Development of a Novel Space Flight Plan to Monitor Female Mice Fertility Using Reduced Crew Time

Ovarian estrogen impacts the normal homeostatic and metabolic processes of all tissues and organ systems within the body: particularly, but not limited to canonical space-flight impacted systems: bone, muscle, immune, wound repair, and cardiovascular. Effects of space flight on the ovarian estrogen production are therefore critical to our understanding of all space flight experiments using female mice, the current paradigm being used on the International Space Station (ISS). Recently, we demonstrated that vaginal wall histology could be used to determine the stage of the estrous cycle in female mice at the time of sacrifice in space. Moreover, this robust technique was completed following two post-flight freezethaw procedures of the carcasses (RR1 experiment). Thus, this technique represents a viable mechanism to determine the estrous cycle status of the female at the time of sacrifice and can be completed in a manner that does not impact primary experimental objectives. We propose that vaginal wall histology become a standard procedure completed on all mice sacrificed in space and that the individual estrous status of each animal be shared with all investigators. While evidence of estrous cyclicity was present in long-term (33 day) RR1 mice, fertility of female mice exposed to weightlessness remains unknown. In preparation for an upcoming funded NASA flight investigating the effects of long duration spaceflight on female fertility, we have refined our experimental design to minimize crew flight time and to accommodate the duration of Dragon capsule berth. These refinements maintain all our proposed primary and secondary experimental objectives. Briefly, in order to evaluate fertility, we will super ovulate mice using standard procedures (PMSG hCG), followed by collection of reproductive tract after follicular stimulation alone (PMSG) or following ovulation (hCG). Ovarian folliculogenesis and ovulation rate will be determined in fixed tissues following return in order to determine fertility. Ovarian and uterine tissues will also be evaluated by hormonal and gene expression profiling using quantitative approaches (radioimmunoassays, western blots, digital droplet PCR). Comparisons will be made to contemporary vivarium and Rodent Research Hardware Transporter and Habitat housed animals maintained on earth. Supported by NNX15AB48G to JST

A detailed analysis of next generation sequencing reads of microRNA expression in Barrett’s Esophagus: absolute versus relative quantification

Background Next generation sequencing (NGS) is a state of the art technology for microRNA (miRNA) analysis. The quantitative interpretation of the primary output of NGS i.e. the read counts for a miRNA sequence that can vary by several orders of magnitude (1 to 107) remains incompletely understood. Findings NGS (SOLiD 3 technology) was performed on biopsies from 6 Barrett’s esophagus (BE) and 5 Gastroesophageal Reflux Disease (GERD) patients. Read sequences were aligned to miRBase 18.0. Differential expression analysis was adjusted for false discovery rate of 5%. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed for 36 miRNA in a validation cohort of 47 patients (27 BE and 20 GERD). Correlation coefficients, accuracy, precision and recall of NGS compared to qRT-PCR were calculated. Increase in NGS reads was associated with progressively lower Cq values, p 1000 vs. 500 vs. 100 vs. <100). The accuracy, precision and recall of NGS to label a miRNA as differentially expressed were 0.71, 0.88 and 0.74 respectively. Conclusion Absolute NGS reads correlated modestly with qRT-PCR but fold changes correlated highly. NGS is robust at relative but not absolute quantification of miRNA levels and accurate for high-throughput identification of differentially expressed miRNA.The current work was supported by a pilot grant from the American Cancer Society (AB and LKC), the American College of Gastroenterology Junior Faculty Development Award (AB) and Hall Family Foundation (LKC)

MicroRNA Expression can be a Promising Strategy for the Detection of Barrett's Esophagus: A Pilot Study

Clinical and Translational Gastroenterology is an open-access journal published by Nature Publishing Group.Patient outcomes for esophageal adenocarcinoma (EAC) have not improved despite huge advances in endoscopic therapy because cancers are being diagnosed late. Barrett's esophagus (BE) is the primary precursor lesion for EAC, and thus the non-endoscopic molecular diagnosis of BE can be an important approach to improve EAC outcomes if robust biomarkers for timely diagnosis are identified. MicroRNAs (miRNAs) are tissue-specific novel biomarkers that regulate gene expression and may satisfy this requirement.The current work was supported by a pilot grant from the American Cancer Society (A.B. and L.K.C.), the American College of Gastroenterology Junior Faculty Development Award (A.B.) and grants from Hall Family Foundation (L.K.C.) and Kansas IDeA Network of Biomedical Research Excellence (A.B., L.K.C.). None of the funding bodies had any role in design, in the collection, analysis and interpretation of data; in the writing of the manuscript; and in the decision to submit the manuscript for publication

Discovery and Validation of Barrett's Esophagus MicroRNA Transcriptome by Next Generation Sequencing

Objective: Barrett's esophagus (BE) is transition from squamous to columnar mucosa as a result of gastroesophageal reflux disease (GERD). The role of microRNA during this transition has not been systematically studied. Design: For initial screening, total RNA from 5 GERD and 6 BE patients was size fractionated. RNA <70 nucleotides was subjected to SOLiD 3 library preparation and next generation sequencing (NGS). Bioinformatics analysis was performed using R package “DEseq”. A p value<0.05 adjusted for a false discovery rate of 5% was considered significant. NGS-identified miRNA were validated using qRT-PCR in an independent group of 40 GERD and 27 BE patients. MicroRNA expression of human BE tissues was also compared with three BE cell lines. Results: NGS detected 19.6 million raw reads per sample. 53.1% of filtered reads mapped to miRBase version 18. NGS analysis followed by qRT-PCR validation found 10 differentially expressed miRNA; several are novel (-708-5p, -944, -224-5p and -3065-5p). Up- or down- regulation predicted by NGS was matched by qRT-PCR in every case. Human BE tissues and BE cell lines showed a high degree of concordance (70–80%) in miRNA expression. Prediction analysis identified targets that mapped to developmental signaling pathways such as TGFβ and Notch and inflammatory pathways such as toll-like receptor signaling and TGFβ. Cluster analysis found similarly regulated (up or down) miRNA to share common targets suggesting coordination between miRNA. Conclusion: Using highly sensitive next-generation sequencing, we have performed a comprehensive genome wide analysis of microRNA in BE and GERD patients. Differentially expressed miRNA between BE and GERD have been further validated. Expression of miRNA between BE human tissues and BE cell lines are highly correlated. These miRNA should be studied in biological models to further understand BE development

Antibiotic-Induced Primary Biles Inhibit SARS-CoV-2 Endoribonuclease Nsp15 Activity in Mouse Gut

The gut microbiome profile of COVID-19 patients was found to correlate with a viral load of SARS-CoV-2, COVID-19 severity, and dysfunctional immune responses, suggesting that gut microbiota may be involved in anti-infection. In order to investigate the role of gut microbiota in anti-infection against SARS-CoV-2, we established a high-throughput in vitro screening system for COVID-19 therapeutics by targeting the endoribonuclease (Nsp15). We also evaluated the activity inhibition of the target by substances of intestinal origin, using a mouse model in an attempt to explore the interactions between gut microbiota and SARS-CoV-2. The results unexpectedly revealed that antibiotic treatment induced the appearance of substances with Nsp15 activity inhibition in the intestine of mice. Comprehensive analysis based on functional profiling of the fecal metagenomes and endoribonuclease assay of antibiotic-enriched bacteria and metabolites demonstrated that the Nsp15 inhibitors were the primary bile acids that accumulated in the gut as a result of antibiotic-induced deficiency of bile acid metabolizing microbes. This study provides a new perspective on the development of COVID-19 therapeutics using primary bile acids

A VQ-motif-containing protein fine-tunes rice immunity and growth by a hierarchical regulatory mechanism.

peer reviewedRice blast and bacterial blight, caused by the fungus Magnaporthe oryzae and the bacterium Xanthomonas oryzae pv. oryzae (Xoo), respectively, are devastating diseases affecting rice. Here, we report that a rice valine-glutamine (VQ) motif-containing protein, OsVQ25, balances broad-spectrum disease resistance and plant growth by interacting with a U-Box E3 ligase, OsPUB73, and a transcription factor, OsWRKY53. We show that OsPUB73 positively regulates rice resistance against M. oryzae and Xoo by interacting with and promoting OsVQ25 degradation via the 26S proteasome pathway. Knockout mutants of OsVQ25 exhibit enhanced resistance to both pathogens without a growth penalty. Furthermore, OsVQ25 interacts with and suppresses the transcriptional activity of OsWRKY53, a positive regulator of plant immunity. OsWRKY53 downstream defense-related genes and brassinosteroid signaling genes are upregulated in osvq25 mutants. Our findings reveal a ubiquitin E3 ligase-VQ protein-transcription factor module that fine-tunes plant immunity and growth at the transcriptional and posttranslational levels

Phase Characters of Optical Dark Solitons with the Third-order Dispersion and Delayed Nonlinear Response

Dark soliton is usually seen as one of the simplest topological solitons, due to the phase jump across its density dip. We investigate the phase jump properties of dark solitons in a single mode optical fiber with the third-order dispersion and delayed nonlinear response, based on exact analytical solutions of Hirota equation. Our analysis indicates that a single-valley dark soliton (SVDS) can admit two distinct phase jumps at the same velocity, in sharp contrast to the dark soliton with only the second-order dispersion and self-phase modulation, which admits a one-to-one match between the velocity and phase jump. We further uncover the different topological vector potentials underlying the distinct phase jumps. The relations between phase jump and velocity of the SVDS can explain the generation of the previously reported double-valley dark soliton (DVDS). The detailed analysis on the two phase jumps characters of the DVDS with one identical velocity enables us to obtain U-shaped type or double-step type phase distribution. We further explore collision properties of the DVDSs by analyzing their topological phase, which can be considered as the generalization of topological phase (Phys. Rev. E 103, L040204). Strikingly, the inelastic collision can lead to the conversion between the two types of phase distributions for DVDS. The results reveal that inelastic or elastic collision can be judged by analyzing the magnetic monopole fields.Comment: 15 pages, 7 figure

A Topology Control with Energy Balance in Underwater Wireless Sensor Networks for IoT-Based Application

As part of the IoT-based application, underwater wireless sensor networks (UWSN), which are typically self-organized heterogeneous wireless network, are one of the research hot-spots using various sensors in marine exploration and water environment monitoring application fields, recently. Due to the serious attenuation of radio in water, acoustic or hybrid communication is a usual way for transmitting information among nodes, which dissipates much more energy to prevent the network failure and guarantee the quality of service (QoS). To address this issue, a topology control with energy balance, namely TCEB, is proposed for UWSN to overcome time-delay and other interference, as well as make the entire network load balance. With the given underwater network model and its specialized energy consumption model, we introduce the non-cooperative-game-based scheme to select the nodes with better performance as the cluster-heads. Afterwards, the intra-cluster and inter-cluster topology construction are, respectively, to form the effective communication links of the intra-cluster and inter-cluster, which aim to build energy-efficient topology to reduce energy consumption. With the demonstration of the simulation, the results show the proposed TCEB has better performance on energy-efficiency and throughput than three other representative algorithms in complex underwater environments

Robust arterial compliance estimation with Katz’s fractal dimension of photoplethysmography

Arterial compliance (AC) plays a crucial role in vascular aging and cardiovascular disease. The ability to continuously estimate aortic AC or its surrogate, pulse pressure (PP), through wearable devices is highly desirable, given its strong association with daily activities. While the single-site photoplethysmography (PPG)-derived arterial stiffness indices show reasonable correlations with AC, they are susceptible to noise interference, limiting their practical use. To overcome this challenge, our study introduces a noise-resistant indicator of AC: Katz’s fractal dimension (KFD) of PPG signals. We showed that KFD integrated the signal complexity arising from compliance changes across a cardiac cycle and vascular structural complexity, thereby decreasing its dependence on individual characteristic points. To assess its capability in measuring AC, we conducted a comprehensive evaluation using both in silico studies with 4374 virtual human data and real-world measurements. In the virtual human studies, KFD demonstrated a strong correlation with AC (r = 0.75), which only experienced a slight decrease to 0.66 at a signal-to-noise ratio of 15dB, surpassing the best PPG-morphology-derived AC measure (r = 0.41) under the same noise condition. In addition, we observed that KFD’s sensitivity to AC varied based on the individual’s hemodynamic status, which may further enhance the accuracy of AC estimations. These in silico findings were supported by real-world measurements encompassing diverse health conditions. In conclusion, our study suggests that PPG-derived KFD has the potential to continuously and reliably monitor arterial compliance, enabling unobtrusive and wearable assessment of cardiovascular health

Research Resource: Preovulatory LH Surge Effects on Follicular Theca and Granulosa Transcriptomes

The molecular mechanisms that regulate the pivotal transformation processes observed in the follicular wall following the preovulatory LH surge, are still not established, particularly for cells of the thecal layer. To elucidate thecal cell (TC) and granulosa cell (GC) type-specific biologic functions and signaling pathways, large dominant bovine follicles were collected before and 21 hours after an exogenous GnRH-induced LH surge. Antral GCs (aGCs; aspirated by follicular puncture) and membrane-associated GCs (mGCs; scraped from the follicular wall) were compared with TC expression profiles determined by mRNA microarrays. Of the approximately 11 000 total genes expressed in the periovulatory follicle, only 2% of thecal vs 25% of the granulosa genes changed in response to the LH surge. The majority of the 203 LH-regulated thecal genes were also LH regulated in GCs, leaving a total of 57 genes as LH-regulated TC-specific genes. Of the 57 thecal-specific LH-regulated genes, 74% were down-regulated including CYP17A1 and NR5A1, whereas most other genes are being identified for the first time within theca. Many of the newly identified up-regulated thecal genes (eg, PTX3, RND3, PPP4R4) were also up-regulated in granulosa. Minimal expression differences were observed between aGCs and mGCs; however, transcripts encoding extracellular proteins (NID2) and matrix modulators (ADAMTS1, SASH1) dominated these differences. We also identified large numbers of unknown LH-regulated GC genes and discuss their putative roles in ovarian function. This Research Resource provides an easy-to-access global evaluation of LH regulation in TCs and GCs that implicates numerous molecular pathways heretofore unknown within the follicle