An inflection point in high-throughput proteomics with Orbitrap Astral: analysis of biofluids, cells, and tissues.

This technical note presents a comprehensive proteomics workflow for the new combination of Orbitrap and Astral mass analyzers across biofluids, cells, and tissues. Central to our workflow is the integration of Adaptive Focused Acoustics (AFA) technology for cells and tissue lysis, to ensure robust and reproducible sample preparation in a high-throughput manner. Furthermore, we automated the detergent-compatible single-pot, solid-phase-enhanced sample Preparation (SP3) method for protein digestion, a technique that streamlines the process by combining purification and digestion steps, thereby reducing sample loss and improving efficiency. The synergy of these advanced methodologies facilitates a robust and high-throughput approach for cells and tissue analysis, an important consideration in translational research. This work disseminates our platform workflow, analyzes the effectiveness, demonstrates reproducibility of the results, and highlights the potential of these technologies in biomarker discovery and disease pathology. For cells and tissues (heart, liver, lung, and intestine) proteomics analysis by data-independent acquisition mode, identifications exceeding 10,000 proteins can be achieved with a 24-minute active gradient. In 200ng injections of HeLa digest across multiple gradients, an average of more than 80% of proteins have a CV less than 20%, and a 45-minute run covers ~90% of the expressed proteome. In plasma samples including naive, depleted, perchloric acid precipitated, and Seer nanoparticle captured, all with a 24-minute gradient length, we identified 87, 108, 96 and 137 out of 216 FDA approved circulating protein biomarkers, respectively. This complete workflow allows for large swaths of the proteome to be identified and is compatible across diverse sample types.

A Novel Transmembrane CXCR4 Variant That Expands the WHIM Genotype-Phenotype Paradigm.

Warts, Hypogammglobulinemia, Infections, Myelokathexis (WHIM) syndrome is a rare immunodeficiency disease that results from impaired leukocyte trafficking (myelokathexis) predominately caused by gain-of-function variants in C-X-C chemokine receptor type 4 (CXCR4). Clinical manifestations of WHIM syndrome can differ in familial forms or in people harboring identical CXCR4 variants. All known pathogenic CXCR4 variants associated with WHIM syndrome (CXCR4WHIM) to date are localized in the intracellular C-terminus of CXCR4. We identified 4 unrelated patients with variable WHIM-like clinical presentations harboring a novel heterozygous CXCR4 variant (c.250G>C; p.D84H) localized at a highly conserved position in the transmembrane domain of the receptor outside the C-terminus. Functional characterization of the CXCR4D84Hvariant (CXCR4D84H) using patient-derived peripheral blood mononuclear cells and in vitro cellular assaysshow decreased CXCR4 internalization and increased chemotaxis in response to CXCL12, similar to known CXCR4WHIM, but also revealed unique features of CXCR4D84H signaling to cAMP, Ca2+ mobilization and AKT/ERK pathways. These findings are consistent with molecular dynamics simulations that show disruption of the Na+ binding pocket by D84H, resulting in collapse of the hydrophobic gate above and destabilization of the inactive state of CXCR4. Mavorixafor, a CXCR4 antagonist being evaluated in clinical trials for chronic neutropenia and WHIM syndrome, normalized CXCL12-mediated chemotaxis of CXCR4D84H patient lymphocytes ex vivo and improved WBC and subset counts in 1 patient with CXCR4D84H enrolled in the chronic neutropenia phase 1b clinical trial (NCT04154488). The present study expands the current understanding of CXCR4 function and genotype-phenotype correlations in WHIM syndrome and in people with WHIM-like phenotypes.

Effect of pyrolysis temperature on characteristics and chloramphenicol adsorption performance of NH2-MIL-53(Al)-derived amine-functionalized porous carbons.

Several activities such as aquaculture, human and feedstock therapies can directly release antibiotics into water. Due to high stability, low hydrolysis and non-biodegradation, they can accumulate in the aqueous environment and transport to aquatic species. Here, we synthesized amine-functionalized porous carbons (ANC) by a direct-pyrolysis process of NH2-MIL-53(Al) as a sacrificial template at between 600 and 900 °C and utilized them to eliminate chloramphenicol antibiotic from water. The NH2-MIL-53(Al)-derived porous carbons obtained high surface areas (304.7-1600 m2 g-1) and chloramphenicol adsorption capacities (148.3-261.5 mg g-1). Several factors such as hydrogen bonding, Yoshida hydrogen bonding, and π-π interaction, hydrophobic interaction possibly controlled adsorption mechanisms. The ANC800 could be reused four cycles along with high stability in structure. As a result, NH2-MIL-53(Al)-derived porous carbons are recommended as recyclable and efficient adsorbents to the treatment of antibiotics in water.

Altered microbial bile acid metabolism exacerbates T cell-driven inflammation during graft-versus-host disease.

Microbial transformation of bile acids affects intestinal immune homoeostasis but its impact on inflammatory pathologies remains largely unknown. Using a mouse model of graft-versus-host disease (GVHD), we found that T cell-driven inflammation decreased the abundance of microbiome-encoded bile salt hydrolase (BSH) genes and reduced the levels of unconjugated and microbe-derived bile acids. Several microbe-derived bile acids attenuated farnesoid X receptor (FXR) activation, suggesting that loss of these metabolites during inflammation may increase FXR activity and exacerbate the course of disease. Indeed, mortality increased with pharmacological activation of FXR and decreased with its genetic ablation in donor T cells during mouse GVHD. Furthermore, patients with GVHD after allogeneic hematopoietic cell transplantation showed similar loss of BSH and the associated reduction in unconjugated and microbe-derived bile acids. In addition, the FXR antagonist ursodeoxycholic acid reduced the proliferation of human T cells and was associated with a lower risk of GVHD-related mortality in patients. We propose that dysbiosis and loss of microbe-derived bile acids during inflammation may be an important mechanism to amplify T cell-mediated diseases.

Deletion of Exoc7, but not Exoc3, in male germ cells causes severe spermatogenesis failure with spermatocyte aggregation in mice.

Vesicular trafficking is essential for the transport of intracellularly produced functional molecules to the plasma membrane and extracellular space. The exocyst complex, composed of eight different proteins, is an important functional machinery for "tethering" in vesicular trafficking. Functional studies have been conducted in laboratory mice to identify the mechanisms by which the deletion of each exocyst factor affect various biological phenomena. Interestingly, each exocyst factor-deficient mutant exhibits a different phenotype. This discrepancy may be due to the function of the exocyst factor beyond its role as a component of the exocyst complex. Male germline-specific conditional knockout (cKO) mice of the Exoc1 gene, which encodes one of the exocyst factors EXOC1 (SEC3), exhibit severe spermatogenesis defects; however, whether this abnormality also occurs in mutants lacking other exocyst factors remains unknown. In this study, we found that exocyst factor EXOC3 (SEC6) was not required for spermatogenesis, but depletion of EXOC7 (EXO70) led to severe spermatogenesis defects. In addition to being a component of the exocyst complex, EXOC1 has other functions. Notably, male germ cell-specific Exoc7 cKO and Exoc1 cKO mice exhibited phenotypic similarities, suggesting the importance of the exocyst complex for spermatogenesis. The results of this study will contribute to further understanding of spermatogenesis from the aspect of vesicular trafficking.

Impact of Frailty in Patients Undergoing Minimally Invasive Mitral Valve Surgery.

OBJECTIVE: Psoas muscle size is a reliable marker of sarcopenia and frailty that correlates with adverse outcomes after cardiac surgery. However, its use in mitral and minimally invasive cardiac surgery is lacking. We sought to determine whether frailty, as measured by psoas muscle index, increases surgical risk for minimally invasive mitral valve surgery. METHODS: Patients undergoing isolated minimally invasive mitral surgery via right minithoracotomy were identified. Patients who underwent maze, tricuspid intervention, and those who were emergent were excluded. Total psoas muscle area was calculated using the average cross-sectional area at the L3 vertebra on computed tomography scan and indexed to body surface area. Sarcopenia was defined as <25th gender-specific percentile. Patients were stratified by sarcopenia status and outcomes compared. RESULTS: Of 287 total patients, 192 patients met inclusion criteria. Sarcopenic patients were 6 years older (66 vs 60 years, P = 0.01), had lower preoperative albumin levels (4.0 vs 4.3 g/dL, P < 0.001), and had higher Society of Thoracic Surgeons risk of morbidity/mortality (13.1% vs 9.0%, P = 0.003). Operative major morbidity or mortality was 6.4% versus 5.5% (P = 0.824), while the 1-year mortality rate was 2.1% versus 0% (P = 0.08). After risk adjustment, psoas index did not predict operative morbidity or mortality. However, sarcopenia was associated with higher odds of readmission (odds ratio = 0.74, P = 0.02). CONCLUSIONS: Contrary to other cardiac operations, for patients undergoing isolated minimally invasive mitral valve surgery, sarcopenia was not associated with increased perioperative risk except for higher readmission rates. Minimally invasive surgical approaches should be strongly considered as the approach of choice in frail patients.

Integrated Sensors for Soft Medical Robotics.

Minimally invasive procedures assisted by soft robots for surgery, diagnostics, and drug delivery have unprecedented benefits over traditional solutions from both patient and surgeon perspectives. However, the translation of such technology into commercialization remains challenging. The lack of perception abilities is one of the obstructive factors paramount for a safe, accurate and efficient robot-assisted intervention. Integrating different types of miniature sensors onto robotic end-effectors is a promising trend to compensate for the perceptual deficiencies in soft robots. For example, haptic feedback with force sensors helps surgeons to control the interaction force at the tool-tissue interface, impedance sensing of tissue electrical properties can be used for tumor detection. The last decade has witnessed significant progress in the development of multimodal sensors built on the advancement in engineering, material science and scalable micromachining technologies. This review article provides a snapshot on common types of integrated sensors for soft medical robots. It covers various sensing mechanisms, examples for practical and clinical applications, standard manufacturing processes, as well as insights on emerging engineering routes for the fabrication of novel and high-performing sensing devices.

Dynamics of macrophage polarization support Salmonella persistence in a whole living organism.

Numerous intracellular bacterial pathogens interfere with macrophage function, including macrophage polarization, to establish a niche and persist. However, the spatiotemporal dynamics of macrophage polarization during infection within host remain to be investigated. Here, we implement a model of persistent Salmonella Typhimurium infection in zebrafish, which allows visualization of polarized macrophages and bacteria in real time at high resolution. While macrophages polarize toward M1-like phenotype to control early infection, during later stages, Salmonella persists inside non-inflammatory clustered macrophages. Transcriptomic profiling of macrophages showed a highly dynamic signature during infection characterized by a switch from pro-inflammatory to anti-inflammatory/pro-regenerative status and revealed a shift in adhesion program. In agreement with this specific adhesion signature, macrophage trajectory tracking identifies motionless macrophages as a permissive niche for persistent Salmonella. Our results demonstrate that zebrafish model provides a unique platform to explore, in a whole organism, the versatile nature of macrophage functional programs during bacterial acute and persistent infections.

Pathogenic/likely pathogenic mutations identified in Vietnamese children diagnosed with autism spectrum disorder using high-resolution SNP genotyping platform.

Among the most prevalent neurodevelopmental disorders, Autism Spectrum Disorder (ASD) is highly diverse showing a broad phenotypic spectrum. ASD also couples with a broad range of mutations, both de novo and inherited. In this study, we used a proprietary SNP genotyping chip to analyze the genomic DNA of 250 Vietnamese children diagnosed with ASD. Our Single Nucleotide Polymorphism (SNP) genotyping chip directly targets more than 800 thousand SNPs in the genome. Our primary focus was to identify pathogenic/likely pathogenic mutations that are potentially linked to more severe symptoms of autism. We identified and validated 23 pathogenic/likely pathogenic mutations in this initial study. The data shows that these mutations were detected in several cases spanning multiple biological pathways. Among the confirmed SNPs, mutations were identified in genes previously known to be strongly associated with ASD such as SLCO1B1, ACADSB, TCF4, HCP5, MOCOS, SRD5A2, MCCC2, DCC, and PRKN while several other mutations are known to associate with autistic traits or other neurodevelopmental disorders. Some mutations were found in multiple patients and some patients carried multiple pathogenic/likely pathogenic mutations. These findings contribute to the identification of potential targets for therapeutic solutions in what is considered a genetically heterogeneous neurodevelopmental disorder.

Guidance of Nerve Stimulator and Ultrasound for Transforaminal Epidural Steroid Injection in Lumbosacral Radicular Pain : A Single Institution Experience in Vietnam.

OBJECTIVE: This study aimed to evaluate the clinical feasibility of the combination of ultrasound and nerve stimulator guidance in transforaminal epidural steroid injections (TESIs) to manage lumbosacral chronic radicular pain. METHODS: Using the combination of nerve stimulator and ultrasound guidance, TESIs were performed in 125 segments of 78 patients who presented with chronic lumbar radicular pain. Demographic characteristics and surgical outcomes were recorded on admission, pre-procedural and post-procedural for 1-week, 1-month, 3-month, and 6-month follow-ups. The result was measured using the Numeric rating scale (NRS) and Oswestry disability index (ODI). RESULTS: Patients who received TESIs showed significant improvements on two evaluation tools (NRS, ODI), compared to that before procedure (p<0.001). No significant complications were observed for 6 months' follow-up. CONCLUSION: The result suggests that a combination of ultrasound and nerve stimulator guidance in transforaminal epidural injections is safe, reliable and effective for short-term management of lumbar disc herniation. It is a promising technique and has shown good results in providing intermediate pain relief.

Towards a single-use, low-cost endoscope for gastroenterological diagnostics.

Early diagnosis and treatment of diseases in the gastrointestinal (GI) tract including colorectal cancers (CRC) via natural orifices have led to a significant increase in patient survival rates. Most screening procedures utilize image-guided techniques via a conventional endoscope. The cost of conventional endoscopes is substantial, ranging in the tens of thousands of USD or more. This presents significant burden for developing countries, which are disproportionally affected by gastroenterological diseases. Conventional endoscopes also require sterilization between use. This increases the chance of cross-infection between patients. To address these problems, this paper introduces a soft endoscope with a disposable insertion tube that can be articulated. This prototype device is hydraulically actuated, capable of a 10 mm bend radius and 180-degree bend angle. The camera system provides 110 degrees field-of-view. The component parts of this disposable endoscope costs less than 200 USD.Clinical relevance-Our low-cost, single-use endoscope eliminates the sterilization step required by conventional systems, thereby reducing the risks of infection and lowering the operating costs. There is also significant scope for our device to be used beyond the human GI track, such as screening for lung or bladder cancers. Given the compact footprint, the minimal cost of the disposable parts, the proposed platform can widen cancer screening programs with quantifiable economic benefit for many patients, particularly those in developing countries.

Phytochemistry and Cytotoxic Activity of Aquilaria crassna Pericarp on MDA-MB-468 Cell Lines.

The extracts of Aquilaria crassna pericarp were investigated on the MDA-MB-468, a breast cancer cell line, at desired concentration (1-50 µg/mL). The results showed that the dichloromethane (DCM) extract exhibited the strongest toxicity and was carried out subsequently. A total of nine compounds were isolated from the DCM extract using column chromatography and recrystallization, of which their structures were determined. Intriguingly, in addition to the previously reported compounds, neocucurbitacin A, a cucurbitacin triterpenoid aglycone with a lactone in ring A, was reported for the first time in the Aquilaria genus. Among the isolated compounds, cucurbitacin E highly inhibited MDA-MB-468 cell growth in a dose-dependent manner. Owing to binding abilities with the SH2 domain in the molecular docking study, cucurbitacin E, neocucurbitan A, neocucurbitan B, and cucurbitacin E 2-O-ß-d-glucopyranoside act as STAT3 inhibitors and are suitable for further research. This study suggests thatAquilaria crassnafruits could serve as a promising source of natural compounds with potential anticancer effects, particularly against breast cancer.

Temperature-Dependent Selection of Reaction Pathways, Reactive Species, and Products during Postsynthetic Selenization of Copper Sulfide Nanoparticles.

Rational design of elaborate, multicomponent nanomaterials is important for the development of many technologies such as optoelectronic devices, photocatalysts, and ion batteries. Combination of metal chalcogenides with different anions, such as in CdS/CdSe structures, is particularly effective for creating heterojunctions with valence band offsets. Seeded growth, often coupled with cation exchange, is commonly used to create various core/shell, dot-in-rod, or multipod geometries. To augment this library of multichalcogenide structures with new geometries, we have developed a method for postsynthetic transformation of copper sulfide nanorods into several different classes of nanoheterostructures containing both copper sulfide and copper selenide. Two distinct temperature-dependent pathways allow us to select from several outcomes-rectangular, faceted Cu2-xS/Cu2-xSe core/shell structures, nanorhombuses with a Cu2-xS core, and triangular deposits of Cu2-xSe or Cu2-x(S,Se) solid solutions. These different outcomes arise due to the evolution of the molecular components in solution. At lower temperatures, slow Cu2-xS dissolution leads to concerted morphology change and Cu2-xSe deposition, while Se-anion exchange dominates at higher temperatures. We present detailed characterization of these Cu2-xS-Cu2-xSe nanoheterostructures by transmission electron microscopy (TEM), powder X-ray diffraction, energy-dispersive X-ray spectroscopy, and scanning TEM-energy-dispersive spectroscopy. Furthermore, we correlate the selenium species present in solution with the roles they play in the temperature dependence of nanoheterostructure formation by comparing the outcomes of the established reaction conditions to use of didecyl diselenide as a transformation precursor.

Identification of a pharyngeal mucosal lymphoid organ in zebrafish and other teleosts: Tonsils in fish?

The constant exposure of the fish branchial cavity to aquatic pathogens causes local mucosal immune responses to be extremely important for their survival. Here, we used a marker for T lymphocytes/natural killer (NK) cells (ZAP70) and advanced imaging techniques to investigate the lymphoid architecture of the zebrafish branchial cavity. We identified a sub-pharyngeal lymphoid organ, which we tentatively named "Nemausean lymphoid organ" (NELO). NELO is enriched in T/NK cells, plasma/B cells, and antigen-presenting cells embedded in a network of reticulated epithelial cells. The presence of activated T cells and lymphocyte proliferation, but not V(D)J recombination or hematopoiesis, suggests that NELO is a secondary lymphoid organ. In response to infection, NELO displays structural changes including the formation of T/NK cell clusters. NELO and gill lymphoid tissues form a cohesive unit within a large mucosal lymphoid network. Collectively, we reveal an unreported mucosal lymphoid organ reminiscent of mammalian tonsils that evolved in multiple teleost fish families.

Antibacterial Activity against Escherichia coli and Cytotoxicity of Maillard Reaction Product of Chitosan and Glucosamine Prepared by Gamma Co-60 Ray Irradiation.

In this study, the gamma ray-induced Maillard reaction method was carried out for chitosan (CTS) and glucosamine (GA) to improve the water solubility and antibacterial activity. The mixture solution of CTS and GA was exposed to gamma rays at a dose of 25 kGy and freeze-dried to obtain a Maillard reaction product (MRP) powder. The physicochemical and biological properties of the CTS-GA MRP powder were investigated. The CTS-GA MRP powder expressed good solubility at a concentration of 0.05 g/mL. In addition, the result of the antibacterial activity test against Escherichia coli revealed that the CTS-GA MRP powder exhibited highly antibacterial activity at pH 7; in particular, bacterial density was reduced by over 4 logs. Furthermore, the cytotoxicity test of the CTS-GA MRP powder on mouse fibroblast cells (L929) showed non-cytotoxicity with high cell viability (>90%) at concentrations of 0.1-1 mg/mL. Owing to the high antibacterial activity and low cytotoxicity, the water-soluble CTS-GA MRP powder can be used as a favorable natural preservative for food and cosmetics.

Identification and Evaluation of the Growth Promotion of Endophytic Bacteria on in vitro Potato Plants.

<b>Background and Objective:</b> Isolation and investigation of plant growth promoting bacteria on potato plants can provide significant information for the application of beneficial bacteria in potato production. This study aims to isolate and characterize endophytic bacteria isolated from potato roots. In addition, the potential application of endophytes in promoting potato growth under <i>in vitro</i> conditions was also investigated. <b>Materials and Methods:</b> The roots from 15 healthy potato plants were excised and surface sterilized by NaOCl and finally rinsed by sterilized water. The confirmed surface-sterilized roots were then aseptically cut into small fragments and spread onto the isolation media, followed by incubation at 27°C for up to 3 days. Six isolates that showed differences in colony morphology were selected for further investigation. All isolates were screened for IAA production, nitrogen fixation, and phosphate solubilization. <b>Results:</b> Five of the isolates were identified as <i>Bacillus</i> and isolate 30 was identified as <i>Paenibacillus alvei</i>. All isolates exhibited good IAA production. While Iso-27 had no nitrogen fixation activity, Iso-28 showed the highest level of nitrogen fixation activity (3.59 mg L¹), four isolates (Iso-9, Iso-10, Iso-11, Iso-28) could solubilize phosphate, ranging from 49.64 g L¹ to 67.98 mg L¹. After being inoculated with <i>in vitro</i> potato plants, isolates 9, 10, 28, 30, improved the stalk length, root number, fresh mass and dried mass of the potato plants. <b>Conclusion:</b> The four isolates can potentially be applied in <i>in vitro</i> potato culture.

A Smart, Textile-Driven, Soft Exosuit for Spinal Assistance.

Work-related musculoskeletal disorders (WMSDs) are often caused by repetitive lifting, making them a significant concern in occupational health. Although wearable assist devices have become the norm for mitigating the risk of back pain, most spinal assist devices still possess a partially rigid structure that impacts the user's comfort and flexibility. This paper addresses this issue by presenting a smart textile-actuated spine assistance robotic exosuit (SARE), which can conform to the back seamlessly without impeding the user's movement and is incredibly lightweight. To detect strain on the spine and to control the smart textile automatically, a soft knitting sensor that utilizes fluid pressure as a sensing element is used. Based on the soft knitting hydraulic sensor, the robotic exosuit can also feature the ability of monitoring and rectifying human posture. The SARE is validated experimentally with human subjects (N = 4). Through wearing the SARE in stoop lifting, the peak electromyography (EMG) signals of the lumbar erector spinae are reduced by 22.8% ± 12 for lifting 5 kg weights and 27.1% ± 14 in empty-handed conditions. Moreover, the integrated EMG decreased by 34.7% ± 11.8 for lifting 5 kg weights and 36% ± 13.3 in empty-handed conditions. In summary, the artificial muscle wearable device represents an anatomical solution to reduce the risk of muscle strain, metabolic energy cost and back pain associated with repetitive lifting tasks.

Optofluidic Sensor Based on Polymer Optical Microresonators for the Specific, Sensitive and Fast Detection of Chemical and Biochemical Species.

The accurate, rapid, and specific detection of DNA strands in solution is becoming increasingly important, especially in biomedical applications such as the trace detection of COVID-19 or cancer diagnosis. In this work we present the design, elaboration and characterization of an optofluidic sensor based on a polymer-based microresonator which shows a quick response time, a low detection limit and good sensitivity. The device is composed of a micro-racetrack waveguide vertically coupled to a bus waveguide and embedded within a microfluidic circuit. The spectral response of the microresonator, in air or immersed in deionised water, shows quality factors up to 72,900 and contrasts up to 0.9. The concentration of DNA strands in water is related to the spectral shift of the microresonator transmission function, as measured at the inflection points of resonance peaks in order to optimize the signal-over-noise ratio. After functionalization by a DNA probe strand on the surface of the microresonator, a specific and real time measurement of the complementary DNA strands in the solution is realized. Additionally, we have inferred the dissociation constant value of the binding equilibrium of the two complementary DNA strands and evidenced a sensitivity of 16.0 pm/µM and a detection limit of 121 nM.

Mechanodetection of neighbor plants elicits adaptive leaf movements through calcium dynamics.

Plants detect their neighbors via various cues, including reflected light and touching of leaf tips, which elicit upward leaf movement (hyponasty). It is currently unknown how touch is sensed and how the signal is transferred from the leaf tip to the petiole base that drives hyponasty. Here, we show that touch-induced hyponasty involves a signal transduction pathway that is distinct from light-mediated hyponasty. We found that mechanostimulation of the leaf tip upon touching causes cytosolic calcium ([Ca2+]cyt induction in leaf tip trichomes that spreads towards the petiole. Both perturbation of the calcium response and the absence of trichomes reduce touch-induced hyponasty. Finally, using plant competition assays, we show that touch-induced hyponasty is adaptive in dense stands of Arabidopsis. We thus establish a novel, adaptive mechanism regulating hyponastic leaf movement in response to mechanostimulation by neighbors in dense vegetation.