Biology subjects

Kaiser, A.

Publications and source records attributed to Kaiser, A..

13 recordsLinked to original sources

bioRxiv2026

Urbanization and wealth alter arthropod biodiversity and pollination services in community gardens

1. As city populations expand globally, understanding how urbanization shapes ecosystem services is increasingly important. Urban agriculture plays a key role in food access, particularly in low-income areas with limited access to fresh produce. Arthropods play important roles in these systems through pollination, herbivory, pest control, and nutrient cycling. Urban development of natural areas often reduces biodiversity, including that of arthropods. Additionally, urban biodiversity frequently correlates positively with socioeconomic conditions, a pattern known as the luxury effect. 2. In this study, we examined how gradients in urbanization and socioeconomic context relate to local and landscape habitat quality, arthropod abundance, and pollination services across 21 community gardens in the Denver, CO Metro Area. To quantify ecosystem services, we employed a sentinel plant, Cucumis sativus (cucumber), and collected arthropods (insects, myriapods, arachnids, isopods), assigning them to functional groups based on their known feeding behavior. We evaluated direct and indirect pathways linking urban matrix characteristics to arthropod-mediated ecosystem services. 3. The abundance of all arthropod groups (including pollinators, herbivores, and natural enemies) declined steeply with increasing impervious surface. Neighborhood wealth was associated only with bee species richness and Shannon diversity and displayed a hump-shaped pattern that peaked at wealth levels 35-46% above the national average, then declined. Multivariate GLMs revealed that Western honeybees (Apis mellifera) were the only species driving differences in bee community composition, with their abundance positively related to neighborhood wealth. 4. We also observed pollen limitation in our cucumber plants, and as bee Shannon diversity increased, cucumber production increased. Environmental covariates alone showed no direct relationship with cucumber production, indicating that insect pollination mediated this effect. This work identifies the biophysical and social-ecological drivers of urban arthropod biodiversity and ecosystem services, revealing where crop production may be most vulnerable to decline in cities.

ecology↗

bioRxiv2026

PDE3A-SLFN12 Molecular Glues Target Multiple KIT D816V Cell Types in Preclinical Models of Mast Cell Malignancies

A drug discovery approach was used to specifically target malignant cells with KIT D816V mutation, which is the predominant disease-causing mutation in clonal mast cell malignancies. To this end, KIT D816V cells derived from induced pluripotent stem cells (iPS cells) of KIT D816V patients were employed to screen a library of FDA approved and experimental drugs for specific killing of KIT D816V cells. We discovered the novel compound LDC 3416, which targets multiple malignant KIT D816V cell types, including hematopoietic stem/progenitor cells and mast cells. Importantly, by exploring the LDC 3416 targeting profile, we identified the phosphodiesterase 3A-Schlafen 12 (PDE3A-SLFN12) molecular glue pathway as a novel approach for specific targeting of malignant KIT D816V cells. We found that the KIT D816V mutant protein leads to increased expression of PDE3A and SLFN12 and thus confers a selective molecular vulnerability to PDE3A-SLFN12 molecular glues. Primary malignant mast cells of KIT D816V patients with indolent and advanced systemic mastocytosis also exhibit increased expression of PDE3A and SLFN12. We extended our study to include additional PDE3A-SLFN12 molecular glues and demonstrate their synergistic action with KIT D816V selective tyrosine kinase inhibitors (TKIs) in killing KIT D816V cells. Furthermore, the PDE3A-SLFN12 molecular glues also target KIT D816V megakaryocytes, a cell type that has been underestimated in malignant mast cell pathophysiology and molecular targeting. The identified molecular glues, along with their synergy with TKIs and their simultaneous targeting of multiple KIT D816V cell types, open novel treatment options for KIT D816V mast cell malignancies and other KIT D816V associated diseases.

cancer biology↗

bioRxiv2025

Ultra-High Field 31P functional Magnetic Resonance Spectroscopy Reveals NAD+ Dynamics in Brain Energy Metabolism during Visual Stimulation.

We investigated dynamic changes in nicotinamide adenine dinucleotide (NAD{square}) metabolism in the human occipital lobe using ultra-high field 31P functional magnetic resonance spectroscopy (fMRS) at 7 Tesla. Twenty-five healthy volunteers (mean age 24 {+/-} 4 years, 10 female) performed a visual task alternating between fixation and flashing checkerboard stimuli. 31P MRS spectra were acquired from a visual cortex voxel functionally localized by prior fMRI. Linear mixed-effects modelling revealed a significant reduction in NAD{square} concentrations during the first stimulation block, while no significant change was observed during the second block. No significant changes were observed for other high-energy phosphate metabolites (ATP, phosphocreatine, and inorganic phosphate), indicating specificity in the NAD{square} response. Exploratory analyses, dividing the blocks in two halves, suggested further reductions in NAD{square} and tNAD in the second halves of both stimulation blocks, though these trends were not statistically significant. Our findings demonstrate the feasibility of using fMRS at 7T to detect stimulus-induced dynamics in cerebral NAD{square} metabolism in vivo, providing insights into the interplay between glycolysis and oxidative phosphorylation during neural activation.

neuroscience↗

bioRxiv2025

Benchmarking the Impact of Anatomical Segmentation on In Vivo Magnetic Resonance Spectroscopy

PurposeEstimation of metabolite concentrations in brain magnetic resonance spectroscopy (MRS) requires correction for differences in tissue water content, relaxation properties, and the proportions of gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF). Accurate knowledge of the relative proportions of these tissue classes within the volume of interest is therefore essential for reliable quantification. Commonly used brain segmentation tools differ in their algorithms, priors, and implementation, potentially introducing variability in MRS-derived concentration estimates. This study investigates the impact of segmentation software on estimated absolute concentrations. MethodsThree segmentation software tools, ANTs, FSL, and SPM, were evaluated. Segmentations were applied to an in vivo test-retest MR dataset to assess (1) differences in estimated tissue fractions, and (2) how these differences propagate into tissue-corrected metabolite concentrations. As an additional validity check and biological benchmark of segmentation performance, age-related associations with GM and total creatine (tCr) were examined. ResultsSignificant differences (p < 0.0001) were observed in tissue fraction estimates between segmentation tools, leading to differences in metabolite concentration estimates of up to 9% under identical acquisition and modeling conditions. Although the strength of the correlation varied between segmentation methods, no statistically significant differences were found. ConclusionThe choice of segmentation methodology contributed substantially to variability in MRS "absolute" metabolite concentration estimates. These results underscore the need for transparent segmentation reporting to ensure reproducibility and cross-study comparability in MRS research. Quantifying the segmentation-driven variability allows researchers to contextualize cross-study differences, helping determine whether observed effects are methodological or biologically meaningful.

neuroscience↗

bioRxiv2025

PglZ from Type I BREX phage defence systems is a metal-dependent nuclease that forms a sub-complex with BrxB

BREX (Bacteriophage Exclusion) systems, identified through shared identity with Pgl (Phage Growth Limitation) systems, are a widespread, highly diverse group of phage defence systems found throughout bacteria and archaea. The varied BREX Types harbour multiple protein subunits (between four and eight) and all encode a conserved putative phosphatase (PglZ aka BrxZ) and an equally conserved, putative ATPase (BrxC). Almost all BREX systems also contain a site-specific methyltransferase (PglX aka BrxX). Despite having determined the structure and fundamental biophysical and biochemical behaviours for the PglX methyltransferase, the BrxL effector, the BrxA DNA-binding protein and the BrxR transcriptional regulator, the mechanism by which BREX impedes phage replication remains largely undetermined. In this study, we identify a stable BREX sub-complex of PglZ:BrxB, validate the structure and dynamic behaviour of that sub-complex, and assess the biochemical activity of PglZ, revealing it to be a metal-dependent nuclease. PglZ can cleave cyclic oligonucleotides, linear oligonucleotides, plasmid DNA and both non-modified and modified linear phage genomes. PglZ nuclease activity has no obvious role in BREX-dependent methylation, but does contribute to BREX phage defence. BrxB binding does not impact PglZ nuclease activity. These data contribute to our growing understanding of the BREX phage defence mechanism.

biochemistry↗

bioRxiv2024

Reward processing in children with Affective Dysregulation

IntroductionAffective dysregulation (AD) in children is characterized by irritability, anger, and frequent intense temper outbursts. Considerable evidence implies altered processing of frustration about missed rewards, but few studies investigated the preceding and thus potentially predictive reward anticipation and initial delivery processing in children with AD. MethodsA total of 103 children aged 8 to 12 years (50 with AD and 53 without AD) were examined during a monetary reward anticipation task with event-related potential (ERP) components resolving reward anticipation (cue-CNV [Contingent Negative Variation]) and reward delivery phases (Reward Positivity and Feedback-Related Negativity). All components were analyzed by repeated measures ANOVA. Regression analyses also evaluated the associations between those ERP components and dimensional AD symptoms. ResultsChildren with AD showed attenuated anticipatory reward processing compared to No-ADs. The CNV at fronto-central site (FCz) showed a significant group effect (No-AD>AD, p=0.017). Post-hoc test showed that this group difference was stronger for the cue monetary condition (monetary cue: p=.007, d=0.56, verbal cue: p=.901, d=0.16), and that only the No-AD group showed a significant difference between conditions (p<0.001). No significant effects were obtained for the delivery phase. Regression analysis showed that a reduced anticipatory CNV at FCz significantly explained AD symptoms, and that anger/irritability and anxiety/depressive symptoms predicted a reduced anticipatory CNV at FCz. ConclusionThis neurophysiological characterization of reward anticipation and delivery in children with AD demonstrates altered neural activity in AD during anticipation of reward rather than following the delivery (or omission) of the reward itself. Our results highlight that altered reward anticipation in AD can occur outside frustration-prone tasks or settings, and underline the important role of both anger/irritability and anxiety/depressive symptoms in the pathophysiology of AD for atypical reward anticipation.

neuroscience↗

bioRxiv2023

Development of selective pyridopyrimidin-7(8H)-one-based Mammalian STE20-like (MST3/4) kinase inhibitors

Mammalian STE20-like (MST) kinases 1-4 play key roles in regulating the Hippo and autophagy pathways, and their dysregulation has been implicated in cancer development. In contrast to the well-studied MST1/2, the roles of MST3/4 are less clear, in part due to the lack of potent and selective MST3/4 inhibitors. Here, we re-evaluated literature compounds, and used structure-guided design to optimize the p21-activated kinase (PAK) inhibitor G-5555 (8) to selectively target MST3/4. These efforts resulted in the development of MR24 (24) and MR30 (27) with good kinome-wide selectivity, high potency for MST3/4, and selectivity towards the closely related MST1/2. In combination with the MST1/2 inhibitor PF-06447475 (2) the two MST3/4 inhibitors can be used to elucidate the multiple roles of MST kinases in cells. We found that MST3/4-selective inhibition caused a cell cycle arrest in the G1 phase, while MST1/2 inhibition resulted in accumulation of cells in the G2/M phase. These data point to distinct functions of these closely related kinases, which can now be addressed with subfamily-selective chemical tool compounds.

biochemistry↗

bioRxiv2023

Synthesis of pyrazole-based macrocycles leads to a highly selective inhibitor for MST3

MST1, MST2, MST3, MST4, and YSK1 are conserved members of the mammalian sterile 20 kinase (MST) family. MSTs regulate key cellular functions such as cell proliferation, cell migration, metabolic regulation, and cell polarity. The MST3 isozyme plays a role in regulation of cell growth, autophagy and apoptosis, and its dysregulation has been linked to the occurrence of high-grade tumors with poor survival prognosis. To date, there are no isoform-selective inhibitors available that could be used for validating the role of MST3 in tumorigenesis and to assess its potential as an anti-cancer target for drug development. To this end, we have designed a new series of 3-aminopyrazole-based macrocycles based on the structure of an acyclic promiscuous kinase inhibitor. By varying moieties targeting the solvent-exposed region and optimizing the linker, macrocycle JA310 (21c) was synthesized. JA310 exhibited high cellular potency for MST3 with an EC50 = 106 nM and excellent kinome-wide selectivity with significantly lower cellular activity on the closely related kinase MST4 (EC50 = 1.4 {micro}M). The high-resolution crystal structure of the MST3-JA310 complex provided intriguing insights into the distinct binding mode of the macrocycle, which was associated with large-scale structural rearrangements, including concerted induced-fit movements of the glycine-rich loop, the C helix, and the activation loop. In summary, the developed macrocyclic MST3 inhibitor, JA310, demonstrates the utility of macrocyclization for the design of highly selective inhibitors and presents a first chemical probe for MST3.

biochemistry↗

bioRxiv2022

Mutation of the Drosophila serotonin transporter dSERT disrupts courtship and feeding and increases both daytime and nighttime sleep

The Serotonin Transporter (SERT) regulates extracellular serotonin levels and is the target of most current drugs used to treat depression. The mechanisms by which inhibition of SERT activity influences behavior are poorly understood. To address this question in the model organism Drosophila melanogaster, we developed new loss of function mutations in Drosophila SERT (dSERT). Previous studies in both flies and mammals have implicated serotonin as an important neuromodulator of sleep, and our newly generated dSERT mutants show an increase in total sleep and altered sleep architecture. Differences in daytime vs. nighttime sleep architecture as well as genetic rescue experiments unexpectedly suggest that distinct serotonergic circuits may modulate daytime versus nighttime sleep. dSERT mutants also show defects in copulation and food intake, akin to the clinical side effects of SSRIs. Starvation did not overcome the sleep drive in the mutants. Additionally in males, but not female dSERT mutants, the drive to mate also failed to overcome sleep drive. dSERT may be used to further explore the mechanisms by which serotonin regulates sleep and its interplay with other complex behaviors. Author SummaryMany medications used to treat depression and anxiety act by changing serotonin levels in the brain. Fruit flies also use serotonin and can be used as a model to study the brain. We have made a fly mutant for the serotonin transporter (SERT), which is the target of antidepressants in humans. The mutants sleep more, eat less, and have a decreased sex drive. These flies can be used to study the neuronal pathways by which serotonin regulates sleep, eating and sexual behaviors and may help us to understand the behavioral effects of antidepressants.

neuroscience↗

bioRxiv2020

CAR T cell entry into tumor islets is a two-step process dependent on IFNγ and ICAM-1

Adoptive transfer of T cells expressing chimeric antigen receptors (CARs) has shown remarkable clinical efficacy against advanced B cell malignancies but not yet against solid tumors. Here, we used fluorescent imaging microscopy and ex vivo assays to compare the early functional responses (migration, Ca2+ and cytotoxicity) of CD20 and EGFR CAR T cells upon contact with malignant B and carcinoma cells. Our results indicate that CD20 CAR T cells rapidly form productive ICAM-1-dependent conjugates with their targets. By comparison, EGFR CAR T cells only interact at first with a subset of carcinoma cells located at the periphery of tumor islets. After this initial peripheral activation, EGFR CAR T cells progressively infiltrate the center of tumor cell regions. The analysis of this two-step entry process shows that activated CAR T cells trigger the upregulation of ICAM-1 on tumor cells in an IFN{gamma}-dependent pathway. The blockade of ICAM-1/LFA-1 interactions prevents CAR T cell recruitment into tumor islets. The requirement for IFN{gamma} and ICAM-1 to enable CAR T cell entry into tumor islets is of significance for improving CAR T strategy in solid tumors.

immunology↗

bioRxiv2020

Longitudinal alterations in fronto-striatal glutamate are associated with functioning during inhibitory control in autism spectrum disorder and obsessive compulsive disorder

BackgroundAutism spectrum disorder (ASD) and obsessive compulsive disorder (OCD) are neurodevelopmental disorders with overlapping symptomatology. Both show deficits in inhibitory control, which are associated with altered functioning and glutamate concentrations in the fronto-striatal circuitry. These parameters have never been examined together. Here we, for the first time, used a multi-center, longitudinal approach to investigate fronto-striatal functioning during an inhibitory control task and its association with fronto-striatal glutamate concentrations across these two disorders. Methods74 adolescents with ASD (24) or OCD (15) and controls (35) aged 8-17 were recruited across three sites of the European TACTICS consortium. They underwent two magnetic resonance imaging (MRI) sessions with a one-year interval. This included proton magnetic resonance spectroscopy (1H-MRS; n=74) and functional MRI during an inhibitory control task (n=57). We used linear mixed effects models to investigate, over time, the relationship between fronto-striatal functioning and glutamate concentrations across these groups and continuous measures of overlapping compulsivity symptoms. ResultsDuring failed inhibitory control, in OCD increased striatal glutamate was associated with increased neural activation of ACC, an effect that decreased over time. During successful inhibitory control, higher ACC glutamate was positively associated with striatal activation in OCD and compulsivity across time. ACC glutamate levels decreased over time in the ASD group compared to controls, while striatal glutamate decreased over time, independent of diagnosis. ConclusionsSignificant differences in fronto-striatal glutamate were observed in ASD and OCD, affecting functional activity during failed- and successful inhibitory control differently, especially in OCD, with effects changing over time.

neuroscience↗

bioRxiv2020

The Development of Cognitive Control in Children with Autism Spectrum Disorders or Obsessive-Compulsive Disorder: A Longitudinal fMRI study

Repetitive behavior is a core symptom of Autism Spectrum Disorder (ASD) and Obsessive-Compulsive Disorder (OCD), and has been associated with impairments in cognitive control. However, it is unclear how cognitive control and associated neural circuitry relate to the development of repetitive behavior in children with these disorders. In a multicenter, longitudinal study (TACTICS; Translational Adolescent and Childhood Therapeutic Interventions in Compulsive Syndromes), the development of cognitive control was assessed during late childhood using a longitudinal fMRI design with a modified stop-signal task in children with ASD or OCD, and typically developing (TD) children (baseline: N=122 (8-12y), follow-up: N=72 (10-14y), average interval: 1.2y). Stop-signal reaction time (SSRT) decreased over development, regardless of diagnosis. Repetitive behavior in children with ASD and OCD was not associated with performance on the stop-signal task. There were no whole-brain between-group differences in brain activity, but ROI-analyses showed increases in activity in right precentral gyrus over development for children with OCD. In sum, even though subtle differences were observed in the development of brain activity in children with OCD, the findings overall suggest that the development of cognitive control, as assessed by the stop signal task, is similar in children with and without ASD or OCD.

neuroscience↗

bioRxiv2020

Controlling the Growth of the Skin Commensal Staphylococcus epidermidis Using D-Alanine Auxotrophy

Using live microbes as therapeutic candidates is a strategy that has gained traction across multiple therapeutic areas. In the skin, commensal microorganisms play a crucial role in maintaining skin barrier function, homeostasis, and cutaneous immunity. Alterations of the homeostatic skin microbiome are associated with a number of skin diseases. Here, we present the design of an engineered commensal organism, Staphylococcus epidermidis, for use as a live biotherapeutic product (LBP) candidate for skin diseases. The development of novel bacterial strains whose growth can be controlled without the use of antibiotics, or genetic elements conferring antibiotic resistance, enables modulation of therapeutic exposure and improves safety. We therefore constructed an auxotrophic strain of S. epidermidis that requires exogenously supplied D-alanine. The S. epidermidis strain, NRRL B-4268 {Delta}alr1{Delta}alr2{Delta}dat (SE{Delta}{Delta}{Delta}) contains deletions of three biosynthetic genes: two alanine racemase genes, alr1 and alr2 (SE1674 and SE1079), and the D-alanine aminotransferase gene, dat (SE1423). These three deletions restricted growth in D-alanine deficient media, pooled human blood, and skin. In the presence of D-alanine, SE{Delta}{Delta}{Delta} colonized and increased expression of human {beta}-defensin 2 in cultured human skin models in vitro. SE{Delta}{Delta}{Delta}, showed a low propensity to revert to D-alanine prototrophy, and did not form biofilms on plastic in vitro. These studies support the potential safety and utility of SE{Delta}{Delta}{Delta} as a live biotherapeutic strain whose growth can be controlled by D-alanine.

microbiology↗