bluuebunny/crossref_metadata_2025 huggingface dataset:
The Application of Exosomal MicroRNAs in the Treatment of Pancreatic Cancer and Its Research Progress
Authors: Li Xin , Jiang Wenkai , Gan Yu , Zhou Wence
Published: December 2020

Despite great progress in the treatment of pancreatic cancer under the efforts of researchers, the survival time of patients with pancreatic cancer is shorter than that of patients with other cancers. Thus, we have a great need for innovative therapeutic methods, including research and development of new drugs and innovation of administration methods. Exosomes are a type of extracellular vesicles wrapped by a lipid bilayer. Thanks to the low clearance ratio and strong specificity of exosomes in circulation, together with in-depth research on the surface protein of exosomes and a targeted modification method, there is a strong potential to apply exosomes in the transfer and even targeted delivery of chemotherapeutics, RNA, and natural products. Particularly, exosomes carrying microRNA show good application prospects in cancer therapy. This article is intended to summarize the progress of research relating to the treatment of pancreatic cancer via exosomal microRNAs.
Multicenter Retrospective Analysis of Chemotherapy for Advanced Pancreatic Acinar Cell Carcinoma
Authors: Takahashi Hideaki , Ikeda Masafumi , Shiba Satoshi , Imaoka Hiroshi , Todaka Akiko , Shioji Kazuhiko , Yane Kei , Kojima Yasushi , Kobayashi Satoshi , Asagi Akinori , Ozaka Masato , Takada Ryoji , Nagashio Yoshikuni , Horiguchi Shigeru , Kasuga Akiyoshi , Suzuki Eiichiro , Terashima Takeshi , Ueno Makoto , Morizane Chigusa , Furuse Junji
Published: December 2020

Objectives

The aim of this multicenter retrospective study was to identify the optimal chemotherapeutic regimen for advanced pancreatic acinar cell carcinoma (PACC).

Methods

Fifty-eight patients with histopathologically confirmed advanced PACC who had received chemotherapy between 1996 and 2013 were enrolled. The clinical characteristics of the patients and the treatment efficacy data were collected from the medical records at 16 Japanese institutions, using standardized data collection instrument.

Results

The most commonly selected treatment regimens were gemcitabine-, fluoropyrimidine-, platinum-, and irinotecan-containing regimens. The overall response rate in the patients who received first-line chemotherapy were 7% and 38%, respectively, and the median overall survival was 13.2 months. When the data for all the treatment lines were aggregated, the response rates to gemcitabine-, fluoropyrimidine-, platinum-, and irinotecan-containing regimens were 7%, 18%, 40%, and 29%, respectively. The overall survival tended to be better in patients who had received a platinum-containing regimen (hazard ratio, 0.50; 95% confidence interval, 0.23–1.11; P = 0.08) or irinotecan-containing regimen (hazard ratio, 0.42; 95% confidence interval, 0.15–1.19; P = 0.09) at least once in the treatment course as compared with those who had not.

Conclusions

Our findings suggested that platinum- and irinotecan-containing regimens exhibited some potential efficacy in patients with advanced PACC.
Causes of Death After Neuroendocrine Tumors Diagnosis
Authors: Sonbol Mohamad Bassam , Saad Anas M. , Gonzalez-Velez Miguel , Starr Jason , Halfdanarson Thorvardur R.
Published: December 2020

Objective

In this study, we aimed to determine the cause of death (COD) after the diagnosis of neuroendocrine tumors (NET).

Methods

We used the Surveillance, Epidemiology and End Results (SEER) Program to review patients diagnosed with NET during 2000 to 2016. Patients were followed until death, and different CODs were determined.

Results

Of 94,399 patients with NETs, 40.9% died during the study period. During the first year of diagnosis, most deaths were from NETs (73%), followed by other cancers (11.2%) and cardiac diseases (4.6%). After more than 10 years, NET deaths decreased to 24.3%, whereas other cancers and cardiac disease became more common. Neuroendocrine tumors were responsible for 42.8%, 63.4%, and 81.2% of deaths in grade I, grade II, and grade III, respectively. For grade I localized NET, other cancers (22.2%) were the most common COD followed by NET (19.7%), whereas in grade 2 localized NET, NET was COD in 31.1% of cases followed by other cancers (22.4%). In metastatic disease, NET was the most common COD regardless of grade.

Conclusions

For low-grade localized NET, deaths were mostly secondary to non-NET causes. In contrast, NET is responsible for most of deaths in metastatic NET regardless of grade.
Validation of a Clinical Prediction Rule to Predict Asymptomatic Chlamydia and Gonorrhea Infections Among Internet-Based Testers
Authors: Ablona Aidan , Falasinnu Titilola , Irvine Michael , Estcourt Claudia , Flowers Paul , Murti Michelle , Gómez-Ramírez Oralia , Fairley Christopher K. , Mishra Sharmistha , Burchell Ann , Grennan Troy , Gilbert Mark
Published: December 2020

Background

Clinical prediction rules (CPRs) can be used in sexually transmitted infection (STI) testing environments to prioritize individuals at the highest risk of infection and optimize resource allocation. We previously derived a CPR to predict asymptomatic chlamydia and/or gonorrhea (CT/NG) infection among women and heterosexual men at in-person STI clinics based on 5 predictors. Population differences between clinic-based and Internet-based testers may limit the tool's application across settings. The primary objective of this study was to assess the validity, sensitivity, and overall performance of this CPR within an Internet-based testing environment (GetCheckedOnline.com).

Methods

We analyzed GetCheckedOnline online risk assessment and laboratory data from October 2015 to June 2019. We compared the STI clinic population used for CPR derivation (data previously published) and the GetCheckedOnline validation population using χ2 tests. Calibration and discrimination were assessed using the Hosmer-Lemeshow goodness-of-fit test and the area under the receiver operating curve, respectively. Sensitivity and the fraction of total screening tests offered were quantified for CPR-predicted risk scores.

Results

Asymptomatic CT/NG infection prevalence in the GetCheckedOnline population (n = 5478) was higher than in the STI clinic population (n = 10,437; 2.4% vs. 1.8%, P = 0.007). When applied to GetCheckedOnline, the CPR had reasonable calibration (Hosmer-Lemeshow, P = 0.90) and discrimination (area under the receiver operating characteristic, 0.64). By screening only individuals with total risk scores ≥4, we would detect 97% of infections and reduce screening by 14%.

Conclusions

The application of an existing CPR to detect asymptomatic CT/NG infection is valid within an Internet-based STI testing environment. Clinical prediction rules applied online can reduce unnecessary STI testing and optimize resource allocation within publicly funded health systems.
Efficacy, Safety, and Immunogenicity of Biosimilar Etanercept (Enerceptan) Versus Its Original Form in Combination With Methotrexate in Patients With Rheumatoid Arthritis
Authors: Strusberg Ingrid , Mysler Eduardo , Citera Gustavo , Siri Daniel , de los Ángeles Correa Maria , Lazaro Maria Alicia , Pardo Hidalgo Rodolfo , Spindler Alberto , Tate Patricio , Venarotti Horacio , Velasco Zamora Jorge , Klimovsky Ezequiel , Federico Andrea , Scheines Eduardo , Gonzalez Eliseo , Cordeiro Lucas , Lago Nestor
Published: December 2020

Background

Enerceptan (EtaBS) has been developed as a proposed biosimilar of etanercept.

Methods

This randomized, multicenter, evaluator-blinded, noninferiority study conducted in Argentina included adults with active, moderate, and severe rheumatoid arthritis with inadequate response to methotrexate. Subjects were randomly assigned to 32 weeks treatment with EtaBS (n = 99) or etanercept (n = 51) at a weekly 50-mg dose administered subcutaneously. Patients were categorized according to prior use of biologic disease-modifying antirheumatic drugs and concomitant use of steroids. The primary efficacy endpoint was ACR20 response rate at week 32. Safety, immunogenicity, and steady-state concentration of both drugs were evaluated. The noninferiority margin for ACR20 was estimated at 12%.

Results

In the per-protocol population, 85 subjects (92.4%) treated with EtaBS and 44 subjects (93.6%) treated with etanercept achieved ACR20 (difference, −1.2%; 95% confidence interval, −10.1% to 7.6%). Frequent adverse drug reactions occurred in 34.3% and 38% of subjects treated with EtaBS and etanercept, respectively. The most common reaction was upper respiratory tract infection. Six and 3 serious adverse events occurred in 4 and 3 subjects treated with EtaBS and etanercept, respectively. Injection site reactions occurred in 67.7% and 66.0% of subjects treated with EtaBS and etanercept, respectively. Two subjects treated with EtaBS and 1 subject treated with etanercept developed antibodies by week 32.

Conclusions

Efficacy outcomes for EtaBS were noninferior to original etanercept in patients with moderate-to-severe rheumatoid arthritis with inadequate response to methotrexate. Safety and immunogenicity results were comparable between the two. This study is a major step toward improving access to biologics in Latin America.
Kangaroos display gazing and gaze alternations during an unsolvable problem task
Authors: McElligott Alan G. , O'Keeffe Kristine H. , Green Alexandra C.
Published: December 2020

Domestication is generally assumed to have resulted in enhanced communication abilities between non-primate mammals and humans, although the number of species studied is very limited (e.g. cats,
Felis catus
; dogs,
Canis familiaris
; wolves,
Canis lupus
; goats,
Capra hircus
; horses,
Equus caballus
). In species without hands for pointing, gazing at humans when dealing with inaccessible food during an unsolvable task, and in particular gaze alternations between a human and the unsolvable task (considered forms of showing), are often interpreted as attempts at referential intentional communication. We report that kangaroos, marsupial mammals that have never been domesticated, actively gazed at an experimenter during an unsolvable problem task (10/11 kangaroos tested), thus challenging the notion that this behaviour results from domestication. Nine of the 10 kangaroos additionally showed gaze alternations between the unsolvable task and experimenter. We propose that the potential occurrence of these behaviours displayed towards humans has been underestimated, owing to a narrow focus on domestic animals, as well as a more general eutherian research bias.
Acute bottlenecks to the survival of juvenile
Pygoscelis
penguins occur immediately after fledging
Authors: Hinke Jefferson T. , Watters George M. , Reiss Christian S. , Santora Jarrod A. , Santos M. Mercedes
Published: December 2020

Estimating when and where survival bottlenecks occur in free-ranging marine predators is critical for effective demographic monitoring and spatial planning. This is particularly relevant to juvenile stages of long-lived species for which direct observations of death are typically not possible. We used satellite telemetry data from fledgling Adélie, chinstrap and gentoo penguins near the Antarctic Peninsula to estimate the spatio-temporal scale of a bottleneck after fledging. Fledglings were tracked up to 106 days over distances of up to 2140 km. Cumulative losses of tags increased to 73% within 16 days of deployment, followed by an order-of-magnitude reduction in loss rates thereafter. The timing and location of tag losses were consistent with at-sea observations of penguin carcasses and bioenergetics simulations of mass loss to thresholds associated with low recruitment probability. A bootstrapping procedure is used to assess tag loss owing to death versus other factors. Results suggest insensitivity in the timing of the bottleneck and quantify plausible ranges of mortality rates within the bottleneck. The weight of evidence indicates that a survival bottleneck for fledgling penguins is acute, attributable to predation and starvation, and may account for at least 33% of juvenile mortality.
Gordon Henry Dixon. 25 March 1930—24 July 2016
Authors: Oliva Rafael , Krawetz Stephen A. , Consortium GHD
Published: December 2020

Gordon H. Dixon was a highly influential scientist who excelled in all the stages of his career and in each laboratory of every institution at which he was a member. Gordon began his graduate career at the University of Cambridge and completed his studies at the University of Toronto on the subject of transpeptidation reactions in biological systems. At an early stage of his career, he developed the technique of starch gel electrophoresis with Oliver Smithies and made important discoveries on the structure of human haptoglobins.

Subsequently, Gordon contributed to the determination of the structure and active sites and mechanisms of action of trypsin and chymotrypsin and made seminal discoveries related to understanding the structure of the protein hormone insulin. However, he is best known for his later studies on the regulation of protamine genes and chromatin transitions in spermatogenesis. He is often considered to be the father of the protamine molecular biology underlying this gene system and his research is continually cited to this day. Gordon contributed to the identification and sequencing of the protamine genes, the discovery that methionine was required for initiation of protamine synthesis, understanding the roles of histone hyperacetylation and protamine phosphorylation, and the generation of the highly compact nucleoprotamine structure present in sperm, primarily using trout as a model system. Gordon is fondly remembered as a brilliant and very generous scientist by all his mentees, representing all levels from undergraduates to PhD and postdoctoral fellows, who provided a scientifically stimulating atmosphere in which they could develop their careers. From a more personal perspective, he also had a fun side and was devoted to his family. Gordon was a person who, owing to his legacy of great science and his fundamental humanity, still lives in the memory of many people.
An experimental design tool to optimize inference precision in data-driven mathematical models of bacterial infections
in vivo
Authors: Vlazaki Myrto , Price David J. , Restif Olivier
Published: December 2020

The management of bacterial diseases calls for a detailed knowledge about the dynamic changes in host–bacteria interactions. Biological insights are gained by integrating experimental data with mechanistic mathematical models to infer experimentally unobservable quantities. This inter-disciplinary field would benefit from experiments with maximal information content yielding high-precision inference. Here, we present a computationally efficient tool for optimizing experimental design in terms of parameter inference in studies using isogenic-tagged strains. We study the effect of three experimental design factors: number of biological replicates, sampling timepoint selection and number of copies per tagged strain. We conduct a simulation study to establish the relationship between our optimality criterion and the size of parameter estimate confidence intervals, and showcase its application in a range of biological scenarios reflecting different dynamics patterns observed in experimental infections. We show that in low-variance systems with low killing and replication rates, predicting high-precision experimental designs is consistently achieved; higher replicate sizes and strategic timepoint selection yield more precise estimates. Finally, we address the question of resource allocation under constraints; given a fixed number of host animals and a constraint on total inoculum size per host, infections with fewer strains at higher copies per strain lead to higher-precision inference.
Identification of
FoxP
circuits involved in locomotion and object fixation in
Drosophila
Authors: Palazzo Ottavia , Rass Mathias , Brembs Björn
Published: December 2020

The
FoxP
family of transcription factors is necessary for operant self-learning, an evolutionary conserved form of motor learning. The expression pattern, molecular function and mechanisms of action of the
Drosophila FoxP
orthologue remain to be elucidated. By editing the genomic locus of
FoxP
with CRISPR/Cas9, we find that the three different
FoxP
isoforms are expressed in neurons, but not in glia and that not all neurons express all isoforms. Furthermore, we detect
FoxP
expression in, e.g. the protocerebral bridge, the fan-shaped body and in motor neurons, but not in the mushroom bodies. Finally, we discover that
FoxP
expression during development, but not adulthood, is required for normal locomotion and landmark fixation in walking flies. While
FoxP
expression in the protocerebral bridge and motor neurons is involved in locomotion and landmark fixation, the
FoxP
gene can be excised from dorsal cluster neurons and mushroom-body Kenyon cells without affecting these behaviours.
Cellular sociology regulates the hierarchical spatial patterning and organization of cells in organisms
Authors: Ganesh Shambavi , Utebay Beliz , Heit Jeremy , Coskun Ahmet F.
Published: December 2020

Advances in single-cell biotechnology have increasingly revealed interactions of cells with their surroundings, suggesting a cellular society at the microscale. Similarities between cells and humans across multiple hierarchical levels have quantitative inference potential for reaching insights about phenotypic interactions that lead to morphological forms across multiple scales of cellular organization, namely cells, tissues and organs. Here, the functional and structural comparisons between how cells and individuals fundamentally socialize to give rise to the spatial organization are investigated. Integrative experimental cell interaction assays and computational predictive methods shape the understanding of societal perspective in the determination of the cellular interactions that create spatially coordinated forms in biological systems. Emerging quantifiable models from a simpler biological microworld such as bacterial interactions and single-cell organisms are explored, providing a route to model spatio-temporal patterning of morphological structures in humans. This analogical reasoning framework sheds light on structural patterning principles as a result of biological interactions across the cellular scale and up.
Geometric morphometrics of endophytic oviposition traces of Odonata (Eocene, Argentina)
Authors: Romero-Lebrón Eugenia , Gleiser Raquel M. , Petrulevičius Julián F.
Published: December 2020

The insertion of the Odonata ovipositor in the plant tissue generates a scar that surrounds the eggs (trace). In insects, individual egg traces are known to vary in size, but their variation in individual shape is mostly unknown. Twenty-four specimens were obtained from the Laguna del Hunco (Lower Eocene, Chubut) and Río Pichileufú (Middle Eocene, Río Negro), Argentina, which had 1346 oviposition traces (MEF Collection). For the first time, a study of the shape and size of a large number of individual Odonata endophytic egg traces was carried out using traditional (general and mixed linear models) and geometric morphometrics (Fourier elliptical series) to elucidate whether there are changes in size or shape of the individual endophytic egg traces associated with the substrate used at the time of oviposition, if the Lower Eocene traces have varied in relation to those of the Middle Eocene, and if the ichnological classification (
Paleoovoidus arcuatus
,
P. bifurcatus
and
P. rectus
) reflects such variations. We found differences in size (
p
< 0.05), but not in shape, in relation to the variables studied. This could reflect that the shape of Odonata eggs (inferred from the traces), unlike their size, could have a strong evolutionary constraint already observed since the Eocene.
The dorsal hippocampus is required for the formation of long-term duration memories in rats
Authors: Hata Toshimichi , Yamashita Tatsuya , Kamada Taisuke
Published: December 2020

Interval timing—the perception of durations mainly in seconds or minutes—is a ubiquitous behavior in organisms. Animal studies have suggested that the hippocampus plays an essential role in duration memory; however, the memory processes involved are unclear. To clarify the role of the dorsal hippocampus in the acquisition of long-term duration memories, we adapted the “time-shift paradigm” to a peak-interval procedure. After a sufficient number of training with an initial target duration (20 s), the rats underwent “shift sessions” with a new target duration (40 s) under a muscimol (0.5 μg per side) infusion into the bilateral dorsal hippocampus. The memory of the new target duration was then tested in drug-free “probe sessions,” including trials in which no lever presses were reinforced. In the probe sessions, the mean response rate distribution of the muscimol group was located leftward to the control group, but these two response rate distributions were superimposed on the standardized time axis, suggesting a scalar property. In the session-by-session analysis, the mean peak time (an index of timing accuracy) of the muscimol group was lower than that of the control group in the probe sessions, but not in the shift sessions. These findings suggest that the dorsal hippocampus is required for the formation of long-term duration memories within the range of interval timing.
The evolutionary history of topological variations in the CPA/AT superfamily
Authors: Govindarajan Sudha , Bassot Claudio , Lamb John , Shu Nanjiang , Huang Yan , Elofsson Arne
Published: December 2020

CPA/AT transporters consist of two structurally and evolutionarily related inverted repeat units, each of them with one core and one scaffold subdomain. During evolution, these families have undergone substantial changes in structure, topology and function. Central to the function of the transporters is the existence of two non-canonical helices that are involved in the transport process. In different families, two different types of these helices have been identified, reentrant and broken. Here, we use an integrated topology annotation method to identify novel topologies in the families. It combines topology prediction, similarity to families with known structure, and the difference in positively charged residues present in inside and outside loops in alternative topological models. We identified families with diverse topologies containing broken or reentrant helix. We classified all families based on 3 distinct evolutionary groups that each share a structurally similar C-terminal repeat unit newly termed as “Fold-types”. Using the evolutionary relationship between families we propose topological transitions including, a transition between broken and reentrant helices, complete change of orientation, changes in the number of scaffold helices and even in some rare cases, losses of core helices. The evolutionary history of the repeat units shows gene duplication and repeat shuffling events to result in these extensive topology variations. The novel structure-based classification, together with supporting structural models and other information, is presented in a searchable database, CPAfold (cpafold.bioinfo.se). Our comprehensive study of topology variations within the CPA superfamily provides better insight about their structure and evolution.
Factors contributing to the disease ecology of brown crab (Cancer pagurus) in a temperate marine protected area
Authors: Davies Charlotte E. , Johnson Andrew F. , Wootton Emma C. , Greenwood Spencer J. , Clark K. Fraser , Vogan Claire L. , Rowley Andrew F.
Published: December 2020

Marine ecosystems are affected by multiple, well-known stressors like fishing and climate change, but a less documented concern is disease. Marine reserves have been successful in replenishing stocks and aiding recruitment but studies have shown that high population abundances in marine reserves may lead to unwanted secondary effects such as increase in predators and competition, altering trophic webs, and disease. Here, we investigate factors contributing to disease prevalence in a brown crab (Cancer pagurus) population around Lundy Island (the UK’s first MPA) after 7 years of no-take protection. Population parameters (size, sex, and abundance), disease (shell disease,Hematodiniumspp. infection) and injury presence (a known precursor to some disease conditions) were assessed over two years in both fished and unfished areas of the MPA. We found no significant difference in prevalence between the disease prevalence in fished and unfished areas, however overall, the number of injured crabs increased significantly over the two years (12%), as did the prevalence of shell disease (15%). The probability of crabs having shell disease increased significantly in male crabs, and in those missing limbs. The probability of crabs being injured increased significantly in crabs below the minimum landing size. In terms of population parameters, crabs were more prevalent in the fished area compared to the unfished area, thought to be a result of an increase in the predatory European lobster. The findings of the present study highlight potential secondary community changes as a result of MPA implementation. Therefore, surveillance for such changes, as part of MPA management, would provide useful information on the health and overall function of the protected ecosystem.
Total recall: episodic memory retrieval, choice, and memory confidence in the rat
Authors: Joo Hannah R. , Liang Hexin , Chung Jason E. , Geaghan-Breiner Charlotte , Fan Jiang Lan , Nachman Benjamin P. , Kepecs Adam , Frank Loren M.
Published: December 2020

Episodic memory enables recollection of past experiences to guide future behavior. Humans know which memories to trust (high confidence) and which to doubt (low confidence). How memory retrieval, memory confidence, and memory-guided decisions are related, however, is not understood. Additionally, whether animals can assess confidence in episodic memories to guide behavior is unknown. We developed a spatial episodic memory task in which rats were incentivized to gamble their time: betting more following a correct choice yielded greater reward. Rat behavior reflected memory confidence, with higher temporal bets following correct choices. We applied modern machine learning to identify a memory decision variable, and built a generative model of memories evolving over time that accurately predicted both choices and confidence reports. Our results reveal in rats an ability thought to exist exclusively in primates, and introduce a unified model of memory dynamics, retrieval, choice, and confidence.
Diverse modes of binocular interactions in the mouse superior colliculus
Authors: Russell Ashley L. , Dixon Karen G. , Triplett Jason W.
Published: December 2020

The superior colliculus (SC) integrates visual and other sensory information to regulate critical reflexive and innate behaviors, such as prey capture. In the mouse, the vast majority of retinal ganglion cells (RGCs) innervate the SC, including inputs from both the contralateral (contra-RGCs) and ipsilateral (ipsi-RGCs) eye. Despite this, previous studies revealed minimal neuronal responses to ipsilateral stimulation and few binocular interactions in the mouse SC. More recent work suggests that ipsi-RGC function and innervation of the SC are critical for efficient prey capture, raising the possibility that binocular interactions in the mouse SC may be more prevalent than previously thought. To explore this possibility, we investigated eye-specific and binocular influences on visual responses and tuning of SC neurons, focusing on the anteromedial region. While the majority of SC neurons were primarily driven by contralateral eye stimulation, we observed that a substantial proportion of units were influenced or driven by ipsilateral stimulation. Clustering based on differential responses to eye-specific stimulus presentation revealed five distinct putative subpopulations and multiple modes of binocular interaction, including facilitation, summation, and suppression. Each of the putative subpopulations exhibited selectivity for orientation, and differences in spatial frequency tuning and spatial summation properties were observed between subpopulations. Further analysis of orientation tuning under different ocular conditions supported differential modes of binocular interaction between putative subtypes. Taken together, these data suggest that binocular interactions in the mouse SC may be more prevalent and diverse than previously understood.
deepBlink: Threshold-independent detection and localization of diffraction-limited spots
Authors: Eichenberger Bastian Th. , Zhan YinXiu , Rempfler Markus , Giorgetti Luca , Chao Jeffrey A.
Published: December 2020

Detection of diffraction-limited spots is traditionally performed with mathematical operators designed for idealized spots. This process requires manual tuning of parameters that is time-consuming and not always reliable. We have developed deepBlink, a neural network-based method to detect and localize spots automatically and demonstrate that deepBlink outperforms state-of-the-art methods across six publicly available datasets. deepBlink is open-sourced on PyPI and GitHub (https://github.com/BBQuercus/deepBlink) as a ready-to-use command-line interface.
A blueprint for high affinity SARS-CoV-2 Mpro inhibitors from activity-based compound library screening guided by analysis of protein dynamics
Authors: Gossen Jonas , Albani Simone , Hanke Anton , Joseph Benjamin P. , Bergh Cathrine , Kuzikov Maria , Costanzi Elisa , Manelfi Candida , Storici Paola , Gribbon Philip , Beccari Andrea R. , Talarico Carmine , Spyrakis Francesca , Lindahl Erik , Zaliani Andrea , Carloni Paolo , Wade Rebecca C. , Musiani Francesco , Kokh Daria B. , Rossetti Giulia
Published: December 2020

The SARS-CoV-2 coronavirus outbreak continues to spread at a rapid rate worldwide. The main protease (Mpro) is an attractive target for anti-COVID-19 agents. Unfortunately, unexpected difficulties have been encountered in the design of specific inhibitors. Here, by analyzing an ensemble of ~30,000 SARS-CoV-2 Mpro conformations from crystallographic studies and molecular simulations, we show that small structural variations in the binding site dramatically impact ligand binding properties. Hence, traditional druggability indices fail to adequately discriminate between highly and poorly druggable conformations of the binding site. By performing ~200 virtual screenings of compound libraries on selected protein structures, we redefine the protein’s druggability as the consensus chemical space arising from the multiple conformations of the binding site formed upon ligand binding. This procedure revealed a unique SARS-CoV-2 Mpro blueprint that led to a definition of a specific structure-based pharmacophore. The latter explains the poor transferability of potent SARS-CoV Mpro inhibitors to SARS-CoV-2 Mpro, despite the identical sequences of the active sites. Importantly, application of the pharmacophore predicted novel high affinity inhibitors of SARS-CoV-2 Mpro, that were validated by in vitro assays performed here and by a newly solved X-ray crystal structure. These results provide a strong basis for effective rational drug design campaigns against SARS-CoV-2 Mpro and a new computational approach to screen protein targets with malleable binding sites.
BiG-MAP: an automated pipeline to profile metabolic gene cluster abundance and expression in microbiomes
Authors: Pascal Andreu Victoria , Augustijn Hannah E. , van den Berg Koen , van der Hooft Justin J. J. , Fischbach Michael A. , Medema Marnix H.
Published: December 2020

Microbial gene clusters encoding the biosynthesis of primary and secondary metabolites play key roles in shaping microbial ecosystems and driving microbiome-associated phenotypes. Although effective approaches exist to evaluate the metabolic potential of such bacteria through identification of metabolic gene clusters in their genomes, no automated pipelines exist to profile the abundance and expression levels of such gene clusters in microbiome samples to generate hypotheses about their functional roles and to find associations with phenotypes of interest. Here, we describe BiG-MAP, a bioinformatic tool to profile abundance and expression levels of gene clusters across metagenomic and metatranscriptomic data and evaluate their differential abundance and expression between different conditions. To illustrate its usefulness, we analyzed 47 metagenomic samples from healthy and caries-associated human oral microbiome samples and identified 58 gene clusters, including unreported ones, that were significantly more abundant in either phenotype. Among them, we found themucoperon, a gene cluster known to be associated to tooth decay. Additionally, we found a putative reuterin biosynthetic gene cluster from aStreptococcusstrain to be enriched but not exclusively found in healthy samples; metabolomic data from the same samples showed masses with fragmentation patterns consistent with (poly)acrolein, which is known to spontaneously form from the products of the reuterin pathway and has been previously shown to inhibit pathogenicStreptococcus mutansstrains. Thus, we show how BiG-MAP can be used to generate new hypotheses on potential drivers of microbiome-associated phenotypes and prioritize the experimental characterization of relevant gene clusters that may mediate them.

Importance

Microbes play an increasingly recognized role in determining host-associated phenotypes by producing small molecules that interact with other microorganisms or host cells. The production of these molecules is often encoded in syntenic genomic regions, also known as gene clusters. With the increasing numbers of (multi-)omics datasets that can help understanding complex ecosystems at a much deeper level, there is a need to create tools that can automate the process of analyzing these gene clusters across omics datasets. The current study presents a new software tool called BiG-MAP, which allows assessing gene cluster abundance and expression in microbiome samples using metagenomic and metatranscriptomic data. In this manuscript, we describe the tool and its functionalities, and how it has been validated using a mock community. Finally, using an oral microbiome dataset, we show how it can be used to generate hypotheses regarding the functional roles of gene clusters in mediating host phenotypes.
The septate junction protein Snakeskin is critical for epithelial barrier function and tissue homeostasis in the Malpighian tubules of adultDrosophila
Authors: Dornan A.J. , Halberg K.A. , Beuter L.-K. , Davies S.-A. , Dow J.A.T.
Published: December 2020

Transporting epithelia provide a protective physical barrier while directing appropriate transport of ions, solutes and water. In invertebrates, epithelial integrity is dependent on formation, and maintenance, of ‘tight’ septate junctions (SJs). We demonstrated thatDrosophilaMalpighian (renal) tubules undergo an age-dependent decline in secretory transport capacity, which correlates with mislocalisation of SJ proteins and coincident progressive degeneration in cellular morphology and tissue homeostasis. By restrictively impairing, in adult tubules, the cell adhesion protein Snakeskin, which is essential for smooth SJ formation, we observed progressive changes in cellular and tissue morphology that phenocopied these effects, including mislocalisation of junctional proteins with concomitant loss of cell polarity and barrier function. Resulting in significant accelerated decline in tubule secretory capacity and organismal viability. Our investigations highlight the tubule’s essential role in maintenance of organismal health, while providing measurable markers of compromised epithelial barrier and tissue function that manifest in advanced morbidity and death.

Abstract Figure

Model for epithelial dysfunction arising from failure of smooth septate junctional complexes as a consequence of impairedSnakeskinexpression.
Nutrition or nature: disentangling the complex forces shaping prokaryote pan-genomes
Authors: Garza Daniel R. , von Meijenfeldt F. A. Bastiaan , van Dijk Bram , Boleij Annemarie , Huynen Martijn A. , Dutilh Bas E.
Published: December 2020

Microbial pan-genomes are shaped by a complex combination of stochastic and deterministic forces. Even closely related genomes often exhibit extensive variation in their gene content. Understanding what drives this variation requires exploring the interactions of genes with each other and with their external environments. However, to date, conceptual models of pan-genome dynamics often represent genes as independent units and provide limited information about their mechanistic interactions. Here, we use pan-reactomes as proxies for pan-genomes since they can explicitly represent the interactions between the genes that code for metabolic reactions and simulate complex phenotypes that interact with the metabolic environment. We interpreted pan-reactomes as dynamic pools of metabolic reactions that are potentially gained or lost and simulated the routes along which different lineages lose reactions in alternative environments. We performed these simulations on the pan-reactomes of 46 bacterial and archaeal families covering a broad taxonomic range. These simulations allowed us to disentangle metabolic reactions whose presence does, and does not depend on the metabolite composition of the external environment, allowing us to identify reactions constrained “by nutrition” and “by nature”, respectively. By comparing the frequency of reactions from the first group with their observed frequencies in bacterial and archaeal families, we predicted the metabolic niches that shaped the genomic composition of these lineages in their evolutionary past. Moreover, we found that the lineages that were shaped by a more diverse metabolic niche also occur in more diverse biomes as assessed by global environmental sequencing datasets. Together, we introduce a computational framework for analyzing and interpreting pan-reactomes that provides new insights into the ecological and evolutionary drivers of pan-genome composition.
Characterization of hormone-producing cell types in the teleost pituitary gland using single-cell RNA-seq
Authors: Siddique Khadeeja , Ager-Wick Eirill , Fontaine Romain , Weltzien Finn-Arne , Henkel Christiaan V.
Published: December 2020

The pituitary is the vertebrate endocrine gland responsible for the production and secretion of several essential peptide hormones. These, in turn, control many aspects of an animal’s physiology and development, including growth, reproduction, homeostasis, metabolism and stress responses. In teleost fish, each hormone is presumably produced by a specific cell type. However, key details on the regulation of, and communication between these cell types remain to be resolved. We have therefore used single-cell sequencing to generate gene expression profiles for 2592 and 3804 individual cells from the pituitaries of female and male adult medaka (Oryzias latipes), respectively. Based on expression profile clustering, we define 15 and 16 distinct cell types in the female and male pituitary, respectively, of which ten are involved in the production of a single peptide hormone. Collectively, our data provide a high-quality reference for studies on pituitary biology and the regulation of hormone production, both in fish and in vertebrates in general.
Brain networks and cognitive impairment in Parkinson’s disease
Authors: Rucco Rosaria , Lardone Anna , Liparoti Marianna , Lopez Emahnuel Troisi , De Micco Rosa , Tessitore Alessandro , Granata Carmine , Mandolesi Laura , Sorrentino Giuseppe , Sorrentino Pierpaolo
Published: December 2020

Aim

The aim of the present study is to investigate the relations between both functional connectivity and brain networks with cognitive decline, in patients with Parkinson’s disease (PD).

Introduction

PD phenotype is not limited to motor impairment but, rather, a wide range of non-motor disturbances can occur, cognitive impairment being one of the commonest. However, how the large-scale organization of brain activity differs in cognitively impaired patients, as opposed to cognitively preserved ones, remains poorly understood.

Methods

Starting from source-reconstructed resting-state magnetoencephalography data, we applied the PLM to estimate functional connectivity, globally and between brain areas, in PD patients with and without cognitive impairment (respectively PD-CI and PD-NC), as compared to healthy subjects (HS). Furthermore, using graph analysis, we characterized the alterations in brain network topology and related these, as well as the functional connectivity, to cognitive performance.

Results

We found reduced global and nodal PLM in several temporal (fusiform gyrus, Heschl’s gyrus and inferior temporal gyrus), parietal (postcentral gyrus), and occipital (lingual gyrus) areas within the left hemisphere, in the gamma band, in PD-CI patients, as compared to PD-NC and HS. With regard to the global topological features, PD-CI patients, as compared to HS and PD-NC patients, showed differences in multi frequencies bands (delta, alpha, gamma) in the Leaf fraction, Tree hierarchy (both higher in PD-CI) and Diameter (lower in PD-CI). Finally, we found statistically significant correlations between the MoCA test and both the Diameter in delta band and the Tree Hierarchy in the alpha band.

Conclusion

Our work points to specific large-scale rearrangements that occur selectively in cognitively compromised PD patients and correlated to cognitive impairment.
A developmental transition in the sensory coding of limb kinematics in primary motor cortex
Authors: Glanz Ryan M. , Dooley James C. , Sokoloff Greta , Blumberg Mark S.
Published: December 2020

Primary motor cortex (M1) undergoes protracted development in mammals, functioning initially as a sensory structure. Throughout the first postnatal week in rats, M1 is strongly activated by self-generated forelimb movements—especially by the twitches that occur during active sleep. Here, we quantify the kinematic features of forelimb movements to reveal receptive-field properties of individual units within the forelimb region of M1. At postnatal day (P) 8, nearly all units were strongly modulated by movement amplitude, especially during active sleep. By P12, only a minority of units continued to exhibit amplitude-tuning, regardless of behavioral state. At both ages, movement direction also modulated M1 activity, though to a lesser extent. Finally, at P12, M1 population-level activity became more sparse and decorrelated, along with a substantial alteration in the statistical distribution of M1 responses to limb movements. These findings reveal a transition toward a more complex and informationally rich representation of movement long before M1 develops its motor functionality.
Pyramidal tract neurons drive feed-forward excitation of striatum through cholinergic interneurons
Authors: Morgenstern Nicolás A. , Isidro Ana Filipa , Israely Inbal , Costa Rui M.
Published: December 2020

Corticostriatal connectivity is central for many cognitive and motor processes, such as reinforcement or action initiation and invigoration. The cortical input to the striatum arises from two main cortical populations: intratelencephalic (IT) and pyramidal tract (PT) neurons. We uncovered a new feedforward excitatory circuit, supported by a polysynaptic motif from PT neurons to cholinergic interneurons (ChIs) to excitatory inputs, which runs in parallel to the canonical monosynaptic corticostriatal connection. This new motif conveys a delayed second phase of excitation to striatal spiny projection neurons (SPNs), through an acetylcholine-dependent glutamate release mechanism, resulting in biphasic corticostriatal signals. These biphasic signals are a hallmark of PT, but not IT, corticostriatal inputs, due to a stronger relative input from PT neurons to ChIs. These results uncover a novel feed-forward circuit mechanism by which PT activity differentially gates excitatory inputs to the striatum, with potential implications for behavior, plasticity and learning.

Highlights

PT, but not IT, corticostriatal inputs convey biphasic excitation to SPNs via a disynaptic circuit involving striatal ChIs.

PT neurons recruit ChIs more efficiently than IT neurons due to a stronger relative input to ChIs.

The second phase of SPN excitation is mediated by nicotinic receptors at long-range glutamatergic axons in the striatum.

Suprathreshold depolarizations of SPNs by PT inputs depend on ChI→SPN excitation and result in delayed spiking.
Integral use of immunopeptidomics and immunoinformatics for the characterization of antigen presentation and rational identification of BoLA-DR-presented peptides and epitopes
Authors: Fisch Andressa , Reynisson Birkir , Benedictus Lindert , Nicastri Annalisa , Vasoya Deepali , Morrison Ivan , Buus Søren , Ferreira Beatriz Rossetti , de Miranda Santos Isabel Kinney Ferreira , Ternette Nicola , Connelley Tim , Nielsen Morten
Published: December 2020

Major histocompatibility complex (MHC) peptide binding and presentation is the most selective event defining the landscape of T cell epitopes. Consequently, understanding the diversity of MHC alleles in a given population and the parameters that define the set of ligands that can be bound and presented by each of these alleles (the immunopeptidome) has an enormous impact on our capacity to predict and manipulate the potential of protein antigens to elicit functional T cell responses. Liquid chromatography-mass spectrometry (LC-MS) analysis of MHC eluted ligands (EL data) has proven to be a powerful technique for identifying such peptidomes, and methods integrating such data for prediction of antigen presentation have reached a high level of accuracy for both MHC class I and class II. Here, we demonstrate how these techniques and prediction methods can be readily extended to the bovine leukocyte antigen class II DR locus (BoLA-DR). BoLA-DR binding motifs were characterized by EL data derived from cell lines expressing a range of DRB3 alleles prevalent in Holstein-Friesian populations. The model generated (NetBoLAIIpan - available as a web-server atwww.cbs.dtu.dk/services/NetBoLAIIpan) was shown to have unprecedented predictive power to identify known BoLA-DR restricted CD4 epitopes. In summary, the results demonstrate the power of an integrated approach combining advanced MS peptidomics with immunoinformatics for characterization of the BoLA-DR antigen presentation system and provide a novel tool that can be utilised to assist in rational evaluation and selection of bovine CD4 T cell epitopes.
MSA: Reproducible mutational signature attribution with confidence based on simulations
Authors: Senkin Sergey
Published: December 2020

Background

Mutational signatures proved to be a useful tool for identifying patterns of mutations in genomes, often providing valuable insights about mutagenic processes or normal DNA damage.De novoextraction of signatures is commonly performed using Non-Negative Matrix Factorisation (NMF) methods, however, accurate attribution of these signatures to individual samples is a distinct problem requiring uncertainty estimation, particularly in noisy scenarios or when the acting signatures have similar shapes. Whilst many packages for signature attribution exist, a few provide accuracy measures, and most are not easily reproducible nor scalable in high-performance computing environments.

Results

We present MSA (Mutational Signature Attribution), a reproducible pipeline designed to assign signatures of different mutation types on a single-sample basis, based on Non-Negative Least Squares (NNLS) method with optimisation. Parametric bootstrap is proposed as a way to measure statistical uncertainties of signature attribution. Supported mutation types include single and doublet base substitutions, indels and structural variants. Results are validated using simulations with reference COSMIC signatures, as well as randomly generated signatures.

Availability and implementation

MSA comprises a set of Python scripts unified in a single Nextflow pipeline with containerisation for cross-platform reproducibility and scalability in high-performance computing environments. The tool is publicly available fromhttps://gitlab.com/s.senkin/MSA