bluuebunny/crossref_metadata_2025 huggingface dataset:
Presacral Ewing's sarcoma mimicking piriformis syndrome
Authors: Liu Kuan-Fu , Chou Chen-Liang , Liu Ding-Hao
Published: May 2021

Rationale:

Piriformis syndrome is caused by entrapment or irritation of the sciatic nerve through a tight or hypertrophic piriformis muscle. Patients usually have buttock pain with sciatica. However, clinical management of piriformis syndrome is still challenging and results in repetitive investigations with potentially misleading diagnoses

Patient concerns:

This was a case of a thirty-six-year-old young woman, who suffered from progressive sciatica on and off for nine months. However, the symptoms progressed under conservative treatment.

Diagnoses:

Piriformis syndrome was diagnosed at first. Ultrasound-guided anesthetic injection over the piriformis muscle was performed, with no alleviation of symptoms. Then Magnetic Resonance Imaging revealed a space-occupying lesion over the presacral region, which was further confirmed by tissue biopsy as Ewing's sarcoma of the sacrum with right S1 and S2 nerve root compression.

Interventions:

The patient received neoadjuvant chemotherapy and tumor excision surgery.

Outcomes:

The patient was followed-up for 15 months with non-progression of residual tumor and complete resolution of sciatica.

Lessons:

Patients with sciatica should be evaluated by history taking and careful physical examination, followed by serial neurophysiological and imaging studies. To manage unresponsive piriformis syndrome, imaging studies should cover the pelvic and hip areas to assess the deep gluteal and pelvic region, because tumors compressing sciatic nerve can mimic piriformis syndrome. This case report aims at raising clinical awareness of the complexity of sciatica and piriformis syndrome.
Correction of the Deepened Labiomental Groove Using Silicone Implants in Advancement Genioplasty
Authors: Hwang Jungil , Park Bumjin
Published: May 2021

Advancement genioplasty is performed to aesthetically improve the lower third of the facial profile. Excessive chin advancement alone may lead to deepened labiomental sulcus and deformed aesthetic results. The purpose of this study was to assess the efficacy of silicone prosthesis placement as an alternative method for effacing an excessively deepened labiomental groove after advancement genioplasty. Three hundred and seventy-six patients underwent genioplasty between January 2014 and October 2017. Among these were 216 cases of advancement genioplasty, of which 79 (62 females and 17 males) underwent advancement procedures using silicone implants. Inserting the silicone implant at the sulcus easily removes the deepened groove. This procedure could be an easy and reliable method for attaining an aesthetically pleasing result in excessive advancement genioplasty.
Effectiveness of BNT162b2 and mRNA-1273 COVID-19 vaccines against symptomatic SARS-CoV-2 infection and severe COVID-19 outcomes in Ontario, Canada: a test-negative design study
Authors: Chung Hannah , He Siyi , Nasreen Sharifa , Sundaram Maria E. , Buchan Sarah A. , Wilson Sarah E. , Chen Branson , Calzavara Andrew , Fell Deshayne B. , Austin Peter C. , Wilson Kumanan , Schwartz Kevin L. , Brown Kevin A. , Gubbay Jonathan B. , Basta Nicole E. , Mahmud Salaheddin M. , Righolt Christiaan H. , Svenson Lawrence W. , MacDonald Shannon E. , Janjua Naveed Z. , Tadrous Mina , Kwong Jeffrey C.
Published: May 2021

Objectives

To estimate the effectiveness of mRNA COVID-19 vaccines against symptomatic infection and severe outcomes.

Design

We applied a test-negative design study to linked laboratory, vaccination, and health administrative databases, and used multivariable logistic regression adjusting for demographic and clinical characteristics associated with SARS-CoV-2 and vaccine receipt to estimate vaccine effectiveness (VE) against symptomatic infection and severe outcomes.

Setting

Ontario, Canada between 14 December 2020 and 19 April 2021.

Participants

Community-dwelling adults aged ≥16 years who had COVID-19 symptoms and were tested for SARS-CoV-2.

Interventions

Pfizer-BioNTech’s BNT162b2 or Moderna’s mRNA-1273 vaccine.

Main outcome measures

Laboratory-confirmed SARS-CoV-2 by RT-PCR; hospitalization/death associated with SARS-CoV-2 infection.

Results

Among 324,033 symptomatic individuals, 53,270 (16.4%) were positive for SARS-CoV-2 and 21,272 (6.6%) received ≥1 vaccine dose. Among test-positive cases, 2,479 (4.7%) had a severe outcome. VE against symptomatic infection ≥14 days after receiving only 1 dose was 60% (95%CI, 57 to 64%), increasing from 48% (95%CI, 41 to 54%) at 14–20 days after the first dose to 71% (95%CI, 63 to 78%) at 35–41 days. VE ≥7 days after 2 doses was 91% (95%CI, 89 to 93%). Against severe outcomes, VE ≥14 days after 1 dose was 70% (95%CI, 60 to 77%), increasing from 62% (95%CI, 44 to 75%) at 14–20 days to 91% (95%CI, 73 to 97%) at ≥35 days, whereas VE ≥7 days after 2 doses was 98% (95%CI, 88 to 100%). For adults aged ≥70 years, VE estimates were lower for intervals shortly after receiving 1 dose, but were comparable to younger adults for all intervals after 28 days. After 2 doses, we observed high VE against E484K-positive variants.

Conclusions

Two doses of mRNA COVID-19 vaccines are highly effective against symptomatic infection and severe outcomes. Single-dose effectiveness is lower, particularly for older adults shortly after the first dose.
DeepNull: Modeling non-linear covariate effects improves phenotype prediction and association power
Authors: McCaw Zachary R. , Colthurst Thomas , Yun Taedong , Furlotte Nicholas A. , Carroll Andrew , Alipanahi Babak , McLean Cory Y. , Hormozdiari Farhad
Published: May 2021

Genome-wide association studies (GWAS) examine the association between genotype and phenotype while adjusting for a set of covariates. Although the covariates may have non-linear or interactive effects, due to the challenge of specifying the model, GWAS often neglect such terms. Here we introduce DeepNull, a method that identifies and adjusts for non-linear and interactive covariate effects using a deep neural network. In analyses of simulated and real data, we demonstrate that DeepNull maintains tight control of the type I error while increasing statistical power by up to 20% in the presence of non-linear and interactive effects. Moreover, in the absence of such effects, DeepNull incurs no loss of power. When applied to 10 phenotypes from the UK Biobank (n=370K), DeepNull discovered more hits (+6%) and loci (+7%), on average, than conventional association analyses, many of which are biologically plausible or have previously been reported. Finally, DeepNull improves upon linear modeling for phenotypic prediction (+23% on average).
Microarrayed human bone marrow organoids for modeling blood stem cell dynamics
Authors: Giger Sonja , Hofer Moritz , Miljkovic-Licina Marijana , Hoehnel Sylke , Brandenberg Nathalie , Guiet Romain , Ehrbar Martin , Kleiner Esther , Gegenschatz Katharina , Matthes Thomas , Lutolf Matthias P.
Published: May 2021

In many leukemia patients, a poor prognosis is attributed either to the development of chemotherapy resistance by leukemic stem cells (LSCs) or to the inefficient engraftment of transplanted hematopoietic stem/progenitor cells (HSPCs) into the bone marrow (BM). Here, we build a 3D in vitro model system of bone marrow organoids (BMOs) that recapitulate several structural and cellular components of native BM. These organoids are formed in a high-throughput manner from the aggregation of endothelial and mesenchymal cells within hydrogel microwells. Accordingly, the mesenchymal compartment shows partial maintenance of its self-renewal and multilineage potential, while endothelial cells self-organize into an interconnected vessel-like network. Intriguingly, such a vascular compartment enhances the recruitment of HSPCs in a chemokine ligand/receptor-dependent manner, reminiscent of HSPC homing behaviorin vivo. Additionally, we also model LSC migration and nesting in BMOs, thus highlighting the potential of this system as a well accessible and scalable preclinical model for candidate drug screening and patient-specific assays.
The sensory and motor components of the cortical hierarchy are coupled to the rhythm of the stomach during rest
Authors: Rebollo Ignacio , Tallon-Baudry Catherine
Published: May 2021

Bodily rhythms appear as novel scaffolding mechanisms orchestrating the spatio-temporal organization of spontaneous brain activity. Here, we follow up on the discovery of the gastric resting-state network (Rebollo et al, 2018), composed of brain regions in which the fMRI signal is phase-synchronized to the slow (0.05 Hz) electrical rhythm of the stomach. Using a larger sample size (n=63 human participants), we further characterize the anatomy and effect sizes of gastric-brain coupling across resting-state networks, a fine grained cortical parcellation, as well as along the main gradients of cortical organization. Most (67%) of the gastric network is included in the somato-motor-auditory (38%) and visual (29%) resting state networks. Gastric brain coupling also occurs in the granular insula and, to a lesser extent, in the piriform cortex. Thus, all sensory and motor cortices corresponding to both exteroceptive and interoceptive modalities are coupled to the gastric rhythm during rest. Conversely, little gastric-brain coupling occurs in cognitive networks and transmodal regions. These results suggest not only that gastric rhythm and sensory-motor processes are likely to interact, but also that gastric-brain coupling might be a mechanism of sensory and motor integration that mostly bypasses cognition, complementing the classical hierarchical organization of the human brain.

Significance statement

While there is growing interest for brain-body communication in general and brain-viscera communication in particular, little is known about how the brain interacts with the gastric rhythm, the slow electrical rhythm continuously produced in the stomach. Here, we show in human participants at rest that the gastric network, composed of brain regions synchronized with delays to the gastric rhythm, includes all motor and sensory (vision, audition, touch and interoception, olfaction) regions, but only few of the transmodal regions associated with higher-level cognition. Such results prompt for a reconsideration of the classical view of cortical organization, where the different sensory modalities are considered as relatively independent modules.
Crossing design shapes patterns of genetic variation in synthetic recombinant populations ofSaccharomyces cerevisiae
Authors: Phillips Mark A. , Kutch Ian C. , McHugh Kaitlin M. , Taggard Savannah K. , Burke Molly K.
Published: May 2021

“Synthetic recombinant” populations have emerged as a useful tool for dissecting the genetics of complex traits. They can be used to derive inbred lines for fine QTL mapping, or the populations themselves can be sampled for experimental evolution. In latter application, investigators generally value maximizing genetic variation in constructed populations. This is because in evolution experiments initiated from such populations, adaptation is primarily fueled by standing genetic variation. Despite this reality, little has been done to systematically evaluate how different methods of constructing synthetic populations shape initial patterns of variation. Here we seek to address this issue by comparing outcomes in synthetic recombinantSaccharomyces cerevisiaepopulations created using one of two strategies: pairwise crossing of isogenic strains or simple mixing of strains in equal proportion. We also explore the impact of the varying the number of parental strains. We find that more genetic variation is initially present and maintained when population construction includes a round of pairwise crossing. As perhaps expected, we also observe that increasing the number of parental strains typically increases genetic diversity. In summary, we suggest that when constructing populations for use in evolution experiments, simply mixing founder strains in equal proportion may limit the adaptive potential.
Machine learning-enabled cancer diagnostics with widefield polarimetric second-harmonic generation microscopy
Authors: Mirsanaye Kamdin , Castaño Leonardo Uribe , Kamaliddin Yasmeen , Golaraei Ahmad , Augulis Renaldas , Kontenis Lukas , Done Susan J. , Žurauskas Edvardas , Wilson Brian C. , Barzda Virginijus
Published: May 2021

The extracellular matrix (ECM) collagen undergoes major remodeling during tumorigenesis. However, alterations to the ECM are not widely considered in cancer diagnostics, due to mostly uniform appearance of collagen fibers in white light images of hematoxylin and eosin-stained tissue sections. Polarimetric second-harmonic generation (P-SHG) microscopy enables label-free visualization and ultrastructural investigation of non-centrosymmetric molecules, which, when combined with texture analysis, provides multiparameter characterization of tissue collagen. This paper demonstrates whole slide imaging of breast tissue microarrays using high-throughput widefield P-SHG microscopy. The resulting P-SHG parameters are used in classification to differentiate tumor tissue from normal with 94.2% accuracy and F1-score, and 6.3% false discovery rate. Subsequently, the trained classifier is employed to predict tumor tissue with 91.3% accuracy, 90.7% F1-score, and 13.8% false omission rate. As such, we show that widefield P-SHG microscopy reveals collagen ultrastructure over large tissue regions and can be utilized as a sensitive biomarker for cancer diagnostics and prognostics studies.
Effect of straw incorporation and nitrification inhibitor on nitrous oxide emission in various cropland soils and its microbial mechanism
Authors: Zhang Ya-Bo , Liu Feng , Wang Jun-Tao , Hu Hang-Wei , He Ji-Zheng , Zhang Li-Mei
Published: May 2021

Nitrification inhibitor and straw incorporation are widely used to improve crop nitrogen use efficiency in agricultural soil, but their effects on nitrous oxide (N2O) emission across different soil types and the microbial mechanisms remain less understood. In this study, we used controlled experiment and DNA-based molecular analysis to study how nitrification inhibitor (dicyandiamide, DCD) and straw incorporation affect soil nitrogen balance, N2O emission and microbial nitrifiers/denitrifers in three distinct agricultural soils (the black, fluvo-aquic and red soils) across China. Both DCD and straw incorporation improved nitrogen balance by increasing NH4+ and decreasing NO3- in all soils. DCD tended to decrease N2O emission from all soils especially the fluvo-aquic one, while straw incorporation reduced N2O emission only in the fluvo-aquic soil but increased N2O emission in the other two especially the red soil (by ∼600%). T-RFLP analysis revealed that the denitriers community structure are distinct among the three soils but was not strongly affected by DCD or straw incorporation. qPCR analysis revealed that DCD or straw incorporation had no significant effect on nitrifier abundance but increased nitrous oxide reductase nosZ gene abundance in the black/fluvo-aquic soil rather than the red soil. Structural equational modelling further confirmed that, when accounting for treatments and soil properties, nosZ gene abundance is the only biological factor significantly determined N2O emission in different soil types. Taken together, our work advanced the knowledge on the agricultural practices and N2O emission in cropland soils, suggesting that straw incorporation may not be a good choice for the red and black soil areas; management practices should be used as per soil type to balance between nitrogen use efficiency and N2O emission.
Functional connectome reorganization relates to post-stroke motor recovery and structural disruption
Authors: Olafson Emily R , Jamison Keith W , Sweeney Elizabeth M , Liu Hesheng , Wang Danhong , Bruss Joel E , Boes Aaron D , Kuceyeski Amy
Published: May 2021

Motor recovery following ischemic stroke is contingent on the ability of surviving brain networks to compensate for damaged tissue. In rodent models, sensory and motor cortical representations have been shown to remap onto intact tissue around the lesion site, but remapping to more distal sites (e.g. in the contralesional hemisphere) has also been observed. Resting state functional connectivity (FC) analysis has been employed to study compensatory network adaptations in humans, but mechanisms and time course of motor recovery are not well understood. Here, we examine longitudinal FC in 23 first-episode ischemic pontine stroke patients (34-74 years old; 8 female, 15 male) and utilize a graph matching approach to identify patterns of regional functional connectivity reorganization during recovery. We quantified functional reorganization between several intervals ranging from 1 week to 6 months following stroke, and demonstrated that the areas that undergo functional reorganization most frequently are in cerebellar/subcortical networks. Brain regions with more structural connectome disruption due to the stroke also had more functional remapping over time. Finally, we show that the amount of functional reorganization between time points is correlated with the extent of motor recovery observed between those time points in the early to late subacute phases, and, furthermore, individuals with greater baseline motor impairment demonstrate more extensive early subacute functional reorganization (from one to two weeks post-stroke) and this reorganization correlates with better motor recovery at 6 months. Taken together, these results suggest that our graph matching approach can quantify recovery-relevant, whole-brain functional connectivity network reorganization after stroke.
Spontaneous polarization and cell guidance on asymmetric nanotopography
Authors: Herr Corey , Winkler Benjamin , Ziebert Falko , Aranson Igor S. , Fourkas John T. , Losert Wolfgang
Published: May 2021

Asymmetric nanotopography with sub-cellular dimensions has recently been demonstrated to be able to provide a unidirectional bias in the migration of cells. The details of this guidance depend both on the type of cell studied and the design of the nanotopography. This behavior is not yet well understood, so there is a pressing need for a predictive description of cell migration on such nanotopography that captures both the initiation of migration and the manner in which cell migration evolves. Here, we employ a three-dimensional, physics-based model to study cell guidance on asymmetric nanosawteeth. In agreement with experimental data, our model predicts that asymmetric sawteeth lead both to spontaneous motion and changes in motion phenotypes. Our model demonstrates that asymmetric nano-sawteeth induce a unidirectional bias in guidance direction that is dependent upon the actin polymerization rate and the sawtooth dimensions. Motivated by this model, an analysis of previously reported experimental data indicates that the degree of guidance by asymmetric nanosawteeth increases with the cell velocity.
Jasmine: Population-scale structural variant comparison and analysis
Authors: Kirsche Melanie , Prabhu Gautam , Sherman Rachel , Ni Bohan , Aganezov Sergey , Schatz Michael C.
Published: May 2021

The increasing availability of long-reads is revolutionizing studies of structural variants (SVs). However, because SVs vary across individuals and are discovered through imprecise read technologies and methods, they can be difficult to compare. Addressing this, we present Jasmine (https://github.com/mkirsche/Jasmine), a fast and accurate method for SV refinement, comparison, and population analysis. Using an SV proximity graph, Jasmine outperforms five widely-used comparison methods, including reducing the rate of Mendelian discordance in trio datasets by more than five-fold, and reveals a set of high confidence de novo SVs confirmed by multiple long-read technologies. We also present a harmonized callset of 205,192 SVs from 31 samples of diverse ancestry sequenced with long reads. We genotype these SVs in 444 short read samples from the 1000 Genomes Project with both DNA and RNA sequencing data and assess their widespread impact on gene expression, including within several medically relevant genes.
A generic systems-theoretic approach to identify biological networks capable of adaptation
Authors: Bhattacharya Priyan , Raman Karthik , Tangirala Arun K.
Published: May 2021

Constructing biological networks capable of performing specific biological functionalities has been of sustained interest in synthetic biology. Adaptation is one such ubiquitous functional property, which enables every living organism to sense a change in its surroundings and return to its operating condition prior to the disturbance. In this paper, we present a generic systems theory-driven method for designing adaptive protein networks. First, we translate the necessary qualitative conditions for adaptation to mathematical constraints using the language of systems theory, which we then map back as ‘design requirements’ for the underlying networks. We go on to prove that a protein network with different input–output nodes (proteins) needs to be at least of third-order in order to provide adaptation. Next, we show that the necessary design principles obtained for a three-node network in adaptation consist of negative feedback or a feed-forward realization. Interestingly, the design principles obtained by the proposed method remain the same for a network of arbitrary size and connectivity. Finally, we prove that the motifs discovered for adaptation are non-retroactive for a canonical downstream connection. This result explains how complex biological networks achieve robustness while keeping the core motifs unchanged in the context of a particular functionality. We corroborate our theoretical results with detailed and thorough numerical simulations. Overall, our results present a generic, systematic and robust framework for designing various kinds of biological networks.
Electrolysis of Bacterial Biofilm
Authors: Bazargani Abdollah , Azimi Arsalan , Farhadi Pouya , Irvani Seyed Sina Naghibi , Moatari Psalm
Published: May 2021

Biofilms are a significant global health problem and are of most important clinical impediments of the century. Biofilms play a crucial role in antimicrobial resistance and chronic infections by acting as reservoir for microorganisms. Therefore greater understanding of biofilm and novel methods to eliminate them are needed. We considered electrolysis as a contrivance to decompose and disperse thePseudomonas aeruginosa biofilmin microtiter dishes. We showed electrolysis effectively eliminated thePseudomonas aeruginosa biofilm with the potential to change our approach in tackling biofilms.
Mitochondria preserve an autarkic one-carbon cycle to confer growth-independent cancer cell migration and metastasis
Authors: Kiweler Nicole , Delbrouck Catherine , Pozdeev Vitaly I. , Neises Laura , Soriano-Baguet Leticia , Eiden Kim , Xian Feng , Benzarti Mohaned , Haase Lara , Koncina Eric , Schmoetten Maryse , Jaeger Christian , Noman Muhammad Zaeem , Vazquez Alexei , Janji Bassam , Dittmar Gunnar , Brenner Dirk , Letellier Elisabeth , Meiser Johannes
Published: May 2021

Progression of primary cancer to metastatic disease is the most common cause of death in cancer patients with minimal treatment options available. Canonical drugs target mainly the proliferative capacity of cancer cells, which often leaves slow-proliferating, persistent cancer cells unaffected. Metabolic determinants that contribute to growth-independent functions supporting resistance and metastatic dissemination are still poorly understood.

In the present study, we revealed that antifolate treatment results in an uncoupled and autarkic mitochondrial one-carbon (1C) metabolism allowing sustained serine catabolism and formate overflow when cytosolic 1C metabolism is impaired. Interestingly, antifolate dependent growth-arrest did not correlate with decreased migration capacity. Therefore, using the antifolate Methotrexate as a tool compound allowed us to disentangle proliferation and migration to profile the metabolic phenotype of migrating (growth-arrested) cells. Supported by an increased NAD/NADH ratio, we observed increased serine de novo synthesis and increased serine catabolism to formate.

Consequently, inhibition of serine de novo synthesis using the competitive PHGDH-inhibitor BI-4916 or direct inhibition of mitochondrial 1C metabolism reduced cancer cell migration. Using an orthotopic breast cancer model, we show that sole inhibition of mitochondrial serine catabolism does not affect primary tumor growth but strongly inhibits pulmonary metastasis.

We conclude that mitochondrial 1C metabolism, despite being dispensable for proliferative capacities, confers an advantage to cancer cells by supporting their motility potential.

Our results improve our understanding of 1C metabolism and of metabolic determinants that support the process of cancer cell migration and metastasis.
NaturalizedDolichogenidea gelechiidivorisMarsh (Hymenoptera: Braconidae) complement the resident parasitoid complex ofTuta absoluta(Meyrick) (Lepidopera:Gelechiidae) in Spain
Authors: Denis Carmen , Riudavets Jordi , Alomar Oscar , Agustí Nuria , Gonzalez-Valero Helena , Cubí Martina , Matas Montserrat , Rodríguez David , van Achterberg Kees , Arnó Judit
Published: May 2021

Our study aimed to assess the contribution of natural parasitism due toNecremnus tutaeRibes & Bernardo (Hymenoptera: Eulophidae) to the biological control ofTuta absoluta(Meyrick) (Lepidopera:Gelechiidae) in commercial plots where an IPM program based on the use of predatory mirid bugs was implemented. During the samplings, the presence of another parasitoid was detected and, therefore, a second part of our study intended to identify this species and to evaluate the importance of its natural populations in the biological control of the pest. Leaflets withT. absolutagalleries were collected during 2017–2020 from commercial tomato plots in the horticultural production area of Catalonia (Northeast Spain), including greenhouses, open fields, and roof covered tunnels that lack side walls. In the laboratory,T. absolutalarvae were classified as ectoparasitized, alive, or dead. Reared parasitoids from ectoparasitized larvae were mostly morphologically identified asNecremnussp. with parasitism rates that peaked in summer months with values between 9 and 15%. Some of these ectoparasitized larvae also yielded another parasitoid identified asDolichogenidea gelechiidivorisMarsh (Hymenoptera: Braconidae) by both morphological and molecular-DNA barcoding methods. In 2020, parasitism rates due toD. gelechiidivoristhat increased with season up to 22%. Our work reports for the first time in Europe the presence of the neotropical speciesD. gelechiidivorisadding this biocontrol agent to the resident parasitoid complex ofT. absolutain Spain.
IN VIVO ANALYSIS OF THE ROLE OF GASDERMIN-B (GSDMB) IN CANCER USING NOVEL KNOCK-IN MOUSE MODELS
Authors: Sarrio David , Rojo-Sebastián Alejandro , Teijo Ana , Pérez-López María , Díaz-Martín Eva , Martínez Lidia , Morales Saleta , García-Sanz Pablo , Palacios José , Moreno-Bueno Gema
Published: May 2021

Background

Gasdermin-B gene (GSDMB) is frequently over-expressed in tumors, and its shortest translated variant (isoform 2; GSDMB2) increases aggressive behavior in breast cancer cells. Paradoxically, GSDMB could have either pro-tumor or tumor suppressor properties depending on the biological context. Since GSDMB gene is not present in the mouse genome, deciphering fully the functional roles of GSDMB in cancer requires novel in vivo models.

Methods

We first generated by gene targeting a conditional knock-in mouse model (R26-STOP-GB2) harboring human GSDMB2 transcript within the ROSA26 locus. We next derived the R26-GB2 model ubiquitously expressing GSDMB2 in multiple tissues (confirmed by western blot and immunohistochemistry) and performed a comprehensive histopathological analysis in multiple tissues from 75 male and female mice up to 18 months of age. Additionally, we produced the double transgenic model R26-GB2/MMTV-PyMT, co-expressing GSDMB2 and the Polyoma-Middle-T oncogene, and assessed breast cancer generation and progression in GSDMB2-homozygous (n=10) and control (n=17) female mice up to 15 weeks of age.

Results

In the R26-GB2 model, which showed different GSDMB2 cytoplasmic and/or nuclear localization among tissues, we investigated if GSDMB2 expression had intrinsic tumorigenic activity. 41% of mice developed spontaneous lung tumors, but neither the frequency nor the histology of these neoplasias was significantly different from wildtype animals. Strikingly, while 17% control mice developed gastric carcinomas, no GSDMB2-positive mice did. No other tumor types or additional histological alterations were frequently seen in these mice. In the R26-GB2/MMTV-PyMT model, the strong nucleus-cytoplasmic GSDMB2 expression in breast cancer cells did not significantly affect cancer formation (number of tumors, latency, tumor weight, histology or proliferation) or lung metastasis potential compared to controls.

Conclusions

GSDMB2 expression alone does not have an overall tumorigenic potential in mice, but it might reduce gastric carcinogenesis. Contrary to human cancers, GSDMB2 upregulation does not significantly affect breast cancer generation and progression in mouse models. However, to evidence the GSDMB functions in cancer and other pathologies in vivo may require the presence of specific stimulus or cellular contexts. Our novel mouse strains will serve as the basis for the future development of more precise tissue-specific and context-dependent cancer models.
Effect of Suppression of Rotational Joint Instability on Cartilage and Meniscus Degeneration in Mouse Osteoarthritis Model
Authors: Arakawa Kohei , Takahata Kei , Oka Yuichiro , Ozone Kaichi , Morosawa Kzuma , Enomoto Saaya , Murata Kenji , Kanemura Naohiko , Kokubun Takanori
Published: May 2021

Objective

Joint instability and meniscal dysfunction contribute to the onset and progression of knee osteoarthritis (OA). In the destabilization of the medial meniscus (DMM) model, secondary OA occurs due to the rotational instability and increases compressive stress resulting from the meniscal dysfunction. We created a new controlled abnormal tibial rotation (CATR) model that reduces the rotational instability that occurs in the DMM model. So, we aimed to investigate whether rotational instability affects articular cartilage degeneration using the DMM and CATR models, as confirmed using histology and immunohistochemistry.

Design

Twelve-week-old male mice were randomized into 3 groups: DMM group, CATR group, and INTACT group (right knee of the DMM group). After 8 and 12 weeks, we performed the tibial rotational test, safranin-O/fast green staining, and immunohistochemical staining for TNF-α and MMP-13.

Results

The rotational instability in the DMM group was significantly higher than that of the other groups. And articular cartilage degeneration was higher in the DMM group than in the other groups. However, meniscal degeneration was observed in both DMM and CATR groups. The TNF-α and MMP-13 positive cell rates in the articular cartilage of the CATR group were lower than those in the DMM group.

Conclusions

We found that the articular cartilage degeneration was effectively suppressed by controlling the rotational instability caused by meniscal dysfunction. These findings suggest that suppression of rotational instability in the knee joint is an effective therapeutic measure for preventing OA progression.
Investigation of extramammary sources of Group BStreptococcusreveals its unusual ecology and epidemiology in camels
Authors: Seligsohn Dinah , Crestani Chiara , Gitahi Nduhiu , Flodin Emelie Lejon , Chenais Erika , Zadoks Ruth N.
Published: May 2021

Camels are vital to food production in the drylands of the Horn of Africa, with milk as their main contribution to food security. A major constraint to camel milk production is mastitis, inflammation of the mammary gland. The condition negatively impacts milk yield and quality as well as household income. The leading cause of mastitis in dairy camels isStreptococcus agalactiae,group BStreptococcus(GBS), which is also a commensal and pathogen of humans. It has been suggested that extramammary reservoirs for this pathogen may contribute to the occurrence of mastitis in camels. We explored the molecular epidemiology of GBS in camels using a cross-sectional study design for sample collection and phenotypic, genomic and phylogenetic analysis of isolates. Among 88 adult camels and 93 calves from six herds in Laikipia County, Kenya, GBS was detected in 20% of 50 milk samples, 25% of 152 nasal swabs, 8% of 90 oral swabs and 3% of 90 rectal swabs, but not in vaginal swabs. Per camel herd, two to four sequence types (ST) were present. More than half of the isolates belonged to ST617 or its single-locus variant, ST1652, with these STs found across all sample types. Serotype VI was detected in 30 of 58 isolates. In three herds, identical STs were detected in milk and swab samples, suggesting that extramammary sources of GBS may contribute to the maintenance and spread of GBS within camel herds. This needs to be considered when developing prevention and control strategies. In addition, the high nasal carriage rate, low recto-vaginal carriage rate, and high prevalence of serotype VI for GBS in camels are in stark contrast to the distribution of GBS in humans and reveal hitherto unknown ecological and molecular features of this bacterial species.
Pathways of savannization in a mesic African savanna-forest mosaic following an extreme fire
Authors: Beckett Heath , Staver A. Carla , Charles-Dominique Tristan , Bond William J.
Published: May 2021

Fires in savannas limit tree cover, thereby promoting flammable grass accumulation and fuelling further frequent fires. Meanwhile, forests and thickets form dense canopies that reduce C4-grass fuel loads and creating a humid microclimate, thereby excluding fires under typical climatic conditions.

However, extreme fires occasionally burn into these closed-canopy systems. Although these rare fires cause substantial tree mortality and can make repeat fires more likely, the long-term consequences of an extreme fire for closed canopy vegetation structure and potential to convert to savanna (hereafter “savannization”) remain largely unknown.

Here, we analysed whether an extreme fire could, alone, alter species composition, vegetation structure, and fire regimes of closed-canopy ecosystems in an intact savanna-forest-thicket mosaic, or whether successive fires after an initial extreme fire were necessary to trigger a biome transition between from forest to savanna.

We found that forests that only burned once recovered, whereas those that burned again following an initial extreme fire transitioned from closed-canopy forests towards open, grassy savannas.

While thickets had less tree mortality in fires than forests, repeat fires nonetheless precipitated a transition towards savannas.

Colonization of the savanna tree community lagged behind the grass community, but also began to transition.

Synthesis

Our results suggest that rare extreme fires, followed by repeated burning can indeed result in savannization in places where savanna and forest represent alternative stable states.
de novo variant calling identifies cancer mutation profiles in the 1000 Genomes Project
Authors: Ng Jeffrey K. , Vats Pankaj , Fritz-Waters Elyn , Sarkar Stephanie , Sams Eleanor I. , Padhi Evin M. , Payne Zachary L. , Leonard Shawn , West Marc A. , Prince Chandler , Trani Lee , Jansen Marshall , Vacek George , Samadi Mehrzad , Harkins Timothy T. , Pohl Craig , Turner Tychele N.
Published: May 2021

Detection of de novo variants (DNVs) is critical for studies of disease-related variation and mutation rates. We developed a GPU-based workflow to rapidly call DNVs (HAT) and demonstrated its effectiveness by applying it to 4,216 Simons Simplex Collection (SSC) whole-genome sequenced parent-child trios from DNA derived from blood. In our SSC DNV data, we identified 78 ± 15 DNVs per individual, 18% ± 5% at CpG sites, 75% ± 9% phased to the paternal chromosome of origin, and an average allele balance of 0.49. These calculations are all in line with DNV expectations. We sought to build a control DNV dataset by running HAT on 602 whole-genome sequenced parent-child trios from DNA derived from lymphoblastoid cell lines (LCLs) from the publicly available 1000 Genomes Project (1000G). In our 1000G DNV data, we identified 740 ± 967 DNVs per individual, 14% ± 4% at CpG sites, 61% ± 11% phased to the paternal chromosome of origin, and an average allele balance of 0.41. Of the 602 trios, 80% had > 100 DNVs and we hypothesized the excess DNVs were cell line artifacts. Several lines of evidence in our data suggest that this is true and that 1000G does not appear to be a static reference. By mutation profile analysis, we tested whether these cell line artifacts were random and found that 40% of individuals in 1000G did not have random DNV profiles; rather they had DNV profiles matching B-cell lymphoma. Furthermore, we saw significant excess of protein-coding DNVs in 1000G in the gene IGLL5 that has already been implicated in this cancer. As a result of cell line artifacts, 1000G has variants present in DNA repair genes and at Clinvar pathogenic or likely-pathogenic sites. Our study elucidates important implications of the use of sequencing data from LCLs for both reference building projects as well as disease-related projects whereby these data are used in variant filtering steps.
Deciphering microbiome impacts on fungal-microalgal interaction in a marine environment using metabolomics
Authors: Berry Olivier , Briand Enora , Bagot Alizé , Chaigne Maud , Meslet-Cladière Laurence , Wang Julien , Grovel Olivier , Jansen Jeroen J. , Ruiz Nicolas , du Pont Thibaut Robiou , François Pouchus Yves , Hess Philipp , Bertrand Samuel
Published: May 2021

The comprehension of microbial interactions is one of the key challenges in microbial ecology. The present study focuses on studying the chemical interaction between the toxic dinoflagellate Prorocentrum lima PL4V strain and associated fungal strains (two Penicillium sp. strains and three Aspergillus sp) among which the Aspergillus pseudoglaucus strain MMS1589 was selected for further co-culture experiment. Such rarely studied interaction (fungal-microalgal) was explored in axenic and non-axenic conditions, in a dedicated microscale marine environment (hybrid solid/liquid conditions), to delineate specialized metabolome alteration in relation to the P. lima and A. pseudoglaucus co-culture in regard to the presence of their associated bacteria. Such alteration was monitored by high-performance liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS). In-depth analysis of the resulting data highlighted (1) the chemical modification associated to fungal-microalgal co-culture, and (2) the impact of associated bacteria in microalgal resilience to fungal interaction. Even if only a very low number of highlighted metabolites were fully characterised due to the poor chemical investigation of the studied species, a clear co-culture induction of the dinoflagellate toxins okadaic acid and dinophysistoxin 1 was observed. Such results highlight the importance to consider microalgal microbiome to study parameters regulating toxin production. Finally, a microscopic observation showed an unusual physical interaction between the fungal mycelium and the dinoflagellates.
Genome-Wide DNA Methylation Profiles of Neurodevelopmental Disorder Genes in Mouse Placenta and Fetal Brain Following Prenatal Exposure to Polychlorinated Biphenyls
Authors: Laufer Benjamin I. , Neier Kari E. , Valenzuela Anthony E. , Yasui Dag H. , Schmidt Rebecca J. , Lein Pamela J. , LaSalle Janine M.
Published: May 2021

Background

Polychlorinated biphenyls (PCBs) are developmental neurotoxicants implicated as environmental risk factors for neurodevelopmental disorders (NDD), including autism spectrum disorders (ASD).

Objective

We examined the effects of prenatal exposure to a human-relevant mixture of PCBs on the DNA methylome of fetal mouse brain and placenta to determine if there was a shared subset of differentially methylated regions (DMRs).

Methods

A PCB mixture formulated to model the 12 most abundant congeners detected in the serum of pregnant women from a prospective high-risk ASD cohort was administered to female mice prior to and during pregnancy. Whole-genome bisulfite sequencing (WGBS) was performed to assess genome-wide DNA methylation profiles of placenta and brain on gestational day 18.

Results

We found thousands of significant (empiricalp< 0.05) DMRs distinguishing placentas and brains from PCB-exposed embryos from sex-matched vehicle controls. In both placenta and brain, PCB-associated DMRs were significantly (p< 0.005) enriched for functions related to neurodevelopment, cellular adhesion, and cellular signaling, and significantly (Odds Ratio > 2.4,q< 0.003) enriched for bivalent chromatin marks. The placenta and brain PCB DMRs overlapped significantly (Z-score = 4.5,p= 0.0001) by genomic coordinate and mapped to a shared subset of genes significantly (q< 0.05) enriched for Wnt signaling, Slit/Robo signaling, and genes differentially expressed in multiple NDD/ASD models. The placenta and brain DMRs also significantly (q< 0.05) overlapped by genomic coordinate with brain samples from humans with Rett syndrome and Dup15q syndrome.

Discussion

These results demonstrate that placenta can be used as a surrogate for embryonic brain DNA methylation changes over genes relevant to NDD/ASD in a mouse model of prenatal PCB exposure.
The Interplay of Electrostatics and Chemical Positioning in the Evolution of Antibiotic Resistance in TEM β-Lactamases
Authors: Schneider Samuel H. , Kozuch Jacek , Boxer Steven G.
Published: May 2021

The interplay of enzyme active site electrostatics and chemical positioning are important for understanding the origin(s) of enzyme catalysis and the design of novel catalysts. We reconstruct the evolutionary trajectory of TEM-1 β-lactamase to TEM-52 towards extended-spectrum activity to better understand the emergence of antibiotic resistance and to provide insights into the structure-function paradigm and non-covalent interactions involved in catalysis. Utilizing a detailed kinetic analysis and the vibrational Stark effect, we quantify the changes in rates and electric fields in the Michaelis and acyl-enzyme complexes for penicillin G and cefotaxime to ascertain the evolutionary role of electric fields to modulate function. These data are combined with MD simulations to interpret and quantify the substrate-dependent structural changes during evolution. We observe that this evolutionary trajectory utilizes a large preorganized electric field and substrate-dependent chemical positioning to facilitate catalysis. This governs the evolvability, substrate promiscuity, and protein fitness landscape in TEM β-lactamase antibiotic resistance.
Protein sensors of bacterial kinase activity reveal antibiotic-dependent kinase activation in single cells
Authors: Zheng Christine R. , Singh Abhyudai , Libby Alexandra , Silver Pamela A. , Libby Elizabeth A.
Published: May 2021

A lack of direct single-cell readouts for bacterial kinase activity remains a major barrier to our understanding of most signaling systems. At the single-cell-level, protein kinase activity is typically inferred by the activity of downstream transcriptional reporters. Complicating this approach in vivo, promoters are often co-regulated by several pathways, making the activity of a specific kinase difficult to deconvolve. Here, we have designed and constructed new, direct and specific sensors of bacterial kinase activity, including FRET-based sensors, as well as a synthetic transcription factor that responds to phosphorylation. We demonstrate the utility of these reporters in measuring kinase activity in population-based and single-cell assays during various growth phases and antibiotic treatments. These sensors respond to a highly conserved bacterial Ser/Thr kinase, PrkC that has no known dedicated transcription factor and whose regulon is known to be convolved with an essential signaling system. We used these new sensors to measure PrkC activity in colonies, bulk culture, and single cells. Together these new sensors provide evidence for considerable heterogeneity in PrkC activity in actively growing populations. We further demonstrate that PrkC activity increases in response to a cell-wall active antibiotic that blocks the late steps in peptidoglycan synthesis (cefotaxime), but not the early steps (fosfomycin). This is consistent with a model where PrkC senses and responds to blocks in the extracellular steps in cell wall synthesis. As the design of these phosphorylation sensors is modular, we anticipate that this work may have broad applications to other bacterial signaling systems in the future.
Personalized chordoma organoids for drug discovery studies
Authors: Shihabi Ahmad Al , Davarifar Ardalan , Lam Nguyen Huyen Thi , Tavanaie Nasrin , Nelson Scott D. , Yanagawa Jane , Federman Noah , Bernthal Nicholas , Hornicek Francis , Soragni Alice
Published: May 2021

Chordomas are rare tumors of notochordal origin, most commonly arising in the sacrum or skull base. Primary treatment of chordoma is surgery, however complete resection is not always feasible due to their anatomic location, and recurrence rates remain high. Chordomas are considered insensitive to conventional chemotherapy, and their rarity complicates running timely and adequately powered trials to identify effective regimens. Therefore, there is a need for discovery of novel therapeutic approaches. Drug discovery efforts in chordoma have been mostly limited to cell line models. Patient-derived organoids can accelerate drug discovery studies and predict patient responses to therapy. In this proof-of-concept study, we successfully established organoids from seven chordoma tumor samples obtained from five patients presenting with tumors in different sites and stages of disease. The organoids recapitulated features of the original parent tumors and inter-as well as intra-patient heterogeneity. High-throughput screenings performed on the organoids highlighted targeted agents such as PI3K/mTOR, EGFR, and JAK2/STAT3 inhibitors among the most effective molecules. Pathway analysis underscored how the NF-kB and IGF-1R pathways are sensitive to perturbations and potential targets to pursue for combination therapy of chordoma.
Levelling out differences in aerobic glycolysis neutralizes the competitive advantage of oncogenicPIK3CAmutant progenitors in the esophagus
Authors: Herms Albert , Colom Bartomeu , Piedrafita Gabriel , Murai Kasumi , Ong Swee Hoe , Fernandez-Antoran David , Bryant Christopher , Frezza Christian , Vanhaesebroeck Bart , Jones Philip H.
Published: May 2021

Normal human tissues progressively accumulate cells carrying mutations. Activating mutations inPIK3CAgenerate large clones in the aging human esophagus, but the underlying cellular mechanisms are unclear. Here, we tracked mutantPIK3CAesophageal progenitor cells in transgenic mice by lineage tracing. Expression of an activating heterozygousPik3caH1047Rmutation in single progenitor cells tilts cell fate towards proliferation, generating mutant clones that outcompete their wild type neighbors. The mutation leads to increased aerobic glycolysis through the activation of Hif1α transcriptional targets compared with wild type cells. We found that interventions that level out the difference in activation of the PI3K/HIF1α/aerobic glycolysis axis between wild type and mutant cells attenuate the competitive advantage ofPik3caH1047Rmutant cellsin vitroandin vivo. Our results suggest that clinically feasible interventions that even out signaling imbalances between wild type and mutant cells may limit the expansion of oncogenic mutants in normal epithelia.