bluuebunny/crossref_metadata_2025 huggingface dataset:
Hypsugo stubbeisp. nov., a novel cryptic bat species of the genusHypsugo(Vespertilionidae, Chiroptera, Mammalia) from Mongolia. Results of the Mongolian-German Biological Expeditions Since 1962, No. 347.
Authors: Dolch D. , Stubbe M. , Batsaikhan N. , Stubbe A. , Steinhauser D.
Published: April 2021

The occurrence of two members of the genusHypsugo, namelyH. alaschanicusandH. savii caucasicus, have been reported for Mongolia in the literature. Due to various taxonomic reassignments within and between genera, the number of records for the genusHypsugoin Mongolia is quite scarce and sometimes not resolved at species or subspecies level. Despite recognition of the two above-mentioned species, recent reports based on genetic analyses describe only new and further records ofH. alaschanicus. Thus, it exists a large uncertainty regarding the occurrence and distribution ofH. savii caucasicusin Mongolia. Here, our efforts in gaining a deeper understanding towards the occurrence and distribution ofHypsugospecies in Mongolia are described.

A combination of genetic and morphological analyses of collected material fromHypsugospecimens revealed the existence of a genetically largely distantHypsugoclade. Therefore, a new and crypticHypsugospecies is proposed which is named after Prof. Dr. Michael Stubbe for his continuous, long-standing and significant contributions into the biological exploration of Mongolia.Hypsugo stubbeisp. nov. differs by at least 8.4 % and 9 % to the closest Western Palearctic distributedH. cf.darwiniiandH. saviias well as at least 11.3 % to the Easter Palearctic (including Mongolia) distributedH. alaschanicusbased on the first 798 nucleotides of the gene encoding the mitochondrial ND1 (subunit one of NADH dehydrogenase). Neither a close proximity species based on the gene encoding the mitochondrial COI (cytochrome oxidase subunit one) could be found in publicly accessible nucleotide databases. While the crypticH. stubbeisp. nov. reveals no obvious cranial and morphological differences, few external characteristics are dissimilar to bothH. alaschanicusandH. savii(caucasicus). Currently,Hypsugo stubbeisp. nov. was found at four different locations in Mongolia. Among the 11 specimens captured, six facilitated a genetic assignment. Based on the current scarce data records, the species seems to occur mainly in the far west of Mongolia inhabiting semi-deserts and steppes up to high mountain areas. An overlapping distribution withH. alaschanicuscannot be excluded based on the limited data currently available.
In silicoanalysis ofcis-elements and identification of transcription factors putatively involved in the regulation of the OAS cluster genesSDI1andSDI2
Authors: Rakpenthai Apidet , Apodiakou Anastasia , Whitcomb Sarah J. , Hoefgen Rainer
Published: April 2021

A. thaliana sulfur deficiency-induced 1andsulfur deficiency-induced 2(SDI1andSDI2) are involved in partitioning sulfur among metabolite pools during sulfur deficiency and their transcription is strongly induced by this condition. However, little is currently known about thecis- andtrans-factors that regulateSDIexpression. To identify potential transcription factors and DNA sequence element regulators ofSDIexpression we performed a comparativein silicoanalysis of their promoter sequences cataloguing known and potentially newcis-elements. We further screened an arrayed library of Arabidopsis transcription factors (TF) for binding to theSDI1andSDI2promoters. In total 14 candidate TF regulators ofSDIs were identified with yeast-one-hybrid analyses, of which five bound to both promoters, 4 were specific toSDI1,and 5 were specificSDI2. Direct association between particularcis-elements in these promoter regions and specific TFs was established via electrophoretic mobility shift assays. SLIM1 was shown to bind SUREcis-element(s) in the proximal promoter region of bothSDI1andSDI2. The bZIP corecis-element in the proximal promoter region ofSDI2was shown to be important for bZIP16, bZIP44, and HYH binding. GBF1 was shown to bind the E-box in the proximal promoter region ofSDI2. Additionally, we performed a meta-analysis of expression changes of these 14 TF candidates in a variety of conditions that alterSDIexpression. These data will allow for more detailed future analysis of the molecular factors required for transcriptional regulation ofSDIs under a range of physiological and metabolic conditions, apart from sulfur deficiency.
The effect of double biofeedback on functional hemispheric asymmetry and activity: a pilot study
Authors: Demareva Valeriia , Mukhina Elena , Bobro Tatiana
Published: April 2021

In the current pilot study, we attempt to find out how double neurofeedback influences functional hemispheric asymmetry and activity. We examined 30 healthy participants (8 males; 22 females, mean age = 29; SD= 8). To measure functional hemispheric asymmetry and activity, we used computer laterometry in the ‘two-source’ lead-lag dichotic paradigm. Double biofeedback included 8 minutes of EEG oscillation recording with five minutes of basic mode. During the basic mode, the current amplitude of the EEG oscillator gets transformed into feedback sounds while the current amplitude of alpha EEG oscillator is used to modulate the intensity of light signals. Double neurofeedback did not directly influence the asymmetry itself but accelerated individual sound perception characteristics during dichotic listening in the preceding effect paradigm. Further research is needed to investigate the effect of double neurofeedback training on functional brain activity and asymmetry taking into account participants’ age, gender, and motivation.
ADAPTATION OF DOLPHINS (TURSIOPS TRUNCATUS) LOCATION SIGNALS WHEN SEARCHING AND RECOGNIZING OBJECTS HIDDEN BY SEA SEDIMENTS
Authors: Zaitseva K. A. , Korolev V. I. , Akhi A. V. , Akhi A. A.
Published: April 2021

An experimental study was conducted to research dolphin’s sonar adaptation capabilities for location of objects obscured by marine sediments. It was shown that dolphins are able to alter spectral and temporal characteristics of their location signals. Adaptive change of length, spectral width, and amplitude of impulses provides optimal tools to fight interference and allows dolphins to effectively identify objects.

This work describes dolphin’s search, location and recognition objects hidden by sea sediments and changes in its location signal structure.
Robust and tunable signal processing in mammalian cells via engineered covalent modification cycles
Authors: Jones Ross D. , Qian Yili , Ilia Katherine , Wang Benjamin , Laub Michael T. , Del Vecchio Domitilla , Weiss Ron
Published: April 2021

Rewired and synthetic signaling networks can impart cells with new functionalities and enable efforts in engineering cell therapies and directing cell development. However, there is a need for tools to build synthetic signaling networks that are tunable, can precisely regulate target gene expression, and are robust to perturbations within the complex context of mammalian cells. Here, we use proteins derived from bacterial two-component signaling pathways to develop synthetic phosphorylation-based and feedback-controlled devices in mammalian cells with such properties. First, we isolate kinase and phosphatase proteins from the bifunctional histidine kinase EnvZ. We then use these proteins to engineer a synthetic covalent modification cycle, in which the kinase and phosphatase competitively regulate phosphorylation of the cognate response regulator OmpR, enabling analog tuning of OmpR-driven gene expression. Further, we show that the phosphorylation cycle can be extended by connecting phosphatase expression to small molecule and miRNA inputs in the cell, with the latter enabling cell-type specific signaling responses and accurate cell type classification. Finally, we implement a tunable negative feedback controller by co-expressing the kinase-driven output gene with the small molecule-tunable phosphatase. This negative feedback substantially reduces cell-to-cell noise in output expression and mitigates the effects of cell context perturbations due to off-target regulation and resource competition. Our work thus lays the foundation for establishing tunable, precise, and robust control over cell behavior with synthetic signaling networks.
Multi-omics approach to identify bacterial polyynes and unveil their antifungal mechanism against Candida albicans
Authors: Lin Ching-Chih , Hoo Sin Yong , Lin Chih , Huang Kai-Fa , Ho Ying-Ning , Sun Chi-Hui , Lee Han-Jung , Chen Pi-Yu , Shu Lin-Jie , Wang Bo-Wei , Hsu Wei-Chen , Yang Yu-Liang
Published: April 2021

Bacterial polyynes are highly active natural products with a broad-spectrum of antimicrobial activities. However, their detailed mechanism of action remains unclear. Through integrating comparative genomics, transcriptomics, functional genetics, and metabolomics analysis, we identified a unique polyyne resistance gene, masL (encoding acetyl-CoA acetyltransferase), from the biosynthesis gene cluster (BGC) dominant for the production of antifungal polyynes (massilin A, massilin B, collimonin C, and collimonin D) in Massilia sp. YMA4. Phylogenic and chemotaxonomic analyses characterized the core architecture of bacterial polyyne BGC. The crystallographic analysis of the MasL-collimonin C complex indicated that bacterial polyynes serve as a covalent inhibitor of acetyl-CoA acetyltransferase. Moreover, we confirmed that the bacterial polyynes disrupted cell membrane integrity and inhibited cell viability of Candida albicans by targeting ERG10 (homolog of MasL). Overall, understanding of the antifungal mechanism of bacterial polyynes presented herein will be useful for the development of polyynes for fungal infections.
An MHV macrodomain mutant predicted to lack ADP-ribose binding activity is severely attenuated, indicating multiple roles for the macrodomain in coronavirus replication
Authors: Voth Lynden S. , O’Connor Joseph J. , Kerr Catherine M. , Doerger Ethan , Schwarting Nancy , Sperstad Parker , Johnson David K. , Fehr Anthony R.
Published: April 2021

All coronaviruses (CoVs) contain a macrodomain, also termed Mac1, in non-structural protein 3 (nsp3) which binds and hydrolyzes ADP-ribose covalently attached to proteins. Despite several reports demonstrating that Mac1 is a prominent virulence factor, there is still a limited understanding of its cellular roles during infection. Currently, most of the information regarding the role of CoV Mac1 during infection is based on a single point mutant of a highly conserved asparagine-to-alanine mutation, which is known to largely eliminate Mac1 ADP-ribosylhydrolase activity. To determine if Mac1 ADP-ribose binding separately contributes to CoV replication, we compared the replication of a murine hepatitis virus (MHV) Mac1 mutant predicted to dramatically reduce ADP-ribose binding, D1329A, to the previously mentioned asparagine mutant, N1347A. D1329A and N1347A both replicated poorly in bone-marrow derived macrophages (BMDMs), were inhibited by PARP enzymes, and were highly attenuatedin vivo. However, D1329A was significantly more attenuated than N1347A in all cell lines tested that were susceptible to MHV infection. In addition, D1329A retained some ability to block IFN-β transcript accumulation compared to N1347A, indicating that these two mutants impacted distinct Mac1 functions. Mac1 mutants predicted to eliminate both binding and hydrolysis activities were unrecoverable, suggesting that the combined activities of Mac1 may be essential for MHV replication. We conclude that Mac1 has multiple roles in promoting the replication of MHV, and that these results provide further evidence that Mac1 could be a prominent target for anti-CoV therapeutics.

IMPORTANCE

In the wake of the COVID-19 epidemic, there has been a surge to better understand how CoVs replicate, and to identify potential therapeutic targets that could mitigate disease caused by SARS-CoV-2 and other prominent CoVs. The highly conserved macrodomain, also termed Mac1, is a small domain within non-structural protein 3. It has received significant attention as a potential drug target as previous studies demonstrated that it is essential for CoV pathogenesis in multiple animal models of infection. However, the various roles and functions of Mac1 during infection remain largely unknown. Here, utilizing recombinant Mac1 mutant viruses, we have determined that different biochemical functions of Mac1 have distinct roles in the replication of MHV, a model CoV. These results indicate that Mac1 is more important for CoV replication than previously appreciated, and could help guide the development of inhibitory compounds that target unique regions of this protein domain.
Genomic Analysis of Human Noroviruses Using Hybrid Illumina-Nanopore Data
Authors: Flint Annika , Reaume Spencer , Harlow Jennifer , Hoover Emily , Weedmark Kelly , Nasheri Neda
Published: April 2021

Whole genome sequence (WGS) analysis of noroviruses is routinely performed by employing a metagenomic approach. While this methodology has several advantages, such as allowing for examination of co-infection, it has some limitations such as the requirement of high viral load to achieve full-length or near full-length genomic sequences. In this study, we used an amplification approach to obtain full-length genomic amplicons from 39 Canadian GII isolates followed by deep sequencing on Illumina and Oxford Nanopore platforms. This approach significantly reduced the required viral titre to obtain full-genome coverage. Herein, we compared the coverage and sequences obtained by both platforms and provided an in-depth genomic analysis of the obtained sequences, including the presence of single nucleotide variants (SNVs) and recombination events.
Mechanisms involved in the active secretion of CTX-M-15 β-lactamase by pathogenicE. coliST131
Authors: Rangama Severine , Lidbury Ian D. E. A , Holden Jennifer M. , Borsetto Chiara , Murphy Andrew R. J. , Hawkey Peter M. , Wellington Elizabeth M. H.
Published: April 2021

Infections caused by antimicrobial resistant bacterial pathogens are fast becoming an important global health issue. Strains ofEscherichia coliare common causal agents of urinary tract infection and can carry multiple resistance genes. This includes the geneblaCTX-M-15that encodes for an extended spectrum beta-lactamase (ESBL). While studying antimicrobial resistance (AMR) in the environment we isolated several strains ofE. coliST131 downstream of a WWTP in a local river. These isolates were surviving in the river sediment and characterisation proved that a multi-resistant phenotype was evident. Here, we show thatE. colistrain 48 (river isolate ST131), provided a protective effect against a third-generation cephalosporin (cefotaxime) for a susceptibleE. colistrain 33 (river isolate ST3576) through secretion of a functional ESBL into the growth medium. Furthermore, extracellular ESBL activity was stable for at least 24 h after secretion. Proteomic and molecular genetic analyses identified CTX-M-15 as the major secreted ESBL responsible for the observed protective effect. In contrast to previous studies, OMVs were not the sole route for CTX-M-15 secretion. Indeed, mutation of the Type I secretion system led to a significant reduction in the growth of the ESBL-producing strain as well as a significantly reduced ability to confer protective effect. We speculate that CTX-M-15 secretion, mediated through active secretion using molecular machinery provides a public goods service by facilitating the survival of otherwise susceptible bacteria in the presence of cefotaxime.

Abstract importance

Infections caused by antimicrobial resistant bacterial pathogens have become an important global health issue. Wastewater treatment plants (WWTPs) have been identified as hotspots for the dissemination of antimicrobial resistant genes/bacteria into the environment. In this study, we investigated resistance enzyme secretion by a multi-drug resistant human pathogenicE. coli, isolated from a UK river, downstream of a WWTP. We present evidence that the resistant strain actively secreted an important resistance enzyme into the surrounding medium which degraded the antibiotic cefotaxime. This research provided evidence for the mechanism for secretion of this enzyme which could indicate a new target to tackle antibiotic resistance pathogens.
Functional, metabolic and transcriptional maturation of stem cell derived beta cells
Authors: Balboa Diego , Barsby Tom , Lithovius Väinö , Saarimäki-Vire Jonna , Omar-Hmeadi Muhmmad , Dyachok Oleg , Montaser Hossam , Lund Per-Eric , Yang Mingyu , Ibrahim Hazem , Näätänen Anna , Chandra Vikash , Vihinen Helena , Jokitalo Eija , Kvist Jouni , Ustinov Jarkko , Nieminen Anni I. , Kuuluvainen Emilia , Hietakangas Ville , Katajisto Pekka , Lau Joey , Carlsson Per-Ola , Barg Sebastian , Tengholm Anders , Otonkoski Timo
Published: April 2021

Transplantation of pancreatic islet cells derived from human pluripotent stem cells is a promising treatment for diabetes. Despite progress in stem cell-derived islet (SC-islet) generation, detailed characterization of their functional properties has not been conducted. Here, we generated functionally mature SC-islets using an optimized protocol and comprehensively benchmarked them against primary adult islets. Biphasic glucose stimulated insulin secretion developed during in vitro maturation, associated with cytoarchitectural reorganization and increased alpha cells. Electrophysiology and exocytosis of SC-islets were comparable to adult islets. Glucose-responsive insulin secretion was achieved despite differences in glycolytic and mitochondrial glucose metabolism. Single-cell transcriptomics of SC-islets in vitro and throughout 6 months of murine engraftment revealed a continuous maturation trajectory culminating in a transcriptional landscape closely resembling that of primary islets. Our thorough evaluation of SC-islet maturation highlights their advanced degree of functionality and supports their use in further efforts to understand and combat diabetes.
Linking Diabetes mellitus to SARS-CoV-2 infection through differential targeting of the microRNAs in the Pancreas tissue
Authors: Bhavya  , Pathak Ekta , Mishra Rajeev
Published: April 2021

Coronavirus Disease 2019 (COVID-19) severity and Diabetes mellitus affect each other bidirectionally. The plus-sense single-stranded RNA (+ssRNA) genome of the SARS-CoV-2 virus can be targeted and suppressed by the host cell’s microRNAs (miRNAs). Using the differential gene expression analysis between the mock-infected and the SARS-CoV-2-infected pancreatic tissue, we report five Diabetes-associated genes that are upregulated due to SARS-CoV-2 infection in the hESC pancreas tissues. Ten miRNAs regulating these five genes can potentially target the SARS-CoV-2 genome. We hypothesize that the SARS-CoV-2 genome copies in the infected human pancreas cell compete with the host cell’s native genes in being regulated by the native miRNAs. It leads to the reduced miRNA-regulation and, thus, the upregulation of the Diabetes-associated native genes. Thus, the resultant new-onset or elevated Diabetic symptoms may worsen the condition of COVID-19 patients.
A tyrosine-based trafficking signal in the simian immunodeficiency virus envelope cytoplasmic domain is strongly selected for in pathogenic SIV infection
Authors: Lawrence Scott P. , Elser Samra E. , Torben Workineh , Blair Robert V. , Pahar Bapi , Aye Pyone P. , Schiro Faith , Szeltner Dawn , Doyle-Meyers Lara A. , Haggarty Beth , Jordan Andrea P.O. , Romano Josephine , Alvarez Xavier , O’Connor David H. , Wiseman Roger W. , Fennessey Christine M. , Li Yuan , Piatak Michael , Lifson Jeffrey D. , LaBranche Celia C. , Lackner Andrew A. , Keele Brandon F. , Maness Nicholas J. , Marsh Mark , Hoxie James A.
Published: April 2021

The HIV/SIV envelope glycoprotein (Env) cytoplasmic domain contains a highly conserved Tyr-dependent trafficking signal that mediates both clathrin-dependent endocytosis and polarized sorting of Env. Despite extensive characterization, the role of these functions in viral infection and pathogenesis is unclear. An SIV molecular clone (SIVmac239) in which the Tyr-based signal is inactivated by deletion of Gly-720 and Tyr-721 (SIVmac239ΔGY) replicates to high levels acutely in pigtail macaques (PTM) but is rapidly controlled. We previously reported that rhesus macaques and PTM can progress to AIDS following SIVmac239ΔGY infection in association with novel amino acid changes in the Env cytoplasmic domain. These included an R722G flanking the ΔGY deletion and a nine nucleotide deletion that encodes amino acids 734-736 (ΔQTH) and overlaps with therevandtatopen reading frames. We show that molecular clones containing these mutations reconstitute signals for both endocytosis and polarized sorting. In one PTM, a novel genotype was selected, which generated a new signal for polarized sorting but not endocytosis. This mutation by itself was sufficient to maintain high viral loads for several months when introduced into naïve PTMs. These findings reveal, for the first time, strong selection pressure for Env endocytosis and, in particular, for polarized sorting during pathogenic SIV infectionin vivo.
Suppression ofcdc13-2-associated senescence bypif1-m2requires Ku-mediated telomerase recruitment
Authors: Fekete-Szücs Enikő , Rosas Bringas Fernando R. , Stinus Sonia , Chang Michael
Published: April 2021

InSaccharomyces cerevisiae, recruitment of telomerase to telomeres requires an interaction between Cdc13, which binds single-stranded telomeric DNA, and the Est1 subunit of telomerase. A second pathway involving an interaction between the yKu complex and telomerase RNA (TLC1) contributes to telomerase recruitment, but cannot sufficiently recruit telomerase on its own to prevent replicative senescence when the primary Cdc13-Est1 pathway is abolished—for example, in thecdc13-2mutant. In this study, we find that mutation ofPIF1, which encodes a helicase that inhibits telomerase, suppresses the replicative senescence ofcdc13-2increasing reliance on the yKu-TLC1 pathway for telomerase recruitment. Our findings reveal new insight into telomerase-mediated telomere maintenance.
JAG1 intracellular domain acts as a transcriptional cofactor that forms an oncogenic transcriptional complex with DDX17/SMAD3/TGIF2
Authors: Kim Eun-Jung , Kim Jung Yun , Kim Sung-Ok , Ham Seok Won , Choi Sang-Hun , Hong Nayoung , Park Min Gi , Jang Junseok , Seo Sunyoung , Lee Kanghun , Jeong Hyeon Ju , Kim Sung Jin , Jeong Sohee , Min Kyungim , Kim Sung-Chan , Jin Xiong , Kim Se Hoon , Kim Sung-Hak , Kim Hyunggee
Published: April 2021

Jagged1 (JAG1) is a Notch ligand that contact-dependently activates Notch receptors and regulates cancer progression. The JAG1 intracellular domain (JICD1) is generated from JAG1, such as the formation of NOTCH1 intracellular domain (NICD1), however, the role of JICD1 in tumorigenicity has not been comprehensively elucidated. Herein, we revealed that JICD1 induced astrocytes to acquire several cancer stem cell properties, including tumor formation, invasiveness, stemness, and resistance to chemotherapy and radiotherapy. The transcriptome, ChIP-sequencing, and proteomic analyses revealed that JICD1 increased SOX2 expression by forming a transcriptional complex with DDX17, SMAD3, and TGIF2. Furthermore, JICD1-driven tumorigenicity was directly regulated by SOX2. Therefore, our results demonstrated that, like NICD1, JICD1 acts as a transcriptional cofactor in the formation of the DDX17/SMAD3/TGIF2 transcriptional complex, leading to oncogenic transformation.
Liquid-to-solid phase transition ofoskarRNP granules is essential for their function in theDrosophilagermline
Authors: Bose Mainak , Mahamid Julia , Ephrussi Anne
Published: April 2021

Asymmetric localization ofoskarRNP granules to the oocyte posterior is crucial for abdominal patterning and germline formation of theDrosophilaembryo. We show thatoskarRNP granules in the oocyte are condensates with solid-like physical properties. Using purifiedoskarRNA and scaffold proteins Bruno and Hrp48, we confirmin vitrothatoskargranules undergo a liquid-to-solid phase transition. Whereas the liquid phase allows RNA incorporation, the solid phase precludes incorporation of additional RNA while allowing RNA-dependent partitioning of specific proteins. Genetic modification of scaffold granule proteins, or tethering the intrinsically disordered region of human Fused in Sarcoma tooskarmRNA, allowed modulation of granule material propertiesin vivo. The resulting liquid-like properties impairedoskarlocalization and translation with severe consequences on embryonic development. Our study reflects how physiological phase transitions shape RNA-protein condensates to regulate localization and expression of a maternal RNA that instructs germline formation.
The effect of histone deacetylase inhibitor Trichostatin A on IL-17A-induced transformation of MRC5 into myofibroblasts and its mechanism
Authors: Zhang Qian , Guo Zexin , Zhang Jing , Zhou Wei , Wu Yueqing , Dong Lixia , Feng Jing , Li Shuo , Cao Jie
Published: April 2021

Objective

To elucidate potential IL-17A- and TSA-mediated regulation of fibroblasts transformation.

Methods

MTT assay, HDAC1 activity assay, cell immunofluorescence and Western blot were employed to detect the expression of related indicators.

Results

MRC5 cells expressed only a small amount of Vimentin. IL-17A treatment upregulated MRC5 cell proliferation, in a concentration-dependent manner. TSA treatment, however, suppressed MRC5 cell proliferation. IL-17A treatment also upregulated HDAC1 activity in MRC5 cells, in a concentration-dependent manner. Using immunofluorescence, we demonstrated that IL-17A-treated MRC5 cells had markedly elevated Vimentin, Collagen-I and a-SMA levels, compared to controls. However, a combined treatment of IL-17A and TSA resulted in markedly reduced levels of the Vimentin, Collagen-I and a-SMA, compared to IL-17A alone, yet the amount was higher than controls. Using western blot analysis, we also revealed that the IL-17A-treated MRC5 cells had markedly elevated levels of Vimentin, a-SMA, HDAC1, p-Smad2, and p-Smad3, and markedly reduced level of Smad7, compared to controls. In TSA intervention group, the expression effect of the above protein was opposite. Moreover, no discernible difference was observed in the levels of Smad2 and Smad3 among the treated and un-treated groups.

Conclusion

IL-17A stimulates proliferation of MRC5 cells and increases HDAC1 activity and protein expression. It also transforms MRC5 cells into myofibroblasts via activation of the TGF -β1/ Smads signaling network. TSA, on the other hand, strongly suppresses TGF -β1/ Smads pathway-mediated fibrosis by ceasing HDAC1 activity and protein expression.
Standing covariation between genomic and epigenomic patterns as source for natural selection in wild strawberry plants
Authors: De Kort Hanne , Toivainen Tuomas , Van Nieuwerburgh Filip , Panis Bart , Hytönen Timo P. , Honnay Olivier
Published: April 2021

Adaptive evolution is generally thought to be the result of natural selection predominantly acting upon pre-existing DNA sequence polymorphisms through gene-environment interactions. Epigenetic inheritance is, however, recently considered an additional molecular force driving adaptive evolution independent of DNA sequence variation. Through comparative analyses of genome-wide genetic (SNPs) and epigenetic (DMCs) variation of wild strawberry plants raised under distinct drought settings, we demonstrate intermediate levels of genome-wide covariation between SNPs and DMCs. Cases of high SNP-DMC covariation were significantly associated with (i) applied stress, (ii) non-adaptive SNPs, and (iii) solitary DMCs (as opposed to DMC islands). We also found that DMCs, drought-responsive DMCs in particular, typically co-vary with hundreds of SNPs, indicating high genomic redundancy as a basis for polygenic adaptation. Our findings suggest that stress-responsive DMCs initially co-vary with many associated SNPs under increased environmental stress (cfr. co-gradient plasticity), and that natural selection acting upon these SNPs subsequently reduce standing covariation with stress-responsive DMCs. In addition, the degree of covariation between SNPs and DMCs appears independent of their respective genomic distance, indicating that trans-acting associations between SNPs and DMCs are as likely as cis-acting associations. Our study is in favor of DNA methylation profiles representing complex quantitative traits rather than independent evolutionary forces, but further research is required to fully rule out SNP-independence of genome-wide DMCs. We provide a conceptual framework for polygenic regulation and adaptation shaping genome-wide methylation patterns.
MetaProClust-MS1: A tool for clustering metaproteomes using rapid MS1 profiling
Authors: Simopoulos Caitlin M.A. , Ning Zhibin , Li Leyuan , Khamis Mona M. , Zhang Xu , Lavallée-Adam Mathieu , Figeys Daniel
Published: April 2021

Metaproteomics is used to explore the composition, dynamics and function of microbial communities. How-ever, acquiring data by tandem mass spectrometry is time consuming and resource intensive. To mediate this challenge, we present MetaProClust-MS1, a computational framework for microbiome screening developed to reduce the time required for data acquisition by mass spectrometry. In this proof-of-concept study, we tested MetaProClust-MS1 on data acquired using short 15 minute MS1-only mass spectrometry gradients and compared the results to those produced using data acquired by a traditional tandem mass spectrometry approach. MetaProClust-MS1 identified robust microbiome shifts caused by xenobiotics in both datasets. Cluster topologies were also significantly correlated. We demonstrate that MetaProClust-MS1 is able to rapidly screen microbiomes using only short MS1 profiles. This approach can be used to prioritize samples for deep metaproteomic analysis and will be especially useful in large-scale metaproteomic screens or in clinical settings where rapid results are required.
CD150-dependent hematopoietic stem cells sensing ofBrucellainstructs myeloid commitment
Authors: Lisiena Hysenaj , Bérengère De Laval , Vilma Arce-Gorvel , Mile Bosilkovski , Gabriela Gonzalez , Guillaume Debroas , Michael Sieweke , Sandrine Sarrazin , Jean-Pierre Gorvel
Published: April 2021

So far, hematopoietic stem cells (HSC) are considered the source of mature immune cells, the latter being the only ones capable of mounting an immune response. Recent evidence shows HSC can also directly sense cytokines released upon infection/inflammation and pathogen-associated molecular pattern interaction, while keeping a long-term memory of previous encountered signals. Direct sensing of danger signals by HSC induces early myeloid commitment, increases myeloid effector cell numbers and contributes to an efficient immune response. Here, using specific genetic tools on both host and pathogen sides, we show that HSC can directly sense B. abortus pathogenic bacteria within the bone marrow via the interaction of the cell surface protein CD150 with the bacterial outer membrane protein Omp25, inducing efficient functional commitment of HSC to the myeloid lineage. This is the first demonstration of a direct recognition of a live pathogen by HSC via CD150, which attests of a very early contribution of HSC to immune response.

This work provides first evidence HSC directly sense Brucella abortus via the bacterial outer membrane protein Omp25 and the HSC surface receptor CD150, leading to functional commitment of HSC to myeloid lineage and very early initiation of immune response.
Predicting skeletal stature using ancient DNA
Authors: Cox Samantha L , Moots Hannah , Stock Jay T , Shbat Andrej , Bitarello Bárbara D , Haak Wolfgang , Rosenstock Eva , Ruff Christopher B , Mathieson Iain
Published: April 2021

Objectives

Ancient DNA provides an opportunity to separate the genetic and environmental bases of complex traits by allowing direct estimation of genetic values in ancient individuals. Here, we test whether genetic scores for height in ancient individuals are predictive of their actual height, as inferred from skeletal remains. We estimate the contributions of genetic and environmental variables to observed phenotypic variation as a first step towards quantifying individual sources of morphological variation.

Materials and Methods

We collected stature estimates and femur lengths from West Eurasian skeletal remains with published genome-wide ancient DNA data (n=167, dating from 33,000-850 BP). We also recorded genetic sex, genetic ancestry, date and paleoclimate data for each individual, andδ13C andδ15N stable isotope values where available (n=67).

Results

A polygenic score (PRS) for height predicts 6.8% of the variance in femur length in our data (n=117, SD=0.0068%, p<0.001), controlling for sex, ancestry, and date. This is consistent with the predictive power of height PRS in present-day populations and the low coverage of ancient samples. Comparatively, sex explains about 15% of the variance in femur length in our sample. Environmental effects also likely play a role in variation, independent of genetics, though with considerable uncertainty (longitude:R2=0.0317, SD=0.009, p=0.019).

Discussion

Polygenic scores explain a small but significant proportion of the variance in height in ancient individuals, though not enough to make useful predictions of individual phenotypes. However, environmental variables also contribute to phenotypic outcomes and understanding their interaction with direct genetic predictions will provide a framework with which to model how plasticity and genetic changes ultimately combine to drive adaptation and evolution.
Microfluidic-based imaging of complete C. elegans larval development
Authors: Berger Simon , Spiri Silvan , deMello Andrew , Hajnal Alex
Published: April 2021

Several microfluidic-based methods for long-term C. elegans imaging have been introduced in recent years, allowing real-time observation of previously inaccessible processes. The existing methods either permit imaging across multiple larval stages without maintaining a stable worm orientation, or allow for very good immobilization but are only suitable for shorter experiments. Here, we present a novel microfluidic imaging method, which allows parallel live-imaging across multiple larval stages, while delivering excellent immobilization and maintaining worm orientation and identity over time. This is achieved by employing an array of microfluidic trap channels carefully tuned to maintain worms in a stable orientation, while allowing growth and molting to occur. Immobilization is supported by an active hydraulic valve, which presses worms onto the cover glass during image acquisition, with the animals remaining free for most of an experiment. Excellent quality images can be acquired of multiple worms in parallel, with little impact of the imaging method on worm viability or developmental timing. The capabilities of this methodology are demonstrated by observing the hypodermal seam cell divisions and, for the first time, the entire process of vulval development from induction to the end of morphogenesis. Moreover, we demonstrate RNAi on-chip, which allows for perturbation of dynamic developmental processes, such as basement membrane breaching during anchor cell invasion.
A spatial multi-scale fluorescence microscopy toolbox discloses entry checkpoints of SARS-CoV-2 variants in Vero E6 cells
Authors: Storti Barbara , Quaranta Paola , Di Primio Cristina , Clementi Nicola , Mancini Nicasio , Criscuolo Elena , Spezia Pietro Giorgio , Carnicelli Vittoria , Lottini Giulia , Paolini Emanuele , Freer Giulia , Lai Michele , Costa Mario , Beltram Fabio , Diaspro Alberto , Pistello Mauro , Zucchi Riccardo , Bianchini Paolo , Signore Giovanni , Bizzarri Ranieri
Published: April 2021

We exploited a multi-scale microscopy imaging toolbox to address some major issues related to SARS-CoV-2 interactions with host cells. Our approach harnesses both conventional and super-resolution fluorescence microscopy and easily matches the spatial scale of single-virus/cell checkpoints. We deployed this toolbox to characterize subtle issues related to the entry phase of SARS-CoV-2 variants in Vero E6 cells. Our results suggest that in these cells the variant of concern B.1.1.7, (aka Alpha variant), became the predominant circulating variant in several countries by a clear transmission advantage. In fact, in these cells B.1.1.7 outcompetes its ancestor B.1.177 in terms of a much faster kinetics of entry. Given the cell-entry scenario dominated by the endosomal “late pathway”, the faster internalization of B.1.1.7 could be directly related to the N501Y mutation in the S protein, which is known to strengthen the binding of Spike receptor binding domain with ACE2. Remarkably, we also directly observed the main role of clathrin as mediator of late-entry endocytosis, reconciling it with the membrane localization of the ACE2 receptor previously attributed to caveolin-enriched rafts. Overall, we believe that our fluorescence microscopy-based approach represents a fertile strategy to investigate the molecular features of SARS-CoV-2 interactions with cells.
A heterochromatic knob reducing the flowering time in maize
Authors: Carvalho Renata Flávia , Aguiar-Perecin Margarida Lopes Rodrigues , Clarindo Wellington Ronildo , Fristche-Neto Roberto , Mondin Mateus
Published: April 2021

Maize flowering time is an important agronomic trait, which has been associated with variations in the genome size and heterochromatic knobs content. We integrated three steps to show this association. Firstly, we selected inbred lines varying for heterochromatic knob composition at specific sites in the homozygous state. Then, we produced homozygous and heterozygous hybrids for knobs. Second, we measured the genome size and flowering time for all materials. Knob composition did not affect the genome size and flowering time. Finally, we developed an association study and identified a knob marker on chromosome 9 showing the strongest association with flowering time. Indeed, modelling allele substitution and dominance effects could offer only one heterochromatic knob locus that could affect flowering time, making it earlier rather than the knob composition.
How does a small molecule bind at a cryptic binding site?
Authors: Shan Yibing , Mysore Venkatesh P. , Leffler Abba E. , Kim Eric T. , Sagawa Shiori , Shaw David E.
Published: April 2021

Protein-protein interactions (PPIs) are ubiquitous biomolecular processes that are central to virtually all aspects of cellular function. Identifying small molecules that modulate specific disease-related PPIs is a strategy with enormous promise for drug discovery. The design of drugs to disrupt PPIs is challenging, however, because many potential drug-binding sites at PPI interfaces are “cryptic”: When unoccupied by a ligand, cryptic sites are often flat and featureless, and thus not readily recognizable in crystal structures, with the geometric and chemical characteristics of typical small-molecule binding sites only emerging upon ligand binding. The rational design of small molecules to inhibit specific PPIs would benefit from a better understanding of how such molecules bind at PPI interfaces. To this end, we have conducted unbiased, all-atom MD simulations of the binding of four small-molecule inhibitors (SP4206 and three SP4206 analogs) to interleukin 2 (IL2)—which performs its function by forming a PPI with its receptor—without incorporating any prior structural information about the ligands’ binding. In multiple binding events, a small molecule settled into a stable binding pose at the PPI interface of IL2, resulting in a protein–small-molecule binding site and pose virtually identical to that observed in an existing crystal structure of the IL2-SP4206 complex. Binding of the small molecule stabilized the IL2 binding groove, which when the small molecule was not bound emerged only transiently and incompletely. Moreover, free energy perturbation (FEP) calculations successfully distinguished between the native and non-native IL2–small-molecule binding poses found in the simulations, suggesting that binding simulations in combination with FEP may provide an effective tool for identifying cryptic binding sites and determining the binding poses of small molecules designed to disrupt PPI interfaces by binding to such sites.
Identification of cardiac afterload dynamics from data
Authors: Pigot Henry , Hansson Jonas , Paskevicius Audrius , Liao Qiuming , Sjöberg Trygve , Steen Stig , Soltesz Kristian
Published: April 2021

The prospect ofex vivofunctional evaluation of donor hearts is considered. Particularly, the dynamics of a synthetic cardiac afterload model are compared to those of normal physiology. A method for identification of continuous-time transfer functions from sampled data is developed and verified against results from the literature. The method relies on exact gradients and Hessians obtained through automatic differentiation. This also enables straightforward sensitivity analyses. Such analyses reveal that the 4-element Windkessel model is not practically identifiable from representative data while the 3-element model underfits the data. Pressure–volume (PV) loops are therefore suggested as an alternative for comparing afterload dynamics.
PCRedux: A Data Mining and Machine Learning Toolkit for qPCR Experiments
Authors: Burdukiewicz Michał , Spiess Andrej-Nikolai , Rafacz Dominik , Blagodatskikh Konstantin , Huggett Jim , McCall Matthew N. , Schierack Peter , Rödiger Stefan
Published: April 2021

Motivation

Quantitative Real-time PCR (qPCR) is a widely used -omics method for the precise quantification of nucleic acids, in which the result is associated with the presence/absence or quantity of a specific nucleic acid sequence. As the amount of qPCR data increases worldwide, the manual assessment of results becomes challenging and difficult to reproduce. To overcome this, some automatable characteristics of amplification curves have been described in the literature, often with an appropriate “rule of thumb”.

Results

We developedPCReduxto analyze and calculate 90 numerical qPCR amplification curve descriptors (‘‘features”) from large datasets of qPCR amplification curves that are aimed for interpretable machine learning and development of decision support systems. In a case study of a diverse dataset with 3181 positive, negative and ambiguous amplification curves, as assessed by three human raters, we demonstrate a sensitivity >99 % and specificity >97 % in detecting positive and negative amplification.PCReduxis unique as it goes beyond traditional qPCR analysis to capture curvature properties that improve the characterization and classification of amplification curves. The calculation of the features is reproducible and objective, sinceRis used as a controllable working environment.PCReduxis not a black box, but open source software following on the principle of mathematically interpretable features. These can be combined with user-defined labels for automatic multi-category classification and regression in machine learning.

Availability

https://cran.r-project.org/package=PCRedux. Web server:http://shtest.evrogen.net/PCRedux-app/. Documentation:https://PCRuniversum.github.io/PCRedux/.
SARS-CoV-2 immune evasion by variant B.1.427/B.1.429
Authors: McCallum Matthew , Bassi Jessica , Marco Anna De , Chen Alex , Walls Alexandra C. , Iulio Julia Di , Tortorici M. Alejandra , Navarro Mary-Jane , Silacci-Fregni Chiara , Saliba Christian , Agostini Maria , Pinto Dora , Culap Katja , Bianchi Siro , Jaconi Stefano , Cameroni Elisabetta , Bowen John E. , Tilles Sasha W , Pizzuto Matteo Samuele , Guastalla Sonja Bernasconi , Bona Giovanni , Pellanda Alessandra Franzetti , Garzoni Christian , Van Voorhis Wesley C. , Rosen Laura E. , Snell Gyorgy , Telenti Amalio , Virgin Herbert W. , Piccoli Luca , Corti Davide , Veesler David
Published: April 2021

SARS-CoV-2 entry is mediated by the spike (S) glycoprotein which contains the receptor-binding domain (RBD) and the N-terminal domain (NTD) as the two main targets of neutralizing antibodies (Abs). A novel variant of concern (VOC) named CAL.20C (B.1.427/B.1.429) was originally detected in California and is currently spreading throughout the US and 29 additional countries. It is unclear whether antibody responses to SARS-CoV-2 infection or to the prototypic Wuhan-1 isolate-based vaccines will be impacted by the three B.1.427/B.1.429 S mutations: S13I, W152C and L452R. Here, we assessed neutralizing Ab responses following natural infection or mRNA vaccination using pseudoviruses expressing the wildtype or the B.1.427/B.1.429 S protein. Plasma from vaccinated or convalescent individuals exhibited neutralizing titers, which were reduced 3-6 fold against the B.1.427/B.1.429 variant relative to wildtype pseudoviruses. The RBD L452R mutation reduced or abolished neutralizing activity of 14 out of 35 RBD-specific monoclonal antibodies (mAbs), including three clinical-stage mAbs. Furthermore, we observed a complete loss of B.1.427/B.1.429 neutralization for a panel of mAbs targeting the N-terminal domain due to a large structural rearrangement of the NTD antigenic supersite involving an S13I-mediated shift of the signal peptide cleavage site. These data warrant closer monitoring of signal peptide variants and their involvement in immune evasion and show that Abs directed to the NTD impose a selection pressure driving SARS-CoV-2 viral evolution through conventional and unconventional escape mechanisms.
Extensive variation in the mouse intelectin gene family: recent duplications, deletions and inactivating variants result in diversity in laboratory strains
Authors: Almalki Faisal , Nonnecke Eric B. , Castillo Patricia A. , Bevin-Holder Alex , Ullrich Kristian K. , Lönnerdal Bo , Odenthal-Hesse Linda , Bevins Charles L. , Hollox Edward J.
Published: April 2021

Intelectins are a family of multimeric secreted proteins that bind microbe-specific glycans. Both genetic and functional studies have suggested that intelectins have an important role in innate immunity and are involved in the etiology of various human diseases, including inflammatory bowel disease. Experiments investigating the role of intelectins in human disease using mouse models are limited by the fact that there is not a clear one-to-one relationship between intelectin genes in humans and mice, and that the number of intelectin genes varies between different mouse strains. In this study we show by gene sequence and gene expression analysis that human intelectin-1 (ITLN1) has multiple orthologues in mice, including a functional homologue Itln1; however, human intelectin-2 has no such orthologue or homologue. We confirm that all sub-strains of the C57-line have a large deletion resulting in retention of only one intelectin gene,Itln1. The majority of laboratory strains have a full complement of six intelectin genes, except wild-derived CAST, SPRET, SKIVE, MOLF and PANCEVO, which are derived from different mouse species/subspecies and encode different complements of intelectin genes. In wild mice, intelectin deletions are polymorphic inMus musculus castaneusandMus musculus domesticus. Further sequence analysis shows thatItln3andItln5are polymorphic pseudogenes due to premature truncating mutations, and that mouseItln1has undergone recent adaptive evolution. Taken together, our study shows extensive diversity in intelectin genes in both laboratory and wild-mice, suggesting a pattern of birth-and-death evolution. In addition, our data provide a foundation for further experimental investigation of the role of intelectins in disease.