bluuebunny/crossref_metadata_2025 huggingface dataset:
Retrospective analysis of adjuvant therapy using dabrafenib plus trametinib in Japanese patients with advanced melanoma: analysis of 36 cases
Authors: Amagai Ryo , Muto Yusuke , Kato Hiroshi , Matsushita Shigeto , Maekawa Takeo , Fukushima Satoshi , Yoshino Koji , Uchi Hiroshi , Fujisawa Yasuhiro , Yamamoto Yuki , Ohuchi Kentaro , Kambayashi Yumi , Fujimura Taku
Published: September 2021

Patients with resected stage IIIB, IIIC and IIID melanomas have a high risk of recurrence. Therefore, an appropriate protocol for stage III melanoma is needed. Since adjuvant dabrafenib plus trametinib (D+T) combined therapy and anti-PD1 antibody (Ab) therapy reduce the risk of recurrence in patients with resected stage III BRAF-mutated melanoma, selecting the adjuvant therapy for BRAF-mutated melanoma is controversial. The efficacy and safety profiles of D+T combined therapy in the adjuvant setting were retrospectively analyzed in 36 Japanese. BRAF-mutated advanced melanoma patients. The relapse-free rate (RFR) at 12 months was 82.1% (95% confidential interval (CI), 63.9–92.6%). In the 21 patients who completed the protocol, the RFR at 12 months was 85.7% (95% CI, 64.5–95.9%). In the seven patients whose protocol was interrupted by adverse events, the RFR was 71.4% (95% CI, 35.2–92.4%). The incidence rate of any AEs for all patients was 69.7% (95% CI, 52.5–82.8%), including 13 cases of pyrexia, five cases of skin rash and four cases of liver dysfunction. The present study suggested that D+T therapy in the adjuvant setting is a useful and very tolerable protocol for BRAF-mutated melanoma in the Japanese population.
Recent progress of biomarkers in oral cancers
Authors: Liang Kung-Hao , Lin Yi-Ying , Chiang Su-Hua , Tsai En-Tung , Lo Wen-Liang , Wang Chia-Lin , Wang Tsui-Ying , Sun Yi-Chen , Kao Shou-Yen , Wu Cheng-Hsien , Hung Kai-Feng
Published: September 2021

Oral cancers are the seventh most common cancer globally. While progresses in oral cancer treatment have been made, not all patients respond to these therapies in the same way. To overcome this difficulty, numerous studies have been devoted to identifying biomarkers, which enable early identification of patients who may benefit from a particular treatment modality or at risk for poor prognosis. Biomarkers are protein molecules, gene expression, DNA variants, or metabolites that are derived from tumors, adjacent normal tissue or bodily fluids, which can be acquired before treatment and during follow-up, thus extending their use to the evaluation of cancer progression and prediction of treatment outcome. In this review, we employed a basic significance level (<0.05) as the minimal requirement for candidate biomarkers. Effect sizes of the biomarkers in terms of odds ratio, hazard ratio, and area under the receiver operating characteristic curves were subsequently used to evaluate the potential of their clinical use. We identified the CCND1 from the tumor, human papillomavirus, HSP70, and IL-17 from the peripheral blood, and high density of CD45RO+ tumor-infiltrating lymphocytes as the clinically relevant biomarkers for oral cancers.
Legacy effect on neuropsychological function in HIV-infected men on combination antiretroviral therapy
Authors: Qu Yang , Weinstein Andrea , Wang Zheng , Cheng Yu , Kingsley Lawrence , Levine Andrew , Martin Eileen , Munro Cynthia , Ragin Ann B. , Rubin Leah H. , Sacktor Ned W. , Seaberg Eric C. , Becker James T.
Published: September 2021

Objective:

To determine whether combination antiretroviral therapy (cART) initiation alters the trajectory of cognitive performance in HIV+ men, and whether cognition prior to cART predicts postcART function.

Design:

Longitudinal cohort study. Multicenter AIDS Cohort Study.

Methods:

From an initial set of 3701 men with complete neuropsychological data, men with HIV infection were initially matched with men without infection on cognitive status, race, age, and timeline (T0 defined as cART initiation). Propensity score matching was then used to match pairs on depressive symptoms at T0, education, T0 cognitive scores, and recruitment cohort. There were 506 matched pairs of infected and uninfected men in the final analysis. Mixed effect models were constructed to analyze the trajectories of cognitive functions and to test the effect of cART and HIV on cognitive functions over time.

Results:

Performance in each cognitive domain did not change following the initiation of cART among HIV-infected men with prior impairment and was comparable to the performance of their matched uninfected men. However, among the infected men who were unimpaired prior to cART, motor function declined significantly faster than it did for uninfected controls.

Conclusions:

Cognitive dysfunction is persistent in HIV-infected men and cART does not alter the trajectory of cognitive decline in men who were impaired prior to effective therapy. This suggests that current cognitive impairment in HIV+ men results from a legacy effect, and from factors other than the HIV itself. Furthermore, motor skills may be uniquely vulnerable to the virus, cART, or age-related co-morbidities.
Elite and viremic HIV-1 controllers in West Africa
Authors: N’takpé Jean Baptiste , Gabillard Delphine , Moh Raoul , Gardiennet Elise , Toni Thomas-d’Aquin , Kouame Gérard M. , Badje Anani , Emieme Arlette , Karcher Sophie , Le Carrou Jérome , Ménan Hervé , Danel Christine , Eholie Serge P. , Rouzioux Christine , Anglaret Xavier , Lambotte Olivier
Published: September 2021

Background:

Data on HIV-1 controllers in Africa are scarce. We report the proportion of HIV-1 controllers in a group of adults prospectively monitored with frequent viral load measurements as part of a clinical trial in West Africa.

Methods:

For the Temprano trial, antiretroviral therapy (ART)-naive HIV-1 infected adults with no criteria for starting ART were randomized to start ART immediately or defer ART until the WHO starting criteria were met. Plasma viral load was measured every 6 months. The trial follow-up was 30 months. We considered all Temprano participants randomized to defer ART. Patients with all semestrial viral <2000 copies/ml and still off ART at month 30 were defined as HIV-1 controllers. Controllers with all viral loads <50 copies/ml were defined as elite controllers, the rest as viremic controllers.

Results:

Of the 1023 HIV-1-infected adults randomized in the Temprano deferred-ART group, 18 (1.8%) met the criteria for classification as HIV controllers, of whom seven (0.7%) were elite controllers and 11 (1.1%) viremic controllers. The HIV-1 controllers had low peripheral blood mononuclear cell HIV-1 DNA and low inflammatory marker levels. They maintained high CD4+ cell count and percentages and had a low morbidity rate.

Discussion:

HIV controllers exist in Africa at a proportion close to that reported elsewhere. They represent a small fraction of all HIV-1-infected patients but raise important questions. Further studies should assess whether starting ART might represent more risk than benefit for some controllers, and where it does, how to identify these patients before they start ART.
Synchronous Recurrence of Metachronous Lung Cancer and Hodgkin Lymphoma Within an Axillary Lymph Node Isolated on 18F-FDG PET/CT
Authors: Lee Marco Enoch , Jiang James Yuheng , Parry Nicholas Mckay , Karikios Deme , Mansberg Robert
Published: September 2021

An 82-year-old man with a background of non-Hodgkin lymphoma in remission, resected left lower lobe adenocarcinoma (stage IA), and resected cutaneous melanoma of the left forearm more than 5 years prior presented with cerebral metastatic disease. Excision biopsy confirmed adenocarcinoma of lung origin. Further evaluation with 18F-FDG PET/CT demonstrated FDG-avid disease in the right thorax, axilla, and lower neck and isolated cutaneous uptake in the right forearm. Lymph node biopsy confirmed synchronous mantle cell lymphoma and metastatic adenocarcinoma of the lung.
A Triphasic Split-bolus Contrast Injection Protocol for Artery-vein Separation During Pulmonary Computed Tomographic Angiography
Authors: Tokurei Shogo , Takegami Kazuki , Ikushima Yoichiro , Sato Shusaku , Kudomi Shohei , Okada Munemasa
Published: September 2021

Purpose:

Accurate artery-vein separation on pulmonary computed tomographic (CT) angiography is desirable for preoperative 3-dimensional image simulation, while using a minimal amount of contrast medium. This study aimed to verify whether a split-bolus contrast enhancement protocol with test-bolus tracking would provide contrast differentiation between the pulmonary arteries (PA) and pulmonary veins (PV) during high-pitch single-pass CT angiography.

Materials and Methods:

Fifty patients underwent pulmonary CT angiography with a triphasic split-bolus injection protocol with the main bolus of contrast medium for 6 seconds, followed by a subsequent bolus of 20% diluted contrast medium/80% saline for another 6 seconds and a 5-second saline chaser. The single-scan timing was individually tailored to the peak enhancement at the left atrium, that is, the pulmonary-venous dominant phase, by monitoring a time-enhancement curve with test bolus.

Results:

Time-enhancement curves of the test bolus demonstrated that the interval times between the peak enhancements at the PA and PV were ~6 seconds. For contrast enhancement image analyses with our protocol, the attenuation measurements at the main PA and left atrium were performed. The mean (SD) CT numbers were 246.4 (50.0) HU at the main PA, and 410.8 (59.0) HU at the left atrium. The mean difference in the CT numbers was 164.4 HU (95% confidence interval: 149.2-179.6, P<0.001) between the main PA and left atrium.

Conclusions:

Our contrast enhancement protocol for high-pitch single-pass pulmonary CT angiography could provide the desired artery-vein separation while maintaining adequate attenuations of the pulmonary vasculature.
Cardiac Magnetic Resonance Tissue Characterization in Ischemic Cardiomyopathy
Authors: Muscogiuri Giuseppe , Ricci Francesca , Scafuri Stefano , Guglielmo Marco , Baggiano Andrea , De Stasio Vincenzo , Di Donna Carlo , Spiritigliozzi Luigi , Chiocchi Marcello , Lee Scott J. , De Cecco Carlo N. , van Assen Marly , Rabbat Mark G. , Pontone Gianluca
Published: September 2021

Ischemic cardiomyopathy (ICM) is one of the most common causes of congestive heart failure. In patients with ICM, tissue characterization with cardiac magnetic resonance imaging (CMR) allows for evaluation of myocardial abnormalities in acute and chronic settings. Myocardial edema, microvascular obstruction (MVO), intracardiac thrombus, intramyocardial hemorrhage, and late gadolinium enhancement of the myocardium are easily depicted using standard CMR sequences. In the acute setting, tissue characterization is mainly focused on assessment of ventricular thrombus and MVO, which are associated with poor prognosis. Conversely, in chronic ICM, it is important to depict late gadolinium enhancement and myocardial ischemia using stress perfusion sequences. Overall, with CMR’s ability to accurately characterize myocardial tissue in acute and chronic ICM, it represents a valuable diagnostic and prognostic imaging method for treatment planning. In particular, tissue characterization abnormalities in the acute setting can provide information regarding the patients that may develop major adverse cardiac event and show the presence of ventricular thrombus; in the chronic setting, evaluation of viable myocardium can be fundamental for planning myocardial revascularization. In this review, the main findings on tissue characterization are illustrated in acute and chronic settings using qualitative and quantitative tissue characterization.
SUIHTER
: a new mathematical model for COVID-19. Application to the analysis of the second epidemic outbreak in Italy
Authors: Parolini N. , Dede’ L. , Antonietti P. F. , Ardenghi G. , Manzoni A. , Miglio E. , Pugliese A. , Verani M. , Quarteroni A.
Published: September 2021

The COVID-19 epidemic is the latest in a long list of pandemics that have affected humankind in the last century. In this paper, we propose a novel mathematical epidemiological model named
SUIHTER
from the names of the seven compartments that it comprises: susceptible uninfected individuals (
S
), undetected (both asymptomatic and symptomatic) infected (
U
), isolated infected (
I
), hospitalized (
H
), threatened (
T
), extinct (
E
) and recovered (
R
). A suitable parameter calibration that is based on the combined use of the least-squares method and the Markov chain Monte Carlo method is proposed with the aim of reproducing the past history of the epidemic in Italy, which surfaced in late February and is still ongoing to date, and of validating
SUIHTER
in terms of its predicting capabilities. A distinctive feature of the new model is that it allows a one-to-one calibration strategy between the model compartments and the data that are made available daily by the Italian Civil Protection Department. The new model is then applied to the analysis of the Italian epidemic with emphasis on the second outbreak, which emerged in autumn 2020. In particular, we show that the epidemiological model
SUIHTER
can be suitably used in a predictive manner to perform scenario analysis at a national level.
Clostridium perfringens necrotizing pancreatitis: an unusual pathogen in pancreatic necrosis infection
Authors: Sánchez-Gollarte Ana , Jiménez-Álvarez Laura , Pérez-González Marina , Vera-Mansilla Cristina , Blázquez-Martín Alma , Díez-Alonso Manuel
Published: September 2021

Pancreatic necrosis infection (PNI) accounts for about 20–40 % of severe acute pancreatitis. PNI caused by anaerobic bacteria is unusual but when they present,

Clostridium perfringens

is the microorganism most commonly involved. We present a 60-year-old patient with a previous history of SARS-CoV-2, diagnosed with acute pancreatitis. During the hospitalisation he developed

Clostridium perfringens

bacteraemia. A CT-scan showed pancreatic gas gangrene and a surgical necrosectomy was performed.

Clostridium perfringens

was isolated in cultures of the pancreatic tissue and collections. The patient’s clinical status improved after surgery and the appropriate medical therapy. He was discharged 76 days after admission. Nowadays, the ‘step-up approach’ is an accepted therapeutic tool in treatment of pancreatic necrosis and peripancreatic fluid collections. However, most authors suggest that Clostridum perfringens infection requires a more aggressive approach due to the high mortality associated to clostridial infection.
Causal effect of C-reactive protein and vitamin D on human cerebral anatomy observed among genetically correlated biomarkers in blood
Authors: Kiltschewskij Dylan J. , Reay William R. , Cairns Murray J.
Published: September 2021

Psychiatric disorders such as schizophrenia are commonly associated with structural brain alterations affecting the cortex, which frequently vary with clinically relevant factors including antipsychotic treatment, duration of illness and age of onset. While the underlying variables mediating these structural changes are poorly understood, recent genetic evidence suggests circulating metabolites and other biochemical traits play a causal role in a number of psychiatric disorders which could be mediated by changes in the cerebral cortex. In the current study, we leveraged publicly available genome-wide association study (GWAS) data to explore shared genetic architecture and evidence for causal relationships between a panel of 50 biochemical traits and measures of cortical thickness and surface area at both the global and regional levels. Linkage disequilibrium score regression identified a total of 20 significant and 156 suggestive genetically correlated biochemical-cortical trait pairings, of which six exhibited strong evidence for causality in a latent causal variable model. Interestingly, a negative causal relationship was identified between a unit increase in serum C-reactive protein levels and thickness of the lingual and lateral occipital regions that was also supported by Mendelian randomisation, while circulating vitamin D (25-hydroxyvitamin D) levels exhibited a positive causal effect on temporal pole thickness. Taken together, our findings suggest a subset of biochemical traits exhibit shared genetic architecture and potentially causal relationships with cortical thickness in functionally distinct regions, which may contribute to alteration of cortical structure in psychiatric disorders.
Drought stress increases the expression of barley defence genes with negative consequences for infesting cereal aphids
Authors: Leybourne Daniel J. , Valentine Tracy A , Binnie Kirsty , Taylor Anna , Karley Alison J , Bos Jorunn IB
Published: September 2021

Crops are exposed to myriad abiotic and biotic stressors with negative consequences. Two stressors that are expected to increase under climate change are drought and infestation with herbivorous insects, including important aphid species. Expanding our understanding of the impact drought has on the plant-aphid relationship will become increasingly important under future climate scenarios. Here we use a previously characterised plant-aphid system comprising a susceptible variety of barley, a wild relative of barley with partial-aphid resistance, and the bird cherry-oat aphid to examine the drought-plant-aphid relationship. We show that drought has a negative effect on plant physiology and aphid fitness and provide evidence to suggest that plant resistance influences aphid responses to drought stress, with the expression of aphid detoxification genes increasing under drought when feeding on the susceptible plant but decreasing on the partially-resistant plant. Furthermore, we show that the expression of thionin genes, plant defensive compounds that contribute aphid resistance, increase ten-fold in susceptible plants exposed to drought stress but remain at constant levels in the partially-resistant plant, suggesting they play an important role in modulating aphid populations. This study highlights the role of plant defensive processes in mediating the interactions between the environment, plants, and herbivorous insects.
Disentangling five dimensions of animacy in human brain and behaviour
Authors: Jozwik Kamila M , Najarro Elias , van den Bosch Jasper JF , Charest Ian , Cichy Radoslaw M , Kriegeskorte Nikolaus
Published: September 2021

Distinguishing animate from inanimate things is of great behavioural importance. Despite distinct brain and behavioural responses to animate and inanimate things, it remains unclear which object properties drive these responses. Here, we investigate the importance of five object dimensions related to animacy (“being alive”, “looking like an animal”, “having agency”, “having mobility”, and “being unpredictable”) in brain (fMRI, EEG) and behaviour (property and similarity judgements) of 19 participants. We used a stimulus set of 128 images, optimized by a genetic algorithm to disentangle these five dimensions. The five dimensions explained much variance in the similarity judgments. Each dimension also explained a modest but significant amount of variance in the brain representations, except, surprisingly, “being alive”. Different brain regions sensitive to animacy may represent distinct dimensions, either as accessible perceptual stepping stones toward detecting whether something is alive or because they are of behavioural importance in their own right.
Fine-tuning functional syndromes for stressful environments: lessons on survival from the South African resurrection plant Myrothamnus flabellifolia
Authors: Marks Rose A. , Mbobe Mpho , Greyling Marilize , Pretorius Jennie , McLetchie D. Nicholas , VanBuren Robert , Farrant Jill M.
Published: September 2021

Resilience to abiotic stress is associated with a suite of functional traits related to defense and longevity. Stress tolerant plants are generally slow growing with extended leave lifespans and reduced allocation to reproduction. Resurrection plants are ideal systems to test for trade-offs associated with stress tolerance due to their extreme resiliency. While, growth defense trade-offs are well-characterized, few studies have tested for natural variation associated with tolerating the harshest environments. Here, we surveyed a suite of functional traits related to stress tolerance, leaf economics, and reproductive allocation in natural populations of the South African resurrection plant Myrothamnus flabellifolia. We selected three distinct field sites in South Africa ranging from mesic to xeric. Despite considerable environmental variation across the study area, M. flabellifolia plants were extremely and similarly stress tolerant at all sites. However, we detected notable variation in other life history and morphological traits. Plants in more mesic sites were larger, faster growing, and had more inflorescences. In contrast, plants from the most xeric sites appeared to invest more in persistence and defense, with lower growth rates and less reproductive allocation. Together, this suggests that desiccation tolerance is a binary trait in M. flabellifolia with little natural variation, but that other phenotypes are more labile. The trait syndromes exhibited by plants at the different study sites align with general expectations about growth defense tradeoffs associated with the colonization of extreme environments. We show that plants from the least stressful sites are more reproductive and faster growing, whereas plants from the most stressful sites were slower growing and less reproductive. These findings suggest that M. flabellifolia plants are finely tuned to their environment.
Non-linear functional brain co-activations in short-term memory distortion tasks
Authors: Ceglarek Anna , Ochab Jeremi K. , Cifre Ignacio , Fąfrowicz Magdalena , Sikora-Wachowicz Barbara , Lewandowska Koryna , Bohaterewicz Bartosz , Marek Tadeusz , Chialvo Dante R.
Published: September 2021

Recent works shed light on the neural correlates of true and false recognition and the influence of time of day on cognitive performance. The current study aimed to investigate the modulation of the false memory formation by the time of day using a non-linear correlation analysis originally designed for fMRI resting-state data. Fifty-four young and healthy participants (32 females, mean age: 24.17 y.o., SD: 3.56 y.o.) performed in MR scanner the modified Deese-Roediger-McDermott paradigm in short-term memory during one session in the morning and another in the evening. Subjects’ responses were modeled with a general linear model, which includes as a predictor the non-linear correlations of regional BOLD activity with the stimuli, separately for encoding and retrieval phases. The results show the dependence of the non-linear correlations measures with the time of day and the type of the probe. In addition, the results indicate differences in the correlations measures with hippocampal regions between positive and lure probes. Besides confirming previous results on the influence of time-of-day on cognitive performance, the study demonstrates the effectiveness of the non-linear correlation analysis method for the characterization of fMRI task paradigms.
Low dose hydroxychloroquine prophylaxis for COVID-19 – a prospective study
Authors:   RE-HCP2 COVID study group, Agarwal Mayank , Ranka Rajat , Panda Prasan Kumar , Kumar Ajay , Chikara Gaurav , Sharma Suresh K , Negi Rizu , Samanta Ramanuj , Walia Rohit , Bahurupi Yogesh Arvind , Saha Sarama , Dhar Minakshi , Sharma Prakhar , Gupta Arvind Kumar , Mishra UB , Gupta Manoj Kumar , Kant Ravi
Published: September 2021

Background

Since the outbreak of COVID-19 pandemic, the world began a frantic search for possible prophylactic options. While trials on hydroxychloroquine (HCQ) prophylaxis are ongoing, concrete evidence is lacking. The study aimed to determine the relative efficacy of various doses of oral HCQ in prophylaxis and mitigating the severity of COVID-19 in healthcare workers.

Methods

This was a prospective cohort with four arms (high, medium, low dose, and control) of HCQ prophylaxis, used by healthcare workers at a tertiary care center in India. Participants were grouped as per their opting for any one arm on a voluntary basis as per institute policy under the Government guidance. The outcomes studied were COVID-19 positivity by RT-PCR and its severity assessed by WHO COVID-19 severity scale.

Results

Total 486 participants were enrolled, of which 29 (6%) opted for low dose, 2 (<1%) medium dose, and none for high dose HCQ while 455 (93.6%) were in the control arm. Of the 164 participants who underwent RT-PCR, 96 (58.2%) tested positive. Out of these 96 positive cases, the majority of them (79 of 96 [82.3%]) were ambulatory and were managed conservatively at home. Only 17.7% (17 of 96) participants, all of them from the control group, required hospitalization with the mild-moderate disease. None of the participants had severe disease, COVID-related complications, ICU stay, or death. The difference in the outcome assessed amongst the various arms was statistically insignificant (p value >0.05).

Conclusion

This single-center study demonstrated that HCQ prophylaxis in healthcare workers does not cause a significant reduction in COVID-19 as well as mitigating its severity in those infected. At present, most of the trials have not shown any benefit. The debate continues to rage, should HCQ prophylaxis be given to healthcare workers for chemoprophylaxis?
Regional Cell Atlas of Human Intestine Shapes Distinct Immune Surveillance
Authors: Wang Yue , Yu Yanbo , Li Lixiang , Zheng Mengqi , Zhou Jiawei , Gong Haifan , Feng Bingcheng , Qu Junyan , Li Zhen , Ji Rui , Lu Ming , Yang Xiaoyun , Zuo Xiuli , Li Shiyang , Li Yanqing
Published: September 2021

Regional intestinal immune surveillance remains obscure. In this study, we integrated single-cell RNA sequencing and spatial transcriptomics to create a regional atlas of fetal and adult intestines, consisting of 59 cell subsets, of which eight new subsets and ILCs transition states were identified. Results revealed that microenvironment determines in-situ cell differentiation and shapes the regional molecular characteristics, allowing different intestinal segments with diverse functions. We characterized the regional expression of mucins, immunoglobulins, and antimicrobial peptides (AMPs) and their shift during development and in inflammatory bowel disease. Notably, α-defensins expressed most abundantly in small intestinal LGR5+ stem cells, rather than in Paneth cells, and down-regulated as cell maturing. Common upstream transcription factors controlled the AMPs expression, illuminating the concurrent change of AMPs during epithelial differentiation, and the spatial co-expression patterns. We demonstrated the correspondence of cell focus of risk genes to diseases’ location susceptibility and identified distinct cell-cell crosstalk and spatial heterogeneity of immune cell homing in different gut segments. Overall, a cross-spatiotemporal approach to transcriptomes at single-cell resolution revealed that the regional milieu of the human intestine determined cellular and molecular cues of immune surveillance, dictating gut homeostasis and disease.
The Lyme Disease agent co-opts adiponectin receptor-mediated signaling in its arthropod vector
Authors: Tang Xiaotian , Cao Yongguo , Arora Gunjan , Hwang Jesse , Sajid Andaleeb , Brown Courtney L. , Mehta Sameet , Marín-López Alejandro , Chuang Yu-Min , Wu Ming-Jie , Ma Hongwei , Pal Utpal , Narasimhan Sukanya , Fikrig Erol
Published: September 2021

Adiponectin-mediated pathways contribute to mammalian homeostasis; however, little is known about adiponectin and adiponectin receptor signaling in arthropods. In this study, we demonstrate that Ixodes scapularis ticks have an adiponectin receptor-like protein (ISARL) but lack adiponectin – suggesting activation by alternative pathways. ISARL expression is significantly upregulated in the tick gut after Borrelia burgdorferi infection suggesting that ISARL-signaling may be co-opted by the Lyme disease agent. Consistent with this, RNA interference (RNAi)-mediated silencing of ISARL significantly reduced the B. burgdorferi burden in the tick. RNA-seq-based transcriptomics and RNAi assays demonstrate that ISARL-mediated phospholipid metabolism by phosphatidylserine synthase I is associated with B. burgdorferi survival. Furthermore, the tick complement C1q-like protein 3 interacts with ISARL, and B. burgdorferi facilitates this process. This study identifies a new tick metabolic pathway that is connected to the life cycle of the Lyme disease spirochete.

Significance Statement

Adiponectin binds to adiponectin receptors and participates in glucose and lipid metabolism in mammals. In this study, we found that ticks have an adiponectin receptor-like protein but lack adiponectin. Importantly, we demonstrated that the Lyme disease agent, Borrelia burgdorferi, takes advantage of the adiponectin receptor signaling pathway to establish infection in its arthropod vector, Ixodes scapularis. Our study sheds light on the understanding of Borrelia-tick interactions and provides insights into how a human infectious disease agent may evolve to manipulate host metabolism for its own benefits. Understanding this pathway may lead to new ways to interfere with the Borrelia life cycle, and this mechanism may be applicable to additional microbes that are transmitted by ticks, mosquitoes or other arthropods.
High interaction valency ensures cohesion and persistence of a microtubule +TIP body at the plus-end of a single specialized microtubule in yeast
Authors: Meier Sandro M. , Farcas Ana-Maria , Kumar Anil , Ijavi Mahdiye , Bill Robert T. , Stelling Jörg , Dufresne Eric , Steinmetz Michel O. , Barral Yves
Published: September 2021

Microtubule plus-end tracking proteins (+TIPs) control microtubule specialization and are as such essential notably during eukaryotic cell division. Here, we investigated interactions and functions of the budding yeast Kar9 network consisting of the core +TIPs components Kar9 (functional homologue of APC, MACF, and SLAIN), Bim1 (orthologue of EB1), and Bik1 (orthologue of CLIP-170). Our data indicate that a redundant, multivalent web of interactions links the three +TIPs together to form a “Kar9 body” at the tip of a single cytoplasmic microtubule. They further suggest that this body is a liquid-like condensate, allowing it to persist on both growing and shrinking microtubule tips, and functions as a mechanical coupling device between microtubules and actin cables during mitosis. Our study underlines the power of dissecting the web of low-affinity interactions driving liquid-liquid phase separation of proteins in order to demonstrate the importance and establish the functional roles of condensation processes in vivo.
Gene duplication and rate variation in the evolution of plastid ACCase and Clp genes in angiosperms
Authors: Williams Alissa M. , Carter Olivia G. , Forsythe Evan S. , Mendoza Hannah K. , Sloan Daniel B.
Published: September 2021

While the chloroplast (plastid) is known for its role in photosynthesis, it is also involved in many other metabolic pathways essential for plant survival. As such, plastids contain an extensive suite of enzymes required for non-photosynthetic processes. The evolution of the associated genes has been especially dynamic in flowering plants (angiosperms), including examples of gene duplication and extensive rate variation. We examined the role of ongoing gene duplication in two key plastid enzymes, the acetyl-CoA carboxylase (ACCase) and the caseinolytic protease (Clp), responsible for fatty acid biosynthesis and protein turnover, respectively. In plants, there are two ACCase complexes—a homomeric version present in the cytosol and a heteromeric version present in the plastid. Duplications of the nuclear-encoded homomeric ACCase gene and retargeting of one resultant protein to the plastid have been previously reported in multiple species. We find that these retargeted homomeric ACCase proteins exhibit elevated rates of sequence evolution, consistent with neofunctionalization and/or relaxation of selection. The plastid Clp complex catalytic core is composed of nine paralogous proteins that arose via ancient gene duplication in the cyanobacterial/plastid lineage. We show that further gene duplication occurred more recently in the nuclear-encoded core subunits of this complex, yielding additional paralogs in many species of angiosperms. Moreover, in six of eight cases, subunits that have undergone recent duplication display increased rates of sequence evolution relative to those that have remained single copy. We also compared substitution patterns between pairs of Clp core paralogs to gain insight into post-duplication evolutionary routes. These results show that gene duplication and rate variation continue to shape the plastid proteome.
Allosteric modulation of the adenosine A2A receptor by cholesterol
Authors: Huang Shuya Kate , Almurad Omar , Pejana Reizel J. , Morrison Zachary A. , Pandey Aditya , Picard Louis-Philippe , Nitz Mark , Sljoka Adnan , Prosser R. Scott
Published: September 2021

Cholesterol is a major component of the cell membrane and commonly regulates membrane protein function. Here, we investigate how cholesterol modulates the conformational equilibria and signaling of the adenosine A2A receptor (A2AR) in reconstituted phospholipid bilayers. GTP hydrolysis assays show that cholesterol is a weak positive allosteric modulator of A2AR, as seen through enhanced basal signaling and a small decrease in agonist EC50. Fluorine nuclear magnetic resonance (19F NMR) spectroscopy suggests that this enhancement arises from an increase in the receptor’s active state populations and stronger G protein coupling. 19F NMR of fluorinated cholesterol analogs reveals transient and non-specific interactions with A2AR, indicating a lack of high-affinity binding sites or direct allosteric modulation. This is confirmed by computational analysis which suggests that cholesterol contacts confer a weak and possibly negative allosteric effect. The combined results suggest that the observed cholesterol allostery in A2AR is likely a result of indirect membrane effects through cholesterol-mediated changes in membrane properties, as shown by membrane fluidity measurements and high-pressure NMR.
Isolation, identification and molecular characterization of Aeromonas spp. from farmed loach (Misgurnus anguillicaudatus)
Authors: Wang Xin , Pan Jiwen , Chen Liqing , Li Roushan , Han Yu , Di Zihao , Ling Bo , Ahmad Ashfaq , Yang Nuo , Fan Lixia , Li Qian , Zeng Jifeng , Guo Guiying , Zheng Jiping
Published: September 2021

Gram-negative Aeromonas bacteria is known to contaminate aquaculture products and retains the ability to infect wide range of host including fishes, shrimps and humans. This study is designed to evaluate the presence of Aeromonas in healthy loaches (Misgurnus anguillicaudatus) collected from the markets in Hainan and Guangdong provinces of China. Based on the molecular sequencing and phylogenetic analysis with single 16S rRNA and concatenated genes (gyrA and ropD), 104 isolates were identified as Aeromonas species followed by further classification to A. veronii (83.65%), A. jandaei (9.62%), A. hydrophila (3.85%) and A. allosaccharophila (2.88%). More than half of the isolates displayed hemolytic activity of 87.5% and were able to form moderate biofilm (78.26%). Fourteen antibiotics from ten representative classes were screened that demonstrated complete resistance to ampicillin, 89.4% and 68.3% to lincomycin and nalidixic acid. Moreover, a notable detection and prevalence was found in screening of ten virulence-related and nine resistance genes. To our knowledge, it is the first report of its kind demonstrating potential threat of the commercial loaches carrying Aeromonas to human health. These findings will assist professionals working in clinical settings to optimize their prescription accordingly and researchers to access the impacts of Aeromonas resistance on human health.

Importance

This study demonstrates high infection rate of loaches by Aeromonas spp. in Hainan and Guangdong provinces of China.

The most prevalent species was Aeromonas veronii.

Most of the isolates displayed hemolytic activity and formed moderate biofilm.

Multiple virulence genes, resistance genes and multi-antibiotic resistance were detected.

Aeromonads risks should be considered in loach industry.
Assessment of CAR-T mediated and targeted cytotoxicity in 3D microfluidic TBNC co-culture models for combination therapy
Authors: Paterson K. , Paterson S. , Mulholland T. , Coffelt S. B. , Zagnoni M.
Published: September 2021

Chimeric antigen receptor (CAR)-T cell therapy is efficacious against many hematological malignancies; however, their therapeutic application to treat solid tumors presents further challenges. A better understanding of how the solid tumor microenvironment (TME) impacts CAR-T anti-tumor effects would enable the selection of effective combination therapies to decipher the optimal course of treatment for patients and to better engineer CAR-Ts. Classical 2Din vitromodels do not provide sufficient recapitulation of the native human TME, andin vivomodels, such as patient-derived xenografts, are costly, complex and labor intensive. Here, we present a novel 3D, miniaturized assay for the evaluation of EGFR-targeted CAR-T cell cytotoxicity and specificity on tumor-stroma triple-negative breast cancer models in microfluidic devices. CAR-T cells were shown to home towards EGFR-expressing cancer cells to elicit a cytotoxic effect, whilst leaving low EGFR-expressing fibroblasts viable, an effect which was enhanced through combination anti-PD-L1 therapy and carboplatin chemotherapy. Hence, we propose this proof-of-concept immunoassay as a future preclinical screening tool for the development of novel immunotherapeutics and for use in personalized medicine.
Convergent clonal selection of donor- and recipient-derived CMV-specific T cells in hematopoietic stem cell transplant patients
Authors: Erickson Jami R. , Stevens-Ayers Terry , Mair Florian , Edmison Bradley , Boeckh Michael , Bradley Philip , Prlic Martin
Published: September 2021

Competition between antigen-specific T cells for peptide:MHC (p:MHC) complexes shapes the ensuing T cell response. Mouse model studies provided compelling evidence that competition is a highly effective mechanism controlling the activation of naïve T cells. However, assessing the effect of T cell competition in the context of a human infection requires defined pathogen kinetics and trackable naïve and memory T cell populations of defined specificity. A unique cohort of non-myeloablative hematopoietic stem cell transplant (nmHSCT) patients allowed us to assess T cell competition in response to CMV reactivation, which was documented with detailed virology data. In our cohort, HSCT donors and recipients were CMV-seronegative and -positive, respectively, thus providing genetically distinct memory and naïve T cell populations. We used single-cell transcriptomics to track donor versus recipient-derived T cell clones over the course of 90 days. We found that donor-derived T cell clones proliferated and expanded substantially following CMV-reactivation. However, for immunodominant CMV epitopes, recipient-derived memory T cells remained the overall dominant population. This dominance was maintained despite more robust clonal expansion of donor-derived T cells in response to CMV reactivation. Interestingly, the donor-derived T cells that were recruited into these immunodominant memory populations shared strikingly similar TCR properties with the recipient-derived memory T cells. This selective recruitment of identical and nearly identical clones from the naïve into the immunodominant memory T cell pool suggests that competition does not interfere with rejuvenating a memory T cell population, but results in selection of convergent clones to the memory T cell pool.

Significance

An existing memory T cell population specific for a single epitope is sufficient to effectively curtail responses to any new antigens if the original epitope is present in a vaccination regimen or heterologous infections. We asked if T cell competition precludes recruitment of any new, naïve T cells to an existing memory T cell pool in context of CMV-specific T cell responses in a cohort of transplant patients. Our data indicate that competition does not prevent recruitment of naïve T cells into the memory T cell pool, but selects for T cells with nearly or fully congruent T cell receptor specificities. We discuss the implications of rejuvenating a memory T cell pool while preserving the T cell receptor repertoire.
Deep learning and CRISPR-Cas13d ortholog discovery for optimized RNA targeting
Authors: Wei Jingyi , Lotfy Peter , Faizi Kian , Baungaard Sara , Gibson Emily , Wang Eleanor , Slabodkin Hannah , Kinnaman Emily , Chandrasekaran Sita , Kitano Hugo , Durrant Matthew G. , Duffy Connor V. , Hsu Patrick D. , Konermann Silvana
Published: September 2021

Transcriptome engineering technologies that can effectively and precisely perturb mammalian RNAs are needed to accelerate biological discovery and RNA therapeutics. However, the broad utility of programmable CRISPR-Cas13 ribonucleases has been hampered by an incomplete understanding of the design rules governing guide RNA activity as well as cellular toxicity resulting from off-target or collateral RNA cleavage. Here, we sought to characterize and develop Cas13d systems for efficient and specific RNA knockdown with low cellular toxicity in human cells. We first quantified the performance of over 127,000 RfxCas13d (CasRx) guide RNAs in the largest-scale screen to date and systematically evaluated three linear, two ensemble, and two deep learning models to build a guide efficiency prediction algorithm validated across multiple human cell types in orthogonal validation experiments (https://www.RNAtargeting.org). Deep learning model interpretation revealed specific sequence motifs at spacer position 15-24 along with favored secondary features for highly efficient guides. We next identified 46 novel Cas13d orthologs through metagenomic mining for activity and cytotoxicity screening, discovering that the metagenome-derived DjCas13d ortholog achieves low cellular toxicity and high transcriptome-wide specificity when deployed against high abundance transcripts or in sensitive cell types, including human embryonic stem cells, neural progenitor cells, and neurons. Finally, our Cas13d guide efficiency model successfully generalized to DjCas13d, highlighting the utility of a comprehensive approach combining machine learning with ortholog discovery to advance RNA targeting in human cells.
Structure of a bacterial Rhs effector exported by the type VI secretion system
Authors: Günther Patrick , Quentin Dennis , Ahmad Shehryar , Sachar Kartik , Gatsogiannis Christos , Whitney John C. , Raunser Stefan
Published: September 2021

The type VI secretion system (T6SS) is a widespread protein export apparatus found in Gram-negative bacteria. The majority of T6SSs deliver toxic effector proteins into competitor bacteria. Yet, the structure, function, and activation of many of these effectors remains poorly understood. Here, we present the structures of the T6SS effector RhsA from Pseudomonas protegens and its cognate T6SS spike protein, VgrG1, at 3.3 Å resolution. The structures reveal that the rearrangement hotspot (Rhs) repeats of RhsA assemble into a closed anticlockwise β-barrel spiral similar to that found in bacterial insecticidal Tc toxins and in metazoan teneurin proteins. We find that the C-terminal toxin domain of RhsA is autoproteolytically cleaved but remains inside the Rhs ‘cocoon’ where, with the exception of three ordered structural elements, most of the toxin is disordered. The N-terminal ‘plug’ domain is unique to T6SS Rhs proteins and resembles a champagne cork that seals the Rhs cocoon at one end while also mediating interactions with VgrG1. Interestingly, this domain is also autoproteolytically cleaved inside the cocoon but remains associated with it. We propose that mechanical force is required to remove the cleaved part of the plug, resulting in the release of the toxin domain as it is delivered into a susceptible bacterial cell by the T6SS.
Extracellular Matrix Stiffness Alters TRPV4 Regulation in Chondrocytes
Authors: Trompeter Nicholas , Farino Cindy J. , Griffin Mallory , Skinner Ryan , Banda Omar A. , Gleghorn Jason P. , Slater John. H , Duncan Randall L.
Published: September 2021

During the progression of osteoarthritis (OA), degradation of the extracellular matrix alters the biomechanical properties of cartilage, especially the compressive modulus. The mechanosensitive ion channel transient receptor potential vanilloid 4 (TRPV4) is required for chondrocyte mechanotransduction However, how OA-mediated cartilage degradation influences TRPV4 signaling remains unknown. To determine if ATDC5 cells alter TRPV4-mediated calcium signaling and cell phenotype in response to softer substrates, we created PEGDA-RGDS hydrogels with Young’s moduli that simulated healthy (~350 kPa), OA (~175 kPa) and severe OA (~35 kPa) tissue. We found that softer substrates reduced the influx of calcium through TRPV4 when challenging chondrocytes with hypotonic swelling (HTS). Chondrocyte apoptosis also increased on the OA and severe OA gels due to elevated basal [Ca2+]i, which is attenuated with pharmacological agonism of TRPV4. Pharmacological agonism of TRPV4 rescued the expression of aggrecan and TRPV4 in chondrocytes cultured on OA gels and enhanced the type II collagen (col2) expression in cells on the normal and OA gels. These data suggest that the biomechanical properties of degraded cartilage alter TRPV4-mediated mechanotransduction in chondrocytes. Given that TRPV4 reduced apoptosis and improved the chondrogenic capacity of cells, TRPV4 stimulation could provide a potential therapeutic target in patients with early to moderate OA.
Direct capsid labeling of infectious HIV-1 by genetic code expansion allows detection of largely complete nuclear capsids and suggests nuclear entry of HIV-1 complexes via common routes
Authors: Schifferdecker Sandra , Zila Vojtech , Müller Thorsten G. , Sakin Volkan , Anders-Össwein Maria , Laketa Vibor , Kräusslich Hans-Georg , Müller Barbara
Published: September 2021

The cone-shaped mature HIV-1 capsid is the main orchestrator of early viral replication. After cytosolic entry, it transports the viral replication complex along microtubules towards the nucleus. While it was initially believed that the reverse transcribed genome is released from the capsid in the cytosol, recent observations indicate that a high amount of capsid protein (CA) remains associated with subviral complexes during import through the nuclear pore complex (NPC). Observation of post-entry events via microscopic detection of HIV-1 CA is challenging, since epitope shielding limits immunodetection and the genetic fragility of CA hampers direct labeling approaches. Here, we present a minimally invasive strategy based on genetic code expansion and click chemistry that allows for site-directed fluorescent labeling of HIV-1 CA, while retaining virus morphology and infectivity. Thereby, we could directly visualize virions and subviral complexes using advanced microscopy, including nanoscopy and correlative imaging. Quantification of signal intensities of subviral complexes revealed an amount of CA associated with nuclear complexes in HeLa-derived cells and primary T cells consistent with a complete capsid and showed that treatment with the small molecule inhibitor PF74 did not result in capsid dissociation from nuclear complexes. Cone-shaped objects detected in the nucleus by electron tomography were clearly identified as capsid-derived structures by correlative microscopy. High-resolution imaging revealed dose-dependent clustering of nuclear capsids, suggesting that incoming particles may follow common entry routes.