bluuebunny/crossref_metadata_2025 huggingface dataset:
Accelerating long-read analysis on modern CPUs
Authors: Kalikar Saurabh , Jain Chirag , Md Vasimuddin , Misra Sanchit
Published: July 2021

Long read sequencing is now routinely used at scale for genomics and transcriptomics applications. Mapping of long reads or a draft genome assembly to a reference sequence is often one of the most time consuming steps in these applications. Here, we present techniques to accelerate minimap2, a widely used software for mapping. We present multiple optimizations using SIMD parallelization, efficient cache utilization and a learned index data structure to accelerate its three main computational modules, i.e., seeding, chaining and pairwise sequence alignment. These result in reduction of end-to-end mapping time of minimap2 by up to 1.8 × while maintaining identical output.
The precedence effect in spatial hearing emerges only late in the auditory pathway
Authors: Li Kongyan , Auksztulewicz Ryszard , Chan Chloe H. K. , Mishra Ambika Prasad , Schnupp Jan W. H.
Published: July 2021

Background

To localize sound sources accurately in a reverberant environment, human binaural hearing strongly favors analyzing the initial wave front of sounds. Behavioral studies of this “precedence effect” have so far largely been confined to human subjects, limiting the scope of complementary physiological approaches. Similarly, physiological studies have mostly looked at neural responses in the inferior colliculus, or used modeling of cochlear mechanics in an attempt to identify likely underlying mechanisms. Studies capable of providing a direct comparison of neural coding and behavioral measures of sound localization under the precedence effect are lacking.

Results

We adapted a “temporal weighting function” paradigm for use in laboratory rats. The animals learned to lateralize click trains in which each click in the train had a different interaural time difference. Computing the “perceptual weight” of each click in the train revealed a strong onset bias, very similar to that reported for humans. Follow-on electrocorticographic recording experiments revealed that onset weighting of ITDs is a robust feature of the cortical population response, but interestingly it often fails to manifest at individual cortical recording sites.

Conclusion

While previous studies suggested that the precedence effect may be caused by cochlear mechanics or inhibitory circuitry in the brainstem and midbrain, our results indicate that the precedence effect is not fully developed at the level of individual recording sites in auditory cortex, but robust and consistent precedence effects are observable at the level of cortical population responses. This indicates that the precedence effect is significantly “higher order” than has hitherto been assumed.
Convergence of MCR-8.2 and chromosome-mediated resistance to colistin and tigecycline in an NDM-5-producing ST656 Klebsiella pneumoniae from a lung transplant patient
Authors: Zhao Jiankang , Li Ziyao , Zhang Yulin , Liu Xinmeng , Xiong Zhujia , Fan Yanyan , Zou Xiaohui , Lu Binghuai , Cao Bin
Published: July 2021

For infection caused by NDM-5-producing Klebsiella pneumoniae, tigecycline and colistin are the last treatment options. In this study, we characterized the first NDM-5 and MCR-8.2 co-harboring K. pneumoniae clinical isolate, combining with chromosomal gene-mediated resistance to colistin and tigecycline. The K. pneumoniae KP32558 was isolated from the bronchoalveolar lavage fluid from a lung transplant male patient. Whole genome sequencing was carried out using Illumina HiSeq sequencing platform as well as nanopore sequencing method. The K. pneumoniae KP32558 was identified as a pan-drug resistant bacteria, belonged to ST656, and harbored plasmid-encoded blaNDM-5 and mcr-8.2 genes. The blaNDM-5 gene was located on an IncX3 type plasmid, which was successfully transferred to Escherichia coli strain J53 without visible fitness cost. The mcr-8.2 gene was located on a conjugative plasmid pKP32558-2-mcr8. It had two replicons, IncFII(K) and IncQ1, harbored previously by another two mcr-8.2-carrying plasmids pMCR8_020135 and pMCR8_095845. These three plasmids were clustered into the same clade and derived from K. pneumoniae isolates of the same clonal complex, indicating that pKP32558-2-mcr8 may come from pMCR8_020135 and pMCR8_095845 related ancestor. The MIC of KP32558 for colistin was 256 mg/L, the 6 amino acid substitutions in the two-component system may involve in the high-level colistin resistance. The truncation in acrR gene, related to tigecycline resistance, was also identified. K. pneumoniae has evolved a variety of complex resistance mechanisms to the last-resort antimicrobials, close surveillance is urgently needed to monitor the prevalence of this clone.
Comparison of infected and vaccinated transplant recipients highlights the role of Tfh and neutralizing IgG in COVID-19 protection
Authors: Charmetant Xavier , Espi Maxime , Benotmane Ilies , Heibel Francoise , Buron Fanny , Gautier-Vargas Gabriela , Delafosse Marion , Perrin Peggy , Koenig Alice , Cognard Noelle , Levi Charlene , Gallais Floriane , Manière Louis , Rossolillo Paola , Soulier Eric , Pierre Florian , Ovize Anne , Morelon Emmanuel , Defrance Thierry , Fafi-Kremer Samira , Caillard Sophie , Thaunat Olivier
Published: July 2021

Transplant recipients, which receive therapeutic immunosuppression to prevent graft rejection, are characterized by high COVID-19-related mortality and defective response to vaccines. Having observed that previous infection by SARS-CoV-2 but not the standard “2 doses” scheme of vaccination, provided complete protection against COVID-19 to transplant recipients, we undertook this translational study to compare the cellular and humoral immune responses of these 2 groups of patients. Neutralizing anti-Receptor Binding Domain (RBD) IgG were identified as the critical immune effectors associated with protection. Generation of anti-RBD IgG was dependent upon spike-specific T follicular helper (Tfh) CD4+ T cells, which acted as limiting checkpoint. Tfh generation was impeded by high dose mycophenolate mofetil in non-responders to vaccine but not in infected patients, suggesting that increasing immunogenicity of vaccine could improve response rate to mRNA vaccine. This theory was validated in two independent prospective cohorts, in which administration of a 3rd dose of vaccine resulted in the generation of anti-RBD IgG in half of non-responders to 2 doses.

One sentence summary

The generation of neutralizing IgG, which protects kidney transplant recipients from COVID-19, requires T follicular helper cells.
Natural Language Word-Embeddings as a glimpse into healthcare at the End Of Life
Authors: Lau Shun , Kraljevic Zeljko , Al-Agil Mohammad , Charing Shelley , Quarterman Alan , Parkes Harold , Metaxa Victoria , Sleeman Katherine , Gao Wei , Dobson Richard , Teo James T , Hopkins Phil
Published: July 2021

Introduction

Planning in advance and personalised discussions on limitation of life sustaining treatment (LST) is an indicator of good care. However, there are many linguistic nuances and misunderstandings around dying in hospital as well as inaccuracy in individual-level prognostication.

Methods

Using unsupervised natural language processing (NLP), we explored real-world terminology using phrase clusters with most similar sematic embeddings to “Ceiling of Treatment” and their prognostication value in the electronic health record of an urban teaching hospital.

Results

Word embeddings with most similar to “Ceiling of Treatment” clustered around phrases describing end-of-life care, ceiling of care and resuscitation discussions. The phrases have differing prognostic profile with the highest 7-day mortality in the phrases most implicitly referring to end of life -“terminal care”, “end of life care” (57.5%) and “unsurvivable” (57.6%).

Conclusion

NLP can quantify and analyse real-world end of life discussions around prognosis and appropriate LST.

Patient-friendly Summary

(by expert patients: Sherry Charing, Alan Quarterman, Harold Parkes)

Discussions between doctors, patients and family in deciding what is the appropriate maximum treatment a specific patient should have based on their clinical condition is complex. Discussions, often involving expressions regarding “End Of Life” care are used to describe the maximum invasive treatments a patient should have or would want. There are a range of expressions used, many with overlapping meanings which can be confusing, not only for the patient and family, but also for doctors reading the patient’s clinical notes. In this study, a computational approach using Artificial Intelligence to read clinical patient notes was carried out by looking at thousands of patient records from a large urban hospital. Expressions that doctors use to describe these discussions were analysed to show the associations of particular words and phrases in relation to mortality. Using a computer analysis for this study it was possible to quantify the use of these expressions and their relation to the “End Of Life”. Through this AI-based approach, real-world use of phrases and language relating “End Of Life” can be analysed to understand how doctors and patients are communicating, and about any possible misunderstandings of language.
Patient stratification reveals the molecular basis of disease comorbidities
Authors: Urda-García Beatriz , Sánchez-Valle Jon , Lepore Rosalba , Valencia Alfonso
Published: July 2021

Epidemiological evidence shows that some diseases tend to co-occur; more exactly, certain groups of patients with a given disease are at a higher risk of developing a specific secondary condition. Despite the considerable interest, only a small number of connections between comorbidities and molecular processes have been identified.

Here we develop a new approach to generate a disease network that uses the accumulating RNA-seq data on human diseases to significantly match a large number of known comorbidities, providing plausible biological models for such co-occurrences. Furthermore, 64% of the known disease pairs can be explained by analysing groups of patients with similar expression profiles, highlighting the importance of patient stratification in the study of comorbidities.

These results solidly support the existence of molecular mechanisms behind many of the known comorbidities. All the information can be explored on a large scale and in detail at http://disease-perception.bsc.es/rgenexcom/.
Complement Regulator Factor H is a Cofactor for Thrombin in both Pro- and Anticoagulant Roles
Authors: McCluskey Genevieve. , Davies Gemma E. , Velounias Rebekah L. , Hughes Tim R. , Morgan B. Paul , Preston Roger J. S. , Collins Peter W. , Jenkins P. Vincent , Heurich Meike
Published: July 2021

Background

Complement FH (FH) is a key regulator of complement activity whereas thrombin (FIIa) is central to hemostasis with both pro- and anticoagulant functions. Both have separately been shown to have auxiliary activities across the two systems. The purpose of this study was to determine the effect of FH on pro- and anti-coagulant functions and investigate the interaction between FH and thrombin.

Methods

Tail bleeding time and hemolysis were measured in FH-deficient mice (CFH−/−). Activated partial thromboplastin time (aPTT) was determined in FH-depleted human plasma. FH effect on fibrin clot generation was investigated in turbidity assays and on activated protein C (APC) generation. Binding affinity of thrombin with FH was determined using surface plasmon resonance (SPR).

Results

Tail bleeding time in CFH−/− mice was significantly prolonged compared to wild type mice. The aPTT in FH-depleted human plasma was elevated compared to normal plasma and restored by adding back FH to depleted plasma. Accordingly, FH enhanced thrombin-mediated fibrin clot generation by shortening lag time, increasing rate of clot formation and maximum turbidity, and affected clot structure. Despite this, FH also increased the rate of thrombin-mediated protein C (PC) activation, both in the presence and absence of soluble recombinant thrombomodulin (TM). Nanomolar affinity binding of FH with thrombin, but not prothrombin, was confirmed.

Conclusion

Complement FH binds thrombin with strong affinity and acts as a novel cofactor that enhances both pro- and anticoagulant actions of thrombin. These data highlight an important role for FH in hemostasis.

Key points

Absence of FH prolongs tail bleeding time in CFH−/− mice and activated partial thromboplastin time (aPTT) is elevated in human FH-depleted plasma.

FH acts a cofactor for thrombin by enhancing fibrin generation, altering fibrin clot structure and enhancing TM-thrombin mediated protein C activation
Combination of High Dose Rate Radiations (10X FFF/2400 MU/min/10 MV X-rays) and Paclitaxel Selectively Eliminates Melanoma Cells
Authors: Lodhi Niraj , Sarojini Sreeja , Keck Michaela , Nagpal Poonam , Chiu Yuk Ming , Parvez Zeenath , Adrianzen Laura , Suh K. Stephen
Published: July 2021

Purpose

Melanoma is one of the most aggressive cancer with 1.6% of total cancer deaths in United States. In recent years treatment options for metastatic melanoma have been improved by the FDA approval of new therapeutic agents. However, these inhibitors based therapies are non-specific and have severe toxicities including hyperkeratosis, photosensitivity, hepatitis, arthralgia and fatigue. The aim of this study is to determine the synthetic lethal effect (paclitaxel and radiations) on melanoma cells and reduce the total radiation doses by increasing the dose rates up to 2400 MU/min.

Methods

We previously reported a radiation treatment (10 MV x-rays, 10X-FFF, dose rate 2400MU/min, low total dose 0.5 Gy) that kills melanoma cells with 80% survival of normal HEM in vitro. In this study we extended the radiation cycle up to four and include paclitaxel treatment to study the synthetic lethal effect on melanoma and two additional normal primary cells, HDF and HEK. Cells were treated with paclitaxel prior to radiations of dose rate of 400 and 2400 MU/min with total radiation dose of only 0.5 Gy. To study induction of apoptosis and cell death, mitochondria respiration assay, DNA damage assay and colony formation assay were performed.

Results

Four days of consequent radiation treatment with paclitaxel significantly reduces the survival of melanoma cells by inducing of apoptosis and mitochondrial damages. After treatment, excessive DNA damage in melanoma cells leads to increase in expression of pro-apoptotic genes (Casp3) and decrease in expression of DNA repair gene (PARP1) and anti-apoptotic gene (Bcl2) to activate apoptosis pathway. Combination of paclitaxel and radiations reduces the survival of melanoma cells colonies when compared to radiation alone.

Conclusion

Our study indicates radiations with paclitaxel has potential synthetic lethal effect on melanoma cells and can be develop as therapy for melanoma without having toxicities or harmful effects to normal primary skin cells.
Not all smokers are alike: The hidden cost of sustained attention during nicotine abstinence
Authors: Deshpande Harshawardhan U. , Fedota John R. , Castillo Juan , Salmeron Betty Jo , Ross Thomas J. , Stein Elliot A.
Published: July 2021

Background

Nicotine Withdrawal Syndrome (NWS)-associated cognitive deficits are heterogeneous, suggesting underlying endophenotypic subgroups. We identified smoker subgroups based on response accuracy during a cognitively demanding Parametric Flanker Task (PFT) and characterized their distinct neuroimaging endophenotypes using a nicotine state manipulation (sated, abstinent).

Methods

Forty-five smokers completed the 25-min PFT in two fMRI sessions (nicotine sated, abstinent). Task-evoked NWS-associated errors of omission (EOm), brain activity, underlying functional connectivity (FC), and brain-behavior correlations between subgroups were assessed.

Results

Based on their response accuracy in the high demand PFT condition, smokers split into high (HTP, n=21) and low task performer (LTP, n=24) subgroups. Behaviorally, HTPs showed greater response accuracy independent of nicotine state and greater vulnerability to abstinence-induced EOm. HTPs showed greater BOLD responses in attentional control brain regions for the [correct responses (–) errors of commission] PFT contrast across states. A whole-brain FC analysis with these subgroup-derived regions as seeds revealed two circuits: L Precentral : R Insula and L Insula : R Occipital, with abstinence-induced FC strength increases only in HTPs. Finally, abstinence-induced brain (FC) and behavior (EOm) differences were positively correlated for HTPs in a L Precentral : R Orbitofrontal cortical circuit.

Conclusion

We used a cognitive stressor (PFT) to fractionate smokers into two subgroups (HTP/LTP). Only the HTPs demonstrated sustained attention deficits during nicotine abstinence, a stressor in dependent smokers. Unpacking underlying smoker heterogeneity with this ‘dual stressor’ approach revealed distinct smoker subgroups with differential attention deficit responses to withdrawal that could be novel targets for therapeutic interventions to improve cessation outcomes.
A Highly Potent SARS-CoV-2 Blocking Lectin Protein
Authors: Ahan Recep Erdem , Hanifehnezhad Alireza , Şahin Kehribar Ebru , Oguzoglu Tuba Cigdem , Földes Katalin , Özçelik Cemile Elif , Filazi Nazlican , Öztop Sıdıka , Önder Sevgen , Bozkurt Eray Ulaş , Ergünay Koray , Özkul Aykut , Şafak Şeker Urartu Özgür
Published: July 2021

COVID-19 pandemic effected more than 180 million people around the globe causing more than four million deaths as of July 2021. Sars-CoV-2, the new coronavirus, has been identified as the primary cause of the infection. The number of vaccinated people is increasing however prophylactic drugs are highly demanded to ensure a secure social contact. There have been a number of drug molecules repurposed to fight against Sars-CoV-2, however the proofs for the effectiveness of these drug candidates is limited. Here we demonstrated griffithsin (GRFT), a lectin protein, to block the entry of the Sars-CoV2 into the Vero6 cell lines and IFNAR-/-mouse models by attaching to spike protein of the Sars-CoV-2. Given the current mutation frequency of the Sars-CoV-2 we believe that GRFT protein-based drugs will have a high impact in preventing the transmission both on Wuhan strain as well as any other emerging variants including delta variant causing high speed spread of COVID-19.
Methylartist: Tools for Visualising Modified Bases from Nanopore Sequence Data
Authors: Cheetham Seth W. , Kindlova Michaela , Ewing Adam D.
Published: July 2021

Methylartist is a consolidated suite of tools for processing, visualising, and analysing nanopore methylation data derived from modified basecalling methods. All detectable methylation types (e.g. 5mCpG, 5hmC, 6mA) are supported, enabling integrated study of base pairs when modified naturally or as part of an experimental protocol.

Background

Covalent modification of nucleobases is an important component of genomic regulatory regimes across all domains of life [1–3] and is harnessed by various genomic footprinting assays, including DamID[4], SMAC-seq[5], and NOMe-seq[6]. Nanopore sequencing offers comprehensive assessment of base modifications from arbitrarily long sequence reads through analysis of electrical current profiles, generally through machine learning models trained to discriminate between modified and unmodified bases [7]. An increasing number of computational tools have been developed or enhanced for calling modified bases [8], including nanopolish [7], megalodon [9], and guppy [10], along with an increasing number of available pre-trained models.
Pectin remodeling belongs to a homeostatic system and triggers transcriptomic and hormonal modulations
Authors: Jobert François , Guénin Stéphanie , Voxeur Aline , Lee Kieran J. D. , Bouton Sophie , Sénéchal Fabien , Hocq Ludivine , Mongelard Gaëlle , Demailly Hervé , Amakorová Petra , Strnad Miroslav , Vernhettes Samantha , Mouille Gregory , Pilard Serge , Knox J. Paul , Novák Ondřej , Pelloux Jérôme , Gutierrez Laurent
Published: July 2021

Here, we focused on the biological modifications arisen from a strong and transient variation of the pectin methylesterification status during the seed-to-seedling transition.

A reverse genetic approach was used to trigger specific reduction of pectin de-methylesterification during the seed maturation stage and the related physiological effects were assessed using a combination of biochemical, transcriptomic and microscopic analyses.

Arabidopsis PME36 is required to implement the characteristic pattern of de-methylesterified pectin in the mature seed. While this pattern is strongly impaired in pme36-1 and pme36-2 mature seed, no phenotypical effect is observed in the knockout mutant during seed germination. By analyzing hormone homeostasis and gene expression regulation, we show a strong and dynamic physiological disorder in the mutant, which reveals the existence of a complex compensatory mechanism overcoming the defect in pectin de-methylesterification.

Our results reveal that pectin methylesterification status acts as upstream modulator involved in an undescribed homeostatic system in which pectin remodeling, hormone signaling and transcriptomic regulations interact to ensure the maintenance of a normal seed-to-seedling developmental program.
A Combination Strategy of Solubility Enhancers for Effective Production of Soluble and Bioactive Human Enterokinase
Authors: Kwon Jinhak , Cho Hyeongjun , Kim Seungmin , Ryu Yiseul , Lee Joong-jae
Published: July 2021

Enterokinase is one of the hydrolases that catalyze hydrolysis to regulate biological processes in intestinal visceral mucosa. Enterokinase plays an essential role in accelerating the process of protein digestion as it converts trypsinogen into active trypsin by accurately recognizing and cleaving a specific peptide sequence, (Asp)4-Lys. Due to its exceptional substrate specificity, enterokinase is widely used as a versatile molecular tool in various bioprocessing, especially in removing fusion tags from recombinant proteins. Despite its biotechnological importance, mass production of soluble enterokinase in bacteria still remains an unsolved challenge. Here, we present an effective production strategy of human enterokinase using tandemly linked solubility enhancers consisting of thioredoxin, phosphoglycerate kinase or maltose-binding protein. The resulting enterokinases exhibited significantly enhanced solubility and bacterial expression level while retaining enzymatic activity, which demonstrates that combinatorial design of fusion proteins has the potential to provide an efficient way to produce recombinant proteins in bacteria.
High-speed imaging of light-induced photoreceptor microsaccades in compound eyes
Authors: Kemppainen Joni , Mansour Neveen , Takalo Jouni , Juusola Mikko
Published: July 2021

Inside compound eyes, photoreceptors contract to light changes, sharpening retinal images of the moving world in time. Current methods to measure these so-called photoreceptor microsaccades in living insects are spatially limited and technically challenging. Here, we present goniometric high-speed deep pseudopupil (GHS-DPP) microscopy to assess how the rhabdomeric insect photoreceptors and their microsaccades are organised across the compound eyes. This method enables non-invasive rhabdomere orientation mapping, whilst their microsaccades can be locally light-activated, revealing the eyes’ underlying active sampling motifs. By comparing the microsaccades in wild-typeDrosophila’s open rhabdom eyes tospam-mutant eyes, reverted to an ancestral fused rhabdom state, and honeybee’s fused rhabdom eyes, we show how different eye types sample light information. These results show different ways compound eyes initiate the conversion of spatial light patterns in the environment into temporal neural signals and highlight how this active sampling can evolve with insects’ visual needs.
Memories in a network with excitatory and inhibitory plasticity are encoded in the spiking irregularity
Authors: Gallinaro Júlia V. , Clopath Claudia
Published: July 2021

Cell assemblies are thought to be the substrate of memory in the brain. Theoretical studies have previously shown that assemblies can be formed in networks with multiple types of plasticity. But how exactly they are formed and how they encode information is yet to be fully understood. One possibility is that memories are stored in silent assemblies. Here we used a computational model to study the formation of silent assemblies in a network of spiking neurons with excitatory and inhibitory plasticity. We found that even though the formed assemblies were silent in terms of mean firing rate, they had an increased coefficient of variation of inter-spike intervals. We also found that this spiking irregularity could be readout with support of short-term plasticity, and that it could contribute to the longevity of memories.
Non-specific adhesive forces between filaments and membraneless organelles
Authors: Böddeker Thomas J. , Rosowski Kathryn A. , Berchtold Doris , Emmanouilidis Leonidas , Han Yaning , Allain Frédéric H. T. , Style Robert W. , Pelkmans Lucas , Dufresne Eric R.
Published: July 2021

Membraneless organelles are liquid-like domains that form inside living cells by phase-separation. While standard physical models of their formation assume their surroundings to be a simple liquid, the cytoplasm is an active viscoelastic environment. To investigate potential coupling of phase separation with the cytoskeleton, we quantify structural correlations of stress granules and microtubules in a human-derived epithelial cell line. We find that microtubule networks are significantly perturbed in the vicinity of stress granules, and that large stress granules conform to the local pore-structure of the microtubule network. When microtubules are depolymerized by nocodazole, tubulin enrichment is localized near the surface of stress granules. We interpret these data using a thermodynamic model of partitioning of particles to the surface and bulk of droplets. This analysis shows that proteins generically have a non-specific affinity for droplet interfaces, which becomes most apparent when they weakly partition to the bulk of droplets and have a large molecular weight. In this framework, our data is consistent with a weak (≲ kbT) affinity of tubulin sub-units for stress granule interfaces. As microtubules polymerize their affinity for interfaces increases, providing sufficient adhesion to deform droplets and/or the network. We validate this basic physical phenomena in vitro through the interaction of a simple protein-RNA condensate with tubulin and microtubules.
Copy number variations with adaptive potential in caribou (Rangifer tarandus): genome architecture and new annotated genome assembly
Authors: Prunier Julien , Carrier Alexandra , Gilbert Isabelle , Poisson William , Albert Vicky , Taillon Joëlle , Bourret Vincent , Côté Steeve D. , Droit Arnaud , Robert Claude
Published: July 2021

Background

Rangifer tarandus (caribou and reindeer) has experienced recent drastic population size reductions throughout its circumpolar distribution. In efforts aimed at preserving caribou in North America and reindeer in Eurasia, genetic diversity conservation is of utmost importance, particularly the adaptive genetic diversity. To facilitate genomic studies of the caribou population, we improved genome assembly and annotation by combining long-read, linked-read and RNA sequencing technologies. As copy number variations (CNVs) are known to impact phenotype and are therefore likely to play a key role in adaptation, we investigated CNVs among the genomes of individuals representing three ecotypes of caribou (migratory, boreal and mountain).

Results

Using de novo transcriptome assembly and similarity with annotated human gene sequences, we identified 17,394 robust gene models embedded in a new highly contiguous genome assembly made of 13,994 scaffolds and presenting the highest N50 reported to date. A BUSCO analysis supported the high accuracy of this assembly, 90% of which being represented by only 131 scaffolds. Genome level comparisons with domestic ruminant species showed high synteny within this clade. A total of 1,698 large CNVs (length > 1kb) were identified, including 332 overlapping coding sequences annotated for functions related to immunity, musculoskeletal development or metabolism regulation and others. While the CNV distribution over the genome revealed 31 CNV hotspots, 43 large CNVs were particularly distinctive of the migratory and sedentary ecotypes and included genes annotated for functions related to cardiac development, fatty acid regulation, cold responses, locomotory behavior or environmental perception (hearing and sight), that can be related to the expected adaptations.

Conclusions

This work includes the first publicly available annotation of the Rangifer tarandus genome and the first genome assembly allowing genome architecture analyses. This robust annotation based on truly expressed sequences showed a distribution overlapping many CNVs that are promising candidates given the annotations supporting their involvement in adaptation. This new highly contiguous assembly will allow relative localization of genetic variations and features and will be a valuable resource for molecular tool development and genomic studies aimed at describing and preserving this species.
AD Informer Set: Chemical tools to facilitate Alzheimer’s disease drug discovery
Authors: Potjewyd Frances M. , Annor-Gyamfi Joel K. , Aubé Jeffrey , Chu Shaoyou , Conlon Ivie L. , Frankowski Kevin J. , Guduru Shiva K. R. , Hardy Brian P. , Hopkins Megan D. , Kinoshita Chizuru , Kireev Dmitri B. , Mason Emily R. , Moerk Charles Travis , Nwogbo Felix , Pearce Kenneth H. , Richardson Timothy , Rogers David A. , Soni Disha M. , Stashko Michael , Wang Xiaodong , Wells Carrow , Willson Timothy M. , Frye Stephen V. , Young Jessica E. , Axtman Alison D.
Published: July 2021

Introduction

The portfolio of novel targets to treat Alzheimer’s disease (AD) has been enriched by the AMP-AD program.

Methods

A cheminformatics-driven effort enabled identification of existing small molecule modulators for many protein targets nominated by AMP-AD and suitable positive control compounds to be included in the set.

Results

We have built an annotated set of 171 small molecule modulators, including mostly inhibitors, targeting 98 unique proteins that have been nominated by AMP-AD consortium members as novel targets for AD treatment. These small molecules vary in their quality and should be considered chemical tools that can be used in efforts to validate therapeutic hypotheses, but which would require further optimization. A physical copy of the AD Informer Set can be ordered via the AD Knowledge Portal.

Discussion

Small molecule tools that enable target validation are important tools for the translation of novel hypotheses into viable therapeutic strategies for AD.
Faces of men with high serum testosterone are less attractive for women during the fertility phase of the menstrual cycle
Authors: Krejza Jaroslaw , Sledziewski Rafal , Tabedzki Marek , Chen Rong , Krzystanek Ewa , Arkuszewski Michal , Odachowska Magdalena , Kwiatkowska Kinga , Marynowska Marcelina , Rogowski Maciej , Ustymowicz Andrzej
Published: July 2021

The attractiveness of the human face plays an essential role in mating as it may signal the genetic suitability of a mate. The controversial ‘ovulatory shift hypothesis’ postulates that women in the fertile phase of the menstrual cycle would prefer faces of masculine men with high testosterone that signals ‘good genes’, whereas in the non-fertile phase they prefer traits signaling the willingness to provide parental care. To examine relationships between men’s testosterone and women’s preferences for men’s faces on day 13 of the menstrual cycle, 19 young women rated the attractiveness of images of the natural faces of 77 young men. Using advanced Bayesian multilevel modeling we showed that the attractiveness of men’s faces is significantly lower in men with a high concentration of serum total testosterone, even taking into account the concentration of serum estrogen in the raters. The average men’s face composited from images of 39 faces rated above pool median attractiveness rate, was slightly narrower than the average face composited from 38 less attractive faces. Our results challenge the ‘ovulatory shift hypothesis’ as faces of males with high circulating testosterone were rated as less attractive than faces of males with lower testosterone by women on the fertile phase of the cycle.
Integrative proteomics and phosphoproteomics reveals phosphorylation networks involved in the maintenance and expression of embryogenic competence in sugarcane callus
Authors: Xavier Lucas R. , Almeida Felipe A. , Pinto Vitor B. , Passamani Lucas Z , Santa-Catarina Claudete , Filho Gonçalo A. de S. , Mooney Brian P. , Thelen Jay J. , Silveira Vanildo
Published: July 2021

Sugarcane (Saccharum spp.) is one of the most important crops for sugar, biofuel, and bioenergy production and has become an important commodity in the worldwide agricultural market in more than 100 countries. In this study, label-free quantitative proteomics and phosphoproteomics analyses were performed to investigate signaling events related to somatic embryo maturation and differentiation in sugarcane. Embryogenic callus (EC) at multiplication (EC0) and after 14 days (EC14) of maturation were compared. The EC14/EC0 comparison found that 251 phosphoproteins and 700 proteins were differentially regulated and accumulated, respectively. Metabolic pathway analysis showed that these proteins and phosphoproteins were enriched in lysine degradation and starch/sucrose metabolism during multiplication, whereas the differentiation of somatic embryos was found to involve the regulation of energetic metabolism, including the TCA cycle, oxidative phosphorylation, and carbon metabolism. Multiplication-related phosphoproteins were mainly associated with abscisic acid responses and transcriptional regulation of the TOPLESS (TPL), SNF1 kinase homolog 10 (KIN10), SEUSS (SEU), and LEUNIG_HOMOLOG (LUH) proteins. Among the maturation-related phosphoproteins, the phosphorylation of light harvesting complex photosystem ii, CURVATURE THYLAKOID 1B, vacuolar proton ATPase A1 and phytochrome interacting factor 3-LIKE 5 was found to be associated with bioenergetic metabolism and carbon fixation. A motif analysis revealed 15 phosphorylation motifs, and among these, the [D-pS/T-x-D] motif was unique among the phosphopeptides identified during somatic embryo differentiation. A coexpression network analysis of proteins and phosphoproteins revealed interactions among SNF1-related protein kinase 2 (SnRK2), abscisic acid responsive elements-binding factor 2 (ABF2), and KIN10, which indicated the role of these proteins in embryogenic competence in EC0. The interactions among ubiquitin-conjugating enzyme 5, ubiquitin-conjugating enzyme 35, small ubiquitin-like modifier 1, and histone deacetylase 1 may be involved in posttranslational protein modification during embryo maturation. Argonaute 1 (AGO1) also interacts with POLTERGEIST (POL) and may integrate gene silencing with the regulation of meristem identity during somatic embryo development. These results reveal novel dynamics of protein regulation in somatic embryogenesis and identify new potential players in somatic embryo differentiation and their phosphosites.
Harnessing the functional diversity of plant cystatins to design inhibitor variants highly active against herbivorous arthropod digestive proteases
Authors: Tremblay Jonathan , Goulet Marie-Claire , Vorster Juan , Goulet Charles , Michaud Dominique
Published: July 2021

Protein engineering approaches have been proposed to improve the inhibitory properties of plant cystatins against herbivorous arthropod digestive proteases. These approaches typically involve the site-directed mutagenesis of functionally relevant amino acids, the production and selection of improved inhibitory variants by molecular phage display procedures, or the design of bi/multifunctional translational fusions integrating one or several cystatin inhibitory domains. Here, we propose a new approach where the function-related structural elements of a cystatin are substituted by the corresponding elements of an alternative cystatin. Cys protease inhibitory assays were first performed with 20 representative plant cystatins and model Cys proteases, including herbivorous arthropod digestive proteases, to appreciate the extent of functional variability among plant cystatin protein family members. The most, and less, potent of these cystatins were then used as ‘donors’ of structural elements to create hybrids of tomato cystatin SlCYS8 used as a model ‘recipient’ inhibitor. Our data confirm the wide variety of cystatin protease inhibitory profiles among plant taxa. They also demonstrate the usefulness of these proteins as a pool of discrete structural elements for the design of cystatin variants with improved potency against herbivorous pest digestive Cys proteases.
iPSC-derived Vascular Smooth Muscle Cells in a Fibronectin Functionalized Collagen Scaffold Augment Endothelial Cell Morphogenesis
Authors: Duan Kaiti , Dash Biraja C. , Sasson Daniel , Hsia Henry C.
Published: July 2021

Tissue-engineered constructs have immense potential as autologous grafts for wound healing. Despite the rapid advancement in fabrication technology, the major limitation is controlling angiogenesis within these constructs to form a vascular network. Here, we aimed to develop a 3D scaffold that can regulate angiogenesis. We tested the effect of fibronectin and vascular smooth muscle cells derived from human induced pluripotent stem cells (hiPSC-VSMC) on the morphogenesis of endothelial cells. The results demonstrate that fibronectin increases the number of endothelial networks. However, hiPSC-VSMC in the presence of fibronectin further substantiated the number and size of endothelial networks. A mechanistic study shows that blocking αvβ3 integrin signaling between hiPSC-VSMC and fibronectin impacts the endothelial network formation. Collectively, this study set forth initial design criteria in developing an improved pre-vascularized construct.
Switching Promotor Recognition of Phage RNA Polymerase in Silico Following Path along Lab Directed Evolution
Authors: Chao E , Dai Liqiang , Yu Jin
Published: July 2021

In this work we computationally investigated how a viral RNA polymerase (RNAP) from bacteriophage T7 evolves into RNAP variants under lab-directed evolution to switch recognition from T7 promoter to T3 promoter in transcription initiation. We first constructed a closed initiation complex for the wild-type T7 RNAP, and then for six mutant RNAPs discovered from phage assisted continuous evolution experiments. All-atom molecular dynamics (MD) simulations up to one microsecond each were conducted on these RNAPs in complex with T7/T3 promoter. Our simulations show notably that protein-DNA electrostatic interactions or stabilities at the RNAP-DNA promoter interface well dictate the promoter recognition preference of the RNAP and variants. Key residues and structural elements that contribute significantly to switching the promoter recognition were identified. Followed by a first point mutation N748D on the specificity loop to slightly disengage the RNAP from the promoter to hinder the original recognition, we found an auxiliary helix (206-225) that takes over switching the promoter recognition upon further mutations (E222K and E207K), by forming additional charge interactions with the promoter DNA and reorientating differently on the T7 and T3 promoter. Further mutations on the AT-rich loop and the specificity loop can fully switch the RNAP-promoter recognition to the T3 promoter. Overall, our studies reveal energetics and structural dynamics details along an exemplary directed evolutionary path of the phage RNAP variants for a rewired promoter recognition function. The findings demonstrate underlying physical mechanisms and are expected to assist knowledge/data learning or rational redesign of the protein enzyme structure-function.
The MKRN1-BRAF exon4-exon9 fusion is a targetable oncogenic driver
Authors: Girtman Megan A. , Richmond Craig S. , Kenny Paraic A.
Published: July 2021

Background

BRAF, when mutated at V600E, is a potent oncogenic driver in melanoma, lung and colorectal cancer with well understood signaling mechanisms and established treatment guidelines. Non-V600E mutations are less common, more functionally diverse and do not yet have clear treatment guidelines. One class of non-V600E mutations are BRAF fusion genes which typically involve the C-terminal kinase domain of BRAF joined to one of a wide repertoire of potential N-terminal fusion partners. Here, we functionally characterized an MKRN1-BRAF fusion gene which we detected in multi-gene panel sequencing of a metastatic colorectal tumor.

Methods

Levels of MEK/ERK pathway activity were evaluated by western blotting in HEK293 cells ectopically expressing MKRN1-BRAF or a series of other BRAF constructs. Dependence on dimerization was evaluated by introducing a dimerization deficiency mutation and drug sensitivity was evaluated by treatment with sorafenib, dabrafenib and trametinib.

Results

MKRN1-BRAF potently activated MEK/ERK signaling and did not require dimerization for activity. Among the inhibitors evaluated, trametinib most effectively suppressed MKRN1-BRAF driven pathway activity.

Conclusion

Our data demonstrate that the MKRN1-BRAF fusion gene encodes an oncoprotein that strongly activates MEK/ERK signaling in a trametinib-sensitive manner.
Novel Class of Psychedelic Iboga Alkaloids Disrupts Opioid Use
Authors: Havel Václav , Kruegel Andrew C. , Bechand Benjamin , McIntosh Scot , Stallings Leia , Hodges Alana , Wulf Madalee G. , Nelson Mel , Hunkele Amanda , Ansonoff Michael , Pintar John E. , Hwu Christopher , Abi-Gerges Najah , Zaidi Saheem A. , Katritch Vsevolod , Yang Mu , Javitch Jonathan A. , Majumdar Susruta , Hemby Scott E. , Sames Dalibor
Published: July 2021

Substance use and related mental health epidemics are causing increasing suffering and death in diverse communities.1,2Despite extensive efforts focused on developing pharmacotherapies for treating substance use disorders, there is an urgent need for radically different therapeutic approaches.3,4Ibogaine provides an important drug prototype in this direction, as a psychoactive iboga alkaloid suggested to have the ability to interrupt opioid use in drug-dependent humans.5However, ibogaine and its major metabolite noribogaine present considerable safety risk associated with cardiac arrhythmias.6We introduce a new class of iboga alkaloids - “oxa-iboga” - defined as benzofuran-containing iboga analogs and created via structural editing of the iboga skeleton. The oxa-iboga compounds act as potent kappa opioid receptor agonistsin vitroandin vivo, but exhibit atypical behavioral features compared to standard kappa psychedelics. We show that oxa-noribogaine has greater therapeutic efficacy in rat models of opioid use, and no cardiac pro-arrhythmic potential, in contrast to noribogaine. Oxa-noribogaine induces long-lasting suppression of morphine and fentanyl intake after a single dose, persistent reduction of morphine intake and reinforcing efficacy after a short treatment regimen, and suppression of morphine and fentanyl drug seeking in relapse models. Oxa-noribogaine also induces a lasting elevation of neurotrophin proteins in the ventral tegmental area and medial prefrontal cortex, consistent with targeted neuroplasticity induction and alteration of addiction-like states. As such, oxa-iboga compounds represent candidates for a novel type of pharmacotherapy for treatment of opioid use disorder.
Phenomics data processing: Extracting dose-response curve parameters from high-resolution temperature courses and repeated field-based wheat height measurements
Authors: Roth Lukas , Piepho Hans-Peter , Hund Andreas
Published: July 2021

Temperature is a main driver of plant growth and development. New phenotyping tools enable quantifying the temperature response of hundreds of genotypes. Yet, for field-derived data, temperature response modeling bears flaws and pitfalls concerning the interpretation of derived parameters. In this study, climate data from five growing seasons with differing temperature distributions served as starting point for a growth simulation of wheat stem elongation, based on a four-parametric temperature response function (Wang-Engel) including all cardinal temperatures. In a novel approach, we re-extracted dose-responses from the simulation by combining high-resolution (hours) temperature courses with low-resolution (days) height data. The collection of such data is common in field phenotyping platforms. To take advantage of the lack of supra-optimal temperatures during the stem elongation, simpler (linear and asymptotic) models to predict temperature-response parameters were investigated. The asymptotic model extracted the base temperature of growth and the maximum absolute growth rate with high precision, whereas simpler, linear models failed to do so. Additionally, the asymptotic model provided a proxy estimate for the optimum temperature. However, when including seasonally changing cardinal temperatures, the prediction accuracy of the asymptotic model was strongly reduced. In a field study with three winter wheat varieties, significant differences were found for all three asymptotic dose-response curve parameters. We conclude that the asymptotic model based on high-resolution temperature courses is suitable to extract meaningful parameters from field-based data.
Regulation of sedimentation rate shapes the evolution of multicellularity in a unicellular relative of animals
Authors: Dudin Omaya , Wielgoss Sébastien , New Aaron M. , Ruiz-Trillo Iñaki
Published: July 2021

Significant increases in sedimentation rate accompany the evolution of multicellularity. These increases should lead to rapid changes in ecological distribution, thereby affecting the costs and benefits of multicellularity and its likelihood to evolve. However, how genetic and cellular traits control this process, their likelihood of emergence over evolutionary timescales, and the variation in these traits as multicellularity evolves, are still poorly understood. Here, using isolates of the ichthyosporean genus Sphaeroforma - close unicellular relatives of animals with brief transient multicellular life stages - we demonstrate that sedimentation rate is a highly variable and evolvable trait affected by at least two distinct physical mechanisms. First, we find extensive (>300x) variation in sedimentation rates for different Sphaeroforma species, mainly driven by size and density during the unicellular-to-multicellular life cycle transition. Second, using experimental evolution with sedimentation rate as a focal trait, we readily obtained, for the first time, fast settling and multicellular S. arctica isolates. Quantitative microscopy showed that increased sedimentation rates most often arose by incomplete cellular separation after cell division, leading to clonal “clumping” multicellular variants with increased size and density. Strikingly, density increases also arose by an acceleration of the nuclear doubling time relative to cell size. Similar size- and density-affecting phenotypes were observed in four additional species from the Sphaeroforma genus, suggesting variation in these traits might be widespread in the marine habitat. By resequencing evolved isolates to high genomic coverage, we identified mutations in regulators of cytokinesis, plasma membrane remodelling, and chromatin condensation that may contribute to both clump formation and the increase in the nuclear number-to-volume ratio. Taken together, this study illustrates how extensive cellular control of density and size drive sedimentation rate variation, likely shaping the onset and further evolution of multicellularity.