Biology subjects

Kern, M.

Publications and source records attributed to Kern, M..

11 recordsLinked to original sources

bioRxiv2024

Control of cholesterol-induced adipocyte inflammation by the Nfe2l1-Atf3 pathway

While adipocytes are critical pillars of energy metabolism, their dysfunction is linked to adipose tissue (AT) inflammation, insulin resistance, and ectopic lipotoxicity in cardiometabolic diseases. However, the mechanisms causing adipocyte inflammation and insulin resistance remain unclear. Here, we show that excess cholesterol induces adipocyte dysfunction, which is suppressed by the transcription factor Nfe2l1 (nuclear factor erythroid derived-2, like-1). Nfe2l1 is required to sustain proteasome function in adipocytes and proteotoxic stress induces adipocyte inflammation via the activation of Atf3. In humans, the Nfe2l1-proteasome pathway is inversely correlated to body mass index (BMI) in an adipose-depot specific manner. In mice, loss of adipocyte Nfe2l1 caused AT inflammation with a pronounced infiltration of macrophages and T cells. Mice lacking adipocyte Nfe2l1 displayed severe adipocyte dysfunction during diet-induced obesity (DIO), characterized by lower adipokine levels, steatosis, glucose intolerance and insulin resistance. Nfe2l1{Delta}AT mice on an Apoe-deficient (Apoe-/-) background fed a cholesterol-rich Western Diet (WD), developed a lipoatrophy-like syndrome, dyslipidemia, and enhanced atherosclerosis. Our results reveal an important role for proteasome-mediated proteostasis in adipocytes and indicate that Nfe2l1 is linked to metabolic health in humans and preclinical mouse models. Promoting proteostasis in adipocytes may thus alleviate inflammation in obesity, potentially averting adverse cardiometabolic outcomes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=191 SRC="FIGDIR/small/604614v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@145e32borg.highwire.dtl.DTLVardef@1454df1org.highwire.dtl.DTLVardef@1002383org.highwire.dtl.DTLVardef@1b7319_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2023

FAM104 proteins promote the nuclear localization of p97/VCP

The ATPase p97 (also known as VCP, Cdc48) has crucial functions in a variety of important cellular processes such as protein quality control, organellar homeostasis and DNA damage repair, and its de-regulation is linked to neuro-muscular diseases and cancer. p97 is tightly controlled by numerous regulatory cofactors, but the full range and function of the p97-cofactor network is unknown. Here, we identify the hitherto uncharacterized FAM104 proteins as a conserved family of p97 interactors. FAM104 proteins bind p97 directly via a novel, alpha-helical motif and associate with the p97- UFD1-NPL4 complex in cells. FAM104 proteins localize to the nucleus and promote both the nuclear import and chromatin binding of p97. Loss of FAM104 proteins results in slow growth and hypersensitivity to p97 inhibition in the absence and presence of DNA damage, suggesting that FAM104 proteins are critical regulators of nuclear p97 functions.

cell biology↗

bioRxiv2023

Cryo-electron tomography sheds light on the elastic nature of the Trypanosoma brucei tripartite attachment complex

Trypanosomes only contain a single mitochondrion per cell. Within that singular mitochondrion, the protist carries a single mitochondrial genome that consists of a complex DNA network, the kinetoplast DNA (kDNA). The replicated kDNA is segregated during cell division by the tripartite attachment complex (TAC), a multi-protein bridge that physically links each daughter kDNA to a basal body (BB). BB movements drive kDNA segregation prior to cell division. How the TAC accommodates constant BB movements while maintaining a stable kDNA anchor throughout the cell cycle has remained unclear. Here we used cryo-electron tomography to image the cytoplasmic part of the TAC in its native context. We resolved the BB, the mitochondrial membranes, and the exclusion zone filaments (EZFs) connecting the BB and pro-BB to the outer mitochondrial membrane (OMM) and quantified the geometry of the region across many cells. EZF lengths spanned 230 to 625 nm in zoid cells and up to 874 nm in NP40-treated cells, and the BB occupied a wide range of positions and orientations relative to the OMM, while the pro-BB sat closer and more constrained. Building on these observations and prior evidence that p197 alone defines the BB-OMM distance, we propose that p197 is a length-variable connector: the length of a tandem array of -helical repeats depends on their relative orientation, and filaments of different lengths coexist at one basal body. How that orientation is set remains open, but such a connector reconciles stable kDNA anchoring with the mechanical demands of BB movement during the cell cycle.

cell biology↗

bioRxiv2022

Standing balance is not affected by estrogen fluctuations during the menstrual cycle

When people stand still, they exhibit a phenomenon called postural sway, or spontaneous movement of the bodys center of pressure, which is related to balance control. In general females show less sway than males, but this difference only begins to appear around puberty, pointing to different levels of sex hormones as one potential mechanism for sway sex differences. In this study, we followed one group of young females using oral contraceptives (n = 32) and one group not using oral contraceptives (n = 19), to investigate associations between estrogen availability and postural sway, both over the course of the menstrual cycle (in the group not using oral contraceptives) and long-term (between the two groups). All participants visited the lab four times over the putative 28-day menstrual cycle. At each visit, we performed blood draws to measure plasma estrogen (estradiol) levels, and tests of postural sway using a force plate. Due to the hormone-stabilizing effects of oral contraceptives, estradiol levels were higher in participants not using oral contraceptives (690.45 pmol/L versus 464.50 pmol/L), reflecting higher estradiol concentrations during the late follicular and luteal phase. Postural sway was similar on average for participants not using oral contraceptives (21.47 cm versus 23.56 cm). Overall, we found no significant effects of the estimated menstrual cycle phase - or absolute levels of estradiol - on postural sway.

physiology↗

bioRxiv2022

Actin nano-architecture of phagocytic podosomes

Podosomes are actin-enriched adhesion structures important for multiple cellular processes, including migration, bone remodeling, and phagocytosis. Here, we characterized the structure and organization of phagocytic podosomes using interferometric photoactivated localization microscopy (iPALM), a super-resolution microscopy technique capable of 15-20 nm resolution, together with structured illumination microscopy (SIM) and localization-based superresolution microscopy. Phagocytic podosomes were observed during frustrated phagocytosis, a model in which cells attempt to engulf micro-patterned IgG antibodies. For circular patterns, this resulted in regular arrays of podosomes with well-defined geometry. Using persistent homology, we developed a pipeline for semi-automatic identification and measurement of podosome features. These studies revealed an "hourglass" shape of the podosome actin core, a protruding "knob" at the bottom of the core, and two actin networks extending from the core. Additionally, the distributions of paxillin, talin, myosin II, -actinin, cortactin, and microtubules relative to actin were characterized.

cell biology↗

bioRxiv2021

Long-term ecosystem nitrogen limitation from foliar δ15N data and a land surface model

The effect of nutrient availability on plant growth and the terrestrial carbon sink under climate change and elevated CO2 remains one of the main uncertainties of the terrestrial carbon cycle. This is partially due to the difficulty of assessing nutrient limitation at large scales over long periods of time. Consistent declines in leaf nitrogen (N) content and leaf {delta}15N have been used to suggest that nitrogen limitation has increased in recent decades, most likely due to the concurrent increase in atmospheric CO2. However, such datasets are often not straightforward to interpret due to the complex factors that contribute to the spatial and temporal variation in leaf N and isotope concentration. We use the land surface model QUINCY, which has the unique capacity to represent N isotopic processes, in conjunction with two large datasets of foliar N and N isotope content. We run the model with different scenarios to test whether foliar {delta}15N isotopic data can be used to infer large scale nitrogen limitation and if the observed trends are caused by increasing atmospheric CO2, changes in climate or changes in sources of anthropogenic N deposition. We show that while the model can capture the observed change in leaf N content and predicts widespread increases in N limitation, it does not capture the pronounced, but very spatially heterogeneous, decrease in foliar {delta}15N observed in the data across the globe. The addition of an observed temporal trend in isotopic composition of N deposition leads to a more pronounced decrease in simulated leaf {delta}15N. Our results show that leaf {delta}15N observations should not, on their own, be used to assess global scale N limitation and that using such a dataset in conjunction with a land surface model can reveal the drivers behind the observed patterns.

ecology↗

bioRxiv2020

Single-nucleus and spatial transcriptomics of archival pancreatic cancer reveals multi-compartment reprogramming after neoadjuvant treatment

Pancreatic ductal adenocarcinoma (PDAC) remains a treatment-refractory disease. Characterizing PDAC by mRNA profiling remains particularly challenging. Previously identified bulk expression subtypes were influenced by contaminating stroma and have not yet informed clinical management, whereas single cell RNA-seq (scRNA-seq) of fresh tumors under-represented key cell types. Here, we developed a robust single-nucleus RNA-seq (snRNA-seq) technique for frozen archival PDAC specimens and used it to study both untreated tumors and those that received neoadjuvant chemotherapy and radiotherapy (CRT). Gene expression programs learned across untreated malignant cell and fibroblast profiles uncovered a clinically relevant molecular taxonomy with improved prognostic stratification compared to prior classifications. Moreover, in the increasingly-adopted neoadjuvant treatment context, there was a depletion of classical-like phenotypes in malignant cells in favor of basal-like phenotypes associated with TNF-NFkB and interferon signaling as well as the presence of novel acinar and neuroendocrine classical-like states, which may be more resilient to cytotoxic treatment. Spatially-resolved transcriptomics revealed an association between malignant cells expressing these basal-like programs and higher immune infiltration with increased lymphocytic content, whereas those exhibiting classical-like programs were linked to sparser macrophage-predominant microniches, perhaps pointing to susceptibility to distinct therapeutic strategies. Our refined molecular taxonomy and spatial resolution can help advance precision oncology in PDAC through informative stratification in clinical trials and insights into differential therapeutic targeting leveraging the immune system.

genomics↗

bioRxiv2020

Validity of the Lumen(R) hand-held metabolic device to measure fuel utilization in healthy young adults

BackgroundMetabolic carts measure the carbon dioxide produced and oxygen consumed from the breath in order to assess metabolic fuel usage (carbohydrates vs. fats). However, these systems are expensive, time-consuming, and only available in the clinic. A small hand-held device capable of measuring metabolic fuel via CO2 from exhaled air has been developed ObjectiveTo evaluate the validity of a novel hand-held device (Lumen(R)) for measuring metabolic fuel utilization in healthy young adults MethodsMetabolic fuel usage was assessed in healthy participants (n = 33; age: 23.1 {+/-} 3.9 y) via respiratory exchange ratio (RER) values from the "gold-standard" metabolic cart as well as %CO2 from the Lumen device. Measurements were performed at rest in two conditions, fasting, and after consuming 150 grams of glucose in order to determine changes in metabolic fuel. Reduced major axis regression was performed as well as Bland-Altman plots and linear regressions to test for agreement between RER and Lumen %CO2. ResultsBoth RER and Lumen %CO2 significantly increased after glucose intake compared with fasting conditions (P < .0001). Regression analyses and Bland-Altman plots revealed an agreement between the two measurements with a systematic bias resulting from the nature of the different units. ConclusionsThis study shows the validity of Lumen(R) to estimate metabolic fuel utilization in a comparable manner with the "gold-standard" metabolic cart, providing the ability for real-time metabolic information for users under any circumstances.

physiology↗

bioRxiv2020

Correlating nuclear morphology and external force with combined atomic force microscopy and light sheet imaging separates roles of chromatin and lamin A/C in nuclear mechanics

Nuclei are constantly under external stress - be it during migration through tight constrictions or compressive pressure by the actin cap - and the mechanical properties of nuclei govern their subsequent deformations. Both altered mechanical properties of nuclei and abnormal nuclear morphologies are hallmarks of a variety of disease states. Little work, however, has been done to link specific changes in nuclear shape to external forces. Here, we utilize a combined atomic force microscope and light sheet microscope (AFM-LS) to show SKOV3 nuclei exhibit a two-regime force response that correlates with changes in nuclear volume and surface area, allowing us to develop an empirical model of nuclear deformation. Our technique further decouples the roles of chromatin and lamin A/C in compression, showing they separately resist changes in nuclear volume and surface area respectively; this insight was not previously accessible by Hertzian analysis. A two-material finite element model supports our conclusions. We also observed that chromatin decompaction leads to lower nuclear curvature under compression, which is important for maintaining nuclear compartmentalization and function. The demonstrated link between specific types of nuclear morphological change and applied force will allow researchers to better understand the stress on nuclei throughout various biological processes.

biophysics↗

bioRxiv2019

Modulating dream experience: Noninvasive brrain stimulation over the sensorimotor cortex reduces dream movement

Recently, cortical correlates of specific dream contents have been reported, such as the activation of the sensorimotor cortex during dreamed hand clenching. Yet, the causal mechanisms underlying specific dream content remain largely elusive. Here, we investigated how alterations in the excitability of sensorimotor areas through transcranial direct current stimulation (tDCS) might alter dream content. Following bihemispheric tDCS or sham stimulation, participants who were awakened from REM sleep filled out a questionnaire on bodily sensations in dreams. tDCS, compared to sham stimulation, significantly decreased reports of dream movement, especially repetitive actions. Contrary to this, other types of bodily experiences, such as tactile or vestibular sensations, were not affected by tDCS, confirming the specificity of stimulation effects. In addition, tDCS reduced interhemispheric coherence in parietal areas and altered the phasic electromyography correlation between the two arms. These findings reveal that a complex reorganization of the motor network co-occurred with the reduction of dream movement, confirming spatial specificity of the stimulation site. We conclude that tDCS over the sensorimotor cortex causally interferes with dream movement during REM sleep.

neuroscience↗

bioRxiv2017

Interactive Visual Exploration And Refinement Of Cluster Assignments

BackgroundWith ever-increasing amounts of data produced in biology research, scientists are in need of efficient data analysis methods. Cluster analysis, combined with visualization of the results, is one such method that can be used to make sense of large data volumes. At the same time, cluster analysis is known to be imperfect and depends on the choice of algorithms, parameters, and distance measures. Most clustering algorithms dont properly account for ambiguity in the source data, as records are often assigned to discrete clusters, even if an assignment is unclear. While there are metrics and visualization techniques that allow analysts to compare clusterings or to judge cluster quality, there is no comprehensive method that allows analysts to evaluate, compare, and refine cluster assignments based on the source data, derived scores, and contextual data.\n\nResultsIn this paper, we introduce a method that explicitly visualizes the quality of cluster assignments, allows comparisons of clustering results and enables analysts to manually curate and refine cluster assignments. Our methods are applicable to matrix data clustered with partitional, hierarchical, and fuzzy clustering algorithms. Furthermore, we enable analysts to explore clustering results in context of other data, for example, to observe whether a clustering of genomic data results in a meaningful differentiation in phenotypes.\n\nConclusionsOur methods are integrated into Caleydo StratomeX, a popular, web-based, disease subtype analysis tool. We show in a usage scenario that our approach can reveal ambiguities in cluster assignments and produce improved clusterings that better differentiate genotypes and phenotypes.

bioinformatics↗