Short tandem repeat profiling via next-generation sequencing for cell line authentication

Cell lines are indispensable models for modern biomedical research. A large part of their usefulness derives from the ability of a cell line to proliferate over multiple passages (often indefinitely), allowing multiple experiments to be performed. However, over time, cell line identity and purity can be compromised by human errors. Cross-contamination from other cell lines and complete misidentification are both possible. Routine cell line authentication is a necessary preventive measure and has become a requirement for many funding applications and publications. Short tandem repeat (STR) profiling is the most common method for cell line authentication and is usually carried out using standard polymerase chain reaction-capillary electrophoresis analysis (STR-CE). Here, we evaluated next-generation sequencing (NGS)-based STR profiling of human and mouse cell lines at 18 and 15 loci, respectively, in a high-throughput format. Using the Python program STRight, we demonstrate that NGS-based analysis (STR-NGS) is superior to standard STR-CE in terms of the ability to report the sequence context of repeat motifs, sensitivity and flexible multiplexing capability. STR-NGS is thus a valuable alternative for cell line authentication

Development of a novel sea surface temperature proxy based on bacterial 3-hydroxy fatty acids

Gram-negative bacterial 3-hydroxy fatty acids (3-OH-FAs) have received recent attention for their potential as palaeoclimate proxies. A novel temperature proxy, the ratio of anteiso to normal C13 3-OH-FA (RAN13), has been proposed for sea surface temperature (SST) reconstruction in the North Pacific Ocean. However, whether this newly proposed temperature proxy is applicable to marginal seas with significant terrigenous input or tropical oligotrophic seas requires further investigation. Here, we analyzed the composition and distribution of 3-OH-FAs and evaluated the possible impact of various environmental parameters (SST, water depth, dissolved oxygen, salinity and nutrient concentration) on their distribution in marine surface sediments from the Bohai Sea (BS) and the South China Sea (SCS). In the BS, the potential source proxy, fractional abundance of anteiso 3-OH-FAs (average 17%), indicates 3-OH-FA geochemical signature are not greatly overprinted by terrigenous inputs. The relative abundance of long-chain 3-OH-FAs (C15-C18) are higher in the SCS (average 41%) compared to those in other seas (average 33% for all marine samples). Massive inputs of terrigenous organic matter to the BS likely result in overestimation of SSTs based on the RAN13 proxy, and limited abundance of anteiso and normal C13 3-OH-FAs in the oligotrophic SCS may increase the uncertainty of the RAN13 estimated SSTs. More importantly, we find that most short-chain 3-OH-FAs are temperature dependent, especially the fractional abundance of i-C12, a-C13, i-C14 and n-C14 with a high determination coefficient (R2 &gt; 0.60). Based on these newly found correlations, we propose a novel proxy: RANs. The RANs index shows a strong linear relationship with SST (R2 = 0.92, p&lt; 0.001, n = 85) and more accurate prediction than the RAN13, especially in tropical samples. Furthermore, the RANs proxy is significantly correlated with TEX86, and RANs-based SSTs are approximate to LDI derived temperature in the SCS, which support the reliability of RANs as a temperature proxy. These findings further suggest 3-OH-FA based proxies have potential for paleo-SST reconstruction, especially at higher and lower ends of the ocean temperature spectrum and even in cases where marginal inputs of terrestrial organic matter and nutrients are high.</p

The spherical distance for intuitionistic fuzzy sets and its application in decision analysis

Different from traditional distances between Intuitionistic Fuzzy Sets (IFS), the spherical distance between two IFSs relies not only on their relative differences but also their absolute values. In this paper, we generalize the properties of spherical distance measures between IFSs, and investigate the applications of spherical distance measures in group decision making, pattern recognition and medical diagnosis. We develop an optimization spherical distance model with IFS preference in group decision making, and demonstrate that this model is feasible and practical with an evaluation model of drought risk. By using comparative analysis method, we show that this new spherical distance can also be applied in other fields such as pattern recognition and medical diagnosis

Altered resting-state functional connectivity of insula in children with primary nocturnal enuresis

ObjectivePrimary nocturnal enuresis (PNE) is a common developmental condition in school-aged children. The objective is to better understand the pathophysiology of PNE by using insula-centered resting-state functional connectivity (rsFC).MethodsWe recruited 66 right-handed participants in our analysis, 33 with PNE and 33 healthy control (HC) children without enuresis matched for gender and age. Functional and structural MRI data were obtained from all the children. Seed-based rsFC was used to examine differences in insular functional connectivity between the PNE and HC groups. Correlation analyses were carried out to explore the relationship between abnormal insula-centered functional connectivity and clinical characteristics in the PNE group.ResultsCompared with HC children, the children with PNE demonstrated decreased left and right insular rsFC with the right medial superior frontal gyrus (SFG). In addition, the bilateral dorsal anterior insula (dAI) seeds also indicated the reduced rsFC with right medial SFG. Furthermore, the right posterior insula (PI) seed showed the weaker rsFC with the right medial SFG, while the left PI seed displayed the weaker rsFC with the right SFG. No statistically significant correlations were detected between aberrant insular rsFC and clinical variables (e.g., micturition desire awakening, bed-wetting frequency, and bladder volume) in results without global signal regression (GSR) in the PNE group. However, before and after setting age as a covariate, significant and positive correlations between bladder volume and the rsFC of the left dAI with right medial SFG and the rsFC of the right PI with right medial SFG were found in results with GSR in the PNE group.ConclusionTo the best of our knowledge, this study explored the rsFC patterns of the insula in children with PNE for the first time. These results uncovered the abnormal rsFC of the insula with the medial prefrontal cortex without and with GSR in the PNE group, suggesting that dysconnectivity of the salience network (SN)-default mode network (DMN) may involve in the underlying pathophysiology of children with PNE. However, the inconsistent associations between bladder volume and dysconnectivity of the SN-DMN in results without and with GSR need further studies

Epidemiological and etiological investigations of hand, foot, and mouth disease in Jiashan, northeastern Zhejiang Province, China, during 2016 to 2022

BackgroundHand, foot, and mouth disease (HFMD) is a common infectious disease in children. Enterovirus A71 (EV71) and coxsackievirus A16 (CA16) have been identified as the predominant pathogens for several decades. In recent years, coxsackievirus A6 (CA6) and coxsackievirus A10 (CA10) have played increasingly important roles in a series of HFMD outbreaks. We performed a retrospective analysis of the epidemiology of HFMD and the spectrum of different viral serotypes, to elucidate the genetic and phylogenetic characteristics of the main serotypes in the Jiashan area during 2016 to 2022.MethodsDescriptive epidemiological methods were used to analyze the time and population distribution of HFMD in Jiashan during 2016 to 2022 based on surveillance data. Molecular diagnostic methods were performed to identify the viral serotypes and etiological characteristics of HFMD. Phylogenetic analyses was based on VP1 region of CA16 and CA6.ResultsThe average annual incidence rate of HFMD fluctuated from 2016 to 2022. Children aged 1–5 years accounted for 81.65% of cases and boys were more frequently affected than girls. Except when HFMD was affected by the COVID-19 epidemic in 2020 and 2022, epidemics usually peak in June to July, followed by a small secondary peak from October to December and a decline in February. Urban areas had a high average incidence and rural areas had the lowest. Among 560 sample collected in Jiashan, 472 (84.29%) were positive for enterovirus. The most frequently identified serotypes were CA6 (296, 52.86%), CA16 (102, 18.21%), EV71 (16, 2.86%), CA10 (14, 2.50%) and other enteroviruses (44, 7.86%). There were 71 and 142 VP1 sequences from CA16 and CA6, respectively. Substitution of N218D, A220L and V251I was detected in CA16 and may have been related to viral infectivity. Phylogenetic analysis showed that CA16 could be assigned to two genogroups, B1a and B1b, while all the CA6 sequences belonged to the D3a genogroup.ConclusionCA6 and CA16 were the two major serotypes of enteroviruses circulating in the Jiashan area during 2016 to 2022. Continuous and comprehensive surveillance for HFMD is needed to better understand and evaluate the prevalence and evolution of the associated pathogens

Management of prolactinoma: a survey of endocrinologists in China

Objective: To assess the current management of prolactinoma among endocrinologists in China. Methods: An online survey of a large sample of endocrinologists was conducted in China. The questionnaire included 21 questions related to controversial issues about the management of prolactinomas. Doctors in the endocrinology department of a university-affiliated hospital or a comprehensive secondary hospital in 12 cities from East, West, South, North and Middle China were surveyed. Results: A total of 290 valid questionnaires were collected, and the response rate was 40%. When hyperprolactinemia occurred, 97% of the respondents would test thyroid-stimulating hormone routinely. 22% of the respondents considered that prolactin levels 250 ng/mL could occur in all the following situations as macroprolactinoma, mircoprolactinoma, macroprolactinemia and drug-induced hyperprolactinemia. Surgery was not recommended by 272 (94%) endocrinologists as the first choice for treating microprolactinomas. 58% and 92% of endocrinologists would start drug treatment for microprolactinomas and macroprolactinomas at diagnosis. 70% and 40% chose to withdraw treatment after 2–3 years of prolactin normalization in microprolactinomas and macroprolactinomas. In case of pregnancy, 57% of the respondents considered bromocriptine as choice for women patients. Drug discontinuation after pregnancy was advocated in 63% and 27% for microprolactinoma and macroprolactinoma. Moreover, 44% of endocrinologists believed that breastfeeding was allowable in both micro- and macroprolactinoma. Conclusion: This is the first study to investigate the management of prolactinomas among endocrinologists in China. We found that the current clinical treatment was not uniform. Therefore, it is necessary to strengthen the training of endocrinologists to improve clinical diagnosis and treatment practices

Interleukin-23-Independent IL-17 Production Regulates Intestinal Epithelial Permeability

SummaryWhether interleukin-17A (IL-17A) has pathogenic and/or protective roles in the gut mucosa is controversial and few studies have analyzed specific cell populations for protective functions within the inflamed colonic tissue. Here we have provided evidence for IL-17A-dependent regulation of the tight junction protein occludin during epithelial injury that limits excessive permeability and maintains barrier integrity. Analysis of epithelial cells showed that in the absence of signaling via the IL-17 receptor adaptor protein Act-1, the protective effect of IL-17A was abrogated and inflammation was enhanced. We have demonstrated that after acute intestinal injury, IL-23R+ γδ T cells in the colonic lamina propria were the primary producers of early, gut-protective IL-17A, and this production of IL-17A was IL-23 independent, leaving protective IL-17 intact in the absence of IL-23. These results suggest that IL-17-producing γδ T cells are important for the maintenance and protection of epithelial barriers in the intestinal mucosa

Functional Connectivity Density, Local Brain Spontaneous Activity, and Their Coupling Strengths in Patients With Borderline Personality Disorder

In this study, combining degree centrality (DC) and fractional amplitude of low frequency fluctuation (fALFF) analyses of resting state (rs)-functional magnetic resonance imaging (fMRI) data, we aimed to explore functional connectivity density, local brain spontaneous activity, and their coupling strengths in borderline personality disorder (BPD). Forty-three BPD patients and 39 demographically-matched controls underwent rs-fMRI after completing a series of psychological tests. Two-sample t-tests were performed to compare DC and fALFF between these two groups. Across-voxel correlation analysis was conducted to assess DC-fALFF coupling strengths in each group. Imaging parameters and psychological variables were correlated by Pearson correlation analysis in the BPD group. Altered DC and fALFF values in the BPD group, compared with the control group, were distributed mainly in default mode network (DMN), and DC-fALFF coupling strengths were decreased in the left middle temporal gyrus (MTG) and right precuneus in the BPD group. Additionally, insecure attachment scores correlated positively with left precuneus DC and negatively with fALFF of the right posterior cingulate cortex (PCC) in the BPD group. These altered DC and fALFF findings indicate that the BPD patients had disturbed functional connectivity density and local spontaneous activity in the DMN compared with control subjects. Their decreased connectivity-amplitude coupling suggests that the left MTG and right precuneus may be functional impairment hubs in BPD. Disturbed rs function in the left precuneus and right PCC might underlie insecure attachment in BPD

Symbiotic diazotrophs in response to yak grazing and Tibetan sheep grazing in Qinghai-Tibetan plateau grassland soils

Grazing by local livestock is the traditional human practice in Qinghai-Tibetan Plateau grassland, and moderate intensity grazing can maintain high productivity and diversity of alpine grassland. Grazing ecosystems are often nitrogen-limited, but N2-fixing communities in response to yak grazing and Tibetan sheep grazing in Qinghai-Tibetan Plateau grassland have remained underexplored. In this study, we applied quantitative PCR quantitation and MiSeq sequencing of nifH under yak grazing and Tibetan grazing through a manipulated grazing experiment on an alpine grassland. The results showed that the grazing treatments significantly increased the soil ammonium nitrogen (AN) and total phosphorus (TP), but reduced the diazotrophs abundance. Compared with no grazing treatment, the composition of diazotrophs could be maximally maintained when the ratio of yak and Tibetan sheep were 1:2. The foraging strategies of grazing livestock reduced the legumes biomass, and thus reduced the diazotrophs abundance. Data analysis suggested that the direct key factors in regulating diazotrophs are AN and TP, and the changes of these two soil chemical properties were affected by the dung and urine of herbivore assemblages. Overall, these results indicated that the mixed grazing with a ratio of yak to Tibetan sheep as 1:2 can stabilize the soil diazotrophsic community, suggesting that MG12 are more reasonable grazing regimes in this region