bluuebunny/crossref_metadata_2025 huggingface dataset:
The Effect of Self-Loading on the Mechano-Stability and Stalk Lodging Resistance of Plant Stems
Authors: Stubbs Christopher J , Oduntan Yusuf , Keep Tyrone , Noble Scott D , Robertson Daniel J.
Published: March 2020

Background

Stalk lodging (breaking of agricultural plant stalks prior to harvest) is a multi-billion dollar a year problem. Stalk lodging occurs when bending moments induced by a combination of external loading (e.g. wind) and self-loading (e.g. the plant’s own weight) exceed the bending strength of plant stems. Previous biomechanical plant stem models have investigated both external loading and self-loading of plants, but have evaluated them as separate and independent phenomena. However, these two types of loading are highly interconnected and mutually dependent. The purpose of this paper is twofold: (1) to investigate the combined effect of external loads and plant weight on the displacement and stress state of plant stems / stalks, and (2) to provide a generalized framework for accounting for self-weight during mechanical phenotyping experiments used to predict stalk lodging resistance.

Results

A method of properly accounting for the interconnected relationship between self-loading and external loading of plants stems is presented. The interconnected set of equations are used to produce user-friendly applications by presenting (1) simplified self-loading correction factors for a number of common external loading configurations of plants, and (2) a generalized Microsoft Excel framework that calculates the influence of self-loading on crop stems. The effect of self-loading on the structural integrity of wheat is examined in detail. A survey of several other plants is conducted and the influence of self-loading on their structural integrity is also presented.

Conclusions

The self-loading of plants plays a potentially critical role on the structural integrity of plant stems. Equations and tools provided herein enable researchers to account for the plant’s weight when investigating the flexural rigidity and bending strength of plant stems.
Hippocampus plays a role in speech feedback processing
Authors: van de Ven Vincent , Waldorp Lourens , Christoffels Ingrid
Published: March 2020

There is increasing evidence that the hippocampus is involved in language production and verbal communication, although little is known about its possible role. According to one view, hippocampus contributes semantic memory to spoken language. Alternatively, hippocampus is involved in the processing the (mis)match between expected sensory consequences of speaking and the perceived speech feedback. In the current study, we re-analysed functional magnetic resonance (fMRI) data of two overt picture-naming studies to test whether hippocampus is involved in speech production and, if so, whether the results can distinguish between a “pure memory” versus an “expectation” account of hippocampal involvement. In both studies, participants overtly named pictures during scanning while hearing their own speech feedback unimpededly or impaired by a superimposed noise mask. Results showed decreased hippocampal activity when speech feedback was impaired, compared to when feedback was unimpeded. Further, we found increased functional coupling between auditory cortex and hippocampus during unimpeded speech feedback, compared to impaired feedback. Finally, we found significant functional coupling between a hippocampal/supplementary motor area (SMA) interaction term and auditory cortex, anterior cingulate cortex and cerebellum during overt picture naming, but not during listening to one’s own pre-recorded voice. These findings indicate that hippocampus plays a role in speech production that is in accordance with an “expectation” view of hippocampal functioning.
Iatrogenic Iron Promotes Neurodegeneration and Activates Self-protection of Neural Cells against Exogenous Iron Attacks
Authors: Xia Maosheng , Liang Shanshan , Li Shuai , Li Zexiong , Zhang Manman , Chen Beina , Dong Chengyi , Chen Binjie , Ji Ming , Gong Wenliang , Guan Dawei , Verkhratsky Alexei , Li Baoman
Published: March 2020

Metal implants are used worldwide, with millions of metal nails, plates and fixtures grafted during orthopaedic surgeries. Iron is the most common element of these metal implants. As time passes metal elements can be corroded and iron can be released from the implants in the form of ferric (Fe3+) or ferrous (Fe2+). These iron ions can permeate the surrounding tissues and enter circulation; importantly both Fe3+and Fe2+freely pass blood brain barrier (BBB). Can iron from implants represent a risk factor for neurological diseases? This remains an unanswered question. In this study, we discovered that the probability of metal implants delivered through orthopaedic surgeries was higher in patients of Parkinson’s diseases (PD) or ischemic stroke than in healthy subjects. This finding instigated subsequent study of iron effects on neuronal cells. In experimentsin vivo, we found that iron selectively decreased presence of divalent metal transporter 1 (DMT1) in neurones through increasing the expression of Ndfip1, which degrades DMT1 and rarely exists in glial cells. At the same time iron accumulation increased expression of DMT1 in astrocytes and microglial cells and triggered reactive astrogliosis and microglial activation. Facing the attack of excess iron, glial cells act as neuroprotectors to uptake more extracellular iron by up-regulating DMT1, whereas neurones limit iron uptake through decreasing DMT1 operation. Cerebral accumulation of iron was associated with impaired cognition, locomotion and mood. Excess iron thus affects neural cells and could increase the risk of neurodegeneration.
Flexible Representations of Odour Categories in the Mouse Olfactory Bulb
Authors: Kudryavitskaya Elena , Marom Eran , Pash David , Mizrahi Adi
Published: March 2020

The ability to group sensory stimuli into categories is crucial for efficient interaction with a rich and ever-changing environment. In olfaction, basic features of categorical representation of odours were observed as early as in the olfactory bulb (OB). Categorical representation was described in mitral cells (MCs) as sudden transitions in responses to odours that were morphed along a continuum. However, it remains unclear to what extent such response dynamics actually reflects perceptual categories and decisions therein. Here, we tested the role of learning on category formation in the mouse OB, usingin vivotwo-photon calcium imaging and behaviour. We imaged MCs responses in naïve mice and in awake behaving mice as they learned two tasks with different classification logic. In one task, a 1-decision boundary task, animals learned to classify odour mixtures based on the dominant compound in the mixtures. As expected, categorical representation of close by odours, which was evident already in naïve animals, further increased following learning. In a second task, a multi-decision boundary task, animals learned to classify odours independent of their chemical similarity. Rather, odour discrimination was based on the meaning ascribed to them (either rewarding or not). Following the second task, odour representations by MCs reorganized according to the odour value in the new category. This functional reorganization was also reflected as a shift from predominantly excitatory odour responses to predominantly inhibitory odour responses. Our data shows that odour representations by MCs is flexible, shaped by task demands, and carry category-related information.
Monodisperse drops templated by 3D-structured microparticles
Authors: Wu Chueh-Yu , Wang Bao , de Rutte Joseph , Ouyang Mengxing , Joo Alexis , Jacobs Matthew , Ha Kyung , Bertozzi Andrea L. , Di Carlo Dino
Published: March 2020

The ability to create uniform sub-nanoliter compartments using microfluidic control has enabled new approaches for analysis of single cells and molecules. However, specialized instruments or expertise have been required, slowing the adoption of these cutting-edge applications. Here, we show that 3D-structured microparticles with sculpted surface chemistries template uniformly-sized aqueous drops when simply mixed with two immiscible fluid phases. In contrast to traditional emulsions, particle-templated drops of a controlled volume occupy a minimum in the interfacial energy of the system, such that a stable monodisperse state results with simple and reproducible formation conditions. We describe techniques to manufacture microscale drop-carrier particles and show that emulsions created with these particles prevent molecular exchange, concentrating reactions within the drops, laying a foundation for sensitive compartmentalized assays with minimal instrumentation.
TheCoxiella burnetiiQpH1 plasmid is a virulence factor for colonizing bone marrow-derived murine macrophages
Authors: Luo Shengdong , Sun Zhihui , Fan Huahao , Lu Shanshan , Hu Yan , Li Ruisheng , An Xiaoping , Tong Yigang , Song Lihua
Published: March 2020

Coxiella burnetiicarries a large conserved plasmid or plasmid-like chromosomally integrated sequence of unknown function. Here we report the curing of QpH1 plasmid fromC. burnetiiNine Mile phase II, the characterization of QpH1-deficientC. burnetiiin in vitro and in vivo infection models, and the characterization of plasmid biology. A shuttle vector pQGK, which is composed of the CBUA0036-0039a region (predicted for QpH1 maintenance), anE. coliplasmid ori, eGFP and kanamycin resistance genes was constructed. The pQGK vector can be stably transformed into Nine Mile II and maintained at a similar low copy like QpH1. Importantly, transformation with pQGK cured the endogenous QpH1 due to plasmid incompatibility. Compared to a Nine Mile II transformant of a RSF1010-based vector, the pQGK transformant shows an identical one-step growth curve in axenic media, a similar growth curve in Buffalo green monkey kidney cells, an evident growth defect in macrophage-like THP-1 cells, and dramatically reduced ability of colonizing bone marrow-derived murine macrophages. In the SCID mouse infection model, the pQGK transformants caused a lesser extent of splenomegaly. Moreover, the plasmid biology was investigated by mutagenesis. We found CBUA0037-0039 are essential for plasmid maintenance, and CBUA0037-0038 account for plasmid compatibility. Taken together, our data suggest that QpH1 encodes factor(s) essential for colonizing murine macrophages, and to a lesser extent for colonizing human macrophages. This study highlights a critical role of QpH1 forC. burnetiipersistence in rodents, and expands the toolkit for genetic studies inC. burnetii.

Author summary

It is postulated thatC. burnetiirecently evolved from an inherited symbiont of ticks by the acquisition of novel virulence factors. AllC. burnetiiisolates carry a large plasmid or have a chromosomally integrated plasmid-like sequence. The plasmid is a candidate virulence factor that contributes toC. burnetiievolution. Here we describe the construction of novel shuttle vectors that allow to make plasmid-deficientC. burnetiimutants. With this plasmid-curing approach, we characterized the role of the QpH1 plasmid inin vitroandin vivo C. burnetiiinfection models. We found that the plasmid plays a critical role forC. burnetiigrowth in macrophages, especially in murine macrophages, but not in axenic media and BGMK cells. Our work highlights an essential role of the plasmid for the acquisition of colonizing capability in rodents byC. burnetii. This study represents a major step toward unravelling the mystery of theC. burnetiicryptic plasmids.
A shared alarmone-GTP switch underlies triggered and spontaneous persistence
Authors: Fung Danny K. , Barra Jessica T. , Schroeder Jeremy W. , Ying David , Wang Jue D.
Published: March 2020

Phenotypically-switched, antibiotic-refractory persisters may prevent pathogen eradication. Although how triggered persistence via starvation-induced (p)ppGpp is well characterized, generation of persisters without starvation are poorly understood. Here we visualized the formation of spontaneous persisters in a small fraction of cells from growing wild type bacteria, revealing a striking single cell rapid switch from growth to dormancy. This switch-like entrance is triggered by GTP dropping beneath a threshold due to stochastic production and self-amplification of (p)ppGpp via allosteric enzyme activation. In addition, persisters are induced by lethal and sublethal concentrations of cell wall antibiotics by inducing (p)ppGpp via cell wall stress response. Thus spontaneous, triggered and antibiotic-induced persisters can all stem from a common metabolic switch: GTP depletion by (p)ppGpp induction, and each pathway of persister formation is activated by different (p)ppGpp synthetases. These persistence pathways are likely conserved in pathogens which may be exploited to potentiate antibiotic efficacy.
Using directed attenuation to enhance vaccine immunity
Authors: Antia Rustom , Ahmed Hasan , Bull James J
Published: March 2020

Many viral infections can be prevented by immunizing with live, attenuated vaccines. Early methods of attenuation were hit-and-miss, and these are now much improved by genetic engineering. But even current attenuation methods operate on the principle of genetic harm, reducing the virus’s ability to grow, which in turn limits the host immune response below that of infection by wild-type. We use mathematical models of the dynamics of virus and its control by innate and adaptive immunity to explore the tradeoff between attenuation of virus growth and the generation of immunity. Our analysis suggests that directed attenuation that disables key viral defenses against the host immune responses may attenuate viral growth without compromising, and potentially even enhancing the generation of immunity. We explore which immune evasion pathways should be attenuated and how attenuating multiple pathways could lead to robust attenuation of pathology with enhancement of immunity.

Author summary

Live attenuated virus vaccines are among the most effective interventions to combat viral infections. Historically, the mechanism of attenuation has been one of genetically reduced viral growth rate, often achieved by adapting the virus to grow in a novel cells. More recent attenuation methods use genetic engineering but also are thought to impair viral growth rate. These classical attenuations typically result in a tradeoff whereby attenuation depresses the within-host viral load and pathology (which is beneficial to vaccine design), but reduces immunity (which is not beneficial). We use models to explore ways of directing the attenuation of a virus to avoid this tradeoff. We show thatdirected attenuationby interfering with (some) viral immune-evasion pathways can yield a mild infection but elicit higher levels of immunity than of the wild-type virus.
Characterisation of the transcriptome and proteome of SARS-CoV-2 using direct RNA sequencing and tandem mass spectrometry reveals evidence for a cell passage induced in-frame deletion in the spike glycoprotein that removes the furin-like cleavage site
Authors: Davidson Andrew D. , Williamson Maia Kavanagh , Lewis Sebastian , Shoemark Deborah , Carroll Miles W. , Heesom Kate , Zambon Maria , Ellis Joanna , Lewis Phillip A. , Hiscox Julian A. , Matthews David A.
Published: March 2020

Direct RNA sequencing using an Oxford Nanopore MinION characterised the transcriptome of SARS-CoV-2 grown in Vero E6 cells. This cell line is being widely used to propagate the novel coronavirus. The viral transcriptome was analysed using a recently developed ORF-centric pipeline. This revealed the pattern of viral transcripts, (i.e. subgenomic mRNAs), generally fitted the predicted replication and transcription model for coronaviruses. A 24 nt in-frame deletion was detected in subgenomic mRNAs encoding the spike (S) glycoprotein. This feature was identified in over half of the mapped transcripts and was predicted to remove a proposed furin cleavage site from the S glycoprotein. This motif directs cleavage of the S glycoprotein into functional subunits during virus entry or exit. Cleavage of the S glycoprotein can be a barrier to zoonotic coronavirus transmission and affect viral pathogenicity. Allied to this transcriptome analysis, tandem mass spectrometry was used to identify over 500 viral peptides and 44 phosphopeptides, covering almost all of the proteins predicted to be encoded by the SARS-CoV-2 genome, including peptides unique to the deleted variant of the S glycoprotein. Detection of an apparently viable deletion in the furin cleavage site of the S glycoprotein reinforces the point that this and other regions of SARS-CoV-2 proteins may readily mutate. This is of clear significance given the interest in the S glycoprotein as a potential vaccine target and the observation that the furin cleavage site likely contributes strongly to the pathogenesis and zoonosis of this virus. The viral genome sequence should be carefully monitored during the growth of viral stocks for research, animal challenge models and, potentially, in clinical samples. Such variations may result in different levels of virulence, morbidity and mortality.
Genetic analysis identifies theOstrea stentina/aupouria/equestrisoyster species complex in Hawai‘i, and resolves its lineage as the western PacificO. equestris
Authors: Sutton Jolene T. , Nishimoto Jared , Schrader Jeremy , Agonias Keinan , Antonio Nicole , Bautista Brandi , Cabarloc Riley , Fakasieiki Maata , Gonong Noreen Aura Mae , Ramangmou Torey , Uehara Lavin , Wong Jade , Wilkie Daniel , Littrell David , Rem-McGeachy Marni , Chandler-‘Īao Rhiannon , Haws Maria
Published: March 2020

Background

Extensive phenotypic plasticity in oysters makes them difficult to identify based on morphology alone, but their identities can be resolved by applying genetic and genomic technologies. In this study, we collected unknown oyster specimens from Hawaiian waters for genetic identification.

Methods

We sequenced two partial gene fragments, mitochondrial 16S ribosomal RNA (16S) and cytochrome c oxidase subunit I (COI), in 48 samples: 27 unidentified oyster specimens collected from two locations on O‘ahu, 13 known specimens from a hatchery in Hilo, Hawai‘i Island, and 8 known specimens from Hilo Bay, Hawai‘i Island.

Results

Molecular data identified approximately 85% of unknown samples as belonging to theOstrea stentina/aupouria/equestrisspecies complex, a globally distributed group with a history of uncertain and controversial taxonomic status. The remaining unknown samples were the nativeDendostrea sandvichensis(G. B. Sowerby II, 1871), and nonnativeCrassostrea gigas(Thunberg, 1793), the latter of which is a commercial species that was introduced to Hawai‘I from multiple sources during the 20th century. Phylogenetic analysis placed Hawai‘iOstreaalongside samples from China, Japan, and New Zealand, grouping them within the recently classified western PacificO. equestris. Until now, four extant species of true oyster have been documented in Hawai‘i. This study expands the known range ofO. equestrisby providing the first verification of its occurrence in Hawai‘i.
Integrative Epigenomic and Transcriptomic Analysis Reveals Robust Metabolic Switching in the Brain During Intermittent Fasting
Authors: Ng Gavin Yong-Quan , Sheng Dominic Paul Lee Kok , Kang Sung Wook , Fann David Yang-Wei , Kim Joonki , Alli-Shaik Asfa , Cho Yoon Suk , Han Jihoon , Sul Jae Hoon , Karamyan Vardan , Okun Eitan , Dheen Thameem , Hande M. Prakash , Vemuganti Raghu , Mallilankaraman Karthik , Kennedy Brian K. , Drummond Grant , Sobey Christopher G. , Gunaratne Jayantha , Mattson Mark P. , Foo Roger Sik-Yin , Jo Dong-Gyu , Arumugam Thiruma V.
Published: March 2020

Intermittent fasting (IF) is a lifestyle intervention comprising a dietary regimen in which energy intake is restricted via alternating periods of fasting andad libitumfood consumption, without compromising nutritional composition. While epigenetic modifications can mediate effects of environmental factors on gene expression, no information is yet available on potential effects of IF on the epigenome. In this study, we found that IF causes modulation of histone H3 lysine 9 trimethylation (H3K9me3) epigenetic mark in the cerebellum of male C57/BL6 mice, which in turn orchestrates a plethora of transcriptomic changes involved in the robust metabolic switching processes commonly observed during IF. Interestingly, both epigenomic and transcriptomic modulation continued to be observed after refeeding, suggesting that memory of the IF-induced epigenetic change is maintained at the locus. Notably though, we found that termination of IF results in a loss of H3K9me3regulation of the transcriptome. Collectively, our study characterizes a novel mechanism of IF in the epigenetic-transcriptomic axis, which controls myriad metabolic process changes. In addition to providing a valuable and innovative resource, our systemic analyses reveal molecular framework for understanding how IF impacts the metaboloepigenetics axis of the brain.

Highlights

○ Intermittent fasting (IF) and refeeding modifies epigenome in the cerebellum

○ Integrative epigenomic and transcriptomic analyses revealed metabolic switching

○ IF affects the metaboloepigenetics axis in regulating metabolic processes

○ Integrative analyses revealed a loss of epigenetic reprogramme following refeeding
Single-cell differential splicing analysis reveals high heterogeneity of liver tumor-infiltrating T cells
Authors: Liu Shang , Zhou Biaofeng , Wu Liang , Sun Yan , Chen Jie , Liu Shiping
Published: March 2020

Recent advances in single-cell RNA sequencing (scRNA-seq), enriched the knowledge of the heterogeneity of the tumor-infiltrating lymphocytes (TIL) for understanding the mechanisms of cancer initiation and progression. However, alternative splicing (AS), as one of the important regulatory factors of heterogeneity, has been poorly investigated. Here, we proposed a computational tool, DESJ-detection, which could fast and accurately detect the differentially expressed splicing junction (DESJ) between cell groups at single-cell level. We analyzed 5,063 T cells of hepatocellular carcinoma (HCC) and identified 1,176 DESJs across 11 T cell subtypes. Cell subtypes with a similar function clustered closer rather than the lineage at the AS level. Meanwhile, we identified two novel cell states, pre-exhaustion and pre-activation with the marker isoform CD103-201 and ARHGAP15-205. In summary, we presented a comprehensive investigation of alternative splicing differences, which provided novel insights for heterogeneity of T cells and can be applied in other full-length scRNA-seq datasets.
Improved segmentation of the intracranial and ventricular volumes in populations with cerebrovascular lesions and atrophy using 3D CNNs
Authors: Ntiri Emmanuel E. , Holmes Melissa F. , Forooshani Parisa M. , Ramirez Joel , Gao Fuqiang , Ozzoude Miracle , Adamo Sabrina , Scott Christopher J.M. , Dowlatshahi Dar , Lawrence-Dewar Jane M. , Kwan Donna , Lang Anthony E. , Symons Sean , Bartha Robert , Strother Stephen , Tardif Jean-Claude , Masellis Mario , Swartz Richard H. , Moody Alan , Black Sandra E. , Goubran Maged
Published: March 2020

Successful segmentation of the total intracranial vault (ICV) and ventricles is of critical importance when studying neurodegeneration through neuroimaging. We present iCVMapper and VentMapper, robust algorithms that use a convolutional neural network (CNN) to segment the ICV and ventricles from both single and multi-contrast MRI data. Our models were trained on a large dataset from two multi-site studies (N=528 subjects for ICV, N=501 for ventricular segmentation) consisting of older adults with varying degrees of cerebrovascular lesions and atrophy, which pose significant challenges for most segmentation approaches. The models were tested on 238 participants, including subjects with vascular cognitive impairment and high white matter hyperintensity burden. Two of the three test sets came from studies not used in the training dataset. We assessed our algorithms relative to four state-of-the-art ICV extraction methods (MONSTR, BET, Deep Extraction, FreeSurfer), as well as a ventricular segmentation tool (FreeSurfer). Our multi-contrast models outperformed other methods across all evaluation metrics, with average Dice coefficients of 0.98 and 0.94 for ICV and ventricular segmentation respectively. Both models were also the most time efficient, segmenting the structures in orders of magnitude faster than some of the other available methods. Our networks showed an increased accuracy with the use of a conditional random field (CRF) as a post-processing step. We further validated both segmentation models, highlighting their robustness to images with lower resolution and signal-to-noise ratio, compared to tested techniques. The pipeline and models are available at:https://icvmapp3r.readthedocs.ioandhttps://ventmapp3r.readthedocs.ioto enable further investigation of the roles of ICV and ventricles in relation to normal aging and neurodegeneration in large multi-site studies.
Elucidating the mechanism ofTrypanosoma cruziacquisition by triatomine insects: evidence from a large field survey ofTriatoma infestans
Authors: Tustin Aaron W. , Castillo-Neyra Ricardo , Tamayo Laura D. , Borini-Mayorí Katty , Salazar Renzo , Levy Michael Z.
Published: March 2020

Blood-sucking triatomine bugs transmit the protozoan parasiteTrypanosoma cruzi, the etiologic agent of Chagas disease. We measured the prevalence ofT. cruziinfection in 58,519Triatoma infestanscaptured in residences in and near Arequipa, Peru. Among bugs from infected colonies,T. cruziprevalence increased with stage from 12% in second instars to 36% in adults. Regression models demonstrated a linear relationship between infection prevalence and developmental stage. Prevalence increased by 5.4 percentage points with each additional stage. We postulate that the probability of acquiring the parasite may be related to the number of feeding events. Transmission of the parasite does not appear to be correlated with the amount of blood ingested during feeding. Similarly, other hypothesized transmission routes such as coprophagy fail to explain the observed pattern of prevalence. Our results could have implications for the feasibility of late-acting control strategies that preferentially kill older insects.
Natural and synthetic potential inhibitors of endoribonuclease Nsp15 encoded by Middle East Respiratory Syndrome Coronavirus (MERS-CoV). Computer modelingin silicoexperiments.p-Coumaric acid, Curcumin and their Boronic acid derivatives compared to Hydroxychloroquine and its Boronic acid derivative
Authors: Barquero Juan F.
Published: March 2020

Based on the structural and biochemical characterization of endoribonuclease Nsp15 in crystal structure PDB code 5YVD, I am providing plausible inhibitors of this enzyme. In this report I intent to signal that is possible to inhibit this enzyme by the use of natural occurring compounds and their boronic acid derivatives, compounds with borono B(OH)2groups. Boronic acids are atracted to serine side chains in the active site of serine proteases, in this case an endoribonuclease. Actual lab tests need to be conducted, nevertheless I venture here to propose four compounds:p-coumaric acid, Curcumin and their boronic acid derivatives with the use of computer modeling,in silicoexperiments. I also compared the above mentioned compounds to Hydroxychloroquine and its boronic acid derivative. I usedAutoDock Vina, UCSF Chimera1.12,DeepView / Swiss-Pdb Viewer4 1.0,Sulp3.0,PubChem, MDL Isis Draw2.5,OpenBabelGUI2.2.3, andMicrosoft WordPad. As hardware I used a VAIO loptop with Intel Core i5 withMicrosoft Windows8.0, and a Dell loptop Inspiron E 1405 with an Intel Core Duo withMicrosoft WindowsXp (off line).
Ultra-Low-Cost Integrated Silicon-based Transducer for On-Site, Genetic Detection of Pathogens
Authors: Nunez-Bajo Estefania , Kasimatis Michael , Cotur Yasin , Asfour Tarek , Collins Alex , Tanriverdi Ugur , Grell Max , Kaisti Matti , Senesi Guglielmo , Stevenson Karen , Güder Firat
Published: March 2020

Rapid screening and low-cost diagnosis play a crucial role in choosing the correct course of interventione.g.,drug therapy, quarantine, no action etc. when dealing with highly infectious pathogens. This is especially important if the disease-causing agent has no effective treatment, such as the novel coronavirus SARS-CoV-2 (the pathogen causing COVID-19), and shows no or similar symptoms to other common infections. We report a silicon-based integrated Point-of-Need (PoN) transducer (TriSilix) that can chemically-amplify and detect pathogen-specific sequences of nucleic acids (NA) quantitatively in real-time. Unlike other silicon-based technologies, TriSilix can be produced at wafer-scale in a standard laboratory; we have developed a series of methodologies based on metal-assisted chemical (wet) etching, electroplating, thermal bonding and laser-cutting to enable a cleanroom-free low-cost fabrication that does not require processing in an advanced semiconductor foundry. TriSilix is, therefore, resilient to disruptions in the global supply chain as the devices can be produced anywhere in the world. To create an ultra-low-cost device, the architecture proposed exploits the intrinsic properties of silicon and integrates three modes of operation in a single chip: i) electrical (Joule) heater, ii) temperature sensor (i.e.thermistor) with a negative temperature coefficient that can provide the precise temperature of the sample solution during reaction and iii) electrochemical sensor for detecting target NA. Using TriSilix, the sample solution can be maintained at a single, specific temperature (needed for isothermal amplification of NA such as Recombinase Polymerase Amplification (RPA) or cycled between different temperatures (with a precision of ±1.3°C) for Polymerase Chain Reaction (PCR) while the exact concentration of amplicons is measured quantitatively and in real-time electrochemically. A single 4-inch Si wafer yields 37 TriSilix chips of 10×10×0.65 mm in size and can be produced in 7 hours, costing ~US $0.35 per device. The system is operated digitally, portable and low power – capable of running up to 35 tests with a 4000 mAh battery (a typical battery capacity of a modern smartphone). We were able to quantitatively detect a 563-bp fragment (Insertion Sequence IS900) of the genomic DNA ofM. aviumsubsp.paratuberculosis(extracted from cultured field samples) through PCR in real-time with a Limit-of-Detection of 20 fg, equivalent to a single bacterium, at the 30thcycle. Using TriSilix, we also detected the cDNA from SARS-CoV-2 (1 pg), through PCR, with high specificity against SARS-CoV (2003).
Grain number and genotype drive nitrogen-dependent yield response in the C4 modelSetaria italica(L.) P. Beauv
Authors: Bandyopadhyay Tirthankar , Swarbreck Stéphanie M , Jaiswal Vandana , Gupta Rajeev , Bentley Alison R. , Griffiths Howard , Prasad Manoj
Published: March 2020

Fertiliser nitrogen (N) drives crop yields and requires the breeding and selection of cultivars that are inherently highly N responsive. For major cereal crops such as wheat (Triticum aestivumL.) breeding over time has led to enhanced N use in modern cultivars however there remains a gap in understanding the N responsiveness of minor cereals grains, many of which are highly relevant to global food security. Here we investigate response to increasing N availability in a diverse population ofSetaria italica(L., foxtail millet) accessions demonstrating that N-driven yield increase is dependent on grain number rather than individual grain weight. Within the population, some accessions responded strongly to increased N availability while others show little yield improvement under high N. Genetic markers were generated to enable investigation of N responsiveness at a genome-wide level, highlighting likely underlying causal loci, especially for grains per plant. Despite the lack of response in terms of yield increase, a non-responsive accession shows a strong transcriptional response suggesting different metabolic functioning under high vs low N. Our results show major differences in N responsiveness inS. italicaand provide novel insight into the genetic and molecular basis for this variation.

One sentence summary

Nitrogen dependent yield response inSetaria italicaL. is driven by grain number and genotypes with low N yield responsive genotypes being more transcriptionally dynamic under varied N levels post-flowering compared to high N yield responsive genotypes.
CATH functional families predict protein functional sites
Authors: Das Sayoni , Scholes Harry M. , Orengo Christine A.
Published: March 2020

Motivation

Identification of functional sites in proteins is essential for functional characterisation, variant interpretation and drug design. Several methods are available for predicting either a generic functional site, or specific types of functional site. Here, we present FunSite, a machine learning predictor that identifies catalytic, ligand-binding and protein-protein interaction functional sites using features derived from protein sequence and structure, and evolutionary data from CATH functional families (FunFams).

Results

FunSite’s prediction performance was rigorously benchmarked using cross-validation and a holdout dataset. FunSite outperformed all publicly-available functional site prediction methods. We show that conserved residues in FunFams are enriched in functional sites. We found FunSite’s performance depends greatly on the quality of functional site annotations and the information content of FunFams in the training data. Finally, we analyse which structural and evolutionary features are most predictive for functional sites.

Availability

The datasets and prediction models are available on request.

Contact

c.orengo@ucl.ac.uk

Supplementary information

Supplementary data are available atBioinformaticsonline.
T606-phosphorylation deprives the function of Kaiso as a transcription and oncogenic factor
Authors: Tian Wei , Yuan Hongfan , Qin Sisi , Liu Wensu , Zhang Baozhen , Gu Liankun , Zhou Jing , Deng Dajun
Published: March 2020

It is well known that Kaiso protein encoded byZBTB33gene is a transcription repressor and that Kaiso–P120ctn interaction increases the shift of Kaiso from the nucleus into the cytoplasm. However, the regulatory mechanisms of Kaiso compartmentalization are far from clear. Here, we reported that AKT1 could phosphorylate 606-threonine residue (T606) within the RSSTIP motif of Kaiso in the cytoplasm. The T606-phosphorylated Kaiso (pT606-Kaiso) could directly bind to 14-3-3 family proteins and the depletion of T606 phosphorylation by T606A mutation abolished most of the Kaiso–14-3-3 binding. In addition, the Kaiso–P120ctn interaction was essential for the pT606-Kaiso accumulation in the cytoplasm. Notably, enforced14-3-3σ(SFN) overexpression could increase the pT606-Kaiso accumulation in the cytoplasm and de-repress the transcription of Kaiso target geneCDH1. Decreased amounts of both pT606-Kaiso and CDH1 proteins were frequently observed in human gastric cancer tissues relative to paired normal controls. The mRNA levels of14-3-3σand Kaiso target geneCDH1were positively and significantly correlated with each other in bioinformatics analyses using publicly available RNA-seq datasets for human normal tissues (n=11688,r=0.60,p<0.001) in the GTEx project and for cancer cell lines (n=1156,r=0.41,p<0.001) in the CCLE project. Furthermore, Kaiso T606A mutant (unable to be phosphorylated) significantly increased the migration and invasion of cancer cellsin vitroas well as boosted the growth of these cellsin vivo. In conclusion, Kaiso could be phosphorylated by AKT1 at the T606 and the pT606-Kaiso accumulates in the cytoplasm through binding to 14-3-3/P120ctn that de-represses the expression of Kaiso target geneCDH1in normal tissues. Decreased Kaiso phosphorylation may contribute to the development of gastrointestinal cancer. The status of Kaiso phosphorylation is a determinant factor for the role of Kaiso in the development of cancer.
Reaching to sounds in virtual reality: A multisensory-motor approach to re-learn sound localisation
Authors: Valzolgher Chiara , Verdelet Grègoire , Salemme Romeo , Lombardi Luigi , Gaveau Valerie , Farné Alessandro , Pavani Francesco
Published: March 2020

When localising sounds in space the brain relies on internal models that specify the correspondence between the auditory input reaching the ears and initial head-position with coordinates in external space. These models can be updated throughout life, setting the basis for re-learning spatial hearing abilities in adulthood. This is particularly important for individuals who experience long-term auditory alterations (e.g., hearing loss, hearing aids, cochlear implants) as well as individuals who have to adapt to novel auditory cues when listening in virtual auditory environments. Until now, several methodological constraints have limited our understanding of the mechanisms involved in spatial hearing re-learning. In particular, the potential role of active listening and head-movements have remained largely overlooked. Here, we overcome these limitations by using a novel methodology, based on virtual reality and real-time kinematic tracking, to study the role of active multisensory-motor interactions with sounds in the updating of sound-space correspondences. Participants were immersed in a virtual reality scenario showing 17 speakers at ear-level. From each visible speaker a free-field real sound could be generated. Two separate groups of participants localised the sound source either by reaching or naming the perceived sound source, under binaural or monaural listening. Participants were free to move their head during the task and received audio-visual feedback on their performance. Results showed that both groups compensated rapidly for the short-term auditory alteration caused by monaural listening, improving sound localisation performance across trials. Crucially, compared to naming, reaching the sounds induced faster and larger sound localisation improvements. Furthermore, more accurate sound localisation was accompanied by progressively wider head-movements. These two measures were significantly correlated selectively for the Reaching group. In conclusion, reaching to sounds in an immersive visual VR context proved most effective for updating altered spatial hearing. Head movements played an important role in this fast updating, pointing to the importance of active listening when implementing training protocols for improving spatial hearing.

HIGHLIGHTS

- We studied spatial hearing re-learning using virtual reality and kinematic tracking

- Audio-visual feedback combined with active listening improved monaural sound localisation

- Reaching to sounds improved performance more than naming sounds

- Monaural listening triggered compensatory head-movement behaviour

- Head-movement behaviour correlated with re-learning only when reaching to sounds
Monoclonal antibody stability can be usefully monitored using the excitation-energy-dependent fluorescence edge-shift
Authors: Knight MK , Woolley RE , Kwok A , Parsons S , Jones HBL , Gulácsy CE , Phaal P , Kassaar O , Dawkins K , Rodriguez E , Marques A , Bowsher L , Wells SA , Watts A , van den Elsen JMH , Turner A , O’Hara J , Pudney CR
Published: March 2020

Among the major challenges in the development of biopharmaceuticals are structural heterogeneity and aggregation. The development of a successful therapeutic monoclonal antibody (mAb) requires both a highly active and also stable molecule. Whilst a range of experimental (biophysical) approaches exist to track changes in stability of proteins, routine prediction of stability remains challenging. The fluorescence red edge excitation shift (REES) phenomenon is sensitive to a range of changes in protein structure. Based on recent work, we have found that quantifying the REES effect is extremely sensitive to changes in protein conformational state and dynamics. Given the extreme sensitivity, potentially this tool could provide a ‘fingerprint’ of the structure and stability of a protein. Such a tool would be useful in the discovery and development of biopharamceuticals and so we have explored our hypothesis with a panel of therapeutic mAbs. We demonstrate that the quantified REES data show remarkable sensitivity, being able to discern between structurally identical antibodies and showing sensitivity to unfolding and aggregation. The approach works across a broad concentration range (μg–mg/ml) and is highly consistent. We show that the approach can be applied alongside traditional characterisation testing within the context of a forced degradation study (FDS). Most importantly, we demonstrate the approach is able to predict the stability of mAbs both in the short (hours), medium (days) and long-term (months). The quantified REES data will find immediate use in the biopharmaceutical industry in quality assurance, formulation and development. The approach benefits from low technical complexity, is rapid and uses instrumentation which exists in most biochemistry laboratories without modification.
Regenerated Interneurons Integrate Into Locomotor Circuitry Following Spinal Cord Injury
Authors: Vasudevan Deeptha , Liu Yen-Chyi , Barrios Joshua P. , Wheeler Maya K. , Douglass Adam D. , Dorsky Richard I.
Published: March 2020

Whereas humans and other adult mammals lack the ability to regain locomotor function after spinal cord injury, zebrafish are able to recover swimming behavior even after complete spinal cord transection. We have previously shown that zebrafish larvae regenerate lost neurons within 9 days post-injury (dpi), but the functional contribution of these neurons to motor recovery is unknown. Here we show that multiple interneuron subtypes known to play a role in locomotor circuitry are regenerated in injured spinal cord segments during the period of functional recovery. Further, we show that one subtype of newly-generated interneurons receives excitatory input and fires synchronously with motor output by 9 dpi. Taken together, our data show that regenerative neurogenesis in the zebrafish spinal cord produces interneurons with the physiological capacity to participate in the recovery of locomotor function.
Flagellar dynamics reveal fluctuations and kinetic limit in theEscherichia colichemotaxis network
Authors: Bano Roshni , Mears Patrick , Golding Ido , Chemla Yann R.
Published: March 2020

TheEscherichia colichemotaxis network, by which bacteria modulate their random run/tumble swimming pattern to navigate their environment, must cope with unavoidable number fluctuations (“noise”) in its molecular constituents like other signaling networks. The probability of clockwise (CW) flagellar rotation, or CW bias, is a measure of the chemotaxis network’s output, and its temporal fluctuations provide a proxy for network noise. Here we quantify fluctuations in the chemotaxis signaling network from the switching statistics of flagella, observed using time-resolved fluorescence microscopy of individual optically trappedE. colicells. This approach allows noise to be quantified across the dynamic range of the network. Large CW bias fluctuations are revealed at steady state, which may play a critical role in driving flagellar switching and cell tumbling. When the network is stimulated chemically to higher activity, fluctuations dramatically decrease. A stochastic theoretical model, inspired by work on gene expression noise, points to CheY activation occurring in bursts, driving CW bias fluctuations. This model also shows that an intrinsic kinetic ceiling on network activity places an upper limit on activated CheY and CW bias, which when encountered suppresses network fluctuations. This limit may also prevent cells from tumbling unproductively in steep gradients.
Organ-specificity of sterol and triterpene accumulation inArabidopsis thaliana
Authors: Lange B. Markus , Poirier Brenton C. , Lange Iris , Schumaker Richard , Rios-Estepa Rigoberto
Published: March 2020

Sterols serve essential functions as membrane constituents and hormones (brassinosteroids) in plants, while non-sterol triterpenoids have been implicated in defense responses. Surprisingly little is known about the sterol and triterpene profiles in different plant organs. To enhance our understanding of organ-specific sterol and triterpene accumulation, we quantified these metabolite classes in four different organs (root, stem, leaf, seed) ofArabidopsis thaliana(L.). Based on these data sets we developed kinetic mathematical models of sterol biosynthesis to capture flux distribution and pathway regulation in different organs. Simulations indicated that an increased flux through the sterol pathway would not only result in an increase of sterol end products but also a concomitant build-up of certain intermediates. These computational predictions turner out to be consistent with experimental data obtained with transgenic plants ectopically overexpressing 3-hydroxy-3-methylglutary-coenzyme A reductase (HMG1gene). The opportunities and limitations of incorporating mathematical modeling into the design of approaches to engineer sterol biosynthesis are discussed.
Maternal vitamin D deficiency increases the risk of obesity in male mice offspring by affecting the immune response
Authors: Li Pei , Li Ping , Liu Yuanlin , Liu Weijiang , Zha Lanlan , Chen Xiaoyu , Zheng Rongxiu , Qi Kemin , zhang Yi
Published: March 2020

Recently, many epidemiological and animal studies have indicated that obesity have their origin in the early stages of life including the inappropriate balance of some nutrients, the objective of this study is to determine the risk of obesity in male mice offspring as a consequence of maternal VD deficiency-mediated disordering of the immune response. Four-week-old C57BL/6J female mice were fed VD-deficient or normal reproductive diets during pregnancy and lactation. Their male offspring were weighted and euthanized after being fed control and high-fat diets (HFD) for 16 weeks starting at the weaning. The serum was collected for biochemical analyses. Epididymal (eWAT) and inguinal (iWAT) white adipose tissues were excised for histological examination, immunohistochemistry, gene expressions of inflammatory factors, and for determining the proportions of immune cells by flow cytometry. Insufficient maternal VD intake exacerbated the development of obesity both in non-obese and obese male offspring as evidenced by larger adipose cells and abnormal glucose and lipid metabolisms. Also, the expression of proinflammatory cytokine genes was increased and that of anti-inflammatory cytokines was decreased in maternal VD-deficient groups in the eWAT and/or iWAT. This was accompanied by higher levels of TNF-α or/and INF-β, and lower levels of IL-4 and IL-10. Insufficient maternal VD intake was also observed to induce a shift in the profiles of immune cells in the eWAT and/or iWAT, resulting in increased percentages of M1 macrophage, ATDCs, and CD4+and CD8+T cells, but caused a significant decrease in the percentage of M2 macrophages, both in non-obese and obese male offspring. All these changes in the immune cell profile were more obvious in the eWAT than in the iWAT. These results indicated that insufficient maternal VD intake promoted the development of obesity in male offspring by modulating the immune cell populations and causing a polarization in the adipose depots.

Importance

Evidence in this study has indicated that insufficient maternal VD intake promotes the development of obesity in the male offspring by modulating the recruitment of immune cell populations and their polarization as well as the expression and secretion of proinflammatory adipokines in the adipose depots in a weight-independent manner, which is more obvious in eWAT than that in the iWAT.