Biology subjects

Fabian, J.

Publications and source records attributed to Fabian, J..

4 recordsLinked to original sources

bioRxiv2024

Extraordinary physiology of polyphosphate-accumulating Beggiatoa mats suggests a key role for phosphate buffering in marine sediments

Filamentous sulfide-oxidizing Beggiatoa spp. are widespread in marine coastal environments and can achieve significant biomass because of their substantial size. Their ability to store phosphates in the polymerized form of polyphosphates makes them potentially key players in altering the phosphorus (P) cycle at the sediment-water interface. This study examined phosphate uptake and polyphosphate formation in a P starved culture of the Beggiatoa sp. 35Flor strain. Remarkably, even after severe P starvation over five generations, the survival of the cultures was 46%, demonstrating considerable plasticity to different levels of phosphate availability. Under these P-depleted conditions, 23% of filaments still contained polyphosphates, underscoring its critical role in their metabolism. Upon reintroduction of phosphate to starved cultures, an extremely rapid phosphate uptake was observed within the first 10 minutes, with rates reaching up to 298 mmol P g-1 protein d-1, which is significantly higher than values previously described in the literature for similar-sized organisms. The high phosphate uptake capacity of Beggiatoa spp., estimated at 0.6 - 6 mmol m-2 d-1 for typical densities of filaments in coastal sediments, suggests that these bacteria may play an important role in buffering the phosphate flux in these environments. Thereby, they reduce primary production and subsequent oxygen consumption by other organisms, creating a negative feedback loop that helps maintain ecosystem stability. ImportanceSulfide-oxidizing bacteria of the genus Beggiatoa occur ubiquitously in marine coastal sediments and have a large potential to influence phosphate fluxes at the sediment-water interface owing to their ability to accumulate polyphosphate and their large size. However, the extent to which these bacteria can contribute to phosphorus (P) sequestration or release remains poorly assessed. The importance of this study lies in demonstrating the unusual flexibility in adaptation of the Beggiatoa sp. 35Flor strain to varying P availability, including extreme P starvation, and its capacity to rapidly uptake and store available phosphate in the form of polyphosphate. When considered at a global scale, these physiological traits could lead to P retention in shallow coastal waters, which, in turn, profoundly impacts ecological stability and ecosystem functioning.

microbiology↗

bioRxiv2024

Proteomic analysis identifies dysregulated proteins in albuminuria: a South African pilot study

Albuminuria may precede decreases in glomerular filtration rate (GFR) and both tests are insensitive predictors of early stages of kidney disease. Our aim was to characterise the urinary proteome in black African individuals with albuminuria and well-preserved GFR from South Africa. A case-controlled study that compared urinary proteomes of 52 normoalbuminuric (urine albumin: creatinine ratio (uACR) <3 mg/mmol) and 56 albuminuric (uACR [≥] 3 mg/mmol) adults of Black African ethnicity. Urine proteins were precipitated, reduced, alkylated, digested, and analysed using an Evosep One LC coupled to a Sciex 5600 Triple-TOF in data-independent acquisition mode. Data were searched on SpectronautTM 15. Differentially abundant proteins (DAPs) were filtered [≥] 2.25-fold change and false discovery rate [≤] 1%. Receiver operating characteristic curves were used to assess the discriminating ability of proteins of interest. Pathway analysis was performed using Enrichr software. The albuminuric group had a higher uACR (7.9 vs 0.55 mg/mmol, p <0.001). The median eGFR (mL/min/1.73m2) showed no difference between the groups (111 vs 114, p=0.707). We identified 80 DAPs in the albuminuria group compared to normoalbuminuria, of which 59 proteins increased while 21 proteins decreased in abundance. We found 12 urinary proteins with AUC > 0.8, and p-value <0.001 in the multivariate analysis. Furthermore, an 80-protein model was developed that showed a high AUC >0.907 and a predictive accuracy of 91.3% between the two groups. Pathway analysis associated with DAPs were involved in insulin growth factor (IGF) functions, innate immunity, platelet degranulation, and extracellular matrix organization. In albuminuric individuals with well-preserved eGFR, pathways involved in preventing the release and uptake of IGF by insulin growth factor binding protein were significantly enriched. These proteins are indicative of a homeostatic imbalance in a variety of cellular processes underlying renal dysfunction and are implicated in chronic kidney disease.

biochemistry↗

bioRxiv2023

Proteomic insights into the pathophysiology of hypertension-associated albuminuria: Pilot study in a South African cohort

BackgroundHypertension is an important public health priority with a high prevalence in Africa. It is also an independent risk factor for kidney outcomes. We aimed to identify potential proteins and pathways involved in hypertension-associated albuminuria by assessing urinary proteomic profiles in black South African participants with combined hypertension and albuminuria compared to those who have neither condition. MethodsThe study included 24 South African cases with both hypertension and albuminuria and 49 control participants who had neither condition. Protein was extracted from urine samples and analysed using ultra-high-performance liquid chromatography coupled with mass spectrometry. Data was generated using data-independent acquisition (DIA) and processed using Spectronaut 15. Statistical and functional data annotation were performed on Perseus and Cytoscape to identify and annotate differentially abundant proteins. Machine learning was applied to the dataset using the OmicLearn platform. ResultsOverall, a mean of 1,225 and 915 proteins were quantified in the control and case groups, respectively. Three hundred and thirty-two differentially abundant proteins were constructed into a network. Pathways associated with these differentially abundant proteins included the immune system (q-value [false discovery rate]=1.4x10-45), innate immune system (q=1.1x10-32), extracellular matrix (ECM) organisation (q=0.03) and activation of matrix metalloproteinases (q=0.04). Proteins with high disease scores (76-100% confidence) for both hypertension and CKD included angiotensinogen (AGT), albumin (ALB), apolipoprotein L1 (APOL1), and uromodulin (UMOD). A machine learning approach was able to identify a set of 20 proteins, differentiating between cases and controls. ConclusionsThe urinary proteomic data combined with the machine learning approach was able to classify disease status and identify proteins and pathways associated with hypertension and albuminuria.

biochemistry↗

bioRxiv2021

Complete neuroanatomy and sensor maps of Odonata wings for fly-by-feel flight control

Can mechanosensors in animal wings allow reconstruction of the wing aeroelastic states? Little is known about how flying animals utilize wing mechanosensation to monitor the dynamic state of their highly deformable wings. Odonata, dragonflies and damselflies, are a basal lineage of flying insects with excellent flight performance, and their wing mechanics have been studied extensively. Here, we present a comprehensive map of the wing sensory system for two Odonata species, including both the external sensor morphologies and internal neuroanatomy. We identified eight morphological classes of sensors; most were mechanosensors innervated by a single neuron. Their innervation patterns and morphologies minimize axon length and allow morphological latency compensation. We further mapped the major veins of another 13 Odonata species across 10 families and identified consistent sensor distribution patterns, with sensor count scaling with wing length. Finally, we constructed a high-fidelity finite element model of a dragonfly wing for structural analysis. Our dynamic loading simulations revealed features of the strain fields that wing sensor arrays could detect to encode different wing deformation states. Taken together, this work marks the first step toward an integrated understanding of fly-by-feel control in animal flight.

neuroscience↗