bluuebunny/crossref_metadata_2025 huggingface dataset:
The SensorOverlord predicts the accuracy of measurements with ratiometric biosensors
Authors: Stanley Julian A. , Johnsen Sean B. , Apfeld Javier
Published: February 2020

Two-state ratiometric biosensors change conformation and spectral properties in response to specific biochemical inputs. Much effort over the past two decades has been devoted to engineering biosensors specific for ions, nucleotides, amino acids, and biochemical potentials. The utility of these biosensors is diminished by empirical errors in fluorescence-ratio signal measurement, which reduce the range of input values biosensors can measure accurately. Here, we present a formal framework and a web-based tool, the SensorOverlord, that predicts the input range of two-state ratiometric biosensors given the experimental error in measuring their signal. We demonstrate the utility of this tool by predicting the range of values that can be measured accurately by biosensors that detect pH, NAD+, NADH, NADPH, histidine, and glutathione redox potential. The SensorOverlord enables users to compare the predicted accuracy of biochemical measurements made with different biosensors, and subsequently select biosensors that are best suited for their experimental needs.
Latrophilins are essential for endothelial junctional fluid shear stress mechanotransduction
Authors: Tanaka Keiichiro , Prendergast Andrew , Hintzen Jared , Kumar Abhishek , Chung Minhwan , Koleske Anthony , Crawford Jason , Nicoli Stefania , Schwartz Martin A.
Published: February 2020

Endothelial cell (EC) responses to fluid shear stress (FSS) are crucial for vascular development, adult physiology and disease. PECAM1 is an important transducer but earlier events remain poorly understood. We therefore investigated heterotrimeric G proteins in FSS sensing. Knockdown (KD) in ECs of single Gα proteins had little effect but combined depletion of Gαi and Gαq/11 blocked all known PECAM1-dependent responses. Re-expression of Gαi2 and Gαq but not Gαi1 and Gαi3 rescued these effects. Sequence alignment and mutational studies identified that K307 in Gαi2 and Gq/11 (Q306 in Gαi1/3), determines participation in flow signaling. We developed pull-down assays for measuring Gα activation and found that this residue, localized to the GPCR interface, determines activation by FSS. We developed a protocol for affinity purification of GPCRs on activated Gα’s, which identified latrophilins (ADGRLs) as specific upstream interactors for Gαi2 and Gq/11. Depletion of latrophilin-2 blocked EC activation of Gαi2 and Gαq, downstream eventsin vitro, and flow-dependent vascular morphogenesis in zebrafish embryos. Surprisingly, latrophilin-2 depletion also blocked flow activation of two additional pathways activated at cell-cell junctions, Smad1/5 and Notch1, independently of Gα proteins. Latrophilins are thus central mediators of junctional shear stress mechanotransduction via Gα protein-dependent and -independent mechanisms.
Tensile Force Induced Cytoskeletal Reorganization: Mechanics Before Chemistry
Authors: Li Xiaona , Ni Qin , He Xiuxiu , Kong Jun , Lim Soon-Mi , Papoian Garegin A. , Trzeciakowski Jerome P. , Trache Andreea , Jiang Yi
Published: February 2020

Understanding cellular remodeling in response to mechanical stimuli is a critical step in elucidating mechano-activation of biochemical signaling pathways. Experimental evidence indicates that external stress-induced subcellular adaptation is accomplished through dynamic cytoskeletal reorganization. To study the interactions between subcellular structures involved in transducing mechanical signals, we combined experimental and computational simulations to evaluate real-time mechanical adaptation of the actin cytoskeletal network. Actin cytoskeleton was imaged at the same time as an external tensile force was applied to live vascular smooth muscle cells using a fibronectin-functionalized atomic force microscope probe. In addition, we performed computational simulations of active cytoskeletal networks under a tensile external force. The experimental data and simulation results suggest that mechanical structural adaptation occurs before chemical adaptation during filament bundle formation: actin filaments first align in the direction of the external force, initializing anisotropic filament orientations, then the chemical evolution of the network follows the anisotropic structures to further develop the bundle-like geometry. This finding presents an alternative, novel explanation for the stress fiber formation and provides new insight into the mechanism of mechanotransduction.

Author Summary

Remodeling the cytoskeletal network in response to external force is key to mechanosensing and locomotion. Despite much focus on cytoskeletal remodeling in recent years, a comprehensive understanding of actin remodeling in real-time in cells under mechanical stimuli is still lacking. We integrated stress-induced 3D actin imaging and 3D computational simulations of actin cytoskeleton to study how the actin cytoskeleton form bundles and how these bundles evolve over time upon external tensile stress. We found a rapid actin alignment and a slower bundle evolution leading to denser bundles. Based on these results, we propose a “mechanics before chemistry” model of actin cytoskeleton remodeling under external force.
Gα/GSA-1 works upstream of PKA/KIN-1 to regulate calcium signaling and contractility in theCaenorhabditis elegansspermatheca
Authors: Castaneda Perla G. , Cecchetelli Alyssa D. , Pettit Hannah N. , Cram Erin J.
Published: February 2020

Correct regulation of cell contractility is critical for the function of many biological systems. The reproductive system of the hermaphroditic nematodeC. eleganscontains a contractile tube of myoepithelial cells known as the spermatheca, which stores sperm and is the site of oocyte fertilization. Regulated contraction of the spermatheca pushes the embryo into the uterus. Cell contractility in the spermatheca is dependent on actin and myosin and is regulated, in part, by Ca2+signaling through the phospholipase PLC-1, which mediates Ca2+release from the endoplasmic reticulum. Here, we describe a novel role for GSA-1/Gαs, and protein kinase A, composed of the catalytic subunit KIN-1/PKA-C and the regulatory subunit KIN-2/PKA-R, in the regulation of Ca2+release and contractility in theC. elegansspermatheca. Without GSA-1/Gαsor KIN-1/PKA-C, Ca2+is not released, and oocytes become trapped in the spermatheca. Conversely, when PKA is activated through either a gain of function allele in GSA-1 (GSA-1(GF)) or by depletion of KIN-2/PKA-R, Ca2+is increased, and waves of Ca2+travel across the spermatheca even in the absence of oocyte entry. In the spermathecal-uterine valve, loss of GSA-1/Gαsor KIN-1/PKA-C results in sustained, high levels of Ca2+and a loss of coordination between the spermathecal bag and sp-ut valve. Additionally, we show that depleting phosphodiesterase PDE-6 levels alters contractility and Ca2+dynamics in the spermatheca, and that the GPB-1 and GPB-2 Gβsubunits play a central role in regulating spermathecal contractility and Ca2+signaling. This work identifies a signaling network in which Ca2+and cAMP pathways work together to coordinate spermathecal contractility.

Author Summary

Organisms are full of biological tubes that transport substances such as food, liquids, and air through the body. Moving these substances in a coordinated manner, with the correct directionality, timing, and rate is critical for organism health. In this study we usedCaenorhabditis elegans, a small transparent worm, to study how cells in biological tubes coordinate how and when they squeeze and relax. TheC. elegansspermatheca is part of the reproductive system, which uses calcium signaling to drive the coordinated contractions that push fertilized eggs out into the uterus. Using genetic analysis and a calcium-sensitive fluorescent protein, we show that the G-protein GSA-1 functions with protein kinase A to regulate calcium release, and contraction of the spermatheca. These findings establish a link between G-protein and cAMP signaling that may apply to similar signaling pathways in other systems.
Prevalence of Staphylococcal Superantigens and their association among bacteremic and Infective Endocarditis patients in Egypt
Authors: Elsherif Heba M. , Helal Zeinab H. , El-Ansary Mona R. , Fahmy Zeinab A. , Eltayeb Wafaa N. , Radwan Sahar , Aboshanab Khaled M.
Published: February 2020

Aim

Infective endocarditis (IE) is a major complication ofStaphylococcus (S.) aureusinfection in humans particularly those with bacteremia. AlthoughStaphylococcusspecies are commensal on or in different parts of the human body, it is also known to be a serious pathogen causing bacteremia and sepsis that could lead to IE. Therefore, our aim was to assess the prevalence as well as phenotypic and genotypic association of the Staphylococcal superantigens (SAgs) among bacteremic and IE patients.

Methods

This study was conducted onStaphylococcusisolates recovered from bacteremic and IE patients. The isolates were screened phenotypically for the detection of SAgs including Staphylococcal enterotoxins (SEs) and toxic shock syndrome toxin-1 (TSST-1). Molecular detection and analysis ofsea, seb, sec, sed, seeand tsst-1, the major SAgs coding genes were performed using PCR and agarose gel electrophoresis, respectively. The obtained findings were statistically analyzed using standard methods.

Results

Detection of SAgs using ELISA revealed that 12 (46%) isolates were positive for enterotoxin production. However, the PCR revealed that 19 (73%) isolates were positive for enterotoxin genes with the highest prevalence of theseagene (79%), followed by theseb(63%), tsst-1 (21%). The least frequent gene was thesed(5.3%). Accordingly, phenotypic and genotypic screening for prevalence of SAgs among Staphylococcal isolates showed significant difference(P value=0.046703), however, no significant correlation could be observed among the coagulase negative Staphylococci (CoNS) isolates (Pvalue=0.248213). Statistical correlations between bacteremic and IE isolates with respect to prevalence of SAgs, showed no significant difference (P-value = 0.139, Effect size = 0.572) indicating no specific association between any of the detected SAgs and IE.

Conclusion

no significant difference has been found between Staphylococcal IE and bacteremia isolates regarding both phenotypic and genotypic detection of the most commonly SAgs. Therefore, all Staphylococcal bacteremic patients are suspected for IE. Also, future work should be conducted for analysis of SAgs gene expression.
Twist, Snail, and Sox9 form an allosterically regulated complex, the EMTosome, on a bipartite E-box site
Authors: McCracken Daniel S , Peng Hongzhuang , Ayyanathan Kasirajan , Jiang Yike Lindy , Welsh Sarah , Yang Jing , Kennedy Eileen , Rauscher Frank J. , Gardini Alessandro , Rauscher Frank J
Published: February 2020

Epithelial-Mesenchymal transition (EMT) of primary tumor cells is a critical trans-differentiation event that contributes to dissemination and metastasis. The process of EMT is controlled by specific DNA-binding transcription factors (TFs) that reprogram the tumor transcriptome. In particular, the canonical EMT-TFs Twist and Snail can induce an EMT program when overexpressed in cancer cells, and both are found upregulated in metastatic cancers. Twist and Snail bind DNA directly, by recognition to variants of the E-Box sequence CANNTG. However, it is unclear how this binding is regulated. We have used a biochemical approach to dissect DNA binding and protein-protein interactions that occur amongst these proteins. We find that Twist preferentially recognizes a dyad repeat of E-boxes that are not directly bound by Snail. Our data suggest that Twist use its WR domain to recruit Snail into a binding complex through the Snail zinc-finger motifs. We analyzed Twist-Snail complexes in the breast carcinoma cell line SUM1315 and found evidence that it contains an additional protein partner, Sox9. Notably, we report that a native Twist complex can be displaced from its dyad binding site by consensus DNA binding sites for Snail and Sox9 even though these proteins do not contact the Twist dyad site. Taken together, our findings suggest that Snail and Sox9 interact with Twist to regulate its DNA binding ability via protein-protein interactions, thereby allosterically regulating Twist DNA binding. We designate this ternary complex EMTosome. These results may inform efforts to therapeutically target the EMT program in order to target cancer metastasis.
A genome engineering resource to uncover principles of cellular organization and tissue architecture by lipid signalling
Authors: Trivedi Deepti , CM Vinitha , Bisht Karishma , Janardan Vishnu , Pandit Awadhesh , Basak Bishal , Raghu Padinjat
Published: February 2020

Phosphoinositides (PI) are key regulators of cellular organization in eukaryotes and genes that tune PI signalling are implicated in human disease mechanisms. Biochemical analyses and studies in cultured cells have identified a large number of proteins that can mediate PI signalling. However, the role of such proteins in regulating cellular processesin vivoand development in metazoans remains to be understood. Here we describe a set of CRISPR based genome engineering tools that allow the manipulation of each of these proteins with spatial and temporal control during metazoan development. We demonstrate the use of these reagents to deplete a set of 103 proteins individually in theDrosophilaeye and identify several new molecules that control eye development. Our work demonstrates the power of this resource in uncovering the molecular basis of tissue homeostasis during normal development and in human disease biology.
Sharp tuning of head direction by somatosensory fast-spiking interneurons
Authors: Long Xiaoyang , Young Calvin K. , Zhang Sheng-Jia
Published: February 2020

Head direction (HD) information is intricately linked to spatial navigation and cognition. We recently reported the co-existence of all currently recognized spatial cell types can be found in the hindlimb primary somatosensory cortex (S1HL). In this study, we carried out an in-depth characterization of HD cells in S1HL. We show fast-spiking (FS), putative inhibitory neurons are over-represented in and sharply tuned to HD compared to regular-spiking (RS), putative excitatory neurons. These FS HD cells are non-conjunctive, rarely theta modulated, not locally connected and are enriched in layer 4/5a. Their co-existence with RS HD cells and angular head velocity (AHV) cells in a layer-specific fashion through the S1HL presents a previously unreported organization of spatial circuits. These findings challenge the notion that FS, putative inhibitory interneurons are weakly tuned to external stimuli in general and present a novel local network configuration not reported in other parts of the brain.
A Bayesian Generative Model of Vestibular Afferent Neuron Spiking
Authors: Paulin Michael , Pullar Kiri , Hoffman Larry
Published: February 2020

Using an information criterion to evaluate models fitted to spike train data from chinchilla semicircular canal afferent neurons, we found that the superficially complex functional organization of the canal nerve branch can be accurately quantified in an elegant mathematical model with only three free parameters. Spontaneous spike trains are samples from stationary renewal processes whose interval distributions are Exwald distributions, convolutions of Inverse Gaussian and Exponential distributions. We show that a neuronal membrane compartment is a natural computer for calculating parameter likelihoods given samples from a point process with such a distribution, which may facilitate fast, accurate, efficient Bayesian neural computation for estimating the kinematic state of the head. The model suggests that Bayesian neural computation is an aspect of a more general principle that has driven the evolution of nervous system design, the energy efficiency of biological information processing.

Significance Statement

Nervous systems ought to have evolved to be Bayesian, because Bayesian inference allows statistically optimal evidence-based decisions and actions. A variety of circumstantial evidence suggests that animal nervous systems are indeed capable of Bayesian inference, but it is unclear how they could do this. We have identified a simple, accurate generative model of vestibular semicircular canal afferent neuron spike trains. If the brain is a Bayesian observer and a Bayes-optimal decision maker, then the initial stage of processing vestibular information must be to compute the posterior density of head kinematic state given sense data of this form. The model suggests how neurons could do this. Head kinematic state estimation given point-process inertial data is a well-defined dynamical inference problem whose solution formed a foundation for vertebrate brain evolution. The new model provides a foundation for developing realistic, testable spiking neuron models of dynamical state estimation in the vestibulo-cerebellum, and other parts of the Bayesian brain.
Forecasting the Wuhan coronavirus (2019-nCoV) epidemics using a simple (simplistic) model
Authors: Hermanowicz Slav W.
Published: February 2020

Abstract and Findings

Confirmed infection cases in mainland China were analyzed using the data up to January 28, 2020 (first13 daysof reliable confirmed cases). In addition, all available data up to February 3 were processed the same way. For the first period the cumulative number of cases followed an exponential function. However, from January 28, we discerned a downward deviation from the exponential growth. This slower-than-exponential growth was also confirmed by a steady decline of the effective reproduction number. A backtrend analysis suggested the original basic reproduction numberR0to be about 2.4 – 2.5. We used a simple logistic growth model that fitted very well withalldatareported until the time of writing. Using this model and the first set of data, we estimate thatthe maximum caseswill be about 21,000 reaching this level in mid-February. Using all available data the maximum number of cases is somewhat higher at 29,000 but its dynamics does not change. These predictions do not account for any possible other secondary sources of infection.
Assessing spread risk of Wuhan novel coronavirus within and beyond China, January-April 2020: a travel network-based modelling study
Authors: Lai Shengjie , Bogoch Isaac I. , Ruktanonchai Nick W , Watts Alexander , Lu Xin , Yang Weizhong , Yu Hongjie , Khan Kamran , Tatem Andrew J
Published: February 2020

Background

A novel coronavirus (2019-nCoV) emerged in Wuhan City, China, at the end of 2019 and has caused an outbreak of human-to-human transmission with a Public Health Emergency of International Concern declared by the World Health Organization on January 30, 2020.

Aim

We aimed to estimate the potential risk and geographic range of Wuhan novel coronavirus (2019-nCoV) spread within and beyond China from January through to April, 2020.

Methods

A series of domestic and international travel network-based connectivity and risk analyses were performed, by using de-identified and aggregated mobile phone data, air passenger itinerary data, and case reports.

Results

The cordon sanitaire of Wuhan is likely to have occurred during the latter stages of peak population numbers leaving the city before Lunar New Year (LNY), with travellers departing into neighbouring cities and other megacities in China. We estimated that 59,912 air passengers, of which 834 (95% UI: 478 - 1349) had 2019-nCoV infection, travelled from Wuhan to 382 cities outside of mainland China during the two weeks prior to Wuhan’s lockdown. The majority of these cities were in Asia, but major hubs in Europe, the US and Australia were also prominent, with strong correlation seen between predicted importation risks and reported cases. Because significant spread has already occurred, a large number of airline travellers (3.3 million under the scenario of 75% travel reduction from normal volumes) may be required to be screened at origin high-risk cities in China and destinations across the globe for the following three months of February to April, 2020 to effectively limit spread beyond its current extent.

Conclusion

Further spread of 2019-nCoV within China and international exportation is likely to occur. All countries, especially vulnerable regions, should be prepared for efforts to contain the 2019-nCoV infection.
A novel mutation inKCNK16causing a gain-of-function in the TALK-1 potassium channel: a new cause of maturity onset diabetes of the young
Authors: Graff Sarah M , Johnson Stephanie R , Leo Paul J , Dadi Prasanna K , Nakhe Arya Y , McInerney-Leo Aideen M , Marshall Mhairi , Brown Matthew A , Jacobson David A , Duncan Emma L
Published: February 2020

Background

Maturity-onset diabetes of the young (MODY) is a heterogeneous group of monogenic disorders of impaired glucose-stimulated insulin secretion (GSIS). Mechanisms include β-cell KATPchannel dysfunction (e.g.,KCNJ11(MODY13) orABCC8(MODY12) mutations); however, no other β-cell channelopathies have been identified in MODY.

Methods

A four-generation family with autosomal dominant non-obese, non-ketotic antibody-negative diabetes, without mutations in known MODY genes, underwent exome sequencing. Whole-cell and single-channel K+currents, Ca2+handling, and GSIS were determined in cells expressing either mutated or wild-type (WT) protein.

Results

We identified a novel non-synonymous genetic mutation inKCNK16(NM_001135105: c.341T>C, p.Leu114Pro) segregating with MODY.KCNK16is the most abundant and β-cell-restricted K+channel transcript and encodes the two-pore-domain K+channel TALK-1. Whole-cell K+currents in transfected HEK293 cells demonstrated drastic (312-fold increase) gain-of-function with TALK-1 Leu144Pro vs. WT, due to greater single channel activity. Glucose-stimulated cytosolic Ca2+influx was inhibited in mouse islets expressing TALK-1 Leu114Pro (area under the curve [AUC] at 20mM glucose: Leu114Pro 60.1 vs. WT 89.1;P=0.030) and less endoplasmic reticulum calcium storage (cyclopiazonic acid-induced release AUC: Leu114Pro 17.5 vs. WT 46.8;P=0.008). TALK-1 Leu114Pro significantly blunted GSIS compared to TALK-1 WT in both mouse (52% decrease,P=0.039) and human (38% decrease,P=0.019) islets.

Conclusions

Our data identify a novel MODY-associated gene,KCNK16; with a gain-of-function mutation limiting Ca2+influx and GSIS. A gain-of-function common polymorphism inKCNK16is associated with type 2 diabetes (T2DM); thus, our findings have therapeutic implications not only forKCNK16-associated MODY but also for T2DM.
Scalable Classification of Organisms into a Taxonomy Using Hierarchical Supervised Learners
Authors: Sohsah Gihad N. , Ibrahimzada Ali Reza , Ayaz Huzeyfe , Cakmak Ali
Published: February 2020

Taxonomy of living organisms gains major importance in making the study of vastly heterogeneous living things easier. In addition, various fields of applied biology (e.g., agriculture) depend on classification of living creatures. Specific fragments of the DNA sequence of a living organism have been defined as DNA barcodes and can be used as markers to identify species efficiently and effectively. The existing DNA barcode-based classification approaches suffer from three major issues: (i) most of them assume that the classification is done within a given taxonomic class and/or input sequences are prealigned, (ii) highly performing classifiers, such as SVM, cannot scale to large taxonomies due to high memory requirements, (iii) mutations and noise in input DNA sequences greatly reduce the taxonomic classification accuracy. In order to address these issues, we propose a multi-level hierarchical classifier framework to automatically assign taxonomy labels to DNA sequences. We utilize an alignment-free approach called spectrum kernel method for feature extraction. We build a proof-of-concept hierarchical classifier with two levels, and evaluated it on real DNA sequence data from BOLD systems. We demonstrate that the proposed framework provides higher accuracy than regular classifiers. Besides, hierarchical framework scales better to large datasets enabling researchers to employ classifiers with high accuracy and high memory requirement on large datasets. Furthermore, we show that the proposed framework is more robust to mutations and noise in sequence data than the non-hierarchical classifiers.
Methylome-based cell-of-origin modeling (Methyl-COOM) identifies aberrant expression of immune regulatory molecules in CLL
Authors: Wierzbinska Justyna A. , Toth Reka , Ishaque Naveed , Rippe Karsten , Mallm Jan-Philipp , Klett Lara , Mertens Daniel , Zenz Thorsten , Hielscher Thomas , Seifert Marc , Küppers Ralf , Assenov Yassen , Lutsik Pavlo , Stilgenbauer Stephan , Roessner Philipp M. , Seiffert Martina , Byrd John , Oakes Christopher C. , Plass Christoph , Lipka Daniel B.
Published: February 2020

Background

In cancer, normal epigenetic patterns are disturbed and contribute to gene expression changes, disease onset and progression. The cancer epigenome is composed of the epigenetic patterns present in the tumor-initiating cell at the time of transformation, and the tumor-specific epigenetic alterations that are acquired during tumor initiation and progression. The precise dissection of these two components of the tumor epigenome will facilitate a better understanding of the biological mechanisms underlying malignant transformation. Chronic lymphocytic leukemia (CLL) originates from differentiating B cells, which undergo extensive epigenetic programming. This poses the challenge to precisely determine the epigenomic ground-state of the cell-of-origin in order to identify CLL-specific epigenetic aberrations.

Methods

We developed a linear regression model, methylome-based cell-of-origin modeling (Methyl-COOM), to map the cell-of-origin for individual CLL patients based on the continuum of epigenomic changes during normal B cell differentiation.

Results

Methyl-COOM accurately maps the cell-of-origin of CLL and identifies CLL-specific aberrant DNA methylation events that are not confounded by physiologic epigenetic B cell programming. Furthermore, Methyl-COOM unmasks abnormal action of transcription factors, altered super-enhancer activities, and aberrant transcript expression in CLL. Among the aberrantly regulated transcripts were many genes that have previously been implicated in T cell biology. Flow cytometry analysis of these markers confirmed their aberrant expression on malignant B cells at the protein level.

Conclusions

Methyl-COOM analysis of CLL identified disease-specific aberrant gene regulation. The aberrantly expressed genes identified in this study might play a role in immune-evasion in CLL and might serve as novel targets for immunotherapy approaches. In summary, we propose a novel framework forin silicomodeling of reference DNA methylomes and for the identification of cancer-specific epigenetic changes, a concept that can be broadly applied to other human malignancies.
Florigen family chromatin recruitment, competition and target genes
Authors: Zhu Yang , Klasfeld Samantha , Jeong Cheol Woong , Jin Run , Goto Koji , Yamaguchi Nobutoshi , Wagner Doris
Published: February 2020

Plants monitor seasonal cues, such as day-length, to optimize life history traits including onset of reproduction and inflorescence architecture1–3. Florigen family transcriptional co-regulators TERMINAL FLOWER 1 (TFL1) and FLOWERING LOCUS T (FT) antagonistically regulate these vital processes4–6yet how TFL1 and FT execute their roles and what the mechanism is for their antagonism remains poorly understood. We show genome-wide, that TFL1 is recruited to the chromatin by the bZIP transcription factor FLOWERING LOCUS D (FD) inArabidopsis. We find that seasonal cue-mediated upregulation of FT competes TFL1 from chromatin-bound FD at key target loci. We identify the master regulator of floral fate,LEAFY(LFY) as a target under dual opposite regulation by TFL1 and FT. Exonic bZIP motifs inLFYare critical for repression by TFL1, upregulation by FT and adoption of floral fate. Transcriptomic identification of target genes directly repressed by the TFL1-FD complex not only identifies key regulators of onset of reproduction and floral fate, but reveals that TFL1-FD repress sugar and hormone signalling pathways and chromatin regulators. Our data provide mechanistic insight into how florigen family member sculpt inflorescence architecture, a trait important for reproductive success and yield.
shanimutation in mouse affects splicing of Spata22 and leads to impaired meiotic recombination
Authors: Petrillo Cynthia , Barroca Vilma , Ribeiro Jonathan , Lailler Nathalie , Livera Gabriel , Keeney Scott , Martini Emmanuelle , Jain Devanshi
Published: February 2020

Recombination is crucial for chromosome pairing and segregation during meiosis. SPATA22, along with its direct binding partner and functional collaborator, MEIOB, is essential for the proper repair of double-strand breaks (DSBs) during meiotic recombination. Here we describe a novel point-mutated allele (shani) of mouseSpata22that we isolated in a forward genetic screen.shanimutant mice phenocopySpata22-null andMeiob-null mice: mutant cells appear to form DSBs and initiate meiotic recombination, but are unable to complete DSB repair, leading to meiotic prophase arrest, apoptosis and sterility.shanimutants show precocious loss of DMC1 foci and improper accumulation of BLM-positive recombination foci, reinforcing the requirement of SPATA22-MEIOB for the proper progression of meiotic recombination events. Theshanimutation lies within aSpata22coding exon and molecular characterization shows that it leads to incorrect splicing of theSpata22mRNA, ultimately resulting in no detectable SPATA22 protein. We propose that theshanimutation alters an exonic splicing enhancer element (ESE) within theSpata22transcript. The affected DNA nucleotide is conserved in most tetrapods examined, suggesting that the splicing regulation we describe here may be a conserved feature ofSpata22regulation.
Small heat shock proteins determine synapse number and neuronal activity during development
Authors: de los Reyes Teresa , Santana Elena , Casas-Tintó Sergio
Published: February 2020

Environmental changes cause stress, Reactive Oxygen Species and unfolded protein accumulation which hamper synaptic activity and trigger cell death. Heat shock proteins (HSPs) assist protein refolding to maintain proteostasis and cellular integrity. Mechanisms regulating the activity of HSPs include transcription factors and posttranslational modifications that ensure a rapid response. HSPs preserve synaptic function in the nervous system upon environmental insults or pathological factors and contribute to the coupling between environmental cues and neuron control of development. We have performed a biased screening inDrosophilamelanogastersearching for synaptogenic modulators among HSPs during development. We explore the role of two small-HSPs (sHSPs), sHSP23 and sHSP26 in synaptogenesis and neuronal activity. Both sHSPs immunoprecipitate together and the equilibrium between both chaperones is required for neuronal development and activity. The molecular mechanism controlling HSP23 and HSP26 accumulation in neurons relies on a novel gene (CG1561), which we namePinkman(pkm). We propose that sHSPs and Pkm are targets to modulate the impact of stress in neurons and to prevent synapse loss.
Molecular characterization of differences between the tomato immune receptors Fls3 and Fls2
Authors: Roberts Robyn , Liu Alexander E. , Wan Lingwei , Geiger Annie M. , Hind Sarah R. , Rosli Hernan G. , Martin Gregory B.
Published: February 2020

Plants mount defense responses by recognizing indications of pathogen invasion, including microbe-associated molecular patterns (MAMPs). Flagellin from the bacterial pathogenPseudomonas syringaepv. tomato (Pst) contains two MAMPs, flg22 and flgII-28, that are recognized by tomato receptors Flagellin sensing 2 (Fls2) and Flagellin sensing 3 (Fls3), respectively. It is unknown to what degree each receptor contributes to immunity and if they promote immune responses using the same molecular mechanisms. Characterization of CRISPR/Cas9-generatedFls2andFls3tomato mutants revealed that the two receptors contribute equally to disease resistance both on the leaf surface and in the apoplast. However, striking differences were observed in certain host responses mediated by the two receptors. Compared to Fls2, Fls3 mediated a more sustained production of reactive oxygen species (ROS) and an increase in transcript abundance of 44 tomato genes, with two genes serving as reporters for Fls3. Fls3 had greaterin vitrokinase activity and interacted differently with thePsteffector AvrPtoB as compared to Fls2. Using chimeric Fls2/Fls3 proteins, we found that no receptor domain was solely responsible for the Fls3 sustained ROS, suggesting involvement of multiple structural features. This work reveals differences in the immunity outputs between Fls2 and Fls3, suggesting they use distinct molecular mechanisms to activate pattern-triggered immunity in response to flagellin-derived MAMPs.
Progesterone shapes medial temporal lobe volume across the human menstrual cycle
Authors: Taylor Caitlin M. , Pritschet Laura , Olsen Rosanna , Layher Evan , Santander Tyler , Grafton Scott T. , Jacobs Emily G.
Published: February 2020

The rhythmic production of sex steroid hormones is a central feature of the mammalian endocrine system. In rodents and nonhuman primates, sex hormones are powerful regulators of hippocampal subfield morphology. However, it remains unknown whether intrinsic fluctuations in sex hormones alter hippocampal morphology in the human brain. In a series of dense-sampling studies, we used high-resolution imaging of the medial temporal lobe (MTL) to determine whether endogenous fluctuations (Study 1) and exogenous manipulation (Study 2) of sex hormones alter MTL volume over time. Across the menstrual cycle, intrinsic fluctuations in progesterone were associated with volumetric changes in CA2/3, entorhinal, perirhinal, and parahippocampal cortex. Chronic progesterone suppression abolished these cycle-dependent effects and led to pronounced volumetric changes in entorhinal cortex and CA2/3 relative to freely cycling conditions. No associations with estradiol were observed. These results establish progesterone’s ability to rapidly and dynamically shape MTL morphology across the human menstrual cycle.

Highlights

Sex hormones are powerful regulators of hippocampal plasticity in mammals.

The impact of hormone fluctuations on hippocampal morphology in humans is unknown.

High resolution imaging of the MTL was conducted across two 30-day periods.

Progesterone dynamically shapes MTL volume across the human menstrual cycle.

Chronic progesterone suppression abolishes cycle-dependent changes.
Nucleoporin 153 links nuclear pore complex to chromatin architecture by mediating CTCF and cohesin binding atcis-regulatory elements and TAD boundaries
Authors: Kadota Shinichi , Ou Jianhong , Shi Yuming , Sun Jiayu , Yildirim Eda
Published: February 2020

The nuclear pore complex (NPC) components, nucleoporins (Nups), have been proposed to mediate spatial and temporal organization of chromatin during gene regulation. Nevertheless, we have little understanding on the molecular mechanisms that underlie Nup-mediated chromatin structure and transcription in mammals. Here, we show that Nucleoporin 153 (NUP153) interacts with the chromatin architectural proteins, CTCF and cohesin, and mediates their binding acrosscis-regulatory elements and TAD boundaries in mouse embryonic stem (ES) cells. NUP153 depletion results in altered CTCF and cohesin occupancy and differential gene expression. This function of NUP153 is most prevalent at the developmental genes that show bivalent chromatin state. To dissect the functional relevance of NUP153-mediated CTCF and cohesin binding during transcriptional activation or silencing, we utilized epidermal growth factor (EGF)-inducible immediate early genes (IEGs). We found that NUP153 binding at thecis-regulatory elements controls CTCF and cohesin binding and subsequent POL II pausing during the transcriptionally silent state. Furthermore, efficient and timely transcription initiation of IEGs relies on NUP153 and occurs around the nuclear periphery suggesting that NUP153 acts as an activator of IEG transcription. Collectively, these results uncover a key role for NUP153 in chromatin architecture and transcription by mediating CTCF and cohesin binding in mammalian cells. We propose that NUP153 links NPCs to chromatin architecture allowing developmental genes and IEGs that are poised to respond rapidly to developmental cues to be properly modulated.
A new mechanism for a familiar mutation – bovineDGAT1K232A modulates gene expression through multi-junction exon splice enhancement
Authors: Fink Tania , Lopdell Thomas J , Tiplady Kathryn , Handley Renee , Johnson Thomas JJ , Spelman Richard J , Davis Stephen R , Snell Russell G , Littlejohn Mathew D
Published: February 2020

TheDGAT1gene encodes an enzyme responsible for catalysing the terminal reaction in mammary triglyceride synthesis, and underpins a well-known pleiotropic quantitative trait locus (QTL) with a large influence on milk composition phenotypes. Since first described over 15 years ago, a protein-coding variant K232A has been assumed as the causative variant underlying these effects, followingin-vitrostudies that demonstrated differing levels of triglyceride synthesis between the two protein isoforms. In the current study, we used a large RNAseq dataset to re-examine the underlying mechanisms of this large milk production QTL, and hereby report novel expression-based functions of the chr14 g.1802265AA>GC variant that encodes theDGAT1K232A substitution. Using expression QTL (eQTL) mapping, we demonstrate a highly-significant mammary eQTL forDGAT1, where the K232A mutation appears as one of the top associated variants for this effect. By conductingin vitroexpression and splicing experiments in bovine mammary cell culture, we further show modulation of splicing efficiency by this mutation, likely through disruption of an exon splice enhancer as a consequence of the allele encoding the 232A variant. Although the relative contributions of the enzymatic and transcription-based mechanisms now attributed to K232A remain unclear, these results suggest that transcriptional impacts contribute to the diversity of lactation effects observed at this locus.
BiGen: Integrative Clinical and Brain-Imaging Genetics Analysis Using Structural Equation Model
Authors: Elsheikh Samar S. M. , Chimusa Emile R. , Crimi Alessandro , Mulder Nicola J.
Published: February 2020

The identification of genetic variants associated with complex brain diseases has evolved in the past decades. Studies in the field have taken different approaches and study designs including genome-wide association studies. Neuroimaging and connectomics have also improved our understanding of the structural connectivity of the human brain and produced reliable measurements. Combining both neuroimaging and genetic characteristics significantly contributes to understand their complex relationship in affecting behaviour and cognition. Throughout this thesis we proposed analysis pipeline to study the association between imaging and genetics of two different types of brain disease, which is, Alzheimer’s disease and glioblastoma. We observe the need for a unified model to study the complex interplay between genetic, environmental and clinical, neuroimaging and phenotype features. In this chapter, we developed BiGen, a mathematical model to measure the inter-correlation structure through the integration of genetic, environmental, neuroimaging and disease measurements. We utilised the structural equation model and used a path construct of latent variables to study the hidden association between genes and brain-related diseases, mediated by connectivity characteristics. We applied BiGen to simulated data and to a dataset from the Alzheimer’s Disease Neuroimaging Initiative.
The cell and stress-specific canonical and non-canonical tRNA cleavage
Authors: Rashad Sherif , Tominaga Teiji , Niizuma Kuniyasu
Published: February 2020

Following stress, tRNA is cleaved to generate tRNA halves (tiRNAs). These stress-induced small RNAs have been shown to regulate translation during stress. To date, angiogenin is considered the main enzyme that cleaves tRNA at its anti-codon site to generate 35 ~ 45 nucleotide long 5′ and 3′ tiRNA halves, however recent reports indicate the presence of angiogenin-independent cleavage. We previously observed tRNA cleavage pattern occurring away from the anti-codon site. To explore this non-canonical cleavage, we analyze tRNA phenotypical cleavage patterns in rat model of ischemia reperfusion and in two rat cell lines.In vivomitochondrial tRNAs were prone to this non-canonical cleavage pattern.In vitro, however, both cytosolic and mitochondrial tRNAs could be cleaved non-canonically. We also evaluated the roles of angiogenin and its inhibitor, RNH1, in regulating tRNA cleavage during stress. Our results suggest that mitochondrial stress has an important regulatory role in angiogenin-mediated tRNA cleavage. Angiogenin does not appear to regulate the non-canonical cleavage pattern of tRNA, and RNH1 does not affect it as well. Finally, we verified our previous findings of the stress-specific role of Alkbh1 in regulating tRNA cleavage and showed a strong influence of stress type on Alkbh1-mediated tRNA cleavage and that Alkbh1 impacts non-canonical tRNA cleavage.
Sputtered porous Pt for wafer-scale manufacture of low-impedance flexible microelectrodes
Authors: Fan Bo , Rodriguez Alexander V. , Vercosa Daniel G. , Kemere Caleb , Robinson Jacob T.
Published: February 2020

Recording electrical activity from individual cells in vivo is a key technology for basic neuroscience and has growing clinical applications. To maximize the number of independent recording channels as well as the longevity, and quality of these recordings, researchers often turn to small and flexible electrodes that minimize tissue damage and can isolate signals from individual neurons. One challenge when creating these small electrodes, however, is to maintain a low interfacial impedance by applying a surface coating that is stable in tissue and does not significantly complicate the fabrication process. Here we use a high-pressure Pt sputtering process to create low-impedance electrodes at the wafer scale using standard microfabrication equipment. Direct-sputtered Pt provides a reliable and well-controlled porous coating that reduces the electrode impedance by 5-9 fold compared to flat Pt and is compatible with the microfabrication technologies used to create flexible electrodes. These porous Pt electrodes show reduced thermal noise that matches theoretical predictions. In addition, we show that these electrodes can be implanted into rat cortex, record single unit activity, and be removed all without disrupting the integrity of the coating. We also demonstrate that the shape of the electrode (in addition to the surface area) has a significant effect on the electrode impedance when the feature sizes are on the order of tens of microns. Overall, porous Pt represents a promising method for manufacturing low-impedance electrodes that can be seamlessly integrated into existing processes for producing flexible neural probes.
Short chain fatty acid butyrate promotes virus infection by repressing interferon stimulated genes
Authors: Chemudupati Mahesh , Smith Anna C. , Fillinger Robert J. , Kenney Adam D. , Zhang Lizhi , Zani Ashley , Liu Shan-Lu , Anderson Matthew Z. , Sharma Amit , Yount Jacob S.
Published: February 2020

Butyrate is an abundant metabolite produced by the gut microbiota and is known to modulate multiple immune system pathways and inflammatory diseases. However, studies of its effects on virus infection of cells are limited and enigmatic. We found that butyrate increases cellular infection and virus replication in influenza virus, reovirus, and human immunodeficiency virus infections. Further exploring this phenomenon, we found that addition of butyrate to cells deficient in type I interferon (IFN) signaling did not increase susceptibility to virus infection. Accordingly, we discovered that butyrate suppressed levels of specific IFN stimulated gene (ISG) products in human and mouse cells. Butyrate did not inhibit IFN-induced phosphorylation of transcription factors STAT1 and STAT2 or their translocation to the nucleus, indicating that IFN signaling was not disrupted. Rather, our data are suggestive of a role for inhibition of histone deacetylase activity by butyrate in limiting ISG induction. Global transcript analysis revealed that butyrate increases expression of more than 800 cellular genes, but represses IFN-induced expression of 60% of ISGs. Overall, we identify a new mechanism by which butyrate promotes virus infection via repression of ISGs. Our findings also add to the growing body of evidence showing that individual ISGs respond differently to type I IFN induction depending on the cellular environment, including the presence of butyrate.

Importance

Butyrate is a lipid produced by intestinal bacteria that can regulate inflammation throughout the body. Here we show for the first time that butyrate influences the innate antiviral immune response mediated by type I IFNs. A majority of antiviral genes induced by type I IFNs were repressed in the presence of butyrate, resulting in increased virus infection and replication in cells. This suggests that butyrate could be broadly used as a tool to increase growth of virus stocks for research and for the generation of vaccines. Our research also indicates that metabolites produced by the gut microbiome can have complex effects on cellular physiology as demonstrated by the dampening of an inflammatory innate immune pathway by butyrate resulting in a pro-viral cellular environment.
Disruption ofAtHAK/KT/KUP9enhances plant cesium accumulation under low potassium supply
Authors: Genies Laure , Martin Ludovic , Kanno Satomi , Chiarenza Serge , Carasco Loïc , Camilleri Virginie , Vavasseur Alain , Henner Pascale , Leonhardt Nathalie
Published: February 2020

Understanding molecular mechanisms which underlie transport of cesium (Cs+) in plants is important to limit entry of its radioisotopes from contaminated area to the food chain. The potentially toxic element Cs+, which is not involved in any biological process, is chemically closed to the macronutrient potassium (K+). Among the multiple K+carriers, the high-affinity K+transporters family HAK/KT/KUP is thought to be relevant in mediating opportunistic Cs+transport. On the 13KUPidentified inArabidopsis thaliana, onlyHAK5, the major contributor to root K+acquisition under low K+supply, has been functionally demonstrated to be involved in Cs+uptakein planta. In the present study, we showed that accumulation of Cs+increased by up to 30% in twoA. thalianamutant lines lackingKUP9and grown under low K+supply. Since further experiments revealed that Cs+release from contaminated plants to the external medium is proportionally lower in the twokup9mutants, we proposed thatKUP9disruption could impair Cs+efflux. By contrast, we did not measure significant impairment of K+status inkup9mutants suggesting thatKUP9disruption does not alter substantially K+transport in experimental conditions used here. Putative primary role of KUP9 in plants is further discussed.