bluuebunny/crossref_metadata_2025 huggingface dataset:
Loss of IKK subunits limits NF-κB signaling in reovirus infected cells
Authors: McNamara Andrew J. , Danthi Pranav
Published: November 2019

Viruses commonly antagonize innate immune pathways that are primarily driven by Nuclear Factor-κB (NF-κB), Interferon Regulatory Factor (IRF) and Signal Transducer and Activator of Transcription (STAT) family of transcription factors. Such a strategy allows viruses to evade immune surveillance and maximize their replication. Using an unbiased RNA-seq based approach to measure gene expression induced by transfected viral genomic RNA (vgRNA) and reovirus infection, we discovered that mammalian reovirus inhibits host cell innate immune signaling. We found that while vgRNA and reovirus infection both induce a similar IRF dependent gene expression program, gene expression driven by the NF-κB family of transcription factors is lower in infected cells. Potent agonists of NF-κB, such as Tumor Necrosis Factor alpha (TNFα) and vgRNA, failed to induce NF-κB dependent gene expression in infected cells. We demonstrate that NF-κB signaling is blocked due to loss of critical members of the Inhibitor of KappaB Kinase (IKK) complex, NF-κB Essential MOdifier (NEMO) and IKKβ. The loss of the IKK complex components prevents nuclear translocation and phosphorylation of NF-κB, thereby preventing gene expression. Our studies demonstrate that reovirus infection selectively blocks NF-κB, likely to counteract its antiviral effects and promote efficient viral replication.

IMPORTANCE

Host cells mount a response to curb virus replication in infected cells and prevent infection of neighboring, as yet uninfected cells. The NF-κB family of proteins is important for the cell to mediate this response. In this study, we show that in cells infected with mammalian reovirus, NF-κB is inactive. Further, we demonstrate that NF-κB is rendered inactive because virus infection results in reduced levels of upstream intermediaries (called IKKs) that are needed for NF-κB function. Based on previous evidence that active NF-κB limits reovirus infection, we conclude that inactivating NF-κB is a viral strategy to produce a cellular environment that is favorable for virus replication.
STRESS-INDUCED GENETIC CHANGE IN FLAX REVEALS GENOME VARIATION MECHANISM
Authors: Li Xiang
Published: November 2019

Inherited genetic change can happen in flax (Linum usitatissimum) due to environmental stress. The change can result in different phenotypes in flax progeny. The genetic changes can be induced during one generation and can result in stable genotypes in the next generation. Also the genetic changes are precise and repeatable that homozygous individuals show the same genome reorganization at specific sites in their progeny. Therefore, the genetic re-arrangements are not the result of a random process but a preference for a particular DNA structure, which indicates that possible new genes or functional fragments are formed during this process. The genomes of different varieties of flax are compared to explain the detail of the rapid but intentional genomic changes and regions of variation identified by whole genome comparisons. Possible mechanisms and the potential causes of these rearrangements bring a new light to modern plant genome studies and molecular evolution research.
Regionalization in the compound eye ofTalitrus saltator(Crustacea, Amphipoda)
Authors: Ciofini Alice , Mercatelli Luca , Yamahama Yumi , Hariyama Takahiko , Ugolini Alberto
Published: November 2019

The crustaceanTalitrus saltatoris known to use many celestial cues during its orientation along the sea-land axis of sandy shores. In this paper, we investigated the existence of the eye regionalization by morphological, electrophysiological and behavioural experiments. Each ommatidium possesses five radially arranged retinular cells producing a square fused rhabdom by R1-R4 cells; the smaller R5 exist between R1 and R4. The size of R5 rhabdomere is largest in dorsal part and becomes gradually smaller in median and ventral part of the eye. Spectral-sensitivity measurements were recorded from either dorsal or ventral parts of the compound eye to clarify the chromatic difference. Results show that the dorsal part is green and UV-blue dichromatic, whereas the ventral part is UV (390 nm) with a substantial population of 450 nm receptors with the responses in the longer wavelength region. To evaluate the orienting behaviour of individuals, their eyes were black painted either in the dorsal or ventral part, under natural sky or a blue filter with or without the vision of the sun. Results show that animals painted on the dorsal part of their eyes tested under the screened sun were more dispersed and in certain cases their directions deflected than other groups of individuals. Furthermore, sandhoppers subjected to the obscuring of this area met in any case high difficulties in their directional choices. Therefore, our present work indicates the existence of a regionalization of the compound eye ofT. saltator.

Summary statement

This work provides evidences of the morphological and electrophysiological regionalization of the compound eye and the visual capabilities for behaviour involved in the recognition of the celestial compass orienting factors in crustaceans.
Telomere shortening produces an inflammatory environment that promotes tumor invasiveness in zebrafish
Authors: Lex Kirsten , Gil Mariana Maia , Figueira Margarida , Marzullo Marta , Lopes-Bastos Bruno , Giannetti Kety , Carvalho Tania , Ferreira Miguel Godinho
Published: November 2019

Cancer incidence increases exponentially with age, when human telomeres are shorter. Similarly, telomerase mutant zebrafish (tert) have premature short telomeres and anticipate cancer incidence to younger ages. However, because short telomeres constitute a road block to cell proliferation, telomere shortening is currently viewed as a tumor suppressor mechanism and should protect from cancer. This conundrum is not fully understood. In our current study, we report that telomere shortening promotes cancer in a non-cell autonomous manner. Using zebrafish chimeras, we show increased incidence of invasive melanoma when WT tumors are generated in tert mutant zebrafish. tert zebrafish show increased levels of senescence (cdkn2a and ink4a/b) and inflammation (TNF-α). In addition, we transferred second generation tert blastula cells into WT to produce embryo chimeras. Cells with very short telomeres induced senescence and increased neutrophil numbers in surrounding larval tissues in a non-cell autonomous manner, creating an inflammatory environment. Considering that inflammation is pro-tumorigenic, we transplanted melanoma-derived cells into second generation tert zebrafish embryos and observed that tissue environment with short telomeres leads to increased micrometastasis. To test if inflammation was necessary for this effect, we treated melanoma transplants with non-steroid anti-inflammatory drugs and show that higher melanoma invasiveness can be averted. Thus, apart from the cell autonomous role of short telomeres in contributing to genome instability, we propose that telomere shortening with age causes systemic chronic inflammation leading to increased tumor incidence.

Significance Statement

Cancer incidence increases exponentially in human midlife. Even though mutation accumulation in somatic tissues results in increased tumorigenesis, it is currently not understood how aging contributes to cancer. Telomeres, the ends of eukaryotic linear chromosomes, shorten with each cell division. Here we show that telomere shortening contributes to cancer in a non-cell autonomous manner. Using embryo chimeras of telomerase deficient zebrafish generated from melanoma-prone fish, we show that tumors arise more frequently and become more invasive in animals with shorter telomeres. Telomere shortening gives rise to increased senescence and systemic inflammation. We observed increased melanoma metastasis dissemination in zebrafish larvae with very short telomeres. Thus, telomere shortening similar to human aging, generates a chronic inflammatory environment that increases cancer incidence.
A Priori Activation of Apoptosis Pathways of Tumor (AAAPT) Technology: Development of Targeted Apoptosis Initiators for Cancer Treatment
Authors: Pandurangi Raghu , Tomasetti Marco , Sekar Thillai Verapazham , Paulmurugan Ramasamy , Ma Cynthia , Sandeep  , Anjanappa Manjushree , Nakshatri Harikrishna
Published: November 2019

Cancer cells develop tactics to circumvent the interventions by desensitizing themselves to interventions. The principle routes of desensitization include a) activation of survival pathways (e.g. NF-kB, PARP) and b) downregulation of cell death pathways (e.g. CD95/CD95L). As a result, it requires high therapeutic dose to achieve tumor regression which, in turn damages normal cells through the collateral damaging effects. Methods are needed to sensitize the low and non-responsive resistant tumor cells including cancer stem cells (CSCs) in order to evoke a better response from the current treatments. Current treatments including chemotherapy can induce cell death only in bulk cancer cells sparing CSCs and cancer resistant cells (CRCs) which are shown to be responsible for high recurrence of disease and low patient survival. Here, we report several novel tumor targeted sensitizers derived from the natural Vitamin E analogue (AMP-001-003). The drug design is based on a novel concept “A priori activation of apoptosis pathways of tumor technology (AAAPT) which is designed to activate specific cell death pathways and inhibit survival pathways simultaneously. Our results indicate that AMP-001-003 sensitize various types of cancer cells including MDA-MB-231 (triple negative breast cancer), PC3 (prostate cancer) and A543 (ling cancer) cells resulting in reducing the IC-50 of doxorubicin in vitro. At higher dose, AMP-001 acts as an anti-tumor agent on its own. The synergy between AMP-001 and doxorubicin could pave a new pathway to use AMP-001 as a neoadjuvant to chemotherapy to achieve a better efficacy and reduced off-target toxicity by the current treatments.

Summary Statement

A Priori Activation of Apoptosis Pathways of Tumor often referred to as “AAAPT” is a novel targeted tumor sensitizing technology which synergizes with chemotherapy to enhance the treatment efficacy.
WolbachiastrainwAu efficiently blocks arbovirus transmission inAedes albopictus
Authors: Mancini Maria Vittoria , Herd Christie S. , Ant Thomas H. , Murdochy Shivan M. , Sinkins Steven P.
Published: November 2019

The global incidence of arboviral diseases transmitted byAedesmosquitoes, including dengue, chikungunya, yellow fever, and Zika, has increased dramatically in recent decades. The release ofAedes aegypticarrying the maternally inherited symbiontWolbachiaas an intervention to control arboviruses is being trialled in several countries. However, these efforts are compromised in many endemic regions due to the co-localization of the secondary vectorAedes albopictus, the Asian tiger mosquito.Ae. albopictushas an expanding global distribution following incursions into a number of new territories. To date, only thewMel andwPip strains ofWolbachiahave been reported to be transferred into and characterized in this vector. AWolbachiastrain naturally infectingDrosophila simulans,wAu, was selected for transfer into a MalaysianAe. albopictusline to create a novel triple-strain infection. The newly generated line showed self-compatibility, moderate fitness cost and complete resistance to Zika and dengue infections.

Author summary

Aedes albopictus, the invasive Asian tiger mosquito, is responsible for numerous outbreaks of important viruses such as dengue and Zika in various regions of the world. The need for alterative control interventions propelled the development of a novel approach that exploits a natural insect symbiont,Wolbachia; when transferred into non-native hosts, these maternally-inherited bacteria are able to interfere with the transmission of mosquito-borne viruses, and also provide reproductive advantages to the host, offering a promising tool for self-sustaining field applications. Currently, several field trials are ongoing for the primary vector of dengue and several other arboviruses,Aedes aegypti, providing encouraging results. In this study,Ae. albopictushas been targeted for a similar approach: this mosquito species naturally carries two strains ofWolbachia. The artificial introduction of a third, non-native strain made this line less able to transmit dengue and Zika viruses and had an impact on its fitness.
The adoptive transfer of BCG-induced T lymphocytes contributes to hippocampal cell proliferation and tempers anxiety-like behavior in immune deficient mice
Authors: Song Dan , Qi Fangfang , Liu ShuaiShuai , Tang Zhongsheng , Duan Jinhai , Yao Zhibin
Published: November 2019

1.

We previously have reported that neonatal Bacillus Calmette-Guerin (BCG) vaccination improves neurogenesis and behavior in early life through affecting the neuroimmune milieu in the brain, but it is uncertain whether activation phenotypes and functional changes in T lymphocytes shape brain development. Here, we studied the effects of BCG vaccination via the adoptive transfer of T lymphocytes from the BALB/c wild-type mice into naive mice. Our results show that mice adoptive BCG-induced lymphocytes (BCG->naive mice) showed anxiolytic and antidepressant-like performance when completing an elevated plus maze (EPM) test. Meanwhile, BCG->naive mice possess more cell proliferation and newborn neurons than PBS->naive and nude mice in the hippocampus. IFN-γ and IL-4 levels in the serum of BCG->naive mice also increased, while TNF-α and IL-1β levels were reduced relative to those of PBS->naive and nude mice. We further found that BCG->naive mice showed different repartition of CD4+ and CD8+ T cell to naive (CD62L+ CD44low), effector memory (CD62L− CD44hi), central memory (CD62L+ CD44hi) and acute/activated effector (CD62L− CD44low) cells in the spleen. Importantly, the adoptive transfer of BCG-induced T lymphocytes infiltrated into the dura mater and brain parenchyma of the nude mice. Activation phenotypes and functional changes in T lymphocytes are very likely to affect the neuroimmune milieu in the brain, and alterations in ratios of splenic CD4+ and CD8+ memory T cells may affect the expression of correlative cytokines in the serum, accounting for our behavioral results. We conclude thus that the adoptive transfer of BCG-induced T lymphocytes contributes to hippocampal cell proliferation and tempers anxiety-like behavior in immune deficient mice. Our work shows that BCG vaccination improves hippocampal cell proliferation outcomes and behaviors, likely as a result of splenic effector/memory T lymphocytes regulating the neuroimmune niche in the brain.
Herpes Simplex Virus Infection, Acyclovir and IVIG Treatment All Independently Cause Gut Dysbiosis
Authors: Ramakrishna Chandran , Mendonca Stacee , Ruegger Paul M. , Kim Jane Hannah , Borneman James , Cantin Edouard
Published: November 2019

Herpes simplex virus 1 (HSV) is a ubiquitous human virus resident in a majority of the global population as a latent infection. Acyclovir (ACV), is the standard of care drug used to treat primary and recurrent infections, supplemented in some patients with intravenous immunoglobulin (IVIG) treatment to suppress deleterious inflammatory responses. We found that HSV, ACV and IVIG can all independently disrupt the gut bacterial community in a sex biased manner when given to uninfected mice. Treatment of HSV infected mice with ACV or IVIG alone or together revealed complex interactions between these drugs and infection that caused pronounced sex biased dysbiosis. ACV reducedBacteroideteslevels in male but not female mice, while levels of the Anti-inflammatory Clostridia (AIC) were reduced in female but not male mice, which is significant as these taxa are associated with protection against the development of GVHD in hematopoietic stem cell transplant (HSCT) patients. Gut barrier dysfunction is associated with GVHD in HSCT patients and ACV also decreasedAkkermansia muciniphila,which is important for maintaining gut barrier functionality. Cumulatively, our data suggest that long-term prophylactic ACV treatment of HSCT patients may contribute to GVHD and potentially impact immune reconstitution. These data have important implications for other clinical settings, including HSV eye disease and genital infections, where ACV is given long-term.

Author Summary

Primary and reactivated HSV and VZV infections are treated with Acyclovir (ACV), an antiviral drug that blocks viral DNA synthesis. In some patients IVIG is used as adjunctive therapy to block deleterious inflammation. Long term preventative treatment of patients who receive stem transplants for various blood cancers has been successful in preventing life threatening reactivated HSV and VZV infections, but GVHD remains a major factor limiting transplant success. Studies reported here reveal that HSV infection, ACV and IVIG given alone can all disrupt the gut microbiota and that complex interactions between these drugs and infection results in even more pronounced sex biased changes in the gut bacteria community structure. Importantly, ACV treatment decreased the levels of specific bacterial taxa, including the anti-inflammatoryClostriodiaandBacteroidetesthat have been shown to protect against development of GVHD in stem cell transplant patients. These data suggest that long term preventative treatment of patients with ACV may contribute to GVHD in transplant patients and have negative consequences in other HSV induced diseases treated long term with ACV. The health effects of long term ACV and IVIG treatments warrant further clinical studies.
WormCat: an online tool for annotation and visualization of Caenorhabditis elegans genome-scale data
Authors: Holdorf Amy D , Higgins Daniel P , Hart Anne C. , Boag Peter R , Pazour Gregory , Walhout Marian (Albertha) , Walker Amy Karol
Published: November 2019

The emergence of large gene expression datasets has revealed the need for improved tools to identify enriched gene categories and visualize enrichment patterns. While Gene Ontogeny (GO) provides a valuable tool for gene set enrichment analysis, it has several limitations. First, it is difficult to graphically compare multiple GO analyses. Second, genes from some model systems are not well represented. For example, around 30% of Caenorhabditis elegans genes are missing from analysis in commonly used databases. To allow categorization and visualization of enriched C. elegans gene sets in different types of genome-scale data, we developed WormCat, a web-based tool that uses a near-complete annotation of the C. elegans genome to identify co-expressed gene sets and scaled heat map for enrichment visualization. We tested the performance of WormCat using a variety of published transcriptomic datasets and show that it reproduces major categories identified by GO. Importantly, we also found previously unidentified categories that are informative for interpreting phenotypes or predicting biological function. For example, we analyzed published RNA-seq data from C. elegans treated with combinations of lifespan-extending drugs where one combination paradoxically shortened lifespan. Using WormCat, we identified sterol metabolism as a category that was not enriched in the single or double combinations but emerged in a triple combination along with the lifespan shortening. Thus, WormCat identified a gene set with potential phenotypic relevance that was not uncovered with previous GO analysis. In conclusion, WormCat provides a powerful tool for the analysis and visualization of gene set enrichment in different types of C. elegans datasets.
Noncoding regions underpin avian bill shape diversification at macroevolutionary scales
Authors: Yusuf Leeban , Heatley Matthew C. , Palmer Joseph P.G. , Barton Henry J. , Cooney Christopher R. , Gossmann Toni I.
Published: November 2019

Recent progress has been made in identifying genomic regions implicated in trait evolution on a microevolutionary scale in many species, but whether these are relevant over macroevolutionary time remains unclear. Here, we directly address this fundamental question using bird beak shape, a key evolutionary innovation linked to patterns of resource use, divergence and speciation, as a model trait. We integrate class-wide geometric-morphometric analyses with evolutionary sequence analyses of 10,322 protein coding genes as well as 229,001 genomic regions spanning 72 species. We identify 1,434 protein coding genes and 39,806 noncoding regions for which molecular rates were significantly related to rates of bill shape evolution. We show that homologs of the identified protein coding genes as well as genes in close proximity to the identified noncoding regions are involved in craniofacial embryo development in mammals. They are associated with embryonic stem cells pathways, including BMP and Wnt signalling, both of which have repeatedly been implicated in the morphological development of avian beaks. This suggests that identifying genotype-phenotype association on a genome wide scale over macroevolutionary time is feasible. While the coding and noncoding gene sets are associated with similar pathways, the actual genes are highly distinct, with significantly reduced overlap between them and bill-related phenotype associations specific to noncoding loci. Evidence for signatures of recent diversifying selection on our identified noncoding loci in Darwin finch populations further suggests that regulatory rather than coding changes are major drivers of morphological diversification over macroevolutionary times.
Impact of different amino acid substitutions in penicillin-binding protein 3 on beta-lactam susceptibility in Haemophilus influenzae
Authors: Reist Josiane , Linnik Janina , Schibli Urs , Egli Adrian , Hinić Vladimira
Published: November 2019

Purpose

Beta-lactam antibiotics in combination with a beta-lactamase inhibitor are the first-line treatment option for Haemophilus influenzae infections. However, beta-lactamase-independent resistance to beta-lactams is increasing. This resistance mechanism has been linked to amino acid substitutions in the penicillin-binding protein 3 (PBP3), but how these substitutions lead to decreased binding affinities to certain beta-lactam antimicrobials remains unknown.

Methods

We investigated beta-lactam resistance and amino acid substitutions in PBP3 from fifty-three clinical isolates of H. influenzae collected in Switzerland from January to April 2016. Identification of key polymorphisms and classification of strains into PBP3 amino acid substitution groups I, II, and M was done as previously described. Based on published PBP3 crystal structures, we investigated how the group-specific amino acid substitutions impact the beta-lactam binding site.

Results

We found that both group I and group II substitutions disrupt the Asn526-Arg517-Glu324 interaction, which might affect the configuration of the beta-lactam binding site. Amino acid substitutions in group M strains are distant from the active site and have most likely no impact on beta-lactam binding. In accordance with this observation, all group M strains showed minimal inhibitory concentrations (MICs) within the susceptible range for all tested antimicrobials and were not significantly different to the wild type (beta-lactamase producers excluded), while group I and group II strains showed significantly higher MICs for beta-lactam antimicrobials.

Conclusion

Group M strains are phenotypically equal to the wild type, while amino acid substitutions of group I and group II might affect the beta-lactam binding through a common mechanism by disrupting the Asn526-Arg517-Glu324 interaction.
Inferring phylogenetic trees from mutational distance of transposable elements
Authors: Bermúdez Juanjo
Published: November 2019

There are many methods for establishing a phylogeny available to researchers. Some of these are based on the mutational distance between ortholog sequences of DNA, and, from these, some are based on the analysis (presence/absence) of transposable elements in specific loci of ortholog sequences. We present a new approach: a method for inferring a phylogeny based on the mutational distance of transposable elements distributed along any segment of DNA. Our method doesn’t require previously having ortholog segments of DNA from every organism. The method can be fully automated, not requiring any previous or posterior data analysis nor data preparation.
qKW9encodes a pentatricopeptide repeat protein affecting photosynthesis and grain filling in maize
Authors: Huang Juan , Lu Gang , Liu Lei , Raihan Mohammad Sharif , Xu Jieting , Jian Liumei , Zhao Lingxiao , Tran Thu M. , Zhang Qinghua , Liu Jie , Li Wenqiang , Wei Cunxu , Braun David M. , Li Qing , Fernie Alisdair R. , Jackson David , Yan Jianbing
Published: November 2019

Kernel weight is an important yield component in maize that was selected during domestication. Many kernel weight genes have been identified through mutant analysis, and are mostly involved in the biogenesis and functional maintenance of organelles or other fundamental cellular activities. However, only a limited number of loci underlying quantitative variation in kernel weight have been cloned. Here we characterize a maize kernel weight QTL,qKW9and find that it encodes a DYW motif pentatricopeptide repeat protein involved in C-to-U editing of NdhB, a subunit of the chloroplast NADH dehydrogenase-like complex. In a nullqKW9background, C-to-U editing of NdhB was abolished, and photosynthesis was reduced, suggesting thatqKW9regulates kernel weight by controling the maternal source of photosynthate for grain filling. Characterization ofqKW9highlights the importance of optimizing photosynthesis on maize grain yield production.
Measurements of the timescale and conformational space of AMPA receptor desensitization
Authors: Salazar Hector , Mischke Sabrina , Plested Andrew J. R.
Published: November 2019

Ionotropic glutamate receptors (iGluRs) are ligand gated ion channels that mediate excitatory synaptic transmission in the central nervous system (CNS). Desensitization of the AMPA-subtype following glutamate binding appears critical for brain function, and involves rearrangement of the ligand binding domains (LBDs). Recently, several full-length structures of iGluRs in putative desensitized states were published. These structures indicate movements of the LBDs that might be trapped by cysteine crosslinks and metal bridges. We found that cysteine mutants at the interface between subunits A and C, and lateral zinc bridges (between subunits C & D or A & B) can trap freely-desensitizing receptors in a spectrum of states with different stabilities. Consistent with close approach of subunits during desensitization processes, introduction of bulky amino acids at the A-C interface produced a receptor with slow recovery from desensitization. Further, in wild-type GluA2 receptors, we detected population of stable desensitized state with a lifetime around 1 second. Using mutations that progressively stabilise deep desensitize states (E713T & Y768R), we were able to selectively protect receptors from crosslinks at both the diagonal and lateral interfaces. Ultrafast perfusion enabled us to perform chemical modification in less than 10 ms, reporting movements associated to desensitization on this timescale within LBD dimers in resting receptors. These observations suggest small disruptions of quaternary structure are sufficient for fast desensitization, and that substantial rearrangements likely correspond to stable desensitized states that are adopted relatively slowly, on a timescale much longer than physiological receptor activation.

Significance statement

iGluRs are central components of fast synaptic transmission in the brain. iGluR desensitization occurs as a natural consequence of receptor activation and can reduce the response of an excitatory synapse. AMPA receptor desensitization also appears necessary for proper brain development. Molecular structures of iGluRs in putative desensitized states predict a range of movements during desensitization. In the present study, we performed a series of crosslinking experiments on mutant receptors that we subjected to similar desensitizing conditions over time periods from milliseconds to minutes. These experiments allowed us to count desensitized configurations and rank them according to their stabilities. These data show that large-scale rearrangements occur during long glutamate exposures that are probably not seen in healthy brain tissue, whereas smaller changes in structure probably suffice for desensitization at synapses.
Integration of Odor-Induced Activity of Kenyon Cells in an Electrotonically CompactDrosophilaMushroom Body Output Neuron (MBON)
Authors: Hafez Omar A. , Escribano Benjamin , Pielage Jan , Niebur Ernst
Published: November 2019

The formation of an ecologically useful lasting memory requires that the brain has an accurate internal representation of the surrounding environment. In addition, it must have the ability to integrate a variety of different sensory stimuli and associate them with rewarding and aversive behavioral outcomes. Over the previous years, a number of studies have dissected the anatomy and elucidated some of the working principles of theDrosophilamushroom body (MB), the fly’s center for learning and memory. As a consequence, we now have a functional understanding of where and how in the MB sensory stimuli converge and are associated. However, the molecular and cellular dynamics at the critical synaptic intersection for this process, the Kenyon cell-mushroom body output neuron (KC-MBON) synapse, are largely unknown. Here, we introduce a first approach to understand this integration process and the physiological changes occurring at the KC-MBON synapse during Kenyon cell (KC) activation. We use the published connectome of theDrosophilaMB to construct a functional computational model of the MBON-α3 dendritic structure. We simulate synaptic input by individual KC-MBON synapses by current injections into precisely (μm) identified local dendritic sections, and the input from a model population of KCs representing an odor by a spatially distributed cluster of current injections. By recording the effect of the simulated current injections on the membrane potential of the neuron, we show that the MBON-α3 is electrotonically compact. This suggests that odor-induced MBON activity is likely governed by input strength while the positions of KC input synapses are largely irrelevant.
Temporal Transcriptome and Promoter Architecture of the African Swine Fever Virus
Authors: Cackett Gwenny , Matelska Dorota , Sýkora Michal , Portugal Raquel , Malecki Michal , Bähler Jürg , Dixon Linda , Werner Finn
Published: November 2019

The African Swine Fever Virus causes haemorrhagic fever in domestic pigs and presents the biggest global threat to animal farming in recorded history. Despite its importance, very little is known the mechanisms and temporal regulation of transcription in ASFV. Here we report the first detailed viral transcriptome analysis of ASFV during early and late infection ofVerocells. In addition to total RNA sequencing, we have characterised the transcription start sites and transcription termination sites at nucleotide-resolution, revealing the distinct DNA consensus motifs of early and late promoters, as well as the sequence determinants for transcription termination. ASFV can utilise alternative promoters to generate distinct proteins from the same transcription unit that differ with respect to the polypeptide N-terminus. Finally, our results reveal that the ASFV-RNAP undergoes transcript slippage at the 5’ end of transcription units that in a promoter sequence-specific manner results in the addition of 5’-AT and 5’-ATAT tails to mRNAs.
Testing Darwin’s naturalization conundrum based on taxonomic, phylogenetic and functional dimensions of vascular plants
Authors: Pinto-Ledezma Jesús N. , Villalobos Fabricio , Reich Peter B. , Larkin Daniel J. , Cavender-Bares Jeannine
Published: November 2019

Charles Darwin posited two alternative hypotheses to explain the success of nonnative species based on their relatedness to incumbent natives: coexistence between them should be (i) more likely with greater relatedness (due to trait similarity that correlates with better matching to the environment), or (ii) less likely (due to biotic interference, such as competition). The paradox raised by the opposing predictions of these two hypotheses has been termed ‘Darwin’s naturalization conundrum’ (DNC). Using plant communities measured repeatedly over a 31-year time span across an experimental fire gradient in an oak savanna (Minnesota, USA) we evaluated the DNC by explicitly incorporating taxonomic, functional and phylogenetic information. Our approach was based on ‘focal-species’ such that the taxonomic, functional and phylogenetic structure of species co-occurring with a given nonnative species in local communities was quantified. We found three main results: first, nonnatives colonizers tended to co-occur most with closely related incumbent natives in recipient communities, except in the extreme ends of the fire gradient (i.e., communities with no fire and those subjected to high fire frequencies); second, with increasing fire frequency, nonnative species were functionally more similar to native species in recipient communities; third, functional similarity of co-occurring nonnatives and natives in recipient communities showed a consistent pattern over time, but the phylogenetic similarity shifted over time, suggesting that external forces (e.g., climate variability) are also relevant in driving the phylogenetic relatedness of nonnatives to natives in invaded communities. Our results provide insights for understanding the invasion dynamics across environmental gradients and highlight the importance of evaluating different dimensions of biodiversity in order to produce more powerful evaluations of species co-occurrence at different spatial and temporal scales.
Antagonistic odor interactions in olfactory sensory neurons are widespread in freely breathing mice
Authors: Zak Joseph D. , Reddy Gautam , Vergassola Massimo , Murthy Venkatesh N.
Published: November 2019

Odor landscapes contain complex blends of discrete molecules that each activate unique, overlapping populations of olfactory sensory neurons (OSNs). Despite the presence of hundreds of OSN subtypes in many animals, the overlapping nature of odor inputs may lead to saturation of neural responses at the early stages of stimulus encoding. Information loss due to saturation could be mitigated by normalizing mechanisms such as antagonism at the level of receptor-ligand interactions, whose existence and prevalence remains uncertain. By imaging OSN axon terminals in olfactory bulb glomeruli as well as OSN cell bodies within the olfactory epithelium in freely breathing mice, we found widespread antagonistic interactions in binary odor mixtures. In complex mixtures of up to 12 odorants, antagonistic interactions became stronger and more prevalent with increasing mixture complexity. Therefore, antagonism is a remarkably common feature of odor mixture encoding in olfactory sensory neurons and helps in normalizing activity to reduce saturation.
Comparative genomics reveals signature regions used to develop a robust and sensitive multiplex TaqMan real-time qPCR assay to detect the genus Dickeya and Dickeya dianthicola
Authors: Dobhal Shefali , Boluk Gamze , Babler Brooke , Stulberg Michael J. , Rascoe John , Nakhla Mark , Chapman Toni A. , Crockford Alex B. , Melzer Michael , Alvarez Anne M. , Arif Mohammad
Published: November 2019

Aims

Dickeya species are high consequence plant pathogenic bacteria listed among the quarantine pathogens of the European Union; associated with potato disease outbreaks and subsequent economic losses worldwide. Early, accurate, and reliable detection of Dickeya spp. is needed to prevent establishment and further dissemination of this pathogen. Therefore, a multiplex TaqMan qPCR was developed for sensitive detection of Dickeya spp. and specifically, D. dianthicola.

Methods and Results

A signature genomic region for the genus Dickeya (mglA/mglC) and unique genomic region for D. dianthicola (alcohol dehydrogenase) were identified using a whole genome based comparative genomics approach. The developed multiplex TaqMan qPCR was validated using extensive inclusivity and exclusivity panels, and naturally/artificially infected samples to confirm broad range detection capability and specificity. Both sensitivity and spiked assays showed detection limit of 10 fg DNA.

Conclusion

The developed multiplex assay is sensitive and reliable to detect Dickeya spp. and D. dianthicola with no false positives or false negatives. It was able to detect mixed infection from naturally and artificially infected plant materials.

Significance and Impact

The developed assay will serve as a practical tool for screening of propagative material, monitoring the presence and distribution, and quantification of target pathogens in a breeding program. The assay also has applications in routine diagnostics, biosecurity and microbial forensics.
Reprogrammed mRNA translation drives resistance to therapeutic targeting of ribosome biogenesis
Authors: Kusnadi E. P. , Trigos A. S. , Cullinane C. , Goode D. L. , Larsson O. , Devlin J. R. , Chan K. T. , De Souza D. P. , McConville M. J. , McArthur G. A. , Thomas G. , Sanij E. , Poortinga G. , Hannan R. D. , Hannan K. M. , Kang J. , Pearson R. B.
Published: November 2019

Elevated ribosome biogenesis in oncogene-driven cancers is commonly targeted by DNA-damaging cytotoxic drugs. Our first-in-human trial of CX-5461, a novel, less genotoxic agent that specifically inhibits ribosome biogenesis via suppression of RNA Polymerase I (Pol I) transcription, revealed single agent efficacy in refractory blood cancers. Despite this clinical response, patients were not cured. In parallel, we demonstrated a marked improvement in thein vivoefficacy of CX-5461 in combination with PI3K/AKT/mTORC1 pathway inhibitors. Here we show that this improved efficacy is associated with specific suppression of translation of mRNAs encoding regulators of cellular metabolism. Importantly, acquired resistance to this co-treatment is driven by translational re-wiring that results in dysregulated cellular metabolism and induction of a cAMP-dependent pathway critical for the survival of blood cancers including lymphoma and acute myeloid leukemia. Our studies identify the molecular mechanisms underpinning the response of blood cancers to selective ribosome biogenesis inhibitors and identify metabolic vulnerabilities that will facilitate the rational design of more effective regimens for Pol I-directed therapies.
Modality-specific and multisensory mechanisms of spatial attention and expectation
Authors: Zuanazzi Arianna , Noppeney Uta
Published: November 2019

In our natural environment, the brain needs to combine signals from multiple sensory modalities into a coherent percept. While spatial attention guides perceptual decisions by prioritizing processing of signals that are task-relevant, spatial expectations encode the probability of signals over space. Previous studies have shown that behavioral effects of spatial attention generalize across sensory modalities. However, because they manipulated spatial attention as signal probability over space, these studies could not dissociate attention and expectation or assess their interaction.

In two experiments, we orthogonally manipulated spatial attention (i.e., task-relevance) and expectation (i.e., signal probability) selectively in one sensory modality (i.e., primary modality) (experiment 1: audition, experiment 2: vision) and assessed their effects on primary and secondary sensory modalities in which attention and expectation were held constant.

Our results show behavioral effects of spatial attention that are comparable for audition and vision as primary modalities; yet, signal probabilities were learnt more slowly in audition, so that spatial expectations were formed later in audition than vision. Critically, when these differences in learning between audition and vision were accounted for, both spatial attention and expectation affected responses more strongly in the primary modality in which they were manipulated, and generalized to the secondary modality only in an attenuated fashion. Collectively, our results suggest that both spatial attention and expectation rely on modality-specific and multisensory mechanisms.
Modulating the cellular context broadly reshapes the mutational landscape of a model enzyme
Authors: Thompson Samuel , Zhang Yang , Ingle Christine , Reynolds Kimberly A. , Kortemme Tanja
Published: November 2019

Protein mutational landscapes are shaped by the cellular environment, but key factors and their quantitative effects are often unknown. Here we show that Lon, a quality control protease naturally absent in common E. coli expression strains, drastically reshapes the mutational landscape of the metabolic enzyme dihydrofolate reductase (DHFR). Selection under conditions that resolve highly active mutants reveals that 23.3% of all single point mutations in DHFR are advantageous in the absence of Lon, but advantageous mutations are largely suppressed when Lon is reintroduced. Protein stability measurements demonstrate extensive activity-stability tradeoffs for the advantageous mutants and provide a mechanistic explanation for Lon’s widespread impact. Our findings suggest possibilities for tuning mutational landscapes by modulating the cellular environment, with implications for protein design and combatting antibiotic resistance.
Phenotypic and physiological responses to salt exposure inSorghumreveal diversity among domesticated landraces
Authors: Henderson Ashley N. , Crim Philip M. , Cumming Jonathan R. , Hawkins Jennifer S.
Published: November 2019

Soil salinity negatively impacts plant function, development, and yield.Sorghum bicoloris a staple crop known to be drought tolerant, to have adapted to a variety of conditions, and to contain significant standing genetic diversity, making it an exemplary species to study phenotypic and physiological variation in salinity tolerance. In our study, a diverse group of sorghum landraces and accessions was first rank-ordered for salinity tolerance and then individuals spanning a wide range of response were analyzed for foliar proline and ion accumulation. We found that, while proline is often a good indicator of osmotic adjustment and is historically associated with increased salt tolerance, proline accumulation in sorghum reflects stress-response injury rather than acclimation. When combining ion profiles with growth responses and stress tolerance indices, the variation observed in tolerance was similarly not a sole result of Na+accumulation, but rather reflected accession-specific mechanisms that may integrate these and other metabolic responses. When we compared variation in tolerance to phylogenetic relationships, we conclude that the most parsimonious explanation for the variation observed among accessions is that salinity tolerance was acquired early during domestication and was subsequently maintained or lost in diverged lineages during improvement in areas that vary in soil salinity.
Preference and switching in the Kill-the-Winner functional response: Diversity, size structure, and synergistic grazing in plankton models
Authors: Archibald Kevin M. , Sosik Heidi M. , Neubert Michael G.
Published: November 2019

Grazing by zooplankton can maintain diversity in phytoplankton communities by allowing coexistence between competitors in situations that would otherwise lead to competitive exclusion. In mathematical models, grazing is represented by a functional response that describes the consumption rate by an individual zooplankter as a function of phytoplankton concentration. Since its initial description, the Kill-the-Winner functional response has been increasingly adopted for large-scale biogeochemical modeling. Here, we analyze how two properties of the Kill-the-Winner functional response—preference and switching—interact to promote coexistence and increase diversity in two simple models: a diamond-shaped nutrient-phytoplankton-zooplankton model and a size-structured phytoplankton community model. We found that, compared to preference, switching leads to coexistence and increased diversity over a much wider range of environmental conditions (nutrient supply and mixing rate). In the absence of switching, preference only allows for coexistence within the narrow range of environmental conditions where the preference is precisely balanced against the competitive difference between phytoplankton types. We also explored a counterintuitive aspect of the Kill-the-Winner functional response that we have termed “synergistic grazing”. Synergistic grazing occurs when the grazing rate on one phytoplankton type increases as the biomass of an alternative phytoplankton type increases. This unrealistic effect is most evident when switching is strong and when zooplankton have a preference for the weaker competitor.
Queue-based features for dynamic waiting time prediction in emergency department
Authors: Benevento Elisabetta , Aloini Davide , Squicciarini Nunzia , Dulmin Riccardo , Mininno Valeria
Published: November 2019

Purpose

The purpose of this study is twofold: exploring new queue-based variables enabled by process mining and evaluating their impact on the accuracy of waiting time prediction. Such queue-based predictors that capture the current state of the emergency department (ED) may lead to a significant improvement in the accuracy of the prediction models.

Design/methodology/approach

Alongside the traditional variables influencing ED waiting time, the authors developed new queue-based predictors exploiting process mining. Process mining techniques allowed the authors to discover the actual patient-flow and derive information about the crowding level of the activities. The proposed predictors were evaluated using linear and nonlinear learning techniques. The authors used real data from an ED.

Findings

As expected, the main results show that integrating the set of predictors with queue-based variables significantly improves the accuracy of waiting time prediction. Specifically, mean square error values were reduced by about 22 and 23 per cent by applying linear and nonlinear learning techniques, respectively.

Practical implications

Accurate estimates of waiting time can enable the ED systems to prevent overcrowding e.g. improving the routing of patients in EDs and managing more efficiently the resources. Providing accurate waiting time information also can lead to decreased patients’ dissatisfaction and elopement.

Originality/value

The novelty of the study relies on the attempt to derive queue-based variables reporting the crowding level of the activities within the ED through process mining techniques. Such information is often unavailable or particularly difficult to extract automatically, due to the characteristics of ED processes.