bluuebunny/crossref_metadata_2025 huggingface dataset:
tRNA fragments (tRFs) populations analysis in mutants affecting tRNAs processing and tRNA methylation
Authors: Molla-Herman Anahi , Angelova Margarita , Carré Clément , Antoniewski Christophe , Huynh Jean-René
Published: December 2019

tRNA fragments (tRFs) are a class of small non-coding RNAs (sncRNAs) derived from tRNAs. tRFs are highly abundant in many cell types including stem cells and cancer cells, and are found in all domains of life. Beyond translation control, tRFs have several functions ranging from transposon silencing to cell proliferation control. However, the analysis of tRFs presents specific challenges and their biogenesis is not well understood. They are very heterogeneous and highly modified by numerous post-transcriptional modifications. Here we describe a bioinformatic pipeline to study tRFs populations and shed light onto tRNA fragments biogenesis. Indeed, we used small RNAs Illumina sequencing datasets extracted from wild type and mutant Drosophila ovaries affecting two different highly conserved steps of tRNA biogenesis: 5’pre-tRNA processing (RNase-P subunit Rpp30) and tRNA 2’-O-methylation (CG7009 and CG5220). Using our pipeline, we show how defects in tRNA biogenesis affect nuclear and mitochondrial tRFs populations and other small non-coding RNAs biogenesis, such as small nucleolar RNAs (snoRNAs). This tRF analysis workflow will advance the current understanding of tRFs biogenesis, which is crucial to better comprehend tRFs roles and their implication in human pathology.
Clumpy coexistence in phytoplankton: The role of functional similarity in community assembly
Authors: Graco-Roza Caio , Segura Angel M , Kruk Carla , Domingos Patrícia , Soininen Janne , Marinho Marcelo Manzi
Published: December 2019

Abstract

Emergent neutrality (EN) suggests that species must be sufficiently similar or sufficiently different in their niches to avoid interspecific competition. Such a scenario results in a transient pattern with clumps and gaps of species abundance along the niche axis (e.g., represented by body size). From this perspective, clumps are groups of coexisting species with negligible fitness differences and stochastic abundance fluctuations. Plankton is an excellent model system for developing and testing ecological theories, especially those related to size structure and species coexistence. We tested EN predictions using the phytoplankton community along the course of a tropical river considering (i) body size structure, (ii) functional clustering of species in terms of morphology-based functional groups (MBFG), and (iii) the functional similarity among species concerning their functional traits. Two main clumps in the body size axis (clump I and II) were conspicuous through time and were detected in different stretches of the river. Clump I comprised medium-sized species from the MBFGs IV, V, and VI while clump II included large-bodied species from the MBFGs V and VI. Pairwise differences in species biovolume correlated with species functional similarity when the whole species pool was considered, but not among species within the same clump. Although clumps comprised multiple MBFGs, the dominant species within the clump belonged always to the same MBFG. Also, within-clump species biovolume increased with functional distinctiveness considering both seasons and stretches, except the lower course. These results suggest that species within clumps behave in a quasi-neutral state, but even minor shifts in trait composition may affect species biovolume. Our findings point that EN belongs to the plausible mechanisms explaining community assembly in river ecosystems.
Ulcerative colitis is characterized by amplified acute inflammation with delayed resolution
Authors: Wysoczanski Riccardo , Kendall Alexandra C , Motwani Madhur , Vega Roser , Rahman Farooq Z , McCartney Sara , Bloom Stuart L , Nicolaou Anna , Gilroy Derek W , Segal Anthony W , Marks Daniel J B
Published: December 2019

The cause of chronic inflammation in ulcerative colitis (UC) is incompletely understood. Here we tested the hypothesis that an excessive acute inflammatory response to bacteria contributes to the pathogenesis. Acute inflammatory responses were provoked in vivo in UC patients and healthy controls by intradermal inoculation with bacteria. Vascular responses were quantified by laser Doppler. Inflammatory exudates were recovered in superimposed suction blisters and cells measured by polychromatic flow cytometry, cytokines by multiplex array, and inflammatory lipids by mass spectrometry. Vascular responses in UC patients were heightened at 24h after bacterial injection (p=0·03), and remained abnormally high at 48h (p=0·0005) and this amplified response was seen in UC with Gram-positive as well as Gram-negative organisms (p=0·01). The cellular infiltrate over the injection site, composed largely of neutrophils at 4 hours a was greater in UC (p=0·002). At 48h, the increased numbers of cells in UC were composed of neutrophils (p=0·001) and CD4 lymphocytes (p=0·001). The exaggerated inflammation in UC was not a cytokine-driven phenomenon. Exaggerated onset was normalised in patients taking 5-aminosalicylates, accompanied by increased concentrations of hydroxy fatty acids 9-oxo-octadecadienoic acid (OxoODE; p=0·05) and 13-OxoODE (p=0·01) in resolving exudates. In vitro, these compounds suppressed macrophage inflammatory cytokine secretion through PPARγ (p<0·0001). Conversely, 5-aminosalicylates did not inhibit early inflammatory reactions in control participants. Acute inflammatory responses to bacteria in UC are both overly exuberant and slow to resolve. Neutrophils accumulate in excess and persist, in keeping with the pathological appearances of disease flares. These studies also provide new insight into the mechanism of 5-aminosalicylate (5ASA) drugs, which act as pro-resolution rather than indiscriminate anti-inflammatory agents by promoting formation of immunomodulatory hydroxy lipids. While production of these lipids is not defective as part of the underlying disease process, this identifies a novel mechanism of drug action harnessing pro-resolution pathways.

Wysoczanski and colleagues demonstrate that the inflammatory response to injected bacteria is exaggerated and prolonged in ulcerative colitis. This disordered inflammation appears to be associated with increased secretion of PGE2. 5-aminosalicylate drugs, which are used to treat this condition, normalize inflammation and PGE2 secretion, and appear to work through PPARγ
Quantification and Discovery of Acyl-ACPs by LC-MS/MS
Authors: Nam Jeong-Won , Jenkins Lauren M. , Li Jia , Evans Bradley S. , Jaworski Jan G. , Allen Doug K.
Published: December 2019

Acyl carrier proteins (ACPs) are the scaffolds for fatty acid biosynthesis in living systems, rendering them essential to a comprehensive understanding of lipid metabolism; however, accurate quantitative methods to assess individual acyl-ACPs do not exist. A robust method was developed to quantify acyl-ACPs at picogram levels. Acyl-ACP elongation intermediates (3-hydroxyacyl-ACPs and 2, 3-trans-enoyl-ACPs), and unexpected medium chain (C10:1, C14:1) and polyunsaturated long chain acyl-ACPs (C16:3) were also identified, indicating the sensitivity of the method and that descriptions of lipid metabolism and ACP function are incomplete. Such ACPs are likely important to medium chain lipid production for fuels and highlight poorly understood lipid remodeling events in the chloroplast. The approach is broadly applicable to Type II FAS systems found in plants, bacteria, and mitochondria of animal and fungal systems because it uses a strategy that capitalizes on a highly conserved Asp-Ser-Leu-Asp (DSLD) amino acid sequence in ACPs to which acyl groups are attached. This allows for sensitive quantification using LC-MS/MS withde novogenerated standards and an isotopic dilution strategy and will fill a gap in understanding, providing insights through quantitative exploration of fatty acid biosynthesis processes for optimal biofuels, renewable feed stocks, and medical studies in health and disease.
Phen2Gene: Rapid Phenotype-Driven Gene Prioritization for Rare Diseases
Authors: Zhao Mengge , Havrilla James M. , Fang Li , Chen Ying , Peng Jacqueline , Liu Cong , Wu Chao , Sarmady Mahdi , Botas Pablo , Isla Julián , Lyon Gholson , Weng Chunhua , Wang Kai
Published: December 2019

Human Phenotype Ontology (HPO) terms are increasingly used in diagnostic settings to aid in the characterization of patient phenotypes. The HPO annotation database is updated frequently and can provide detailed phenotype knowledge on various human diseases, and many HPO terms are now mapped to candidate causal genes with binary relationships. To further improve the genetic diagnosis of rare diseases, we incorporated these HPO annotations, gene-disease databases, and gene-gene databases in a probabilistic model to build a novel HPO-driven gene prioritization tool, Phen2Gene. Phen2Gene accesses a database built upon this information called the HPO2Gene Knowledgebase (H2GKB), which provides weighted and ranked gene lists for every HPO term. Phen2Gene is then able to access the H2GKB for patient-specific lists of HPO terms or PhenoPackets descriptions supported by GA4GH (http://phenopackets.org/), calculate a prioritized gene list based on a probabilistic model, and output gene-disease relationships with great accuracy. Phen2Gene outperforms existing gene prioritization tools in speed, and acts as a real-time phenotype driven gene prioritization tool to aid the clinical diagnosis of rare undiagnosed diseases. In addition to a command line tool released under the MIT license (https://github.com/WGLab/Phen2Gene), we also developed a web server and web service (https://phen2gene.wglab.org/) for running the tool via web interface or RESTful API queries. Finally, we have curated a large amount of benchmarking data for phenotype-to-gene tools involving 197 patients across 76 scientific articles and 85 patients’ de-identified HPO term data from CHOP.
Mechanism of duration perception in artificial brains suggests new model of attentional entrainment
Authors: Tehrani-Saleh Ali , McAuley J. Devin , Adami Christoph
Published: December 2019

While cognitive theory has advanced several candidate frameworks to explain attentional entrainment, the neural basis for the temporal allocation of attention is unknown. Here we present a new model of attentional entrainment that is guided by empirical evidence obtained using a cohort of 50 artificial brains. These brains were evolvedin silicoto perform a duration judgement task similar to one where human subjects perform duration judgements in auditory oddball paradigms1. We found that the artificial brains display psychometric characteristics remarkably similar to those of human listeners, and also exhibit similar patterns of distortions of perception when presented with out-of-rhythm oddballs. A detailed analysis of mechanisms behind the duration distortion in the artificial brains suggests that their attention peaks at the end of the tone, which is inconsistent with previous attentional entrainment models. Instead, our extended model of entrainment emphasises increased attention to those aspects of the stimulus that the brain expects to be highly informative.
Identification of GABAergic neurons innervating the zebrafish lateral habenula
Authors: Ramaswamy Mahathi , Cheng Ruey-Kuang , Jesuthasan Suresh
Published: December 2019

Habenula neurons are constantly active. The level of activity affects mood and behaviour, with increased activity in the lateral habenula reflecting exposure to punishment and a switch to passive coping and depression. Here, we identify GABAergic neurons that could reduce activity in the lateral habenula of larval zebrafish. GAD65/67 immunohistochemistry and imaging of gad1b:DsRed transgenic fish suggest the presence of GABAergic terminals in the neuropil and between cell bodies in the lateral habenula. Retrograde tracing with the lipophilic dye DiD suggests that the former derives from the thalamus, while the latter originates from a group of cells in the posterior hypothalamus that are located between the posterior tuberal nucleus and hypothalamic lobes. Two-photon calcium imaging indicates that blue light causes excitation of thalamic GABAergic neurons and terminals in the neuropil, while a subpopulation of lateral habenula neurons show reduced intracellular calcium levels. Whole-cell electrophysiological recording indicates that blue-light reduces membrane potential of lateral habenula neurons. These observations suggest that GABAergic input from the thalamus may mediate inhibition in the zebrafish lateral habenula. Mechanisms governing release of GABA from the neurons in the posterior hypothalamus, which are likely to be in the tuberomammillary nucleus, remain to be defined.
Curvature-sensitive trans-assembly of human Atg8-family proteins in autophagy-related membrane tethering
Authors: Taniguchi Saki , Toyoshima Masayuki , Takamatsu Tomoyo , Mima Joji
Published: December 2019

In macroautophagy, de novo formation of the double membrane-bound organelles, termed autophagosomes, is essential for engulfing and sequestering the cytoplasmic contents to be degraded in the lytic compartments such as vacuoles and lysosomes. Atg8-family proteins have been known to be responsible for autophagosome formation via membrane tethering and fusion events of precursor membrane structures. Nevertheless, how Atg8 proteins act directly upon autophagosome formation still remains enigmatic. Here, to further gain molecular insights into Atg8-mediated autophagic membrane dynamics, we study the two representative human Atg8 orthologs, LC3B and GATE-16, by quantitatively evaluating their intrinsic potency to physically tether lipid membranes in a chemically defined reconstitution system using purified Atg8 proteins and synthetic liposomes. Both LC3B and GATE-16 retained the capacities to trigger efficient membrane tethering at the protein-to-lipid molar ratios ranging from 1:100 to 1:5,000. These human Atg8-mediated membrane tethering reactions require trans-assembly between the membrane-anchored forms of LC3B and GATE-16 and can be reversibly and strictly controlled by the membrane attachment and detachment cycles. Strikingly, we further uncovered distinct membrane curvature dependences of LC3B- and GATE-16-mediated membrane tethering reactions: LC3B can drive tethering more efficiently than GATE-16 for highly-curved small vesicles (e.g. 50 nm in diameter), although GATE-16 turns out to be a more potent tether than LC3B for flatter large vesicles (e.g. 200 and 400 nm in diameter). Our findings establish curvature-sensitive trans-assembly of human Atg8-family proteins in reconstituted membrane tethering, which recapitulates an essential subreaction of the biogenesis of autophagosomes in vivo.
Astrocytic regulation of synchronous bursting in cortical cultures: from local to global
Authors: Kumar Ravi , Huang Yu-Ting , Chen Chun-Chung , Tzeng Shun-Fen , Chan C. K.
Published: December 2019

Synchronous bursting (SB) is ubiquitous in neuronal networks. It is known for a long time that SB is driven by glutamatergic neurotransmissions but its underlying mechanism is still unclear. Recent studies show that local glutamate recycle by astrocytes can affect neuronal activities nearby. Since SB is independent of network structure, it is conceivable that the local dynamics might also be the origin of SB in networks. We investigated the effects of local glutamate dynamics on SBs in both cultures developed on multi-electrode array (MEA) systems and a tripartite synapse simulation model. In our experiments, local glutamate recycle dynamics are studied by pharmacologically targeting the astrocytic glutamate transporters (GLT-1), while neuronal firing activities and synaptic glutamate level are simultaneously monitored with MEA and glutamate sensor (iGluSnFR) expressed on surface of astrocytes respectively. We found SBs to be synchronized with glutamate transients and the manipulation of local glutamate dynamics can indeed alter the global properties of the SBs. Detailed simulation of a network with astrocytic glutamate uptake and recycle mechanisms conforming with the experimental observations revealed that astrocytes function as a slow negative feedback for the neuronal activities in the network. With this model, SB can be understood as the alternation between the positive and negative feedback in the neurons and astrocytes in the network respectively. An understanding of this glutamate trafficking dynamics is of general application to explain disordered phenomena in neuronal systems, and therefore can provide new insights into the origin of fatal seizure-like behavior.

Significance

Synchronous bursting (SB) is a hallmark of neuronal circuits. Contrary to the common belief that the SB is governed mainly by neuron-neuron interactions, this study shows that SBs are orchestrated through a generic neuron-astrocyte tripartite interactions. These interactions, identified as glutamate uptake and recycle processes in astrocytes, control the excitability of neuronal networks and shape the overall SB patterns. Our simulation results suggest that astrocytes traffic more glutamate than neurons and actively regulating glutamate proceedings around synapses. A bipartite synapse is a good approximation of a tripartite synapse provided that astrocyte-dependent glutamate content is taken into account. Our findings provide key insights into the ubiquity of SB and the origin of fatal seizure-like behavior in brain arising from astrocytic malfunction.
SpecHap: a diploid phasing algorithm based on spectral graph theory
Authors: Yu Yonghan , Chen Lingxi , Miao Xinyao , Li Shuai Cheng
Published: December 2019

Haplotype phasing is essential to study diploid eukaryotic organisms. High-throughput sequencing, including next-generation sequencing and third-generation sequencing from different technologies, brings possibilities for haplotype assembly. Although there exist multiple haplotype phasing algorithms, only a few are portable across sequencing technologies with the premise of efficiency and accuracy. Herein, we proposed SpecHap, a novel haplotype assembly tool that leverages spectral graph theory, transforming haplotype phasing into an algebraic problem. On both in silico and whole-genome-sequencing datasets, SpecHap consumed less memory and required less CPU time, yet achieved comparable accuracy comparing to state-of-art methods across all the test instances of next-generation sequencing, linked-reads, high-throughput chromosome conformation capture sequencing, PacBio single-molecule real-time sequencing and Oxford Nanopore long-reads sequencing data. Furthermore, SpecHap successfully phased an individual Ambystoma mexicanumm, a species with gigantic diploid genomes, within 6 CPU hours and 945MB peak memory usage, while other tools failed to yield results either due to a memory overflow (40GB) or a time limit excess (5 days). Our results demonstrated that SpecHap is scalable, efficient and accurate for diploid phasing, supporting diverse sequencing platforms.
Activation of macrophages by lysophosphatidic acid through the lysophosphatidic acid receptor 1 as a novel mechanism in multiple sclerosis pathogenesis
Authors: Fransson Jennifer , Gómez Ana Isabel , Romero-Imbroda Jesús , Fernández Oscar , Leyva Laura , de Fonseca Fernando Rodriguez , Chun Jerold , Louapre Celine , Van-Evercooren Anne Baron , Zujovic Violetta , Estivill-Torrús Guillermo , García-Díaz Beatriz
Published: December 2019

Multiple sclerosis (MS) is a neuro-inflammatory disease for which the pathogenesis remains largely unclear. Lysophosphatidic acid (LPA) is an endogenous phospholipid that is involved in multiple immune cell functions and is dysregulated in MS. Its receptor LPA1 is expressed in macrophages and regulates their activation, which is of interest due to the role of macrophage activation in MS in both destruction and repair.

In this study, we studied the viable Malaga variant of LPA1-null mutation as well as pharmaceutical inhibition of LPA1 in mice with experimental autoimmune encephalomyelitis (EAE), a model of MS. LPA1 expression was also analyzed in both wild-type EAE mice and MS patient immune cells. The effect of LPA and LPA1 on macrophage activation was studied in human monocyte-derived macrophages.

We show that lack of LPA1 activity induces a milder clinical course in EAE, and that Lpar1 expression in peripheral blood mononuclear cells (PBMCs) correlates with onset of relapses and severity in wild-type EAE mice. We see the same over-expression in PBMCs from MS patients during relapse compared to progressive forms of the disease, and in monocyte-derived macrophages after exposure to pro-inflammatory stimuli. In addition, LPA induced a pro-inflammatory-like response in macrophages through LPA1, providing a plausible way in which LPA and LPA1 dysregulation can lead to the inflammation seen in MS.

These data show a new mechanism of LPA signaling in the pathogenesis of MS, prompting further research into its use as a therapeutic target biomarker.
Mutagenesis of two homologs ATP Binding cassette protein in tomato by CRISPR/Cas9 provide resistance against the plant parasite Phelipanche aegyptiaca
Authors: Bari Vinay Kumar , Nassar Jackline Abu , Meir Ayala , Aly Radi
Published: December 2019

Plant parasitic weed Phelipanche aegyptiaca and Orobanche spp. are obligate plant parasites that cause heavy damage to agricultural crop plants. Germination of the parasite seeds require exposure to specific chemical known as strigolactone [SL]. The plant hormone SL is derived from plant carotenoids via cleavage by CCD7 and CCD8 enzymes and exuded by the host roots to the rhizosphere. Here, we provide evidence that CRISPR/Cas9 mediated targeted mutagenesis of two homologues ATP Binding cassette (ABC) protein in tomato (Solyc08g067610 and Solyc08g067620), significantly reduced the germination of the parasitic weed P.aegyptiaca. Constructs harboring specific single guide RNA were prepared and targeted against conserved region in the above tomato genes (Solyc08g067610 and Solyc08g067620). Selected T0-mutated tomato plants showed different type of deletions at both locuses. Furthermore, genotype analysis of T1 plants showed that the introduced mutations stably inherited to next generation with no identified off-targets. Mutated tomato lines, showed more branching, enhanced growth of axillary buds, reduced length of primary stems and significantly reduced development of the parasitic weed P. aegyptiaca as compared to wild type plants. Moreover, in ABCCas9 mutants the expression level of the genes (CCD8 and MAX1) related to SL biosynthesis were decreased, without alteration in the root extract orobanchol [SL] as compared to control plants. Development of genetic resistance based on genome editing of host key genes are novel approaches for enhancing host-parasite resistance. The current study offers insights into ABC protein homologs and mutagenesis of ABC protein that could be used in the development of efficient method to reduce parasitic weed germination.
In vitroinduced floral reversion in switchgrass (Panicum VirgatumL.)
Authors: Wang Yongfeng , Xie Kunliang , Sun Fengli , Zhang Chao , Liu Shudong , Xi Yajun
Published: December 2019

Switchgrass (Panicum VirgatumL.) is a warm-season perennial grass native to North America, it was used as forage and vegetative filter strips in early days, and have developed into a bioenergy crop in recent years. In this study, we found that the switchgrass cultivar ‘Alamo’ at elongation stage 4 have developed inflorescences about 1 cm in length, andin vitroincubation of the shoot apexes harboring inflorescences on Murashige and Skoog’s basal medium supplemented with 3 mg/L 6-benzylaminopurine generated multiple shoot clumps. Anatomical study showed that some of the regenerated shoots originated from axillary buds on the explants, some of them originated from adventurous buds and some of them originated from young florets. Further study of shoots originated from young florets found that the floral organs degenerated or developed into leaf-like organs, and the flower terminal transformed into a vegetative shoot apical meristem, that’s to say these shoots arise from flower reversion.In vitroinduction of floral reversion provided a novel protocol to manipulate flower development in switchgrass, which might contribute a fundamental for flower development study in switchgrass and other plants.
Disentangling spatial and environmental effects: flexible methods for community ecology and macroecology
Authors: Viana Duarte S. , Keil Petr , Jeliazkov Alienor
Published: December 2019

Community ecologists and macroecologists have long sought to evaluate the importance of environmental conditions in determining species distributions, community composition, and diversity across sites. Different methods have been used to estimate species-environment relationships, but their differences to jointly fit and disentangle spatial autocorrelation and structure remain poorly studied. We compared how methods in four broad families of statistical models estimated the contribution of the environment and space to variation in species binary occurrence and abundance. These methods included distance-based regression, generalized linear models (GLM, and the special case of RDA), generalized additive models (GAM), and tree-based machine learning (ML): regression trees, boosted regression trees (BRT), and random forests. The spatial component of the model consisted of spatial distance (in distance-based regression), Moran’s Eigenvector Maps (MEM; in GLM and ML), smooth spatial splines (in GAM), or tree-based non-linear modelling of spatial coordinates (in ML). We simulated typical site-by-species data to assess the methods’ performance in (1) fitting environmental and spatial models, and (2) partitioning the variation explained by environmental and spatial predictors. We observed marked differences in performance mostly caused by imbalanced performance in estimating environmental and spatial effects. Such differences also manifested when analyzing eight different empirical datasets. GLM and BRT with MEMs were generally the most reliable methods for partitioning the variation explained by environmental and spatial effects across a wide range of simulated scenarios. The remaining methods tended to underfit simulated spatial structures, causing underestimation of spatial fractions of variation. Our results suggest that previously overlooked methods for performing variation partitioning, especially tree-based ML, offer flexible approaches to analyze site-by-species matrices. We provide general guidelines on the usefulness of different models under different ecological and sampling scenarios, for species distribution modelling, community ecology, and macroecology.
Characteristics of a novel NMR-based metabolomics platform for dogs
Authors: Ottka Claudia , Vapalahti Katariina , Puurunen Jenni , Vahtera Laura , Lohi Hannes
Published: December 2019

Metabolomics has proven itself an invaluable research tool, providing comprehensive insight to systemic metabolism. However, the lack of scalable and quantitative methods with known reference intervals and documented reproducibility has prevented the use of metabolomics in the clinical setting. This study describes the development and validation of a quantitative nuclear magnetic resonance (NMR) -based metabolomics platform for canine serum and plasma samples. Altogether 8247 canine samples were analyzed using a Bruker’s 500 MHz NMR spectrometer. Using statistical approaches derived from international guidelines, we defined reference intervals for 123 biomarkers, studied method precision, analyte storage stability, the effect of prolonged contact to red blood cells, differences of blood collection tubes, interference of lipemia, hemolysis and bilirubinemia, method comparison, and demonstrated the method’s practical relevance in a hyperglycemic cohort. Owing to the advantages of quantitative results, high reproducibility, and scalability, this canine metabolomics platform holds great potential for numerous clinical and research applications to improve canine health and well-being.
FLS2 is a CDK-like kinase that directly binds IFT70 and is required for proper ciliary disassembly inChlamydomonas
Authors: Zhao Qin , Li Shufen , Shao Shangjin , Wang Zhengmao , Pan Junmin
Published: December 2019

Intraflagellar transport (IFT) is required for ciliary assembly and maintenance. While disruption of IFT may trigger ciliary disassembly, we show here that IFT mediated transport of a CDK-like kinase ensures proper ciliary disassembly. Mutations in flagellar shortening 2 (FLS2), encoding a CDK-like kinase, lead to retardation of cilia resorption and delay of cell cycle progression. Stimulation for ciliary disassembly induces gradual dephosphorylation of FLS2 accompanied with gradual inactivation. Loss of FLS2 or its kinase activity induces early onset of kinesin13 phosphorylation in cilia. FLS2 is predominantly localized in the cell body, however, it is transported to cilia upon induction of ciliary disassembly. FLS2 directly interacts with IFT70 and loss of this interaction inhibits its ciliary transport, leading to dysregulation of kinesin13 phosphorylation and retardation of ciliary disassembly. Thus, this work demonstrates that IFT plays active roles in controlling proper ciliary disassembly by transporting a protein kinase to cilia to regulate a microtubule depolymerizer.

Author Summary

Cilia or eukaryotic flagella are cellular surface protrusions that function in cell motility as well as sensing. They are dynamic structures that undergo assembly and disassembly. Cilia are resorbed during cell cycle progression. Dysregulation of cilia resorption may cause delay of cell cycle progression, which underlies aberrant cell differentiation and even cancer. Ciliary resorption requires depolmerization of axonemal microtubules that is mediated by kinesin13. Using the unicellular green alga,Chlamydomonas, we have identified a CDK-like kinase FLS2 that when mutated retards cilia resorption, leading to delay of cell cycle progression. FLS2, a cell body protein, is transported to cilia via intraflagellar transport upon induction of cilia resorption. FLS2 directly interacts with IFT70 and loss of this interaction inhibits transport of FLS2 to cilia and fails to regulate proper phosphorylation of kinesin13 in cilia.
Repeated exposure to nanosecond high power pulsed microwaves increases cancer incidence in rat
Authors: Seze René de , Poutriquet Carole , Gamez Christelle , Maillot-Maréchal Emmanuelle , Robidel Franck , Lecomte Anthony , Fonta Caroline
Published: December 2019

High-power microwaves are used to inhibit electronics of threatening military or civilian vehicles. This work aims to assess health hazards of high-power microwaves and helps define hazard threshold levels of modulated radiofrequency exposures such as those emitted by the first generations of mobile phones.

Rats were exposed to the highest possible field levels, under single acute or repetitive exposures for eight weeks. Intense microwave electric fields at 1 MV/m of nanoseconds duration were applied from two sources at different carrier frequencies of 10 and 3.7 GHz. The repetition rate was 100 pps, and the duration of train pulses lasted from 10 s to twice 8 min. The effects were studied on the central nervous system, by labelling brain inflammation marker GFAP and by performing different behavioural tests: rotarod, T-maze, beam-walking, open-field, and avoidance test. Long-time survival was measured in animals repeatedly exposed, and anatomopathological analysis was performed on animals sacrificed at two years of life or at death if earlier. One group was sham exposed.

Few effects were observed on behaviour. With acute exposure, an avoidance reflex was shown at very high, thermal level (22 W/kg); GFAP was increased some days after exposure. Most importantly, with repeated exposures, survival time was 4-month shorter in the exposed group, with eleven animals exhibiting a large sub-cutaneous tumour, compared to two in the sham group. A residual X-ray exposure was also present in the beam (0.8 Gy), which is not a bias for the observed result.

High power microwaves below thermal level in average, can increase cancer incidence and decrease survival time in rats, without clear effects on behaviour. The parameters of this effect need to be explored further, and a more precise dosimetry to be performed.
Mitochondrial localization of SESN2
Authors: Kovaleva Irina E. , Tokarchuk Artem V. , Zeltukhin Andrei O. , Safronov Grigoriy , Evstafieva Aleksandra G. , Dalina Alexandra A. , Lyamzaev Konstantin G. , Chumakov Peter M. , Budanov Andrei V.
Published: December 2019

SESN2 is a member of evolutionarily conserved sestrin protein family found in most of Metazoa species. SESN2 is transcriptionally activated by many stress factors including metabolic derangements, oxidants and DNA-damage. As a result, SESN2 controls ROS accumulation, metabolism and cell viability. The best known function of SESN2 is the regulation of mechanistic target of rapamycin complex 1 kinase (mTORC1) that plays the central role in the stimulation of cell growth and suppression of autophagy. SESN2 inhibits mTORC1 activity through interaction with the GATOR2 protein complex that suppresses an inhibitory effect of GATOR2 on the GATOR1 protein complex. GATOR1 inhibits mTORC1 through its GAP activity toward the small GTPase RagA/B which in complex with RagC/D proteins stimulate mTORC1 translocation to the lysosomes where this kinase is activated by small GTPase Rheb. Despite the well-established role of SESN2 in mTORC1 inhibition, the other SESN2 activities are not well characterised. We recently showed that SESN2 can control mitochondrial function and cell death via mTORC1-independent mechanisms and these activities might be explained by direct effects of SESN2 on mitochondria. In this work we examined mitochondrial localization of SESN2 and demonstrated that SESN2 is located on mitochondria and can be directly involved in the regulation of mitochondrial functions.
CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content
Authors: Borry Maxime , Cordova Bryan , Perri Angela , Wibowo Marsha C. , Honap Tanvi , Jada Ko Wing Tung , Yu Jie , Britton Kate , Flink Linus Girdland , Power Robert C. , Stuijts Ingelise , Garcia Domingo Salazar , Hofman Courtney A. , Hagan Richard W. , Kagone Thérèse Samdapawindé , Meda Nicolas , Carabin Hélène , Jacobson David , Reinhard Karl , Lewis Cecil M. , Kostic Aleksandar , Jeong Choongwon , Herbig Alexander , Hübner Alexander , Warinner Christina
Published: December 2019

Shotgun metagenomics applied to archaeological feces (paleofeces) can bring new insights into the composition and functions of human and animal gut microbiota from the past. However, paleofeces often undergo physical distortions in archaeological sediments, making their source species difficult to identify on the basis of fecal morphology or microscopic features alone. Here we present a reproducible and scalable pipeline using both host and microbial DNA to infer the host source of fecal material. We apply this pipeline to newly sequenced archaeological specimens and show that we are able to distinguish morphologically similar human and canine paleofeces, as well as non-fecal sediments, from a range of archaeological contexts.
Getting to know each other: PPIMem, a novel approach for predicting transmembrane protein-protein complexes
Authors: Khazen Georges , Gyulkhandanian Aram , Issa Tina , Maroun Rachid C.
Published: December 2019

Because of their considerable number and diversity, membrane proteins and their macromolecular complexes represent the functional units of cells. Their quaternary structure may be stabilized by interactions between the α-helices of different proteins in the hydrophobic region of the cell membrane. Membrane proteins also represent potential pharmacological targets par excellence for various diseases. Unfortunately, their experimental 3D structure and that of their complexes with intramembrane interacting partners are scarce due to technical difficulties. To overcome this key problem, we devised PPIMem, a computational approach for the specific prediction of higher-order structures of α-helical transmembrane proteins. The novel approach involves identification of the amino acid residues at the interface of complexes with a 3D structure. The identified residues compose then interaction motifs that are conveniently expressed as mathematical regular expressions. These are used for motif search in databases, and for the prediction of intramembrane protein-protein complexes. Our template interface-based approach predicted 21, 544 binary complexes between 1, 504 eukaryotic plasma membrane proteins across 39 species. We compared our predictions to experimental datasets of protein-protein interactions as a first validation method. The PPIMem online database with the annotated predicted interactions is implemented as a web server and can be accessed directly at https://transint.shinyapps.io/transint/.
Fate mapping quantifies the dynamics of B cell development and activation throughout life
Authors: Verheijen Melissa , Rane Sanket , Pearson Claire , Yates Andrew J. , Seddon Benedict
Published: December 2019

Follicular mature (FM) and germinal centre (GC) B cells underpin humoral immunity but the dynamics of their generation and maintenance are not clearly defined. Here we exploited a fate-mapping system in mice that tracks B cells as they develop into peripheral subsets, together with a cell division fate reporter mouse and mathematical models. We find that FM cells are kinetically homogeneous, recirculate freely, continually replenished from transitional populations, and self-renew rarely. In contrast, GC B cell lineages persist for weeks with rapid turnover and site-specific dynamics. Those in the spleen derive from transitional cells and are kinetically homogeneous, while those in lymph nodes derive from FM B cells and comprise both transient and persistent clones. These differences likely derive from the nature of antigen exposure at the different sites. Our integrative approach also reveals how the host environment drives cell-extrinsic, age-related changes in B cell homeostasis.
Identification of the C. sordellii lethal toxin receptor elucidates principles of receptor specificity in clostridial toxins
Authors: Lee Hunsang , Beilhartz Greg L. , Kucharska Iga , Raman Swetha , Cui Hong , Lam Mandy Hiu Yi , Rubinstein John L. , Schramek Daniel , Julien Jean-Philippe , Melnyk Roman A. , Taipale Mikko
Published: December 2019

Clostridium sordellii lethal toxin (TcsL) is responsible for an almost invariably lethal toxic shock syndrome associated with gynecological C. sordellii infections. Here, using CRISPR/Cas9 screening, we identify semaphorins SEMA6A and SEMA6B as the cellular receptors for TcsL and demonstrate that soluble extracellular SEMA6A can protect mice from TcsL-induced edema. A 3.3 Å cryo-EM structure shows that TcsL binds SEMA6A with the same region that the highly related C. difficile TcdB toxin uses to bind structurally unrelated Frizzled receptors. Remarkably, reciprocal mutations in this evolutionarily divergent surface are sufficient to switch receptor specificity between the toxins. Our findings establish semaphorins as physiologically relevant receptors for TcsL, and reveal the molecular basis for the difference in tissue targeting and disease pathogenesis between highly related toxins.
Pharmacological and fasting-induced activation of SIRT1/LXRα signaling alleviates diabetes-induced retinopathy
Authors: Hammer Sandra S. , Vieira Cristiano P. , McFarland Delaney , Sandler Maximilian , Levitsky Yan , Dorweiler Tim F. , Lydic Todd , Asare-Bediako Bright , Adu-Agyeiwaah Yvonne , Sielski Micheli Severo , Dupont Mariana , Longhini Ana Leda , Calzi Sergio Li , Chakraborty Dibyendu , Seigel Gail M. , Proshlyakov Denis A. , Grant Maria B. , Busik Julia V.
Published: December 2019

In diabetes, the retina, a tissue with unique metabolic needs, demonstrates dysregulation of the intricate balance between nutrient availability and utilization. This results in cholesterol accumulation, pro-inflammatory and pro-apoptotic changes, and consequently neurovascular damage. Sirtuin 1 (SIRT1), a nutrient sensing deacetylase, is downregulated in the diabetic retina. In this study, the effect of SIRT1 stimulation by fasting or by pharmacological activation using SRT1720, was evaluated on retinal cholesterol metabolism, inflammation and neurovascular damage. SIRT1 activation, in retinal endothelial cells (REC) and neuronal retinal progenitor cells (R28), led to Liver X Receptor alpha (LXRα) deacetylation and subsequent increased activity, as measured by increased ATP-binding cassette transporter (ABC) A1 and G1 mRNA expression. In turn, increased cholesterol export resulted in decreased REC cholesterol levels. SIRT1 activation also led to decreased inflammation. SIRT1 activation, in vivo, prevented diabetes-induced inflammation and vascular and neural degeneration. Diabetes-induced visual function impairment, as measured by electroretinogram and optokinetic response, was significantly improved as a result of SIRT1 activation. Taken together, activation of SIRT1 signaling is an effective therapeutic strategy that provides a mechanistic link between the advantageous effects associated with fasting regimes and prevention of diabetic retinopathy (DR).
Nanopore sequencing reveals U2AF1 S34F-associated full-length isoforms
Authors: Soulette Cameron M. , Hrabeta-Robinson Eva , Tang Alison , Marin Maximillian G. , Brooks Angela N.
Published: December 2019

U2AF1 S34F is one of the most recurrent splicing factor mutations in lung adenocarcinoma (ADC) and has been shown to cause transcriptome-wide pre-mRNA splicing alterations. While U2AF1 S34F-associated splicing alterations have been described, the function of altered mRNA isoform changes remains largely unexplored. To better understand the impact U2AF1 S34F has on isoform fate and function, we conducted high-throughput long-read cDNA sequencing from isogenic human bronchial epithelial cells with and without U2AF1 S34F mutation. We found that nearly 75% (49,366) of our long-read constructed multiexon isoforms do not overlap GENCODE or short-read assembled isoforms. We found 198 transcript isoforms with significant expression and usage changes caused by U2AF1 S34F mutation, including a novel lncRNA. Isoforms from immune-related genes were largely downregulated in mutant cells, none of which were found to have splicing changes. Finally, isoforms likely targeted by nonsense-mediated decay were preferentially downregulated in U2AF1 S34F cells, suggesting that the impact of observed isoform changes may alter the translational output of affected genes. Altogether, long-read sequencing provided additional insights into transcriptome alterations and downstream functional consequences associated with U2AF1 S34F mutation.
Escherichia coliNusG links the lead ribosome with the transcription elongation complex
Authors: Washburn Robert S. , Zuber Philipp K. , Sun Ming , Hashem Yaser , Shen Bingxin , Li Wen , Harvey Sho , Knauer Stefan H. , Frank Joachim , Gottesman Max E.
Published: December 2019

It has been known for more than 50 years that transcription and translation are physically coupled in bacteria, but whether or not this coupling may be mediated by the two-domain protein N-utilization substance (Nus) G inEscherichia coliis still heavily debated. Here, we combine integrative structural biology and functional analyses to provide conclusive evidence that NusG can physically link transcription with translation by contacting both RNA polymerase and the ribosome. We present a cryo-electron microscopy structure of a NusG:70S ribosome complex and nuclear magnetic resonance spectroscopy data revealing simultaneous binding of NusG to RNAP and the intact 70S ribosome, providing the first direct structural evidence for NusG-mediated coupling. Furthermore,in vivoreporter assays show that recruitment of NusG occurs late in transcription and strongly depends on translation. Thus, our data suggest that coupling occurs initially via direct RNAP:ribosome contacts and is then mediated by NusG.
Genome sequencing for early-onset or atypical dementia: high diagnostic yield and frequent observation of multiple contributory alleles
Authors: Cochran J. Nicholas , McKinley Emily C. , Cochran Meagan , Amaral Michelle D. , Moyers Bryan A. , Lasseigne Brittany N. , Gray David E. , Lawlor James M.J. , Prokop Jeremy W. , Geier Ethan G. , Holt James M. , Thompson Michelle L. , Newberry J. Scott , Yokoyama Jennifer S. , Worthey Elizabeth A. , Geldmacher David S. , Love Marissa Natelson , Cooper Gregory M. , Myers Richard M. , Roberson Erik D.
Published: December 2019

We assessed the results of genome sequencing for early-onset dementia. Participants were selected from a memory disorders clinic. Genome sequencing was performed along with C9orf72 repeat expansion testing. All returned sequencing results were Sanger-validated. Prior clinical diagnoses included Alzheimer's disease, frontotemporal dementia, and unspecified dementia. The mean age of onset was 54 (41–76). Fifty percent of patients had a strong family history, 37.5% had some, and 12.5% had no known family history. Nine of 32 patients (28%) had a variant defined as pathogenic or likely pathogenic (P/LP) by American College of Medical Genetics and Genomics standards, including variants in APP, C9orf72, CSF1R, and MAPT. Nine patients (including three with P/LP variants) harbored established risk alleles with moderate penetrance (odds ratios of ∼2–5) in ABCA7, AKAP9, GBA, PLD3, SORL1, and TREM2. All six patients harboring these moderate penetrance variants but not P/LP variants also had one or two APOE ε4 alleles. One patient had two APOE ε4 alleles with no other established contributors. In total, 16 patients (50%) harbored one or more genetic variants likely to explain symptoms. We identified variants of uncertain significance (VUSs) in ABI3, ADAM10, ARSA, GRID2IP, MME, NOTCH3, PLCD1, PSEN1, TM2D3, TNK1, TTC3, and VPS13C, also often along with other variants. In summary, genome sequencing for early-onset dementia frequently identified multiple established or possible contributory alleles. These observations add support for an oligogenic model for early-onset dementia.
The impact of credit on productivity of smallholder farmers in Ghana
Authors: Nordjo Ralph Essem , Adjasi Charles K.D.
Published: December 2019

Purpose

The purpose of this paper is to evaluate the impact of access to production credit on the productivity of smallholder farmers.

Design/methodology/approach

Data for the study were drawn from the Agricultural Value Chain Facility (AVCF), which was implemented in the Northern Region of Ghana. This paper uses the Propensity Score Matching (PSM) to estimate the average treatment effect of access to production credit on the productivity of smallholder farmers. The rationale for the choice of this estimation technique is to control for selection bias since the treatment variable (access to production credit) was not randomised. The authors also test for the effect of hidden bias using “Rosenbaum bounds” sensitivity analysis. The study uses two control groups to examine the net effect of credit on productivity.

Findings

The results reveal that smallholder farmers with access to production credit increased productivity through investment in farm inputs. For the impact of credit on productivity using control Group 1, the result shows that farmers with access to credit increased their productivity by 0.170 metric tonnes per hectare and for control Group 2, the result shows an increase of 0.252 metric tonnes per hectare more than farmers who are without access to production credit.

Practical implications

The evidence as provided by this paper is that access to production credit is significant to meet the credit needs of smallholder farmers and therefore contributes to the policy debate on whether access to credit has impact on the productivity of smallholder farmers.

Originality/value

The paper shows the importance of production credit in augmenting the production function of smallholder farmers.