bluuebunny/crossref_metadata_2025 huggingface dataset:
Upon microbial challenge human neutrophils undergo rapid changes in nuclear architecture to orchestrate an immediate inflammatory gene program
Authors: Denholtz Matthew , Zhu Yina , He Zhaoren , Lu Hanbin , Isoda Takeshi , Döhrmann Simon , Nizet Victor , Murre Cornelis
Published: October 2019

Differentiating neutrophils undergo large-scale changes in nuclear morphology. How such alterations in structure are established and modulated upon exposure to microbial agents is largely unknown. Here, we found that prior to encounter with bacteria, an armamentarium of inflammatory genes was positioned in a transcriptionally passive environment suppressing premature transcriptional activation. Upon microbial exposure, however, human neutrophils rapidly (<3 hours) repositioned the ensemble of pro-inflammatory genes towards the transcriptionally permissive compartment. We show that the repositioning of genes was closely associated with the swift recruitment of cohesin across the inflammatory enhancer landscape permitting an immediate transcriptional response upon bacterial exposure. These data reveal at the mechanistic level how upon microbial challenge human neutrophils undergo rapid changes in nuclear architecture to orchestrate an immediate inflammatory gene program.
Development of CRSIPR-Cas13a-based antimicrobials capable of sequence-specific killing of target bacteria
Authors: Kiga Kotaro , Tan Xin-Ee , Ibarra-Chávez Rodrigo , Watanabe Shinya , Aiba Yoshifumi , Sato’o Yusuke , Li Feng-Yu , Sasahara Teppei , Cui Bintao , Kawauchi Moriyuki , Boonsiri Tanit , Thitiananpakorn Kanate , Taki Yusuke , Azam Aa Haeruman , Suzuki Masato , Penadés José R , Cui Longzhu
Published: October 2019

Emergence of antimicrobial-resistant bacteria is an increasingly serious threat to global health, necessitating the development of innovative antimicrobials. We established a series of CRISPR-Cas13a-based antibacterial nucleocapsid, termed CapsidCas13a(s), capable of sequence-specific killing of carbapenem-resistant Escherichia coli and methicillin-resistant Staphylococcus aureus through promiscuous RNA cleavage after recognizing corresponding antimicrobial resistance genes. CapsidCas13a constructs were generated by packaging CRISPR-Cas13a into a bacteriophage capsid to target antimicrobial resistance genes. Contrary to Cas9-based antimicrobials that lack bacterial killing capacity when the target genes are located on a plasmid, the CapsidCas13a(s) exhibited strong bacterial killing activities upon recognizing target genes regardless of their location. The antimicrobials’ treatment efficacy was confirmed using a Galleria mellonella larvae model. Further, we demonstrated that the CapsidCas13a(s) can assist in bacterial gene detection without employing nucleic acid amplification and optical devices.
Impact of upstream landslide on perialpine lake ecosystem: an assessment using multi-temporal satellite data
Authors: Villa Paolo , Bresciani Mariano , Bolpagni Rossano , Braga Federica , Bellingeri Dario , Giardino Claudia
Published: October 2019

Monitoring freshwater and wetland systems and their response to stressors of natural or anthropogenic origin is critical for ecosystem conservation.

A multi-temporal set of 87 images acquired by Sentinel-2 satellites over three years (2016-2018) provided quantitative information for assessing the temporal evolution of key ecosystem variables in the perialpine Lake Mezzola (northern Italy), which was suffered from the impacts of a massive landslide that took place upstream of the lake basin in summer 2017.

Sentinel-2 derived products revealed an increase in lake turbidity triggered by the landslide that amounted to twice the average values scored in the years preceding and following the event. Hotspots of turbidity within the lake were in particular highlighted. Moreover both submerged and riparian vegetation showed harmful impacts due to sediment deposition. A partial loss of submerged macrophyte cover was found, with delayed growth and a possible community shift in favor of species adapted to inorganic substrates. Satellite-derived seasonal dynamics showed that exceptional sediment load can overwrite climatic factors in controlling phenology of riparian reed beds, resulting in two consecutive years with shorter than normal growing season, and roughly 20% drop in productivity according to spectral proxies: compared to 2016, senescence came earlier by around 20 days on average in 2017 season, and green-up was delayed by up to 50 days (20 days, on average) in 2018, following the landslide.

The approach presented could be easily implemented for continuous monitoring of similar ecosystems subject to external pressures with periods of high sediment loads.
Bread feeding is a robust and more physiological enteropathogen administration method compared to oral gavage
Authors: Derbise Anne , Echenique-Rivera Hebert , Garcia-Lopez Marta , Beau Rémi , Mattei Myriam , Dersch Petra , Pizarro-Cerdá Javier
Published: October 2019

Oral administration is a preferred model for studying infection by bacterial enteropathogens such asYersinia. In the mouse model, the most frequent method for oral infection consists of oral gavage with a feeding needle directly introduced in the animal stomach via the esophagus. In this study, we compared needle gavage to bread feeding as an alternative mode of bacterial administration. Using a bioluminescence-expressing strain ofYersinia pseudotuberculosis, we detected very early upon needle gavage a bioluminescent signal in the neck area together with a signal in the abdominal region, highlighting the presence of two independent sites of bacterial colonization and multiplication. Bacteria were often detected in the esophagus and trachea, as well as in the lymph nodes draining the salivary glands, suggesting that lesions made during needle introduction into the animal oral cavity lead to rapid bacterial draining to proximal lymph nodes. We then tested an alternative mode of bacterial administration using small pieces of white bread containing bacteria. Upon bread feeding infection, mice exhibited a stronger bioluminescent signal in the abdominal region as compared to needle gavage, and no signal was detected in the neck area. Moreover,Y. pseudotuberculosisincorporated in the bread is less susceptible to the acidic environment of the stomach and is therefore more efficient in causing intestinal infections. Based on our observations, bread feeding constitutes a natural and more efficient administration method which does not require specialized skills, is less traumatic for the animal, and results in diseases that more closely mimic food-borne intestinal infection.
Ageing before birth: pace and stability of prenatal growth affect telomere dynamics
Authors: Stier Antoine , Metcalfe Neil B. , Monaghan Pat
Published: October 2019

Pre-natal effects on telomere length are increasingly recognized as a potential contributor to the developmental origin of health and adult diseases. While it is becoming clear that telomere length is strongly influenced by pre-natal conditions, the factors affecting telomere dynamics during embryogenesis remain poorly understood. We manipulated both the pace and stability of prenatal growth using incubation temperature in Japanese quail and investigated the impact on telomere dynamics from embryogenesis to adulthood, along with potential drivers of telomere shortening such as oxidative damage and prenatal glucocorticoid levels. Telomere length was not affected by these manipulations for the first 75% of prenatal development, but was reduced at hatching in response to both experimentally induced fast embryo growth and growth instability. These early-life effects on telomere length persisted until adulthood. The effect of developmental instability on telomere length at hatching was potentially mediated by an increased secretion of glucocorticoid hormones during development. Both the pace and the stability of prenatal growth appear as key factors determining telomere length and dynamics up to adulthood, with fast and unstable embryo growth leading to short telomeres with the potential for adverse associated outcomes in terms of reduced longevity and greater risk of disease.
Breeding behaviour and productivity of Black-necked crane (Grus nigricolis) in Ladakh, Indian Trans-Himalaya
Authors: Chandan Pankaj , Ahmed Tanveer , Khan Afifullah
Published: October 2019

A long-term study was conducted to understand some aspects of breeding biology of Black-necked crane (Grus nigricollis) in Changthang, Ladakh. Data on aspects such as the breeding season, courtship, mating, egg laying and incubation period, nest site fidelity, egg morphometry, breeding productivity and recruitment rate were collected between 2003 and 2012. Black-necked crane started arriving from last week of March to first half of April and showed fidelity at ten nesting sites. Courtship and mating peaked early morning (0700 hours), around noon (1100 hours) and in late evening (0600 hours) while the nest building at evening (1600 hours). The egg laying period initiated in May and extended up to July. The average incubation period was 33.88±0.3 days. Hatching success, nest survival rate and fledgling increment rate of the bird were 73.3%, 0.55 ± 0.03 and 0.41 ± 0.02 respectively with an overall breeding productivity of 0.73. The present population of Black-necked crane in Changthang, Ladakh seems to stable with an average recruitment rate of 15.7±1.4.
Genetic determinants of multi-drug resistance inAcinetobacter baumanniiat an academic hospital in Pretoria, South Africa
Authors: Nogbou Noel-David , Thabiso Phofa Dikwata , Nchabeleng Maphoshane , Musyoki Andrew Munyalo
Published: October 2019

Antimicrobial resistance is now globally recognised as the greatest threat to human health.Acinetobacter baumanniis’(A. baumannii) clinical significance has been driven by its ability to obtain and transmit antimicrobial resistance factors. In South Africa,A. baumanniiis a leading cause of healthcare associated infections (HAI). In this study, we investigated the genetic determinants of multi-drug resistantA. baumannii(MDRAB) at a teaching hospital in Pretoria, South Africa.

One hundred non repetitive isolates ofA. baumanniiwere collected for the study at Dr George Mukhari Tertiary Laboratory (DGMTL). Antimicrobial susceptibility testing was performed using the VITEK2 system (bioMerieux, France). The prevalence of common resistance associated genes and AdeABC efflux pump system associated genes were investigated using conventional PCR. Genetic relatedness of isolates was then determined using rep-PCR.

Seventy (70) of 100 isolates collected were confirmed to be multi-drug resistant and wereblaOXA51positive. Phenotypically, the isolates where resistant to almost all tested antibiotics. However, one isolate showed intermediate susceptibility to tigecycline while all were susceptible to colistin. Oxacillinase encoding geneblaOXA-23was the most detected at 99% and only 1% was positive forblaOXA-40. The PCR results for metallo-betalactamase (MBL) encoding genes showed that MBLblaVIMwas the most frequently detected at 86% andblaSIM-1at 3% was the least detected. Out of 70 isolates, 56 isolates had the required gene combination for an active efflux pump. The most prevalent clone was clone A at 69% of the isolates. Regarding treatment; colistin and tigecycline are the most effective against strains encountered at DGMTL as all tested carbapenems seem to have lost their effectiveness.

The major genotypic determinants for drug resistances are oxacillinases:blaOXA-51(100%) andblaOXA-23(99%). The study reports for the first time,blaOXA-40andblaSIM-1detection inA. baumanniiin South Africa.
Isolation of the Astacin-like metalloprotease coding gene (astl) and assessment of its insecticidal activity againstSpodoptera littoralisandSitophilus oryzae
Authors: Diab Mervat R. , Hussein Ibtissam H.A. , Ahmed Mahmoud M. , Mohammed Ahmed
Published: October 2019

Astacin- like metalloprotease (astl) is a multi-domain metallopeptidase that has protease activity against a number of organisms; including fish, frogs, birds and insects. In this present investigation, the full length ofastlcDNA was cloned from spider species,Hasarius adansoni. Sequencing of the clonedastlcDNA proved that its full length including 802 bp with 714bp open reading frame encoding for 238 amino acids. The catalytic domain comprised of 489 nts was cloned and expressed by the yeast expression systemPichia pastorisand its insecticidal activity was determined against two species of agricultural insectsSpodoptera littoralis(Lepidoptera:Noctuidae) andSitophilus oryzae(Coleoptera:Curculionidae). Bioassay was performed using three concentrations (100,500 and 1000 ppm) for four days forS. littoralisand 14 days forS. oryzae.In addition, the astl was fused to the GNA snowdrop lectin in the same frame and expressed inP. pastoris. The synergistic effect of astl and GNA was examined on theS. littoralislarvae andS. oryzaeadults. The mortality percentages of the fused protein (Ha-astl/GNA) “1000 ppm” after 4 days, were 78.6%± 4.16 and 71.66% ±3.51 for first and second spodpotera larval instars, respectively. While, lower mortality of the fused protein of the same concentration was observed onS. oryzaeadults, 49.3±2.08 %.
TLR2 signaling pathway combats Streptococcus uberis infection by inducing production of mitochondrial reactive oxygen species
Authors: Li Bin , Wan Zhixin , Wang Zhenglei , Zuo Jiakun , Xu Yuanyuan , Han Xiangan , Phouthapane Vanhnaseng , Miao Jinfeng
Published: October 2019

Mastitis caused by Streptococcus uberis is a hazardous clinical disease in dairy animals. In this study, the role of Toll-like receptors (TLRs) and TLR-mediated signaling pathways in mastitis caused by S. uberis was investigated using mouse models and mammary epithelial cells (MECs). We used S. uberis to infect mammary glands of wild type, TLR2−/− and TLR4−/− mice and quantified the adaptor molecules in TLR signaling pathways, proinflammatory cytokines, tissue damage and bacterial count in mammary glands. When compared with TLR4 deficiency, TLR2 deficiency induced more severe pathological changes through myeloid differentiation primary response 88 (MyD88)-mediated signaling pathways during S. uberis infection. In MECs, TLR2 detected S. uberis infection and induced mitochondrial reactive oxygen species (mROS) to assist host control of secretion of inflammatory factors and elimination of intracellular S. uberis. Our results demonstrate that TLR2-mediated mROS have a significant effect on S. uberis-induced host defense responses in mammary glands as well as MECs.

Author summary

S. uberis contributes significantly to global mastitis and remains a major obstacle for inflammation elimination due to its ability to form persistent infection in mammary tissue. The Toll-like receptor (TLR) family plays a significant role in identifying infections of intracellular bacteria and further triggering inflammatory reactions in immune cells. However, the detailed molecular mechanism by which TLR is regulated, and whether MECs, as the main cells in mammary gland, are tightly involved in these processes is poorly understood. Here, we used S. uberis to infect mammary glands of wild type, TLR2−/−, TLR4−/− mice and MECs to assess pathogenesis, proinflammatory cytokines, ROS as well as mROS levels during infection. We found that during S.uberis infection, it is TLR2 deficiency that induced more severe pathological changes through MyD88-mediated signaling pathways. In addition, our work demonstrates that mROS mediated by TLR2 has an important role in host defense response to combat S. uberis infection in mammary glands as well as MECs.
Salt-inducible kinases (SIKs) regulate TGFβ-mediated transcriptional and apoptotic responses
Authors: Hutchinson Luke D. , Darling Nicola J. , Nicolaou Stephanos , Gori Ilaria , Squair Daniel R. , Cohen Philip , Hill Caroline S. , Sapkota Gopal P.
Published: October 2019

Abstract

The signalling pathways initiated by members of the transforming growth factor-β (TGFβ) family of cytokines control many metazoan cellular processes, including proliferation and differentiation, epithelial-mesenchymal transition (EMT), and apoptosis. TGFβ signalling is therefore strictly regulated to ensure appropriate context-dependent physiological responses. In an attempt to identify novel regulatory components of the TGFβ signalling pathway, we performed a pharmacological screen using a cell line engineered to report the endogenous transcription of the TGFβ-responsive target genePAI-1. The screen revealed that small-molecular inhibitors of salt-inducible kinases (SIKs) attenuate TGFβ-mediated transcription ofPAI-1without affecting receptor-mediated SMAD phosphorylation, SMAD complex formation or nuclear translocation. We provide evidence that genetic inactivation of SIK isoforms also attenuates TGFβ-dependent transcriptional responses. Pharmacological inhibition of SIKs using multiple small-molecule inhibitors potentiated apoptotic cell death induced by TGFβ stimulation. Our data therefore provides evidence for a novel function of SIKs in modulating TGFβ-mediated transcriptional and cellular responses.
RecA levels modulate biofilm development inAcinetobacter baumannii
Authors: Ching Carly , Brychcy Merlin , Nguyen Brian , Muller Paul , Reverdy Alicyn , Downs Margaret , Regan Samuel , Isley Breanna , Fowle William , Chai Yunrong , Godoy Veronica G.
Published: October 2019

Infections caused byAcinetobacter baumannii,a Gram-negative opportunistic pathogen, are difficult to eradicate due to the bacterium’s propensity to quickly gain antibiotic resistances and form biofilms, a protective bacterial multicellular community. TheA. baumanniiDNA damage response (DDR) mediates the antibiotic resistance acquisition and regulates RecA in an atypical fashion; both RecALowand RecAHighcell types are formed in response to DNA damage. The findings of this study demonstrate that the levels of RecA can influence the development, formation and dispersal, of biofilms through the global biofilm regulatorbfmR. RecA loss results in surface attachment and prominent biofilms, while elevated RecA leads to diminished attachment and dispersal. These findings suggest that the challenge to treatA. baumanniiinfections may be explained by the induction of the DDR, common during infection, as well as the delicate balance between maintaining biofilms in low RecA cells, and promoting mutagenesis and dispersal in high RecA cells. This study underscores the importance of understanding the fundamental biology of bacteria to develop more effective treatments for infections.
Inferring the structures of signaling motifs from paired dynamic traces of single cells
Authors: Haggerty R. A. , Purvis Jeremy E.
Published: October 2019

Individual cells show variability in their signaling dynamics that often correlates with phenotypic responses, indicating that cell-to-cell variability is not merely noise but can have functional consequences. Based on this observation, we reasoned that cell-to-cell variability under the same treatment condition could be explained by a single signaling motif that deterministically maps different upstream signals into a corresponding set of downstream responses. If this assumption holds, then repeated measurements of upstream and downstream signaling dynamics in single cells could provide information about the underlying signaling motif for a given pathway, even when no prior knowledge of that motif exists. To test these two hypotheses, we developed a computer algorithm called MISC (Motif Inference from Single Cells) that infers the underlying signaling motif from paired time-series measurements from individual cells. When applied to measurements of transcription factor and reporter gene expression in the yeast stress response, MISC predicted signaling motifs that were consistent with previous mechanistic models of transcription. The ability to detect the underlying mechanism became less certain when a cell’s upstream signal was randomly paired with another cell’s downstream response, demonstrating how averaging time-series measurements across a population obscures information about the underlying signaling mechanism. In some cases, motif predictions improved as more cells were added to the analysis. These results provide evidence that mechanistic information about cellular signaling networks can be embedded within the dynamical patterns of single cells.

Author Summary

Cells use molecular signaling networks to translate dynamically changing stimuli into appropriate downstream responses. Specialized network structures, or motifs, allow cells to properly decode a variety of temporal input signals. In this paper, we present an algorithm that infers signaling motifs from multiple examples of an upstream signal paired with its downstream response in the same cell. We compare the predictive power of single-cell versus averaged time-series traces and the incremental benefit of adding more single-cell traces to the algorithm. We use this approach to understand how yeast respond to environmental stresses.
Evolutionary impact of size-selective harvesting on shoaling behavior: Individual-level mechanisms and possible consequences for natural and fishing mortality
Authors: Sbragaglia Valerio , Klamser Pascal P. , Romanczuk Pawel , Arlinghaus Robert
Published: October 2019

Intensive and size-selective harvesting is an evolutionary driver of life-history as well as individual behavioral traits. Yet, whether and to what degree harvesting modifies the collective behavior of exploited species is largely unknown. We present a multi-generation harvest selection experiment with zebrafish (Danio rerio) as a model species to understand the effects of size-selective harvesting on shoaling behavior. The experimental system is based on a large-harvested (typical of most wild capture fisheries targeting larger size classes) and small-harvested (typical of specialized fisheries and gape-limited predators targeting smaller size classes) selection lines. By combining high resolution tracking of fish behavior with computational agent-based modeling we show that shoal cohesion changed in the direction expected by a trade-off between vigilance and the use of social cues. In particular, we document a decrease of vigilance in the small-harvested line, which was linked to an increase in the attention to social cues, favoring more cohesive shoals. Opposing outcomes were found for the large-harvested line, which formed less cohesive shoals. Using the agent-based model we outline possible consequences of changes is shoaling behavior for both fishing and natural mortality. The changes in shoaling induced by large size-selective harvesting may decrease fishing mortality, but increase mortality by natural predators. Our work suggests an insofar overlooked evolutionary mechanism by which size-selective harvesting can affect mortality and in turn population dynamics of exploited fish.
Involvement of orexin/hypocretin in the expression of social play behaviour in juvenile rats
Authors: Reppucci Christina J. , Gergely Cassandra K. , Bredewold Remco , Veenema Alexa H.
Published: October 2019

Social play is a highly rewarding and motivated behaviour displayed by juveniles of many mammalian species. We hypothesized that the orexin/hypocretin (ORX) system is involved in the expression of juvenile social play behaviour because this system is interconnected with brain regions that comprise the social behaviour and mesocorticolimbic reward networks. We found that exposure to social play increased recruitment of ORX-A neurons in juvenile rats. Furthermore, central administration of ORX-A decreased social play duration, while central blockade of ORX-1 receptors differentially altered social play duration in juvenile rats with low versus high baseline levels of social play (increasing social play in low baseline social play individuals and decreasing social play in high baseline social play individuals). Together, our results provided the first evidence of a role for the ORX system in the modulation of juvenile social play behaviour.
Synchronized eye movements predict test scores in online video education
Authors: Madsen Jens , Julio Sara U. , Gucik Pawel J. , Steinberg Richard , Parra Lucas C.
Published: October 2019

Experienced teachers pay close attention to their students, adjusting their teaching when students seem lost. This dynamic interaction is missing in online education. We propose to measure attention to online videos remotely by tracking eye movements, as we hypothesize that attentive students follow videos similarly with their eyes. Here we show that inter-subject correlation of eye-movements during instructional video presentation is substantially higher for attentive students, and that synchronized eye movement are predictive of individual test scores on the material presented in the video. These findings replicate for videos in a variety of production styles, learning scenarios and for recall and comprehension questions alike. We reproduce the result using standard web cameras to capture eye-movements in a classroom setting, and with over 1,000 participants at-home without the need to transmit user data. Our results suggest that online education could be made adaptive to a student’s level of attention in real-time.
Optimal Multichannel Artifact Prediction and Removal for Brain Machine Interfaces and Neural Prosthetics
Authors: Sadeghi Najafabadi Mina , Chen Longtu , Dutta Kelsey , Norris Ashley , Feng Bin , Schnupp Jan WH , Rosskothen-Kuhl Nicole , Read Heather , Escabi Monty
Published: October 2019

Neural implants that electrically stimulate neural tissue such as deep brain stimulators, cochlear implants (CI), and vagal nerve stimulators are becoming the routine treatment options for various diseases. Optimizing electrical stimulation paradigms requires closed-loop stimulation using simultaneous recordings of evoked neural activity in real time. Stimulus-evoked artifacts at the recording site are generally orders of magnitude larger than the neural signals, which challenge the interpretation of evoked neural activity. We developed a generalized artifact removal algorithm that can be applied in a variety of neural recording modalities. The procedure leverages known electrical stimulation currents to derive optimal filters that are used to predict and remove artifacts. We validated the procedure using paired recordings and electrical stimulation from sciatic nerve axons, high-rate bilateral CI stimulation, and concurrent multichannel stimulation in auditory midbrain and recordings in auditory cortex. We demonstrate a vast enhancement in the quality of recording even for high-throughput multi-site stimulation with typical improvements in the signal-to-noise ratio between 20-40 dB. The algorithm is efficient, can be scaled to arbitrary number of sites, and is applicable in range of recording modalities. It has numerous benefits over existing approaches and thus should be valuable for emerging neural recording and stimulation technologies.
Individual neuronal subtypes control initial myelin sheath growth and stabilization
Authors: Nelson Heather N. , Treichel Anthony J. , Eggum Erin N. , Martell Madeline R. , Kaiser Amanda J. , Trudel Allie G. , Gronseth James R. , Maas Samantha T. , Bergen Silas , Hines Jacob H.
Published: October 2019

Background

In the developing central nervous system, pre-myelinating oligodendrocytes sample candidate nerve axons by extending and retracting process extensions. Some contacts stabilize, leading to the initiation of axon wrapping, nascent myelin sheath formation, concentric wrapping and sheath elongation, and sheath stabilization or pruning by oligodendrocytes. Although axonal signals influence the overall process of myelination, the precise oligodendrocyte behaviors that require signaling from axons are not completely understood. In this study, we investigated whether oligodendrocyte behaviors during the early events of myelination are mediated by an oligodendrocyte-intrinsic myelination program or are over-ridden by axonal factors.

Methods

To address this, we utilized in vivo time-lapse imaging in embryonic and larval zebrafish spinal cord during the initial hours and days of axon wrapping and myelination. Transgenic reporter lines marked individual axon subtypes or oligodendrocyte membranes.

Results

In the larval zebrafish spinal cord, individual axon subtypes supported distinct nascent sheath growth rates and stabilization frequencies. Oligodendrocytes ensheathed individual axon subtypes at different rates during a two-day period after initial axon wrapping. When descending reticulospinal axons were ablated, local spinal axons supported a constant ensheathment rate despite the increased ratio of oligodendrocytes to target axons.

Conclusion

We conclude that properties of individual axon subtypes instruct oligodendrocyte behaviors during initial stages of myelination by differentially controlling nascent sheath growth and stabilization.
Mother machine image analysis with MM3
Authors: Sauls John T. , Schroeder Jeremy W. , Brown Steven D. , Treut Guillaume Le , Si Fangwei , Li Dongyang , Wang Jue D. , Jun Suckjoon
Published: October 2019

The mother machine is a microfluidic device for high-throughput time-lapse imaging of microbes. Here, we present MM3, a complete and modular image analysis pipeline. MM3 turns raw mother machine images, both phase contrast and fluorescence, into a data structure containing cells with their measured features. MM3 employs machine learning and non-learning algorithms, and is implemented in Python. MM3 is easy to run as a command line tool with the occasional graphical user interface on a PC or Mac. A typical mother machine experiment can be analyzed within one day. It has been extensively tested, is well documented and publicly available via Github.
Presence or absence of Ras-dimerization shows distinct kinetic signature in Ras-Raf interaction
Authors: Sarkar Sumantra , Garcia Angel E.
Published: October 2019

In eukaryotes, MAPK pathways play a central role in making several important cellular decisions, including cell proliferation and development of an organism. Ras, a small GTPase, interacts with the protein Raf to create activated Ras-Raf complex (Raf dimer) that activates the downstream effectors in the ERK pathway, one of the many MAPK pathways. Malfunctioning Ras-Raf “switches” cause almost 30% of all known cancer. Hence, understanding Ras-Raf interaction is of paramount importance. Despite decades of research, the detailed mechanism of Ras-Raf interaction is still unclear. It has been hypothesized that Ras dimerization is necessary to create the activated Raf dimer. Although there are circumstantial evidences supporting the Ras dimerization hypothesis, direct proof of Ras dimerization is still inconclusive. In the absence of conclusive direct experimental proof, this hypothesis can only be examined through indirect evidences of Ras dimerization. In this paper, using a multi-scale simulation technique, we provide multiple criteria that distinguishes an activation mechanism involving Ras dimerization from another mechanism that does not involve Ras dimerization. The provided criteria will be useful in the investigation of not only Ras-Raf interaction but also other two-protein interactions.
Integrating ensemble systems biology feature selection and bimodal deep neural network for breast cancer prognosis prediction
Authors: Cheng Li-Hsin , Lin Che
Published: October 2019

Motivation

Breast cancer is a heterogeneous disease. In order to guide proper treatment decisions for each individual patient, there is an urgent need for robust prognostic biomarkers that allow reliable prognosis prediction. Gene feature selection on microarray data is an approach to systematically discover potential biomarkers. However, common pure-statistical feature selection approaches often fail to incorporate prior biological knowledge and thus tend to select genes that lack biological insights. In addition, due to the high dimensionality and low sample size properties of microarray data, selecting robust gene features is an intrinsically challenging problem. We therefore combined systems biology feature selection with ensemble learning in this study, aiming to address the above challenges and select genes with biological insights, as well as robust prognostic predictive power. Moreover, in order to capture the complex molecular processes of breast cancer, where multiple disease-contributing genes may exist and interact, we adopted a multi-gene approach to predict the prognosis status using machine learning classifiers.

Results

We systematically evaluated three different ensemble approaches that all improved the original systems biology feature selector. We found that compared to the most popular data-perturbation approach, function perturbation can produce significant improvement with just a few ensembles. Among all, the hybrid ensemble approach led to the most robust feature selection result, and the identified genes were shown to be highly involved in pathways, such as ubiquitination and cell cycle. Final prognosis prediction models were constructed using the identified genes and clinical information as input features. Among all models, bimodal deep neural network (DNN) achieved the highest AUC (area under receiver operating characteristic curve) in test performance evaluation, where subsequent survival analysis also verified its ability to differentiate patients with different prognosis statuses. In summary, the study demonstrated the potential of ensemble learning to improve gene feature selection robustness, as well as the potential of bimodal DNN in providing reliable prognosis prediction and guiding precision medicine.
Paradigm of Vanadium pentoxide nanoparticle-induced autophagy and apoptosis in triple-negative breast cancer cells
Authors: Pillai Suma Parvathy Radhakrishna , Padmanabhan Renjini A. , Telukutla Srinivasa Reddy , Ravindran Rishith , Velikkakath Anoop Kumar G. , Dekiwadia Chaitali D. , Paul Willi , Shenoy Sachin J. , Laloraya Malini , Srinivasula Srinivasa M. , Bhosale Sheshanath V. , Jayasree Ramapurath S.
Published: October 2019

Chemo-resistance remains the main hurdle to cancer therapy, challenging the improvement of clinical outcomes in cancer patients. Therefore, exploratory studies to address chemo-resistance through various approaches are highly rewarding. Nanomedicine is a promising recent advancement in this direction. Comprehensive studies to understand the precise molecular interactions of nanomaterials is necessary to validate their specific “nano induced” effects. Here, we illustrate in detail the specific biological interactions of vanadium pentoxide nanoparticles (VnNp) on triple-negative breast cancer cells and provide initial insights towards its potential in breast cancer management at the cellular level. VnNp shows a time-dependent anti-oxidant and pro-oxidant property in vitro. These nanoparticles specifically accumulate in the lysosomes and mitochondria, modulate various cellular processes including impaired lysosomal function, mitochondrial damage, and induce autophagy. At more extended periods, VnNp influences cell cycle arrest and inhibits cell migration potentiating the onset of apoptosis. Preliminary in vivo studies, on exposing healthy Swiss albino mice to VnNp demonstrated normal blood parameters, organ distribution, and tissue redox balance which further indicated the absence of any adverse organ toxicity. Hence, we foresee tumor-targeting VnNp as a potential drug molecule for future cancer management.
Estimates of cortical column orientation improve MEG source inversion
Authors: Bonaiuto James J , Afdideh Fardin , Ferez Maxime , Wagstyl Konrad , Mattout Jérémie , Bonnefond Mathilde , Barnes Gareth R , Bestmann Sven
Published: October 2019

Determining the anatomical source of brain activity non-invasively measured from EEG or MEG sensors is challenging. In order to simplify the source localization problem, many techniques introduce the assumption that current sources lie on the cortical surface. Another common assumption is that this current flow is orthogonal to the cortical surface, thereby approximating the orientation of cortical columns. However, it is not clear which cortical surface to use to define the current source locations, and normal vectors computed from a single cortical surface may not be the best approximation to the orientation of cortical columns. We compared three different surface location priors and five different approaches for estimating dipole vector orientation, both in simulations and visual and motor evoked MEG responses. We show that models with source locations on the white matter surface and using methods based on establishing correspondences between white matter and pial cortical surfaces dramatically outperform models with source locations on the pial or combined pial/white surfaces and which use methods based on the geometry of a single cortical surface in fitting evoked visual and motor responses. These methods can be easily implemented and adopted in most M/EEG analysis pipelines, with the potential to significantly improve source localization of evoked responses.
Mechano-modulatory synthetic niches for liver organoid derivation
Authors: Sorrentino Giovanni , Rezakhani Saba , Yildiz Ece , Nuciforo Sandro , Heim Markus H. , Lutolf Matthias P. , Schoonjans Kristina
Published: October 2019

The recent demonstration that primary cells from the liver can be expanded in vitro as organoids holds enormous promise for regenerative medicine and disease modeling1–5. The use of three-dimensional (3D) cultures based on ill-defined and potentially immunogenic matrices, however, hampers the translation of liver organoid technology into real-life applications6. We here used chemically defined hydrogels for the efficient derivation of both mouse and human hepatic organoids. Organoid growth was found to be highly stiffness-sensitive and dependent on yes-associated protein 1 (YAP) activity. However, in contrast to intestinal organoids7, YAP-mediated stiffness sensitivity was independent of acto-myosin contractility, requiring instead activation of the Src family of kinases (SFKs). Aberrant matrix stiffness on the other hand led to a shift in the progenitor phenotype, resulting in compromised proliferative capacity. Finally, we demonstrate the unprecedented establishment of biopsy-derived human liver organoids without the use of animal components at any step of the process. Our approach thus opens up exciting perspectives for the establishment of protocols for liver organoid-based regenerative medicine.
Analysis of genetically independent phenotypes identifies shared genetic factors associated with chronic musculoskeletal pain at different anatomic sites
Authors: Tsepilov Yakov A. , Freidin Maxim B. , Shadrina Alexandra S. , Sharapov Sodbo Z. , Elgaeva Elizaveta E. , van Zundert Jan , Karssen Lennart C. , Suri Pradeep , Williams Frances M.K. , Aulchenko Yurii S.
Published: October 2019

Chronic musculoskeletal pain has a negative impact on all aspects of human life. Genetic studies of pain are complicated by the high complexity and heterogeneity of pain phenotypes. In this research, we aimed to reduce phenotype heterogeneity and reveal genes and pathways shared by chronic musculoskeletal pain at four locations: back, neck/shoulder, hip, and knee. Our study was based on the results of genome-wide association studies performed using UK Biobank data with a total sample size of 456,000 individuals. We applied principal component analysis based on the matrix of genetic covariances between the studied pain traits and constructed four genetically independent phenotypes (GIPs). The leading GIP (GIP1) explains the largest proportion of the genetic variance of and covariance between the analyzed phenotypes (78.4%), and the later GIPs (GIP2-4) explain progressively less. We identified and replicated five loci associated with GIP1 and one locus associated with GIP2. The genes decisively prioritized for the GIP1-associated loci were SLC39A8, ECM1, and FOXP2. For the remaining two GIP1-associated loci, we proposed several candidates (AMIGO3, BSN, RBM6, FAM212A, RNF123, UBA7 and MIR7114, NSMF, NOXA1, GRIN1), but were unable to prioritize any of them convincingly. The most likely causal gene in the locus associated with GIP2 was GDF5. For GIP1, gene set/tissue/cell type enrichment analyses identified multiple terms related to the nervous system. Genetic correlations analysis revealed a genetic overlap between GIP1 and osteoarthritis as well as a set of anthropometric (such as overweight and waist circumference), sociodemographic (such as age of first birth and college completion) and psychiatric/personality (such as depressive symptoms and neuroticism) traits. We suggest that GIP1 represents a biopsychological component of chronic musculoskeletal pain, related to physiological and psychological aspects and likely reflecting pain perception and processing.
Empirical Analysis of Phylogenetic Quasi-Terraces
Authors: Breitling Paula , Stamatakis Alexandros , Chernomor Olga , Bettisworth Ben , Reszczynski Lukasz
Published: October 2019

Abstract

Terraces in phylogenetic tree space are, among other things, important for the design of tree space search strategies. While the phenomenon of phylogenetic terraces is already known for unlinked partition models on partitioned phylogenomic data sets, it has not yet been studied if an analogous structure is present under linked and scaled partition models. To this end, we analyze aspects such as the log-likelihood distributions, likelihood-based significance tests, and nearest neighborhood interchanges on the trees residing on a terrace and compare their distributions among unlinked, linked, and scaled partition models. Our study shows that there exists a terrace-like structure under linked and scaled partition models as well. We denote this phenomenon as quasi-terrace. Therefore quasi-terraces should be taken into account in the design of tree search algorithms as well as when reporting results on ‘the’ final tree topology in empirical phylogenetic studies.
Tandem paired nicking promotes precise genome editing with scarce interference by p53
Authors: Hyodo Toshinori , Rahman Md Lutfur , Karnan Sivasundaram , Ito Takuji , Toyoda Atsushi , Ota Akinobu , Wahiduzzaman Md , Tsuzuki Shinobu , Okada Yohei , Hosokawa Yoshitaka , Konishi Hiroyuki
Published: October 2019

Targeted knock-in mediated by double-stranded DNA cleavage is accompanied by unwanted insertions and deletions (indels) at on-target and off-target sites. A nick-mediated approach scarcely generates indels but exhibits reduced efficiency of targeted knock-in. Here, we demonstrate that tandem paired nicking, a method for targeted knock-in involving two Cas9 nickases that create nicks at the homologous regions of the donor DNA and the genome in the same strand, scarcely creates indels at the edited genomic loci, while permitting the efficiency of targeted knock-in largely equivalent to that of the Cas9 nuclease-based approach. Tandem paired nicking seems to accomplish targeted knock-in via DNA recombination analogous to Holliday’s model, and creates intended genetic changes in the genome without introducing additional nucleotide changes such as silent mutations. Targeted knock-in through tandem paired nicking neither triggers significant p53 activation nor occurs preferentially in p53-suppressed cells. These properties of tandem paired nicking demonstrate its utility in precision genome engineering.
Accurate chromosome-scale haplotype-resolved assembly of human genomes
Authors: Garg Shilpa , Fungtammasan Arkarachai , Carroll Andrew , Chou Mike , Schmitt Anthony , Zhou Xiang , Mac Stephen , Peluso Paul , Hatas Emily , Ghurye Jay , Maguire Jared , Mahmoud Medhat , Cheng Haoyu , Heller David , Zook Justin M. , Moemke Tobias , Marschall Tobias , Sedlazeck Fritz J. , Aach John , Chin Chen-Shan , Church George M. , Li Heng
Published: October 2019

Haplotype-resolved or phased sequence assembly provides a complete picture of genomes and complex genetic variations. However, current phased assembly algorithms either fail to generate chromosome-scale phasing or require pedigree information, which limits their application. We present a method that leverages long accurate reads and long-range conformation data for single individuals to generate chromosome-scale phased assembly within a day. Applied to three public human genomes, PGP1, HG002 and NA12878, our method produced haplotype-resolved assemblies with contig NG50 up to 25 Mb and phased ∼99.5% of heterozygous sites to 98–99% accuracy, outperforming other approaches in terms of both contiguity and phasing completeness. We demonstrate the importance of chromosome-scale phased assemblies to discover structural variants (SVs), including thousands of new transposon insertions, and of highly polymorphic and medically important regions such as HLA and KIR. Our improved method will enable high-quality precision medicine and facilitate new studies of individual haplotype variation and population diversity.
Genotypic Variation in Below-to Aboveground Systemic Induction of Glucosinolates Mediates Plant Fitness Consequences under Herbivore Attack
Authors: Bakhtiari Moe , Rasmann Sergio
Published: October 2019

Plants defend themselves against herbivore attack by constitutively producing toxic secondary metabolites, as well as by inducing them during herbivore feeding. Induction of secondary metabolites can cross plant tissue boundaries, such as from root to shoot. However, whether the potential for plants to systemically induce secondary metabolites from roots to shoots shows genetic variability, and thus, potentially, is under selection conferring fitness benefits to the plants is an open question. To address this question, we induced 26 maternal plant families of the wild speciesCardamine hirsutabelowground (BG) using the wound-mimicking phytohormone jasmonic acid (JA). We measured resistance against a generalist (Spodoptera littoralis) and a specialist (Pieris brassicae) herbivore species, as well as the production of glucosinolates (GSLs) in plants. We showed that BG induction increased AG resistance against the generalist but not against the specialist, and found substantial plant family-level variation for resistance and GSL induction. We further found that the systemic induction of several GSLs tempered the negative effects of herbivory on total seed set production. Using a widespread natural system, we thus confirm that BG to AG induction has a strong genetic component, and it can be under positive selection by increasing plant fitness. We suggest that natural variation in systemic induction is in part dictated by allocation trade-offs between constitutive and inducible GSL production, as well as natural variation in AG and BG herbivore attack in nature.