The unfolding and folding dynamics of TNfnALL probed by single molecule force-ramp spectroscopy

Abstract Tenascin, an important extracellular matrix protein, is subject to stretching force under physiological conditions and plays important roles in regulating the cell-matrix interactions. Using the recently developed single molecule force-ramp spectroscopy, we investigated the unfoldingfolding kinetics of a recombinant tenascin fragment TNfnALL. Our results showed that all the 15 FnIII domains in TNfnALL have similar spontaneous unfolding rate constant at zero force, but show great difference in their folding rate constants. Our results demonstrated that single molecule force-ramp spectroscopy is a powerful tool for accurate determination of the kinetic parameters that characterize the unfolding and folding reactions. We anticipate that single molecule force-ramp spectroscopy will become a versatile addition to the single molecule manipulation tool box and greatly expand the scope of single molecule force spectroscopy.

A Microeconomics-Based Fuzzy QoS Unicast Routing Scheme in NGI

Abstract. Due to the difficulty on exact measurement and expression of NGI (Next-Generation Internet) network status, the necessary QoS routing information is fuzzy. With the gradual commercialization of network operation, paying for network usage calls for QoS pricing and accounting. In this paper, a microeconomics-based fuzzy QoS unicast routing scheme is proposed, consisting of three phases: edge evaluation, game analysis, and route selection. It attempts to make both network provider and user utilities maximized along the found route, with not only the user QoS requirements satisfied but also the Pareto-optimum under the Nash equilibrium on their utilities achieved

Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes

Explosive growth in the study of microbial epigenetics has revealed a diversity of chemical structures and biological functions of DNA modifications in restriction-modification (R-M) and basic genetic processes. Here, we describe the discovery of shared consensus sequences for two seemingly unrelated DNA modification systems, [superscript 6m]A methylation and phosphorothioation (PT), in which sulfur replaces a nonbridging oxygen in the DNA backbone. Mass spectrometric analysis of DNA from Escherichia coli B7A and Salmonella enterica serovar Cerro 87, strains possessing PT-based R-M genes, revealed d(G[subscript PS] [superscript 6m]A) dinucleotides in the G[subscript PS] [superscript 6m]AAC consensus representing ∼5% of the 1,100 to 1,300 PT-modified d(G[subscript PS] A) motifs per genome, with [superscript 6m]A arising from a yet-to-be-identified methyltransferase. To further explore PT and 6m A in another consensus sequence, G[subscript PS] [superscript 6m]ATC, we engineered a strain of E. coli HST04 to express Dnd genes from Hahella chejuensis KCTC2396 (PT in G[subscript PS] ATC) and Dam methyltransferase from E. coli DH10B ( [superscript 6m] A in G [superscript 6m] ATC). Based on this model, in vitro studies revealed reduced Dam activity in G PS ATC-containing oligonucleotides whereas single-molecule real-time sequencing of HST04 DNA revealed [superscript 6m] A in all 2,058 G[subscript PS] ATC sites (5% of 37,698 total GATC sites). This model system also revealed temperature-sensitive restriction by DndFGH in KCTC2396 and B7A, which was exploited to discover that [superscript 6m] A can substitute for PT to confer resistance to restriction by the DndFGH system. These results point to complex but unappreciated interactions between DNA modification systems and raise the possibility of coevolution of interacting systems to facilitate the function of each

Effects of Delayed Cord Clamping on 4-Month Ferritin Levels, Brain Myelin Content, and Neurodevelopment: A Randomized Controlled Trial

Objective To evaluate whether placental transfusion influences brain myelination at 4 months of age. Study design A partially blinded, randomized controlled trial was conducted at a level III maternity hospital in the US. Seventy-three healthy term pregnant women and their singleton fetuses were randomized to either delayed umbilical cord clamping (DCC, \u3e5 minutes) or immediate clamping (ICC, \u3c20 \u3eseconds). At 4 months of age, blood was drawn for ferritin levels. Neurodevelopmental testing (Mullen Scales of Early Learning) was administered, and brain myelin content was measured with magnetic resonance imaging. Correlations between myelin content and ferritin levels and group-wise DCC vs ICC brain myelin content were completed. Results In the DCC and ICC groups, clamping time was 172 ± 188 seconds vs 28 ± 76 seconds (P \u3c .002), respectively; the 48-hour hematocrit was 57.6% vs 53.1% (P \u3c .01). At 4 months, infants with DCC had significantly greater ferritin levels (96.4 vs 65.3 ng/dL, P = .03). There was a positive relationship between ferritin and myelin content. Infants randomized to the DCC group had greater myelin content in the internal capsule and other early maturing brain regions associated with motor, visual, and sensory processing/function. No differences were seen between groups in the Mullen testing. Conclusion At 4 months, infants born at term receiving DCC had greater ferritin levels and increased brain myelin in areas important for early life functional development. Endowment of iron-rich red blood cells obtained through DCC may offer a longitudinal advantage for early white matter development

Dopamine and Serotonin Modulate Free Amino Acids Production and Na+/K+ Pump Activity in Chinese Mitten Crab Eriocheir sinensis Under Acute Salinity Stress

The Chinese mitten crab Eriocheir sinensis lives in saline or fresh water during different life stages and exhibits a complex life history, making it an ideal model to study the salinity adaptation of euryhaline animals. In this study, RNA-seq techniques, and determinations of free amino acids (FAAs), monoamine neurotransmitters, and Na+/K+ pump activity, were employed to understand the osmoregulatory mechanism in Chinese mitten crab. A total of 15,138 differentially expressed genes were obtained from 12 transcriptome libraries. GO enrichment analysis revealed that the mRNA expression profiles were completely remodeled from 12 to 24 h after salinity stress. The neuroendocrine system was activated under stimulation, and the monoamine neurotransmitters including dopamine (DA) and serotonin (5-HT) were released to modulate osmoregulation. Furthermore, the Na+/K+ pump in crab hemocytes was significantly inhibited post salinity stress, resulting in increased intracellular ion concentrations and osmotic pressure to sustain the osmotic balance. Moreover, six key FAAs, including alanine (Ala), proline (Pro), glycine (Gly), glutamate (Glu), arginine (Arg), and aspartate (Asp), were overexpressed to modulate the extracellular osmotic balance during salinity adaptation. Interestingly, the immune genes were not enriched in the GO analysis, implying that the immune system might not contribute fundamentally to the tolerance upon fluctuating ambient salinity in the Chinese mitten crab. These results collectively demonstrated that the Chinese mitten crab had evolved an efficient regulation mechanism by modulating the FAAs production and Na+/K+ pump activity to sustain the osmotic balance independent of the immune system, in which the neuroendocrine modulation, especially generated by the monoamine neurotransmitter, played an indispensable role

Association between tertiary lymphoid structures and clinical outcomes in cancer patients treated with immune checkpoint inhibitors: an updated meta-analysis

BackgroundAlthough numerous studies have reported the association between tertiary lymphoid structures (TLSs) and clinical outcomes in cancer patients treated with immune checkpoint inhibitors (ICIs), there remains a lack of a newer and more comprehensive meta-analysis. The main objective of this study is to explore prognostic biomarkers in immunotherapy-related patients, through analyzing the associations between tertiary lymphoid structures (TLSs) and clinical outcomes in cancer patients treated with ICIs, so as to investigate their prognostic value in cancer patients treated with ICIs.MethodsA comprehensive search was conducted until February 2024 across PubMed, Embase, Web of Science, and the Cochrane Library databases to identify relevant studies evaluating the association between tertiary lymphoid structures and clinical outcomes in cancer patients treated with ICIs. The clinical outcomes were overall survival (OS), progression‐free survival (PFS), and objective response rate (ORR).ResultsThirteen studies were incorporated in this meta-analysis, among which nine evaluated the prognostic value of TLSs. The results showed the high levels of TLSs predicted a significantly prolonged OS (pooled HR = 0.35, 95% CI: 0.24–0.53, p < 0.001) and PFS (pooled HR = 0.47, 95% CI: 0.31–0.72, p < 0.001), while lower ORR (pooled OR = 3.78, 95% CI: 2.26–6.33, p < 0.001) in cancer patients treated with ICIs.ConclusionOur results indicated that high levels of TLSs could predict a favorable prognosis for cancer patients treated with ICIs and have the potential to become a prognostic biomarker of immunotherapy-related patients

PAR6, A Potential Marker for the Germ Cells Selected to Form Primordial Follicles in Mouse Ovary

Partitioning-defective proteins (PAR) are detected to express mainly in the cytoplast, and play an important role in cell polarity. However, we showed here that PAR6, one kind of PAR protein, was localized in the nuclei of mouse oocytes that formed primordial follicles during the perinatal period, suggesting a new role of PAR protein. It is the first time we found that, in mouse fetal ovaries, PAR6 appeared in somatic cell cytoplasm and fell weak when somatic cells invaded germ cell cysts at 17.5 days post coitus (dpc). Meanwhile, the expression of PAR6 was observed in cysts, and became strong in the nuclei of some germ cells at 19.5 dpc and all primordial follicular oocytes at 3 day post parturition (dpp), and then obviously declined when the primordial follicles entered the folliculogenic growth phase. During the primordial follicle pool foundation, the number of PAR6 positive germ cells remained steady and was consistent with that of formed follicles at 3 dpp. There were no TUNEL (apoptosis examination) positive germ cells stained with PAR6 at any time studied. The number of follicles significantly declined when 15.5 dpc ovaries were treated with the anti-PAR6 antibody and PAR6 RNA interference. Carbenoxolone (CBX, a known blocker of gap junctions) inhibited the expression of PAR6 in germ cells and the formation of follicles. Our results suggest that PAR6 could be used as a potential marker of germ cells for the primordial follicle formation, and the expression of PAR6 by a gap junction-dependent process may contribute to the formation of primordial follicles and the maintenance of oocytes at the diplotene stage