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Biology subjects

Lang, C.

Publications and source records attributed to Lang, C..

15 recordsLinked to original sources

Deep-learning-based fMRI decoding of real-world size for hand-held objects

Real-world object size is a fundamental dimension of visual cognition, supporting effective interaction with the environment and object manipulation. However, neural mechanisms encoding size have largely been inferred from extreme size comparisons, leaving the neural representation of subtle size differences within a manipulable, "hand-scale" range poorly understood. Here, we applied a three-dimensional deep neural network (3D DNN) to decode real-world size from whole-brain fMRI data (N = 50) using objects that all fall within a graspable range. The 3D DNN successfully decoded subtle size differences, achieving predictive accuracies comparable to multivariate pattern analysis. Crucially, Guided Gradient-weighted Class Activation Mapping (Guided Grad-CAM) revealed that discriminative size information was not confined to the ventral occipito-temporal cortex but extended to a distributed network. Notably, these regions spatially overlap with the specific brain areas implicated in size-perception distortions following brain damage. Our findings suggest that the brain represents subtle variations in object size through a non-linear, distributed network that transcends the traditional visual hierarchy. Specifically, this system likely orchestrates the integration of visual properties with semantic scaling and the multimodal convergence of vision, space, and memory.

neuroscience↗

How do we tread? Differences in stability-related foot placement control between overground and treadmill walking in young adults

Step-by-step foot placement control, accommodating for natural variations in center-of-mass state, ensures stability during steady-state gait. Current understanding of this foot placement mechanisms is primarily based on findings during treadmill walking. However, contextual differences might hamper generalization of these findings towards overground walking, and ultimately daily life gait. This study investigated whether foot placement control manifests itself differently during overground as compared to treadmill walking in healthy young adults. 14 young adults walked at comfortable walking speed, both on the treadmill and overground in a figure-8 path. During overground walking we found a significant relationship between the step width/step length and the center-of-mass state during the swing phase of walking, capturing foot placement control with the same linear model as during treadmill walking. Contrary to what was hypothesized, we found a significant lower foot placement precision during overground walking for the step width model with center-of-mass state at the start of the swing phase as predictor, complemented by a wider average step width. Moreover, during overground walking participants responded less strongly to a deviation in center-of-mass position, yet significantly stronger to deviations in center-of-mass velocity at the end of the step for both the step width/step length models. Exploratory analysis showed a larger relative contribution of velocity feedback during over ground walking as compared to treadmill walking. These differences warrant caution in generalizing foot placement findings during treadmill walking to overground walking and might be promising for the estimation of foot placement control in daily life gait.

physiology↗

Foot placement coordination is impaired in people with Parkinson's Disease

BackgroundGait instability is a common and disabling symptom of Parkinsons disease (PD), contributing to frequent falls and reduced quality of life. While clinical balance tests and spatiotemporal gait measures can predict fall risk, they do not fully explain the underlying control mechanisms. In healthy individuals, foot placement is actively adjusted based on an internal estimate of the center of mass state to maintain gait stability, known as foot placement control. This estimation relies on the integration of multisensory information, which has been shown to be impaired in PD, potentially disrupting the control of gait stability through foot placement. ObjectiveTo investigate whether foot placement coordination during overground walking is impaired in people with PD. MethodsFifty people with PD and 51 healthy older adults walked overground for ten minutes at self-selected, comfortable walking speed. Foot placement errors were quantified as the deviation between the actual foot placement and the predicted placement derived from the center of mass kinematic state during the preceding swing phase. ResultsFoot placement errors were significantly higher in people with PD than in healthy older adults in both mediolateral (p < .05) and anteroposterior directions (p < .0001), at both mid-swing and terminal swing. Relative explained variance in mediolateral direction was significantly higher in people with PD compared to healthy older adults (p < .005). ConclusionWe provide first evidence of impaired coordination between the center of mass and foot placement in PD. Future work should investigate a causal relationship between impaired foot placement control, sensorimotor integration and gait instability.

pathology↗

Rapid enzymatic detection of Shigatoxin-producing E. coli using fluorescence-labeled oligonucleotide substrates

Shigatoxin-producing E. coli (STEC) are important human pathogens causing disease ranging from diarrhea to severe hemolytic uremic syndrome. As STEC are transmitted via animals, food, and water, and may produce large outbreaks, their timely and qualified detection including isolate recovery is of high importance, but challenging and labor-intense. Thus, the availability of an easy-to-perform rapid test would be a tremendous advance. Since the common feature and major virulence factor of otherwise multifaceted STEC is the Shiga toxin (Stx), we developed a detection method for Stx, specifically for its catalytic RNA-N-glycosidase activity targeting the Sarcin Ricin Loop (SRL) of 28S ribosomal RNA. To this end, synthetic ssDNA substrates mimicking the SRL were designed and linked to a fluorophore and quencher pair, which conferred a fluorescence signal after cleavage by Stx. Optimal results using bacterial culture supernatants or single colonies were achieved for substrate StxSense 4 following 30 to 60 minutes incubation. Importantly, different Stx1 and Stx2 subtypes, diverse STEC serotypes, and Shigella were detected. In conclusion, the assay offers rapid and facile detection of STEC based on a real-time readout for Stx activity. Therefore, it may improve STEC risk evaluation, therapy decisions, outbreak and source detection, and simplify research for antimicrobials.

microbiology↗

Single-cycle SARS-CoV-2 vaccine elicits high protection and sterilizing immunity in hamsters

Vaccines have been central in ending the COVID-19 pandemic, but newly emerging SARS-CoV-2 variants increasingly escape first-generation vaccine protection. To fill this gap, live particle-based vaccines mimicking natural infection aim at protecting against a broader spectrum of virus variants. We designed "single-cycle SARS-CoV-2 viruses" (SCVs) that lack essential viral genes, possess superior immune-modulatory features and provide an excellent safety profile in the Syrian hamster model. Full protection of all intranasally vaccinated animals was achieved against an autologous challenge with SARS-CoV-2 virus using an Envelope-gene-deleted vaccine candidate. By deleting key immune-downregulating genes, sterilizing immunity was achieved with an advanced candidate without virus spread to contact animals. Hence, SCVs have the potential to induce a broad and durable protection against COVID-19 superior to a natural infection.

molecular biology↗

Structure-function relationships underpin disulfide loop cleavage-dependent activation of Legionella pneumophila lysophosholipase A PlaA

Legionella pneumophila, the causative agent of a life-threatening pneumonia, intracellularly replicates in a specialized compartment in lung macrophages, the Legionella-containing vacuole (LCV). Secreted proteins of the pathogen govern important steps in the intracellular life cycle including bacterial egress. Among these is the type II secreted PlaA which, together with PlaC and PlaD, belongs to the GDSL phospholipase family found in L. pneumophila. PlaA shows lysophospholipase A (LPLA) activity which increases after secretion and subsequent processing by the zinc metalloproteinase ProA at residue E266/L267 located within a disulfide loop. Activity of PlaA contributes to the destabilization of the LCV in the absence of the type IVB-secreted effector SdhA. We here present the 3D structure of PlaA which shows a typical /{beta} hydrolase fold and reveals that the uncleaved disulfide loop forms a lid structure covering the catalytic triad S30/D278/H282. This leads to reduction of both substrate access and membrane interaction before activation; however, the catalytic and membrane interaction site gets more accessible when the disulfide loop is processed. After structural modelling, a similar activation process is suggested for the GDSL hydrolase PlaC, but not for PlaD. Furthermore, the size of the PlaA substrate binding site indicated preference towards phospholipids comprising ~16 carbon fatty acid residues which was verified by lipid hydrolysis, suggesting a molecular ruler mechanism. Indeed, mutational analysis changed the substrate profile with respect to fatty acid chain length. In conclusion, our analysis revealed the structural basis for the regulated activation and substrate preference of PlaA.

biochemistry↗

Early striatal hyperexcitability in an in vitro human striatal microcircuit model carrying the Parkinson's GBA-N370S mutation

Understanding medium spiny neuron (MSN) physiology is essential to understand motor impairments in Parkinsons disease (PD) given the architecture of the basal ganglia. Here, we developed a custom three-chamber microfluidic platform and established a cortico-striato-nigral microcircuit recapitulating the striatal presynaptic triad in vitro using induced pluripotent stem cell (iPSC)-derived neurons. We found that, although cortical glutamatergic projections facilitated MSN synaptic activity, dopaminergic transmission was essential for excitability maturation of MSNs in vitro. Replacement of wild-type iPSC-dopamine neurons (iPSC-DaNs) in the striatal microcircuit with those carrying the PD-related GBA-N370S mutation induced early hyperexcitability in iPSC-MSNs through reduction of voltage-gated sodium and potassium intrinsic currents. Such deficits were resolved in aged cultures or with antagonism of protein kinase A activity in nigrostriatal iPSC-DaNs. Hence, our results highlight the unique utility of modelling striatal neurons in a modular and highly physiological circuit which is essential to reveal mechanistic insights of the loss of electrical functional integrity in the striata of GBA1 PD patients.

neuroscience↗

Recent O-antigen diversification masks highly pathogenic STEC O104:H4

Shiga toxin-producing E. coli (STEC) can give rise to a range of clinical outcomes from diarrhea to the life-threatening systemic condition, hemolytic uremic syndrome (HUS). Although STEC O157:H7 is the serotype most frequently associated with HUS, a major outbreak of HUS occurred in 2011 in Germany, and was caused by a rare serotype, STEC O104:H4. Prior to 2011 and since the outbreak, STEC O104:H4 strains have only rarely been associated with human infections. From 2012 to 2020 intensified STEC surveillance was performed in Germany where subtyping of [~]8,000 clinical isolates by molecular methods including whole genome sequencing was carried out. A rare STEC serotype O181:H4 associated with HUS was identified and, like the STEC O104:H4 outbreak strain, this strain belongs to sequence type (ST) 678. Genomic and virulence comparisons revealed that the two strains are phylogenetically related and differ principally in the gene cluster encoding their respective lipopolysaccharide O-antigens but exhibit similar virulence phenotypes. In addition, five other serotypes belonging to ST678 from human clinical infection, such as OX13:H4, O127:H4, OgN-RKI9:H4, O131:H4, and O69:H4, were identified from diverse locations worldwide. ImportanceOur data suggest the high virulence ensemble of the STEC O104:H4 outbreak strain remains a global threat because genomically similar strains cause disease worldwide, but that horizontal acquisition of O-antigen gene clusters has diversified the O-antigens of strains belonging to ST678. Thus, identification of these highly pathogenic strains is masked by diverse and rare O-antigens, thereby confounding the interpretation of their potential risk.

microbiology↗

Triterpenoid production with a minimally engineered Saccharomyces cerevisiae chassis

Triterpenoids, one of the most diverse classes of natural products, have been used for centuries as active ingredients in essential oils and Chinese medicines and are of interest for many industrial applications ranging from low-calorie sweeteners to cosmetic ingredients and vaccine adjuvants. However, not only can the extraction from plant material be cumbersome due to low concentrations of the specific triterpenoid, but concerns are also increasing regarding the sustainability of wild plant harvest while meeting market demands. The alternative is to produce triterpenoids with engineered microbes. Here, we present a generally applicable strategy for triterpenoid production in the yeast Saccharomyces cerevisiae based on a modified oxidosqualene cyclase Erg7. The modification reduces the flux into the sterol pathway while increasing the precursor supply for triterpenoid production. The minimally engineered strain was exploited for the exemplary production of the lupane triterpenoids betulin, betulin aldehyde, and betulinic acid at a total titer above 6 g/L, the highest reported so far. To further highlight the chassis concept, squalene, oleanane- and dammarane-type triterpenoids were synthesized to titers at a similar gram scale. We propose the developed bakers yeast as a host for the thousands of triterpenoid synthesis pathways from plants, reducing the pressure on the natural resources.

bioengineering↗

Development of a 3D atlas of the embryonic pancreas for topological and quantitative analysis of heterologous cell interactions

Generating comprehensive image maps, while preserving spatial 3D context, is essential to quantitatively assess and locate specific cellular features and cell-cell interactions during organ development. Despite the recent advances in 3D imaging approaches, our current knowledge of the spatial organization of distinct cell types in the embryonic pancreatic tissue is still largely based on 2D histological sections. Here, we present a light-sheet fluorescence microscopy approach to image the pancreas in 3D and map tissue interactions at key development time points in the mouse embryo. We used transgenic mouse models and antibodies to visualize the three main cellular components within the developing pancreas, including epithelial, mesenchymal and endothelial cell populations. We demonstrated the utility of the approach by providing volumetric data, 3D distribution of distinct progenitor populations and quantification of relative cellular abundance within the tissue. Lastly, our image data were combined in an open source online repository (referred to as Pancreas Embryonic Cell Atlas). This image dataset will serve the scientific community by enabling further investigation on pancreas organogenesis but also for devising strategies for the in vitro generation of transplantable pancreatic tissue for regenerative therapies.

developmental biology↗

NAD(H)-mediated tetramerization controls the activity of Legionella pneumophila phospholipase PlaB

The virulence factor and phospholipase PlaB promotes lung colonization, tissue destruction, and intracellular replication of Legionella pneumophila, the causative agent of Legionnaires disease. It is exposed at the bacterial surface and shows an extraordinary activation mechanism by tetramer deoligomerization. To unravel the molecular basis for enzyme activation and localization, we determined the crystal structure of PlaB in its tetrameric form. We found that the tetramer is a dimer of identical dimers, and a monomer consists of an N-terminal phospholipase /{beta}-hydrolase domain augmented by two non-canonical two-stranded {beta}-sheets, {beta}6/{beta}7 and {beta}9/{beta}10. The C- terminal domain reveals a novel fold displaying a bilobed {beta}-sandwich with a hook structure that is required for dimer formation and complementation of the phospholipase domain in the neighboring monomer. Unexpectedly, we observed eight NAD(H) molecules at the dimer/dimer interface, suggesting that these molecules stabilize the tetramer and hence lead to enzyme inactivation. Indeed, addition of NAD(H) increased the fraction of the tetrameric form and concomitantly reduced activity. {beta}9/{beta}10 mutants revealed a decrease in the tetrameric fraction, altered activity profiles, and mislocalization. Protein variants lacking the hook or strands {beta}6/{beta}7 were unaffected in terms of localization but lost their activity, and lid mutants changed substrate specificity. Together, these data reveal structural elements and an unprecedented NAD(H)- mediated tetramerization mechanism required for spatial and enzymatic control of a phospholipase virulence factor. The regulatory process identified is ideally suited to fine tune PlaB in a way that protects L. pneumophila from self-inflicted lysis while ensuring its activity at the pathogen-host interface.

microbiology↗

Direct Antimicrobial Resistance Prediction from MALDI-TOF mass spectra profile in clinical isolates through Machine Learning

Early administration of effective antimicrobial treatments is critical for the outcome of infections. Antimicrobial resistance testing enables the selection of optimal antibiotic treatments, but current culture-based techniques take up to 72 hours. We have developed a novel machine learning approach to predict antimicrobial resistance directly from MALDI-TOF mass spectra profiles of clinical samples. We trained calibrated classifiers on a newly-created publicly available database of mass spectra profiles from clinically most relevant isolates with linked antimicrobial susceptibility phenotypes. The dataset combines more than 300,000 mass spectra with more than 750,000 antimicrobial resistance phenotypes from four medical institutions. Validation against a panel of clinically important pathogens, including Staphylococcus aureus, Escherichia coli, and Klebsiella pneumoniae, resulting in AUROC values of 0.8, 0.74, and 0.74 respectively, demonstrated the potential of using machine learning to substantially accelerate antimicrobial resistance determination and change of clinical management. Furthermore, a retrospective clinical case study found that implementation of this approach would have resulted in a beneficial change in the clinical treatment in 88% (8/9) of cases. MALDI-TOF mass spectra based machine learning may thus be an important new tool for antibiotic stewardship.

microbiology↗

The Biomechanical Basis of Biased Epithelial Tube Elongation

During lung development, epithelial branches expand preferentially in longitudinal direction. This bias in outgrowth has been linked to a bias in cell shape and in the cell division plane. How this bias arises is unknown. Here, we show that biased epithelial outgrowth occurs independent of the surrounding mesenchyme, of preferential turn-over of the extracellular matrix at the bud tips, and of FGF signalling. There is also no evidence for actin-rich filopodia at the bud tips. Rather, we find epithelial tubes to be collapsed during early lung and kidney development, and we observe fluid flow in the narrow tubes. By simulating the measured fluid flow inside segmented narrow epithelial tubes, we show that the shear stress levels on the apical surface are sufficient to explain the reported bias in cell shape and outgrowth. We use a cell-based vertex model to confirm that apical shear forces, unlike constricting forces, can give rise to both the observed bias in cell shapes and tube elongation. We conclude that shear stress may be a more general driver of biased tube elongation beyond its established role in angiogenesis. Summary StatementWe systematically analysed the requirements for biased elongating outgrowth of epithelial tubes during lung and kidney development, and provide evidence that fluid-flow induced shear stress drives their biased elongation.

developmental biology↗

Germline RNA helicases couple RNA binding to P granule assembly at nuclear periphery

P granules are phase-separated liquid droplets that play important roles in the maintenance of the germ cell fate in C. elegans. The localization and formation of P granules are highly dynamic, but mechanisms that regulate such processes remain poorly understood. Here we show that germline RNA helicases (GLHs) control the formation and disassembly of germ granules through their binding and release of RNAs, respectively. In addition, the FGG repeats in the GLHs promote the formation of germ granules at the perinucleus. Proteomic analyses of a mutation that traps RNA-bound GLH-1 complex revealed transient interactions of GLH-1 with several Argonautes and RNA binding proteins. Finally, we found that defects in perinuclear P granule formation correlate with the fertility defects observed in various GLH mutants. Together, our results highlight the versatile roles of RNA helicases in controlling the formation of liquid droplets in space and time.

cell biology↗

Effect of different forage-to-concentrate ratios on the structure of rumen bacteria and its relationship with nutrition levels and real-time methane production in sheep

Emission from ruminants has become the largest source of anthropogenic emission of methane in China. The structure of the rumen flora has a significant effect on methane production. To establish a more accurate prediction model for methane production, the rumen flora should be one of the most important parameters. The objective of the present study was to investigate the relationship among changes in rumen flora, nutrient levels, and methane production in sheep fed with the diets of different forage-to-concentration ratios, as well as to screen for significantly different dominant genera. Nine rumen-cannulated hybrid sheep were separated into three groups and fed three diets with forage-to-concentration ratios of 50:50, 70:30, and 90:10. Three proportions of the diets were fed according to a 3 x 3 incomplete Latin square, design during three periods of 15 d each. The ruminal fluid was collected for real-time qPCR, high-throughput sequencing and in vitro rumen fermentation in a new real-time fermentation system wit. Twenty-two genera were screened, the abundance of which varied linearly with forage-to-concentration ratios and methane production. In addition, during the 12-hour in vitro fermentation, the appearance of peak concentration was delayed by 26-27 min with the different structure of rumen bacteria. The fiber-degrading bacteria were positively correlated with this phenomenon, but starch-degrading and protein-degrading bacteria were negative correlated. These results would facilitate macro-control of rumen microorganisms and better management of diets for improved nutrition in ruminants. In addition, our findings would help in screening bacterial genera that are highly correlated with methane production.

microbiology↗