bluuebunny/crossref_metadata_2025 huggingface dataset:
ABPP-HT - High-Throughput Activity-Based Profiling of Deubiquitylating Enzyme Inhibitors in a Cellular Context
Authors: Jones Hannah B. L. , Heilig Raphael , Fischer Roman , Kessler Benedikt M. , Pinto-Fernández Adán
Published: February 2021

The potency and selectivity of a small molecule inhibitor are key parameters to assess during the early stages of drug discovery. In particular, it is very informative for characterizing compounds in a relevant cellular context in order to reveal potential off-target effects and drug efficacy. Activity-based probes are valuable tools for that purpose, however, obtaining cellular target engagement data in a high-throughput format has been particularly challenging. Here, we describe a new methodology named ABPP-HT (high-throughput-compatible activity-based protein profiling), implementing a semi-automated proteomic sample preparation workflow that increases the throughput capabilities of the classical ABPP workflow approximately ten times while preserving its enzyme profiling characteristics. Using a panel of deubiquitylating enzyme (DUB) inhibitors, we demonstrate the feasibility of ABPP-HT to provide compound selectivity profiles of endogenous DUBs in a cellular context at a fraction of time as compared to previous methodologies.
Engineered Bacteria of MG1363-pMG36e-GLP-1 Attenuated Obesity-Induced by High Fat Diet in Mice
Authors: Wang Lingfang , Chen Tingtao , Wang Huan , Wu Xiaoli , Cao Qing , Wen Ke , Deng Ke-Yu , Xin Hongbo
Published: February 2021

Background

Although gut hormone glucagon-like peptide 1 (GLP-1) has been widely used for treating diabetes, the extremely short half-life greatly limits its application. The purpose of this study is to explore the effects of an engineered bacteria with expression of GLP-1 on obese mice induced by high fat diet (HFD).

Methods

The engineered strain of MG1363-pMG36e-GLP-1 (M-GLP-1) was constructed and its anti-obesity effects were evaluated in vivo. The bodyweight, the morphology of adipose and liver tissue, and liver function were examined. Quantitative RT-PCR and Western blot were used to measure the expressions of the genes involved in fatty acid oxidation synthesis. The intestinal microbial diversity was detected with high-throughput sequencing analysis.

Results

The engineered bacteria could produce GLP-1. It also significantly decreased the bodyweight and improved the glucose intolerance in the obese mice induced by HFD. Moreover, the strain also reduced the triglyceride (TG) in serum, protected liver, as well as decreased the intracellular TG in liver tissues of the obese mice. Furthermore, our results showed that the expressions of the genes including peroxisome proliferator-activated receptors α (PPARα) and its target genes were enhanced in liver tissues when mice treated with M-GLP-1. Finally, we found that the engineered strain markedly increased intestinal microbial diversity.

Conclusion

Our results suggested the genetically engineered bacteria that constitutively secreted GLP-1 could improve obesity and the mechanism may be related to promoting fatty acid oxidation and increasing intestinal microbial diversity of the obese mice.
Amentoflavone as an Ally in the Treatment of Cutaneous Leishmaniasis: Analysis of Its Antioxidant/Prooxidant Mechanisms
Authors: Rizk Yasmin Silva , Santos-Pereira Sandy , Gervazoni Luiza , Hardoim Daiana de Jesus , Cardoso Flávia de Oliveira , de Souza Celeste da Silva Freitas , Pelajo-Machado Marcelo , Carollo Carlos Alexandre , de Arruda Carla Cardozo Pinto , Almeida-Amaral Elmo Eduardo , Zaverucha-do-Valle Tânia , Calabrese Kátia da Silva
Published: February 2021

Treatment of leishmaniasis is a challenging subject. Although available, chemotherapy is limited, presenting toxicity and adverse effects. New drugs with antileishmanial activity are being investigated, such as antiparasitic compounds derived from plants. In this work, we investigated the antileishmanial activity of the biflavonoid amentoflavone on the protozoanLeishmania amazonensis. Although the antileishmanial activity of amentoflavone has already been reportedin vitro, the mechanisms involved in the parasite death, as well as its actionin vivo, remain unknown. Amentoflavone demonstrated activity on intracellular amastigotes in macrophages obtained from BALB/c mice (IC502.3 ± 0.93 μM). No cytotoxicity was observed and the selectivity index was estimated as greater than 10. Using BALB/c mice infected withL. amazonensiswe verified the effect of an intralesional treatment with amentoflavone (0.05 mg/kg/dose, in a total of 5 doses every 4 days). Parasite quantification demonstrated that amentoflavone reduced the parasite load in treated footpads (46.3% reduction by limiting dilution assay and 56.5% reduction by Real Time Polymerase Chain Reaction). Amentoflavone decreased the nitric oxide production in peritoneal macrophages obtained from treated animals. The treatment also increased the expression of ferritin and decreased iNOS expression at the site of infection. Furthemore, it increased the production of ROS in peritoneal macrophages infectedin vitro. The increase of ROSin vitro, associated with the reduction of NO and iNOS expressionin vivo, points to the antioxidant/prooxidant potential of amentoflavone, which may play an important role in the balance between inflammatory and anti-inflammatory patterns at the infection site. Taken together these results suggest that amentoflavone has the potential to be used in the treatment of cutaneous leishmaniasis, working as an ally in the control and development of the lesion.
Development and Evaluation of the Rapid and Sensitive RPA Assays for Specific Detection of Salmonella spp. in Food Samples
Authors: Zhao Liwei , Wang Jianchang , Sun Xiao Xia , Wang Jinfeng , Chen Zhimin , Xu Xiangdong , Dong Mengyuan , Guo Ya-nan , Wang Yuanyuan , Chen Pingping , Gao Weijuan , Geng Yunyun
Published: February 2021

Salmonella spp. is among the main foodborne pathogens which cause serious foodborne diseases. An isothermal real-time recombinase polymerase amplification (RPA) and lateral flow strip detection (LFS RPA) were used to detect Salmonella spp. targeting the conserved sequence of invasion protein A (invA). The Real-time RPA was performed in a portable florescence scanner at 39°C for 20 min. The LFS RPA was performed in an incubator block at 39°C for 15 min, under the same condition that the amplifications could be inspected by the naked eyes on the LFS within 5 min. The detection limit of Salmonella spp. DNA using real-time RPA was 1.1 × 101 fg, which was the same with real-time PCR but 10 times higher than that of LFS RPA assay. Moreover, the practicality of discovering Salmonella spp. was validated with artificially contaminated lamb, chicken, and broccoli samples. The analyzing time dropped from 60 min to proximately 5–12 min on the basis of the real-time and LFS RPA assays compared with the real-time PCR assay. Real-time and LFS RPA assays’ results were equally reliable. There was no cross-reactivity with other pathogens in both assays. In addition, the assays had good stability. All of these helped to show that the developed RPA assays were simple, rapid, sensitive, credible, and could be a potential point-of-need (PON) test required mere resources.
Early Detection of Checkpoint Inhibitor-Associated Myocarditis Using 68Ga-FAPI PET/CT
Authors: Finke Daniel , Heckmann Markus B. , Herpel Esther , Katus Hugo A. , Haberkorn Uwe , Leuschner Florian , Lehmann Lorenz H.
Published: February 2021

Objective: Checkpoint inhibitors (ICIs) have gained importance in recent years regarding the treatment of a variety of oncologic diseases. The possibilities of diagnosing cardiac adverse autoimmune effects of ICIs are still limited. We aimed to implement FAPI PET/CT imaging in detecting ICI-associated myocarditis.

Methods: In a retrospective study, FAPI PET/CT scans of 26 patients who received ICIs from 01/2017 to 10/2019 were analyzed. We compared tracer enrichment in the heart of patients without any signs of a cardiac disease (n = 23) to three patients with suspected ICI-associated myocarditis. To exclude any significant coronary heart disease, cardiac catherization was performed. All three patients' myocardial biopsies were examined for inflammatory cells.

Results: Three patients showed clinical manifestations of an ICI syndrome including myocarditis with elevated levels of hsTnT (175 pg/ml, 1,771 pg/ml, 157 pg/ml). Further cardiological assessments revealed ECG abnormalities, lymphocyte infiltration of the myocardium in the biopsies or wall motion abnormalities in echocardiography. These patients' FAPI PET/CTs showed cardiac enrichment of the marker which was less distinct or absent in patients receiving ICIs without any signs of immunological adverse effects or cardiac impairment (n = 23) [Median SUV myocarditis patients: 1.79 (IQR: 1.65, 1.85), median SUV non-myocarditis patients: 1.15 (IQR: 0.955, 1.52)].

Conclusions: Apart from the successful implementation of ICIs in oncological treatments, ICI-associated myocarditis is still a challenging adverse effect. FAPI PET/CT may be used in order to identify affected patients at an early stage. Moreover, when integrated into cancer stage diagnostics, it contributes to cardiac risk stratification besides biomarker, ECG and echocardiography.
Trends in Heart-Rate Variability Signal Analysis
Authors: Ishaque Syem , Khan Naimul , Krishnan Sri
Published: February 2021

Heart rate variability (HRV) is the rate of variability between each heartbeat with respect to time. It is used to analyse the Autonomic Nervous System (ANS), a control system used to modulate the body's unconscious action such as cardiac function, respiration, digestion, blood pressure, urination, and dilation/constriction of the pupil. This review article presents a summary and analysis of various research works that analyzed HRV associated with morbidity, pain, drowsiness, stress and exercise through signal processing and machine learning methods. The points of emphasis with regards to HRV research as well as the gaps associated with processes which can be improved to enhance the quality of the research have been discussed meticulously. Restricting the physiological signals to Electrocardiogram (ECG), Electrodermal activity (EDA), photoplethysmography (PPG), and respiration (RESP) analysis resulted in 25 articles which examined the cause and effect of increased/reduced HRV. Reduced HRV was generally associated with increased morbidity and stress. High HRV normally indicated good health, and in some instances, it could signify clinical events of interest such as drowsiness. Effective analysis of HRV during ambulatory and motion situations such as exercise, video gaming, and driving could have a significant impact toward improving social well-being. Detection of HRV in motion is far from perfect, situations involving exercise or driving reported accuracy as high as 85% and as low as 59%. HRV detection in motion can be improved further by harnessing the advancements in machine learning techniques.
Earthquake Shocks Around Delhi-NCR and the Adjoining Himalayan Front: A Seismotectonic Perspective
Authors: Khan Prosanta Kumar , Mohanty Sarada P. , Chakraborty Partha P. , Singh Rashmi
Published: February 2021

An increase in the number of earthquakes and subsequent clustering in northwest India, particularly around the Delhi-National Capital Region (NCR) and adjacent NW Himalayan front, provides a good opportunity to understand the underpinning tectonic controls and the likelihood of any large earthquake in the future. The 2001 Mw7.7 Bhuj, 2011 Mw6.9 Sikkim and 2015 Mw7.8 and 7.3 Nepal earthquakes (and 2004 Mw9.2 Sumatra event) are important in this context. We analyzed the seismicity around the Delhi-NCR and the adjoining Himalayan front, including event clustering and the spatio-temporal distribution of b-values, in the context of kinematics and the regional geodynamics. The overall moderate-to-low b-values, both in time and space, since 2016, provide information regarding an increase and subsequent stabilization of the stress field in the study area. The analysis led to the identification of (1) a structurally guided stress field in the region between the Kachchh and the NW Himalaya that coincides with the direction of Indian plate convergence and (2) frequent occurrences of earthquakes particularly in the Delhi, Kangra and Uttarkashi areas. We propose that faults in western Peninsular India, which pass through the margins of the Aravalli Range, the Marwar basin, and the isostatically over-compensated Indo-Gangetic Plains beneath the under-plated Indian lithosphere, act as stress guides; concentrating and increasing stress in regions of lithospheric flexure. This enhanced stress may trigger a large earthquake.
Exploring Class Enumeration in Bayesian Growth Mixture Modeling Based on Conditional Medians
Authors: Kim Seohyun , Tong Xin , Ke Zijun
Published: February 2021

Growth mixture modeling is a popular analytic tool for longitudinal data analysis. It detects latent groups based on the shapes of growth trajectories. Traditional growth mixture modeling assumes that outcome variables are normally distributed within each class. When data violate this normality assumption, however, it is well documented that the traditional growth mixture modeling mislead researchers in determining the number of latent classes as well as in estimating parameters. To address nonnormal data in growth mixture modeling, robust methods based on various nonnormal distributions have been developed. As a new robust approach, growth mixture modeling based on conditional medians has been proposed. In this article, we present the results of two simulation studies that evaluate the performance of the median-based growth mixture modeling in identifying the correct number of latent classes when data follow the normality assumption or have outliers. We also compared the performance of the median-based growth mixture modeling to the performance of traditional growth mixture modeling as well as robust growth mixture modeling based on t distributions. For identifying the number of latent classes in growth mixture modeling, the following three Bayesian model comparison criteria were considered: deviance information criterion, Watanabe-Akaike information criterion, and leave-one-out cross validation. For the median-based growth mixture modeling and t-based growth mixture modeling, our results showed that they maintained quite high model selection accuracy across all conditions in this study (ranged from 87 to 100%). In the traditional growth mixture modeling, however, the model selection accuracy was greatly influenced by the proportion of outliers. When sample size was 500 and the proportion of outliers was 0.05, the correct model was preferred in about 90% of the replications, but the percentage dropped to about 40% as the proportion of outliers increased to 0.15.
The Effect of Metformin on Self-Selected Exercise Intensity in Healthy, Lean Males: A Randomized, Crossover, Counterbalanced Trial
Authors: Pilmark Nanna Skytt , Petersen-Bønding Christina , Holm Nielse Frederich Rose , Johansen Mette Yun , Pedersen Bente Klarlund , Hansen Katrine Bagge , Karstoft Kristian
Published: February 2021

Introduction

In general, patients with type 2 diabetes have lower cardiorespiratory fitness levels and perform exercise at lower intensities compared to healthy controls. Since metformin (MET) has been shown to increase the rate of perceived exertion (RPE) during exercise with a fixed intensity, MET per se may reduce self-selected exercise intensity. The aim of this study was to assess the effect of MET on self-selected exercise intensity.

Methods

Healthy males were eligible for this crossover, counterbalanced study with two treatment periods: MET and placebo (PLA), each lasting 17 days. Treatment dose was gradually increased and reached 2 g/day on treatment day 9, and continued at that level for the rest of the treatment period. The two periods were performed in randomized order. Two experimental days (A+B) were conducted on Day 15 (A) and Day 17 (B) of each period, respectively. Day A consisted of an exercise bout with self-selected exercise intensity (equal to RPE = 14–15 on the Borg Scale). Day B consisted of an exercise bout with fixed intensity (70% of VO2peak). Oxygen consumption rate was assessed continuously during both exercise bouts.

Results

Fifteen males (age 23.7 ± 0.6 years, BMI 22.3 ± 2.0, VO2peak 3.5 ± 0.6 L/min) were included in the study. On Day B, RPE was higher in MET compared to PLA (14.8 ± 0.4 vs. 14.0 ± 0.3, P = 0.045). On Day A, no difference in self-selected exercise intensity measured by oxygen consumption rate (PLA 2.33 ± 0.09 L O2/min, MET 2.42 ± 0.10 L O2/min, P = 0.09) was seen between treatment periods.

Conclusions

Self-selected exercise intensity was not reduced by MET in healthy males, despite the fact that MET increased RPE during an exercise bout with fixed intensity.
Clinical Characteristics of Primary Hyperparathyroidism: 15-Year Experience of 457 Patients in a Single Center in China
Authors: Lin Xiaoyun , Fan Youben , Zhang Zhenlin , Yue Hua
Published: February 2021

Objective

Primary hyperparathyroidism (PHPT) is a common endocrine disorder of calcium metabolism. However, data concerning a large cohort of PHPT patients in the Chinese population are scarce. Thus, the objective of this study was to determine the general clinical signatures of 457 Chinese PHPT patients and explore the clinical characteristic differences between benign and malignant PHPT.

Methods

A single-center retrospective study was designed. Medical records between preoperation and postoperative follow-up, were assessed and statistical analysis of the clinical data was performed.

Results

Patients with PHPT aged 12–87 years, with a mean onset age of 56.16 ± 14.60 years, were included. Most patients (68.7%) in our center had symptomatic patterns described as bone pain (74.8%), urolithiasis (25.5%), fatigue (17.5%), and pathological fracture (13.1%), but an increasing tendency has been established in the proportion of patients with asymptomatic forms. Correlation analysis revealed that patients with higher serum levels of parathyroid hormone (PTH) and calcium presented higher serum levels of bone turnover markers (BTMs) and lower 25-hydroxy-vitamin D (25OHD) values (P<0.001). Gains in bone mineral density (BMD) at L1–4, the femoral neck and the total hip were observed 1–2 years after parathyroidectomy (9.6, 5.9, and 6.8%). Parathyroid carcinoma patients presented prominently higher serum PTH and calcium levels and BTMs and lower BMD at femoral neck and total hip than benign PHPT patients (P<0.05), while no significant differences in age, sex, and serum 25OHD concentration were observed between benign and malignant PHPT patients.

Conclusions

PHPT should be paid attention to in the patients with bone pain. While, BMD and BTMs can differentiate parathyroid carcinoma from parathyroid adenoma and hyperplasia to some extent. In addition, anti-osteoporosis drugs could be used when necessary to avoid hip fractures in patients with parathyroid carcinoma.
Familial Hyperparathyroidism
Authors: Blau Jenny E. , Simonds William F.
Published: February 2021

Regulation of the serum calcium level in humans is achieved by the endocrine action of parathyroid glands working in concert with vitamin D and a set of critical target cells and tissues including osteoblasts, osteoclasts, the renal tubules, and the small intestine. The parathyroid glands, small highly vascularized endocrine organs located behind the thyroid gland, secrete parathyroid hormone (PTH) into the systemic circulation as is needed to keep the serum free calcium concentration within a tight physiologic range. Primary hyperparathyroidism (HPT), a disorder of mineral metabolism usually associated with abnormally elevated serum calcium, results from the uncontrolled release of PTH from one or several abnormal parathyroid glands. Although in the vast majority of cases HPT is a sporadic disease, it can also present as a manifestation of a familial syndrome. Many benign and malignant sporadic parathyroid neoplasms are caused by loss-of-function mutations in tumor suppressor genes that were initially identified by the study of genomic DNA from patients who developed HPT as a manifestation of an inherited syndrome. Somatic and inherited mutations in certain proto-oncogenes can also result in the development of parathyroid tumors. The clinical and genetic investigation of familial HPT in kindreds found to lack germline variants in the already known HPT-predisposition genes represents a promising future direction for the discovery of novel genes relevant to parathyroid tumor development.
Current Understanding of the Etiology, Symptomatology, and Treatment Options in Premature Ovarian Insufficiency (POI)
Authors: Ishizuka Bunpei
Published: February 2021

Premature ovarian insufficiency (POI) occurs in at least 1% of all women and causes life-long health problems and psychological stress. Infertility caused by POI used to be considered absolute, with infertility treatment having little or no value. Generally, it has been thought that medicine can provide little service to these patients. The etiology of POI has been found to be genetic, chromosomal, and autoimmune. In addition, the increasing numbers of cancer survivors are candidates for iatrogenic POI, along with patients who have undergone ovarian surgery, especially laparoscopic surgery. Over 50 genes are known to be causally related to POI, and the disease course of some cases has been clarified, but in most cases, the genetic background remains unexplained, suggesting that more genes associated with the etiology of POI need to be discovered. Thus, in most cases, the genetic background of POI has not been clarified. Monosomy X is well known to manifest as Turner’s syndrome and is associated with primary amenorrhea, but recent studies have shown that some women with numerical abnormalities of the X chromosome can have spontaneous menstruation up to their twenties and thirties, and some even conceive. Hormone replacement therapy (HRT) is recommended for women with POI from many perspectives. It alleviates vasomotor and genitourinary symptoms and prevents bone loss and cardiovascular disease. POI has been reported to reduce quality of life and life expectancy, and HRT may help improve both. Most of the problems that may occur with HRT in postmenopausal women do not apply to women with POI; thus, in POI, HRT should be considered physiological replacement of estrogen (+progesterone). This review describes some new approaches to infertility treatment in POI patients that may lead to new treatments for POI, along with the development of more sensitive markers of secondary/preantral follicles and genetic diagnosis.
Vitamin D Association With Macrophage-Derived Cytokines in Polycystic Ovary Syndrome: An Enhanced Risk of COVID-19 Infection?
Authors: Moin Abu Saleh Md , Sathyapalan Thozhukat , Butler Alexandra E. , Atkin Stephen L.
Published: February 2021

Background

Women with polycystic ovary syndrome (PCOS) often have vitamin D deficiency, a known risk factor for severe COVID-19 disease. Alveolar macrophage-derived cytokines contribute to the inflammation underlying pulmonary disease in COVID-19. We sought to determine if basal macrophage activation, as a risk factor for COVID-19 infection, was present in PCOS and, if so, was further enhanced by vitamin D deficiency.

Methods

A cross-sectional study in 99 PCOS and 68 control women who presented sequentially. Plasma levels of a macrophage-derived cytokine panel were determined by Slow Off-rate Modified Aptamer (SOMA)-scan plasma protein measurement. Vitamin D was measured by tandem mass spectroscopy.

Results

Vitamin D was lower in PCOS women (p<0.0001) and correlated negatively with body mass index (BMI) in PCOS (r=0.28, p=0.0046). Basal macrophage activation markers CXCL5, CD163 and MMP9 were elevated, whilst protective CD200 was decreased (p<0.05); changes in these variables were related to, and fully accounted for, by BMI. PCOS and control women were then stratified according to vitamin D concentration. Vitamin D deficiency was associated with decreased CD80 and IFN-γ in PCOS and IL-12 in both groups (p<0.05). These factors, important in initiating and maintaining the immune response, were again accounted for by BMI.

Conclusion

Basal macrophage activation was higher in PCOS with macrophage changes related with increased infection risk associating with vitamin D; all changes were BMI dependent, suggesting that obese PCOS with vitamin D deficiency may be at greater risk of more severe COVID-19 infection, but that it is obesity-related rather than an independent PCOS factor.
Understanding People’s Relationship With Wildlife in Trans-Himalayan Folklore
Authors: Bhatia Saloni , Suryawanshi Kulbhushansingh , Redpath Stephen Mark , Namgail Stanzin , Mishra Charudutt
Published: February 2021

People’s views and values for wild animals are often a result of their experiences and traditional knowledge. Local folklore represents a resource that can enable an understanding of the nature of human-wildlife interactions, especially the underlying cultural values. Using archival searches and semi-structured interviews, we collected narratives about the ibex (Capra sibirica) (n = 69), and its predators, the wolf (Canis lupus) (n = 52) and the snow leopard (Panthera uncia) (n = 43), in Ladakh, India. We compared these stories to those of a mythical carnivore called seng ge or snow lion (n = 19), frequently referenced in local Tibetan Buddhist folklore and believed to share many of the traits commonly associated with snow leopards (except for livestock depredation). We then categorized the values along social-cultural, ecological and psychological dimensions. We found that the ibex was predominantly associated with utilitarianism and positive symbolism. Both snow leopard and wolf narratives referenced negative affective and negative symbolic values, though more frequently in the case of wolves. Snow leopard narratives largely focused on utilitarian and ecologistic values. In contrast, snow lion narratives were mostly associated with positive symbolism. Our results suggest that especially for snow leopards and wolves, any potentially positive symbolic associations appeared to be overwhelmed by negative sentiments because of their tendency to prey on livestock, unlike in the case of the snow lion. Since these values reflect people’s real and multifarious interactions with wildlife, we recommend paying greater attention to understanding the overlaps between natural and cultural heritage conservation to facilitate human-wildlife coexistence.
Regulatory Mechanisms Underlying the Differentiation of Neotenic Reproductives in Termites: Partial Release From Arrested Development
Authors: Oguchi Kohei , Maekawa Kiyoto , Miura Toru
Published: February 2021

Eusocial insects exhibit reproductive division of labor, in which only a part of colony members differentiates into reproductives. In termite colonies, the division of labors is performed among multiple types of individuals (i.e., castes), such as reproductives, workers, and soldiers to organize their society. Caste differentiation occurs according to extrinsic factors, such as social interactions, leading to developmental modifications during postembryonic development, and consequently, the caste ratio in a colony is appropriately coordinated. In particular, when the current reproductives die or become senescent, some immature individuals molt into supplementary reproductives, also known as “neotenics,” that take over the reproductive task in their natal colony. Neotenics exhibit variety of larval features, such as winglessness, and thus, immature individuals are suggested to differentiate by a partial release from arrested development, particularly in the reproductive organs. These neotenic features, which have long been assumed to develop via heterochronic regulation, provide us opportunities to understand the developmental mechanisms and evolutionary origin of the novel caste. This article overviews the accumulated data on the physiological and developmental mechanisms that regulate the neotenic differentiation in termites. Furthermore, the evolutionary trajectories leading to neotenic differentiation are discussed, namely the acquisition of a regulatory mechanism that enable the partial release from a developmentally arrested state.
Identification of the QTL-allele System Underlying Two High-Throughput Physiological Traits in the Chinese Soybean Germplasm Population
Authors: Wang Lei , Liu Fangdong , Hao Xiaoshuai , Wang Wubin , Xing Guangnan , Luo Jingjing , Zhou Guodong , He Jianbo , Gai Junyi
Published: February 2021

The QTL-allele system underlying two spectral reflectance physiological traits, NDVI (normalized difference vegetation index) and CHL (chlorophyll index), related to plant growth and yield was studied in the Chinese soybean germplasm population (CSGP), which consisted of 341 wild accessions (WA), farmer landraces (LR), and released cultivars (RC). Samples were evaluated in the Photosynthetic System II imaging platform at Nanjing Agricultural University. The NDVI and CHL data were obtained from hyperspectral reflectance images in a randomized incomplete block design experiment with two replicates. The NDVI and CHL ranged from 0.05–0.18 and 1.20–4.78, had averages of 0.11 and 3.57, and had heritabilities of 78.3% and 69.2%, respectively; the values of NDVI and CHL were both significantly higher in LR and RC than in WA. Using the RTM-GWAS (restricted two-stage multi-locus genome-wide association study) method, 38 and 32 QTLs with 89 and 82 alleles and 2–4 and 2–6 alleles per locus were identified for NDVI and CHL, respectively, which explained 48.36% and 51.35% of the phenotypic variation for NDVI and CHL, respectively. The QTL-allele matrices were established and separated into WA, LR, and RC submatrices. From WA to LR + RC, 4 alleles and 2 new loci emerged, and 1 allele was excluded for NDVI, whereas 6 alleles emerged, and no alleles were excluded, in LR + RC for CHL. Recombination was the major motivation of evolutionary differences. For NDVI and CHL, 39 and 32 candidate genes were annotated and assigned to GO groups, respectively, indicating a complex gene network. The NDVI and CHL were upstream traits that were relatively conservative in their genetic changes compared with those of downstream agronomic traits. High-throughput phenotyping integrated with RTM-GWAS provides an efficient procedure for studying the population genetics of traits.
Interpretable Machine Learning Reveals Dissimilarities Between Subtypes of Autism Spectrum Disorder
Authors: Garbulowski Mateusz , Smolinska Karolina , Diamanti Klev , Pan Gang , Maqbool Khurram , Feuk Lars , Komorowski Jan
Published: February 2021

Autism spectrum disorder (ASD) is a heterogeneous neuropsychiatric disorder with a complex genetic background. Analysis of altered molecular processes in ASD patients requires linear and nonlinear methods that provide interpretable solutions. Interpretable machine learning provides legible models that allow explaining biological mechanisms and support analysis of clinical subgroups. In this work, we investigated several case-control studies of gene expression measurements of ASD individuals. We constructed a rule-based learning model from three independent datasets that we further visualized as a nonlinear gene-gene co-predictive network. To find dissimilarities between ASD subtypes, we scrutinized a topological structure of the network and estimated a centrality distance. Our analysis revealed that autism is the most severe subtype of ASD, while pervasive developmental disorder-not otherwise specified and Asperger syndrome are closely related and milder ASD subtypes. Furthermore, we analyzed the most important ASD-related features that were described in terms of gene co-predictors. Among others, we found a strong co-predictive mechanism between EMC4 and TMEM30A, which may suggest a co-regulation between these genes. The present study demonstrates the potential of applying interpretable machine learning in bioinformatics analyses. Although the proposed methodology was designed for transcriptomics data, it can be applied to other omics disciplines.
Genetic Parameters and Genome-Wide Association Studies of Eight Longevity Traits Representing Either Full or Partial Lifespan in Chinese Holsteins
Authors: Zhang Hailiang , Liu Aoxing , Wang Yachun , Luo Hanpeng , Yan Xinyi , Guo Xiangyu , Li Xiang , Liu Lin , Su Guosheng
Published: February 2021

Due to the complexity of longevity trait in dairy cattle, two groups of trait definitions are widely used to measure longevity, either covering the full lifespan or representing only a part of it to achieve an early selection. Usually, only one group of longevity definition is used in breeding program for one population, and genetic studies on the comparisons of two groups of trait definitions are scarce. Based on the data of eight traits well representing the both groups of trait definitions, the current study investigated genetic parameters and genetic architectures of longevity in Holsteins. Heritabilities and correlations of eight longevity traits were estimated using single-trait and multi-trait animal models, with the data from 103,479 cows. Among the cows with phenotypes, 2,630 cows were genotyped with the 150K-SNP panel. A single-trait fixed and random Circuitous Probability Unification model was performed to detect candidate genes for eight longevity traits. Generally, all eight longevity traits had low heritabilities, ranging from 0.038 for total productive life and herd life to 0.090 for days from the first calving to the end of first lactation or culling. High genetic correlations were observed among the traits within the same definition group: from 0.946 to 0.997 for three traits reflecting full lifespan and from 0.666 to 0.997 for five traits reflecting partial productive life. Genetic correlations between two groups of traits ranged from 0.648 to 0.963, and increased gradually with the extension of lactations number regarding the partial productive life traits. A total of 55 SNPs located on 25 chromosomes were found genome-wide significantly associated with longevity, in which 12 SNPs were associated with more than one trait, even across traits of different definition groups. This is the first study to investigate the genetic architecture of longevity representing both full and the partial lifespan simultaneously, which will assist the selection of an appropriate trait definition for genetic improvement of longevity. Because of high genetic correlations with the full lifespan traits and higher heritability, the partial productive life trait measured as the days from the first calving to the end of the third lactation or culling could be a good alternative for early selection on longevity. The candidate genes identified by this study, such as RPRM, GRIA3, GTF2H5, CA5A, CACNA2D1, FGF10, and DNAJA3, could be used to pinpoint causative mutations for longevity and further benefit the genomic improvement of longevity in dairy cattle.
Induction of Therapeutic Protection in an HPV16-Associated Mouse Tumor Model Through Targeting the Human Papillomavirus-16 E5 Protein to Dendritic Cells
Authors: Badillo-Godinez Oscar , Pedroza-Saavedra Adolfo , Valverde-Garduño Veronica , Bermudez-Morales Victor , Maldonado-Gama Minerva , Leon-Letelier Ricardo , Bonifaz Laura C. , Esquivel-Guadarrama Fernando , Gutierrez-Xicotencatl Lourdes
Published: February 2021

HPV E5 is an oncoprotein mainly expressed in premalignant lesions, which makes it an important target for a vaccine to prevent or cure cervical cancer (CC). In this study, we evaluated whether E5 targeted to DEC-205, present in dendritic cells (DCs), could induce a therapeutic protection against HPV16-induced tumor cells in a mouse model. The HPV-16 E5 (16E5) protein was cross-linked to a monoclonal antibody (mAb) specific to mouse DEC-205 (anti-DEC-205:16E5) or to an isotype control mAb (isotype:16E5). Rotavirus VP6 was cross-linked to the mouse anti-DEC-205 mAb (anti-DEC-205:VP6) as a non-specific antigen control. BALB/c mice were inoculated subcutaneously (s.c.) with the 16E5-expressing BMK-16/myc tumor cells, and 7 and 14 days later the mice were immunized s.c. with the conjugates, free 16E5 or PBS in the presence of adjuvant. Tumor growth was monitored to evaluate protection. A strong protective immune response against the tumor cells was induced when the mice were inoculated with the anti-DEC-205:16E5 conjugate, since 70% of the mice controlled the tumor growth and survived, whereas the remaining 30% developed tumors and died by day 72. In contrast, 100% of the mice in the control groups died by day 30. The anti-DEC-205:16E5 conjugate was found to induce 16E5-specific memory T cells, with a Th1/Th17 profile. Both CD4+ and CD8+ T cells contributed to the observed protection. Finally, treating mice that had developed tumors with an anti-PD-1 mAb, delayed the tumor growth for more than 20 days. These results show that targeting 16E5 to DEC-205, alone or combined with an immune checkpoint blockade, could be a promising protocol for the treatment of the early stages of HPV-associated cancer.
Dietary Inclusion of Black Soldier Fly (Hermetia Illucens) Larvae Meal and Paste Improved Gut Health but Had Minor Effects on Skin Mucus Proteome and Immune Response in Atlantic Salmon (Salmo Salar)
Authors: Weththasinghe Pabodha , Lagos Leidy , Cortés Marcos , Hansen Jon Øvrum , Øverland Margareth
Published: February 2021

The present study investigated effects of dietary inclusion of black soldier fly larvae (BSFL) (Hermetia illucens) meal and paste on gut health, plasma biochemical parameters, immune response and skin mucus proteome in pre-smolt Atlantic salmon (Salmo salar). The seven-week experiment consisted of seven experimental diets: a control diet based on fishmeal and plant protein (Control-1); three BSFL meal diets, substituting 6.25% (6.25IM), 12.5% (12.5IM) and 25% (25IM) of protein; two BSFL paste diets, substituting 3.7% (3.7IP) and 6.7% (6.7IP) of protein and an extra control diet with 0.88% of formic acid (Control-2). The 6.25IM diet reduced enterocyte steatosis in pyloric caeca, improved distal intestine histology, and reduced IgM in distal intestine. The fish fed 12.5IM diet reduced enterocyte steatosis in pyloric caeca, improved distal intestine histology, had a higher plasma lysozyme content compared to 6.25IM, and tend to increase phagocytic activity in head-kidney macrophages-like cells. On the other hand, 25IM diet improved distal intestine histology, but showed mild-moderate enterocyte steatosis in pyloric caeca, increased IFNγ and reduced IgM in distal intestine. In the case of BSFL paste diets, 3.7IP diet caused mild inflammatory changes in distal intestine, although it reduced enterocyte steatosis in pyloric caeca. The 6.7IP diet reduced enterocyte steatosis in pyloric caeca and improved distal intestine histology. Increasing level of BSFL meal in the diet linearly decreased plasma C-reactive protein, whereas increasing level of BSFL paste linearly increased plasma antioxidant capacity. Dietary inclusion of BSFL meal and paste had minor effects on the expression profile of proteins in skin mucus and no effects on immune markers in splenocytes. BSFL meal showed no negative effect on liver and muscle health as indicated by plasma alanine aminotranseferase, asparate aminotransferase and creatine kinase. The present study showed that replacing conventional protein sources with low to moderate levels of BSFL meal (6.25% and 12.5%) or paste (3.7% and 6.7%) reduced enterocyte steatosis in pyloric caeca, while replacing up to 25% with BSFL meal or 6.7% with paste improved distal intestine histology. Further, dietary inclusion of BSFL meal and paste had minor effects on skin mucus proteome and immune response in Atlantic salmon.
Hijacking Factor H for Complement Immune Evasion
Authors: Moore Sara R. , Menon Smrithi S. , Cortes Claudio , Ferreira Viviana P.
Published: February 2021

The complement system is an essential player in innate and adaptive immunity. It consists of three pathways (alternative, classical, and lectin) that initiate either spontaneously (alternative) or in response to danger (all pathways). Complement leads to numerous outcomes detrimental to invaders, including direct killing by formation of the pore-forming membrane attack complex, recruitment of immune cells to sites of invasion, facilitation of phagocytosis, and enhancement of cellular immune responses. Pathogens must overcome the complement system to survive in the host. A common strategy used by pathogens to evade complement is hijacking host complement regulators. Complement regulators prevent attack of host cells and include a collection of membrane-bound and fluid phase proteins. Factor H (FH), a fluid phase complement regulatory protein, controls the alternative pathway (AP) both in the fluid phase of the human body and on cell surfaces. In order to prevent complement activation and amplification on host cells and tissues, FH recognizes host cell-specific polyanionic markers in combination with complement C3 fragments. FH suppresses AP complement-mediated attack by accelerating decay of convertases and by helping to inactivate C3 fragments on host cells. Pathogens, most of which do not have polyanionic markers, are not recognized by FH. Numerous pathogens, including certain bacteria, viruses, protozoa, helminths, and fungi, can recruit FH to protect themselves against host-mediated complement attack, using either specific receptors and/or molecular mimicry to appear more like a host cell. This review will explore pathogen complement evasion mechanisms involving FH recruitment with an emphasis on: (a) characterizing the structural properties and expression patterns of pathogen FH binding proteins, as well as other strategies used by pathogens to capture FH; (b) classifying domains of FH important in pathogen interaction; and (c) discussing existing and potential treatment strategies that target FH interactions with pathogens. Overall, many pathogens use FH to avoid complement attack and appreciating the commonalities across these diverse microorganisms deepens the understanding of complement in microbiology.
Therapeutic Targeting of Neutrophil Extracellular Traps Improves Primary and Secondary Intention Wound Healing in Mice
Authors: Heuer Annika , Stiel Carolin , Elrod Julia , Königs Ingo , Vincent Deirdre , Schlegel Patrick , Trochimiuk Magdalena , Appl Birgit , Reinshagen Konrad , Raluy Laia Pagerols , Boettcher Michael
Published: February 2021

Background

Neutrophils are the first responders in wound healing after injury that mediate pro- and anti-inflammatory activities i.a. through the formation of extracellular traps (NETs). However, excessive NETs presence in wound tissue can cause local hyperinflammation and -coagulation resulting in delayed wound healing. To improve wound healing, we aimed to examine the role of NETs and DNase1 on primary and secondary wound healing.

Methods

The study included 93 C57BL/6 mice, with 3 different genotypes: wildtype, Pad4-, and DNase1-Knockout (KO). Pad4-KO mice show limited NETs formation, while DNase1-KO mice cannot disintegrate them. All 3 genotypes were included in (1) a laparotomy group and (2) a thermal injury group. Animals in both groups either received DNase1 or a vehicle i.p. post wound induction and wound assessment and euthanasia were conducted. Laparotomy and burn scars were assessed using the stony brook scar evaluation scale and modified Yeong scale respectively. Tissue was analyzed histologically using H&E staining. Ly6g, Collagen I and III, SMA, and Fibrinogen were visualized and neutrophils activation (NE, MPO) and NETs (H3cit) formation assessed.

Results

All animals survived with no complications. DNase1 treatment led to a significantly improved scar appearance in both groups, which was also seen in Pad4-KO mice. In the laparotomy group DNase1 improved collagen deposition and fibrin concentration was significantly reduced by DNase1 treatment. Markers of neutrophil activation were significantly reduced in the treatment and Pad4-KO group. In the thermal injury group wound closure time was significantly reduced after DNase1 treatment and in the Pad4-KO group. Even though inflammation remained high in the thermal injury model over time, neutrophil activation and NETs formation were significantly reduced by DNase1 treatment compared to controls.

Discussion

Primary and secondary intention wound healing is improved by targeting NETs through DNase1 treatment or genetic KO, as assessed by wound closure time and scar appearances. Additionally, wound stability was not affected by DNASE treatment. The results suggest that overall wound healing is accelerated and DNase1 appears to be a promising option to reduce scar formation; which should be evaluated in humans.
Pin1 Promotes NLRP3 Inflammasome Activation by Phosphorylation of p38 MAPK Pathway in Septic Shock
Authors: Dong Ruijie , Xue Zhenyi , Fan Guangyue , Zhang Na , Wang Chengzhi , Li Guangliang , Da Yurong
Published: February 2021

Pin1 is the only known peptidyl-prolyl cis-trans isomerase (PPIase) that can specifically recognize and isomerize the phosphorylated Serine/Threonine-Proline (pSer/Thr-Pro) motif, change the conformation of proteins through protein phosphorylation, thus regulate various cellular processes in the body. Pin1 plays an important role in cancer, Alzheimer’s disease, and autoimmune diseases. However, the specific mechanism of Pin1 regulation in LPS-induced septic shock is unclear. Here, we found that lack of Pin1 reduced shock mortality and organ damage in mice, and NLRP3 inflammasome activation also was reduced in this process. We further confirmed that Pin1 can affect the expression of NLRP3, ASC, Caspase1, and this process can be regulated through the p38 MAPK pathway. We analyzed that p38 MAPK signaling pathway was highly expressed in septic shock and showed a positive correlation with Pin1 in the Gene Expression Omnibus database. We found that Pin1 could affect the phosphorylation of p38 MAPK, have no obvious difference in extracellular signal-regulated kinases (ERK) and Jun-amino-terminal kinase (JNK) signaling. We further found that Pin1 and p-p38 MAPK interacted, but not directly. In addition, Pin1 deficiency inhibited the cleavage of gasdermin D (GSDMD) and promoted the death of macrophages with LPS treatment, and reduced secretion of inflammatory cytokines including IL-1β and IL-18. In general, our results suggest that Pin1 regulates the NLRP3 inflammasome activation by p38 MAPK signaling pathway in macrophages. Thus, Pin1 may be a potential target for the treatment of inflammatory diseases such as septic shock.
Insights Into the Involvement of Circular RNAs in Autoimmune Diseases
Authors: Zhai Xingyu , Zhang Yunfei , Xin Shuyu , Cao Pengfei , Lu Jianhong
Published: February 2021

Circular RNAs (circRNAs) are single-stranded, endogenous, non-coding RNA (ncRNA) molecules formed by the backsplicing of messenger RNA (mRNA) precursors and have covalently closed circular structures without 5′-end caps and 3′-end polyadenylation [poly(A)] tails. CircRNAs are characterized by abundant species, stable structures, conserved sequences, cell- or tissue-specific expression, and widespread and stable presence in many organisms. Therefore, circRNAs can be used as biomarkers for the prediction, diagnosis, and treatment of a variety of diseases. Autoimmune diseases (AIDs) are caused by defects in immune tolerance or abnormal immune regulation, which leads to damage to host organs. Due to the complexity of the pathophysiological processes of AIDs, clinical therapeutics have been suboptimal. The emergence of circRNAs sheds new light on the treatment of AIDs. In particular, circRNAs mainly participate in the occurrence and development of AIDs by sponging targets. This review systematically explains the formation, function, mechanism, and characteristics of circRNAs in the context of AIDs. With a deeper understanding of the pathophysiological functions of circRNAs in the pathogenesis of AIDs, circRNAs may become reasonable, accurate, and effective biomarkers for the diagnosis and treatment of AIDs in the future.