strategies of these pervasive pests. Eriophyid mites exhibit a complex life cycle and reproductive strategy, with their habitat preferences and distribution heavily influenced by environmental factors and host-plant interactions. Advances in molecular biology have provided more profound insights into their genetics and interactions at the molecular level, revealing crucial information for developing targeted pest management strategies. Control strategies for eriophyid mites encompass chemical methods, such as applying acaricides and understanding resistance mechanisms, as well as biological control using natural predators and parasitoids. Cultural and physical control methods, including crop rotation and mechanical removal, play vital roles in integrated pest management (IPM). Emerging approaches like RNA interference (RNAi) and semiochemical-based controls offer promising alternatives for sustainable pest management. This review underscores the importance of a multifaceted approach to effectively manage eriophyid mite infestations, integrating traditional and novel strategies. Future research should focus on overcoming current challenges, enhancing the efficacy of control methods, and further exploring the molecular mechanisms underlying mite-plant interactions

DSCI: a database of synthetic biology components for innate immunity and cell engineering decision-making processes

Although significant progress of clinical strategy has been made in gene editing and cell engineering in immunotherapy, it is now apparent that design and modification in terms of complex signaling pathways and motifs on medical synthetic biology are still full of challenges. Innate immunity, the first line of host defense against pathogens, is critical for anti-pathogens immune response as well as regulating durable and protective T cell-mediated anti-tumor responses. Here, we introduce DSCI (Database of Synthetic Biology Components for Innate Immunity, https://dsci.renlab.cn/), a web-accessible and integrative database that provides better insights and strategies for innate immune signaling circuit design in biosynthesis. Users can interactively navigate comprehensive and carefully curated components resources that presented as visualized signaling motifs that participate in innate immunity. The current release of DSCI incorporates 1240 independent components and more than 4000 specific entries contextually annotated from public literature with experimental verification. The data integrated into DSCI includes the components of pathways, relationships between regulators, signal motifs based on regulatory cascades, and loop graphs, all of which have been comprehensively annotated to help guide modifications to gene circuits. With the support of DSCI, users can easily obtain guidance of gene circuits construction to make decision of cell engineering based on innate immunity. DSCI not only provides comprehensive and specialized resource on the biological components of innate immune synthesis, but also serves as a useful tool to offer modification or generation strategies for medical synthetic biology.

Development of a green Komagataella phaffii cell factory for sustainable production of plant-derived sesquiterpene (–)-α-bisabolol

(–)-α-Bisabolol is a plant-derived sesquiterpene derived from Eremanthus erythropappus, which can be used as a raw material in cosmetics and has anti-inflammatory function. In this study, we designed six mutation sites of the (–)-α-bisabolol synthase BOS using the plmDCA algorithm. Among these, the F324Y mutation demonstrated exceptional performance, increasing the product yield by 73 %. We constructed a de novo (–)-α-bisabolol biosynthesis pathways through systematic synthetic biology strategies, including the enzyme design of BOS, selection of different linkers in fusion expression, and optimization of the mevalonate pathway, weakening the branching metabolic flow and multi-copy strategies, the yield of (–)-α-bisabolol was significantly increased, which was nearly 35-fold higher than that of the original strain (2.03 mg/L). The engineered strain was capable of producing 69.7 mg/L in shake flasks. To the best of our knowledge, this is the first report on the biosynthesis of (–)-α-bisabolol in Komagataella phaffii, implying this is a robust cell factory for sustainable production of other terpenoids.

Repetitive Sequence Stability in Embryonic Stem Cells.

Repetitive sequences play an indispensable role in gene expression, transcriptional regulation, and chromosome arrangements through trans and cis regulation. In this review, focusing on recent advances, we summarize the epigenetic regulatory mechanisms of repetitive sequences in embryonic stem cells. We aim to bridge the knowledge gap by discussing DNA damage repair pathway choices on repetitive sequences and summarizing the significance of chromatin organization on repetitive sequences in response to DNA damage. By consolidating these insights, we underscore the critical relationship between the stability of repetitive sequences and early embryonic development, seeking to provide a deeper understanding of repetitive sequence stability and setting the stage for further research and potential therapeutic strategies in developmental biology and regenerative medicine.

Managing fruit rot diseases of Vaccinium corymbosum.

Blueberry is an important perennial fruit crop with expanding consumption and production worldwide. Consumer demand for blueberries has grown due to the desirable flavor and numerous health benefits, and fresh market production in the U.S. has risen in turn. U.S. imports have also increased to satisfy year-round consumer demand for fresh blueberries. Pre- and post-harvest fruit diseases such as anthracnose (caused by Colletotrichum spp.) and botrytis fruit rot (caused by Botrytis spp.) have a significant impact on fruit quality and consumer acceptance. These are also among the most difficult diseases to control in the blueberry cropping system. These latent pathogens can cause significant losses both in the field, and especially during transport and marketplace storage. Although both diseases result in rotted fruit, the biology and infection strategies of the causal pathogens are very different, and the management strategies differ. Innovations for management, such as improved molecular detection assays for fungicide resistance, postharvest imaging, breeding resistant cultivars, and biopesticides have been developed for improved fruit quality. Development and integration of new strategies is critical for the long-term success of the blueberry industry.

Generation and characterization of human-derived induced pluripotent stem cell line (IGIBi010-A) from a patient with neurodegenerative disease phenotype carrying mutation in SQSTM1/p62 gene

SQSTM1 (Sequestosome 1) also known as p62, plays several important physiological roles in the cell. It regulates autophagy and mitochondrial homeostasis and can further lead to metabolic reprogramming. Pathogenic variants in SQSTM1 gene are known to cause Neurodegeneration with ataxia, dystonia, and gaze palsy in autosomal recessive inheritance fashion. We report here, the generation of induced pluripotent stem cell (iPSC) line (IGIBi010-A) carrying a novel homozygous frameshift variant in SQSTM1 i.e. p.Leu251SerfsTer4. In future, this iPSC line will be used as a resource to elucidate the molecular pathway, targeting strategies for disease biology derived by variation in SQSTM1 gene.

Incompatibility in cell adhesion constitutes a barrier to interspecies chimerism

Interspecies blastocyst complementation holds great potential to address the global shortage of transplantable organs by growing human organs in animals. However, a major challenge in this approach is the limited chimerism of human cells in evolutionarily distant animal hosts due to various xenogeneic barriers. Here, we reveal that human pluripotent stem cells (PSCs) struggle to adhere to animal PSCs. To overcome this barrier, we developed a synthetic biology strategy that leverages nanobody-antigen interactions to enhance interspecies cell adhesion. We engineered cells to express nanobodies and their corresponding antigens on their outer membranes, significantly improving adhesion between different species' PSCs during invitro assays and increasing the chimerism of human PSCs in mouse embryos. Studying and manipulating interspecies pluripotent cell adhesion will provide valuable insights into cell interaction dynamics during chimera formation and early embryogenesis.

A new era of synthetic biology-microbial community design.

Synthetic biology conceptualizes biological complexity as a network of biological parts, devices, and systems with predetermined functionalities and has had a revolutionary impact on fundamental and applied research. With the unprecedented ability to synthesize and transfer any DNA and RNA across organisms, the scope of synthetic biology is expanding and being recreated in previously unimaginable ways. The field has matured to a level where highly complex networks, such as artificial communities of synthetic organisms, can be constructed. In parallel, computational biology became an integral part of biological studies, with computational models aiding the unravelling of the escalating complexity and emerging properties of biological phenomena. However, there is still a vast untapped potential for the complete integration of modelling into the synthetic design process, presenting exciting opportunities for scientific advancements. Here, we first highlight the most recent advances in computer-aided design of microbial communities. Next, we propose that such a design can benefit from an organism-free modular modelling approach that places its emphasis on modules of organismal function towards the design of multispecies communities. We argue for a shift in perspective from single organism-centred approaches to emphasizing the functional contributions of organisms within the community. By assembling synthetic biological systems using modular computational models with mathematical descriptions of parts and circuits, we can tailor organisms to fulfil specific functional roles within the community. This approach aligns with synthetic biology strategies and presents exciting possibilities for the design of artificial communities. Graphical Abstract.

Single-cell genomics details the maturation block in BCP-ALL and identifies therapeutic vulnerabilities in DUX4-r cases

AbstractB-cell progenitor acute lymphoblastic leukemia (BCP-ALL) is the most common childhood malignancy and is driven by multiple genetic alterations that cause maturation arrest and accumulation of abnormal progenitor B cells. Current treatment protocols with chemotherapy have led to favorable outcomes but are associated with significant toxicity and risk of side effects, highlighting the necessity for highly effective, less toxic, targeted drugs, even in subtypes with a favorable outcome. Here, we used multimodal single-cell sequencing to delineate the transcriptional, epigenetic, and immunophenotypic characteristics of 23 childhood BCP-ALLs belonging to the BCR::ABL1+, ETV6::RUNX1+, high hyperdiploid, and recently discovered DUX4-rearranged (DUX4-r) subtypes. Projection of the ALL cells along the normal hematopoietic differentiation axis revealed a diversity in the maturation pattern between the different BCP-ALL subtypes. Although the BCR::ABL1+, ETV6::RUNX1+, and high hyperdiploidy cells mainly showed similarities to normal pro-B cells, DUX4-r ALL cells also displayed transcriptional signatures resembling mature B cells. Focusing on the DUX4-r subtype, we found that the blast population displayed not only multilineage priming toward nonhematopoietic cells, myeloid, and T-cell lineages, but also an activation of phosphatidylinositol 3-kinase (PI3K)/AKT signaling that sensitized the cells to PI3K inhibition in vivo. Given the multilineage priming of DUX4-r blasts with aberrant expression of myeloid marker CD371 (CLL-1), we generated chimeric antigen receptor T cells, which effectively eliminated DUX4-r ALL cells in vivo. These results provide a detailed characterization of BCP-ALL at the single-cell level and reveal therapeutic vulnerabilities in the DUX4-r subtype, with implications for the understanding of ALL biology and new therapeutic strategies.

Abstract PO-021: Modeling marginal zone lymphomagenesis

Abstract Introduction: Marginal zone lymphomas (MZL) are the second most prevalent subtype of indolent Non-Hodgkin Lymphomas (iNHL), yet lack a unique cytogenetic identifying abnormality. The B-cell receptor signaling pathway is activated in B-cell malignancy and mediates its activity mainly through the Phosphoinositide 3-kinase (PI3K), protein kinase B (Akt), mammalian target of rapamycin (mTOR) pathway. PI3K inhibitors have demonstrated impressive clinical activity in several indolent lymphomas including MZL, underscoring the pivotal role of the PI3K-AKT-mTOR (PAM) pathway in MZL pathogenesis. Furthermore, iNHL overexpress the antiapoptotic protein Bcl-2. Methods: We developed a genetically engineered mouse model with heterozygous global knockout alleles of both the tumor suppressor genes Phosphatase and Tensin Homolog (PTEN) and Liver Kinase B1 (LKB1), resulting in heightened PAM pathway activation across all tissues. We closely monitored these mice for tumor formation via regular physical assessments over several months. Upon tumor detection, mice were euthanized, and tumors were histologically examined. For a more precise representation of B-cell biology akin to the human disease, we employed the Cre-LoxP system to create the CD19-Cre-PTENfl/fl/LKB1fl/fl and CD19-Cre-PTENfl/fl/Eµ-Bcl2. Results: Thirty mice of global KO PTEN+/- LKB1+/- succumbed to or were euthanized due to disease progression, defined as either lymph node enlargement and/or splenomegaly. By Kaplan-Meier analysis, we saw a steady decrease in both tumor-free and overall survival after 3 months of age. Median survival time was 6 months (95% CI: 6, 8). Immunohistochemical analysis of the 51 lymph nodes revealed iNHL in 61.5% (N=32), with all of the MZL subtype. The penetrance rate was 37%. Then, we looked at the absolute B cells, and the major B subtypes in age-matched mice (N=3 per group): WT, CD19-Cre-PTENfl/fl/LKB1fl/fl, CD19-Cre-PTENfl/fl/Eµ-Bcl2. We observed the following preliminary results in the absolute B cells (23,489,812; 1,550,430; 140,476,875), Marginal zone cells (1,087,883; 452,470; 42,658,701), follicular cells (19,078,598; 203,286; 57,212,627), B1 cells (962,192; 939,386; 1,803,060), and plasma cells (211,725; 202,790; 10,531,585) respectively. Then, Kruskal-Wallis tests were used to test the main effect of these three models (WT, CD19-Cre-PTENfl/fl/LKB1fl/fl and CD19-Cre-PTENfl/fl/Bcl2) on absolute cell counts for each cell type: B cells (p=0.027), follicular (p=0.061), Marginal zone (p=0.027), B1 (p=0.43), and plasma cell (p=0.066). The test results indicate that there were statistically discernible differences in absolute cell counts among the three models for B cells and MZ. Conclusion: Marginal zone lymphoma remains an incurable lymphoma with a dearth of reliable preclinical models. Our data provides, for the first time, evidence supporting the involvement of the PAM pathway in MZL pathogenesis, laying the groundwork for further research elucidating the disease biology and rational therapeutic strategies for this incurable malignancy. Citation Format: Emily Harris, Ariel Sindel, Jian He, Roy Sabo, Alden Chesney, Guanhua Lai, Adolpho Mauro, Rebecca Martins, Jennifer Koblinski, Joelene Windle, Victor Yazbeck. Modeling marginal zone lymphomagenesis [abstract]. In: Proceedings of the Fourth AACR International Meeting on Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2024 Jun 19-22; Philadelphia, PA. Philadelphia (PA): AACR; Blood Cancer Discov 2024;5(3_Suppl):Abstract nr PO-021.

An engineering biology approach to automated workflow and biodesign

Abstract The paper addresses the application of engineering biology strategies and techniques to the automation of laboratory workflow—primarily in the context of biofoundries and biodesign applications based on the Design, Build, Test and Learn paradigm. The trend toward greater automation comes with its own set of challenges. On the one hand, automation is associated with higher throughput and higher replicability. On the other hand, the implementation of an automated workflow requires an instruction set that is far more extensive than that required for a manual workflow. Automated tasks must also be conducted in the order specified in the workflow, with the right logic, utilizing suitable biofoundry resources, and at scale—while simultaneously collecting measurements and associated data. The paper describes an approach to an automated workflow that is being trialed at the London Biofoundry at SynbiCITE. The solution represents workflows with directed graphs, uses orchestrators for their execution, and relies on existing standards. The approach is highly flexible and applies to not only workflow automation in single locations but also distributed workflows (e.g. for biomanufacturing). The final section presents an overview of the implementation—using the simple example of an assay based on a dilution, measurement, and data analysis workflow.

Dual role of phage terminase in Salmonella enterica oxidative stress response

The adaptive survival mechanisms of bacterial pathogens under host-induced stress are crucial for understanding pathogenesis. Recently, Uppalapati et al. revealed a unique dual function of the Gifsy-1 prophage terminase in Salmonella enterica: it acts as a transfer ribonuclease (tRNase) under oxidative stress. The Gifsy-1 prophage terminase targets and fragments tRNALeu to halt translation and temporarily impairs bacterial growth when exposed to high levels of ROS generated by the host immune cells. This response not only preserves genomic integrity by facilitating DNA repair but also inhibits prophage mobilization, thereby aiding in bacterial survival within vertebrate hosts. This study highlights a novel intersection between phage biology and bacterial adaptive strategies.