bluuebunny/crossref_metadata_2025 huggingface dataset:
CHIME: CMOS-hosted in-vivo microelectrodes for massively scalable neuronal recordings
Authors: Kollo Mihaly , Racz Romeo R , Hanna Mina-Elraheb S , Obaid Abdulmalik M , Angle Matthew R , Wray William , Kong Yifan , Hierlemann Andreas , Müller Jan , Melosh Nicholas A , Schaefer Andreas T
Published: March 2019

Mammalian brains consist of 10s of millions to 100s of billions of neurons operating at millisecond time scales, of which current recording techniques only capture a tiny fraction. Recording techniques capable of sampling neural activity at such temporal resolution have been difficult to scale: The most intensively studied mammalian neuronal networks, such as the neocortex, show layered architecture, where the optimal recording technology samples densely over large areas. However, the need for application-specific designs as well as the mismatch between the threedimensional architecture of the brain and largely two-dimensional microfabrication techniques profoundly limits both neurophysiological research and neural prosthetics.

Here, we propose a novel strategy for scalable neuronal recording by combining bundles of glass-ensheathed microwires with large-scale amplifier arrays derived from commercial CMOS of in-vitro MEA systems or high-speed infrared cameras. High signal-to-noise ratio (<20 μV RMS noise floor, SNR up to 25) is achieved due to the high conductivity of core metals in glass-ensheathed microwires allowing for ultrathin metal cores (down to <1 μm) and negligible stray capacitance. Multi-step electrochemical modification of the tip enables ultra-low access impedance with minimal geometric area and largely independent of core diameter. We show that microwire size can be reduced to virtually eliminate damage to the blood-brain-barrier upon insertion and demonstrate that microwire arrays can stably record single unit activity.

Combining microwire bundles and CMOS arrays allows for a highly scalable neuronal recording approach, linking the progress of electrical neuronal recording to the rapid scaling of silicon microfabrication. The modular design of the system allows for custom arrangement of recording sites. Our approach of employing bundles of minimally invasive, highly insulated and functionalized microwires to lift a 2-dimensional CMOS architecture into the 3rd dimension can be translated to other CMOS arrays such as electrical stimulation devices.
Few Effects of a 5-week Computerized Cognitive Training Program in Healthy Older Adults
Authors: Rabipour Sheida , Morrison Cassandra , Crompton Jessica , Petrucelli Marcelo , de Oliveira Gonçalves Germano Murillo , Popescu Anita , Davidson Patrick S. R.
Published: March 2019

Computerized cognitive training programs are becoming increasingly popular and practical for cognitive aging. Nevertheless, basic questions remain about the benefits of such programs, and about the degree to which participant expectations might influence training and transfer. Here we examined a commercial cognitive training program (Activate) in a 5-week double-blind, pseudo-randomized placebo-controlled trial. Based on a priori power analysis, we recruited 99 healthy older adults 59-91 years of age (M = 68.87, SD = 6.31; 69 women), assigning them to either the intervention or an active control program (Sudoku and n-back working memory exercises). We subdivided both groups into high and low expectation priming conditions, to probe for effects of participants’ expectations on training and transfer. We assessed transfer using a battery of standard neuropsychological and psychosocial measures that had been agreed to by the training program developers. We planned and pre-registered our analyses (on osf.io). The majority (88%) of participants progressed through the training, and most provided positive feedback about it. Similarly, the majority (80%) of participants believed they were truly training their brains. Yet, transfer of training was minimal. Also minimal were any effects of expectations on training and transfer, although participants who received high expectation priming tended to engage more with their assigned program overall. Our findings suggest limited benefits ofActivatetraining on cognition and psychosocial wellbeing in healthy older adults, at least under the conditions we used.
Selective Liposomal Transport Through Blood Brain Barrier Disruption in Ischaemic Stroke Reveals Two Distinct Therapeutic Opportunities
Authors: Al-Ahmady Zahraa S. , Jasim Dhifaf , Ahmad Sabahuddin Syed , Wong Raymond , Haley Michael , Coutts Graham , Schiessl Ingo , Allan Stuart M. , Kostarelos Kostas
Published: March 2019

The development of new therapies for stroke continues to face repeated translational failures. Brain endothelial cells form paracellular and transcellular barriers to many blood-borne therapies and the development of efficient delivery strategies is highly warranted. Here, in a mouse model of stroke, we show selective recruitment of clinically used liposomes into the ischaemic brain that correlates with biphasic blood brain barrier (BBB) breakdown. Intravenous administration of liposomes into mice exposed to transient middle cerebral artery occlusion took place at early (0.5h and 4h) and delayed (24h and 48h) timepoints, covering different phases of BBB disruption after stroke. Using a combination of in vivo real-time imaging and histological analysis we show that selective liposomal brain accumulation coincides with biphasic enhancement in transcellular transport followed by a delayed impairment to the paracellular barrier. This process precedes neurological damage in the acute phase and maintains long-term liposomal co-localisation within the neurovascular unit, which could have great potential for neuroprotection. Levels of liposomal uptake by glial cells are similarly selectively enhanced in the ischaemic region late after experimental stroke (2-3 days), highlighting their potential for blocking delayed inflammatory responses or shifting the polarization of microglia/macrophages towards brain repair.

These findings demonstrate the capability of liposomes to maximise selective translocation into the brain after stroke and identify for the first time two windows for therapeutic manipulation. This emphasizes the benefits of selective drug delivery for efficient tailoring of new stroke treatments.
Bicarbonate Resensitization of Methicillin-ResistantStaphylococcus aureusto β-Lactam Antibiotics
Authors: Ersoy Selvi C. , Abdelhady Wessam , Li Liang , Chambers Henry F. , Xiong Yan Q. , Bayer Arnold S.
Published: March 2019

Endovascular infections caused by methicillin-resistantStaphylococcus aureus(MRSA) are a major healthcare concern, especially infective endocarditis (IE). Standard antimicrobial susceptibility testing (AST) defines most MRSA strains as ‘resistant’ to β-lactams, often leading to use of costly and/or toxic treatment regimens. In this investigation, five prototype MRSA strains, representing the range of genotypes in current clinical circulation, were studied. We identified two distinct MRSA phenotypes upon AST using standard media, with or without sodium bicarbonate (NaHCO3) supplementation: one highly susceptible to the anti-staphylococcal β-lactams, oxacillin and cefazolin (‘NaHCO3-responsive’) and one resistant to such agents (‘NaHCO3-nonresponsive’). These phenotypes accurately predicted clearance profiles of MRSA from target tissues in experimental MRSA IE treated with each β-lactam. Mechanistically, NaHCO3reduced expression of two key genes involved in the MRSA phenotype,mecAandsarA,leading to decreased production of penicillin-binding protein (PBP) 2a (that mediates methicillin resistance), in NaHCO3-responsive (but not in NaHCO3-nonresponsive) strains. Moreover, both cefazolin and oxacillin synergistically killed NaHCO3-responsive strains in the presence of the host defense antimicrobial peptide (LL-37) in NaHCO3-supplemented media. These findings suggest that AST of MRSA strains in NaHCO3-containing media may potentially identify infections caused by NaHCO3-responsive strains that are appropriate for β-lactam therapy.
Conserving unprotected important coastal habitats in the Yellow Sea: Shorebird occurrence, distribution and food resources at Lianyungang
Authors: Chan Ying-Chi , Peng He-Bo , Han Yong-Xiang , Chung Sheena Suet-Wah , Li Jing , Zhang Lin , Piersma Theunis
Published: March 2019

The authors have withdrawn their manuscript since this preprint contain errors which have been corrected in the version published in the journal ‘Global Ecology and Conservation’ (doi: 10.1016/j.gecco.2019.e00724). Therefore, the authors do not wish this preprint to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Pulcherrimin formation controls growth arrest of theBacillus subtilisbiofilm
Authors: Arnaouteli Sofia , Matoz-Fernandez Daniel , Porter Michael , Kalamara Margarita , Abbott James , MacPhee Cait E. , Davidson Fordyce A. , Stanley-Wall Nicola R.
Published: March 2019

Biofilm formation byBacillus subtilisis a communal process that culminates in the formation of architecturally complex multicellular communities. Here we reveal that the transition of the biofilm into a non-expanding phase constitutes a distinct step in the process of biofilm development. Using genetic analysis we show thatB. subtilisstrains lacking the ability to synthesize pulcherriminic acid form biofilms that sustain the expansion phase, thereby linking pulcherriminic acid to growth arrest. However, production of pulcherriminic acid is not sufficient to block expansion of the biofilm. It needs to be secreted into the extracellular environment where it chelates Fe3+from the growth medium in a non-enzymatic reaction. Utilizing mathematical modelling and a series of experimental methodologies we show that when the level of freely available iron in the environment drops below a critical threshold, expansion of the biofilm stops. Bioinformatics analysis allows us to identify the genes required for pulcherriminic acid synthesis in other Firmicutes but the patchwork presence both within and across closely related species suggests loss of these genes through multiple independent recombination events. The seemingly counterintuitive self-restriction of growth led us to explore if there were any benefits associated pulcherriminic acid production. We identified that pulcherriminic acid producers can prevent invasion from neighbouring communities through the generation of an “iron free” zone thereby addressing the paradox of pulcherriminic acid production byB. subtilis.

Significance

Understanding the processes that underpin the mechanism of biofilm formation, dispersal, and inhibition are critical to allow exploitation and to understand how microbes thrive in the environment. Here, we reveal that the formation of an extracellular iron chelate restricts the expansion of a biofilm. The countering benefit to self-restriction of growth is protection of an environmental niche. These findings highlight the complex options and outcomes that bacteria need to balance in order to modulate their local environment to maximise colonisation, and therefore survival.
Altered structural brain asymmetry in autism spectrum disorder: large-scale analysis via the ENIGMA Consortium
Authors: Postema Merel C. , van Rooij Daan , Anagnostou Evdokia , Arango Celso , Auzias Guillaume , Behrmann Marlene , Filho Geraldo Busatto , Calderoni Sara , Calvo Rossa , Daly Eileen , Deruelle Christine , Di Martino Adriana , Dinstein Ilan , Duran Fabio Luis S. , Durston Sarah , Ecker Christine , Ehrlich Stefan , Fair Damien , Fedor Jennifer , Feng Xin , Fitzgerald Jackie , Floris Dorothea L. , Freitag Christine M. , Gallagher Louise , Glahn David C. , Gori Ilaria , Haar Shlomi , Hoekstra Liesbeth , Jahanshad Neda , Jahanshad Neda , Jalbrzikowski Maria , Janssen Joost , King Joseph A. , Zaro Luisa L , Lerch Jason P. , Luna Beatriz , Martinho Mauricio M. , McGrath Jane , Medland Sarah E. , Muratori Filippo , Murphy Clodagh M. , Murphy Declan G.M. , O’Hearn Kirsten , Oranje Bob , Parellada Mara , Puig Olga , Retico Alessandra , Rosa Pedro , Rubia Katya , Shook Devon , Taylor Margot , Tosetti Michela , Wallace Gregory L. , Zhou Fengfeng , Thompson Paul , Fisher Simon E. , Buitelaar Jan K. , Francks Clyde
Published: March 2019

Background

Left-right asymmetry is an important organizing feature of the healthy brain. Various studies have reported altered structural brain asymmetry in autism spectrum disorder (ASD). However, findings have been inconsistent, likely due to limited sample sizes and low statistical power.

Methods

We investigated 1,774 subjects with ASD and 1,809 controls, from 54 datasets, for differences in the asymmetry of thickness and surface area of 34 cerebral cortical regions. We also examined global hemispheric measures of cortical thickness and area asymmetry, and volumetric asymmetries of subcortical structures. Data were obtained via the ASD Working Group of the ENIGMA (Enhancing NeuroImaging Genetics through Meta-Analysis) consortium. T1-weighted MRI data were processed with a single protocol using FreeSurfer and the Desikan-Killiany atlas.

Results

ASD was significantly associated with reduced leftward asymmetry of total hemispheric average cortical thickness, compared to controls. Eight regional thickness asymmetries, distributed over the cortex, also showed significant associations with diagnosis after correction for multiple comparisons, for which asymmetry was again generally lower in ASD versus controls. In addition, the medial orbitofrontal surface area was less rightward asymmetric in ASD than controls, and the putamen volume was more leftward asymmetric in ASD than controls. The largest effect size had Cohen’sd= 0.15. Most effects did not depend on age, sex, IQ, or disorder severity.

Conclusion

Altered lateralized neurodevelopment is suggested in ASD, affecting widespread cortical regions with diverse functions. Large-scale analysis was necessary to reliably detect, and accurately describe, subtle alterations of structural brain asymmetry in this disorder.
Comparison Between Normobaric Hypoxia Altitude Simulation Test and Altitude Hypoxia Predictive Equations in Cystic Fibrosis Patients
Authors: Costa Christine , Barros André , Rodrigues João Valença , Staats Richard , Alves Mariana , Cardim Pilar , Lopes Carlos , Barbara Cristina , Moita Luís F. , Moreira Susana
Published: March 2019

Background:

The Hypoxia Altitude Simulation Test (HAST) is the Gold Standard to evaluate hypoxia in response to altitude and to decide on in-flight requirements for oxygen supplementation. Several equations are available to predict PaO2 in altitude (PaO2alt), but it remains unclear whether their predictive value is equivalent. We aimed to compare the results obtained by the available methods in a population of cystic fibrosis (CF) adults.

Methods:

Eighty-eight adults (58 healthy controls and 30 CF patients) performed a spirometry followed by an HAST. HAST results were compared with the predicted PaO2alt made by five equations: 1st: PaO2alt= 0,410 x PaO2ground + 1,7652; 2nd: PaO2alt= 0,519 x PaO2ground + 11,855 x FEV1 (L) − 1,760; 3rd: PaO2alt= 0,453 x PaO2ground + 0,386 x FEV1 (%) + 2,44; 4th: PaO2alt= 0,88 + 0,68 x PaO2ground; 5th: PaO2alt= PaO2ground − 26,6.

Results:

None of the controls required in-flight oxygen neither by HAST or by the five predictive equations. Eleven CF-patients had PaO2alt < 50 mmHg, accessed by HAST. The positive predictive value was 50% (1st), 87.5% (2nd and 3rd), 77.78% (4th) and 58.33% (5th). Areas under the curve were 78.95% (1st), 84.69% (2nd), 88.04% (3rd) and 78.95% (4th and 5th). FEV1 and PaO2ground were correlated with HAST results.

Conclusions:

The 3rd equation gave the best predictions in comparison with results obtained by HAST. However, because the individual differences found were substantial for all equations, we still recommend performing a HAST whenever possible to confidently access in-flight hypoxia and the need for oxygen.
Modulation of Rapid Visual Responses during Reaching by Multimodal Stimuli
Authors: Glover Isabel S , Baker Stuart N
Published: March 2019

The reticulospinal tract plays an important role in primate upper limb function, but methods for assessing its activity are limited. One promising approach is to measure rapid visual responses (RVRs) in arm muscle activity during a visually-cued reaching task; these may arise from a tecto-reticulospinal pathway. We investigated whether changes in reticulospinal excitability can be assessed non-invasively using RVRs, by pairing the visual stimuli of the reaching task with electrical stimulation of the median nerve, galvanic vestibular stimulation or loud sounds, all of which are known to activate the reticular formation.

Surface electromyogram recordings were made from the right deltoid of healthy human subjects as they performed fast reaching movements towards visual targets. Stimuli were delivered up to 200ms before target appearance and RVR was quantified as the EMG amplitude in a window 75-125ms after visual target onset. Median nerve, vestibular and auditory stimuli all consistently facilitated the RVRs, as well as reducing the latency of responses. We propose that this reflects modulation of tecto-reticulospinal excitability, suggesting that the amplitude of RVRs can be used to assess changes in brainstem excitability non-invasively in humans.

New & Noteworthy

Short latency responses in arm muscles evoked during a visually-driven reaching task have previously been proposed to be tecto-reticulospinal in origin. We demonstrate that these responses can be facilitated by pairing the appearance of a visual target with stimuli that activate the reticular formation – median nerve, vestibular and auditory stimuli. We propose that this reflects non-invasive measurement and modulation of reticulospinal excitability.
Notch signaling restricts FGF pathway activation in parapineal cells to promote their collective migration
Authors: Wei Lu , Blader Patrick , Roussigné Myriam
Published: March 2019

Coordinated migration of cell collectives is important during embryonic development and relies on cells integrating multiple mechanical and chemical cues. Recently, we described that focal activation of the FGF pathway promotes the migration of the parapineal in the zebrafish epithalamus. How FGF activity is restricted to leading cells in this system is, however, unclear. Here, we address the role of Notch signaling in modulating FGF activity within the parapineal. While Notch loss-of-function results in an increased number of parapineal cells activating the FGF pathway, global activation of Notch signaling decreases it; both contexts result in defects in parapineal migration and specification. Decreasing or increasing FGF signaling in a Notch loss-of-function context respectively rescues or aggravates parapineal migration defects without affecting parapineal cells specification. We propose that Notch signaling controls the migration of the parapineal through its capacity to restrict FGF pathway activation to a few leading cells.
Challenges and Strategies for Recruiting Type 1 Diabetes Families in Kuwait with Strong Beliefs in Familism
Authors: Rahme Zahra , Taha Nehad , Abdalla Hidaia , Abraham Smitha , Alhubail Asma , AlSanae Hala , AlMahdi Maria , Aljaser Fahed , Abdelrasoul Majda , Khawari Mona Al , Jahromi Mohamed
Published: March 2019

Type 1 diabetes (T1D) is one of the most common endocrine and metabolic conditions in children. In fact, this disease in children and adolescents has been increasing exponentially, with Kuwait being ranked second highest in the world regarding the number of T1D incidences. Kuwait is an oil-rich country known for its strong sense of familism, affiliative obedience, and filial obligation. Therefore, a familial study of this disease may disclose certain causative agents responsible for passing the disease on to subsequent generations.

To recruit T1D patients and their family members, three different scenarios were developed. First, since Kuwaiti families are generally obedient to their doctors, the authors decided to recruit the patients through their endocrine physicians. Second, home visits were performed for meeting the families’ requirements. In this case, a team consisting of one nurse, two phlebotomists (a male and a female, since some refused to be seen by the opposite gender), and a driver of the institute’s car was arranged. Finally, two diabetes educators were employed to resolve any issues raised during the recruitment process. Utilizing these approaches helped convince the culturally and religiously oriented Kuwaiti families to participate in this study. In this case, the doctors and educators were not only aware of the obstacles in this population but also sensitive to the families’ beliefs. This paper reports on our experience in recruitment and presents a roadmap for any future familial studies on culturally tailored societies i.e. Arab populations.
Short translational ramp determines efficiency of protein synthesis
Authors: Verma Manasvi , Choi Junhong , Cottrell Kyle A. , Lavagnino Zeno , Thomas Erica N. , Pavlovic-Djuranovic Slavica , Szczesny Pawel , Piston David W. , Zaher Hani , Puglisi Joseph D. , Djuranovic Sergej
Published: March 2019

It is generally assumed that translation efficiency is governed by translation initiation. However, the efficiency of protein synthesis is regulated by multiple factors including tRNA abundance, codon composition, mRNA motifs and amino-acid sequence1–4. These factors influence the rate of protein synthesis beyond the initiation phase of translation, typically by modulating the rate of peptide-bond formation and to a lesser extent that of translocation. The slowdown in translation during the early elongation phase, known as the 5’ translational ramp, likely contributes to the efficiency of protein synthesis 5–9. Multiple mechanisms, which could explain the molecular basis for this translational ramp, have been proposed that include tRNA abundance bias6,9, the rate of translation initiation10–15, mRNA and ribosome structure 11,12,14,16–18, or retention of initiation factors during early elongation events 19. Here, we show that the amount of synthesized protein (translation efficiency) depends on a short translational ramp that comprises the first 5 codons in mRNA. Using a library of more than 250,000 reporter sequences combined with in vitro and in vivo protein expression assays, we show that differences in the short ramp can lead to 3 to 4 orders of magnitude changes in protein abundance. The observed difference is not dependent on tRNA abundance, efficiency of translation initiation, or overall mRNA structure. Instead, we show that translation is regulated by amino-acid-sequence composition and local mRNA sequence. Single-molecule measurements of translation kinetics indicate substantial pausing of ribosome and abortion of protein synthesis on the 4th or 5th codon for distinct amino acid or nucleotide compositions. Introduction of preferred sequence motifs, only at the exact positions within the mRNA, improves protein synthesis for recombinant proteins, indicating an evolutionarily conserved mechanism for controlling translational efficiency.
Identification of the relative timing of infectiousness and symptom onset for outbreak control
Authors: Cope Robert C. , Ross Joshua V.
Published: March 2019

In an outbreak of an emerging disease the epidemiological characteristics of the pathogen may be largely unknown. A key determinant of ability to control the outbreak is the relative timing of infectiousness and symptom onset. We provide a method for identifying this relationship with high accuracy based on data from household-stratified symptom-onset data. Further, this can be achieved with observations taken on only a few specific days, chosen optimally, within each household. This constitutes an important tool for outbreak response. An accurate and computationally-efficient heuristic for determining the optimal surveillance scheme is introduced. This heuristic provides a novel approach to optimal design for Bayesian model discrimination.
Targeted DNA transposition using a dCas9-transposase fusion protein
Authors: Bhatt Shivam , Chalmers Ronald
Published: March 2019

Homology directed genome engineering is limited by transgene size. Although DNA transposons are more efficient with large transgenes, random integrations are potentially mutagenic. Catalytically inactive Cas9 is attractive candidate for targeting a transposase fusion-protein because of its high specificity and affinity for its binding site. Here we demonstrate efficient Cas9 targeting of a mariner transposon. Targeted integrations were tightly constrained at two adjacent TA dinucleotides about 20 bp to one side of the gRNA binding site. Biochemical analysis of the nucleoprotein complexes demonstrated that the transposase and Cas9 moieties of the fusion protein can bind their respective substrates independently. In the presence of the Cas9 target DNA, kinetic analysis revealed a delay between first and second strand cleavage at the transposon end. This step involves a significant conformational change that may be hindered by the properties of the interdomainal linker. Otherwise, the transposase behaved normally and was proficient for integration in vitro and in vivo.
Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics
Authors: Davis Luke K. , Ford Ian J. , Šarić Anđela , Hoogenboom Bart W.
Published: March 2019

In the nuclear pore complex (NPC), intrinsically disordered nuclear pore proteins (FG nups) form a selective barrier for transport into and out of the cell nucleus, in a way that remains poorly understood. The collective FG nup behaviour has long been conceptualized either as a polymer brush, dominated by entropic and excluded-volume (repulsive) interactions, or as a hydrogel, dominated by cohesive (attractive) interactions between FG nups. Here we compare mesoscale computational simulations with a wide range of experimental data to demonstrate that FG nups are at the crossover point between these two regimes. Specifically, we find that repulsive and attractive interactions are balanced, resulting in morphologies and dynamics that are close to those of ideal polymer chains. We demonstrate that this property of FG nups yields sufficient cohesion to seal the transport barrier, and yet maintains fast dynamics at the molecular scale, permitting the rapid polymer rearrangements needed for transport events.
Connectional heterogeneity in the mouse auditory corticocollicular system
Authors: Yudintsev Georgiy , Asilador Alexander , Coppinger Macey , Nair Kavyakrishna , Prasad Masumi , Llano Daniel A.
Published: March 2019

The auditory cortex (AC) sends long-range projections to virtually all subcortical structures important for hearing. One of the largest and most complex of these - the projection between AC and inferior colliculus (IC, the corticocollicular pathway) - has attracted attention due to its potential to alter IC response properties. The corticocollicular pathway comprises a component originating from layer 5, but recent evidence suggests a significant contribution from deep layer 6, constituting 25% of corticocollicular neurons in mouse. The functions of layer-specific corticocollicular projections are poorly understood. Here, using a combination of tracers and in vivo imaging, we observed that layer 5 and layer 6 corticocollicular neurons differ in their cortical areas of origin, as well as IC termination patterns. Layer 5 corticocollicular neurons are concentrated in primary AC areas while layer 6 corticocollicular neurons emanate from broad auditory and non-auditory areas of temporal cortex. In addition, layer 5 projects to three IC subdivisions with axo-somatic terminals in the central nucleus, while layer 6 projects to non-central nuclei and targets the most superficial layers. These findings suggest that layer 5 corticocollicular neurons form a direct connection between primary AC and IC while the layer 6 projection is more diffusely organized and carries non-auditory information to modulate IC.
A novel Ca2+-binding protein influences photosynthetic electron transport inAnabaenasp. PCC 7120
Authors: Walter Julia , Selim Khaled A. , Leganés Francisco , Fernández-Piñas Francisca , Vothknecht Ute C. , Forchhammer Karl , Aro Eva-Mari , Gollan Peter J.
Published: March 2019

Ca2+is a potent signalling molecule that regulates many cellular processes. In cyanobacteria, Ca2+has been linked to cell growth, stress response and photosynthesis, and to the development of specialist heterocyst cells in certain nitrogen-fixing species. Despite this, the pathways of calcium signal transduction in cyanobacteria are poorly understood, and only a few protein components are known. The current study describes a previously unreported calcium-binding protein which was called the Calcium Sensor EF-hand (CSE), which is conserved in filamentous, nitrogen-fixing cyanobacteria. CSE is shown to bind calcium, which induces a conformational change in the protein structure. Poor growth of a strain ofAnabaenasp. PCC 7120 overexpressing CSE was attributed to diminished photosynthetic performance. Transcriptomics, biophysics and proteomics analyses revealed modifications in the light-harvesting phycobilisome and photosynthetic reaction center-protein complexes, and downregulated respiration.
Fertility intentions and influential factors in Dalian urban city ---A cross-sectional study based on Universal Two-child policy in China
Authors: Qiu Hongyan , Zhang Qun , Zhang Jin , Ren Yangjie , Zhou Xujuan , Li Shuangyue , Liang Hong , Luo Jiajia , Wang Qingshan , Hou Liyan
Published: March 2019

Background

In October, 2015, Chinese government announced that one-child policy had finally been replaced by a universal two-child policy. However, the effects of new policy may be far less than expected. So we conducted this research to explore potential influential factors of fertility intention.

Methods

This cross-sectional study was conducted and a self-administered questionnaire was designed for collecting socio-demographic information, future fertility intention and influential factors of individual reproductive behavior. The analyses were performed using the SPSS 19.0 statistical software package.

Results

A total of 1370 respondents were interviewed. Our research indicated that the mean ideal number of children was only 1.73 and urban respondents’ sex preference was symmetrical preference. 79.1% (884) married people had the first child already, only 7.6% (71) respondents had two children. Among 1370 participants, 30.4% respondents stated that they would have a second child; while 69.6% respondents refused to have two children in future (just wanted only a child). Binary logistic regression analysis (model 1) showed that female, older age, lower education lever, birth place was Dalian, lower family income, the ideal number of children were associated with having 1 child in the future. Model 2 (only respondents with childbearing experience) showed that female, lower family income, couldn’t get additional financial support from parents were more likely refused to have two children; in additional, the ideal number of children and childbearing experience were significantly influences on future fertility intention.

Conclusion

Fertility intention and reproductive behavior still below replacement in Dalian city. Our results suggest that several factors (including socioeconomic characteristics, economic factors, desired number of child, childbearing experience) have distinctive effects on fertility intention.
Microsecond Molecular Dynamics Simulations of Diphtheria Toxin Translocation T-Domain pH-Dependent Unfolding in Solution
Authors: Flores-Canales Jose C. , Simakov Nikolay A. , Kurnikova Maria
Published: March 2019

Diphtheria toxin is a multi-domain protein that invades cells by using their own endocytosis mechanism. In endocytosis, an endosome, a lipid bilayer vesicle, is formed to encapsulate an extracellular molecule. Subsequent acidification of endosome internal solution induces conformational rearrangements and membrane insertion of such encapsulated diphtheria toxin translocation domain (T-domain). In solution at neutral pH, a stand-alone T-domain adopts an all alpha-helical globular structure; however, atomistic details of the pH-dependent conformational changes of the protein are not completely understood. We model structural rearrangements in T-domain in 18 µs long molecular dynamics (MD) simulations of neutral and low pH T-domain models in explicit solvent. At low pH, six histidine residues of the protein were protonated. Two independent MD trajectories resulted in partial protein unfolding at low pH, in which similar regions of the protein conformational subspace were explored. Notably, a pH induced unfolding transition was initiated by partial unfolding of helix TH4 followed by unfolding of helix TH1. Helix TH2 repeatedly unfolds in the low pH T-domain model, which is consequently predicted to be disordered by a consensus of disorder prediction algorithms. Protonation of histidines disrupted a hydrophobic core containing a putative transmembrane helix TH8, which is encircled by hydrophobic surfaces of helices TH3, TH5 and TH9. Afterwards, the low pH T-domain model was reorganized into an ensemble of partially unfolded structures with increased solvent exposure of hydrophobic and charged sites. Thus, MD simulations suggest the destabilizing role of protonation of histidines, in the neutral pH conformation in solution, which may facilitate the initial stages of T-domain membrane binding. The simulation at neutral pH samples conformations in the vicinity of the native structure of the protein. However, significant fluctuations of the protein, including unfolding and refolding of α-helices were observed at these simulation time-scales.
Genetic analysis ofTP53gene mutations in exon 4 and exon 8 among esophageal cancer patients in Sudan
Authors: Eltaher Sulafa Mohamed , Idris Abeer Babiker , Mahmoud A. H , Yousif Mawadah Yousif Mohamed , Mohamed Nouh Saad , Hamid Muzamil M. Abdel , Elsiddig Kamal Elzaki , Hassan Mohamed A. , Yousif Galal Mohammed
Published: March 2019

Background

Esophageal carcinoma (EC) represents the 1strank among all gastrointestinal cancers in Sudan. Despite little publications, there is a deep absence of literature about the molecular pathogenesis of EC considering TP53 gene from Sudanese population.

Aims

In this study, we performed the expression analysis on p53 protein level by immunohistochemical staining and examined its overexpression with p53 mutations in exons 4 and 8 among esophageal cancer patients in Sudan.

Material and Methods

Fixed tissue with 10% buffered formalin was stained by Hematoxlin and Eosin (H&E), Alcian blue-Periodic Acid Schiff (PAS) and Immunohistochemistry stain. PCR-RFLP was used to study the frequencies of p53 codon 72 R/P polymorphism. Conventional PCR and sanger sequencing were applied for exon 4 and exon 8. Then detection and functional analysis of SNPs and mutations were performed using various in bioinformatics tools.

Result

Nuclear accumulations for p53 protein was detected in all of the esophageal carcinomas examined while no accumulations were observed in normal control sections. Four patients with immune-positive for p53 showed no mutations in p53 gene (exon4 and exon8). The incidence of the homozygous mutant variant Pro/Pro was higher in esophageal cancerous patients comparing to healthy control subject 20(71. 4%) vs. 1(10%), respectively (p=0.0026). In exon 4, no mutation was detected other than NG_017013.2:g. 16397C>G. While in exon 8, g.18783-18784AG>TT, g.18803A>C, g.18860A>C, g.18845A>T and g.18863_ 18864 InsT were observed.

Conclusion

we found a significant association between the overexpression of TP53 protein and mutation in exon 4 and 8. A silent mutation P301P was detected in all of examined cases. Two patients who diagnosed with small cell sarcoma have shared the same mutations in exon8. Further studies with large sample size are required to demonstrate the usefulness of these mutations in the screening of EC especially SCCE.
Risky Decision-Making Predicts Dopamine Release Dynamics in Nucleus Accumbens Shell
Authors: Freels Timothy G. , Gabriel Daniel B. K. , Lester Deranda B. , Simon Nicholas W.
Published: March 2019

The risky decision-making task (RDT) measures risk-taking in a rat model by assessing preference between a small, safe reward and a large reward with increasing risk of punishment (mild foot shock). It is well-established that dopaminergic drugs modulate risk-taking; however, little is known about how differences in baseline phasic dopamine signaling drive individual differences in risk preference. Here, we usedin vivofixed potential amperometry in male Long-Evans rats to test if phasic nucleus accumbens shell (NACs) dopamine dynamics are associated with risk-taking. We observed a positive correlation between medial forebrain bundle-evoked dopamine release in the NACs and risky decision-making, suggesting that risk-taking is associated with elevated dopamine sensitivity. Moreover, “risk-taking” subjects were found to demonstrate greater phasic dopamine release than “risk-averse” subjects. Risky decision-making also predicted enhanced sensitivity to nomifensine, a dopamine reuptake inhibitor, quantified as elevated latency for dopamine to clear from the synapse. Importantly, this hyperdopaminergic phenotype was selective for risky decision-making, as delay discounting performance was not predictive of phasic dopamine release or dopamine supply. These data identify phasic NACs dopamine release as a possible therapeutic target for alleviating the excessive risk-taking observed across multiple forms of psychopathology.

Significance Statement

Excessive risky decision-making is a hallmark of addiction, promoting ongoing drug seeking despite the risk of social, financial, and physical consequences. However, punishment-driven risk-taking is understudied in preclinical models. Here, we examined the relationship between individual differences in risk-taking and dopamine release properties in the rat nucleus accumbens shell, a brain region associated with motivation and decision-making. We observed that high risk taking predicted elevated phasic dopamine release and sensitivity to the dopamine transporter blocker nomifensine. This hypersensitive dopamine system was not observed in rats with high impulsive choice, another behavior associated with substance use disorder. This provides critical information about neurobiological factors underlying a form of decision-making that promotes vulnerability to substance abuse.
DNA damage-specific effects of Tel1/ATM and γH2A/γH2AX on checkpoint signaling inSaccharomyces cerevisiae
Authors: Siler Jasmine , Guo Na , Liu Zhengfeng , Qin Yuhua , Bi Xin
Published: March 2019

DNA lesions trigger the activation of DNA damage checkpoints (DDCs) that stop cell cycle progression and promote DNA damage repair.Saccharomyces cerevisiaeTel1 is a homolog of mammalian ATM kinase that plays an auxiliary role in DDC signaling. γH2A, equivalent to γH2AX in mammals, is an early chromatin mark induced by DNA damage that is recognized by a group of DDC and DNA repair factors. We find that both Tel1 and γH2A negatively impact G2/M checkpoint in response to DNA topoisomerase I poison camptothecin independently of each other. γH2A also negatively regulates DDC induced by DNA alkylating agent methyl methanesulfonate. These results, together with prior findings demonstrating positive or no roles of Tel1 and γH2A in DDC in response to other DNA damaging agents such as phleomycin and ionizing radiation, suggest that Tel1 and γH2A have DNA damage-specific effects on DDC. We present data indicating that Tel1 acts in the same pathway as Mre11-Rad50-Xrs2 complex to suppress CPT induced DDC possibly by repairing topoisomerase I-DNA crosslink. On the other hand, we find evidence consistent with the notion that γH2A regulates DDC by mediating the competitive recruitment of DDC mediator Rad9 and DNA repair factor Rtt107 to sites of DNA damage. We propose that γH2A serves to create a dynamic balance between DDC and DNA repair that is influenced by the nature of DNA damage.
Mechanism of pharmacochaperoning in KATP channels revealed by cryo-EM
Authors: Martin Gregory M. , Sung Min Woo , Yang Zhongying , Innes Laura M. , Kandasamy Balamurugan , David Larry L. , Yoshioka Craig , Shyng Show-Ling
Published: March 2019

ATP-sensitive potassium (KATP) channels composed of a pore-forming Kir6.2 potassium channel and a regulatory ABC transporter sulfonylurea receptor 1 (SUR1) regulate insulin secretion in pancreatic β-cells to maintain glucose homeostasis. Mutations that impair channel folding or assembly prevent cell surface expression and cause congenital hyperinsulinism. Structurally diverse KATPinhibitors have been shown to act as pharmacochaperones to correct mutant channel expression, but the mechanism is unknown. Here, we compare cryoEM structures of KATPchannels bound to pharmacochaperones glibenclamide, repaglinide, and carbamazepine. We found all three drugs bind within a common pocket in SUR1. Further, we found the N-terminus of Kir6.2 inserted within the central cavity of the SUR1 ABC core, adjacent the drug binding pocket. The findings reveal a common mechanism by which diverse compounds stabilize the Kir6.2 N-terminus within the SUR1 ABC core, allowing it to act as a firm “handle” for the assembly of metastable mutant SUR1-Kir6.2 complexes.
The Developmental Transcriptome forLytechinus variegatusExhibits Temporally Punctuated Gene Expression Changes
Authors: Hogan John D. , Keenan Jessica L. , Luo Lingqi , Hawkins Dakota Y. , Ibn-Salem Jonas , Lamba Arjun , Schatzberg Daphne , Piacentino Michael L. , Zuch Daniel T. , Core Amanda B. , Blumberg Carolyn , Timmermann Bernd , Grau José Horacio , Speranza Emily , Andrade-Narravo Miguel A. , Irie Naoki , Poustka Albert J. , Bradham Cynthia A.
Published: March 2019

Embryonic development is arguably the most complex process an organism undergoes during its lifetime, and understanding this complexity is best approached with a systems-level perspective. The sea urchin has become a highly valuable model organism for understanding developmental specification, morphogenesis, and evolution. As a non-chordate deuterostome, the sea urchin occupies an important evolutionary niche between protostomes and vertebrates.Lytechinus variegatus(Lv) is an Atlantic species that has been well studied, and which has provided important insights into signal transduction, patterning, and morphogenetic changes during embryonic and larval development. The Pacific species,Strongylocentrotus purpuratus(Sp), is another well-studied sea urchin, particularly for gene regulatory networks (GRNs) andcis-regulatory analyses. A well-annotated genome and transcriptome for Sp are available, but similar resources have not been developed for Lv. Here, we provide an analysis of the Lv transcriptome at 11 timepoints during embryonic and larval development. The data indicate that the gene regulatory networks that underlie specification are well-conserved among sea urchin species. We show that the major transitions in variation of embryonic transcription divide the developmental time series into four distinct, temporally sequential phases. Our work shows that sea urchin development occurs via sequential intervals of relatively stable gene expression states that are punctuated by abrupt transitions.
Visual awareness judgments are sensitive to accuracy feedback in stimulus discrimination task
Authors: Siedlecka Marta , Wereszczyński Michał , Paulewicz Borysław , Wierzchoń Michał
Published: March 2019

In this study we tested the hypothesis that perceptual awareness judgments are sensitive to the accuracy feedback about previous behaviour. We used a perceptual discrimination task in which participants reported their stimulus awareness. We created two conditions: No-feedback and Feedback (discrimination accuracy feedback was provided at the end of each trial). The results showed that visual awareness judgments are related to the accuracy of current and previous responses. Participants reported lower stimulus awareness for incorrectly versus correctly discriminated stimuli in both conditions; they also reported lower stimulus awareness in trials preceded by incorrect discrimination responses, compared to trials preceded by correct discrimination. This difference was significantly stronger in the Feedback condition. Moreover, in the Feedback condition we also observed larger post-error slowing for PAS ratings. We discuss the relation between the effects of performance monitoring and visual awareness and interpret the results in the context of current theories of consciousness.
Charting shared developmental trajectories of cortical thickness and structural connectivity in childhood and adolescence
Authors: Ball G. , Beare R. , Seal M. L.
Published: March 2019

The cortex is organised into broadly hierarchical functional systems with distinct neuroanatomical characteristics reflected by macroscopic measures of cortical morphology. Diffusion-weighted MRI allows the delineation of areal connectivity, changes to which reflect the ongoing maturation of white matter tracts. These developmental processes are intrinsically linked with timing coincident with the development of cognitive function.

In this study, we use a data-driven multivariate approach, non-negative matrix factorisation, to define cortical regions that co-vary together across a large paediatric cohort (n=456) and are associated with specific subnetworks of cortical connectivity.

We find that age between 3 and 21 years is associated with accelerated cortical thinning in fronto-parietal regions, whereas relative thinning of primary motor and sensory regions is slower. Together, the subject-specific weights of the derived set of components can be combined to predict chronological age. Structural connectivity networks reveal a relative increase in strength in connection within, as opposed to between hemispheres that vary in line with cortical changes. We confirm our findings in an independent sample.
The ER membrane protein complex is required to ensure correct topology and stable expression of flavivirus polyproteins
Authors: Ngo Ashley M , Shurtleff Matthew J , Popova Katerina D , Kulsuptrakul Jessie , Weissman Jonathan S , Puschnik Andreas S
Published: March 2019

Flaviviruses translate their genomes as multi-pass transmembrane proteins at the endoplasmic reticulum (ER) membrane. Here, we show that the ER membrane protein complex (EMC) is indispensable for the expression of viral polyproteins. We demonstrated that EMC was essential for accurate folding and post-translational stability rather than translation efficiency. Specifically, we revealed degradation of NS4A-NS4B, a region rich in transmembrane domains, in absence of EMC. Orthogonally, by serial passaging of virus on EMC-deficient cells, we identified two non-synonymous point mutations in NS4A and NS4B, which rescued viral replication. Finally, we showed a physical interaction between EMC and viral NS4B and that the NS4A-4B region adopts an aberrant topology in the absence of the EMC leading to degradation. Together, our data highlight how flaviviruses hijack the EMC for transmembrane protein biogenesis to achieve optimal expression of their polyproteins, which reinforces a role for the EMC in stabilizing challenging transmembrane proteins during synthesis.