bluuebunny/crossref_metadata_2025 huggingface dataset:
SSTP1, a Host Defense Peptide, Exploits the Immunomodulatory IL6 Pathway to Induce Apoptosis in Cancer Cells
Authors: Gopalakrishnan Shyla , Uma Soumya Krishnan , Mohan Gayathri , Mohan Amrutha , Shanmugam Geetha , Kumar Vineeth T. V. , J Sreekumar , Chandrika Sivakumar K. , Vasudevan Dileep , Nori Sai Ravi Chandra , Sathi Shijulal Nelson , George Sanil , Maliekal Tessy Thomas
Published: November 2021

While the immunomodulatory pathways initiated in immune cells contribute to therapeutic response, their activation in cancer cells play a role in cancer progression. Also, many of the aberrantly expressed immunomodulators on cancer cells are considered as therapeutic targets. Here, we introduce host defense peptide (HDP), a known immuomodulator, as a therapeutic agent to target them. The cationic host defense peptides (HDPs), an integral part of the innate immune system, possess membranolytic activity, which imparts antimicrobial and antitumor efficacy to it. They act as immunomodulators by activating the immune cells. Though their antimicrobial function has been recently reassigned to immunoregulation, their antitumor activity is still attributed to its membranolytic activity. This membrane pore formation ability, which is proportional to the concentration of the peptide, also leads to side effects like hemolysis, limiting their therapeutic application. So, despite the identification of a variety of anticancer HDPs, their clinical utility is limited. Though HDPs are shown to exert the immunomodulatory activity through specific membrane targets on immune cells, their targets on cancer cells are unknown. We show that SSTP1, a novel HDP identified by shotgun cloning, binds to the active IL6/IL6Rα/gp130 complex on cancer cells, rearranging the active site residues. In contrast to the IL6 blockers inhibiting JAK/STAT activity, SSTP1 shifts the proliferative IL6/JAK/STAT signaling to the apoptotic IL6/JNK/AP1 pathway. In IL6Rα-overexpressing cancer cells, SSTP1 induces apoptosis at low concentration through JNK pathway, without causing significant membrane disruption. We highlight the importance of immunomodulatory pathways in cancer apoptosis, apart from its established role in immune cell regulation and cancer cell proliferation. Our study suggests that identification of the membrane targets for the promising anticancer HDPs might lead to the identification of new drugs for targeted therapy.
How to Prepare Spectral Flow Cytometry Datasets for High Dimensional Data Analysis: A Practical Workflow
Authors: den Braanker Hannah , Bongenaar Margot , Lubberts Erik
Published: November 2021

Spectral flow cytometry is an upcoming technique that allows for extensive multicolor panels, enabling simultaneous investigation of a large number of cellular parameters in a single experiment. To fully explore the resulting high-dimensional single cell datasets, high-dimensional analysis is needed, as opposed to the common practice of manual gating in conventional flow cytometry. However, preparing spectral flow cytometry data for high-dimensional analysis can be challenging, because of several technical aspects. In this article, we will give insight into the pitfalls of handling spectral flow cytometry datasets. Moreover, we will describe a workflow to properly prepare spectral flow cytometry data for high dimensional analysis and tools for integrating new data at later time points. Using healthy control data as example, we will go through the concepts of quality control, data cleaning, transformation, correcting for batch effects, subsampling, clustering and data integration. This methods article provides an R-based pipeline based on previously published packages, that are readily available to use. Application of our workflow will aid spectral flow cytometry users to obtain valid and reproducible results.
Pre-Existing Cross-Reactive Antibody Responses Do Not Significantly Impact Inactivated COVID-19 Vaccine-Induced Neutralization
Authors: Wang Jin , Guo Cheng , Cai Lin , Liao Conghui , Yi Huaimin , Li Qianlin , Hu Huan , Deng Qiang , Lu Yuying , Guo Zhongmin , Chen Zeliang , Lu Jiahai
Published: November 2021

Recent exposure to seasonal coronaviruses (sCoVs) may stimulate cross-reactive antibody responses against severe acute respiratory syndrome CoV 2 (SARS-CoV-2). However, previous studies have produced divergent results regarding protective or damaging immunity induced by prior sCoV exposure. It remains unknown whether pre-existing humoral immunity plays a role in vaccine-induced neutralization and antibody responses. In this study, we collected 36 paired sera samples from 36 healthy volunteers before and after immunization with inactivated whole-virion SARS-CoV-2 vaccines for COVID-19, and analyzed the distribution and intensity of pre-existing antibody responses at the epitope level pre-vaccination as well as the relationship between pre-existing sCoV immunity and vaccine-induced neutralization. We observed large amounts of pre-existing cross-reactive antibodies in the conserved regions among sCoVs, especially the S2 subunit. Excep t for a few peptides, the IgG and IgM fluorescence intensities against S, M and N peptides did not differ significantly between pre-vaccination and post-vaccination sera of vaccinees who developed a neutralization inhibition rate (%inhibition) <40 and %inhibition ≥40 after two doses of the COVID-19 vaccine. Participants with strong and weak pre-existing cross-reactive antibodies (strong pre-CRA; weak pre-CRA) had similar %inhibition pre-vaccination (10.9% ± 2.9% vs. 12.0% ± 2.2%, P=0.990) and post-vaccination (43.8% ± 25.1% vs. 44.6% ± 21.5%, P=0.997). Overall, the strong pre-CRA group did not show a significantly greater increase in antibody responses to the S protein linear peptides post-vaccination compared with the weak pre-CRA group. Therefore, we found no evidence for a significant impact of pre-existing antibody responses on inactivated vaccine-induced neutralization and antibody responses. Our research provides an important basis for inactivated SARS-CoV-2 vaccine use in the context of high sCoV seroprevalence.
Melanocortin 1 Receptor Deficiency in Hematopoietic Cells Promotes the Expansion of Inflammatory Leukocytes in Atherosclerotic Mice
Authors: Kadiri James J. , Tadayon Sina , Thapa Keshav , Suominen Anni , Hollmén Maija , Rinne Petteri
Published: November 2021

Melanocortin receptor 1 (MC1-R) is expressed in leukocytes, where it mediates anti-inflammatory actions. We have previously observed that global deficiency of MC1-R signaling perturbs cholesterol homeostasis, increases arterial leukocyte accumulation and accelerates atherosclerosis in apolipoprotein E knockout (Apoe-/-) mice. Since various cell types besides leukocytes express MC1-R, we aimed at investigating the specific contribution of leukocyte MC1-R to the development of atherosclerosis. For this purpose, male Apoe-/-mice were irradiated, received bone marrow from either female Apoe-/-mice or MC1-R deficient Apoe-/-mice (Apoe-/-Mc1re/e) and were analyzed for tissue leukocyte profiles and atherosclerotic plaque phenotype. Hematopoietic MC1-R deficiency significantly elevated total leukocyte counts in the blood, bone marrow and spleen, an effect that was amplified by feeding mice a cholesterol-rich diet. The increased leukocyte counts were largely attributable to expanded lymphocyte populations, particularly CD4+T cells. Furthermore, the number of monocytes was elevated in Apoe-/-Mc1re/echimeric mice and it paralleled an increase in hematopoietic stem cell count in the bone marrow. Despite robust leukocytosis, atherosclerotic plaque size and composition as well as arterial leukocyte counts were unaffected by MC1-R deficiency. To address this discrepancy, we performed anin vivohoming assay and found that MC1-R deficient CD4+T cells and monocytes were preferentially entering the spleen rather than homing in peri-aortic lymph nodes. This was mechanistically associated with compromised chemokine receptor 5 (CCR5)-dependent migration of CD4+T cells and a defect in the recycling capacity of CCR5. Finally, our data demonstrate for the first time that CD4+T cells also express MC1-R. In conclusion, MC1-R regulates hematopoietic stem cell proliferation and tissue leukocyte counts but its deficiency in leukocytes impairs cell migrationviaa CCR5-dependent mechanism.
CCR5 Receptor Occupancy Analysis Reveals Increased Peripheral Blood CCR5+CD4+ T Cells Following Treatment With the Anti-CCR5 Antibody Leronlimab
Authors: Chang Xiao L. , Wu Helen L. , Webb Gabriela M. , Tiwary Meenakshi , Hughes Colette , Reed Jason S. , Hwang Joseph , Waytashek Courtney , Boyle Carla , Pessoa Cleiton , Sylwester Andrew W. , Morrow David , Belica Karina , Fischer Miranda , Kelly Scott , Pourhassan Nader , Bochart Rachele M. , Smedley Jeremy , Recknor Christopher P. , Hansen Scott G. , Sacha Jonah B.
Published: November 2021

CCR5 plays a central role in infectious disease, host defense, and cancer progression, thereby making it an ideal target for therapeutic development. Notably, CCR5 is the major HIV entry co-receptor, where its surface density correlates with HIV plasma viremia. The level of CCR5 receptor occupancy (RO) achieved by a CCR5-targeting therapeutic is therefore a critical predictor of its efficacy. However, current methods to measure CCR5 RO lack sensitivity, resulting in high background and overcalculation. Here, we report on two independent, flow cytometric methods of calculating CCR5 RO using the anti-CCR5 antibody, Leronlimab. We show that both methods led to comparable CCR5 RO values, with low background on untreated CCR5+CD4+ T cells and sensitive measurements of occupancy on both blood and tissue-resident CD4+ T cells that correlated longitudinally with plasma concentrations in Leronlimab-treated macaques. Using these assays, we found that Leronlimab stabilized cell surface CCR5, leading to an increase in the levels of circulating and tissue-resident CCR5+CD4+ T cells in vivo in Leronlimab-treated macaques. Weekly Leronlimab treatment in a chronically SIV-infected macaque led to increased CCR5+CD4+ T cells levels and fully suppressed plasma viremia, both concomitant with full CCR5 RO on peripheral blood CD4+ T cells, demonstrating that CCR5+CD4+ T cells were protected from viral replication by Leronlimab binding. Finally, we extended these results to Leronlimab-treated humans and found that weekly 700 mg Leronlimab led to complete CCR5 RO on peripheral blood CD4+ T cells and a statistically significant increase in CCR5+CD4+ T cells in peripheral blood. Collectively, these results establish two RO calculation methods for longitudinal monitoring of anti-CCR5 therapeutic antibody blockade efficacy in both macaques and humans, demonstrate that CCR5+CD4+ T cell levels temporarily increase with Leronlimab treatment, and facilitate future detailed investigations into the immunological impacts of CCR5 inhibition in multiple pathophysiological processes.
Prevalence of Methicillin-Resistant Staphylococcus Species Among Filarial Lymphedema Patients in Ahanta West District of Ghana
Authors: Wireko Solomon , Asiedu Samuel Opoku , Kini Priscilla , Aglomasa Bill Clinton , Amewu Emmanuel Kobla Atsu , Asiedu Ebenezer , Osei-Akoto Freda , Boahen Kennedy Gyau , Obiri-Yeboah Dorcas , Amato Katherine Ryan , Kwarteng Alexander
Published: November 2021

Background

Filarial pathologies such as lymphedema may be associated with complications such as chronic non-healing wounds. Nonetheless, the role of bacterial population colonizing the lymphedematous legs has been posited to worsen the conditions of those living with the infection. These bacteria are usually composed of staphylococcal species partly because they are commensals. Thus, this present study sought to type the methicillin-resistant Staphylococcus aureus (MRSA) prevalence among individuals presenting with filarial lymphedema, particularly as MRSA tends to affect treatments options.

Methods

We recruited individuals (n = 321) with stages I–VII of lymphedema in a cross-sectional study in the Ahanta West district of the Western Region of Ghana. Swabs from lymphedematous limb ulcers, pus, and cutaneous surfaces were cultured using standard culture-based techniques. The culture isolates were later identified using Matrix-assisted Laser Desorption/Ionization Time of Flight (MALDI-TOF) mass spectrometry.

Results

A total of 192 Staphylococci species were isolated, with an overall prevalence of 39.7% (95% CI: 35%–44%; N = 483). S. hominis was the most prevalent species (23.95%), followed by S. haemolyticus (20.83%), S. epidermidis (15.10%), S. aureus (10.41%), and S. saprophyticus (9.32%). The remaining 20.34% were distributed among S. wanneri, S. sciuri, S. pasteuri, S. xylosus, S. simulans, S. cohnii, S. caprae, S. lugdunensis, and S. capitis. MRSA, containing mecA gene, was detected in 21 out of 31 Staphylococci isolates tested, with an overall prevalence of 68% (95% CI: 51%–84%). In addition, a virulent gene, Panton–Valentine leukocidin (PVL), which is usually associated with S. aureus, was detected in 20/31 (64.5%) S. aureus in the study.

Conclusion

These results suggest that MRSA species may pose a challenge to the treatment of filarial lymphedema with antibiotics particularly, as doxycycline is currently being piloted in some endemic areas to treat the infection. Thus, intensive antimicrobial resistance surveillance should be conducted in endemic areas by health authorities to forestall the dilemma of multidrug resistance not only against lymphatic filariasis (LF) infection but other diseases.
Public Perceptions of the Ocean: Lessons for Marine Conservation From a Global Research Review
Authors: Jefferson Rebecca , McKinley Emma , Griffin Holly , Nimmo Alison , Fletcher Stephen
Published: November 2021

Insights into how public audiences perceive and relate to the ocean are pivotal to successful societal engagement and integration of human dimensions in marine conservation. Perceptions research explores how people understand, value or engage with an environment, issue or management response, and in the context of marine conservation, provides crucial insights for the development, delivery and evaluation of effective conservation interventions. This review of 349 peer reviewed studies explores the current state of research into public perceptions of the ocean. Using an extensive data extraction process, the review examined the geographical spread of ocean perceptions research, the topics of research focus, and the methods used. The review identifies gaps in current research activity, and opportunities for maximizing the impact of ocean perceptions research in current and future marine conservation. Key findings of the review include evidence that the rate of research is growing, with 59% of studies published between 2013–2017. However, a clear geographical skew is evident, with the majority of studies being undertaken in higher income countries. Furthermore, there has been a tendency to focus on charismatic species, or issues and spaces of clear human-ocean interaction (e.g., beaches), highlighting significant gaps in the topics and themes currently covered by ocean perceptions research. An additional gap identified is the underutilization of available methods to explore the complexity of marine perceptions. In a bid to address these gaps, the paper concludes with a series of recommendations designed to stimulate and support ocean perceptions research as being fundamental to the success of marine conservation efforts. While ocean perceptions research may be young, the growing research effort evidenced in this review gives optimism for realizing its potential and continuing to improve the integration of ocean perceptions research effectively into marine conservation.
When Imagery and Physical Sampling Work Together: Toward an Integrative Methodology of Deep-Sea Image-Based Megafauna Identification
Authors: Hanafi-Portier Mélissa , Samadi Sarah , Corbari Laure , Chan Tin-Yam , Chen Wei-Jen , Chen Jhen-Nien , Lee Mao-Ying , Mah Christopher , Saucède Thomas , Borremans Catherine , Olu Karine
Published: November 2021

Imagery has become a key tool for assessing deep-sea megafaunal biodiversity, historically based on physical sampling using fishing gears. Image datasets provide quantitative and repeatable estimates, small-scale spatial patterns and habitat descriptions. However, taxon identification from images is challenging and often relies on morphotypes without considering a taxonomic framework. Taxon identification is particularly challenging in regions where the fauna is poorly known and/or highly diverse. Furthermore, the efficiency of imagery and physical sampling may vary among habitat types. Here, we compared biodiversity metrics (alpha and gamma diversity, composition) based on physical sampling (dredging and trawling) and towed-camera still images (1) along the upper continental slope of Papua New Guinea (sedimented slope with wood-falls, a canyon and cold seeps), and (2) on the outer slopes of the volcanic islands of Mayotte, dominated by hard bottoms. The comparison was done on selected taxa (Pisces, Crustacea, Echinoidea, and Asteroidea), which are good candidates for identification from images. Taxonomic identification ranks obtained for the images varied among these taxa (e.g., family/order for fishes, genus for echinoderms). At these ranks, imagery provided a higher taxonomic richness for hard-bottom and complex habitats, partially explained by the poor performance of trawling on these rough substrates. For the same reason, the gamma diversity of Pisces and Crustacea was also higher from images, but no difference was observed for echinoderms. On soft bottoms, physical sampling provided higher alpha and gamma diversity for fishes and crustaceans, but these differences tended to decrease for crustaceans identified to the species/morphospecies level from images. Physical sampling and imagery were selective against some taxa (e.g., according to size or behavior), therefore providing different facets of biodiversity. In addition, specimens collected at a larger scale facilitated megafauna identification from images. Based on this complementary approach, we propose a robust methodology for image-based faunal identification relying on a taxonomic framework, from collaborative work with taxonomists. An original outcome of this collaborative work is the creation of identification keys dedicated specifically to in situ images and which take into account the state of the taxonomic knowledge for the explored sites.
Improvement in Tear Ferning Patterns of Sheep Tears After Addition of Various Electrolyte Solutions
Authors: Fagehi Raied , El-Hiti Gamal A. , Alqarni Bayh M. , Alanazi Mana A. , Masmali Ali M. , Almubrad Turki
Published: November 2021

Objective: This study aimed to improve the tear ferning (TF) patterns in the sheep tears after the addition of various electrolyte solutions in different proportions.

Animal Studied: Sheep were located at a small farm in the outskirts of Riyadh, Saudi Arabia. The sheep had no ocular disorders or diseases, and none of the female sheep were pregnant.

Methods: Tear samples (20 μl) were collected from the right eyes of seven healthy sheep (five female sheep and two male sheep; age 7–36 months with an average of 17.0 ± 10.3 months). A tear sample (1 μl) from each sheep was dried on a microscopic glass slide at 22°C and <40% humidity. The TF patterns were graded based on the five-point grading scale in 0.1 increments. Homogenous mixtures were prepared by mixing tears from each sheep (0.5 μl) with various electrolyte solutions in different proportions (1:1, 1:2, 1:4, 1:6, 1:8, and 1:10). A sample of each mixture (1 μl) was dried on a glass slide, and the TF patterns for each mixture were observed, recorded, graded, and compared with those of the corresponding pure sheep tears. In addition, each sheep tear sample (0.5 μl) was diluted with pure water (0.5 μl) and the TF images were recorded and graded to test the dilution effect.

Results: General improvement was noted in TF grades after the addition of electrolyte solutions, ranging from 1.7–1.4 to 1.3–0.3 regardless of the ratio between the electrolyte solutions and sheep tears within the mixture. TF grades of sheep tear samples improved significantly after adding different volumes of calcium chloride solution. Similar improvements in TF grades were observed when magnesium chloride hexahydrate and sodium dihydrogen phosphate solutions were used as the electrolytes. Some improvements in the TF grades occurred with the addition of potassium chloride to sheep tear samples. There was little improvement in TF grades after the addition of sodium chloride solution.

Conclusion: Tear ferning grades of sheep tear samples improved when mixed with a number of electrolyte solutions at different volumes, in particular with calcium chloride or magnesium chloride solutions. Some improvements in TF grades were seen with sodium dihydrogen phosphate or potassium chloride solution added as the electrolyte. Clearly, divalent electrolytes lead to a greater improvement in TF grades of sheep tear samples as compared with sodium dihydrogen phosphate or monovalent electrolytes.
Predictive Performance of Placental Protein 13 for Screening Preeclampsia in the First Trimester: A Systematic Review and Meta-Analysis
Authors: Wu Yifan , Liu Yang , Ding Yiling
Published: November 2021

Preeclampsia is a pregnancy-specific syndrome that affects maternal and neonatal mortality. Several serum biomarkers can be used to predict preeclampsia. Among these proteins, placental protein 13 (PP13) has received progressively more interest in recent studies. The decrease in PP13 expression is one of the earliest signs for the development of preeclampsia and has shown its predictive performance for preeclampsia. In this meta-analysis, we collected 17 observational studies with 40,474 pregnant women. The overall sensitivity of PP13 to predict preeclampsia was 0.62 [95% confidence interval (CI) = 0.49–0.74], the specificity was 0.84 (95%CI = 0.81–0.86), and the diagnostic odds ratio was nine (95%CI = 5–15). The area under the curve for summary receiver operating characteristic was 0.84. We then chose the early-onset preeclampsia as a subgroup. The sensitivity of early-onset subgroup was 0.63 (95%CI = 0.58–0.76), the specificity was 0.85 (95%CI = 0.82–0.88), and the diagnostic odds ratio was 10 (95%CI = 6–18). The findings of our meta-analysis indicate that PP13 may be an effective serum biomarker for the predictive screening of preeclampsia. Nonetheless, large prospective cohort studies and randomized controlled trials are expected to uncover its application in clinical practice. The heterogeneity of the original trials may limit the clinical application of PP13.

Systematic Review Registration:https://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=188948 The meta-analysis was registered in PROSPERO (CRD42020188948).
Is There Limited Utility for Lifestyle Recommendations for Diabetes Prevention Among Overweight or Obese Depressed Patients?
Authors: Mainous Arch G. , Rooks Benjamin J. , Orlando Frank A.
Published: November 2021

Background: Lifestyle interventions like diet and exercise are commonly recommended for diabetes prevention, but it is unclear if depression modifies the likelihood of adherence. We evaluated the relationship between high depressive symptomatology and adherence to lifestyle interventions among patients with pre-diabetes.

Methods: We conducted an analysis of the nationally representative National Health and Nutrition Examination Survey (NHANES) 2017–2018. Adults, aged ≥18 years old who were overweight or obese (BMI ≥25) and had diagnosed or undiagnosed pre-diabetes (HbA1c 5.7–6.4) were included. Depressive symptomatology was classified by the Patient Health Questionniare-9 (PHQ-9). We used self-reported adherence to physician suggested lifestyle changes of diet and exercise.

Results: In this nationally representative survey of overweight or obese adults with pre-diabetes, 14.8% also have high depressive symptomatology. In unadjusted analyses, an interaction was observed with high depressive symptomatology acting as an effect modifier for adherence to exercise oriented interventions among patients with diagnosed pre-diabetes (p = 0.027). In logistic regressions, adjusting for age, sex, race, outpatient medical care in the past 12 months, and obesity, among patients with diagnosed pre-diabetes, depressed patients were less likely to attempt to exercise more (OR = 0.31; 95% CI: 0.10, 0.94) and no association between high depressive symptomatology and attempting to lose weight was observed (OR = 0.45; 95% CI: 0.14, 1.42).

Conclusions: The findings of this nationally representative study of US adults, high depressive symptomatology decreases the likelihood of adherence to exercise based lifestyle recommendations among patients with diagnosed pre-diabetes.
The Role of circRNAs in the Diagnosis of Colorectal Cancer: A Meta-Analysis
Authors: Li Ru-Dong , Guan Min , Zhou Zhe , Dong Shu-Xiao , Liu Qian
Published: November 2021

Background: A novel category of non-coding circular RNAs (circRNAs) has been found to be dysregulated in colorectal cancer (CRC) and significantly contribute to its progression. However, the feasibility of using circRNA as a diagnostic biomarker for CRC remains to be elucidated. Herein, we aimed to comprehensively collect and analyze evidence regarding the potential application of circRNAs as diagnostic indicators for CRC.

Methods: A comprehensive retrieval of relevant studies dating from January, 2015 to December 2020, was carried out in PubMed, Cochrane Library, and Web of Science. Data regarding the diagnostic accuracy of circRNA for CRC, including sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and area under the curve (AUC), were obtained from the included studies. Quality assessment of diagnostic accuracy studies (QUADAS-2) was used to assess the methodological quality of each study. Statistical analysis was performed using STAT and RevMan software.

Results: Eighteen studies, involving a total of 2021 individuals, were included in the present meta-analysis. The specimens examined included tissue, serum, and plasma. The pooled sensitivity, specificity, DOR, PLR, NLR, and AUC, with a 95% confidence interval (CI), of circRNAs in the diagnosis of CRC were 0.78 (0.71–0.83), 0.73 (0.68–0.78), 9.68 (6.76–13.85), 2.92 (2.45–3.50), 0.30 (0.23–0.39), and 0.81 (0.78–0.85), respectively. Subgroup analysis showed that the upregulated circRNAs in the tissue or plasma possessed relatively higher diagnostic values for CRC than the downregulated circRNAs. There was no significant difference between the tissue-derived and non-tissue-derived circRNA subgroups.

Conclusion: circRNA may be used as a diagnostic biomarker for CRC because of its relatively high diagnostic accuracy in distinguishing CRC patients from normal controls. Further prospective studies are needed to identify more representative circRNAs as diagnostic markers for CRC.
Foot-and-Mouth Disease Virus 3C Protease Antagonizes Interferon Signaling and C142T Substitution Attenuates the FMD Virus
Authors: Ekanayaka Pathum , Shin Sung Ho , Weeratunga Prasanna , Lee Hyuncheol , Kim Tae-Hwan , Chathuranga Kiramage , Subasinghe Ashan , Park Jong-Hyeon , Lee Jong-Soo
Published: November 2021

3C protease (3Cpro), a chymotrypsin-like cysteine protease encoded by the foot-and-mouth disease virus (FMDV), plays an essential role in processing the FMDV P1 polyprotein into individual viral capsid proteins in FMDV replication. Previously, it has been shown that 3Cpro is involved in the blockage of the host type-I interferon (IFN) responses by FMDV. However, the underlying mechanisms are poorly understood. Here, we demonstrated that the protease activity of 3Cpro contributed to the degradation of RIG-I and MDA5, key cytosolic sensors of the type-I IFN signaling cascade in proteasome, lysosome and caspase-independent manner. And also, we examined the degradation ability on RIG-I and MDA5 of wild-type FMDV 3Cpro and FMDV 3Cpro C142T mutant which is known to significantly alter the enzymatic activity of 3Cpro. The results showed that the FMDV 3Cpro C142T mutant dramatically reduce the degradation of RIG-I and MDA5 due to weakened protease activity. Thus, the protease activity of FMDV 3Cpro governs its RIG-I and MDA5 degradation ability and subsequent negative regulation of the type-I IFN signaling. Importantly, FMD viruses harboring 3Cpro C142T mutant showed the moderate attenuation of FMDV in a pig model. In conclusion, our results indicate that a novel mechanism evolved by FMDV 3Cpro to counteract host type-I IFN responses and a rational approach to virus attenuation that could be utilized for future vaccine development.
The FtcR-Like Protein ActR in Azorhizobium caulinodans ORS571 Is Involved in Bacterial Motility and Symbiosis With the Host Plant
Authors: Sun Li , Wang Dandan , Yin Zhiqiu , Zhang Chengsheng , Bible Amber , Xie Zhihong
Published: November 2021

Bacterial signal transduction pathways are important for a variety of adaptive responses to environment, such as two-component systems (TCSs). In this paper, we reported the characterization of a transcriptional regulator in Azorhizobium caulinodans ORS571, ActR, with an N-terminal receiver domain and one C-terminal OmpR/PhoB-type DNA binding domain. Sequence analysis showed that ActR shared a high similarity with FtcR regulator of Brucella melitensis 16M known to be involved in flagellar regulation. The structural gene of this regulator was largely distributed in Alphaproteobacteria, in particular in Rhizobiales and Rhodobacterales, and was located within clusters of genes related to motility functions. Furthermore, we studied the biological function of ActR in A. caulinodans grown at the free-living state or in association with Sesbania rostrata by constructing actR gene deletion mutant. In the free-living state, the bacterial flagellum and motility ability were entirely deleted, the expression of flagellar genes was downregulated; and the exopolysaccharide production, biofilm formation, and cell flocculation decreased significantly compared with those of the wild-type strain. In the symbiotic state, ΔactR mutant strain showed weakly competitive colonization and nodulation on the host plant. These results illustrated that FtcR-like regulator in A. caulinodans is involved in flagellar biosynthesis and provide bacteria with an effective competitive nodulation for symbiosis. These findings improved our knowledge of FtcR-like transcriptional regulator in A. caulinodans.
Acidic Microenvironment Determines Antibiotic Susceptibility and Biofilm Formation of Pseudomonas aeruginosa
Authors: Lin Qiao , Pilewski Joseph M. , Di Y. Peter
Published: November 2021

Pseudomonas aeruginosais the most prevalent bacterial species that contribute to cystic fibrosis (CF) respiratory failure. The impaired function of CF transmembrane conductance regulator leads to abnormal epithelial Cl–/HCO3–transport and acidification of airway surface liquid. However, it remains unclear why the CF lung is most commonly infected byPseudomonas aeruginosaversus other pathogens. We carried out studies to investigate if lower pH helpsPseudomonas aeruginosaadapt and thrive in the CF-like acidic lung environment. Our results revealed thatPseudomonas aeruginosagenerally forms more biofilm, induces antibiotic resistance faster in acidic conditions, and can be reversed by returning the acidic environment to physiologically neutral conditions.Pseudomonas aeruginosaappears to be highly adaptive to the CF-like acidic pH environment. By studying the effects of an acidic environment on bacterial response, we may provide a new therapeutic option in preventing chronicPseudomonas aeruginosainfection and colonization.
The Temperature-Dependent Expression of the High-Pathogenicity Island Encoding Piscibactin in Vibrionaceae Results From the Combined Effect of the AraC-Like Transcriptional Activator PbtA and Regulatory Factors From the Recipient Genome
Authors: Lages Marta A. , Lemos Manuel L. , Balado Miguel
Published: November 2021

The high-pathogenicity island irp-HPI is widespread among Vibrionaceae encoding the piscibactin siderophore system. The expression of piscibactin genes in the fish pathogen Vibrio anguillarum is favored by low temperatures. However, information about the regulatory mechanism behind irp-HPI gene expression is scarce. In this work, in-frame deletion mutants of V. anguillarum defective in the putative regulators AraC1 and AraC2, encoded by irp-HPI, and in the global regulators H-NS and ToxRS, were constructed and their effect on irp-HPI gene expression was analyzed at 15 and 25°C. The results proved that only AraC1 (renamed as PbtA) is required for the expression of piscibactin biosynthesis and transport genes. PbtA inactivation led to an inability to grow under iron restriction, a loss of the outer membrane piscibactin transporter FrpA, and a significant decrease in virulence for fish. Inactivation of the global repressor H-NS, which is involved in silencing of horizontally acquired genes, also resulted in a lower transcriptional activity of the frpA promoter. Deletion of toxR-S, however, did not have a relevant effect on the expression of the irp-HPI genes. Therefore, while irp-HPI would not be part of the ToxR regulon, H-NS must exert an indirect effect on piscibactin gene expression. Thus, the temperature-dependent expression of the piscibactin-encoding pathogenicity island described in V. anguillarum is the result of the combined effect of the AraC-like transcriptional activator PbtA, harbored in the island, and other not yet defined regulator(s) encoded by the genome. Furthermore, different expression patterns were detected within different irp-HPI evolutionary lineages, which supports a long-term evolution of the irp-HPI genomic island within Vibrionaceae. The mechanism that modulates piscibactin gene expression could also be involved in global regulation of virulence factors in response to temperature changes.
Risk Factors and Prevalence of mcr-1-Positive Escherichia coli in Fecal Carriages Among Community Children in Southern Taiwan
Authors: Wu Pin-Chieh , Cheng Ming-Fang , Chen Wan-Ling , Hung Wan-Yu , Wang Jiun-Ling , Hung Chih-Hsin
Published: November 2021

Colistin is the last resort antimicrobial for treating multidrug-resistant gram-negative bacterial infections. The plasmid-mediated colistin resistance gene, mcr-1, crucially influences colistin’s resistance transmission. Human fecal carriages of mcr-1-positive Escherichia coli (E. coli) were detected in many regions worldwide; however, only a few studies have focused on children. Therefore, we identified the prevalence and risk factors of mcr-1-positive E. coli in fecal carriages among community children in Southern Taiwan. In this study, 510 stool samples were collected from April 2016 to August 2019 from the pediatric department at a medical center in Southern Taiwan. These samples were collected within 3 days after admission and were all screened for the presence of the mcr-1 gene. Diet habits, travel history, pet contact, and medical history were also obtained from participants to analyze the risk factors of their fecal carriages to mcr-1-positive E. coli. Antimicrobial susceptibility testing was determined using the VITEK 2 system and the broth microdilution test. Twelve mcr-1-positive E. coli. were isolated from 2.4% of the fecal samples. Through multivariate analysis, frequent chicken consumption (at least 3 times per week) had a significantly positive association with the presence of mcr-1-positive E. coli in fecal carriages (adjust odds ratio 6.60, 95% confidence interval1.58– 27.62, p = 0.033). Additionally, multidrug resistance was more common in mcr-1-positive E. coli. (75.0% vs. 39.5%, p = 0.031) than in non-mcr-1-positive Escherichia coli. Furthermore, the percentage of extraintestinal pathogenic E. coli in mcr-1-positive isolates was 83.3%. Some multi-locus sequence types in our mcr-1-positive E. coli were also similar to those isolated from food animals in the literature. The prevalence of fecal carriages of mcr-1-positive E. coli was low among community children in Southern Taiwan. Our data shows that chicken consumption with a higher frequency increases the risk of mcr-1-positive E. coli. in fecal carriages.
Multiomics Study Reveals Enterococcus and Subdoligranulum Are Beneficial to Necrotizing Enterocolitis
Authors: Lin Hao , Guo Qingqing , Ran Yun , Lin Lijian , Chen Pengcheng , He Jianquan , Chen Ye , Wen Jianbo
Published: November 2021

Necrotizing enterocolitis (NEC) is a life-threatening disease for premature infants with low body weight. Due to its fragile gut microbiome and successful treatment of fecal microbiota transplantation (FMT) for intestinal disease, we aimed to reveal the multiple-omics changes after FMT and/or sulperazone treatment. In this study, 2-week-old newborn rabbits were used to simulate the NEC model and grouped into healthy control, NEC, sulperazone treatment, FTM treatment, and FMT and sulperazone combination treatment. We evaluated the intestinal pathology and survival to define the benefit from each treatment and performed microbiome and transcriptome analysis to reveal the changes in microcosmic level, which could be helpful to understand the pathogenesis of NEC and develop new strategy. We found NEC rabbits benefit more from the combination of FMT and sulperazone treatment. Combination treatment reverses a lot of microorganisms dysregulated by NEC and showed the most similar transcript profiler with healthy control. Moreover, a combination of FMT and sulperazone significantly prolonged the survival of NEC rabbits. Function enrichment showed that metabolism and viral life cycle are the most significant changes in NEC. FMT is a common therapy method for NEC. Meanwhile, in the severe situation of NEC with intestinal infection, the first therapy strategy is preferred the third-generation cephalosporin, among which sulperazone is used widely and the effect is remarkable. So, we used sulperazone to treat the rabbits with the NEC. In this research, we aim to explore the different effects on NEC between FMT and sulperazone as well as the combination. Considering the microbiome and transcriptome result, we make a conclusion that the Enterococcus and Subdoligranulum benefits NEC by influencing the bacterial phages and butyrate production, respectively.
Antitheilerial Activity of the Anticancer Histone Deacetylase Inhibitors
Authors: Barman Madhumanti , Kamble Sonam , Roy Sonti , Bhandari Vasundhra , Singothu Siva , Dandasena Debabrata , Suresh Akash , Sharma Paresh
Published: November 2021

The apicomplexan parasite, Theileria annulata, is the most prevalent hemoprotozoan in livestock, causing significant economic losses worldwide. It is essential to develop new and improved therapeutics, as current control measures are compromised by the development of resistance against the only available antitheilerial drug, buparvaquone (BPQ). Histone deacetylase inhibitors (HDACi) were shown to treat cancer effectively and revealed in vitro antiparasitic activity against apicomplexan parasites such as Plasmodium and Toxoplasma. In this study, we investigated the antitheilerial activity of the four anti-cancer HDACi (vorinostat, romidepsin, belinostat, and panobinostat) against the schizont stage of T. annulata parasites. All four HDACi showed potent activity and increased hyperacetylation of the histone-4 protein. However, based on the low host cell cytotoxicity and IC50 values, vorinostat (0.103 μM) and belinostat (0.069 μM) were the most effective showing antiparasitic activity. The parasite-specific activities of the HDACi (vorinostat and belinostat) were evaluated by western blotting using parasite-specific antibodies and in silico analysis. Both vorinostat and belinostat reduced the Theileria infected cell viability by downregulating anti-apoptotic proteins and mitochondrial dysfunction, leading to caspase-dependent cell apoptosis. The HDACi caused irreversible and antiproliferative effects on the Theileria infected cell lines. Our results collectively showed that vorinostat and belinostat could be used as an alternative therapy for treating Theileria parasites.
Heterologous Expression of Two Malate Transporters From an Oleaginous Fungus Mucor circinelloides Improved the Lipid Accumulation in Mucor lusitanicus
Authors: Wang Xiuwen , Mohamed Hassan , Bao Yonghong , Wu Chen , Shi Wenyue , Song Yuanda , Yang Junhuan
Published: November 2021

The fungus,Mucor lusitanicus, is of great interest for microbial lipids, because of its ability to accumulate intracellular lipid using various carbon sources. The biosynthesis of fatty acid requires the reducing power NADPH, and acetyl-CoA, which is produced by the cleavage of citrate in cytosol. In this study, we employed different strategies to increase lipid accumulation in the low lipid-producing fungi via metabolic engineering technology. Hence, we constructed the engineered strain ofM. lusitanicusCBS 277.49 by using malate transporter (mt) and 2-oxoglutarate: malate antiporter (sodit)fromM. circinelloidesWJ11. In comparison with the control strain, the lipid content of the overexpressed strains ofmtandsoditgenes were increased by 24.6 and 33.8%, respectively. These results showed thatmtandsoditcan affect the distribution of malate in mitochondria and cytosol, provide the substrates for the synthesis of citrate in the mitochondria, and accelerate the transfer of citrate from mitochondria to cytosol, which could play a significant regulatory role in fatty acid synthesis leading to lipids over accumulation.
Dynamically Accumulating Homologous Recombination Deficiency Score Served as an Important Prognosis Factor in High-Grade Serous Ovarian Cancer
Authors: Su Rongjia , Liu Yuan , Wu Xiaomei , Xiang Jiangdong , Xi Xiaowei
Published: November 2021

Background: The homologous recombination (HR) pathway defects in cancers induced abrogation of cell cycle checkpoints, resulting in the accumulation of DNA damage, mitotic catastrophe, and cell death. Cancers with BRCA1/2 loss and other accumulation of similar genomic scars resulting in HRD displayed increased sensitivity to chemotherapy. Our study aimed to explore HRD score genetic mechanisms and subsequent clinical outcomes in human cancers, especially ovarian cancer.

Methods: We analyzed TCGA data of HRD score in 33 cancer types and evaluated HRD score distribution and difference among tumor stages and between primary and recurrent tumor tissues. A weighted gene co-expression network analysis (WGCNA) was performed to identify highly correlated genes representing essential modules contributing to the HRD score and distinguish the hub genes and significant pathways. We verified HRD status predicting roles in patients’ overall survival (OS) with univariate and multivariate Cox regression analyses and built the predicting model for patient survival.

Results: We found that the HRD score increased with the rise in tumor stage, except for stage IV. The HRD score tended to grow up higher in recurrent tumor tissue than in their primary counterparts (p = 0.083). We constructed 15 co-expression modules with WGCNA, identified co-expressed genes and pathways impacting the HRD score, and concluded that the HRD score was tightly associated with tumor cells replication and proliferation. A combined HRD score ≥42 was associated with shorter OS in 33 cancer types (HR = 1.010, 95% CI: 1.008–1.011, p < 0.001). However, in ovarian cancer, which ranked the highest HRD score among other cancers, HRD ≥42 cohort was significantly associated with longer OS (HR = 0.99, 95% CI: 0.98–0.99, p < 0.0001). We also built a predicting model for 3 and 5 years survival in HGSC patients.

Conclusion: A quantitative HRD score representing the accumulated genomic scars was dynamically increasing in proliferating tumor cells since the HRD score was tightly correlated to tumor cell division and replication. We highlighted HRD score biomarker role in prognosis prediction of ovarian cancer.
Ad-Apoptin-hTERTp-E1a Regulates Autophagy Through the AMPK-mTOR-eIF4F Signaling Axis to Reduce Drug Resistance of MCF-7/ADR Cells
Authors: Li Yaru , Zhu Yilong , Han Jicheng , Fang Jinbo , Xiu Zhiru , Li Shanzhi , Li Wenjie , Yang Xia , Jin Ningyi , Sun Lili , Li Xiao , Li Yiquan
Published: November 2021

Ad-VT (Ad-Apoptin-hTERTp-E1a) is a type of oncolytic adenovirus with dual specific tumor cell death ability. It can effectively induce cell death of breast cancer cells and has better effect when used in combination with chemotherapy drugs. However, it has not been reported whether Ad-VT reduces the resistance of breast cancer cells to chemotherapy drugs. The purpose of this study is to investigate the effect of Ad-VT on drug resistance of Adriamycin-resistant breast cancer cells. For this, the effects of different doses of Ad-VT on the resistance of breast cancer cells to Adriamycin were analyzed using qualitative and quantitative experiments in vitro and in vivo. The Ad-VT can reduce the resistance of MCF-7/ADR to adriamycin, which is caused by the reduction of MRP1 protein level in MCF-7/ADR cells after treatment with Ad-VT, and MRP1 can be interfered with by autophagy inhibitors. Subsequently, the upstream signal of autophagy was analyzed and it was found that Ad-VT reduced the resistance of cells to doxorubicin by reducing the level of mTOR, and then the analysis of the upstream and downstream proteins of mTOR found that Ad-VT increased the sensitivity of MCF-7/ADR cells to adriamycin by activating AMPK-mTOR-eIF4F signaling axis. Ad-VT can not only significantly induce cell death in MCF-7/ADR cells, but also improved their sensitivity to Adriamycin. Therefore, the combination of Ad-VT and chemotherapy drugs may become a new strategy for the treatment of breast cancer in overcoming Adriamycin resistance.
Single-Molecule Microscopy Meets Molecular Dynamics Simulations for Characterizing the Molecular Action of Proteins on DNA and in Liquid Condensates
Authors: Kamagata Kiyoto
Published: November 2021

DNA-binding proteins trigger various cellular functions and determine cellular fate. Before performing functions such as transcription, DNA repair, and DNA recombination, DNA-binding proteins need to search for and bind to their target sites in genomic DNA. Under evolutionary pressure, DNA-binding proteins have gained accurate and rapid target search and binding strategies that combine three-dimensional search in solution, one-dimensional sliding along DNA, hopping and jumping on DNA, and intersegmental transfer between two DNA molecules. These mechanisms can be achieved by the unique structural and dynamic properties of these proteins. Single-molecule fluorescence microscopy and molecular dynamics simulations have characterized the molecular actions of DNA-binding proteins in detail. Furthermore, these methodologies have begun to characterize liquid condensates induced by liquid-liquid phase separation, e.g., molecular principles of uptake and dynamics in droplets. This review discusses the molecular action of DNA-binding proteins on DNA and in liquid condensate based on the latest studies that mainly focused on the model protein p53.