Biology subjects

Saleh, S.

Publications and source records attributed to Saleh, S..

12 recordsLinked to original sources

bioRxiv2026

Gastric resection and restriction yield distinct neuroendocrine and metabolic outcomes in obese mice

Whether the metabolic benefits of sleeve gastrectomy arise from gastric restriction alone or also depend on tissue resection remains unclear. We compared sleeve gastrectomy (SG) with a surgical sleeve gastroplasty (GP) model that restricts the stomach without removing tissue. Diet-induced obese male C57BL mice were randomized to SG, GP, or sham surgery and evaluated over six weeks for energy balance, glucose regulation, hepatic lipid accumulation, circulating hormones and branched chain amino acids (BCAAs), and hypothalamic neuropeptide expression. SG and GP produced comparable weight loss of 12 and 11 percent, respectively, without significant differences in energy expenditure. However, the procedures differed in the timing of reduced food intake, and only SG produced smaller, more frequent meals. Both procedures improved glucose handling, with greater improvement after SG. SG also selectively reduced hepatic triglyceride content and circulating BCAAs. Hypothalamic POMC expression decreased after both procedures, whereas NPY and AgRP expression decreased only after SG. SG further produced a distinct hormonal profile, including higher fasting GLP1 and PYY, lower ghrelin, and greater glucose-stimulated increases in several gut and pancreatic hormones. Thus, comparable short-term weight loss after gastric resection and non-resection restriction was accompanied by distinct metabolic and neuroendocrine responses. These findings support a contribution of gastric resection beyond restriction alone and identify candidate gut-brain and metabolic pathways for developing less invasive interventions that reproduce the broader benefits of sleeve gastrectomy.

molecular biology↗

bioRxiv2026

Machine learning guided cell-free expression maps the biochemical landscape of carbonic anhydrase

Carbonic anhydrases are among the fastest known biocatalysts, reversibly facilitating the hydration of CO2 to HCO3- at rates up to 107 s-1, which warrants their investigation for industrial carbon capture technologies. However, engineering carbonic anhydrases to maintain stability under harsh industrial process conditions remains a key challenge, and sequence-to-function datasets compatible with machine learning to inform forward engineering are lacking. Here, we developed a high-throughput platform that couples cell-free gene expression with a gaseous CO2 colorimetric assay to map the fitness landscapes of carbonic anhydrases. From 96 diverse natural homologs, we identified a robust variant from the Aquificota phylum and conducted an exhaustive mutational scan and functional assessment of this enzyme at 70{degrees}C and 90{degrees}C, covering >99% of all single-amino acid substitutions (totaling 4,365 mutations assayed in 39,285 reactions). This biochemical landscape was used to benchmark 22 zero-shot protein fitness models and identify critical mutations that improved enzyme stability at 90{degrees}C by more than three-fold. We then used both zero-shot protein language models and supervised learning to filter 419 model-generated variants from a ProteinMPNN library of 100,000 sequences, leading to a best-in-class enzyme that retained activity after incubation at 95{degrees}C. This work demonstrates that integrating cell-free enzyme engineering with machine learning enables opportunities for high-throughput experimental measurements to benchmark and improve protein language models, accelerate design loops, and expand functional exploration within protein families where experimental information is limited.

synthetic biology↗

bioRxiv2026

Expanding the scope of redox-balance growth coupling techniques with a carbon cofeeding strategy

Metabolic engineering to produce molecules not naturally synthesized by the host often requires directed evolution to improve pathway enzyme performance. Growth-coupled selection can dramatically increase directed-evolution throughput, and manipulation of redox balance has proven effective for tying reductase fitness to microbial growth. However, most redox-balance selections require feeding the reductase substrate because of stoichiometric constraints. This is impractical for many biosynthetic pathways either due to practical limitations on cost or complexity of bulk substrate synthesis, or the lack of an ability to transport substrate into cells, for example intracellular acyl-CoA/ACP intermediates. Here we define stoichiometric constraints that make substrate feeding necessary for many acetyl-CoA-derived reduction pathways in NADPH-imbalanced hosts. We overcome these constraints with a dual-feedstock strategy in which glucose provides reducing power while acetate supplies additional acetyl-CoA without directly perturbing redox balance. In an engineered E. coli selection strain, acetate co-feeding enabled growth coupling of acetaldehyde, 3-hydroxybutyrate, and mevalonate production and produced a linear correlation between product formation and growth. We then used this selection to evolve a class II HMG-CoA reductase (HMGR) from Delftia acidovorans toward NADPH utilization, enriching variants with improved NADPH-dependent activity. Finally, propionate co-feeding enabled growth coupling of propionyl-CoA reduction, supporting the generality of carbon co-feeding for selecting enzymes in pathways involving acyl-chain elongation and reduction. HighlightsO_LIStoichiometric limits of redox-balance growth coupling are defined C_LIO_LIAcetate co-feeding supplies acetyl-CoA without perturbing redox balance C_LIO_LICo-feeding enables growth coupling of acetaldehyde, 3-HB, and mevalonate C_LIO_LIGrowth coupling enables evolution of HMGR toward NADPH specificity C_LIO_LIPropionate co-feeding extends growth coupling to additional acyl-CoA substrates C_LI

bioengineering↗

bioRxiv2025

Ultraflexible, Biodegradable ECoG Arrays via Rapid Fabrication Enables High-Resolution Cortical Mapping and Seizure Network Classification In Vivo

Neural interfaces are essential tools for diagnosing and managing neurological disorders, yet conventional electrocorticography (ECoG) devices are limited by mechanical mismatch with brain tissue, chronic inflammation, and poor scalability. Here, we introduce a fully inkjet-printed, flexible, and biodegradable ECoG array fabricated on ultrathin polycaprolactone films with gold nanoparticle electrodes. The arrays achieve among the highest electrode densities reported for additive manufacturing (7.44 electrodes/mm{superscript 2}) while maintaining low impedance (10.6 k{Omega} at 1 kHz) and high-fidelity recordings (SNR 28 dB). A rapid, maskless prototyping process relying on photonic sintering enables scalable, cost-effective fabrication. In vivo, the devices conformally mapped cortical seizure propagation and resolved distinct ictal dynamics in a rat model. Histology at 30 days confirmed preserved neuronal density and astrocytic response comparable to controls, indicating minimal chronic inflammation. A convolutional neural network trained on recorded signals classified seizure stages with >95% accuracy, underscoring the translational potential for real-time monitoring and closed-loop neuromodulation. This platform unites rapid prototyping, biodegradability, and high performance, providing a scalable route toward next-generation, patient-specific, and disposable neural interfaces for epilepsy and other neuroengineering applications.

bioengineering↗

bioRxiv2025

A Sequence Motif Enables Widespread Use of Non-Canonical Redox Cofactors in Natural Enzymes

Non-canonical redox cofactors (NRCs) are promising alternatives to nicotinamide adenine dinucleotide (phosphate) (NAD(P)+) for biomanufacturing due to low cost and exquisite electron delivery control, yet their adoption is limited by the scarcity of compatible enzymes. Here, we screened the aldehyde dehydrogenase (ALDH) protein family and identified a conserved RH/QxxR sequence motif that enables widespread NRC activity among natural enzymes. Bos taurus ALDH3a1 and Pseudanabaena biceps ALDH exhibit unprecedented turnover with nicotinamide mononucleotide (NMN+), with kcat values matching or exceeding that of NAD+ and surpassing most engineered NRC-active enzymes by 10 to 105-fold, based on the relative NRC to native activity. Structural and dynamic analyses reveal this motif reinforces cofactor positioning and pre-organizes the active site without dependence on the adenosine monophosphate moiety of NAD+. When introduced into diverse ALDH scaffolds, the RH/QxxR motif enhances NMN+ activity up to 60-fold. In addition to NMN+, this motif also supports activity across multiple non-nucleotide, simple synthetic NRCs such as 1-(2-carbamoylmethyl)nicotinamide (AmNA+). These findings elucidate Natures solution to the engineering challenge of obtaining NRC-active enzymes and offers a blueprint to mine latent evolutionary plasticity in natural enzymes that serve as superior engineering starting points.

synthetic biology↗

bioRxiv2025

Activation-Free Upgrading of Carboxylic Acids to Aldehydes and Alcohols

Advances in organic and gas waste valorization have enabled high-yield production of carboxylic acids, positioning them as promising feedstocks for the bioeconomy. However, carboxylic acids must be activated before downstream use, typically requiring ATP, CoA, or reduced ferredoxin to overcome unfavorable thermodynamics. These activators are costly to generate and divert carboxylic acids into CO2-releasing pathways, reducing carbon efficiency. Here, we demonstrate that aldehyde dehydrogenases (ALDHs) can directly reduce carboxylic acids to aldehydes without prior activation, a process previously thought to be biologically inaccessible. Screening 133 ALDHs revealed that this activity is remarkably widespread within the protein family, enabling production of aliphatic aldehydes and alcohols, diols, and aromatic alcohols, at titers >1 g/L, in some cases, after optimization of thermodynamic driving forces. Additionally, we applied this system to upgrade waste-derived carboxylic acid effluent streams from wastewater sludge, food waste, and waste gas (CO2). This activation-free process, termed "reverse aldehyde oxidation" (rAOX), establishes a broadly applicable, energy-efficient platform for carboxylic acid valorization at 100% carbon yield. Analogous to the reverse tricarboxylic acid cycle (rTCA) and reverse {beta}-oxidation (rBOX), rAOX exemplifies that metabolic reactions classically defined as unidirectional may have unexpected plasticity to operate in reverse and open new avenues in biomanufacturing.

synthetic biology↗

bioRxiv2025

Agonistic interactions between slender mudskippers (Periophthalmus gracilis) in Singapore

Mudskippers engage in frequent territorial interactions. Few studies of mudskipper agonistic behavioral sequences exist. The slender mudskipper (Periophthalmus gracilis) inhabits intertidal zones of mangrove forests across Southeast Asia. Here, we describe common behavioral sequences of winners and losers among unmanipulated, wild slender mudskipper interactions in Singapore. Winning mudskippers showed more approach behaviors than losers, such as "Crawl towards", and more behaviors that may indicate aggression, such as "Pectoral wave", "Flag", and "Head up". Losers showed more evasive behaviors, like "Jump" and "Crawl away". We found evidence of agonistic behavioral matching. Larger mudskippers won contests more frequently than smaller mudskippers.

animal behavior and cognition↗

bioRxiv2024

Rapid SARS-CoV-2 Detection Using High-Sensitivity Thickness Shear Mode Sensors

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has emphasized the urgent need for accurate and readily available diagnostic tools. Conventional diagnostic methods, such as reverse transcription real-time polymerase chain reaction (RT-qPCR), are often labor-intensive and time-consuming, which highlights the necessity for rapid point-of-care diagnostic solutions. This study introduces an innovative, low-cost, and highly sensitive diagnostic platform for swift COVID-19 detection. Our platform utilizes the mass sensing properties of thickness shear mode (TSM) transducers to detect and quantify the SARS-CoV-2 nucleocapsid protein through polyethylene glycol (PEG)-based chemistry (1). To confirm surface functionalization and evaluate the effects of the virus lysis buffer, we employed surface characterization techniques including Digital Holographic Microscopy (DHM), Scanning Electron Microscopy (SEM) with Energy-Dispersive X-ray spectroscopy (EDX), and Raman spectroscopy. Sensitivity tests with heat-inactivated SARS-CoV-2 samples demonstrated a sensitivity of about 0.256 Hz/TCID50/mL and a limit of detection (LOD) of roughly 150 TCID50/mL. Specificity was verified through cross-reactivity testing. Our detailed characterization and sensitivity analysis underscore the platforms reliability, making it a promising candidate for efficient and accessible COVID-19 diagnosis at the point of care.

bioengineering↗

bioRxiv2022

Identifying the Neural Correlates of Balance Deficits in Traumatic Brain Injury using the Partial Least Squares Correlation (PLSC) analysis

BackgroundBalance impairment is one of the most debilitating consequences of Traumatic Brain Injury (TBI). To study the neurophysiological underpinnings of balance impairment, the brain functional connectivity during perturbation tasks can provide new insights. To better characterize the association between the task-relevant functional connectivity and the degree of balance deficits in TBI, the analysis needs to be performed on the data stratified based on the balance impairment. However, such stratification is not straightforward, and it warrants a data-driven approach. ApproachWe conducted a study to assess the balance control using a computerized posturography platform in 17 individuals with TBI and 15 age-matched healthy controls. We stratified the TBI participants into balance-impaired and non-impaired TBI using k -means clustering of either center of pressure (COP) displacement during a balance perturbation task or Berg Balance Scale (BBS) score as a functional outcome measure. We analyzed brain functional connectivity using the imaginary part of coherence across different cortical regions in various frequency bands. These connectivity features are then studied using the mean-centered partial least squares correlation (MC-PLSC) analysis, which is a multivariate statistical framework with the advantage of handling more features than the number of samples, thus making it suitable for a small-sample study. Main ResultsBased on the nonparametric significance testing using permutation and bootstrap procedure, we noticed that the theta-band connectivity strength in the following regions of interest significantly contributed to distinguishing balance impaired from non-impaired population, regardless of the type of strat-ification: left middle frontal gyrus, right paracentral lobule, precuneus, and bilateral middle occipital gyri. SignificanceIdentifying neural regions linked to balance impairment enhances our understanding of TBI-related balance dysfunction and could inform new treatment strategies. Future work will explore the impact of balance platform training on sensorimotor and visuomotor connectivity.

neuroscience↗

bioRxiv2021

Preclinical studies for plant-based oral enzyme replacement therapy (Oral-ERT) in Pompe disease knockout mice with transgenic tobacco seeds expressing human GAA (tobrhGAA)

Genetic deficiency of acid -glucosidase (GAA) results in glycogen storage disease type II (GSDII) or Pompe disease (PD) encompassing at least four clinical subtypes of varying severity (infantile; childhood, juvenile and late onset). Our objective is to develop an innovative and affordable approach for enzyme replacement therapy (ERT) via oral administration (Oral-ERT) to maintain a sustained, therapeutic level of enzyme on a daily basis to improve efficacy of treatment and quality of life for people living with Pompe disease. A consensus at a 2019 US Acid Maltase Deficiency (AMDA) conference suggested that a multi-pronged approach including gene therapy, diet, exercise, etc. must be evaluated for a successful treatment of Pompe disease. Tobacco seeds contain the metabolic machinery that is more compatible with mammalian glycosylation-phosphorylation and processing. Previously, we have shown that a lysate from transgenic tobacco seeds expressing human GAA (tobrhGAA) was enzymatically active and can correct enzyme deficiency in cultured PD cells and in adult lymphocytes of Pompe patients and in vivo in disease-relevant tissues in GAA knockout (KO) mice when administered IP. We have extended these pre-clinical studies in PD knockout (KO) mice with ground tobrhGAA seeds that supports proof-of-concept for Oral-ERT for future clinical trials. Briefly in GAA KO mice, Oral-ERT with ground tobrhGAA seeds showed significant reversal of fore-limb and hind-limb muscle weakness, increased motor coordination/balance/strength and mobility, improved spontaneous learning, increased GAA baseline activity in tissues, reduced glycogen in tissues and negible serum titers to GAA. Pharmacokinetics showed maximum serum GAA concentration (Cs) at 8-10 hr and peak urine excretion at 10-12 hr. The tobrhGAA was taken up in PD fibroblast, lymphoid and myoblast cells. Enzyme kinetics compared favorably or superior to placental hGAA, plus alglucosidase alfa or other rhGAAs for Km, Vmax, pH optima, thermal heat stability and IC50 for inhibitors. The tobrhGAA in seeds was extremely stable stored for 15 years at room temperature. NGS-genome sequencing of the tobrhGAA and wild-type plants and RNA expression profiles was performed and will be posted on our website. Thus, Oral-ERT with ground tobrhGAA seeds is an innovative approach that overcomes some of the challenges of alglucosidase alfa-ERT and provides a more effective, safe and significantly less expensive treatment.

genetics↗

bioRxiv2021

EEG-Based Spectral Analysis ShowingBrainwave Changes Related to ModulatingProgressive Fatigue During a ProlongedIntermittent Motor Task

Repeatedly performing a submaximal motor task for a prolonged period of time leads to muscle fatigue comprising a central and peripheral component, which demands a gradually increasing effort. However, the brain contribution to the enhancement of effort to cope with progressing fatigue lacks a complete understanding. The intermittent motor tasks (IMTs) closely resemble many activities of daily living (ADL), thus remaining physiologically relevant to study fatigue. The scope of this study is therefore to investigate the EEG-based brain activation patterns in healthy subjects performing IMT until self-perceived exhaustion. Fourteen participants (median age 51.5 years; age range 26-72 years; 5 males) repeated elbow flexion contractions at 40% maximum voluntary contraction by following visual cues displayed on an oscilloscope screen until subjective exhaustion. Each contraction lasted for approximately 5 s with a 2-s rest between trials. The force, EEG, and surface EMG (from elbow joint muscles) data were simultaneously collected. After preprocessing, we selected a subset of trials at the beginning, middle, and end of the study session representing brain activities germane to mild, moderate, and severe fatigue conditions, respectively, to compare and contrast the changes in the EEG time-frequency (TF) characteristics across the conditions. The outcome of channel- and source-level TF analyses reveals that the theta, alpha, and beta power spectral densities vary in proportion to fatigue levels in cortical motor areas. We observed a statistically significant change in the band-specific spectral power in relation to the graded fatigue from both the steady- and post-contraction EEG data. The findings would enhance our understanding on the etiology and physiology of voluntary motor-action-related fatigue and provide pointers to counteract the perception of muscle weakness and lack of motor endurance associated with ADL. The study outcome would help rationalize why certain patients experience exacerbated fatigue while carrying out mundane tasks, evaluate how clinical conditions such as neurological disorders and cancer treatment alter neural mechanisms underlying fatigue in future studies, and develop therapeutic strategies for restoring the patients ability to participate in ADL by mitigating the central and muscle fatigue.

neuroscience↗

bioRxiv2020

Graph-theoretical Analysis of EEG Functional Connectivity during Balance Perturbation in Traumatic Brain Injury.

Traumatic Brain Injury (TBI) often results in balance impairment, increasing the risk of falls, and the chances of further injuries. However, the underlying neurophysiological mechanisms of postural control after TBI are not well understood. To this end, we conducted a pilot study with a multimodal approach of EEG, MRI, and Diffusion Tensor Imaging (DTI) to explore the neural mechanisms of unpredictable balance perturbations in 17 chronic TBI participants and 15 matched Healthy Controls (HC). As quantitative measures of the functional integration and segregation of the brain networks during the postural task, we computed the global graph-theoretic network measures (global efficiency and modularity) of brain functional connectivity derived from source-space EEG in different frequency bands. We observed that the TBI group showed a lower balance performance as measured by the Center of Pressure (COP) displacement during the task, and the Berg Balance Scale. They also showed altered brain activation and connectivity during the balance task. In particular, the task modulation of brain network segregation in alpha-band was reduced in TBI. Moreover, the DTI findings revealed that the structural damage is associated with reduced network connectivity and integration. In terms of the neural correlates, we observed a distinct role played by different frequency bands; greater theta-band modularity during the task was strongly correlated with the BBS in TBI group; alpha-band and beta-band graph-theoretic measures were associated with the measures of white matter structural integrity. Our future studies will focus on how postural training will modulate the functional brain networks in TBI.

neuroscience↗