bluuebunny/crossref_metadata_2025 huggingface dataset:
Activated regulatory T-cells, dysfunctional and senescent T-cells dominate the microenvironment of pancreatic cancer
Authors: Sivakumar Shivan , Abu-Shah Enas , Ahern David J , Arbe-Barnes Edward H , Mangal Nagina , Reddy Srikanth , Rendek Aniko , Easton Alistair , Kurz Elke , Silva Michael , Soonawalla Zahir , Heij Lara R , Bashford- Rogers Rachael , Middleton Mark R , Dustin Michael L
Published: June 2020

Pancreatic cancer has the worst prognosis of any human malignancy and leukocyte infiltration is a major prognostic marker of the disease. As current immunotherapies confer negligible survival benefits, there is a need to better characterise leukocytes in pancreatic cancer to identify better therapeutic strategies.

In this study, we analysed 32 human pancreatic cancer patients from two independent cohorts. A multi-parameter mass-cytometry analysis was performed on 32,000 T-cells from eight patients. Single-cell RNA sequencing dataset analysis was performed on a cohort of 24 patients. Multiplex immunohistochemistry imaging and spatial analysis were performed to map immune infiltration into the tumour microenvironment.

Regulatory T-cell populations demonstrated highly immunosuppressive states with high TIGIT, ICOS and CD39 expression. CD8+T-cells were found to be either in senescence or an exhausted state. The exhausted CD8 T-cells had low PD-1 expression but high TIGIT and CD39 expression. These findings were corroborated in an independent pancreatic cancer single-cell RNA dataset from additional 24 patients.

These data suggest that T-cells are major players in the suppressive microenvironment of pancreatic cancer. Our work identifies novel therapeutic targets that should form the basis for rational design of a new generation of clinical trials in pancreatic ductal adenocarcinoma.
Dufour’s gland analysis reveals caste and physiology specific signals inBombus impatiens
Authors: Derstine Nathan T. , Villar Gabriel , Orlova Margarita , Hefetz Abraham , Millar Jocelyn , Amsalem Etya
Published: June 2020

Reproductive division of labor in insect societies is regulated through multiple concurrent mechanisms, primarily chemical and behavioral. Here, we examined if the Dufour’s gland secretion in the primitively eusocial bumble beeBombus impatienssignals information about caste, social condition, and reproductive status. We chemically analyzed Dufour’s gland contents across castes, age groups, social and reproductive conditions, and examined worker behavioral and antennal responses to gland extracts.

We found that workers and queens each possess caste-specific compounds in their Dufour’s glands. Queens and gynes differed from workers based on the presence of diterpene compounds which were absent in workers, whereas four esters were exclusive to workers. These esters, as well as the total amounts of hydrocarbons in the gland, provided a separation between castes and also between fertile and sterile workers. Olfactometer bioassays demonstrated attraction of workers to Dufour’s gland extracts that did not represent a reproductive conflict, while electroantennogram recordings showed higher overall antennal sensitivity in queenless workers. Our results demonstrate that compounds in the Dufour’s gland act as caste- and physiology-specific signals and are used by workers to discriminate between workers of different social and reproductive status.
Unique K-mer sequences for validating cancer-related substitution, insertion and deletion mutations
Authors: Lee HoJoon , Shuaibi Ahmed , Bell John M. , Pavlichin Dmitri S. , Ji Hanlee P.
Published: June 2020

The cancer genome sequencing has led to important discoveries such as identifying cancer gene. However, challenges remain in the analysis of cancer genome sequencing. One significant issue is that mutations identified by multiple variant callers are frequently discordant even when using the same genome sequencing data. For insertion and deletion mutations, oftentimes there is no agreement among different callers. Identifying somatic mutations involves read mapping and variant calling, a complicated process that uses many parameters and model tuning. To validate the identification of true mutations, we developed a method using k-mer sequences. First, we characterized the landscape of unique versus non-unique k-mers in the human genome. Second, we developed a software package, KmerVC, to validate the given somatic mutations from sequencing data. Our program validates the occurrence of a mutation based on statistically significant difference in frequency of k-mers with and without a mutation from matched normal and tumor sequences. Third, we tested our method on both simulated and cancer genome sequencing data. Counting k-mer involving mutations effectively validated true positive mutations including insertions and deletions across different individual samples in a reproducible manner. Thus, we demonstrated a straightforward approach for rapidly validating mutations from cancer genome sequencing data.
Individual cell-based modeling of tumor cell plasticity-induced immune escape after CAR-T therapy
Authors: Zhang Can , Shao Changrong , Jiao Xiaopei , Bai Yue , Li Miao , Shi Hanping , Lei Jinzhi , Zhong Xiaosong
Published: June 2020

Chimeric antigen receptor (CAR) therapy targeting CD19 is an effective treatment for refractory B cell malignancies, especially B cell acute lymphoblastic leukemia (B-ALL). The majority of patients achieve a complete response following a single infusion of CD19-targeted CAR-modified T cells (CAR-19 T cells); however, many patients suffer relapse after therapy, and the underlying mechanism remains unclear. To better understand the mechanism of tumor relapse, we developed an individual cell based computational model for tumor cell plasticity and the heterogeneous responses to the CAR-T treatment. Model simulations reproduced the process of tumor relapse, and predicted that CAR-T stress-induced cell plasticity can lead to tumor relapse in B-ALL. Model predictions were verified by applying the second-generation CAR-T cells to mice injected with NALM-6-GL leukemic cells, in which 60% of the mice relapse within 3 months, and relapsed tumors retained CD19 expression but exhibited a subpopulation of cells with CD34 transcription. These findings lead to a mechanism of tumor replace by which CAR-T treatment induced tumor cells to transition to hematopoietic stem-like cells (HSLCs) and myeloid-like cells and hence escape of CAR-T targeting. The computational model framework was successfully developed to recapitulate the individual evolutionary dynamics, which could predict clinical survival outcomes in B-ALL patients after CAR-T therapy.
A combined characterization of coelomic fluid cell types in the spiny starfishMarthasterias glacialis– inputs from flow cytometry and imaging
Authors: Oliveira Bárbara , Guatelli Silvia , Martinez Pedro , Simões Beatriz , Bispo Claúdia , Andrade Claúdia , Ferrario Cinzia , Bonasoro Francesco , Rino José , Sugni Michela , Gardner Rui , Zilhão Rita , Coelho Ana Varela
Published: June 2020

Coelomocytes is a generic name for a collection of cellular morphotypes, present in many coelomate animals, that has been reported as highly variable across echinoderm classes. The roles attributed to the major types of the free circulating cells present in the coelomic fluid of echinoderms include immune response, phagocytic digestion and clotting. The main aim of the present study is the thorough characterization of coelomocytes present in the coelomic fluid ofMarthasterias glacialis(class Asteroidea) through the combined use of flow cytometry (FC) and fluorescence plus transmission electron microscopy. Two coelomocyte populations (here named P1 and P2) were identified by flow cytometry and subsequently studied in terms of abundance, morphology, ultrastructure, cell viability and cell cycle profiles. Ultrastructurally, P2 diploid cells showed two main morphotypes, similar to phagocytes and vertebrate thrombocytes, whereas the small P1 haploid cellular population was characterized by a low mitotic activity, relatively undifferentiated cytotype and a high nucleus/cytoplasm ratio. These last cells resemble stem-cell types present in other animals. P1 and P2 cells differ also in cell viability and cell cycle profiles. Additionally, two other morphotypes were only detected by fluorescence microscopy and a third one when using a combined microscopy/FC approach.
Critical care demand and intensive care supply for patients in Japan with COVID-19 at the time of the state of emergency declaration in April 2020: a descriptive analysis.
Authors: Fujii Yosuke , Hirota Kiichi
Published: June 2020

Background

The coronavirus disease 2019 (COVID-19) pandemic, due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), threatened to overwhelm Japan’s intensive care capacity due to the rising numbers of infected patients. This study aimed to determine the number of critically ill patients with COVID-19 who required intensive care, including mechanical ventilation and extracorporeal membrane oxygenation (ECMO), during the pandemic and to compare these patient numbers with Japan’s overall intensive care capacity.

Methods

Japanese Society of Intensive Care Medicine datasets were used to obtain the number of confirmed patients with COVID-19 who had undergone mechanical ventilation and ECMO between February 15 and June 4 2020, to determine and compare intensive care unit (ICU) and attending bed needs for patients with COVID-19, and to estimate peak ICU demands in Japan.

Results

In total, 17968 ICU days, 15171 mechanical ventilation days, and 2797 ECMO days were attributable to patients with COVID-19. There was a median (interquartile range) 143 (63-255) patients in ICU, 124 (51-225) patients on mechanical ventilation, and 18 (15-36) patients on ECMO machines. During the epidemic peak in late April, 11443 patients (1.03 per 10000 adults) had been infected, 373 patients (0.034 per 10000 adults) were in ICU, 312 patients (0.028 per 10000 adults) were receiving mechanical ventilation, and 62 patients (0.0056 per 10000 adults) were on ECMO machines per day. The number of infected patients at the peak of the epidemic was 651% of total designated beds and the number of patients requiring intensive care at the peak of the epidemic was 6.0% of total ICU beds in Japan, 19.1% of total board-certified intensivists in Japan and 106% of total designated medical institutions for Category II infectious diseases in Japan, respectively.

Conclusions

Following the state of emergency declaration on April 7 2020, the number of patients with COVID-19 and the number of critically ill patients continued to rise, exceeding the number of designated beds but not exceeding ICU capacity. Urgent nationwide and regional planning is needed to prevent an overwhelming burden on ICUs in relation to critically ill patients with COVID-19 in Japan.
Real-time image processing toolbox for all-optical closed-loop control of neuronal activities
Authors: Sheng Weihao , Zhao Xueyang , Huang Xinrui , Yang Yang
Published: June 2020

The development ofin vivoimaging and optogenetic tools makes it possible to control neural circuit activities in an all-optical, closed-loop manner [1], but such applications are limited by the lack of software for online analysis of neuronal imaging data. We developed an analysis software ORCA (Online Real-time activity and offline Cross-session Analysis), which performs image registration, neuron segmentation, and activity extraction at over 100 frames per second, fast enough to support real-time detection and readout of neural activity. Our active neuron detection algorithm is purely statistical, achieving much higher speed than previous methods. We demonstrated closed-loop control of neurons that were identified on the fly, without prior recording or image processing. ORCA also includes a cross-session alignment module that efficiently tracks neurons across multiple sessions. In summary, ORCA is a powerful toolbox for fast imaging data analysis, and provides a solution for all-optical closed-loop control of neuronal activity.
Glucose promotes resistance of human commensalEscherichia coliagainst contact-killing by pandemicVibrio cholerae
Authors: Crisan Cristian V , Nichols Holly , Wiesenfeld Sophia , Steinbach Gabi , Yunker Peter J , Hammer Brian K
Published: June 2020

Evolutionary arms races among organisms are broadly prevalent and bacteria have evolved defensive strategies against various attackers. A common microbial aggression mechanism is the Type VI Secretion System (T6SS), a contact-dependent bacterial weapon used to deliver toxic effector proteins into adjacent target cells. Sibling cells constitutively express immunity proteins that neutralize effectors. However, less is known about mechanisms that allow non-sibling bacteria to respond to external cues and survive T6SS attacks independently of immunity proteins. In this study, we show that resistance to T6SS attacks is promoted by a genetically controlled response to exogenous glucose. We observe that multiple humanEscherichia colicommensal strains lacking immunity proteins are sensitive to T6SS attacks from pandemicVibrio choleraeon nutrient-rich media. By contrast,E. colicells become resistant to attacks when co-cultured on the same media with glucose. We confirm that glucose does not impairV. choleraeT6SS activity. Instead, we find that cAMP receptor protein (CRP), which alters expression of hundreds of genes in response to glucose, controls resistance to T6SS attacks inE. colicells. Consistent with the observed resistance on media with glucose, anE. coli crpdisruption mutant survives significantly better againstV. choleraeT6SS attacks even in the absence of glucose. Finally, we also show that resistance to T6SS attacks depends on the pH of the medium and varies based on the target and killer strains.

IMPORTANCE

Many Gram-negative bacteria, including important pathogens, encode T6SS genes to deliver toxic effectors and eliminate competitors. Our results uncover a novel defense mechanism against T6SS attacks that is triggered by an external stimulus and mediated by a metabolic response in non-kin target cells. In microbiomes such as those in gastrointestinal tracts where T6SS activity is known to occur, signaling by metabolites like glucose may affect the efficacy of T6SS attacks and alter microbial community composition. Our findings could have vast implications for microbial interactions during pathogen colonization of hosts and survival of bacterial cells in environmental communities. Furthermore, the glucose-mediated resistance observed here might provide a novel example of an evolutionary arms race between killer T6SS cells and target bacteria.
Expert-level prenatal detection of complex congenital heart disease from screening ultrasound using deep learning
Authors: Arnaout Rima , Curran Lara , Zhao Yili , Levine Jami C. , Chinn Erin , Moon-Grady Anita J.
Published: June 2020

Congenital heart disease (CHD) is the most common birth defect. Fetal survey ultrasound is recommended worldwide, including five views of the heart that together could detect 90% of complex CHD. In practice, however, sensitivity is as low as 30%. We hypothesized poor detection results from challenges in acquiring and interpreting diagnostic-quality cardiac views, and that deep learning could improve complex CHD detection. Using 107,823 images from 1,326 retrospective echocardiograms and surveys from 18-24 week fetuses, we trained an ensemble of neural networks to (i) identify recommended cardiac views and (ii) distinguish between normal hearts and complex CHD. Finally, (iii) we used segmentation models to calculate standard fetal cardiothoracic measurements. In a test set of 4,108 fetal surveys (0.9% CHD, >4.4 million images, about 400 times the size of the training dataset) the model achieved an AUC of 0.99, 95% sensitivity (95%CI, 84-99), 96% specificity (95%CI, 95-97), and 100% NPV in distinguishing normal from abnormal hearts. Sensitivity was comparable to clinicians’ task-for-task and remained robust on external and lower-quality images. The model’s decisions were based on clinically relevant features. Cardiac measurements correlated with reported measures for normal and abnormal hearts. Applied to guidelines-recommended imaging, ensemble learning models could significantly improve detection of fetal CHD and expand telehealth options for prenatal care at a time when the COVID-19 pandemic has further limited patient access to trained providers. This is the first use of deep learning to ∼double standard clinical performance on a critical and global diagnostic challenge.
Prelimbic-dependent activation of amygdala somatostatin interneurons signals non-aversive cues to promote discrimination
Authors: Stujenske J.M. , O’Neill P.K. , Nahmoud I , Goldberg S. , Diaz L. , Labkovich M. , Hardin W. , Bolkan S.S. , Reardon T.R. , Spellman T.J. , Salzman C.D. , Gordon J.A. , Likhtik E.
Published: June 2020

The amygdala and prelimbic cortex (PL) communicate during fear discrimination retrieval, but how they coordinate to discriminate a non-threatening stimulus is unknown. Here, we show that somatostatin interneurons (SOM) in the basolateral amygdala (BLA) become active specifically during learned non-threatening cues, when they block sensory-evoked phase resetting of theta-oscillations. Further, we show that SOM activation is PL-dependent, and promotes discrimination of non-threat. Thus, fear discrimination engages PL-dependent coordination of BLA SOM responses to non-threatening stimuli.
Response of Regulatory Genetic Variation in Gene Expression to Environmental Change inDrosophila melanogaster
Authors: Huang Wen , Carbone Mary Anna , Lyman Richard F. , Anholt Robert H. H. , Mackay Trudy F. C.
Published: June 2020

The genetics of phenotypic responses to changing environments remains elusive. Using whole genome quantitative gene expression as a model, we studied how the genetic architecture of regulatory variation in gene expression changed in a population of fully sequenced inbredDrosophila melanogasterstrains when flies developed at different environments (25 °C and 18 °C). We found a substantial fraction of the transcriptome exhibited genotype by environment interaction, implicating environmentally plastic genetic architecture of gene expression. Genetic variance in expression increased at 18 °C relative to 25 °C for most genes that had a change in genetic variance. Although the majority of expression quantitative trait loci (eQTLs) for the gene expression traits in the two environments were shared and had similar effects, analysis of the environment-specific eQTLs revealed enrichment of binding sites for two transcription factors. Finally, although genotype by environment interaction in gene expression could potentially disrupt genetic networks, the co-expression networks were highly conserved across environments. Genes with higher network connectivity were under stronger stabilizing selection, suggesting that stabilizing selection on expression plays an important role in promoting network robustness.
Non-invasive Amelioration of Essential Tremor via Phase-Locked Disruption of its Temporal Coherence
Authors: Schreglmann Sebastian R. , Wang David , Peach Robert , Li Junheng , Zhang Xu , Latorre Anna , Rhodes Edward , Panella Emanuele , Boyden Edward S. , Barahona Mauricio , Santaniello Sabato , Bhatia Kailash P. , Rothwell John , Grossman Nir
Published: June 2020

Aberrant neural oscillations hallmark numerous brain disorders. Here, we first report a method to track the phase of neural oscillations in real-time via endpoint-corrected Hilbert transform (ecHT) that mitigates the characteristic Gibbs distortion. We then used ecHT to show that the aberrant neural oscillation that hallmarks essential tremor (ET) syndrome, the most common adult movement disorder, can be noninvasively suppressed via electrical stimulation of the cerebellum phase-locked to the tremor. The tremor suppression is sustained after the end of the stimulation and can be phenomenologically predicted. Finally, using feature-based statistical-learning and neurophysiological-modelling we show that the suppression of ET is mechanistically attributed to a disruption of the temporal coherence of the oscillation via perturbation of the tremor generating a cascade of synchronous activity in the olivocerebellar loop. The suppression of aberrant neural oscillation via phase-locked driven disruption of temporal coherence may represent a powerful neuromodulatory strategy to treat brain disorders.
A hybrid additive manufacturing platform to create bulk and surface composition gradients on scaffolds for tissue regeneration
Authors: Sinha Ravi , Cámara-Torres Maria , Scopece Paolo , Falzacappa Emanuele Verga , Patelli Alessandro , Moroni Lorenzo , Mota Carlos
Published: June 2020

Scaffolds with gradients of physico-chemical properties and controlled 3D architectures are crucial for engineering complex tissues. These can be produced using multi-material additive manufacturing (AM) techniques. However, they typically only achieve discrete gradients using separate printheads to vary compositions. Achieving continuous composition gradients, to better mimic tissues, requires material dosing and mixing controls. No such AM solution exists for most biomaterials. Existing AM techniques also cannot selectively modify scaffold surfaces to locally stimulate cell adhesion. We report a hybrid AM solution to cover these needs. On one platform, we combine a novel dosing- and mixing-enabled, dual-material printhead with an atmospheric pressure plasma jet to selectively activate/coat scaffold filaments during manufacturing. We fabricated continuous composition gradients in both 2D hydrogels and 3D thermoplastic scaffolds. We demonstrated an improvement in mechanical properties of continuous gradients compared to discrete gradients in the 3D scaffolds, and the ability to selectively enhance cell adhesion.
IMPACT OF PHENOLIC ACIDS ON THE ENERGY METABOLISM AND LONGEVITY INC. ELEGANS
Authors: Dilberger Benjamin , Weppler Selina , Eckert Gunter P
Published: June 2020

Introduction

Aging represents one of the major risk factors for metabolic diseases, such as diabetes and obesity, or neurodegeneration. Polyphenols and its metabolites, especially simple phenolic acids, have gained more and more attention as a preventive strategy for age-related, non-communicable diseases, due to their hormetic potential. Using the nematodeCaenorhabditis elegans(C. elegans) we investigate the effect of protocatechuic, gallic and vanillic acid to improve mitochondrial function and health associated parameters as a preventive measure.

Methods

Lifespan, heat-stress resistance and chemotaxis ofC. elegansstrain PX627, as a specific model for aging, were assessed in 2-day and 10-day old nematodes. Mitochondrial membrane potential (ΔΨm) and ATP generation of young and aged nematodes were measured. mRNA expression levels of longevity and energy metabolism-related genes were determined using qRT-PCR.

Results

All phenolic acids were able to significantly increase the nematodes lifespan, heat-stress resistance and chemotaxis at micromolar concentrations. While ΔΨm was only affected by age, vanillic acid significantly decreased ATP concentrations in aged nematodes. Genetic analysis revealed increased glycolytic activity mediated through vanillic acid, suggesting improved thermogenesis.

Conclusion

While life- and health-span parameters are positively affected by the investigated phenolic acids, the concentrations applied were unable to impact mitochondrial performance, suggesting hormesis. In contrast to the other phenolic acids, vanillic acid showed potential in regulating glucose homeostasis, making it a prime candidate for future diabetes and obesity focused approaches.
Fatty acid photodecarboxylase is an ancient photoenzyme responsible for hydrocarbon formation in the thylakoid membranes of algae
Authors: Moulin Solène , Beyly Audrey , Blangy Stéphanie , Légeret Bertrand , Floriani Magali , Burlacot Adrien , Sorigué Damien , Li-Beisson Yonghua , Peltier Gilles , Beisson Fred
Published: June 2020

Fatty acid photodecarboxylase (FAP) is one of the three enzymes that require light for their catalytic cycle (photoenzymes). FAP has been first identified in the green microalgaChlorella variabilisNC64A and belongs an algae-specific subgroup of the glucose-methanol-choline oxidoreductase family. While the FAP fromChlorellaand itsChlamydomonas reinhardtiihomolog CrFAP have demonstratedin vitroactivity, their activity and physiological function have not been studiedin vivo. Besides, the conservation of FAP activity beyond green microalgae remains hypothetical. Here, using aChlamydomonasFAP knockout line (fap), we show that CrFAP is responsible for the formation of 7-heptadecene, the only hydrocarbon present in this alga. We further show that CrFAP is associated to the thylakoids and that 90% of 7-heptadecene is recovered in this cell fraction. In thefapmutant, photosynthesis activity was not affected under standard growth conditions but was reduced after cold acclimation. A phylogenetic analysis including sequences from Tara Ocean identified almost 200 putative FAPs and indicated that FAP was acquired early after primary endosymbiosis. Within Bikonta, FAP was kept in photosynthetic secondary endosymbiosis lineages but absent in those that lost the plastid. Characterization of recombinant FAPs from various algal genera (Nannochloropsis, Ectocarpus, Galdieria, Chondrus) provided experimental evidence that FAP activity is conserved in red and brown algae and is not limited to unicellular species. These results thus indicate that FAP has been conserved during evolution of most algal lineages when photosynthesis was kept and suggest that its function is linked to photosynthetic membranes.

One sentence summary

FAP is present in thylakoids and conserved beyond green algae.
CRISPR-targeted display of functional T cell receptors enables engineering of enhanced specificity and prediction of cross-reactivity
Authors: Vazquez-Lombardi Rodrigo , Jung Johanna S. , Bieberich Florian , Kapetanovic Edo , Aznauryan Erik , Weber Cédric R. , Reddy Sai T.
Published: June 2020

T cell receptor (TCR) gene therapy is a promising cell therapy approach for the treatment of cancer. However, most naturally occurring TCRs display low affinities to their peptide-MHC targets, and engineering of TCRs for enhanced affinity is complicated by the risk of introducing cross-reactivity and the poor correlation between affinity and function. Here we report the establishment of the TCR-accepting T cell (TnT) platform through five sequential CRISPR-Cas9 genome editing steps of a human T cell line, and demonstrate its application for functional engineering of TCRs and prediction of cross-reactivity. Using the TnT platform, we profile the mutational landscapes of tumor-specific TCRs at high-throughput to reveal a substantial discordance between antigen binding and antigen-induced signaling. Furthermore, we combine CRISPR-targeting, functional selection and deep sequencing to screen TCR mutagenesis libraries and identify variants with enhanced recognition of the cancer-testis antigen MAGE-A3. Finally, functional cross-reactivity profiling using TnT cells was able to accurately predict off-targets and identify engineered TCRs with exquisite specificity to MAGE-A3. Thus, the TnT platform represents a valuable technology for the engineering of TCRs with enhanced functional and safety profiles.
A Computer-aided Method for Identifying the Presence of Softwood Growth Ring Boundaries
Authors: Lin Qi-Zhao , He Tuo , Sun Yong-Ke , He Xin , Qiu Jian
Published: June 2020

The objective of this study was to develop a computer-aided method to quantify the obvious degree of growth ring boundaries of softwood species, based on data analysis with some image processing technologies. For this purpose, a 5× magnified cross-section color micro-image of softwood was cropped into 20 sub-images, then every image is binarized as a gray image according to an automatic threshold value. After that, the number of black pixels in the gray image was counted row by row and the number of black pixels was binarized to 0 or 100. Finally, a transition band from earlywood to latewood on the sub-image was identified. If this was successful, the growth ring boundaries of the sub-image are distinct, otherwise they were indistinct or absent. If 10 of the 20 sub-images are distinct, with the majority voting method, the growth ring boundaries of softwood are distinct, otherwise they are indistinct or absent. The proposed method has been visualized as a growth-ring-boundary detecting system based on the .NET Framework. A sample of 100 micro-images (Supplementary Images) of softwood cross-sections were selected for evaluation purposes. In short, this detecting system computes the obvious degree of growth ring boundaries of softwood species by image processing involved image importing, image cropping, image reading, image grayscale, image binarization, data analysis. The results showed that the method used avoided mistakes made by the manual comparison method of identifying the presence of growth ring boundaries, and it has a high accuracy of 98%.
Nuclear lamin A/C promotes cancer cell survival and lung metastasis without restricting transendothelial migration
Authors: Roncato Francesco , Regev Ofer , Feigelson Sara W. , Yadav Sandeep Kumar , Kaczmarczyk Lukasz , Levi Nehora , Drago-Garcia Diana , Ovadia Samuel , Kizner Marina , Addadi Yoseph , Sabino João C. , Ovadya Yossi , de Almeida Sérgio F. , Feldmesser Ester , Gerlitz Gabi , Alon Ronen
Published: June 2020

The mechanisms by which the nuclear lamina of tumor cells controls their migration and survival are poorly understood. Lamin A and its variant lamin C are key nuclear lamina proteins that control nucleus stiffness and chromatin conformation. Downregulation of lamin A/C levels in two metastatic lines, B16F10 melanoma and E0771 breast carcinoma, facilitated cell squeezing through rigid pores, elevated nuclear deformability and reduced heterochromatin. Unexpectedly, the transendothelial migration of both cancer cells in vitro and in vivo, through lung capillaries, was not elevated by lamin A/C knockdown. Both cancer cells with lamin A/C knockdown grew normally in primary tumors and in vitro on rigid surfaces. Strikingly, however, both lamin A/C deficient melanoma and breast cancer cells grew poorly in 3D spheroids expanded in soft agar cultures. Experimental lung metastasis of both lamin A/C knockdown cells was also markedly reduced. Taken together, our results suggest that high content of lamin A/C in multiple cancer cells promotes cancer cell survival and ability to generate lung metastasis without compromising cancer cell emigration from lung vessels.
Genetic and Genomic Resources to Study Natural Variation inBrassica rapa
Authors: Lou Ping , Woody Scott , Greenham Kathleen , VanBuren Robert , Colle Marivi , Edger Patrick P. , Sartor Ryan , Zheng Yakun , Levendoski Nathan , Lim Jan , So Calvin , Stoveken Brian , Woody Timothy , Zhao Jianjun , Shen Shuxing , Amasino Richard M. , McClung C. Robertson
Published: June 2020

The globally important cropBrassica rapa, a close relative of Arabidopsis, is an excellent system for modeling our current knowledge of plant growth on a morphologically diverse crop. The long history ofB. rapadomestication across Asia and Europe provides a unique collection of locally adapted varieties that span large climatic regions with various abiotic and biotic stress tolerance traits. This diverse gene pool provides a rich source of targets with the potential for manipulation towards the enhancement of productivity of crops both within and outside the Brassicaceae. To expand the genetic resources available to study natural variation inB. rapa, we constructed an Advanced Intercross Recombinant Inbred (AI-RIL) population usingB. rapasubsp.trilocularis(Yellow Sarson) R500 and theB. rapasubsp.parachinensis(Cai Xin) variety L58. Our current understanding of genomic structure variation across crops suggests that a single reference genome is insufficient for capturing the genetic diversity within a species. To complement this AI-RIL population and current and futureB. rapagenomic resources, we generated ade novogenome assembly of theB. rapasubsp.trilocularis(Yellow Sarson) variety R500, the maternal parent of the AI-RIL population. The genetic map for the R500 x L58 population generated using thisde novogenome was used to map QTL for seed coat color and revealed the improved mapping resolution afforded by this new assembly.
IMIX: A multivariate mixture model approach to integrative analysis of multiple types of omics data
Authors: Wang Ziqiao , Wei Peng
Published: June 2020

Motivation

Integrative genomic analysis is a powerful tool to study the biological mechanisms underlying a complex disease or trait across multiplatform high-dimensional data, such as DNA methylation, copy number variation (CNV), and gene expression. It is common to perform large-scale genome-wide association analysis of an outcome for each data type separately and combine the resultsad hoc, leading to loss of statistical power and uncontrolled overall false discovery rate (FDR).

Results

We propose a multivariate mixture model framework (IMIX) that integrates multiple types of genomic data and allows examining and relaxing the commonly adopted conditional independence assumption. We investigate across-data-type FDR control in IMIX, and show the gain in lower misclassification rates at controlled over-all FDR compared with established individual data type analysis strategies, such as Benjamini-Hochberg FDR control, the q-value, and the local FDR control by extensive simulations. IMIX features statistically-principled model selection, FDR control, and computational efficiency. Applications to the Cancer Genome Atlas (TCGA) data provide novel multi-omic insights into the luminal/basal subtyping of bladder cancer and the prognosis of pancreatic cancer.

Availability and implementation

We have implemented our method in R package “IMIX” with instructions and examples available athttps://github.com/ziqiaow/IMIX.
Capsaicin inhibits arginine kinase and exerts anti-Trypanosoma cruziactivity
Authors: Valera-Vera Edward A. , Reigada Chantal , Sayé Melisa , Digirolamo Fabio A. , Miranda Mariana R. , Pereira Claudio A.
Published: June 2020

Trypanosoma cruziis the causative agent of Chagas disease, considered within the list of twenty neglected diseases according to the World Health Organization. There are only two therapeutic drugs for Chagas disease, both of them unsuitable for the chronic phase, therefore the development of new drugs is a priority.

T. cruziarginine kinase (TcAK) is a promising drug target since it is absent in humans and it is involved in cellular stress responses. In a previous study from our laboratory, possible TcAK inhibitors were identified through computer simulations, resulting in the best-scoring compounds cyanidin derivatives and capsaicin. Considering these results, in this work we evaluate the effect of capsaicin on TcAK activity and its trypanocidal effect. Although capsaicin produced a weak inhibition on the recombinant TcAK activity (IC50≈ 800 µM), it had a strong trypanocidal effect on epimastigotes and trypomastigotes (IC50= 6.26 µM and 0.26 µM, respectively) being 20-fold more active on trypomastigotes than mammalian cells. Epimastigotes that overexpress TcAK were 37% more resistant to capsaicin than wild type parasites, suggesting that trypanocidal activity could be due, in part, to the enzyme inhibition. However, the difference between the concentrations at which the enzyme is inhibited and the parasite death is caused implies the presence of other targets. In this sense, the prohibitin-2 and calmodulin were identified as other possible capsaicin targets. Capsaicin is a strong and selective trypanocidal agent active in nanomolar concentrations, with an IC5057-fold lower than benznidazole, the drug currently used for treating Chagas disease.
The proteomic landscape of centromeric chromatin reveals an essential role for the Ctf19CCANcomplex in meiotic kinetochore assembly
Authors: Borek Weronika E. , Vincenten Nadine , Duro Eris , Makrantoni Vasso , Spanos Christos , Sarangapani Krishna K. , Alves Flavia de Lima , Kelly David A. , Asbury Charles L. , Rappsilber Juri , Marston Adele L.
Published: June 2020

Kinetochores direct chromosome segregation in mitosis and meiosis. Faithful gamete formation through meiosis requires that kinetochores take on new functions that impact homolog pairing, recombination and the orientation of kinetochore attachment to microtubules in meiosis I. Using an unbiased proteomics pipeline, we determined the composition of centromeric chromatin and kinetochores at distinct cell-cycle stages, revealing extensive reorganisation of kinetochores during meiosis. The data uncover a network of meiotic chromosome axis and recombination proteins that replace the microtubule-binding outer kinetochore sub-complexes during meiotic prophase. We show that this kinetochore remodelling in meiosis requires the Ctf19cCCANinner kinetochore complex. Through functional analyses, we identify a Ctf19cCCAN-dependent kinetochore assembly pathway that is dispensable for mitotic growth, but becomes critical upon meiotic entry. Therefore, extensive kinetochore remodelling and a distinct assembly pathway direct the specialization of meiotic kinetochores for successful gametogenesis.
Photoacoustic imaging resolves species-specific differences in haemoglobin concentration and oxygenation
Authors: Hacker Lina , Brunker Joanna , St. John Smith Ewan , Quiros-Gonzalez Isabel , Bohndiek Sarah E.
Published: June 2020

Introduction

Photoacoustic imaging (PAI) enables the detection of blood haemoglobin (HB) concentration and oxygenation (SO2) with high contrast and resolution. To date, the relationship between photoacoustically determined total Haemoglobin (THbMSOT) and oxygen saturation (SO2) biomarkers and the underlying biochemical blood parameters has yet to be established. We sought to explore these relationships in a species-specific manner.

Methods

Experiments were performedin vitrousing tissue-mimicking agar phantoms. Blood was extracted from mouse, rat, human and naked mole-rat (Heterocephalus glaber), anticoagulated in EDTA and measured within 48 hours. THbMSOTand SO2MSOTwere measured using a commercial photoacoustic tomography system (InVision 128, iThera Medical GmBH). Biochemical blood parameters such as haemoglobin concentration (HB, g/dL), haematocrit (HCT, %) and red blood cell count (RBC, μL-1) were assessed using a haematology analyser (Mythic 18 Vet, Woodley Equipment).

Results

A significant correlation was observed between THbMSOTand biochemical HB, HCT and RBC in mouse and rat blood. Moreover, PAI accurately recapitulated inter-species variations in HB and HCT between mouse and rat blood and resolved differences in the oxygen dissociation curves between human, mouse and rat. With these validation data in hand, we applied PAI to studies of blood obtained from naked mole-rats and could confirm the high oxygen affinity of this species in comparison to other rodents of similar size.

Conclusion

In summary, our results demonstrate the high sensitivity of photoacoustically determined biomarkers towards species-specific variationsin vitro.
Ecologically relevant thermal fluctuations enhance offspring fitness: biological and methodological implications for studies of thermal developmental plasticity
Authors: Hall Joshua M. , Warner Daniel A.
Published: June 2020

Natural thermal environments are notably complex and challenging to mimic in controlled studies. Consequently, our understanding of the ecological relevance and underlying mechanisms of organismal responses to thermal environments is often limited. For example, studies of thermal developmental plasticity have provided key insights into the ecological consequences of temperature variation, but most laboratory studies use treatments that do not reflect natural thermal regimes. While controlling other important factors, we compared the effects of naturally fluctuating temperatures to commonly used laboratory regimes on development of lizard embryos and offspring phenotypes and survival. We incubated eggs in 4 treatments – 3 that followed procedures commonly used in the literature, and one that precisely mimicked naturally fluctuating nest temperatures. To explore context-dependent effects, we replicated these treatments across two seasonal regimes: relatively cool temperatures from nests constructed early in the season and warm temperatures from late-season nests. We show that natural thermal fluctuations have a relatively small effect on developmental variables but enhance hatchling performance and survival at cooler temperatures. Thus, natural thermal fluctuations are important for successful development and simpler approximations (e.g. repeated sine waves, constant temperatures) may poorly reflect natural systems under some conditions. Thus, the benefits of precisely replicating real-world temperatures in controlled studies may outweigh logistical costs. Although patterns might vary according to study system and research goals, our methodological approach demonstrates the importance of incorporating natural variation into controlled studies and provides biologists interested in thermal ecology with a framework for validating the effectiveness of commonly used methods.
The role of Ca2+and protein scaffolding in the formation in nature’s water oxidizing complex
Authors: Avramov Anton P. , Hwang Hong J. , Burnap Robert L.
Published: June 2020

The photosystem II (PSII) complex catalyzing the H2O-oxidation reaction of photosynthesis is highly prone to photodamage. Nature has evolved synthesis and repair mechanisms that include the photooxidative self-assembly, termed photoactivation, of the Mn4CaO5metal cluster responsible for H2O-oxidation. Assembly is a multi-step light-driven process that proceeds with low quantum yield, involves a critical molecular rearrangement between light-activated steps, and is prone to photoinactivation and mis-assembly. A sensitive polarographic technique was used to track the assembly process under flash illumination as a function of the constituent Mn2+and Ca2+ions in genetically engineered samples to elucidate the action of Ca2+and peripheral proteins. We show that the protein scaffolding that organizes this process is modulated allosterically by the assembly protein Psb27, which together with Ca2+, stabilizes the intermediates of photoactivation, a feature especially evident at long intervals between photoactivating flashes. Besides stabilizing intermediates, the Ca2+ion is also critical to prevent photoinactivation due to inappropriate binding of Mn2+. Overexpression of Psb27, deletion of extrinsic protein PsbO, and excess Ca2+characteristically modify these processes and retard the dark rearrangement. The results suggest the involvement of three metal binding sites, two Mn and one Ca with occupation of the Ca site by Ca2+critical for the suppression of inactivation and the long-observed competition between Mn2+and Ca2+occurring at the second Mn site necessary for trapping the first stable assembly intermediates.

Significance Statement

The oxidation of water by the photosystem II is the foundation of bioproductivity on Earth and represents a blueprint for sustainable, carbon neutral technologies. Water oxidation is catalyzed by a metal cluster containing of 4 Mn and 1 Ca atoms linked via oxo bridges. The initial assembly is a complex sequential reaction harnessing the photochemical reaction center to photooxidatively incorporate Mn2+and Ca2+ions into the catalytic unit embedded in the protein matrix. This photoassembly is crucial for both de novo biosynthesis and as part of the ‘self-healing’ mechanism to cope with incessant photodamage that photosynthetic organisms experience. The results have implications for the natural mechanism as well as the highly desirable biomimetic devices currently envisioned for solar energy production.
Opposing directions of stage-specific body length change in a close relative ofC. elegans
Authors: Hammerschmith Eric W. , Woodruff Gavin C. , Phillips Patrick C.
Published: June 2020

Background

Body size is a fundamental organismal trait. However, as body size and ecological contexts change across developmental time, evolutionary divergence may cause unexpected patterns of body size diversity among developmental stages. This may be particularly evident in polyphenic developmental stages specialized for dispersal. The dauer larva is such a stage in nematodes, andCaenorhabditisspecies disperse by traveling on invertebrate carriers. Here, we describe the morphology of the dispersal dauer larva of the nematodeCaenorhabditis inopinata, whose adults can grow to be nearly twice as long as its close relative, the model organismC. elegans.

Results

We find that theC. inopinatadauer larva is shorter and fatter than those of its close relativesC. elegans, C. briggsae, andC. tropicalis, despite its much longer adult stage. Additionally, manyC. inopinatadauer larvae were ensheathed, an apparent novelty in this lineage reminiscent of the infective juveniles of parasitic nematodes. We also found abundant variation in dauer formation frequency among twenty-four wild isolates ofC. inopinata, with many strains unable to produce dauer larvae under laboratory conditions.

Conclusion

MostCaenorhabditisspecies thrive on rotting plants and disperse on snails, slugs, or isopods (among others) whereasC. inopinatais ecologically divergent and thrives in freshFicus septicafigs and disperses on their pollinating wasps. These wasps are at least an order of magnitude smaller in length than the vectors of otherCaenorhabditisspecies. While there is some unknown factor of the fig environment that promotes elongated body size inC. inopinataadults, the smaller size of its fig wasp carrier may be driving the reduced body length of its dauer larva. Thus ecological divergence across multiple developmental stages can promote unexpected and opposing changes in body size within a single species.
De novo deletions and duplications at recombination hotspots in mouse germlines
Authors: Lukaszewicz Agnieszka , Lange Julian , Keeney Scott , Jasin Maria
Published: June 2020

Numerous DNA double-strand breaks (DSBs) arise during meiosis to initiate homologous recombination. These DSBs are usually repaired faithfully, but here we uncover a new type of mutational event in which deletions form via joining of ends from two closely spaced DSBs (double cuts) within a single hotspot or at adjacent hotspots on the same or different chromatids. Deletions occur in normal meiosis but are much more frequent when DSB formation is dysregulated in the absence of the ATM kinase. Events between chromosome homologs point to multi-chromatid damage and aborted gap repair. Some deletions contain DNA from other hotspots, indicating that double cutting at distant sites creates substrates for insertional mutagenesis. End joining at double cuts can also yield tandem duplications or extrachromosomal circles. Our findings highlight the importance of DSB regulation and reveal a previously hidden potential for meiotic mutagenesis that is likely to affect human health and genome evolution.