Genetic Response Research Articles

Crop Diversity in Agroecosystems for Pest Management and Food Production.

During the past 30 years, there has been a growing belief in and promotion of agroecosystem diversity for pest management and future food production as an agroecological or nature-based approach. Monoculture agriculture, which produces most of our food, is considered to be highly vulnerable to pests in contrast to plant species-diverse agroecosystems which may possess a greater abundance of natural enemies, keeping pest populations under control. In this paper, we question the role of crop diversity for pest management and explore the relationship between crop and associated diversity and pests through the following processes: environmental stresses that favor monodominance; evolutionary adaptations that resist insect herbivores (genetic resistance response); mechanisms of spatial escape from insect herbivores (escape response); and the role of crop-associated biodiversity. We present strong evidence that not only questions the high vulnerability of monocultures to pest damage but also supports why monocultures continue to produce most of the world's food. Reference is made to the importance of targeted plant breeding and the role of trans-continental crop introduction supported by efficient quarantine for pest management. We conclude that-with the exception of irrigated rice-much more research is needed to better understand the role of crop diversity in agroecosystems for pest management and food production.

Optimization of Process Parameters for Turning Operation on D3 Die Steel

This research aims to determine the optimal Surface Roughness for machining D3 die steel alloy with uncoated carbide inserts. It will do this by studying the most efficient turning parameters, such as cutting speed, feed, and depth of cut. Models have been generated using a variety of statistical modeling approaches, including Genetic Algorithm with Response Surface Methodology. This research aimed to use the regression technique to develop a model that could predict surface roughness. It has also been investigated if the Taguchi Technique may be used to optimize process parameters. To decide the primary boundaries affecting Surface Unpleasantness, we used Signal-to-Noise (S/N) ratio and Analysis of Variance (ANOVA) tests. This paper aims to contribute valuable insights into achieving the best Surface Roughness outcomes in the machining process for D3 die steel alloy with Uncoated Carbide Inserts. The utilization of Genetic Algorithm and Response Surface Methodology showcases a robust approach for modelling intricate parameter interactions. If you know the values of the parameters, you may use the Regression Technique to forecast the surface roughness. Process parameter optimization may be made more systematic with the use of the Taguchi Technique.

Association of CIITA (rs8048002) and CLEC2D (rs2114870) gene variants and type 1 diabetes mellitus.

Type I diabetes mellitus (T1DM) is a significant health challenge, especially for children, owing to its chronic autoimmune nature. Although the exact etiology of T1DM remains elusive, the interplay of genetic predisposition, immune responses, and environmental factors are postulated. Genetic factors control immune reactivity against β-cells. Given the pivotal roles of CIITA and CLEC2D genes in modulating a variety of immune pathologies, we hypothesized that genetic variations in CIITA and CLEC2D genes may impact T1DM disease predisposition. This study was designed to explore the association between gene polymorphisms in CIITA (rs8048002) and CLEC2D (rs2114870) and type 1 diabetes (T1DM), with a focus on analyzing the functional consequence of those gene variants. The study enlisted 178 healthy controls and 148 individuals with type 1 diabetes (T1DM) from Suez Canal University Hospital. Genotyping for CIITA and CLEC2D was done using allelic-discrimination polymerase chain reaction (PCR). Levels of glycated hemoglobin (HbA1c) and lipid profiles were determined through automated analyzer, while fasting blood glucose and insulin serum levels were measured using the enzyme-linked immunosorbent assay (ELISA) technique. RegulomeDB was used to examine the regulatory functions of CIITA (rs8048002) and CLEC2D (rs2114870) gene variants. Analysis of the genotype distribution of the CIITA rs8048002 polymorphism revealed a significantly higher prevalence of the rare C allele in T1DM patients compared to the control group (OR = 1.77; P = 0.001). Both the CIITA rs8048002 heterozygote TC genotype (OR = 1.93; P = 0.005) and the rare homozygote CC genotype (OR = 3.62; P = 0.006) were significantly more frequent in children with T1DM when compared to the control group. Conversely, the rare A allele of CLEC2D rs2114870 was found to be significantly less frequent in T1DM children relative to the control group (OR = 0.58; P = 0.002). The heterozygote GA genotype (OR = 0.61; P = 0.033) and the rare homozygote AA genotype (OR = 0.25; P = 0.004) were also significantly less frequent in T1DM patients compared to the control group. Both CIITA (rs8048002) and CLEC2D (rs2114870) gene variants were predicted to have regulatory functions, indicated by a RegulomeDB score of (1f) for each. The rare C allele of CIITA rs8048002 genetic variant was associated with an increased risk of developing T1DM, while the less common A allele of CLEC2D rs2114870 was associated with a reduced risk of T1DM. The online version contains supplementary material available at 10.1007/s40200-024-01402-w.

Application of ionic liquid ultrasound-assisted extraction (IL-UAE) of lycopene from guava (Psidium guajava L.) by response surface methodology and artificial neural network-genetic algorithm

Lycopene-rich guava (Psidium guajava L.) exhibits significant economic potential as a functional food ingredient, making it highly valuable for the pharmaceutical and agro-food industries. However, there is a need to enhance the extraction methods of lycopene to fully exploit its beneficial uses. In this study, we evaluated various ionic liquids to identify the most effective one for extracting lycopene from guava. Among thirteen ionic liquids with varying carbon chains or anions, 1-butyl-3-methylimidazolium chloride demonstrated the highest productivity. Subsequently, a single-factor experiment was employed to test the impact of several parameters on the efficiency of lycopene extraction using this selected ionic liquid. These parameters included extraction time, ultrasonic power, liquid-solid ratio, concentration of the ionic liquid, as well as material particle size. Moreover, models of artificial neural networks using genetic algorithms (ANN-GA) and response surface methodology (RSM) were employed to comprehensively assess the first four key parameters. The optimized conditions for ionic liquid ultrasound-assisted extraction (IL-UAE) were determined as follows: 33 min of extraction time, 225 W of ultrasonic power, 22 mL/g of liquid-solid ratio, 3.0 mol/L of IL concentration, and extraction cycles of three. Under these conditions, lycopene production reached an impressive yield of 9.35 ± 0.36 mg/g while offering advantages such as high efficiency, time savings, preservation benefits, and most importantly environmental friendliness.

Study of promising novel biomarkers on cardio vascular diseases

An excellent paper that provides a comprehensive analysis of biomarkers, which can disclose a variety of information about health or illness, such as the kind or extent of environmental exposure, genetic Vulnarability, genetic responses to exposures, indicators of preclinical or clinical illness, or indications of the treatment response. Indicators of disease trait , disease stage (preclinical or clinical), or illness rate are thus a basic approach to conceptualize biomarkers. A trait that can be objectively measured and evaluated is called a biomarker. as a gauge for biological activities that are pathogenic, healthy, or pharmaceutical responses to a treatment As a result, this paper examines the wealth of research on the function of bioactive compounds in a range of pathological processes associated with different

High-risk multiple myeloma: Redefining genetic, clinical, and functional high-risk disease in the era of molecular medicine and immunotherapy.

Multiple myeloma (MM) exhibits significant heterogeneity in its presentation, genetics, and treatment response. Despite therapeutic advances, some patients continue to relapse early (ER, <18-months) and rapidly cycle through therapies. Myriad prognostic factors have been identified and incorporated into risk stratification models; however, these produce discordant, often three-tiered outputs that fail to identify many patients destined for ER. Treatment strategies are increasingly focused on disease biology and trials enriched for high-risk (HR)MM, but consensus on the minimum required testing and a succinct, specific, and clinically meaningful definition for HRMM remains elusive. We review the risk-factors, definitions, and future directions for HRMM.

Saccharomyces cerevisiae strains performing similarly during fermentation of lignocellulosic hydrolysates show pronounced differences in transcriptional stress responses.

The need for sustainable alternatives to oil-based production of biochemicals and biofuels is undisputable. Saccharomyces cerevisiae is the most commonly used industrial fermentation workhorse. The fermentation of lignocellulosic hydrolysates, second-generation biomass unsuited for food and feed, is still hampered by lowered productivities as the raw material is inhibitory for the cells. In order to map the genetic responses of different S. cerevisiae strains, we performed RNA sequencing of a CEN.PK laboratory strain, two industrial strains (KE6-12 and Ethanol Red), and two wild-type isolates of the LBCM collection when cultivated anaerobically in wheat straw hydrolysate. While the response to inhibitors of S. cerevisiae has been studied earlier, this has in previous studies been done in aerobic conditions. The transcriptomic analysis highlights different evolutionary adaptations among the different S. cerevisiae strains and suggests novel gene targets for improving fermentation performance and robustness.

The potential of artificial intelligence in early diagnosis and personalized treatment: Advances and challenges in modern medicine

Carrying out this study is justified by its academic, scientific and social relevance, based on presenting technological advances involving artificial intelligence in healthcare. Therefore, the objective of this research focuses on highlighting the applications and benefits of Artificial Intelligence in Medicine. This study was carried out through an integrative literature review, with an exploratory approach, whose institute was limited to investigating, through already published articles, relevant information that answered the guiding question. Thus, data collection took place in scientific bases: SCIELO and LILACS. One of the main advantages of using AI in early diagnosis is the ability to process large volumes of data quickly and accurately, identifying patterns and signals that may be imperceptible to human healthcare professionals. This makes it possible to detect serious medical conditions early, such as cancer and heart disease, when treatment is most effective and the chances of recovery are greatest. Furthermore, AI can significantly contribute to personalized treatment, adapting therapeutic approaches based on the individual characteristics of each patient. By analyzing genetic data, medical history, and response to previous treatments, AI algorithms can help doctors develop treatment plans that are more effective and have fewer side effects.

Genetic analysis of feed efficiency and novel feeding behavior traits measured in group-housed broilers using electronic feeders

This study aimed to estimate genetic parameters for feeding behavior (FB) traits and to assess their genetic relationship with performance traits in group-housed broilers. In total, 99,472,151 visits were recorded for 95,711 birds between 2017 and 2022 using electronic feeders. The visits were first clustered into 2,667,617 daily observations for ten FB traits: daily feed intake (DFI), daily number of visits (NVIS), time spent at the feeders (TSF), number of visited feeders (NVF), visiting activity interval (VAI), feeding rate (FR), daily number of meals (NMEAL), average intake per meal (INTMEAL), number of visits per meal (VISMEAL) and interval between meals (MEALIVL). All FB traits were then considered as the average per bird across the feeding test period. Three growth traits (body weight at the start - SBW and at the end of the feeding test - FBW, and weight gain over the test period - BWG), and 2 feed efficiency (FE) traits (Feed Conversion Rate - FCR and Residual Feed Intake - RFI) were also recorded. The (co)variance components were estimated using multitrait animal mixed models. For growth and FE, the heritability (h2) estimates were moderate, ranging from 0.20 ± 0.01 (BWG) to 0.32 ± 0.02 (RFI). Overall, the h2 estimates for FB traits were higher than for productive traits, ranging from 0.31 ± 0.01 (DFI) to 0.56 ± 0.02 (TSF). DFI presented high genetic correlations (0.53-0.86) with all performance traits. Conversely, the remaining FB traits presented null to moderate genetic correlations with these traits, ranging from -0.38 to 0.42 for growth traits and between -0.14 and 0.25 for FE traits. Genetic selection for favorable feeding behavior is expected to exhibit a fast genetic response. The results suggest that it is possible to consider different feeding strategies without compromising the genetic progress of FE. Conversely, breeding strategies prioritizing a higher bird activity might result in lighter broiler lines in the long term, given the negative genetic correlations between visit-related traits (NV, NVF, and NMEAL) and growth traits (SBW and FBW).

A Method to Estimate Climate Drivers of Maize Yield Predictability Leveraging Genetic-by-Environment Interactions in the US and Canada

Throughout history, the pursuit of diagnosing and predicting crop yields has evidenced genetics, environment, and management practices intertwined in achieving food security. However, the sensitivity of crop phenotypes and genetic responses to climate still hampers the identification of the underlying abilities of plants to adapt to climate change. We hypothesize that the PiAnosi and WagNer (PAWN) global sensitivity analysis (GSA) coupled with a genetic by environment (GxE) model built of environmental covariance and genetic markers structures, can evidence the contributions of climate on the predictability of maize yields in the U.S. and Ontario, Canada. The GSA-GxE framework estimates the relative contribution of climate variables to improving maize yield predictions. Using an enhanced version of the Genomes to Fields initiative database, the GSA-GxE framework shows that the spatially aggregated sensitivity of maize yield predictability is attributed to solar radiation, followed by temperature, rainfall, and relative humidity. In one-third of the individually assessed locations, rainfall was the primary responsible for maize yield predictability. Also, a consistent pattern of top sensitivities (Relative Humidity, Solar Radiation, and Temperature) as the main or the second most relevant drivers of maize yield predictability shed some light on the drivers of genetic improvement in response to climate change.

Vaccinomics: Paving the Way for Personalized Immunization.

Vaccines are one of the most important medical advancements in human history. They have been successfully used to control and limit the spread of many of the lethal diseases that have plagued us, such as smallpox and polio. Previous vaccine design methodologies were based on the model of "isolate-inactivateinject", which amounts to giving the same vaccine dose to everyone susceptible to infection. In recent years, the importance of how the host genetic background alters vaccine response necessitated the introduction of vaccinomics, which is aimed at studying the variability of vaccine efficacy by associating genetic variability and immune response to vaccination. Despite the rapid developments in variant screening, data obtained from association studies is often inconclusive and cannot be used to guide the new generation of vaccines. This review aims to compile the polymorphisms in HLA and immune system genes and examine the link with their immune response to vaccination. The compiled data can be used to guide the development of new strategies for vaccination for vulnerable groups. Overall, the highly polymorphic HLA locus had the highest correlation with vaccine response variability for most of the studied vaccines, and it was linked to variation in multiple stages of the immune response to the vaccines for both humoral and cellular immunity. Designing new vaccine technologies and immunization regiments to accommodate for this variability is an important step for reaching a vaccinomics-based approach to vaccination.

Exposure to Sublethal Concentrations of Lead (Pb) Affects Ecologically Relevant Behaviors in House Sparrows (Passer domesticus)

Global contamination of environments with lead (Pb) poses threats to many ecosystems and populations. While exposure to Pb is toxic at high concentrations, recent literature has shown that lower concentrations can also cause sublethal, deleterious effects. However, there remains relatively little causal investigation of how exposure to lower concentrations of environmental Pb affects ecologically important behaviors. Behaviors often represent first-line responses of an organism and its internal physiological, molecular, and genetic responses to a changing environment. Hence, better understanding how behaviors are influenced by pollutants such as Pb generates crucial information on how species are coping with the effects of pollution more broadly. To better understand the effects of sublethal Pb on behavior, we chronically exposed adult wild-caught, captive house sparrows (Passer domesticus) to Pb-exposed drinking water and quantified a suite of behavioral outcomes: takeoff flight performance, activity in a novel environment, and in-hand struggling and breathing rate while being handled by an experimenter. Compared to controls (un-exposed drinking water), sparrows exposed to environmentally relevant concentrations of Pb exhibited decreases in takeoff flight performance and reduced movements in a novel environment following 9–10 weeks of exposure. We interpret this suite of results to be consistent with Pb influencing fundamental neuro-muscular abilities, making it more difficult for exposed birds to mount faster movements and activities. It is likely that suppression of takeoff flight and reduced movements would increase the predation risk of similar birds in the wild; hence, we also conclude that the effects we observed could influence fitness outcomes for individuals and populations altering ecological interactions within more naturalistic settings.

The impact of magnesium sulfate on the gene expression of Bordetella pertussis (ptxP1 and ptxP3) strains and the incidence of whooping cough in Nineveh

IntroductionThe incidence of Bordetella pertussis infections in the Nineveh is affected by living conditions and the density of the population in specific geographic regions. AimThis study amid to assess the monitoring pertussis in Nineveh between 2017 and 2021. MethodsThis work focused on how MgSO4 impacts the activity of ptxP1 and ptxP3 genes in B. pertussis strains. ResultsMosul, Al-Baaj, and Sinjar recorded higher rates of infection compared to other regions due to population density. The expression BfrD, ptxE, ptxD, ptxB, ptxA, and ptxC was exhibited elevation when exposed to MgSO4 of 0 and 5 mM conc. On the other hand, WbpT, VipC, and KpsM showed high expression at a concentration of 50 mM of MgSO4. Pgm demonstrated elevated expression across all concentrations of MgSO4 for the ptxP1 strain, while maintaining consistently low expression for the ptxP3 strain. The potential of Pgm as a distinct marker, effectively distinguishing between the 2 strains of B. pertussis. This approach will allow for a more detailed exploration of the variations between bacterial strains regarding their genetic responses to MgSO4 concentrations. ConclusionsData analysis of microarray was indicated that ptxP3 strains are less affected by the inhibitory effects of sulfate root on undesirable gene expression. This investigation may lead for further studies into the role of sulfite root in pertussis's pathogenicity.

Genome-wide association studies and transcriptomics reveal mechanisms explaining the diversity of wheat root responses to nutrient availability.

Nutrient availability profoundly influences plant root system architecture, which critically determines crop productivity. While Arabidopsis has provided important insights into the genetic responses to nutrient deficiency, translating this knowledge to crops, particularly wheat, remains a subject of inquiry. Here, examining a diverse wheat population under varying nitrogen (N), phosphorus (P), potassium (K), and iron (Fe) levels, we uncover a spectrum of root responses, spanning from growth inhibition to stimulation, highlighting genotype-specific strategies. Furthermore, we reveal a nuanced interplay between macronutrient deficiency (N, P, and K) and Fe availability, emphasizing the central role of Fe in modulating root architecture. Through genome-wide association mapping, we identify 11 quantitative trait loci underlying root traits under varying nutrient availabilities, including homologous genes previously validated in Arabidopsis, supporting our findings. In addition, utilizing transcriptomics, ROS imaging, and antioxidant treatment, we uncover that wheat root growth inhibition by nutrient deficiency is attributed to ROS accumulation, akin to the role of ROS in governing Arabidopsis root responses to nutrient deficiency. Therefore, our study reveals the conservation of molecular and physiological mechanisms between Arabidopsis and wheat to adjust root growth to nutrient availability, paving the way for targeted crop improvement strategies aimed at increasing nutrient use efficiency.

Update in lean metabolic dysfunction-associated steatotic liver disease.

A new nomenclature consensus has emerged for liver diseases that were previously known as non-alcoholic fatty liver disease (NAFLD) and metabolic dysfunction-associated fatty liver disease (MAFLD). They are now defined as metabolic dysfunction-associated steatotic liver disease (MASLD), which includes cardiometabolic criteria in adults. This condition, extensively studied in obese or overweight patients, constitutes around 30% of the population, with a steady increase worldwide. Lean patients account for approximately 10%-15% of the MASLD population. However, the pathogenesis is complex and is not well understood. To systematically review the literature on the diagnosis, pathogenesis, characteristics, and prognosis in lean MASLD patients and provide an interpretation of these new criteria. We conducted a comprehensive database search on PubMed and Google Scholar between January 2012 and September 2023, specifically focusing on lean NAFLD, MAFLD, or MASLD patients. We include original articles with patients aged 18 years or older, with a lean body mass index categorized according to the World Health Organization criteria, using a cutoff of 25 kg/m2 for the general population and 23 kg/m2 for the Asian population. We include 85 studies in our analysis. Our findings revealed that, for lean NAFLD patients, the prevalence rate varied widely, ranging from 3.8% to 34.1%. The precise pathogenesis mechanism remained elusive, with associations found in genetic variants, epigenetic modifications, and adaptative metabolic response. Common risk factors included metabolic syndrome, hypertension, and type 2 diabetes mellitus, but their prevalence varied based on the comparison group involving lean patients. Regarding non-invasive tools, Fibrosis-4 index outperformed the NAFLD fibrosis score in lean patients. Lifestyle modifications aided in reducing hepatic steatosis and improving cardiometabolic profiles, with some medications showing efficacy to a lesser extent. However, lean NAFLD patients exhibited a worse prognosis compared to the obese or overweight counterpart. MASLD is a complex disease comprising epigenetic, genetic, and metabolic factors in its pathogenesis. Results vary across populations, gender, and age. Limited data exists on clinical practice guidelines for lean patients. Future studies employing this new nomenclature can contribute to standardizing and generalizing results among lean patients with steatotic liver disease.

Evaluation of genetic response of mesenchymal stem cells to nanosecond pulsed electric fields by whole transcriptome sequencing.

Mesenchymal stem cells (MSCs) modulated by various exogenous signals have been applied extensively in regenerative medicine research. Notably, nanosecond pulsed electric fields (nsPEFs), characterized by short duration and high strength, significantly influence cell phenotypes and regulate MSCs differentiation via multiple pathways. Consequently, we used transcriptomics to study changes in messenger RNA (mRNA), long noncoding RNA (lncRNA), microRNA (miRNA), and circular RNA expression during nsPEFs application. To explore gene expression profiles and potential transcriptional regulatory mechanisms in MSCs pretreated with nsPEFs. The impact of nsPEFs on the MSCs transcriptome was investigated through whole transcriptome sequencing. MSCs were pretreated with 5-pulse nsPEFs (100 ns at 10 kV/cm, 1 Hz), followed by total RNA isolation. Each transcript was normalized by fragments per kilobase per million. Fold change and difference significance were applied to screen the differentially expressed genes (DEGs). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed to elucidate gene functions, complemented by quantitative polymerase chain reaction verification. In total, 263 DEGs were discovered, with 92 upregulated and 171 downregulated. DEGs were predominantly enriched in epithelial cell proliferation, osteoblast differentiation, mesenchymal cell differentiation, nuclear division, and wound healing. Regarding cellular components, DEGs are primarily involved in condensed chromosome, chromosomal region, actin cytoskeleton, and kinetochore. From aspect of molecular functions, DEGs are mainly involved in glycosaminoglycan binding, integrin binding, nuclear steroid receptor activity, cytoskeletal motor activity, and steroid binding. Quantitative real-time polymerase chain reaction confirmed targeted transcript regulation. Our systematic investigation of the wide-ranging transcriptional pattern modulated by nsPEFs revealed the differential expression of 263 mRNAs, 2 miRNAs, and 65 lncRNAs. Our study demonstrates that nsPEFs may affect stem cells through several signaling pathways, which are involved in vesicular transport, calcium ion transport, cytoskeleton, and cell differentiation.

Abstract 7046: Proteogenomic and immunologic profiles of head and neck cancer patients of African ancestry

Abstract Blacks/African Americans (BAAs) with head and neck squamous cell carcinoma (HNSCC) have worse survival than Whites. However, the complex molecular biomarkers and signatures of HNSCC among BAAs and molecular distinction associated with HNSCC disparities are largely unknown. Here we show the results of a multi-omics analysis of 500 patients (48 BAAs and 452 Whites). Comparative analyses between the racial groups were performed at the level of genomics, pathways, molecular subtype, tumor immune infiltration, protein alterations and prognosis. We found that overall survival in BAAs with HPV-unrelated HNSCC is significantly shorter than in White patients. Ancestry-related differential mutation spectrum, DNA methylation, gene and protein expression pattern and immune infiltration landscape were identified. Particularly, FAT1 mutation is significantly associated with its gene expression in BAA HNSCC and poor overall survival in this group. In BAA HNSCC, SALL3 gene expression is positively associated with its gene CNVs, while RTP4 gene expression is inversely correlated with its methylation. High EGFR_pY1068 and RAD50 levels correlate with poor prognosis in BAAs with HNSCC. The immune infiltration enrichment scores of Th17 cells, activated dendritic cells, monocytes and neutrophils in BAA HNSCC were significantly lower than those in White HNSCC. By combining multi-omics analysis and data validation using in-house-made tumor tissue arrays, this study comprehensively elucidates the genetic landscape, immune response, and tumor biology in BAA and White HNSCC patients, providing a molecular basis for future research in identifying appropriate screening modalities and therapeutic interventions leading to improved outcomes in BAAs with HNSCC. Citation Format: Fan Yang, Fanghui Chen, Chloe Shay, Nabil F. Saba, Yong Teng. Proteogenomic and immunologic profiles of head and neck cancer patients of African ancestry [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7046.

Insights into metal tolerance and resistance mechanisms in Trichoderma asperellum unveiled by de novo transcriptome analysis during bioleaching

This study investigates the genetic responses of the fungus Trichoderma asperellum (T. asperellum) during bioleaching of ore and tailing samples, comparing one-step, two-step, and spent media bioleaching processes. HPLC analysis quantified oxalic acid, citric acid, and propionic acids, with oxalic acid identified as the primary organic acid involved in metal bioleaching. Metal analysis revealed differences in recovery between ore and tailing samples and among bioleaching processes. The two-step bioleaching process yielded the highest zinc (>54%) and nickel (>60%) recovery in tailings and ore, respectively. Nickel's efficient recovery in ore bioleaching was attributed to the presence of manganese, while its precipitation as nickel oxalate in tailings hindered recovery. Additional metals such as Co, Mn, Mg, Cu, and As were also successfully recovered. Transcriptomic analyses showed significant upregulation of genes associated with biological processes and cellular components, particularly those related to cell membrane structure and function, indicating T. asperellum's adaptation to environmental stresses during metal bioleaching. These findings enhance our understanding of the diverse mechanisms influencing metal recovery rates in bioleaching processes.

Abstract 60: Functional mapping of glioblastoma recurrence reveals targetable dependencies in an axonal guidance pathway in highly invasive brain cancers

Abstract Resistance to genotoxic therapies and tumor recurrence are hallmarks of glioblastoma (GBM), an aggressive brain tumor. Here, we explore the functional drivers of post-treatment recurrent GBM. By conducting genome-wide CRISPR-Cas9 screens in patient-derived GBM models, we uncover distinct genetic dependencies in recurrent tumor cells that were absent in their patient-matched primary predecessors, accompanied by increased mutational burden and differential transcript and protein expression. These analyses map a multilayered genetic response to drive tumor recurrence, identifying protein tyrosine phosphatase 4A2 (PTP4A2) as a novel modulator of self-renewal, proliferation and tumorigenicity at GBM recurrence. Genetic perturbation or small molecule inhibition of PTP4A2 represses axon guidance activity through a dephosphorylation axis with roundabout guidance receptor 1 (ROBO1), exploiting a functional dependency on ROBO signaling. Importantly, engineered anti-ROBO1 single-domain antibodies also mimic effects of PTP4A2 inhibition. Since a pan-PTP4A inhibitor was limited by poor penetrance across the blood brain barrier (BBB) in vivo, a second-generation chimeric antigen receptor (CAR)-T cell therapy was engineered against ROBO1 that elicits specific and potent anti-tumor responses in vivo. A single dose of anti-ROBO1 CAR-T cells doubles median survival in patient-derived xenograft (PDX) models of recurrent glioblastoma, and also eradicates tumors in around 50% of mice engrafted with PDX models of lung-to-brain metastases and pediatric relapsed medulloblastoma. We conclude that functional reprogramming drives tumorigenicity and dependence on a multi-targetable PTP4A-ROBO1 signaling axis at GBM recurrence, with potential in other malignant brain tumors. Citation Format: Sheila Kumari Singh, Chirayu Chokshi, Vaseem Shaikh, Benjamin Brakel, Alisha Anand, Chitra Venugopal, Thomas Kislinger, Kevin Henry, Martin Rossotti, Kevin Brown, John Lazo, Jason Moffat. Functional mapping of glioblastoma recurrence reveals targetable dependencies in an axonal guidance pathway in highly invasive brain cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 60.

CRISPR/Cas9-mediated editing of ACTB in induced pluripotent stem cells: A model for investigating human ACTB loss-of-function and genetic adaptive responses

Heterozygous beta-actin (ACTB) indel and nonsense mutations are linked to developmental disorders. We generated two CRISPR/Cas9 human induced pluripotent stem cell (iPSC) lines, WTSIi018-B-19 and WTSIi018-B-20, carrying heterozygous and homozygous indel mutations in ACTB exon 4. Both iPSCs exhibited normal cell morphology, expression of pluripotency markers, and the ability to differentiate into the three primary germ layers. While iPSCs with a heterozygous ACTB mutation maintain genome integrity, homozygous mutants showed a loss of heterozygosity in chromosome three. These mutants provide a powerful model to study the onset, progression, and complex interplay of genetic compensation and phenotypic variation of ACTB-related diseases.