bluuebunny/crossref_metadata_2025 huggingface dataset:
A Stem Cell Surge During Thyroid Regeneration
Authors: Ma Risheng , Morshed Syed A. , Latif Rauf , Davies Terry F.
Published: January 2021

Background

Many tissues, including the thyroid, contain resident (adult) stem cells that are responsible for regeneration and repair after injury. The mechanisms of thyroid regeneration and the role of thyroid stem cells and thyroid progenitor cells in this process are not well understood. We have now used a new mouse thyroid injury model to gain insight into this phenomenon.

Methods

Tamoxifen induced TPO-Cre mice (TPOCreER2) were crossed with inducible Diphtheria Toxin Receptor homozygous mice (ROSA26iDTR) to give rise to TPOCreER2/iDTR mice, allowing for the Cre-mediated expression of the DTR and rendering TPO expressing thyroid cells highly sensitive to diphtheria toxin (DT). This model of TPOCreER2/iDTR mice allowed us to study the repair/regeneration of thyroid follicles after diphtheria toxin induced thyroid damage by measuring serum thyroid hormones and cell fate.

Results

In TPOCreER2/iDTR double transgenic mice we observed severe thyroid damage as early as 2 weeks after initiating intraperitoneal DT injections. There was marked thyroid tissue apoptosis and a ~50% drop in serum T4 levels (from 5.86 to 2.43 ug/dl) and a corresponding increase in serum TSH (from 0.18 to 8.39 ng/dl). In addition, there was a ~50% decrease in transcription of thyroid specific genes (thyroglobulin, TSH receptor, and sodium-iodide symporter). After suspending the DT administration, the thyroid rapidly recovered over a 4-week period during which we observed a transient surge in stem cell marker expression (including Oct4, Nanog, Sox2, and Rex1). In addition, cells immunostaining with stem cell markers Oct4 and Ssea-1 were found in clusters around new thyroid follicles in TPOCreER2/iDTR double transgenic mice. Furthermore, the presence of clusters of thyroid progenitor cells was also identified by Pax8 staining of thyroglobulin negative cells. This recovery of the injured gland was followed by a rapid and sequential restoration of thyroid function.

Conclusion

These data demonstrate that a new model of thyroid cell damage induced by DT can be used to study the mobilization of resident adult stem cells. Furthermore, the model clearly demonstrates the involvement of both stem and progenitor cells in the in vivo regeneration of the thyroid after severe destruction.
Variations in the Mitochondrial Genome of a Goldfish-Like Hybrid [Koi Carp (♀) × Blunt Snout Bream (♂)] Indicate Paternal Leakage
Authors: Wang Yude , Sun Wenzhen , Gu Qianhong , Yao Jiajun , Tan Huifang , Huang Xu , Qin Qinbo , Tao Min , Zhang Chun , Liu Shaojun
Published: January 2021

Previously, a homodiploid goldfish-like fish (2n = 100; GF-L) was spontaneously generated by self-crossing a homodiploid red crucian carp-like fish (2n = 100; RCC-L), which was in turn produced via the distant hybridization of female koi carp (Cyprinus carpio haematopterus, KOC, 2n = 100) and male blunt snout bream (Megalobrama amblycephala, BSB, 2n = 48). The phenotypes and genotypes of RCC-L and GF-L differed from those of the parental species but were similar to diploid red crucian carp (2n = 100; RCC) and goldfish (2n = 100; GF), respectively. We sequenced the complete mitochondrial DNAs (mtDNAs) of the KOC, BSB, RCC-L, GF-L, and subsequent generations produced by self-crossing [the self-mating offspring of RCC-L (RCC-L-F2) to the self-mating offspring of RCC-L-F2 (RCC-L-F3) and the self-mating offspring of GF-L (GF-L-F2)]. Paternal mtDNA fragments were stably embedded in the mtDNAs of both lineages, forming chimeric DNA fragments. In addition to these chimeras, several nucleotide positions in the RCC-L and GF-L lineages differed from the parental bases, and were instead identical with RCC and GF, respectively. Moreover, RCC-L and GF-L mtDNA organization and nucleotide composition were more similar to those of RCC and GF, respectively, compared to parental mtDNA. Finally, phylogenetic analyses indicated that RCC-L and GF-L clustered with RCC and GF, not with the parental species. The molecular dating time shows that the divergence time of KOC and GF was about 21.26 Mya [95% highest posterior density (HPD): 24.41–16.67 Mya], which fell within the period of recent. The heritable chimeric DNA fragments and mutant loci identified in the mtDNA of the RCC-L and GF-L lineages provided important evidence that hybridizations might lead to changes in the mtDNA and the subsequent generation of new lineages. Our findings also demonstrated for the first time that the paternal mtDNA was transmitted into the mtDNA of homodiploid lineages (RCC-L and GF-L), which provided evidence that paternal DNA plays a role in inherited mtDNA. These evolutionary analyses in mtDNA suggest that GF might have diverged from RCC after RCC diverged from koi carp.
Distinct Immunophenotypes of T Cells in Bronchoalveolar Lavage Fluid From Leukemia Patients With Immune Checkpoint Inhibitors-Related Pulmonary Complications
Authors: Kim Sang T. , Sheshadri Ajay , Shannon Vickie , Kontoyiannis Dimitrios P. , Kantarjian Hagop , Garcia-Manero Guillermo , Ravandi Farhad , Im Jin S. , Boddu Prajwal , Bashoura Lara , Balachandran Diwakar D. , Evans Scott E. , Faiz Saadia , Ruiz Vazquez Wilfredo , Divenko Margarita , Mathur Rohit , Tippen Samantha P. , Gumbs Curtis , Neelapu Sattva S. , Naing Aung , Wang Linghua , Diab Adi , Futreal Andrew , Nurieva Roza , Daver Naval
Published: January 2021

Patients with acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS) treated with immune checkpoint inhibitors (ICIs) are at risk of pneumonitis as well as pneumonia (combined henceforth as ICI-related pulmonary complications). Little is known about the cellular and molecular mechanisms underlying ICI-related pulmonary complications. We characterized lymphocytes from bronchoalveolar lavage (BAL) fluid and peripheral blood from seven AML/MDS patients with pulmonary symptoms after ICI-based therapy (ICI group) and four ICI-naïve AML/MDS patients with extracellular bacterial or fungal pneumonias (controls). BAL T cells in the ICI group were clonally expanded, and BAL IFNγ+ IL-17− CD8+ T and CXCR3+ CCR6+ Th17/Th1 cells were enriched in the ICI group. Our data suggest that these cells may play a critical role in the pathophysiology of ICI-related pulmonary complications. Understanding of these cell populations may also provide predictive and diagnostic biomarkers of ICI-related pulmonary complications, eventually enabling differentiation of pneumonitis from pneumonia in AML/MDS patients receiving ICI-based therapies.
Understanding Early-Life Adaptive Immunity to Guide Interventions for Pediatric Health
Authors: Semmes Eleanor C. , Chen Jui-Lin , Goswami Ria , Burt Trevor D. , Permar Sallie R. , Fouda Genevieve G.
Published: January 2021

Infants are capable of mounting adaptive immune responses, but their ability to develop long-lasting immunity is limited. Understanding the particularities of the neonatal adaptive immune system is therefore critical to guide the design of immune-based interventions, including vaccines, in early life. In this review, we present a thorough summary of T cell, B cell, and humoral immunity in early life and discuss infant adaptive immune responses to pathogens and vaccines. We focus on the differences between T and B cell responses in early life and adulthood, which hinder the generation of long-lasting adaptive immune responses in infancy. We discuss how knowledge of early life adaptive immunity can be applied when developing vaccine strategies for this unique period of immune development. In particular, we emphasize the use of novel vaccine adjuvants and optimization of infant vaccine schedules. We also propose integrating maternal and infant immunization strategies to ensure optimal neonatal protection through passive maternal antibody transfer while avoiding hindering infant vaccine responses. Our review highlights that the infant adaptive immune system is functionally distinct and uniquely regulated compared to later life and that these particularities should be considered when designing interventions to promote pediatric health.
Nonmicrobial Activation of TLRs Controls Intestinal Growth, Wound Repair, and Radioprotection
Authors: Stenson William F. , Ciorba Matthew A.
Published: January 2021

TLRs, key components of the innate immune system, recognize microbial molecules. However, TLRs also recognize some nonmicrobial molecules. In particular, TLR2 and TLR4 recognize hyaluronic acid, a glycosaminoglycan in the extracellular matrix. In neonatal mice endogenous hyaluronic acid binding to TLR4 drives normal intestinal growth. Hyaluronic acid binding to TLR4 in pericryptal macrophages results in cyclooxygenase2- dependent PGE2 production, which transactivates EGFR in LGR5+ crypt epithelial stem cells leading to increased proliferation. The expanded population of LGR5+ stem cells leads to crypt fission and lengthening of the intestine and colon. Blocking this pathway at any point (TLR4 activation, PGE2 production, EGFR transactivation) results in diminished intestinal and colonic growth. A similar pathway leads to epithelial proliferation in wound repair. The repair phase of dextran sodium sulfate colitis is marked by increased epithelial proliferation. In this model, TLR2 and TLR4 in pericryptal macrophages are activated by microbial products or by host hyaluronic acid, resulting in production of CXCL12, a chemokine. CXCL12 induces the migration of cyclooxygenase2-expressing mesenchymal stem cells from the lamina propria of the upper colonic crypts to a site adjacent to LGR5+ epithelial stem cells. PGE2 released by these mesenchymal stem cells transactivates EGFR in LGR5+ epithelial stem cells leading to increased proliferation. Several TLR2 and TLR4 agonists, including hyaluronic acid, are radioprotective in the intestine through the inhibition of radiation-induced apoptosis in LGR5+ epithelial stem cells. Administration of exogenous TLR2 or TLR4 agonists activates TLR2/TLR4 on pericryptal macrophages inducing CXCL12 production with migration of cyclooxygenase2-expressing mesenchymal stem cells from the lamina propria of the villi to a site adjacent to LGR5+ epithelial stem cells. PGE2 produced by these mesenchymal stem cells, blocks radiation-induced apoptosis in LGR5+ epithelial stem cells by an EGFR mediated pathway.
Planktonic and Parasitic Sea Lice Abundance on Three Commercial Salmon Farms in Norway Throughout a Production Cycle
Authors: Jevne Lone S. , Guttu Maria , Båtnes Anna S. , Olsen Yngvar , Reitan Kjell I.
Published: January 2021

The present article reports the densities of planktonic sea lice (Lepeophtheirus salmonis and Caligus elongatus) in three Atlantic salmon (Salmo salar) localities, and the relationship between the abundance of adult sea lice on the salmon and the densities of planktonic sea lice stages, during a complete production cycle followed by a fallowing period. Samples were taken downstream inside and immediately outside of cages, at one locality with lice skirts and two localities without lice skirts. There were no differences in densities of planktonic sea lice in samples taken from the inside or the outside of cages for any of the localities. However, the proportion-non-zero of planktonic sea lice samples taken from inside the cage was higher during months with a temperature above 9°C (mean abundance: 0.40–2.5 individuals m–3) than months with temperature below 9°C (mean abundance: 0.02–0.21 individuals m–3, odds ratio of the proportion-non-zero: p < 0.01). Densities of planktonic sea lice correlated most strongly with temperature in the first year (τ = 0.44–0.57, p < 0.05). A significant correlation between the number of adult female lice on salmon and average density of plankton sea lice was found in the locality with lice skirts during the second year (τ = 0.43 inside cages, τ = 0.58 outside cages, both p values < 0.05). Background levels of planktonic sea lice in the succeeding fallowing period showed neither L. salmonis nor C. elongatus planktonic sea lice, suggesting that there was successful reduction of the densities of planktonic sea lice for this area during the fallowing period.
Infrared Thermographic and Ultrasonic Inspection of Randomly-Oriented Short-Natural Fiber-Reinforced Polymeric Composites
Authors: Loganathan Tamil Moli , Sultan Mohamed Thariq Hameed , Muhammad Amir Siti Madiha , Jamil Jeffry , Yusof Mohd Reusmaazran , Md Shah Ain Umaira
Published: January 2021

Non-destructive testing (NDT) is not only primarily concerned with the detection of discontinuities, but also with the mechanical properties. However, the usage of NDT in understanding the mechanical effect that leads to a failure of composites and the damage mechanisms are still not thoroughly studied, as much of the NDT approaches are widely used to maintain the structural integrity to preserve quality assurance. This work aims to investigate the application of infrared thermographic and ultrasonic in evaluating randomly-oriented short-natural-fiber-reinforced phenolic composites. The composites were made from short palm fibers of various sizes between 1.18–0.6 mm, 0.6–0.3 mm, and less than 0.3 mm at 20 and 40 wt%, respectively. The tensile results obtained from the parallel testing of the composites using infrared thermography, where the temperature and time changes on the tested samples were continuously recorded. The peak in the temperature-time graph indicated a macro crack growth and matrix cracking in the form of dissipated energy. Ultrasonic inspection were carried out on the impacted specimens. A scan of the ultrasonic testing on the phenolic composites found presence of a back wall in neat phenolic and was eradicated with fiber reinforcement due to attenuation and energy dissipation. The attenuation coefficient of composites was calculated with the aid of the A-scan. Therefore, it is concluded that ultrasonic inspection on the natural fiber is limited due to the large scattering of wave and energy loss due to attenuation, while infrared thermography is suitable to inspect natural-fiber-reinforced composites when monotonic loadings are applied.
Shear Fatigue Performance of Epoxy Resin Waterproof Adhesive Layer on Steel Bridge Deck Pavement
Authors: Xu Ying , Lv Xinpeng , Ma Chunfeng , Liang Fengming , Qi Jiafei , Chou Zhijing , Xu Shifa
Published: January 2021

In this study, the effects of temperature, shear stress, and coating quantity of waterproof adhesive layer on the shear fatigue performance of a steel bridge deck pavement were investigated. Direct shear fatigue tests of a pavement comprising an epoxy resin waterproof adhesive layer with stone matrix asphalt were conducted at different temperatures, stress levels, and coating quantities. The results show that temperature and stress have significant effects on the shear fatigue life. With increasing temperature and stress, the shear fatigue life of the waterproof adhesive layer decreased gradually. Therefore, for steel bridge deck pavements under high temperatures and heavy loads, the use of asphalt waterproof adhesive layers or pavement layers should be evaluated carefully while limiting the traffic of heavily loaded vehicles. Shear failure occurs at the waterproof adhesive layer–pavement interface and not at the steel–waterproof adhesive layer interface. The shear strength of the epoxy resin waterproof adhesive layer is mainly provided by the bond strength between the waterproof adhesive and pavement mixture as well as the interlocking force between the cured epoxy resin and the bottom interface of uneven pavement mixture. The shear strength increases with the coating quantity of the waterproof adhesive layer; however, after reaching the maximum value, the shear strength becomes stable. In contrast, the interlaminar shear fatigue life increases continuously with the coating quantity of the waterproof adhesive layer. Appropriately increasing the coating quantity is beneficial for improving the resistance of the waterproof adhesive layer to interlaminar shear fatigue failure.
Role of Palm Oil Vitamin E in Preventing Pre-eclampsia: A Secondary Analysis of a Randomized Clinical Trial Following ISSHP Reclassification
Authors: Aminuddin Nurul Afzan , Sutan Rosnah , Mahdy Zaleha Abdullah
Published: January 2021

Background: Preeclampsia is a significant cause of maternal and perinatal mortality worldwide. Oxidative stress plays a key role in its pathophysiology, hence antioxidants such as tocotrienol may be preventive against preeclampsia. In 2018, the ISSHP revised the definition of preeclampsia. In accordance with the new definition, we report a secondary data analysis from a clinical trial comparing palm oil vitamin E in the form of tocotrienol-rich fraction (TRF) against placebo, in preventing preeclampsia.

Method: A randomized double-blind controlled trial was conducted in 2002–2005 to assess the benefits of TRF in preeclampsia prevention. A total of 299 primigravidae were recruited. The intervention group was supplemented with TRF 100 mg daily in super-olein capsules, whereas the placebo group was prescribed super-olein capsules without TRF, beginning from 12 to 16 gestational weeks until delivery. The primary outcome measure was incidence of preeclampsia.

Results: The total incidence of pregnancy induced hypertension (PIH) was 5%, whereas the incidence of preeclampsia was 2.3%. The odds of developing PIH (adjusted OR 0.254; 95% CI: 0.07–0.93; p–value 0.038) and preeclampsia (adjusted OR 0.030; 95% CI: 0.001–0.65; p-value 0.025) were significantly lower in the TRF arm compared to the placebo arm.

Conclusion: Antenatal supplementation with palm oil vitamin E in the form of TRF is associated with significant reductions in the incidence of preeclampsia and PIH in a single urban tertiary hospital. Palm oil vitamin E deserves further scrutiny as a potential public health preventive measure against preeclampsia and PIH.
Encrusted Uropathy: A Comprehensive Overview—To the Bottom of the Crust
Authors: Van de Perre Els , Reichman Gina , De Geyter Deborah , Geers Caroline , Wissing Karl M. , Letavernier Emmanuel
Published: January 2021

Encrusted uropathy is a rare subacute to chronic inflammatory disorder caused by infection with urease-producing bacteria, mainlyCorynebacterium urealyticum. The disorder is characterized by urothelial deposition of struvite and carbonated apatite, resulting in encrustations and ulceronecrotic inflammation of the urothelium and surrounding tissues. Most commonly, encrusted uropathy is encountered in patients with predisposing conditions. The disease remains underdiagnosed. High urinary pH and negative conventional urine cultures should raise suspicion of the diagnosis. Prognosis is dependent on timely diagnosis and treatment installment, which consists of urological removal of encrustations in combination with urinary acidification and long-term antibiotic therapy.
Keep Your Friends Close, but Your Enemies Closer: Role of Acid Sphingomyelinase During Infection and Host Response
Authors: Chung Ha-Yeun , Claus Ralf A.
Published: January 2021

Breakdown of the inert and constitutive membrane building block sphingomyelin to the highly active lipid mediator ceramide by extracellularly active acid sphingomyelinase is tightly regulated during stress response and opens the gate for invading pathogens, triggering the immune response, development of remote organ failure, and tissue repair following severe infection. How do one enzyme and one mediator manage all of these affairs? Under physiological conditions, the enzyme is located in the lysosomes and takes part in the noiseless metabolism of sphingolipids, but following stress the protein is secreted into circulation. When secreted, acid sphingomyelinase (ASM) is able to hydrolyze sphingomyelin present at the outer leaflet of membranes to ceramide. Its generation troubles the biophysical context of cellular membranes resulting in functional assembly and reorganization of proteins and receptors, also embedded in highly conserved response mechanisms. As a consequence of cellular signaling, not only induction of cell death but also proliferation, differentiation, and fibrogenesis are affected. Here, we discuss the current state of the art on both the impact and function of the enzyme during host response and damage control. Also, the potential role of lysosomotropic agents as functional inhibitors of this upstream alarming cascade is highlighted.
Physiological and Pathological Functions of SLC26A6
Authors: Wang Juan , Wang Wenkang , Wang Hui , Tuo Biguang
Published: January 2021

Solute Carrier Family 26 (SLC26) is a conserved anion transporter family with 10 members in human (SLC26A1-A11, A10 being a pseudogene). All SLC26 genes except for SLC26A5 (prestin) are versatile anion exchangers with notable ability to transport a variety of anions. SLC26A6 has the most extensive exchange functions in the SLC26 family and is widely expressed in various organs and tissues of mammals. SLC26A6 has some special properties that make it play a particularly important role in ion homeostasis and acid-base balance. In the past few years, the function of SLC26A6 in the diseases has received increasing attention. SLC26A6 not only participates in the development of intestinal and pancreatic diseases but also serves a significant role in mediating nephrolithiasis, fetal skeletal dysplasia and arrhythmia. This review aims to explore the role of SLC26A6 in physiology and pathophysiology of relative mammalian organs to guide in-depth studies about related diseases of human.
Can GPR4 Be a Potential Therapeutic Target for COVID-19?
Authors: Yang Li V. , Oppelt Karen A. , Thomassen Mary Jane , Marie Mona A. , Nik Akhtar Shayan , McCallen Justin D.
Published: January 2021

Coronavirus disease 19 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first emerged in late 2019 and has since rapidly become a global pandemic. SARS-CoV-2 infection causes damages to the lung and other organs. The clinical manifestations of COVID-19 range widely from asymptomatic infection, mild respiratory illness to severe pneumonia with respiratory failure and death. Autopsy studies demonstrate that diffuse alveolar damage, inflammatory cell infiltration, edema, proteinaceous exudates, and vascular thromboembolism in the lung as well as extrapulmonary injuries in other organs represent key pathological findings. Herein, we hypothesize that GPR4 plays an integral role in COVID-19 pathophysiology and is a potential therapeutic target for the treatment of COVID-19. GPR4 is a pro-inflammatory G protein-coupled receptor (GPCR) highly expressed in vascular endothelial cells and serves as a “gatekeeper” to regulate endothelium-blood cell interaction and leukocyte infiltration. GPR4 also regulates vascular permeability and tissue edema under inflammatory conditions. Therefore, we hypothesize that GPR4 antagonism can potentially be exploited to mitigate the hyper-inflammatory response, vessel hyper-permeability, pulmonary edema, exudate formation, vascular thromboembolism and tissue injury associated with COVID-19.
ACE Gene I/D Polymorphism and Acute Pulmonary Embolism in COVID19 Pneumonia: A Potential Predisposing Role
Authors: Calabrese Cecilia , Annunziata Anna , Coppola Antonietta , Pafundi Pia Clara , Guarino Salvatore , Di Spirito Valentina , Maddaloni Valeria , Pepe Nicola , Fiorentino Giuseppe
Published: January 2021

Most recent studies have stressed a high risk of thromboembolism in patients with SARS-CoV-2 infection, particularly in those with severe COVID-19 pneumonia. Counterbalance between angiotensin-converting-enzyme (ACE) and ACE2 activities in COVID-19 disease may be crucially involved in the thrombo-inflammatory process. Currently, no study has investigated ACE I/D polymorphism involvement in COVID-19 disease complicated by pulmonary embolism, hence the aim of the present pilot study. This is a retrospective, single-center observational case-control study, conducted at the Sub-Intensive Care Unit of A.O.R.N. Ospedali dei Colli, Cotugno Hospital, Naples (Italy). We included 68 subjects with severe/critical COVID-19 pneumonia. COVID-19 patients were divided according to occurrence of PE (PE+, n = 25) or absence of thromboembolic complications (PE−, n = 43). Assessment of ACE I/D polymorphisms showed a statistically significant difference between PE+ and PE− patients (p = 0.029). Particularly, prevalence of D/D homozygous polymorphism was significantly higher in PE+ COVID-19 patients than in PE− (72 vs. 46.5%; p = 0.048), while heterozygote I/D polymorphism was significantly lower expressed in PE+ patients than in PE− (16 vs. 48.8%; p = 0.009). Computed tomographic pulmonary angiography showed predominantly mono/bilateral sub-segmental embolisms. In conclusion, our findings let us hypothesize a genetic susceptibility to thromboembolism in COVID-19 disease. ACE D/D polymorphism might represent a genetic risk factor, although studies on larger populations are needed.
Spectroscopic and Microscopic Approaches for Investigating the Dynamic Interactions of Anti-microbial Peptides With Membranes and Cells
Authors: Clayton Andrew H. A.
Published: January 2021

The emergence of microbes resistant to conventional antibiotics is a burgeoning threat to humanity with significant impacts on the health of people and on the health system itself. Antimicrobial peptides (AMPs) hold promise as potential future alternatives to conventional drugs because they form an integral part of the defense systems of other species in the animal, plant, and fungal kingdoms. To aid the design of the next generation of AMPs optimized for human use, we must first understand the mechanism of action of existing AMPs with their targets, ideally in the context of the complex landscape of the living (microbial) cell. Advances in lasers, optics, detectors, fluid dynamics and various probes has enabled the experimentalist to measure the kinetics of molecule–membrane, molecule–molecule, and molecule–cell interactions with increasing spatial and temporal resolution. The purpose of this review is to highlight studies into these dynamic interactions with a view to improving our understanding of AMP mechanisms.
Direct Evidence of Abortive Lytic Infection-Mediated Establishment of Epstein-Barr Virus Latency During B-Cell Infection
Authors: Inagaki Tomoki , Sato Yoshitaka , Ito Jumpei , Takaki Mitsuaki , Okuno Yusuke , Yaguchi Masahiro , Masud H. M. Abdullah Al , Watanabe Takahiro , Sato Kei , Iwami Shingo , Murata Takayuki , Kimura Hiroshi
Published: January 2021

Viral infection induces dynamic changes in transcriptional profiles. Virus-induced and antiviral responses are intertwined during the infection. Epstein-Barr virus (EBV) is a human gammaherpesvirus that provides a model of herpesvirus latency. To measure the transcriptome changes during the establishment of EBV latency, we infected EBV-negative Akata cells with EBV-EGFP and performed transcriptome sequencing (RNA-seq) at 0, 2, 4, 7, 10, and 14 days after infection. We found transient downregulation of mitotic division-related genes, reflecting reprogramming of cell growth by EBV, and a burst of viral lytic gene expression in the early phase of infection. Experimental and mathematical investigations demonstrate that infectious virions were not produced in the pre-latent phase, suggesting the presence of an abortive lytic infection. Fate mapping using recombinant EBV provided direct evidence that the abortive lytic infection in the pre-latent phase converges to latent infection during EBV infection of B-cells, shedding light on novel roles of viral lytic gene(s) in establishing latency. Furthermore, we find that the BZLF1 protein, which is a key regulator of reactivation, was dispensable for abortive lytic infection in the pre-latent phase, suggesting the divergent regulation of viral gene expressions from a productive lytic infection.
Microbial Grazers May Aid in Controlling Infections Caused by the Aquatic Zoosporic Fungus Batrachochytrium dendrobatidis
Authors: Farthing Hazel N. , Jiang Jiamei , Henwood Alexandra J. , Fenton Andy , Garner Trent W. J. , Daversa David R. , Fisher Matthew C. , Montagnes David J. S.
Published: January 2021

Free-living eukaryotic microbes may reduce animal diseases. We evaluated the dynamics by which micrograzers (primarily protozoa) apply top-down control on the chytrid Batrachochytrium dendrobatidis (Bd) a devastating, panzootic pathogen of amphibians. Although micrograzers consumed zoospores (∼3 μm), the dispersal stage of chytrids, not all species grew monoxenically on zoospores. However, the ubiquitous ciliate Tetrahymena pyriformis, which likely co-occurs with Bd, grew at near its maximum rate (r = 1.7 d–1). A functional response (ingestion vs. prey abundance) for T. pyriformis, measured using spore-surrogates (microspheres) revealed maximum ingestion (Imax) of 1.63 × 103 zoospores d–1, with a half saturation constant (k) of 5.75 × 103 zoospores ml–1. Using these growth and grazing data we developed and assessed a population model that incorporated chytrid-host and micrograzer dynamics. Simulations using our data and realistic parameters obtained from the literature suggested that micrograzers could control Bd and potentially prevent chytridiomycosis (defined as 104 sporangia host–1). However, simulated inferior micrograzers (0.7 × Imax and 1.5 × k) did not prevent chytridiomycosis, although they ultimately reduced pathogen abundance to below levels resulting in disease. These findings indicate how micrograzer responses can be applied when modeling disease dynamics for Bd and other zoosporic fungi.
Functional Insights From KpfR, a New Transcriptional Regulator of Fimbrial Expression That Is Crucial for Klebsiella pneumoniae Pathogenicity
Authors: Gomes Ana Érika Inácio , Pacheco Thaisy , Santos Cristiane da Silva dos , Pereira José Aires , Ribeiro Marcelo Lima , Darrieux Michelle , Ferraz Lúcio Fábio Caldas
Published: January 2021

Although originally known as an opportunistic pathogen, Klebsiella pneumoniae has been considered a worldwide health threat nowadays due to the emergence of hypervirulent and antibiotic-resistant strains capable of causing severe infections not only on immunocompromised patients but also on healthy individuals. Fimbriae is an essential virulence factor for K. pneumoniae, especially in urinary tract infections (UTIs), because it allows the pathogen to adhere and invade urothelial cells and to form biofilms on biotic and abiotic surfaces. The importance of fimbriae for K. pneumoniae pathogenicity is highlighted by the large number of fimbrial gene clusters on the bacterium genome, which requires a coordinated and finely adjusted system to control the synthesis of these structures. In this work, we describe KpfR as a new transcriptional repressor of fimbrial expression in K. pneumoniae and discuss its role in the bacterium pathogenicity. K. pneumoniae with disrupted kpfR gene exhibited a hyperfimbriated phenotype with enhanced biofilm formation and greater adhesion to and replication within epithelial host cells. Nonetheless, the mutant strain was attenuated for colonization of the bladder in a murine model of urinary tract infection. These results indicate that KpfR is an important transcriptional repressor that, by negatively controlling the expression of fimbriae, prevents K. pneumoniae from having a hyperfimbriated phenotype and from being recognized and eliminated by the host immune system.
Antiproliferative Sorbicillinoids From the Deep-Sea-Derived Penicillium allii-sativi
Authors: Xie Chun-Lan , Zhang Duo , Lin Ting , He Zhi-Hui , Yan Qing-Xiang , Cai Qi , Zhang Xiao-Kun , Yang Xian-Wen , Chen Hai-Feng
Published: January 2021

Two new (1–2) and three known (3–5) sorbicillinoids were isolated from the deep-sea-derived fungus Penicillium allii-sativi MCCC 3A00580. Compounds 1 and 2, named sorbicatechols C and D, were two new hybrid dihydrosorbillinoids. Their structures were established mainly by spectroscopic analyses and electronic circular dichroism (ECD) calculations. All five isolates were tested for antiproliferative activities against four tumor cell lines of MCF-7, HT-29, HuH-7, and LNCap. Compounds 2 and 5 inhibited HT-29 cells in a good dose-dependent manner. Mechanism investigation uncovered that they could significantly induce cell cycle G2-M phase arresting by increasing the protein levels of p-H3 and cyclin B1.
BioMaster: An Integrated Database and Analytic Platform to Provide Comprehensive Information About BioBrick Parts
Authors: Wang Beibei , Yang Huayi , Sun Jianan , Dou Chuhao , Huang Jian , Guo Feng-Biao
Published: January 2021

Synthetic biology seeks to create new biological parts, devices, and systems, and to reconfigure existing natural biological systems for custom-designed purposes. The standardized BioBrick parts are the foundation of synthetic biology. The incomplete and flawed metadata of BioBrick parts, however, are a major obstacle for designing genetic circuit easily, quickly, and accurately. Here, a database termed BioMaster http://www.biomaster-uestc.cn was developed to extensively complement information about BioBrick parts, which includes 47,934 items of BioBrick parts from the international Genetically Engineered Machine (iGEM) Registry with more comprehensive information integrated from 10 databases, providing corresponding information about functions, activities, interactions, and related literature. Moreover, BioMaster is also a user-friendly platform for retrieval and analyses of relevant information on BioBrick parts.
DeepT3_4: A Hybrid Deep Neural Network Model for the Distinction Between Bacterial Type III and IV Secreted Effectors
Authors: Yu Lezheng , Liu Fengjuan , Li Yizhou , Luo Jiesi , Jing Runyu
Published: January 2021

Gram-negative bacteria can deliver secreted proteins (also known as secreted effectors) directly into host cells through type III secretion system (T3SS), type IV secretion system (T4SS), and type VI secretion system (T6SS) and cause various diseases. These secreted effectors are heavily involved in the interactions between bacteria and host cells, so their identification is crucial for the discovery and development of novel anti-bacterial drugs. It is currently challenging to accurately distinguish type III secreted effectors (T3SEs) and type IV secreted effectors (T4SEs) because neither T3SEs nor T4SEs contain N-terminal signal peptides, and some of these effectors have similar evolutionary conserved profiles and sequence motifs. To address this challenge, we develop a deep learning (DL) approach called DeepT3_4 to correctly classify T3SEs and T4SEs. We generate amino-acid character dictionary and sequence-based features extracted from effector proteins and subsequently implement these features into a hybrid model that integrates recurrent neural networks (RNNs) and deep neural networks (DNNs). After training the model, the hybrid neural network classifies secreted effectors into two different classes with an accuracy, F-value, and recall of over 80.0%. Our approach stands for the first DL approach for the classification of T3SEs and T4SEs, providing a promising supplementary tool for further secretome studies.
The GTPase-Activating Protein FgGyp1 Is Important for Vegetative Growth, Conidiation, and Virulence and Negatively Regulates DON Biosynthesis in Fusarium graminearum
Authors: Zheng Qiaojia , Yu Zhi , Yuan Yanping , Sun Danli , Abubakar Yakubu Saddeeq , Zhou Jie , Wang Zonghua , Zheng Huawei
Published: January 2021

Ypt1 is a small Rab GTPase in yeast, Gyp1 functions at the Golgi as a negative regulator of Ypt1. Gyp1 homologs are conserved in filamentous fungi. However, the roles of Gyp1 in phytopathogenic fungi are still unclear. Herein, we investigated the functions of FgGyp1 in the wheat pathogen Fusarium graminearum by live-cell imaging, genetic, and pathological analyses. Targeted gene replacement method was used to delete FgGYP1 in F. graminearum. Phenotypic analyses showed that FgGyp1 is critically important not only for the vegetative growth of F. graminearum but also its conidiation. The mutant’s vegetative growth was significantly reduced by 70% compared to the wild type PH-1. The virulence of FgGYP1 deletion mutant was significantly decreased when compared with the wild type PH-1. We further found that FgGyp1 negatively regulates DON production of the fungus. Live-cell imaging clearly demonstrated that FgGyp1 mainly localizes to the Golgi apparatus. Moreover, the TBC domain, C-terminal, and N-terminal regions of FgGyp1 are found to be indispensable for its biological functions and normal localization. The Arg357 residue of FgGyp1 is essential for its functions but dispensable for the normal localization of the protein, while the Arg284 residue is not required for both the functions and normal localization of the protein. Furthermore, we showed that FgGyp1 essentially hydrolyzes the GTP-bound FgRab1 (activated form) to its corresponding GDP-bound (inactive) form in vitro, suggesting that FgGyp1 is a GTPase-activating protein (GAP) for FgRab1. Finally, FgGyp1 was found to be important for FgSnc1-mediated fusion of secretory vesicles from the Golgi with the plasma membrane in F. graminearum. Put together, these data demonstrate that FgGyp1 functions as a GAP for FgRab1 and is important for vegetative growth, conidiation and virulence, and negatively regulates DON biosynthesis in F. graminearum.
From Paths to Routes: A Method for Path Classification
Authors: Gonsek Andrea , Jeschke Manon , Rönnau Silvia , Bertrand Olivier J. N.
Published: January 2021

Many animals establish, learn and optimize routes between locations to commute efficiently. One step in understanding route following is defining measures of similarities between the paths taken by the animals. Paths have commonly been compared by using several descriptors (e.g., the speed, distance traveled, or the amount of meandering) or were visually classified into categories by the experimenters. However, similar quantities obtained from such descriptors do not guarantee similar paths, and qualitative classification by experimenters is prone to observer biases. Here we propose a novel method to classify paths based on their similarity with different distance functions and clustering algorithms based on the trajectories of bumblebees flying through a cluttered environment. We established a method based on two distance functions (Dynamic Time Warping and Fréchet Distance). For all combinations of trajectories, the distance was calculated with each measure. Based on these distance values, we grouped similar trajectories by applying the Monte Carlo Reference-Based Consensus Clustering algorithm. Our procedure provides new options for trajectory analysis based on path similarities in a variety of experimental paradigms.
Alzheimer’s Disease Projection From Normal to Mild Dementia Reflected in Functional Network Connectivity: A Longitudinal Study
Authors: Sendi Mohammad S. E. , Zendehrouh Elaheh , Miller Robyn L. , Fu Zening , Du Yuhui , Liu Jingyu , Mormino Elizabeth C. , Salat David H. , Calhoun Vince D.
Published: January 2021

Background

Alzheimer’s disease (AD) is the most common age-related problem and progresses in different stages, including mild cognitive impairment (early stage), mild dementia (middle-stage), and severe dementia (late-stage). Recent studies showed changes in functional network connectivity obtained from resting-state functional magnetic resonance imaging (rs-fMRI) during the transition from healthy aging to AD. By assuming that the brain interaction is static during the scanning time, most prior studies are focused on static functional or functional network connectivity (sFNC). Dynamic functional network connectivity (dFNC) explores temporal patterns of functional connectivity and provides additional information to its static counterpart.

Method

We used longitudinal rs-fMRI from 1385 scans (from 910 subjects) at different stages of AD (from normal to very mild AD or vmAD). We used group-independent component analysis (group-ICA) and extracted 53 maximally independent components (ICs) for the whole brain. Next, we used a sliding-window approach to estimate dFNC from the extracted 53 ICs, then group them into 3 different brain states using a clustering method. Then, we estimated a hidden Markov model (HMM) and the occupancy rate (OCR) for each subject. Finally, we investigated the link between the clinical rate of each subject with state-specific FNC, OCR, and HMM.

Results

All states showed significant disruption during progression normal brain to vmAD one. Specifically, we found that subcortical network, auditory network, visual network, sensorimotor network, and cerebellar network connectivity decrease in vmAD compared with those of a healthy brain. We also found reorganized patterns (i.e., both increases and decreases) in the cognitive control network and default mode network connectivity by progression from normal to mild dementia. Similarly, we found a reorganized pattern of between-network connectivity when the brain transits from normal to mild dementia. However, the connectivity between visual and sensorimotor network connectivity decreases in vmAD compared with that of a healthy brain. Finally, we found a normal brain spends more time in a state with higher connectivity between visual and sensorimotor networks.

Conclusion

Our results showed the temporal and spatial pattern of whole-brain FNC differentiates AD form healthy control and suggested substantial disruptions across multiple dynamic states. In more detail, our results suggested that the sensory network is affected more than other brain network, and default mode network is one of the last brain networks get affected by AD In addition, abnormal patterns of whole-brain dFNC were identified in the early stage of AD, and some abnormalities were correlated with the clinical score.
Magnetic Resonance Imaging and Gait Analysis Indicate Similar Outcomes Between Yucatan and Landrace Porcine Ischemic Stroke Models
Authors: Sneed Sydney E. , Scheulin Kelly M. , Kaiser Erin E. , Fagan Madison M. , Jurgielewicz Brian J. , Waters Elizabeth S. , Spellicy Samantha E. , Duberstein Kylee J. , Platt Simon R. , Baker Emily W. , Stice Steven L. , Kinder Holly A. , West Franklin D.
Published: January 2021

The Stroke Therapy Academic Industry Roundtable (STAIR) has recommended that novel therapeutics be tested in a large animal model with similar anatomy and physiology to humans. The pig is an attractive model due to similarities in brain size, organization, and composition relative to humans. However, multiple pig breeds have been used to study ischemic stroke with potentially differing cerebral anatomy, architecture and, consequently, ischemic stroke pathologies. The objective of this study was to characterize brain anatomy and assess spatiotemporal gait parameters in Yucatan (YC) and Landrace (LR) pigs pre- and post-stroke using magnetic resonance imaging (MRI) and gait analysis, respectively. Ischemic stroke was induced via permanent middle cerebral artery occlusion (MCAO). MRI was performed pre-stroke and 1-day post-stroke. Structural and diffusion-tensor sequences were performed at both timepoints and analyzed for cerebral characteristics, lesion diffusivity, and white matter changes. Spatiotemporal and relative pressure gait measurements were collected pre- and 2-days post-stroke to characterize and compare acute functional deficits. The results from this study demonstrated that YC and LR pigs exhibit differences in gross brain anatomy and gait patterns pre-stroke with MRI and gait analysis showing statistical differences in the majority of parameters. However, stroke pathologies in YC and LR pigs were highly comparable post-stroke for most evaluated MRI parameters, including lesion volume and diffusivity, hemisphere swelling, ventricle compression, caudal transtentorial and foramen magnum herniation, showing no statistical difference between the breeds. In addition, post-stroke changes in velocity, cycle time, swing percent, cadence, and mean hoof pressure showed no statistical difference between the breeds. These results indicate significant differences between pig breeds in brain size, anatomy, and motor function pre-stroke, yet both demonstrate comparable brain pathophysiology and motor outcomes post-stroke. The conclusions of this study suggest pigs of these different breeds generally show a similar ischemic stroke response and findings can be compared across porcine stroke studies that use different breeds.
Economic Evaluation Protocol and Statistical Analysis Plan for the Cost-Effectiveness of a Novel Australian Stroke Telemedicine Program; the Victorian Stroke Telemedicine (VST) program
Authors: Cadilhac Dominique A. , Sheppard Lauren , Kim Joosup , Tan Elise , Gao Lan , Sookram Garveeta , Dewey Helen M. , Bladin Christopher F. , Moodie Marj
Published: January 2021

Introduction:Telemedicine can address limited access to medical specialists in rural hospitals. Stroke provides an important case study because: it is a major cause of disease burden; effective treatments to reduce disability (e.g., thrombolysis) can be provided within the initial hours of stroke onset; careful selection of patients is needed by skilled doctors to minimize adverse events from thrombolysis; and there are major treatment gaps (only about half of regional hospitals in Australia provide thrombolysis for stroke). Few economic analyses have been undertaken on telestroke and the majority have been simulation models. The aim of this protocol and statistical analysis plan is to outline the methods for the cost-effectiveness evaluation of a large, multicentre acute stroke telemedicine program being conducted in Victoria, Australia.

Methods:Using a historical- and prospective-controlled design, we will compare patient-level data obtained in the 12 months prior to the Victorian Stroke Telemedicine (VST) program implementation and during the first 12 months of VST to determine the incremental difference in costs and patient outcomes at 3 and 12 months. Secondary aims include assessing the cost per additional patient receiving intravenous thrombolysis and the cost per additional patient receiving intravenous thrombolysis within 60 min. Tertiary aims include assessing the potential longer-term cost-effectiveness in the second year of the program at the hospitals to determine whether any program benefits are sustained once site coordinators are no longer employed; and modeling the potential net life-time costs and benefits from a societal perspective. Multivariable uncertainty and one-way sensitivity analyses will be performed to assess the robustness of results.

Results:Sixteen hospitals participated. Patient-level data collection including 12-month outcomes for the cohorts obtained in the first and second year of the program for each hospital was completed in January 2020.

Conclusion:The results from this real-world study with patient-level data will provide high quality evidence of the costs, health benefits and policy implications of telestroke programs, including the potential for application in other locations within Australia or other countries with similar health system delivery and financing.