bluuebunny/crossref_metadata_2025 huggingface dataset:
“Dual protease type XIII/pepsin digestion offers superior resolution and overlap for the analysis of histone tails by HX-MS”
Authors: Mullahoo James , Zhang Terry , Clauser Karl , Carr Steven A. , Jaffe Jacob D. , Papanastasiou Malvina
Published: October 2019

The N-terminal regions of histone proteins (tails) are dynamic elements that protrude from the nucleosome and are involved in many aspects of chromatin organization. Their epigenetic role is well-established, and post-translational modifications (PTMs) present on these regions contribute to transcriptional regulation. While hydrogen/deuterium exchange mass spectrometry (HX-MS) is well-suited for the analysis of dynamic structures, it has seldom been employed to analyze histones due to the poor N-terminal coverage obtained using pepsin. Here, we test the applicability of a dual protease type XIII/pepsin digestion column to this class of proteins. We optimize online digestion conditions using the H4 monomer, and extend the method to the analysis of histones in monomeric states and nucleosome core particles (NCPs). We show that the dual protease column generates many short and overlapping N-terminal peptides. We evaluate our method by performing hydrogen exchange experiments of NCPs for different time points and present full coverage of the tails at excellent resolution. We further employ electron transfer dissociation (ETD) and showcase an unprecedented degree of overlap across multiple peptides that is several fold higher than previously reported methods. The method we report here may be readily applied to the HX-MS investigation of histone dynamics and to the footprints of histone binding proteins on nucleosomes.
Lipid Chaperoning of a Thylakoid Protease Whose Stability is Modified by the Protonmotive Force
Authors: McKinnon Lucas J. , Fukushima Jeremy , Inoue Kentaro , Theg Steven M.
Published: October 2019

Protein folding is a complex cellular process often assisted by chaperones but can also be facilitated by interactions with lipids. Disulfide bond formation is a common mechanism to stabilize a protein. This can help maintain functionality amidst changes in the biochemical milieu which are especially common across energy-transducing membranes. Plastidic Type I Signal Peptidase 1 (Plsp1) is an integral thylakoid membrane signal peptidase which requires an intramolecular disulfide bond forin vitroactivity. We have investigated the interplay between disulfide bond formation, lipids, and pH in the folding and activity of Plsp1. By combining biochemical approaches with a genetic complementation assay, we provide evidence that interactions with lipids in the thylakoid membrane have chaperoning activity towards Plsp1. Further, the disulfide bridge appears to prevent an inhibitory conformational change resulting from proton motive force-mimicking pH conditions. Broader implications related to the folding of proteins in energy-transducing membranes are discussed.
A Lamin Associated Chromatin Model for Chromosome Organization
Authors: Maji Ajoy , Ahmed Jahir , Roy Shubhankar , Chakrabarti Buddhapriya , Mitra Mithun K.
Published: October 2019

We propose a simple model for chromatin organization based on the interaction of the chromatin fibres with Lamin proteins along the nuclear membrane. Lamin proteins are known to be a major factor that influences chromatin organization, and hence gene expression in the cells. Our polymer model explains the formation of lamin associated domains, and for heteropolymers with sequence control, can reproduce observed length distributions of LADs. In particular, lamin mediated interaction can enhance the formation of chromosome territories as well as the organization of chromatin into tightly packed heterochromatin and the loosely-packed gene-rich euchromatin regions.
Promoting neuronal outgrowth using ridged scaffolds coated with extracellular matrix proteins
Authors: Siddiqui Ahad M. , Brunner Rosa , Harris Gregory M. , Miller Alan.L. , Waletzki Brian E. , Schwarzbauer Jean E. , Schwartz Jeffrey , Yaszemski Michael J. , Windebank Anthony J. , Madigan Nicolas N.
Published: October 2019

Spinal cord injury (SCI) results in cell death, demyelination, and axonal loss. The spinal cord has a limited ability to regenerate and current clinical therapies for SCI are not effective in helping promote neurologic recovery. We have developed a novel scaffold biomaterial that is fabricated from the biodegradable hydrogel oligo[poly(ethylene glycol)fumarate] (OPF). We have previously shown that positively charged OPF scaffolds (OPF+) in an open spaced, multichannel design can be loaded with Schwann cells to support axonal generation and functional recovery following SCI. We have now developed a hybrid OPF+ biomaterial that increases the surface area available for cell attachment and that contains an aligned microarchitecture and extracellular matrix (ECM) proteins to better support axonal regeneration. OPF+ was fabricated as 0.08 mm thick sheets containing 100 μm high polymer ridges that self-assembles into a spiral shape when hydrated. Laminin, fibronectin, or collagen I coating promoted neuron attachment and axonal outgrowth on the scaffold surface. In addition, the ridges aligned axons in a longitudinal bipolar orientation. Decreasing the space between the ridges increased the number of cells and neurites aligned in the direction of the ridge. Schwann cells seeded on laminin coated OPF+ sheets aligned along the ridges over a 6-day period and could myelinate dorsal root ganglion neurons over 4 weeks. The OPF+ sheets support axonal regeneration when implanted into the transected spinal cord. This novel scaffold design, with closer spaced ridges and Schwann cells is a novel biomaterial construct to promote regeneration after SCI.

Graphical Abstract
Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data
Authors: Nouri Nima , Kleinstein Steven H.
Published: October 2019

Motivation

Adaptive immune receptor repertoire sequencing (AIRR-Seq) offers the possibility of identifying and tracking B cell clonal expansions during adaptive immune responses. Members of a B cell clone are descended from a common ancestor and share the same initial V(D)J rearrangement, but their B cell receptore (BCR) sequence may differ due to the accumulation of somatic hypermutations (SHMs). Clonal relationships are learned from AIRR-seq data by analyzing the BCR sequence, with the most common methods focused on the highly diverse junction region. However, clonally related cells often share SHMs which have been accumulated during affinity maturation. Here, we investigate whether shared SHMs in the V and J segments of the BCR can be leveraged along with the junction sequence to improve the ability to identify clonally related sequences. We develop independent distance functions that capture junction similarity and shared mutations, and combine these in a spectral clustering framework to infer the BCR clonal relationships. Using both simulated and experimental data, we show that this model improves both the sensitivity and specificity for identifying B cell clones.

Availability

Source code for this method is freely available in theSCOPer(Spectral Clustering for clOne Partitioning) R package (version 0.2 or later) in the Immcantation framework:www.immcantation.orgunder the CC BY-SA 4.0 license.

Contact

steven.kleinstein@yale.edu
Retromer subunit, VPS29, regulates synaptic transmission and is required for endolysosomal function in the aging brain
Authors: Ye Hui , Ojelade Shamsideen , Li-Kroeger David , Zuo Zhongyuan , Wang Liping , Li Yarong , Gu Jessica Y. J. , Tepass Ulrich , Rodal Avital A. , Bellen Hugo J. , Shulman Joshua M.
Published: October 2019

Retromer, including Vps35, Vps26, and Vps29, is a protein complex responsible for recycling proteins within the endolysosomal pathway. Although implicated in both Parkinson’s and Alzheimer’s disease, our understanding of retromer function in the adult brain remains limited, in part becauseVps35andVps26are essential for development. InDrosophila, we find thatVps29is dispensable for embryogenesis but required for retromer function in aging adults, including for synaptic transmission, survival, and locomotion. Unexpectedly, inVps29mutants, Vps35 and Vps26 proteins are normally expressed and associated, but retromer is mislocalized from neuropil to soma with the Rab7 GTPase. Further,Vps29phenotypes are suppressed by reducing Rab7 or overexpressing the GTPase activating protein, TBC1D5. With aging, retromer insufficiency triggers progressive endolysosomal dysfunction, with ultrastructural evidence of impaired substrate clearance and lysosomal stress. Our results reveal the role of Vps29 in retromer localization and function, highlighting requirements for brain homeostasis in aging.

Impact Statement

Vps29 promotes retromer localization in the adultDrosophilabrain, engaging Rab7 and TBC1D5, and its loss triggers age-dependent neuronal impairments in endolysosomal trafficking and synaptic transmission.
Circadian- and sex-dependent increases in intravenous cocaine self-administration inNpas2mutant mice
Authors: DePoy Lauren M. , Becker-Krail Darius D. , Zong Wei , Petersen Kaitlyn , Shah Neha M. , Brandon Jessica H. , Miguelino Alyssa M. , Tseng George C. , Logan Ryan W. , McClung Colleen A.
Published: October 2019

Substance use disorder is associated with disruptions in circadian rhythms. The circadian transcription factor neuronal PAS domain protein 2 (NPAS2) is enriched in reward-related brain regions and regulates reward, but its role in substance use is unclear. To examine the role of NPAS2 in drug taking, we measured intravenous cocaine self-administration (acquisition, dose-response, progressive ratio, extinction, cue-induced reinstatement) in wild-type (WT) andNpas2mutant mice at different times of day. In the light (inactive) phase, cocaine reinforcement was increased in allNpas2mutants, while self-administration and motivation were affected sex-dependently. These sex differences were amplified during the dark (active) phase withNpas2mutation increasing self-administration, reinforcement, motivation, extinction responding and reinstatement in females, but only reinforcement in males. To determine whether circulating hormones are driving these sex differences, we ovariectomized WT andNpas2mutant females and confirmed that unlike sham controls, ovariectomized mutant mice showed no increase in self-administration. To identify whether striatal brain regions are activated inNpas2mutant females, we measured cocaine-induced ΔFosB expression. Relative to WT, ΔFosB expression was increased in D1+ neurons in the nucleus accumbens core and dorsolateral striatum inNpas2mutant females after dark phase self-administration. We also identified potential target genes that may underlie the behavioral responses to cocaine inNpas2mutant females. These results suggest NPAS2 regulates reward and activity in specific striatal regions in a sex and time of day specific manner. Striatal activation could be augmented by circulating sex hormones, leading to an increased effect ofNpas2mutation in females.

Significance Statement

Circadian disruptions are a common symptom of substance use disorders and chronic exposure to drugs of abuse alters circadian rhythms, which may contribute to subsequent substance use. Diurnal rhythms are commonly found in behavioral responses to drugs of abuse with drug sensitivity and motivation peaking during the dark (active) phase in nocturnal rodents. Emerging evidence links disrupted circadian genes to substance use vulnerability and drug-induced alterations to these genes may augment drug-seeking. The circadian transcription factor NPAS2 is enriched in reward-related brain regions and regulates reward, but its role in substance use is unclear. To examine the role of NPAS2 in drug taking, we measured intravenous cocaine self-administration in wild-type andNpas2mutant mice at different times of day.
Relationship between simultaneously recorded spiking activity and fluorescence signal in GCaMP6 transgenic mice
Authors: Huang Lawrence , Knoblich Ulf , Ledochowitsch Peter , Lecoq Jérôme , Reid R. Clay , de Vries Saskia E. J. , Buice Michael A. , Murphy Gabe J. , Waters Jack , Koch Christof , Zeng Hongkui , Li Lu
Published: October 2019

Two-photon calcium imaging is often used with genetically encoded calcium indicators (GECIs) to investigate neural dynamics, but the relationship between fluorescence and action potentials (spikes) remains unclear. Pioneering work linked electrophysiology and calcium imaging in vivo with viral GECI expression, albeit in a small number of cells. Here we characterized the spikefluorescence transfer function in vivo of 91 layer 2/3 pyramidal neurons in primary visual cortex in four transgenic mouse lines expressing GCaMP6s or GCaMP6f. We found that GCaMP6s cells have spike-triggered fluorescence responses of larger amplitude, lower variability and greater single-spike detectability than GCaMP6f. Mean single-spike detection rates at high spatiotemporal resolution measured in our data was >70% for GCaMP6s and ~40-50% for GCaMP6f (at 5% false positive rate). These rates are estimated to decrease to 25-35% for GCaMP6f under generally used population imaging conditions. Our ground-truth dataset thus supports more refined inference of neuronal activity from calcium imaging.
Genome-wide quantitative trait loci mapping on Verticillium wilt resistance in 300 chromosome segment substitution lines from Gossypium hirsutum × Gossypium barbadense
Authors: Rashid Md Harun or , Li Peng-tao , Chen Tingting , Palanga Koffi Kibalou , Gong Wan-kui , Ge Qun , Gong Ju-wu , Liu Ai-ying , Lu Quan-wei , Diouf Latyr , Sarfraz Zareen , Jamshed Muhammad , Shi Yu-zhen , Yuan You-lu
Published: October 2019

Cotton Verticillium wilt (VW) is a devastating disease seriously affecting fiber yield and quality, and the most effective and economical prevention measure at present is selection and extension of Gossypium varieties harboring high resistant VW. However, multiple attempts to improve the VW resistance of the most widely cultivated Upland cotton have brought in little significant progress, and it seems necessary and urgent to develop Chromosome segment substitution lines (CSSLs) for merging the superior genes related with high yield and wide adaptation from G. hirsutum and VW resistance and excellent fiber quality from G. barbadense. In this study, 300 CSSLs were chosen from the developed BC5F3:5 CSSLs constructed by G. hirsutum CCRI36 and G. barbadense Hai1 to conduct quantitative trait locus (QTL) mapping on VW resistance, and a total of 53 QTLs relevant to VW disease index (DI) were identified together with the phenotypic data of 2 years investigations in two fields with two replications per year. All the QTLs were distributed on 20 chromosomes with phenotypic variation of 3.74-11.89%, of which 29 stable ones were consistent in at least two environments. Based on Meta-analysis on the 53 QTLs, 43 novel ones were identified, while 10 ones consistent to previously identified QTLs. Meanwhile, 32 QTL hotspot regions were detected, including 15 ones were novel. This study concentrates on QTL identification and screening hotspot region related with VW in the 300 CSSLs, which lay a solid platform not only for revealing the genetic and molecular mechanisms of VW resistance, but also for further fine mapping, gene cloning and molecular designing in breeding program for resistant cotton varieties.
Genomic Competition for Noise Reduction Shaped Evolutionary Landscape of Mir-4673
Authors: Farahani Ramin M , Rezaei-Lotfi Saba , Hunter Neil
Published: October 2019

The genomic platform that informs evolution of microRNA cascades remains unknown. Here we capitalized on the recent evolutionary trajectory of hominin-specific miRNA-4673 (Dokumcu et al., 2018) encoded in intron 4 of notch-1 to uncover the identity of one such precursor genomic element and the selective forces acting upon it. The miRNA targets genes that regulate Wnt/β-catenin signalling cascade. Primary sequence of the microRNA and its target region in Wnt modulating genes evolved from homologous signatures mapped to homotypic cis-clusters recognised by TCF3/4 and TFAP2A/B/C families. Integration of homologous TFAP2A/B/C cis-clusters (short range inhibitor of β-catenin (Li and Dashwood, 2004)) into the transcriptional landscape of Wnt cascade genes can reduce noise in gene expression (Blake et al., 2003). Probabilistic adoption of miRNA secondary structure by one such cis-signature in notch-1 reflected selection for superhelical curvature symmetry of precursor DNA to localize a nucleosome that overlapped the latter cis-cluster. By replicating the cis-cluster signature, non-random interactions of the miRNA with key Wnt modulator genes expanded the transcriptional noise buffering capacity via a coherent feed-forward loop mechanism (Hornstein and Shomron, 2006). In consequence, an autonomous transcriptional noise dampener (the cis-cluster/nucleosome) evolved into a post-transcriptional one (the miRNA). The findings suggest a latent potential for remodelling of transcriptional landscape by miRNAs that capitalize on non-random distribution of genomic cis-signatures.
Isolation and Characterization of aRhizobiumBacterium Associated with the Toxic DinoflagellateGambierdiscus balechii
Authors: Wu Zhen , Yang Xiaohong , Lin Senjie , Lee Wai Hin , Lam Paul K.S.
Published: October 2019

Algae-bacteria associations are increasingly being recognized to be important in shaping the growth of both algae and bacteria. Bacteria belonging to order Rhizobiales are important symbionts of legumes often developing as nodules on plant roots, but have not been widely documented in association with algae. Here, we detected, isolated, and characterized aRhizobiumspecies from the toxic benthic dinoflagellateGambierdiscusculture. The sequence of 16S rDNA showed 99% identity with that ofRhizobium rosettiformans. To further characterize the bacterium, we amplified and sequenced a cell wall hydrolase (CWH)-encoding gene; phylogenetic analysis indicated that this sequence was similar to the homologs ofMartellelasp. andHoefleasp, of order Rhizobiales. We performed PCR usingnifH primers to determine whether this bacterium can fix N2; however, the results of sequencing analysis showed that it was closer to chlorophyllideareductase-encoding gene (bchX), which is similar tonifH. Results of 16S rDNA qPCR showed that compared to that in the early exponential phase, the abundance of this bacterium increased during the late exponential growth phase ofGambierdiscus. When the dinoflagellate culture was subjected to N limitation, the abundance of the bacterium represented by both 16S rDNA and CWH increased. Based on these results and published literature, it is apparent that thisRhizobiumbacterium benefits from the association withGambierdiscusby hydrolyzing and utilizing the extracellular organic matter exudates released by the dinoflagellate. This is the first report ofRhizobiumspecies being associated with dinoflagellates, which will shed light on the algae-bacteria relationships.

IMPORTANCE

Phytoplankton are the undisputed primary producers in the aquatic ecosystems and contribute approximately half of the global net primary productivity.

Dinoflagellates are one of the most important phytoplankton in the marine ecosystems. Commonly, they do not exist autonomously in the marine environment but rather co-live with many bacteria that interact with dinoflagellates, producing a dynamic microbial ecosystem. Their interactions play a major role in important processes such as carbon fluxes and nutrient regeneration in the ocean, ultimately influencing the global carbon cycle and the climate. Hence, there is a need to understand the association and relationships between dinoflagellates and bacteria. Here, we tried to elucidate these interactions through isolating and characterizing a bacterium from a benthic toxic dinoflagellate culture. Our study is the first report of such bacterium being recorded to be associated with a dinoflagellate in this genus, providing new insights into the dinoflagellate-bacteria association for future research.
Spatially explicit ecological modeling improves empirical characterization of dispersal
Authors: Karisto Petteri , Suffert Frédéric , Mikaberidze Alexey
Published: October 2019

Dispersal is a key ecological process, but remains difficult to measure. By recording numbers of dispersed individuals at different distances from the source one can acquire a dispersal gradient. Although dispersal gradients contain information on dispersal, they are influenced by the spatial extent of the source. How can we separate the two contributions to extract knowledge on dispersal?

One could use a small, point-like source for which a dispersal gradient represents a dispersal kernel, which quantifies the probability of an individual dispersal event from a source to a destination point. However, the validity of this approximation cannot be established before conducting measurements.

We formulated a theory that incorporates the spatial extent of sources to estimate dispersal kernels from dispersal gradients. We re-analyzed published dispersal gradients for three major plant pathogens. We also demonstrated using simulations that this approach provides more accurate estimates of dispersal kernels across biologically plausible scenarios. We concluded that the three plant pathogens disperse over substantially shorter distances compared to conventional estimates. Using this method, a significant proportion of published dispersal gradients can be re-analyzed to improve our knowledge about spatial scales of dispersal. Thus, our results can boost progress in characterization of dispersal across taxa.
The roles ofhox 13genes in newt limb development and regeneration
Authors: Takeuchi Takashi , Minamitani Fumina , Koriyama Kazuki , Satoh Yukio , Suzuki Ken-ichi , Shigenobu Shuji , Inoue Takeshi , Agata Kiyokazu , Hayashi Toshinori
Published: October 2019

PosteriorHoxgenes play crucial roles in limb development and specify regions in the proximal-distal (PD) axis of limbs. However, there is no direct genetic evidence thatHoxgenes are essential for limb regeneration. Moreover, if essential, it is totally unknown whichHoxgenes have the same or distinct functions between development and regeneration. Here, we mutatedhox13using an efficient CRISPR/Cas9 system in newts (Pleurodeles waltl), which have strong regenerative capacities in various tissues. Triple or double mutants ofhox13paralogs lost their digit and metacarpal/metatarsal bones. Limb regeneration progressed but regenerates lacked the same autopod region. These results showed thathox13paralogs have the same functions in limb development and regeneration.
Looking for mimicry in a snake assemblage using deep learning
Authors: de Solan Thomas , Renoult Julien Pierre , Geniez Philippe , David Patrice , Crochet Pierre-Andre
Published: October 2019

Batesian mimicry, with its highly colorful species and astonishing mimic-model resemblance, is a canonical example of evolution by natural selection. However, Batesian mimicry could also occur in inconspicuous species and rely on subtle resemblance. Although potentially widespread, such instances have been rarely investigated, such that the real frequency of Batesian mimicry has remained largely unknown. To fill this gap, we developed a new approach using deep learning to quantify the resemblance between putative mimics and models from photographs. We applied this method to quantify the frequency of Batesian mimicry in Western Palearctic snakes. Potential mimics were revealed by an excess of resemblance with sympatric venomous snakes compared to random expectations. We found that 8% of the non-venomous species were potential mimics, among which all were imperfect mimics. This study is the first to quantify the frequency of Batesian mimicry in a whole community of vertebrates, and shows that even concealed species can be reliably identified as potential models. Our approach should prove useful to detect mimicry in other communities, and more generally it highlights the benefits of deep learning for quantitative studies of phenotypic resemblance.
Differential Effects of SUMO1/2 on Circadian Protein PER2 Stability and Function
Authors: Chen Ling-Chih , Hsieh Yung-Lin , Kuo Tai-Yun , Chou Yu-Chi , Hsu Pang-Hung , Hwang-Verslues Wendy W.
Published: October 2019

Posttranslational modification (PTM) of core circadian clock proteins, including Period2 (PER2), is required for proper circadian regulation. PER2 function is regulated by casein kinase 1 (CK1)-mediated phosphorylation and ubiquitination but little is known about other PER2 PTMs or their interaction with PER2 phosphorylation. We found that PER2 can be SUMOylated by both SUMO1 and SUMO2; however, SUMO1 versus SUMO2 conjugation had different effects on PER2 turnover and transcriptional suppressor function. SUMO2 conjugation facilitated PER2-β-TrCP interaction leading to PER2 proteasomal degradation. In contrast, SUMO1 conjugation, mediated by E3 SUMO-protein ligase RanBP2, enhanced CK1-mediated PER2S662 phosphorylation and increased PER2 transcriptional suppressor function. PER2 K736 was critical for both SUMO1- and SUMO2-conjugation. A PER2K736R mutation was sufficient to alter circadian periodicity and reduce PER2-mediated transcriptional suppression. Together, our data revealed SUMO1 versus SUMO2 conjugation acts as an upstream determinant of PER2 phosphorylation and thereby affects the circadian regulatory system and circadian periodicity.
CtIP promotes the motor activity of DNA2 to accelerate long-range DNA end resection
Authors: Ceppi Ilaria , Howard Sean M. , Kasaciunaite Kristina , Pinto Cosimo , Anand Roopesh , Seidel Ralf , Cejka Petr
Published: October 2019

BLM or WRN helicases function with the DNA2 helicase-nuclease to resect DNA doublestrand breaks and initiate homologous recombination. Upon DNA unwinding by BLM/WRN, RPA directs the DNA2 nuclease to degrade the 5’-strand, revealing the 3’ overhang needed for recombination. RPA bound to ssDNA also represents a barrier, explaining the need for the motor activity of DNA2 to displace RPA prior to resection. Using ensemble and single molecule biochemistry, we show that phosphorylated CtIP dramatically stimulates the ATP hydrolysis driven motor activity of DNA2. This activation in turn strongly promotes the degradation of RPA-coated ssDNA by DNA2. The domains of CtIP required to stimulate DNA2 are separable from those that regulate the MRN complex. These results establish that CtIP couples both MRE11-dependent short and DNA2-dependent long-range resection, and show how the motor activity of DNA2 promotes resection. Our data explain the less severe resection defects of MRE11 nuclease-deficient cells compared to those lacking CtIP.

Highlights

Phosphorylated CtIP stimulates the motor activity of DNA2

The activated DNA2 translocase facilitates degradation of RPA-coated ssDNA

CtIP promotes both MRN and DNA2 nucleases coupling short and long-range resection

The CtIP domains required to promote DNA2 and MRN are distinct and fully separable
Metabolic remodeling by TIGAR overexpression is a therapeutic target in esophageal squamous-cell carcinoma
Authors: Chu Jiahui , Niu Xiangjie , Chang Jiang , Shao Mingming , Peng Linna , Xi Yiyi , Lin Ai , Wang Chengcheng , Cui Qionghua , Luo Yingying , Fan Wenyi , Chen Yamei , Sun Yanxia , Guo Wenjia , Tan Wen , Lin Dongxin , Wu Chen
Published: October 2019

Whole-genome sequencing has identified many amplified genes in esophageal squamous-cell carcinoma (ESCC); however, their roles and the clinical relevance have yet elucidated. Here we show TP53-induced glycolysis and apoptosis regulator (TIGAR) is a major player in ESCC progression and chemoresistance. TIGAR reprograms glucose metabolism from glycolysis to the glutamine pathway through AMP-activated kinase, and its overexpression is correlated with poor disease outcomes. Tigar knockout mice have reduced ESCC growth and tumor burden. Treatment of TIGAR-overexpressed ESCC cell xenografts and patient-derived tumor xenografts in mice with combination of glutaminase inhibitor and chemotherapeutic agents achieves significant more efficacy than chemotherapy alone. These findings shed light on an important role of TIGAR in ESCC and provide evidence for targeted treatment of TIGAR-overexpressed ESCC.

Significance

Effective and target therapies are required for ESCC, one of the most common types of digestive OR cancer. Little has been known about the biology of ESCC progression or potential molecular targets OR for treatment. Whole-genome sequencing and RNA sequencing studies in ESCC have identified OR many recurrent copy number gain genes; however, the roles and druggable relevance of these OR genes remains poorly understood. Herein we demonstrate that TIGAR overexpression leads to OR metabolic remodeling, promoting ESCC progression and resistance to chemotherapeutic agents. OR Inhibiting the glutamine pathway significantly represses TIGAR-overexpressing ESCC growth and OR enhances tumor cell sensitization to cytotoxic agents. These findings might provide the rationale OR for clinical trials testing glutamine pathway inhibitors in combination with chemotherapy in OR TIGAR-expressing ESCC.
Genetic diversity and multiplicity of infection in Fasciola gigantica isolates of Pakistani livestock
Authors: Rehman Zia Ur , Zahid Osama , Rashid Imran , Ali Qasim , Akbar Muhammad Haroon , Oneeb Muhammad , Shehzad Wasim , Ashraf Kamran , Sargison Neil D. , Chaudhry Umer
Published: October 2019

Fasciola gigantica liver flukes are responsible for over 3 billion US dollars of production loss annually in farmed livestock and cause widespread zoonotic disease. Nevertheless, the understating of the emergence and spread of the trematode species is poor. The multiplicity of F. gigantica infection and its spread is potentially influenced by multiple factors, including the abundance of suitable intermediate hosts, climatic conditions favoring the completion of the parasite’s lifecycle, and translocation of infected animals or free-living parasite stages between regions. Here we describe the development of a ‘tremabiome’ metabarcoding sequencing method to explore the numbers of F. gigantica genotypes per infection and patterns of parasite spread, based on genetic characteristics of the mitochondrial NADH dehydrogenase 1 (mt-ND-1) locus. We collected F. gigantica from three abattoirs in the Punjab and Balochistan provinces of Pakistan, and our results show a high level of genetic diversity in 20 F. gigantica populations derived from small and large ruminants consigned to slaughter in both provinces. This implies that F. gigantica can reproduce in its definitive hosts through meiosis involving cross- and self-breeding, as described in the closely related species, Fasciola hepatica. The genetic diversity between the 20 populations derived from different locations also illustrates the impact of animal movements on gene flow. Our results demonstrate the predominance of single haplotypes, consistent with a single introduction of F. gigantica infection in 85% of the hosts from which the parasite populations were derived. This is consistent with clonal reproduction in the intermediate snail hosts.
Time-Space Fourier κώ Filter for Motion Artifacts Compensation during Transcranial Fluorescence Brain Imaging
Authors: Molodij Guillaume , Meglinski Igor , Sdobnov Anton , Kuznetsov Yuri , Harmelin Alon , Kalchenko Vyacheslav
Published: October 2019

Intravital imaging of brain vasculature through the intact craniumin vivois based on the evolution of the fluorescence intensity and provides an ability to characterize various physiological processes in the natural context of cellular resolution. The involuntary motions of the examined subjects often limitin vivonon-invasive functional optical imaging. Conventional imaging diagnostic modalities encounter serious difficulties in correction of artificial motions, associated with the rapid structural variations and fast high dynamics of the intensity values in the collected image sequences, when a common reference cannot be provided. In current report, we introduce an alternative solution that utilizes a Fourier Kappa-Omega filtering approach. We demonstrate that the proposed approach is effective for image stabilization of fast dynamic image sequences. The validation of the Fourier Kappa-Omega filtering was performed on the images obtaining during mouse transcranial brain imaging using fluorescent microscope as well as on the simulated sequences of images. The proposed technique can be used autonomously without supervision and assignation of a reference image.
Neurobiological successor features for spatial navigation
Authors: de Cothi William , Barry Caswell
Published: October 2019

The hippocampus has long been observed to encode a representation of an animal’s position in space. Recent evidence suggests that the nature of this representation is somewhat predictive and can be modelled by learning a successor representation (SR) between distinct positions in an environment. However, this discretisation of space is subjective making it difficult to formulate predictions about how some environmental manipulations should impact the hippocampal representation. Here we present a model of place and grid cell firing as a consequence of learning a SR from a basis set of known neurobiological features – boundary vector cells (BVCs). The model describes place cell firing as the successor features of the SR, with grid cells forming a low-dimensional representation of these successor features. We show that the place and grid cells generated using the BVC-SR model provide a good account of biological data for a variety of environmental manipulations, including dimensional stretches, barrier insertions, and the influence of environmental geometry on the hippocampal representation of space.
The effect of Rosovitine on mPSM explants: a real time analysis
Authors: Moya Lucas J. Morales , Bailey Charlotte S. L. , Dale J. Kim , Murray Philip J.
Published: October 2019

Previously we showed, using fixed tissue techniques, that treatment of chick embryos with a family of pharmacological inhibitors yields increased levels of NICD, an increased NICD half life and longer segments (Wiederman et al., 2015). Here we measure the effect of one of the pharmacological perturbations (Roscovtine) using a real time reporter of the somitogenesis clock. After processing the reporter signal using empirical mode decomposition, we measure the oscillator period in mPSM explants and find, in agreement with the previous study, that the period of the segmentation clock increases upon Roscovitine treatment. However, we also make the novel discovery that the differentiation rate of the mPSM tissue also increases upon Roscovitine treatment. Returning to the previous study, we find that the measured increases in somite size and oscillator period are only consistent with the clock and wavefront model if the wavefront velocity also increased.
β-cell dedifferentiation is associated with epithelial-mesenchymal transition triggered by miR-7-mediated repression of mSwi/Snf complex
Authors: Mak Tracy CS , von Ohlen Yorrick , Wang Yi Fang , Kane Eva , Jurgaityte Kaste , Ervilha Pedro , Chabosseau Pauline , Distaso Walter , Salem Victoria , Tomas Alejandra , Stoffel Markus , Marchetti Piero , Shapiro A.M. James , Rutter Guy A. , Latreille Mathieu
Published: October 2019

β-cell dedifferentiation has been revealed as a pathological mechanism underlying pancreatic dysfunction in diabetes. However, little is known on the genetic and epigenetic changes linked with the dedifferentiation of β-cells. We now report that β-cell dedifferentiation is associated with epithelial to mesenchymal transition (EMT) triggered by miR-7-mediated repression of Smarca4/Brg1 expression, a catalytic subunit of the mSwi/Snf chromatin remodeling complexes essential for β-cell transcription factors (β-TFs) activity. miR-7-mediated repression of Brg1 expression in diabetes causes an overall compaction of chromatin structure preventing β-TFs from accessing and transactivating genes maintaining the functional and epithelial identity of β-cells. Concomitantly, loss of β-cell identity impairs the ability of β-TFs Pdx1, Nkx6-1, Neurod1 to repress non-β-cell genes enriched selectively in mesenchymal cells leading to EMT, change in islet microenvironment, and fibrosis. Remarkably, anti-EMT agents normalized glucose tolerance of diabetic mice, thus revealing mesenchymal reprogramming of β-cells as a novel therapeutic target in diabetes. This study sheds light on the genetic signature of dedifferentiated β-cells and highlights how loss of mSwi/Snf activity in diabetes initiating a step-wise remodeling of epigenetic landscapes of β-cells leading to the induction of an EMT process reminiscent of a response to tissue injury.
Both Determinants of Allosteric and Active Sites Responsible for Catalytic Activity of Delta 12 Fatty Acid Desaturase by Domain Swapping
Authors: Shi Haisu , Tian Jinlong , Wu Chen , Li Mo , An Feiyu , Wu Rina , Shao Junhua , Zheng Yan , Luo Xue , Tao Dongbing , Chen Xu , Pi Yuzhen , Zhao Chunyan , Yue Xiqing , Wu Junrui
Published: October 2019

Cheese lacks essential fatty acids (EFAs). Delta 12 fatty acid desaturase (FADS12) is a critical enzyme required for EFA biosynthesis in fermentation of the predominant strains of cheese. Previously, we identified theFADS12gene and characterized its function for the first time inGeotrichum candidum, a dominant strain used to manufacture soft cheese with white rind. In this study, we analyzed the molecular mechanism ofFADS12function by swapping domains fromMortierella alpinaandG. candidumthat had, respectively, high and low oleic acid conversion rates. The results revealed three regions that are essential to this process, including regions from the end of the second transmembrane domain to the beginning of the third transmembrane domain, from the end of the third transmembrane domain to the beginning of the fourth transmembrane domain, and from the 30-amino acid from the end of the sixth transmembrane domain to the C-terminal end region. Based on our domain swapping analyses, nine pairs of amino acids including H112, S118, H156, Q161, K301, R306, E307, A309 and S323 in MaFADS12 (K123, A129, N167, M172, T302, D307, I308, E310 and D324 in GcFADS12) were identified as having a significantly effect onFADS12catalytic efficiency, and linoleic acid and its analogues (12,13-cyclopropenoid fatty acid) were found to inhibit the catalytic activity ofFADS12and related recombinant enzymes. Furthermore, the molecular mechanism ofFADS12inhibition was analyzed. The results revealed two allosteric domains, including one domain from the N-terminal region to the beginning of the first transmembrane domain and another from the 31stamino acid from the end of the sixth transmembrane domain to the C terminus. Y4 and F398 amino acid residues fromMaFADS12and eight pairs of amino acids including G56, L60, L344, G10, Q13, S24, K326 and L344 in MaFADS12 (while Y66, F70, F345, F20, Y23, Y34, F327 and F345 in GcFADS12) played a pivotal role inFADS12inhibition. Finally, we found that both allosteric and active sites were responsible for the catalytic activity ofFADS12at various temperatures, pH, and times. This study offers a solid theoretical basis to develop preconditioning methods to increase the rate at whichGcFADS12converts oleic and linoleic acids to produce higher levels of EFAs in cheese.
Paracrine control of α-cell glucagon exocytosis is compromised in human type-2 diabetes
Authors: Omar-Hmeadi Muhmmad , Lund Per-Eric , Gandasi Nikhil R , Tengholm Anders , Barg Sebastian
Published: October 2019

Glucagon is secreted from pancreatic α-cells to activate gluconeogenesis and other pathways that raise blood glucose during hypoglycemia. Glucose-dependent regulation of glucagon secretion involves both α-cell-intrinsic mechanisms and paracrine control through insulin and somatostatin. In type-2 diabetes (T2D) inadequately high glucagon levels contribute to hyperglycemia. To understand these disease-associated changes at the cellular level, and to isolate intrinsic and paracrine effects, we analyzed glucagon granule exocytosis and membrane excitability in isolated α-cells from 56 non-diabetic (ND) and 15 T2D human donors. High resolution imaging showed that glucagon granule exocytosis had a U-shaped sensitivity to glucose, with the slowest rate around 7 mM glucose, and accelerated rates at <5 and >10 mM glucose. Exocytosis was reduced in T2D α-cells, but their glucose sensitivity remained intact and there were no changes in voltage-dependent ion currents or granule trafficking. Instead, α-cells from T2D donors were markedly insensitive to somatostatin and insulin, which rapidly inhibited exocytosis and electrical activity in ND cells. Thus, intrinsic mechanisms do not inhibit glucagon secretion at hyperglycemia, and elevated glucagon levels in human T2D reflect an insensitivity of α-cells to paracrine inhibition.
Single-molecule imaging reveals control of parental histone recycling by free histones during DNA replication
Authors: Gruszka Dominika T. , Xie Sherry , Kimura Hiroshi , Yardimci Hasan
Published: October 2019

Faithful replication of chromatin domains during cell division is fundamental to eukaryotic development. During replication, nucleosomes are disrupted ahead of the replication fork, followed by their rapid reassembly on daughter strands from the pool of recycled parental and newly synthesized histones. Here, we use single-molecule imaging and replication assays in Xenopus laevis egg extracts to determine the outcome of replication fork encounters with nucleosomes. Contrary to current models, the majority of parental histones are evicted from the DNA, with histone recycling, nucleosome sliding and replication fork stalling also occurring but at lower frequencies. The anticipated local histone transfer only becomes dominant upon depletion of free histones from extracts. Our studies provide the first direct evidence that parental histones remain in close proximity to their original locus during recycling and reveal that provision of excess histones results in impaired histone recycling, which has the potential to affect epigenetic memory.
Novel repellents for the blood-sucking insectsRhodnius prolixusandTriatoma infestans, vectors of Chagas disease
Authors: Ramírez Melanie , Ortiz Mario I. , Guerenstein Pablo , Molina Jorge
Published: October 2019

Background

Studying the behavioral response of blood-sucking, disease-vector insects to potentially repellent volatile compounds could shed light on the development of new control strategies. Volatiles released by human facial skin microbiota play different roles in the host-seeking behavior of triatomines. We assessed the repellency effect of such compounds of bacterial origin onTriatoma infestansandRhodnius prolixus, two important vectors of Chagas disease in Latin America.

Methods

Using an exposure device, insects were presented to human odor alone (negative control) and in the presence of three individual tested compounds (2-mercaptoethanol, dimethyl sulfide and 2-phenylethanol, which was only tested inR. prolixus) and the gold-standard repellent NN-diethyl-3-methylbenzamide–DEET (positive control). We quantified the time the insects spent in the proximity of the host and performed nonparametric statistical tests to determine if any of the compounds evaluated affected the behavior of the insect.

Results

We found volatiles that significantly reduced the time spent in the proximity of the host. These were 2-phenylethanol and 2-mercaptoethanol forR. prolixus, and dimethyl sulfide and 2-mercaptoethanol forT. infestans. Such an effect was also observed in both species when DEET was presented, although only at the higher doses tested.

Conclusions

The new repellents modulated the behavior of two Chagas disease vectors belonging to two different triatomine tribes, and this was achieved using a dose up to three orders of magnitude lower than that needed to evoke the same effect with DEET. Future efforts in understanding deeply the mechanism of action of repellent compounds such as 2-mercaptoethanol, as well as an assessment of their temporal and spatial repellent properties, could lead to the development of novel control strategies for insect vectors refractory to DEET.
Allium roseum L. extract inhibits amyloid beta aggregation and toxicity involved in Alzheimer’s disease
Authors: Boubakri Abdelbasset , Leri Manuela , Bucciantini Monica , Najjaa Hanen , Ben Arfa Abdelkarim , Stefani Massimo , Neffati Mohamed
Published: October 2019

Allium roseum is an important medicinal and aromatic plant, specific to the North African flora and a rich source of important nutrients and bioactive molecules including flavonoids and organosulfur compounds whose biological activities and pharmacological properties are well known. In the present study, the inhibition of amyloid beta protein toxicity by the ethanolic extract of this plant is investigated for the first time. Preliminary biochemical analyses identified kæmpferol and Luteolin-7-o-glucoside as the more abundant phenolic compounds. The effects of A. roseum extract (ARE) on amyloid beta-42 (Aβ42) aggregation and aggregate cytotoxicity, were investigated by biophysical (ThT assay, Dynamic light scattering and transmission electron microscopy) and cellular assays (cytotoxicity, aggregate immunolocalization, ROS measurement and intracellular Ca2+ imaging). The biophysical data suggest that ARE affects the structure of Aβ42 peptide, inhibits its polymerization, and interferes with the path of fibrillogenesis. The data with cultured cells shows that ARE reduces Aß42 aggregate toxicity by inhibiting aggregate binding to the cell membrane and by decreasing both oxidative stress and intracellular Ca2+. Accordingly, ARE could act as a neuroprotective factor against Aβ aggregate toxicity in Alzheimer’s disease.
Feasibility of real-time in vivo89Zr-DFO-labeled CAR T-cell trafficking using PET imaging
Authors: Lee Suk Hyun , Soh Hyunsu , Chung Jin Hwa , Cho Eun Hyae , Lee Sang Joo , Ju Ji-Min , Shin Joong Hyuk , Kim Hyori , Oh Seung Jun , Lee Sang-Jin , Chung Junho , Kim Seog-Young , Ryu Jin-Sook
Published: October 2019

Introduction

Chimeric antigen receptor (CAR) T-cells have been developed recently, producing impressive outcomes in patients with hematologic malignancies. However, there is no standardized method for cell trafficking and in vivo CAR T-cell monitoring. We assessed the feasibility of real-time in vivo89Zr-p-Isothiocyanatobenzyl-desferrioxamine (Df-Bz-NCS, DFO) labeled CAR T-cell trafficking using positron emission tomography (PET).

Results

The 89Zr-DFO radiolabeling efficiency of Jurkat/CAR and human peripheral blood mononuclear cells (hPBMC)/CAR T-cells was 70–79%, and cell radiolabeling activity was 98.1–103.6 kBq/106 cells. Cell viability after radiolabeling was >95%. Compared with unlabeled cells, cell proliferation was not significantly different during the early period after injection; however, the proliferative capacity decreased over time (p = 0.02, day 7 after labeling). IL-2 or IFN-γ secretion was not significantly different between unlabeled and labeled CAR T-cells. PET/magnetic resonance images in the xenograft model showed that most of the 89Zr-DFO-labeled Jurkat/CAR T-cells were distributed in the lung (24.4% ± 3.4%ID) and liver (22.9% ± 5.6%ID) by 1 hour after injection. The cells gradually migrated from lung to the liver and spleen by day 1, and remained stably until day 7 (on day 7: lung 3.9% ± 0.3%ID, liver 36.4% ± 2.7%ID, spleen 1.4% ± 0.3%ID). No significant accumulation of labeled cells was identified in tumors. A similar pattern was observed in ex vivo biodistributions on day 7 (lung 3.0% ± 1.0%ID, liver 19.8% ± 2.2%ID, spleen 2.3% ± 1.7%ID). 89Zr-DFO-labeled hPBMC/CAR T-cells showed the similar distribution on serial PET images as Jurkat/CAR T-cells. The distribution of CAR T-cells was cross-confirmed by flow cytometry, Alu polymerase chain reaction, and immunohistochemistry.

Conclusion

Using PET imaging of 89Zr-DFO-labeled CAR T-cells, real time in vivo cell trafficking is feasible. It can be used to investigate cellular kinetics, initial in vivo biodistribution, and the safety profile in future CAR T-cell development.