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1.
NPJ Precis Oncol ; 8(1): 99, 2024 Jun 03.
Article in English | MEDLINE | ID: mdl-38831114

ABSTRACT

Fetal adenocarcinoma of the lung (FLAC) is a rare form of lung adenocarcinoma and was divided into high-grade (H-FLAC) and low-grade (L-FLAC) subtypes. Despite the existence of some small case series studies, a comprehensive multi-omics study of FLAC has yet to be undertaken. In this study, we depicted the multi-omics landscapes of this rare lung cancer type by performing multi-regional sampling on 20 FLAC cases. A comparison of multi-omics profiles revealed significant differences between H-FLAC and L-FLAC in a multi-omic landscape. Two subtypes also showed distinct relationships between multi-layer intratumor heterogeneity (ITH). We discovered that a lower genetic ITH was significantly associated with worse recurrence-free survival and overall survival in FLAC patients, whereas higher methylation ITH in H-FLAC patients suggested a short survival. Our findings highlight the complex interplay between genetic and transcriptional heterogeneity in FLAC and suggest that different types of ITH may have distinct implications for patient prognosis.

2.
J Nanobiotechnology ; 22(1): 308, 2024 Jun 02.
Article in English | MEDLINE | ID: mdl-38825711

ABSTRACT

Research into mRNA vaccines is advancing rapidly, with proven efficacy against coronavirus disease 2019 and promising therapeutic potential against a variety of solid tumors. Adjuvants, critical components of mRNA vaccines, significantly enhance vaccine effectiveness and are integral to numerous mRNA vaccine formulations. However, the development and selection of adjuvant platforms are still in their nascent stages, and the mechanisms of many adjuvants remain poorly understood. Additionally, the immunostimulatory capabilities of certain novel drug delivery systems (DDS) challenge the traditional definition of adjuvants, suggesting that a revision of this concept is necessary. This review offers a comprehensive exploration of the mechanisms and applications of adjuvants and self-adjuvant DDS. It thoroughly addresses existing issues mentioned above and details three main challenges of immune-related adverse event, unclear mechanisms, and unsatisfactory outcomes in old age group in the design and practical application of cancer mRNA vaccine adjuvants. Ultimately, this review proposes three optimization strategies which consists of exploring the mechanisms of adjuvant, optimizing DDS, and improving route of administration to improve effectiveness and application of adjuvants and self-adjuvant DDS.


Subject(s)
Adjuvants, Immunologic , Cancer Vaccines , Nanotechnology , Neoplasms , mRNA Vaccines , Humans , Cancer Vaccines/immunology , Nanotechnology/methods , Neoplasms/therapy , Neoplasms/immunology , Animals , Drug Delivery Systems/methods , COVID-19/prevention & control , Adjuvants, Vaccine , RNA, Messenger/genetics , SARS-CoV-2/immunology , Vaccines, Synthetic/immunology
3.
J Dig Dis ; 25(3): 176-190, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38697922

ABSTRACT

OBJECTIVES: Functional constipation (FC), a common functional gastrointestinal disorder, is usually overlapping with upper gastrointestinal symptoms (UGS). We aimed to explore the clinical characteristics of patients with FC overlapping UGS along with the related risk factors. METHODS: The differences in the severity of constipation symptoms, psychological state, quality of life (QoL), anorectal motility and perception function, autonomic function, and the effect of biofeedback therapy (BFT) among patients with FC in different groups were analyzed, along with the risk factors of overlapping UGS. RESULTS: Compared with patients with FC alone, those with FC overlapping UGS had higher scores in the Patient Assessment of Constipation Symptoms and Self-Rating Anxiety Scale and lower scores in the Short Form-36 health survey (P < 0.05). Patients with FC overlapping UGS also had lower rectal propulsion, more negative autonomic nervous function, and worse BFT efficacy (P < 0.05). Overlapping UGS, especially overlapping functional dyspepsia, considerably affected the severity of FC. Logistic regression model showed that age, body mass index (BMI), anxiety, exercise, and sleep quality were independent factors influencing overlapping UGS in patients with FC. CONCLUSIONS: Overlapping UGS reduces the physical and mental health and the QoL of patients with FC. It also increases the difficulty in the treatment of FC. Patient's age, BMI, anxiety, physical exercise, and sleep quality might be predictors for FC overlapping UGS.


Subject(s)
Constipation , Quality of Life , Humans , Constipation/physiopathology , Constipation/psychology , Constipation/etiology , Female , Male , Middle Aged , Risk Factors , Adult , Severity of Illness Index , Biofeedback, Psychology , Anxiety , Gastrointestinal Diseases/psychology , Gastrointestinal Diseases/physiopathology , Gastrointestinal Diseases/etiology , Aged , Gastrointestinal Motility/physiology
4.
Article in English | MEDLINE | ID: mdl-38703823

ABSTRACT

BACKGROUND: As a central hub in cognitive and emotional brain circuits, the striatum is considered likely to be integrally involved in the psychopathology of bipolar disorder (BD). However, it remains unclear how alterations in striatal function contribute to distinct symptomatology of BD during different mood states. METHODS: Behavioral assessment (i.e., emotional symptoms and cognitive performance) and neuroimaging data were collected from 125 participants comprising 31 (hypo)manic, 31 depressive and 31 euthymic patients with BD, and 32 healthy controls. We compared the functional connectivity (FC) of striatal subregions across BD mood states with healthy controls and then used a multivariate data-driven approach to explore dimensional associations between striatal connectivity and behavioral performance. Finally, we compared the FC and behavioral composite scores, which reflect the individual weighted representation of the associations, among different mood states. RESULTS: Patients in all mood states exhibited increased FC between the bilateral ventral rostral putamen (VRP) and ventrolateral thalamus. Bipolar (hypo)mania uniquely exhibited increased VRP connectivity and superior ventral striatum connectivity. One latent component was identified, whereby increased FCs of striatal subregions were associated with distinct psychopathological symptomatology (more manic symptoms, elevated positive mood, less depressive symptoms and worse cognitive performance). Bipolar (hypo)manic patients had the highest FC and behavioral composite scores while bipolar depressive patients had the lowest. CONCLUSIONS: Our data demonstrated both trait features of BD and state features specific to bipolar (hypo) mania. The findings underscored the fundamental role of the striatum in the pathophysiological processes underlying specific symptomatology across all mood states.

5.
J Hosp Infect ; 2024 May 03.
Article in English | MEDLINE | ID: mdl-38705475

ABSTRACT

INTRODUCTION: The prevention and control of hospital-acquired infections remain a significant challenge worldwide, as textiles used in hospital wards are highly involved in transmission processes. Herein, we report a new antibacterial medical fabric used to prepare hospital pillowcases, bottom sheets, and quilt covers for controlling and reducing hospital-acquired infections. METHOD: The medical fabric was composed of blended yarns of staple polyester and degradable poly(3-hydroxybutyrate co-3-hydroxyvalerate)/polylactide fibres, which were then coated with polylactide oligomers, an environmentally friendly and safe antimicrobial agent with excellent thermal stability in high-temperature laundry. A clinical trial was conducted with emphasis on the bacterial species that were closely related to the infection cases in the trial hospital. RESULT: After 7 days of usage, 94% of PET/PHBV/PLA-PLAO fabric could keep less than 20 CFU/100 cm2 of total bacterial amount, meeting hygiene and cleanliness standards. CONCLUSION: This study demonstrates the potential of fabrics containing polyhydroxyalkanoate oligomers as highly effective, safe, and long-lasting antimicrobial medical textiles that can effectively reduce the incidence of hospital-acquired infections.

6.
Neuron ; 2024 Apr 22.
Article in English | MEDLINE | ID: mdl-38697111

ABSTRACT

Mutations in human nonsense-mediated mRNA decay (NMD) factors are enriched in neurodevelopmental disorders. We show that deletion of key NMD factor Upf2 in mouse embryonic neural progenitor cells causes perinatal microcephaly but deletion in immature neurons does not, indicating NMD's critical roles in progenitors. Upf2 knockout (KO) prolongs the cell cycle of radial glia progenitor cells, promotes their transition into intermediate progenitors, and leads to reduced upper-layer neurons. CRISPRi screening identified Trp53 knockdown rescuing Upf2KO progenitors without globally reversing NMD inhibition, implying marginal contributions of most NMD targets to the cell cycle defect. Integrated functional genomics shows that NMD degrades selective TRP53 downstream targets, including Cdkn1a, which, without NMD suppression, slow the cell cycle. Trp53KO restores the progenitor cell pool and rescues the microcephaly of Upf2KO mice. Therefore, one physiological role of NMD in the developing brain is to degrade selective TRP53 targets to control progenitor cell cycle and brain size.

7.
Water Res ; 257: 121743, 2024 Jun 15.
Article in English | MEDLINE | ID: mdl-38728775

ABSTRACT

Effective deep-dewatering is crucial for wastewater sludge management. Currently, the dominant methods focus on promoting cell lysis to release intracellular water, but these techniques often lead to secondary pollution and require stringent conditions, limiting their practical use. This study explores an innovative method using a commercially available complex quaternary ammonium salt surfactant, known as G-agent. This agent remarkably reduces the sludge water content from 98.6 % to 56.8 % with a low dosage (50 mg/g DS) and under neutral pH conditions. This approach surpasses Fenton oxidation in terms of dewatering efficiency and avoids the necessity for cell lysis and bound water release, thereby reducing the risk of secondary pollution in the filtrate, including heavy metals, nitrogen, phosphorus, and other contaminants. The G-agent plays a significant role in destabilizing flocs and enhancing flocculation during the conditioning and initial dewatering stages, effectively reducing the solid-liquid interfacial affinity of the sludge. In the compression filtration stage, the agent's solidification effect is crucial in forming a robust skeleton that improves pore connectivity within the filter cake, leading to increased water permeability, drainage performance and water flow-out efficiency. This facilitates deep dewatering of sludge without cell lysis. The study reveals that the G-agent primarily improves water flow-out efficiency rather than water flowability, indicating that cell lysis and bound water release are not indispensable prerequisites for sludge deep-dewatering. Furthermore, it presents an encouraging prospect for overcoming the limitations associated with conventional sludge deep-dewatering processes.


Subject(s)
Flocculation , Sewage , Waste Disposal, Fluid , Waste Disposal, Fluid/methods , Filtration , Water/chemistry , Surface-Active Agents/chemistry
8.
Front Bioeng Biotechnol ; 12: 1340765, 2024.
Article in English | MEDLINE | ID: mdl-38737537

ABSTRACT

Objective: This study aimed to estimate the effects of the volume of preperitoneal balloon (PPB) on arterial and venous hemorrhage in a swine pelvic fracture model. Methods: Twenty-four swine were randomized into 0-mL, 500-mL, 800-mL, and 1000-mL intra-hematoma PPB groups. They were subjected to open-book pelvic fracture and reproducible injuries in the external iliac artery and vein. The pelvic binder and IH-PPBs with different volumes of fluid were applied to control the active hemorrhage after arterial and venous injuries. The survival time and rate during 60-min observation and digital subtraction angiography (DSA) images were the primary endpoints in this study. Secondary endpoints included survival rate within 70 min, peritoneal pressure, hemodynamics, blood loss, infusion fluid, blood pH, and lactate concentration. Results: Our results indicated that the 800-mL and 1000-mL groups had a higher survival rate (0%, 50%, 100% and 100% for 0, 500, 800, and 1000-mL groups respectively; p < 0.0001) and longer survival time (13.83 ± 2.64, 24.50 ± 6.29, 55.00 ± 6.33, and 60.00 ± 0.00 min for 0, 500, 800, and 1,000 groups respectively; p < 0.0005) than the 0-mL or 500-mL groups during the 60 min observation. Contrastingly, survival rate and time were comparable between 800-mL and 1000-mL groups during the 60-min observation. The IH-PPB volume was associated with an increase in the pressure of the balloon and the preperitoneal pressure but had no effect on the bladder pressure. Lastly, the 1000-mL group had a higher mean arterial pressure and systemic vascular resistance than the 800-mL group. Conclusion: IH-PPB volume-dependently controls vascular bleeding after pelvic fracture in the swine model. IH-PPB with a volume of 800 mL and 1000 mL efficiently managed pelvic fracture-associated arterial and venous hemorrhage and enhanced survival time and rate in the swine model without evidences of visceral injury.

9.
Trends Microbiol ; 2024 May 14.
Article in English | MEDLINE | ID: mdl-38749772

ABSTRACT

Dengue is a mosquito-borne viral disease which causes significant morbidity and mortality each year. Previous research has proposed several mechanisms of pathogenicity that mainly involve the dengue virus and host humoral immunity. However, innate immune cells, such as neutrophils, may also play an important role in dengue, albeit a much less defined role. In this review, we discuss the emerging roles of neutrophils in dengue and their involvement in pathologies associated with severe dengue. We also describe the potential use of several neutrophil proteins as biomarkers for severe dengue. These studies suggest that neutrophils are important players in dengue, and a better understanding of neutrophil-dengue biology is urgently needed.

10.
Nat Prod Res ; : 1-7, 2024 May 16.
Article in English | MEDLINE | ID: mdl-38752874

ABSTRACT

Two new withanolides named physaminilides L (1) and M (2), together with four known ones (3-6) were isolated from the Physalis minima L. The structures were established by analysis of the HR ESIMS, IR and NMR spectroscopic data. The absolute configurations were determined through NOESY and ECD spectra. For compounds 1-5 assayed at 20 µM and compound 6 at 10 µM, inhibition rates of hepatic fibrosis were 22.19%, 15.29%, 37.07%, 9.27%, 12.45%, and 37.03%, respectively.

11.
Laryngoscope Investig Otolaryngol ; 9(3): e1262, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38741682

ABSTRACT

Background: Eustachian tube dysfunction (ETD) is the predominant cause of otitis media with effusion in children and adults. Balloon dilatation of the Eustachian tube (BDET) provides a new method for restoring the ventilatory function of Eustachian tube (ET). However, the differences in age-related morphological changes in the dimensions and positions of ET in children and adults are unclear. Purpose: This study aimed to examine age-related morphological changes in bony and cartilage segments of the ET in a three-dimensional space in normal population. Methods: A total of 71 randomly selected computed tomography (CT) images of the temporal bones of 46 people were retrospectively studied in four age groups: A (0-3 years old); B (4-8 years old), C (9-18 years old), and D (19-65 years old). Space analytic geometry was assessed to calculate the dimensions and positions of ET. Results: The bony segment of ET lengthened from infancy to adulthood with age in groups A, B and C (r = 0.562**/0.000). The cartilage segment of ET mostly extended with age from infancy to 8 years old in children (r = 0.633**/0.000), but with bending close to the sagittal plane and away from the horizontal plane with age in groups A, B and C (P < .05), and with a constant angle to the coronal plane among the four groups (P > .05). Conclusion: The bony and cartilaginous segments of ET exhibit distinct morphological changes in space with age. The bony segment of ET extends in a constant position from infancy to adulthood. In contrast, the cartilaginous segment of the ET indicates multidimensional positional changes until adulthood, in addition to the elongation from infancy to children. This may provide an accurate morphological basis for comparing the differences in ETD pathogenesis and surgical treatment between children and adults.

12.
MedComm (2020) ; 5(5): e577, 2024 May.
Article in English | MEDLINE | ID: mdl-38741888

ABSTRACT

The study by Rahim et al., focusing on preoperative immunotherapy, highlights the pivotal role of CD8+ T cells within lymph nodes in response to neoadjuvant immunotherapy, suggesting that preserving lymph node integrity could bolster the treatment's efficacy by activating antitumor T cells. This underlines the importance of lymph node preservation and supports the use of immunotherapy as a neoadjuvant approach in cancer treatment.

13.
Cardiovasc Diabetol ; 23(1): 162, 2024 May 09.
Article in English | MEDLINE | ID: mdl-38724999

ABSTRACT

BACKGROUND: The triglyceride glucose-body mass index (TyG-BMI) is recognized as a reliable surrogate for evaluating insulin resistance and an effective predictor of cardiovascular disease. However, the link between TyG-BMI index and adverse outcomes in heart failure (HF) patients remains unclear. This study examines the correlation of the TyG-BMI index with long-term adverse outcomes in HF patients with coronary heart disease (CHD). METHODS: This single-center, prospective cohort study included 823 HF patients with CHD. The TyG-BMI index was calculated as follows: ln [fasting triglyceride (mg/dL) × fasting blood glucose (mg/dL)/2] × BMI. To explore the association between the TyG-BMI index and the occurrences of all-cause mortality and HF rehospitalization, we utilized multivariate Cox regression models and restricted cubic splines with threshold analysis. RESULTS: Over a follow-up period of 9.4 years, 425 patients died, and 484 were rehospitalized due to HF. Threshold analysis revealed a significant reverse "J"-shaped relationship between the TyG-BMI index and all-cause mortality, indicating a decreased risk of all-cause mortality with higher TyG-BMI index values below 240.0 (adjusted model: HR 0.90, 95% CI 0.86-0.93; Log-likelihood ratio p = 0.003). A distinct "U"-shaped nonlinear relationship was observed with HF rehospitalization, with the inflection point at 228.56 (adjusted model: below: HR 0.95, 95% CI 0.91-0.98; above: HR 1.08, 95% CI 1.03-1.13; Log-likelihood ratio p < 0.001). CONCLUSIONS: This study reveals a nonlinear association between the TyG-BMI index and both all-cause mortality and HF rehospitalization in HF patients with CHD, positioning the TyG-BMI index as a significant prognostic marker in this population.


Subject(s)
Biomarkers , Blood Glucose , Body Mass Index , Coronary Disease , Heart Failure , Patient Readmission , Triglycerides , Humans , Male , Female , Heart Failure/mortality , Heart Failure/blood , Heart Failure/diagnosis , Triglycerides/blood , Middle Aged , Aged , Prospective Studies , Blood Glucose/metabolism , Time Factors , Biomarkers/blood , Risk Assessment , Risk Factors , Coronary Disease/mortality , Coronary Disease/blood , Coronary Disease/diagnosis , Coronary Disease/epidemiology , Prognosis , Cause of Death , Insulin Resistance , Predictive Value of Tests
14.
J Neuroinflammation ; 21(1): 123, 2024 May 09.
Article in English | MEDLINE | ID: mdl-38725082

ABSTRACT

BACKGROUND: Hepatic encephalopathy (HE) is closely associated with inflammatory responses. However, as a crucial regulator of the immune and inflammatory responses, the role of leucine-rich repeat kinase 2 (LRRK2) in the pathogenesis of HE remains unraveled. Herein, we investigated this issue in thioacetamide (TAA)-induced HE following acute liver failure (ALF). METHODS: TAA-induced HE mouse models of LRRK2 wild type (WT), LRRK2 G2019S mutation (Lrrk2G2019S) and LRRK2 knockout (Lrrk2-/-) were established. A battery of neurobehavioral experiments was conducted. The biochemical indexes and pro-inflammatory cytokines were detected. The prefrontal cortex (PFC), striatum (STR), hippocampus (HIP), and liver were examined by pathology and electron microscopy. The changes of autophagy-lysosomal pathway and activity of critical Rab GTPases were analyzed. RESULTS: The Lrrk2-/--HE model reported a significantly lower survival rate than the other two models (24% vs. 48%, respectively, p < 0.05), with no difference found between the WT-HE and Lrrk2G2019S-HE groups. Compared with the other groups, after the TAA injection, the Lrrk2-/- group displayed a significant increase in ammonium and pro-inflammatory cytokines, aggravated hepatic inflammation/necrosis, decreased autophagy, and abnormal phosphorylation of lysosomal Rab10. All three models reported microglial activation, neuronal loss, disordered vesicle transmission, and damaged myelin structure. The Lrrk2-/--HE mice presented no severer neuronal injury than the other genotypes. CONCLUSIONS: LRRK2 deficiency may exacerbate TAA-induced ALF and HE in mice, in which inflammatory response is evident in the brain and aggravated in the liver. These novel findings indicate a need of sufficient clinical awareness of the adverse effects of LRRK2 inhibitors on the liver.


Subject(s)
Hepatic Encephalopathy , Leucine-Rich Repeat Serine-Threonine Protein Kinase-2 , Liver Failure, Acute , Mice, Knockout , Thioacetamide , Animals , Leucine-Rich Repeat Serine-Threonine Protein Kinase-2/genetics , Leucine-Rich Repeat Serine-Threonine Protein Kinase-2/metabolism , Thioacetamide/toxicity , Mice , Hepatic Encephalopathy/pathology , Hepatic Encephalopathy/genetics , Liver Failure, Acute/chemically induced , Liver Failure, Acute/pathology , Liver Failure, Acute/genetics , Male , Mice, Inbred C57BL
15.
Article in English | MEDLINE | ID: mdl-38734818

ABSTRACT

The ventral subiculum (vSUB), the major output structure of the hippocampal formation, regulates motivation, stress integration, and anxiety-like behaviors that rely on heightened arousal. However, the roles and underlying neural circuits of the vSUB in wakefulness are poorly known. Using in vivo fiber photometry and multichannel electrophysiological recordings in mice, we found that the vSUB glutamatergic neurons exhibited high activities during wakefulness. Moreover, activation of vSUB glutamatergic neurons caused an increase in wakefulness and anxiety-like behaviors and induced a rapid transition from sleep to wakefulness. In addition, optogenetic stimulation of vSUB glutamatergic terminals and retrograde-targeted chemogenetic activation of vSUB glutamatergic neurons revealed that vSUB promoted arousal by innervating the lateral hypothalamus (LH), nucleus accumbens (NAc) shell, and prefrontal cortex (PFC). Nevertheless, local microinjection of dopamine D1 or D2/D3 receptor antagonist blocked the wake-promoting effect induced by chemogenetic activation of vSUB pathways. Finally, chemogenetic inhibition of vSUB glutamatergic neurons decreased arousal. Altogether, our findings reveal a prominent contribution of vSUB glutamatergic neurons to the control of wakefulness through several pathways.

16.
Adv Sci (Weinh) ; : e2309992, 2024 May 22.
Article in English | MEDLINE | ID: mdl-38774946

ABSTRACT

Radiotherapy demonstrates a synergistic effect with immunotherapy by inducing a transformation of "immune cold" tumors into "immune hot" tumors in triple negative breast cancer (TNBC). Nevertheless, the effectiveness of immunotherapy is constrained by low expression of tumor-exposed antigens, inadequate inflammation, and insufficient tumor infiltrating lymphocyte (TILs). To address this predicament, novel lutecium-based rare earth nanoparticles (RENPs) are synthesized with the aim of amplifying radiation effect and tumor immune response. The nanoprobe is characterized by neodymium-based down-conversion fluorescence, demonstrating robust photostability, biocompatibility, and targetability. The conjugation of RENPs with a CXCR4 targeted drug enables precise delineation of breast tumors using a near-infrared imaging system and improves radiation efficacy via lutetium-based radio-sensitizer in vivo. Furthermore, the study shows a notable enhancement of immune response through the induction of immunogenic cell death and recruitment of TILs, resulting in the inhibition of tumor progression both in vitro and in vivo models following the administration of nanoparticles. Hence, the novel multifunctional nanoprobes incorporating various lanthanide elements offer the potential for imaging-guided tumor delineation, radio-sensitization, and immune activation post-radiation, thus presenting an efficient radio-immunotherapeutic approach for TNBC.

17.
J Hazard Mater ; 473: 134613, 2024 May 14.
Article in English | MEDLINE | ID: mdl-38788571

ABSTRACT

Bacteria are pivotal to drinking water treatment and public health. However, the mechanisms of bacterial assembly and their impact on species coexistence remain largely unexplored. This study explored the assembly and succession of bacterial communities in two full-scale drinking water systems over one year. We observed a decline in bacterial biomass, diversity, and co-occurrence network complexity along the treatment processes, except for the biological activated carbon filtration stage. The conventional plant showed higher bacterial diversity than the advanced plant, despite similar bacterial concentrations and better removal efficiency. The biological activated carbon filter exhibited high phylogenetic diversity, indicating enhanced bacterial metabolic functionality for organic matter removal. Chlorination inactivated most bacteria but favored some chlorination-resistant and potentially pathogenic species, such as Burkholderia, Bosea, Brevundimonas, and Acinetobacter. Moreover, the spatiotemporal dynamics of the bacterial continuum were primarily driven by stochastic processes, explaining more than 78% of the relative importance. The advanced plant's bacterial community was less influenced by dispersal limitation and more by homogeneous selection. The stochastic process regulated bacterial diversity and influenced the complexity of the species co-occurrence network. These findings deepen our understanding of microbial ecological mechanisms and species interactions, offering insights for enhancing hygienic safety in drinking water systems.

18.
Sci Adv ; 10(21): eadj8184, 2024 May 24.
Article in English | MEDLINE | ID: mdl-38781332

ABSTRACT

Sinking particles are a critical conduit for the transport of surface microbes to the ocean's interior. Vertical connectivity of phylogenetic composition has been shown; however, the functional vertical connectivity of microbial communities has not yet been explored in detail. We investigated protein and taxa profiles of both free-living and particle-attached microbial communities from the surface to 3000 m depth using a combined metaproteomic and 16S rRNA amplicon sequencing approach. A clear compositional and functional vertical connectivity of microbial communities was observed throughout the water column with Oceanospirillales, Alteromonadales, and Rhodobacterales as key taxa. The surface-derived particle-associated microbes increased the expression of proteins involved in basic metabolism, organic matter processing, and environmental stress response in deep waters. This study highlights the functional vertical connectivity between surface and deep-sea microbial communities via sinking particles and reveals that a considerable proportion of the deep-sea microbes might originate from surface waters and have a major impact on the biogeochemical cycles in the deep sea.


Subject(s)
Microbiota , Oceans and Seas , Phylogeny , RNA, Ribosomal, 16S , Seawater , RNA, Ribosomal, 16S/genetics , Seawater/microbiology , Bacteria/genetics , Bacteria/classification
19.
Nat Commun ; 15(1): 4376, 2024 May 23.
Article in English | MEDLINE | ID: mdl-38782890

ABSTRACT

Topologically associating domains (TADs), megabase-scale features of chromatin spatial architecture, are organized in a domain-within-domain TAD hierarchy. Within TADs, the inner and smaller subTADs not only manifest cell-to-cell variability, but also precisely regulate transcription and differentiation. Although over 20 TAD callers are able to detect TAD, their usability in biomedicine is confined by a disagreement of outputs and a limit in understanding TAD hierarchy. We compare 13 computational tools across various conditions and develop a metric to evaluate the similarity of TAD hierarchy. Although outputs of TAD hierarchy at each level vary among callers, data resolutions, sequencing depths, and matrices normalization, they are more consistent when they have a higher similarity of larger TADs. We present comprehensive benchmarking of TAD hierarchy callers and operational guidance to researchers of life science researchers. Moreover, by simulating the mixing of different types of cells, we confirm that TAD hierarchy is generated not simply from stacking Hi-C heatmaps of heterogeneous cells. Finally, we propose an air conditioner model to decipher the role of TAD hierarchy in transcription.


Subject(s)
Benchmarking , Chromatin , Chromatin/chemistry , Humans , Computational Biology/methods , Software , Chromatin Assembly and Disassembly
20.
Reprod Sci ; 2024 May 20.
Article in English | MEDLINE | ID: mdl-38769248

ABSTRACT

Endometrial elasticity is a potential new marker for assessing endometrial receptivity and pregnancy outcomes based on endometrial thickness and type. Currently, little research has been conducted on the elasticity of the endometrium using shear wave elasticity imaging (SWEI). This study aimed to explore whether endometrial elasticity is an ultrasound marker for predicting clinical pregnancy outcomes after embryo transfer. A total of 245 infertile women underwent ultrasonography before embryo transfer at the Peking University Third Hospital. We compared the endometrial elasticity and sub-endometrial blood flow rate using SWEI in the groups with different pregnancy outcomes. Trends in clinical pregnancy outcomes across the quartiles of endometrial elasticity in the fundus of the uterus (E1) were assessed. Logistic regression analysis was performed to obtain odds ratios for clinical pregnancy outcomes based on the quartiles of E1, with or without adjusting for potential confounding variables. Women in the clinical pregnancy group had higher E1 values and sub-endometrial blood flow rates in the uterine fundus than those in the non-pregnancy group. Women in the highest quartile of E1 had the most favorable clinical pregnancy rates. Endometrial elasticity measured using SWEI is a promising ultrasound marker for predicting clinical pregnancy outcomes after embryo transfer.

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