bluuebunny/crossref_metadata_2025_split huggingface dataset:
Harnessing CRISPR-Cas9 for genome editing inStreptococcus pneumoniae
Authors: Synefiaridou Dimitra , Veening Jan-Willem 
Published: June 2020

AbstractCRISPR systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by detection and cleavage of invading foreign DNA. Modified versions of this system can be exploited as a biotechnological tool for precise genome editing at a targeted locus. Here, we developed a novel, replicative plasmid that carries the CRISPR-Cas9 system for RNA-programmable, genome editing by counterselection in the opportunistic human pathogenStreptococcus pneumoniae. Specifically, we demonstrate an approach for making targeted, marker-less gene knockouts and large genome deletions. After a precise double-stranded break (DSB) is introduced, the cells’ DNA repair mechanism of homology-directed repair (HDR) pathway is being exploited to select successful transformants. This is achieved through the transformation of a template DNA fragment that will recombine in the genome and eliminate recognition of the target of the Cas9 endonuclease. Next, the newly engineered strain, can be easily cured from the plasmid that is temperature-sensitive for replication, by growing it at the non-permissive temperature. This allows for consecutive rounds of genome editing. Using this system, we engineered a strain with three major virulence factors deleted. The here developed approaches should be readily transportable to other Gram-positive bacteria.ImportanceStreptococcus pneumoniae(the pneumococcus) is an important opportunistic human pathogen killing over a million people each year. Having the availability of a system capable of easy genome editing would significantly facilitate drug discovery and vaccine candidate efforts. Here, we introduced an easy to use system to perform multiple rounds of genome editing in the pneumococcus by putting the CRISPR-Cas9 system on a temperature-sensitive replicative plasmid. The here used approaches will advance genome editing projects in this important human pathogen.
Multi-epitope Based Peptide Vaccine Design Using Three Structural Proteins (S, E, and M) of SARS-CoV-2: AnIn SilicoApproach
Authors: Roy Arpita Singha , Tonmoy Mahafujul Islam Quadery , Fariha Atqiya , Hami Ithmam , Afif Ibrahim Khalil , Munim Md. Adnan , Alam Mohammad Rahanur , Hossain Md. Shahadat 
Published: June 2020

AbstractSevere Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the novel coronavirus responsible for the ongoing pandemic of coronavirus disease (COVID-19). No sustainable treatment option is available so far to tackle such a public health threat. Therefore, designing a suitable vaccine to overcome this hurdle asks for immediate attention. In this study, we targeted for a design of multi-epitope based vaccine using immunoinformatics tools. We considered the structural proteins S, E and, M of SARS-CoV-2, since they facilitate the infection of the virus into host cell and using different bioinformatics tools and servers, we predicted multiple B-cell and T-cell epitopes having potential for the required vaccine design. Phylogenetic analysis provided insight on ancestral molecular changes and molecular evolutionary relationship of S, E, and M proteins. Based on the antigenicity and surface accessibility of these proteins, eight epitopes were selected by various B cell and T cell epitope prediction tools. Molecular docking was executed to interpret the binding interactions of these epitopes and three potential epitopes WTAGAAAYY, YVYSRVKNL, and GTITVEELK were selected for their noticeable higher binding affinity scores −9.1, −7.4, and −7.0 kcal/mol, respectively. Targeted epitopes had 91.09% population coverage worldwide. In summary, we identified three epitopes having the most significant properties of designing the peptide-based vaccine against SARS-CoV-2.
Microglial activation results in neuron-type-specific increase in mPFC GABAergic transmission and abnormal behavior in mice
Authors: Tang Binliang , Jiang Jinxiang , Wang Lei , Misrani Afzal , Huo Qingwei , Han Yuanyuan , Long Cheng , Yang Li 
Published: June 2020

AbstractNeuroinflammation and synaptic dysfunction are two early symptoms of most neurological diseases. However, the mechanisms underlying microglia-associated neuroinflammation in the regulation of synaptic activity remain obscure. We report here that acute neuroinflammation induced by a single-dose proinflammatory cytokine inducer, lipopolysaccharide (LPS), results in enhanced inhibitory postsynaptic currents (IPSCs) of glutamatergic neurons, upregulated levels of GABAAR subunits, glutamine synthetase (GS) and vGAT, and downregulated BDNF and pTrkB levels, due to enhanced activation of microglia in the medial prefrontal cortex (mPFC). Blockage of microglial activation by minocycline ameliorated LPS-induced aberrant mIPSCs and associated aberrant protein expression and behavior. Exogenous application of BDNF prior to LPS challenge also ameliorated LPS-induced abnormal mIPSCs. Thus, this study elucidates a critical role for microglia in the neurobiology of GABAergic synaptic dysfunction induced by neuroinflammation, revealing a novel GABAergic signaling pathway that might be targeted therapeutically to treat neuroinflammation-induced abnormal synaptic activity and associated aberrant behavior.
CDC6 regulates mitotic CDK1 via cyclin B and not cyclin A and acts through abona fideCDK inhibitor Xic1
Authors: El Dika Mohammed , Wechselberger Lisa , Djeghout Bilal , Benouareth Djamel Eddine , Jęderka Krystyna , Lewicki Sławomir , Prigent Claude , Kloc Malgorzata , Kubiak Jacek Z. 
Published: June 2020

AbstractThe timing of the M-phase entry and its progression are precisely controlled by a CDC6-dependent mechanism that inhibits the major mitotic kinase CDK1, and, thus, regulates the dynamic of CDK1 during the M-phase. In this paper, we describe the differential regulation of the mitotic CDK1 dynamics by exogenous cyclin A or a non-degradable cyclin B added to theXenopus laevisembryo cycling extracts. We showed that the variations in the level of cyclin B modify both CDK1 activity and the timing of the M-phase progression, while the cyclin A levels modify only CDK1 activity without changing the timing of the M-phase events. In consequence, CDC6 regulates the M-phase through endogenous cyclin B, but not cyclin A, which we demonstrated directly by the depletion of cyclin A, and the addition of CDC6 to the cycling extracts. Further, we showed, by p9 precipitation (p9 protein associates with Cyclin-Dependent Kinases, CDK), followed by the Western blotting that CDC6, and thebona fideCDK1 inhibitor Xic1, associate with CDK1 and/or another CDK present in Xenopus embryos, the CDK2. Finally, we demonstrated that the Xic1 temoprarily separates from the mitotic CDK complexes during the peak of CDK1 activity. These data show the differential coordination of the M-phase progression by CDK1/cyclin A and CDK1/cyclin B, confirm the critical role of the CDC6-dependent CDK1 inhibition in this process and show that CDC6 acts through the cyclin B- and not cyclin A/CDK complexes. This CDC6- and cyclin B-dependent mechanism may also depend on the precisely regulated association of Xic1 with the CDK complexes. We postulate that the dissociation of Xic1 from the CDK complexes allows the maximal activation of CDK1 during the M-phase.
Microbial Diversity of Deep-Sea Ferromanganese Crust Field in the Rio Grande Rise, Southwestern Atlantic Ocean
Authors: Bergo Natascha Menezes , Bendia Amanda Gonçalves , Ferreira Juliana Correa Neiva , Murton Bramley , Brandini Frederico Pereira , Pellizari Vivian Helena 
Published: June 2020

AbstractSeamounts are often covered with Fe and Mn oxides, known as ferromanganese (Fe-Mn) crusts. Future mining of these crusts is predicted to have significant effects on biodiversity in mined areas. Although microorganisms have been reported on Fe–Mn crusts, little is known about the role of crusts in shaping microbial communities. Here, we investigated microbial community based on 16S rRNA gene sequences retrieved from Fe-Mn crusts, coral skeleton, calcarenite and biofilm at crusts of the Rio Grande Rise (RGR). RGR is a prominent topographic feature in the deep southwestern Atlantic Ocean with Fe-Mn crusts. Our results revealed that crust field of the RGR harbors a usual deep-sea microbiome. We observed differences of microbial structure according to the sampling location and depth, suggesting an influence of water circulation and availability of particulate organic matter. Bacterial and archaeal groups related to oxidation of nitrogen compounds, such as Nitrospirae, Nitrospinae phyla, Nitrosopumilus within Thaumarchaeota group were present on those substrates. Additionally, we detected abundant assemblages belonging to methane oxidation, i. e. Ca. Methylomirabilales (NC10) and SAR324 (Deltaproteobacteria). The chemolithoautotrophs associated with ammonia-oxidizing archaea and nitrite-oxidizing bacteria potentially play an important role as primary producers in the Fe-Mn substrates from RGR. These results provide the first insights into the microbial diversity and potential ecological processes in Fe-Mn substrates from the Atlantic Ocean. This may also support draft regulations for deep-sea mining in the region.
Dendritic cell actin dynamics controls T cell priming efficiency at the immunological synapse
Authors: Leithner Alexander , Altenburger Lukas M. , Hauschild Robert , Assen Frank , Rottner Klemens , Stradal Theresia E.B. , Stein Jens V. , Sixt Michael 
Published: June 2020

AbstractDendritic cells (DCs) are crucial for the priming of naïve T cells and the initiation of adaptive immunity. Priming is initiated at a heterologous cell-cell contact, the immunological synapse (IS). While it is established that actin dynamics regulates signalling at the T cell side of the contact, little is known about the cytoskeletal contribution on the DC side. We show that that the DC cytoskeleton is decisive for the formation of a multifocal synaptic structure, which correlates with T cell priming efficiency. We demonstrate that DC actin appears in transient foci at the IS and that these foci are dynamized by the WAVE complex. Absence of WAVE in DCs leads to stabilized contacts with T cells, caused by an increase in ICAM1-integrin mediated cell-cell adhesions. This results in a lower number of activated and proliferating T cells. Our results reveal an important role of DC actin in the regulation of synaptic contacts with crucial relevance for full T cell expansion.
Sex differences in vocalizations to familiar or unfamiliar females in mice
Authors: Sasaki Eri , Tomita Yuiri , Kanno Kouta 
Published: June 2020

AbstractMice, both wild and laboratory strains, emit ultrasound to communicate. The sex differences between male to female (male–female) and female to female (female– female) ultrasonic vocalizations (USVs) have been discussed for decades. In the present study, we compared the number of USVs emitted to familiar and unfamiliar females by both males (male–female USVs) and females (female–female USVs). We found that females vocalized more to unfamiliar than to familiar females. In contrast, males exhibited more USVs to familiar partners. This sexually dimorphic behavior suggests that mice change their vocal behavior in response to the social context, and their perception of the context is based on social cognition and memory. In addition, because males vocalized more to familiar females, USVs appear to be not just a response to novel things or individuals, but also to be a social response.
Steady-State Regulation of COPII-Dependent Secretory Cargo Sorting by Inositol Trisphosphate Receptors, Calcium, and Penta EF Hand Proteins
Authors: Held Aaron , Lapka Jacob , Sargeant John , Hojanazarova Jennet , Madreiter-Sokolowski Corina , Malli Roland , Graier Wolfgang F. , Hay Jesse C. 
Published: June 2020

ABSTRACTRecently, we demonstrated that agonist-stimulated Ca2+signaling involving IP3 receptors modulates ER export rates through activation of the penta-EF Hand (PEF) proteins apoptosis-linked gene-2 (ALG-2) and peflin. It is unknown, however, whether IP3Rs and PEF proteins regulate ER export rates at steady state. Here we tested this idea in normal rat kidney (NRK) epithelial cells by manipulation of IP3R isoform expression. Under standard growth conditions, spontaneous cytosolic Ca2+oscillations occurred simultaneously in successive groups of contiguous cells, generating intercellular Ca2+waves (ICWs) that moved across the monolayer periodically. Depletion of IP3R-3, typically the least promiscuous IP3R isoform, caused increased cell participation in ICWs in unstimulated cells. The increased spontaneous signaling was sufficient to cause increased ALG-2 and Sec31A, and decreased peflin localization at ER exit sites (ERES), resulting in increased ER-to-Golgi transport of the COPII client cargo VSV-G. The elevated ER-to-Golgi transport caused greater concentration of VSV-G at ERES and had reciprocal effects on transport of VSV-G and a bulk-flow cargo, though both cargos equally required Sec31A. Inactivation of client cargo sorting using 4-phenylbutyrate (4-PBA) had opposing reciprocal effects on client and bulk-flow cargo and neutralized any effect of ALG-2 activation on transport. This work extends our knowledge of ALG-2 mechanisms and indicates that in NRK cells, IP3R isoforms regulate homeostatic Ca2+signaling that helps determine the basal secretion rate and stringency of COPII-dependent cargo sorting.
Visual processing and fold-change detection by the larva of the simple chordateCiona
Authors: Borba Cezar , Kourakis Matthew J. , Schwennicke Shea , Brasnic Lorena , Smith William C. 
Published: June 2020

AbstractVisual processing transforms the complex visual world into useful information.Ciona, a close relative of vertebrates, has one of the simplest nervous systems known, yet has a range of visuomotor behaviors. Among them are negative phototaxis and a looming-shadow response. These two behaviors are mediated by separate photoreceptor groups acting via distinct, but overlapping, neural circuits. We show here that processing circuits underlying both behaviors transform visual inputs to generate fold-change detection (FCD) outputs. In FCD, the response scales with the relative fold changes in input, but is invariant to the overall magnitude of the stimulus. Several different circuit architectures can generate FCD responses. Both the behavioral outputs and the putative circuitry for the two visuomotor behaviors point to them using different FCD circuits. Pharmacological treatment points to circuits in the posterior brain vesicle ofCiona, a region we speculate shares homology with the vertebrate midbrain, as important for FCD.
The BCG dilemma: linear versus non-linear correlation models over the time of the COVID-19 pandemic
Authors: Lopez-Campos Guillermo , Hawthorne Christopher , Valvano Miguel A. 
Published: June 2020

AbstractIn this work we have analysed the use of two different correlation metrics and two different datasets, detecting differences in the extent and directionality of the correlation between COVID-19 infection and BCG immunization. Correlation between COVID-19 infection, death rates and BCG immunization is strongly affected by the correlation metrics and so will be their biological interpretation.
Sentinel surveillance of SARS-CoV-2 in wastewater anticipates the occurrence of COVID-19 cases
Authors: Chavarria-Miró Gemma , Anfruns-Estrada Eduard , Guix Susana , Paraira Miquel , Galofré Belén , Sánchez Gloria , Pintó Rosa M. , Bosch Albert 
Published: June 2020

AbstractSARS-CoV-2 was detected in Barcelona sewage long before the declaration of the first COVID-19 case, indicating that the infection was present in the population before the first imported case was reported. Sentinel surveillance of SARS-CoV-2 in wastewater would enable adoption of immediate measures in the event of future COVID-19 waves.Article Summary LineSARS-CoV-2 genomes occur in sewage long before the declaration of COVID-19 cases among the population.
Impacts of regional climate on the COVID-19 fatality in 88 countries
Authors: Wen Minneng , Chen Liyuan 
Published: June 2020

AbstractThe COVID-19 pandemic had led to 500000 confirmed death by June 30, 2020. We combined the number of monthly confirmed new cases and deaths with latitude, temperature, humidity, rainfall, and sunshine ultraviolet (UV) to explore the climate impacts on COVID-19 fatality in 88 countries. There was a significant decrease in overall case-fatality rate in May and June (from 8.17% to 4.99% and 3.22%). The fatality in temperate marine regions was the highest (11.13%). The fatality was 5.71% in high latitudes (≥30°) but only 3.73% in low latitudes (<30°). The fatality was 6.76% in cold regions (<20°C) but only 3.90% in hot regions (≥20°C). The fatality was 5.87% in rainy regions (≥40mm) but only 3.33% in rainless regions (<40mm). The fatality was 6.57% in cloudy regions (<50) but only 3.86% in sunny regions (≥50). Traveling to hot sunny regions without pollution is a strategy for risk reduction.
Short‐term change in water availability influences thermoregulation behaviours in a dry‐skinned ectotherm
Authors: Rozen‐Rechels David , Farigoule Pauline , Agostini Simon , Badiane Arnaud , Meylan Sandrine , Le Galliard Jean‐François 
Published: June 2020

Abstract

Mechanistic models of terrestrial ectotherms predict that climate warming will induce activity restriction due to heat stress and loss of shade, leading to the extinction of numerous populations. Such models rely on the assumption that activity patterns are dictated by simple temperature thresholds independent of changes in water availability. However, changes in water availability may further influence thermoregulation behaviour of ectotherms through dehydration risk perception, changes in water balance or changes in microclimatic conditions.

Here, we experimentally assess the interactive effects of thermal conditions and water availability on activity patterns, shade selection and thermoregulation efficiency in a model ectothermic species.

Thermoregulation behaviour of adult common lizards Zootoca vivipara was monitored in outdoor mesocosms as we manipulated water availability, providing water as mist in the morning and free‐standing water during the daytime. We recorded operative temperatures and micro‐meteorological conditions to infer thermal constraints and dehydration risk.

Activity and shade selection were better predicted by continuous changes in thermal conditions and dehydration risk, respectively, than by threshold functions. In addition, water supplementation increased activity in males and reduced shade selection in both sexes, most probably as a behavioural response to the perception of a stronger dehydration risk. Water supplementation also influenced the thermal quality of the environment, which in turn altered daily activity patterns and thermoregulation statistics.

This demonstrates that dual effects of heat and water stress on activity patterns may lead to stronger activity restriction as a result of climate change than currently predicted.
Impacts of selective logging on the oxidative status of tropical understorey birds
Authors: Messina Simone , Edwards David P. , AbdElgawad Hamada , Beemster Gerrit T. S. , Tomassi Suzanne , Benedick Suzan , Eens Marcel , Costantini David 
Published: June 2020

Abstract

Selective logging is the dominant form of human disturbance in tropical forests, driving changes in the abundance of vertebrate and invertebrate populations relative to undisturbed old‐growth forests.

A key unresolved question is understanding which physiological mechanisms underlie different responses of species and functional groups to selective logging. Regulation of oxidative status is thought to be one major physiological mechanism underlying the capability of species to cope with environmental changes.

Using a correlational cross‐sectional approach, we compared a number of oxidative status markers among 15 understorey bird species in unlogged and selectively logged forest in Borneo in relation to their feeding guild. We then tested how variation of markers between forest types was associated with that in population abundance.

Birds living in logged forests had a higher activity of the antioxidant enzyme superoxide dismutase and a different regulation of the glutathione cycle compared to conspecific birds in unlogged forest. However, neither oxidative damage nor oxidized glutathione differed between forest types. We also found that omnivores and insectivores differed significantly in all markers related to the key cellular antioxidant glutathione irrespective of the forest type. Species with higher levels of certain antioxidant markers in a given type of forest were less abundant in that forest type compared to the other.

Our results suggest that there was little long‐term effect of logging (last logging rotation occurred ~15 years prior to the study) on the oxidative status of understorey bird species. However, it is unclear if this was owing to plasticity or evolutionary change. Our correlative results also point to a potential negative association between some antioxidants and population abundance irrespective of the forest type.
Vaginal compared with intramuscular progestogen for preventing preterm birth in high‐risk pregnant women (VICTORIA study): a multicentre, open‐label randomised trial and meta‐analysis
Authors: Choi S‐J , Kwak DW , Kil K , Kim S‐C , Kwon J‐Y , Kim YH , Na S , Bae J‐G , Cha H‐H , Shim J‐Y , Oh KY , Lee KA , Kim SM , Cho IA , Lee SM , Cho GJ , Jo YS , Choi GY , Choi SK , Hur SE , Hwang HS , Kim YJ ,   from The Preterm Birth Research Committee of the Korean Society of Maternal Fetal Medicine
Published: June 2020

ObjectiveTo compare the efficacy of two types of progestogen therapy for preventing preterm birth (PTB) and to review the relevant literature.DesignA multicentre, randomised, open‐label, equivalence trial and a meta‐analysis.SettingTertiary referral hospitals in South Korea.PopulationPregnant women with a history of spontaneous PTB or short cervical length (<25 mm).MethodsEligible women were screened and randomised at 16‒22 weeks of gestation to receive either 200 mg of vaginal micronised progesterone daily (vaginal group) or an intramuscular injection of 250 mg 17α‐hydroxyprogesterone caproate weekly (IM group). Stratified randomisation was carried out according to participating centres and indications for progestogen therapy. This trial was registered at ClinicalTrials.gov (NCT02304237).Main outcome measurePreterm birth (PTB) before 37 weeks of gestation.ResultsA total of 266 women were randomly assigned and a total of 247 women (119 and 128 women in the vaginal and IM groups, respectively) were available for the intention‐to‐treat analysis. Risks of PTB before 37 weeks of gestation did not significantly differ between the two groups (22.7 versus 25.8%, P = 0.571). The difference in PTB risk between the two groups was 3.1% (95% CI −7.6 to 13.8%), which was within the equivalence margin of 15%. The meta‐analysis results showed no significant differences in the risk of PTB between the vaginal and IM progestogen treatments.ConclusionCompared with vaginal progesterone, treatment with intramuscular progestin might increase the risk of PTB before 37 weeks of gestation by as much as 13.8%, or reduce the risk by as much as 7.6%, in women with a history of spontaneous PTB or with short cervical length.Tweetable abstractVaginal and intramuscular progestogen showed equivalent efficacy for preventing preterm birth before 37 weeks of gestation.