bluuebunny/crossref_metadata_2025 huggingface dataset:
Liver perfusion strategies: what is best and do ischemia times still matter?
Authors: Panconesi Rebecca , Carvalho Mauricio Flores , Muiesan Paolo , Dutkowski Philipp , Schlegel Andrea
Published: February 2022

Purpose of review

This review describes recent developments in the field of liver perfusion techniques.

Recent findings

Dynamic preservation techniques are increasingly tested due to the urgent need to improve the overall poor donor utilization. With their exposure to warm ischemia, livers from donors after circulatory death (DCD) transmit additional risk for severe complications after transplantation. Although the superiority of dynamic approaches compared to static-cold-storage is widely accepted, the number of good quality studies remains limited. Most risk factors, particularly donor warm ischemia, and accepted thresholds are inconsistently reported, leading to difficulties to assess the impact of new preservation technologies. Normothermic regional perfusion (NRP) leads to good outcomes after DCD liver transplantation, with however short ischemia times. While randomized controlled trials (RCT) with NRP are lacking, results from the first RCTs with ex-situ perfusion were reported. Hypothermic oxygenated perfusion was shown to protect DCD liver recipients from ischemic cholangiopathy. In contrast, endischemic normothermic perfusion seems to not impact on the development of biliary complications, although this evidence is only available from retrospective studies.

Dynamic perfusion strategies impact posttransplant outcomes and are increasingly commissioned in various countries along with more evidence from RCTs. Transparent reporting of risk and utilization with uniform definitions is required to compare the role of different preservation strategies in DCD livers with prolonged ischemia times.
Decision-making context of women who have undergone surgical treatment for breast cancer: a qualitative exploration of patient perspectives
Authors: Darmonkow Georgia , Dicks Elizabeth , Roome Rebecca , Chafe Joanne , Simmonds Charlene , Etchegary Holly
Published: February 2022

Background:

Mastectomy (MT) rates are higher in Newfoundland and Labrador (NL) than in any other province in Canada, even in women diagnosed with early-stage breast cancer. In this article, we present qualitative data from women who made a surgical breast cancer treatment decision to better understand the decision-making environment and process.

Methods:

A descriptive, qualitative design was employed. Semi-structured interviews and focus groups were held with women in NL who underwent surgical treatment for breast cancer, including breast-conserving surgery (BCS) or mastectomy (MT).

Results:

Thirty-five women participated. 74.3% had MT, whereas only 11.4% had BCS. Additionally, 14.3% had BCS initially followed by MT. The surgical treatment decision-making context was heterogeneous. Women reported varying levels of time they had to make a surgical decision, diverse perceptions of decisional choice, opinions on the adequacy of information provided to inform a decision, and different levels of available formal and informal supports. Most reported they were satisfied with their surgical decision, although the context in which these decisions were made was clearly a challenging one.

Conclusions:

Although most women were pleased with the surgical care they received, adequate time and thorough pre-surgical discussion were noted as necessary but not always available. Women explained the importance of thinking through their personal circumstances and values so as to make informed surgical decisions. Postsurgical care and discussion of available psychosocial supports were proposed as areas that could be improved.
Enhancing access to sustainable cancer supportive modalities: the roles of interactive health communication and trained volunteers
Authors: Attieh Samar , Loiselle Carmen G.
Published: February 2022

Background:

Addressing the unmet needs of individuals with cancer in a timely manner is imperative for true implementation of person-centered care. Interactive health communication (ie, people's interactions with health information technologies) and more sustainable forms of support (eg, trained volunteers), are increasingly recognized as promising means to address the many barriers to accessing cancer-related support. This pilot study is timely as it tested an accessible cancer supportive approach that included e-handouts on 25 cancer distress-related topics and supportive phone calls by trained volunteers. The study objectives were to document participants’ preferences for the types of support offered, assess changes in distress pre and post, and determine the usability of the approach.

Methods:

Individuals with various types and stages of cancer (N = 88), diagnosed within the past 6 months were recruited from a university-affiliated cancer center in Montreal, Quebec, Canada. Participants completed the Cancer Support Community Distress measure at baseline, and they were prompted to request different types of support. Participants completed a follow-up questionnaire including the distress measure one to four weeks post support provision.

Results:

Of the 88 participants who filled out baseline questionnaires, 68 completed the follow up measures. Of the former, 76% (n = 67) made at least one request (e-handouts/phone calls/or both). The most frequently requested e-handout addressed pain/physical discomfort (37 requests) and phone calls were requested mostly for sleep problems (8 requests). Participants who requested both support modalities reported significantly lower distress [F (3,64) = 3.52, P = .02] at follow-up compared to those who made no requests. Ninety-two percent of participants who requested e-handouts reported that other patients would benefit from these. Participants who requested phone calls agreed or strongly agreed that volunteers were knowledgeable. The usability score was excellent (mean = 85.5/100; SD = 16.36).

Conclusion:

Preliminary findings indicate that this supportive approach is promising. Future work would document the differential contributions of supportive modalities that compare, for instance, professional versus lay (trained) support.
Requests to Amend Cause and Manner of Death Determinations by Medical Examiners in Maryland, 2015–2021
Authors: Weedn Victor W. , Goldfarb Bruce
Published: February 2022

A 1989 state law in Maryland allows family members to contest cause and manner of death determinations of medical examiners. A previous article described the experience with this law involving 12 appeals over a 3-year period (2012–2015). We now update the experience with the law involving 10 appeals that occurred over a subsequent period (2015 to September 2021) and a resultant change in the law. This unique appellate scheme has proven to be a valuable tool for medical examiners and families and has to date prevented resort to judicial courts. It is a model statutory scheme that is recommended for other jurisdictions to consider.
Difficult removal of exposed peripheral nerve stimulator leads: a report of 2 cases
Authors: Uppal Pushpinder , Wright Thelma B. , Dahbour Layth , Watterworth Blake , Lee Seung J. , Gattu Kanchana , Stansbury Lynn G. , Benoit Justin
Published: February 2022

Introduction:

Peripheral nerve stimulators have emerged as a new generation of advanced modalities to treat chronic pain and avoid opioids. They transmit electrical stimulation through implanted leads and wireless, wearable, external generators. Common complications include infection, nerve damage, and migration of stimulating leads. This article describes 2 cases of complications from lead migration.

Methods:

Case 1 describes a 61-year-old man with chronic groin pain who underwent an uncomplicated ultrasound-guided ilioinguinal peripheral nerve lead implantation. Case 2 describes a 54-year-old woman with left shoulder pain who underwent an uncomplicated ultrasound-guided percutaneous lead placement near the axillary nerve through a deltoid approach. Both peripheral nerve stimulators were confirmed with fluoroscopy, and each patient was followed up every 2 months for the following 2 years.

Results:

Both patients experienced lead migration to the skin resulting in erythema and need for lead removal. Initial unsuccessful removal by traction resulted in retained fragments and need for open surgical removal.

Discussion:

Neurologic complications of peripheral nerve stimulator implantation are rare, but device-associated complications, specifically lead migration, remain a source of long-term problems that can result in decreased coverage of the intended neural target.

Conclusion:

Thorough patient education, early postimplantation assessment, and extended routine follow-up are necessary to decrease lead-associated complications. If migration does occur, the potential impact of scar tissue on removal should be considered.
The Failed Breast Implant in Postmastectomy Reconstruction
Authors: Bucher Florian , Vogt Peter M.
Published: February 2022

Background

Breast cancer is the most diagnosed malignant neoplasia of female patients worldwide in 2019. Survival has increased making it necessary to offer breast reconstructive procedures to improve quality of life and self-esteem. Implant-based breast reconstruction is the most common approach, making it necessary to quantify the associated complications.

Methods

A systematic literature review of the PubMed, Cochrane, and Web of Science databases was performed. A total of 9608 citations were identified, and 44 studies met the inclusion criteria.

Results

Studies included reported the incidence of complications either per patient or per breast leading consequently to 2 complication rates depending on the type of reporting. A total of 14.3% of patient-related and 28.8% of breast-related complications while undergoing implant-based reconstruction were reported.

Among total complications reported, 72.6% of patient-related and 48.5% of breast-related complications were classified as major complications.

A total of 37.6% of patients respectively 15.1% of breasts required prosthesis explantation due to severe complications. Depending on reporting, 9.7% of patients and 4% of breasts required autologous flap reconstruction due to reconstructive failure.

Conclusions

High complication and failure rates are associated with implant-based breast reconstruction. Lacking randomized controlled trials, the choice between implant-based and autologous breast reconstruction has to be made individually for each patient.
Interest in Plastic Surgery Residency
Authors: Maisner Rose S. , Ayyala Haripriya S.
Published: February 2022

Background

Since 2010, the number of programs and available positions for integrated plastic surgery residency has increased, yet the match rate remains one of the lowest of all specialties, and the applicant pool remains one of the most competitive. We sought to investigate whether this increased interest in integrated programs has translated to increased online search volume regarding plastic surgery residency.

Methods

Our study uses Google Trends, a powerful online tool that analyzes changes in Google search volume over time and across various regions, to study temporal and geographic trends in search interest for terms related to plastic surgery residency from July 2009 to 2020 in the United States.

Results

Terms related to plastic surgery research, step 1 and 2 scores, and residency interviews had the most search results, whereas terms related to away rotations and Alpha Omega Alpha had the least. “Independent plastic surgery track” had more total search results on Google than “integrated plastic surgery residency,” and “plastic surgery fellowship” declined in search interest from July 2009 to March 2010. There was a rise in search volume for a plastic surgeon's salary and a fall in search volume for plastic surgery research between July 2009 and July 2020. However, other terms related to residency or residency applications showed no sustained trends over time. “Plastic surgery residency” was most searched in Pennsylvania, New York, Ohio, and Missouri, whereas “plastic surgeon salary” was most searched in Louisiana, Texas, Arizona, and Georgia.

Conclusions

This Google Trends analysis showed discordance between the upward trend in integrated plastic surgery residency positions offered through the National Residency Match Program and relatively unchanging search interest in factors related to the plastic surgery residency application. However, interest in a plastic surgeon's salary has increased over time, but this is not specific to plastic surgery. Although online search tools can be of important predictive value, this study demonstrates that there are clearly other factors that influence medical students' interest in plastic surgery residency besides Internet research.
Muricauda aurea sp. nov. and Muricauda profundi sp. nov., two marine bacteria isolated from deep sea sediment of Pacific Ocean
Authors: Zhao Sufang , Liu Renju , Lai Qiliang , Shao Zongze
Published: February 2022

Two novel Gram-stain-negative, aerobic, rod-shaped, carotenoid-pigmented and non-flagellated bacteria, designated BC31-1-A7T and BC31-3-A3T, were isolated from polyethylene-terephthalate-degrading bacterial consortia enriched from deep-sea sediment collected in the Pacific Ocean. Optimal growth of both strains was observed at 28–32 °C, at pH 7.5 and in the presence of 3–4% (w/v) NaCl. The 16S rRNA gene sequence analysis revealed that strains BC31-1-A7T and BC31-3-A3T were closely related to

Muricauda aquimarina

JCM 11811T,

Muricauda lutimaris

KCTC 22173T,

Muricauda ruestringensis

DSM 13258T,

Muricauda zhangzhouensis

DSM 25030T,

Muricauda oceani

JCM 33902T and

Muricauda oceanensis

KCTC 72200T with 96.8–98.9% sequence similarity. The 16S rRNA gene sequence similarity between strains BC31-1-A7T and BC31-3-A3T was 97.5%. The genomic G+C contents of strains BC31-1-A7T and BC31-3-A3T were 42.1 and 41.6 mol%, respectively. The average nucleotide identity and digital DNA–DNA hybridization values between strain BC31-3-A3T, strain BC31-1-A7T and their six closely related type strains were 77.6–84.3% and 20.5–27.9%, respectively. Menaquinone-6 was detected as the major isoprenoid quinone in all strains. Their major fatty acids were iso-C15:0, iso-C15:1 G and iso-C17:0 3-OH. The major polar lipids of strains BC31-1-A7T and BC31-3-A3T were identified as one phosphatidylethanolamine, some unidentified polar lipids and one aminolipid. Based on their distinct taxonomic characteristics, strains BC31-1-A7T and BC31-3-A3T represent two novel species in the genus

Muricauda

. The names proposed to accommodate these two strains are Muricauda aurea sp. nov. and Muricauda profundi sp. nov., and the type strains are BC31-1-A7T (=MCCC M23246T=KCTC 82569T) and BC31-3-A3T (=MCCC M23216T=KCTC 82302T), respectively.
Electroencephalographic Signatures of Canine Cognitive Dysfunction
Authors: Mondino Alejandra , Gutiérrez Mary , González Camila , Mateos Diego , Torterolo Pablo , Olby Natasha , Delucchi Luis
Published: February 2022

Canine cognitive dysfunction (CCD) is a highly prevalent neurodegenerative disease considered the canine analog of Alzheimer’s disease (AD). Unfortunately, CCD cannot be cured. However, early therapeutic interventions can slow the progression of cognitive decline and improve quality of life of the patients; therefore, early diagnosis is ideal. In humans, electroencephalogram (EEG) findings specific to AD have been described, and some of them have successfully detect early stages of the disease. In this study we characterized the EEG correlates of CCD, and we compared them with the EEGs of healthy aging dogs and dogs at risk of developing CCD. EEG recordings were performed in 25 senior dogs during wakefulness. Dogs were categorized in normal, at risk of CCD or with CCD according to their score in the Rofina questionnaire. We demonstrated that, quantitative EEG can detect differences between normal dogs and dogs with CCD. Dogs with CCD experience a reduction in beta and gamma interhemispheric coherence, and higher Joint Lempel Ziv complexity. Dogs at risk of developing CCD, had higher alpha power and interhemispheric coherence, making these features potential markers of early stages of the disease. These results demonstrate that EEG could be an additional biomarker that can contribute to the diagnosis of CCD, and reinforce the CCD as a translational model of AD.
The course of COVID-19 in allergic rhinitis patients receiving allergen spesific immunotherapy
Authors: Atayik Emel , Aytekіn Gökhan
Published: February 2022

Introduction

The aims of presenting study were trying to expose the course of SARS-CoV-2 (severe acute respiratory syndrome-related coronavirus) in patients with allergic rhinitis (AR), to compare the prevalence of SARS-CoV-2 infection, hospitalization and pneumonia rates in patients with AR receiving allergen immunotherapy (AIT) and patients did not receive AIT (non-receivers) and to define possible risk factors for SARS-CoV-2 positivity in patients with AR.

Materials and Methods

A total of 419 patients with AR who were being followed up in a tertiary allergy clinic between 1 June 2020 and 31 December 2020, were selected for the study. Only patients who were receiving active-continuous treatment for allergic rhinitis during the study period, were included in the study.

Results

Seventy-nine patients (18.9%) became infected with the SARS-CoV-2 [32 patients (19.6%) in AR patients with AIT and 47 patients (19.0%) in non-receivers] and the rate of pneumonia was 2.4% [12.7% of SARS-CoV-2 (+) patients]. There was no significant difference was determined between the AR patients with AIT and the non-receivers in regard to the rate of SARS-CoV-2 infection, pneumonia, and hospitalization (p: 0.864, p: 0.081, p: 0.113). There was a significant difference between the groups in terms of gender, duration of disease, sensitivity to allergens (atopy), and serum IgE levels (p: 0.009, p: 0.001, p: 0.001, and p: 0.001). The accompanying comorbidities, eosinophil count, AIT, and duration of AIT were not found to be associated with an increased risk SARS-CoV-2 PCR positivity. However, the female gender was shown to be associated with a decreased risk for SARS-CoV-2 PCR positivity (OR, 0.571; 95% confidence interval, 0.330-0.987; p: 0.045)

Conclusion

The course of SARS-CoV-2 is similar in patients with AR who underwent AIT and patients with AR who did not undergo AIT, and AIT does not seem to increase the risk for SARS-CoV-2 infection.
The efficacy of omalizumab treatment in patients with non-atopic severe asthma
Authors: Atayik Emel , Aytekіn Gökhan
Published: February 2022

Introduction

Non-atopic asthmatic patients generally have more severe clinical manifestations frequently accompanied by chronic sinusitis and nasal polyps, with more limited therapeutic options as compared to atopic asthmatic patients. This has led to a search for novel therapeutic approaches including omalizumab for non-atopic asthmatic patients who are not adequately controlled with current therapies.

Materials and Methods

In this retrospective study undertaken between 1st August 2020 and 31st December 2021 at a tertiary allergy clinic, data from 61 non-atopic asthmatic patients inadequately controlled with optimum therapy was examined.

Results

A total of 61 patients with severe asthma were included in the study [Female: 48 (78.7%), male: 13 (21.3%], mean age: 49 (18-71) years). The mean duration of asthma was 60 (18-160) months. A statistically significant increase in FEV1 (Forced expiratory volume in one second), FVC (forced vital capacity), and ACT (asthma control test) scores were found after 1 year of omalizumab treatment (p < 0.001, for all parameters). Omalizumab treatment was associated with a significant decrease in the number of asthma exacerbations, asthma-related hospitalization, duration of hospitalization, and the number of unplanned emergency room visits after 1 year (p < 0.001, for all parameters). One year treatment with omalizumab led to significant changes in eosinophil counts and serum IgE levels as well (p < 0.001 and p< 0.001)

Conclusion

In the atopic severe asthma patient group omalizumab treatment provided similar clinical benefits to those observed in patients with severe atopic asthma, suggesting that it may be a useful therapeutic option in patients with non-atopic asthma who failed to benefit from step 4 and step 5 treatments.
Spatiotemporal dissociation of brain network connectivity in salience processing: A simultaneous pupillometry-EEG-fMRI study
Authors: He Hengda , Hong Linbi , Sajda Paul
Published: February 2022

The processing of salient stimuli involves a wide range of both bottom-up and top-down processes. Previous neuroimaging studies have identified multiple brain areas and networks for salience processing, including the salience network (SN), dorsal attention network (DAN), and the locus coeruleus-norepinephrine (LC-NE) neuromodulatory system. However, interactions among these networks and the cortico-subcortical systems in salience processing remain unclear. Here, we simultaneously recorded pupillometry, electroencephalogram (EEG), and functional magnetic resonance imaging (fMRI) during an auditory oddball paradigm. Using EEG-informed fMRI analysis, we temporally dissociated the target stimulus evoked activation, allowing us to identify the cascades of cortical areas associated with salience processing. Furthermore, functional connectivity analysis uncovered spatiotemporal functional network organizations of these salience processing neural correlates. Using pupillometry as a psychophysiological marker of LC-NE activity, we also assessed brain-pupil relationships. With state-space modeling of target modulated effective connectivity, we found that the target evoked pupillary response is associated with the network causal couplings from late to early subsystems, as well as the network switching initiated by the SN. These findings indicate that the SN might cooperate with pupil-indexed brainstem neuromodulatory systems, such as the LC-NE system, in the reorganization and dynamic switching of cortical networks, and shed light on the implications of their integrative framework in various cognitive processes and neurological diseases.
Guiding Irregular Nuclear Morphology on Nanopillar Array for Malignancy Differentiation in Tumor cells
Authors: Zeng Yongpeng , Zhuang Yinyin , Mitra Aninda , Chen Peng , Saggio Isabella , Shivashankar G. V. , Gao Weibo , Zhao Wenting
Published: February 2022

For more than a century, abnormal nuclei in tumor cells, presenting subnuclear invaginations and folds on the nuclear envelope, have been known to be associated with high malignancy and poor prognosis. However, current nuclear morphology analysis focuses on the features of the entire nucleus, overlooking the malignancy-related subnuclear features in nanometer scale. The main technical challenge is to probe such tiny and randomly distributed features inside cells. We here employ nanopillar arrays to guide subnuclear features into ordered patterns enabling their quantification as a strong indicator of cell malignancy. Both breast and liver cancer cells were validated, as well as the quantification of nuclear abnormality heterogeneity. The alterations of subnuclear patterns were also explored as effective readouts for drug treatment. We envision this nanopillar-enabled quantification of subnuclear abnormal features in tumor cells opens a new angle in characterizing malignant cells and studying the unique nuclear biology in cancer.

Teaser

A nanopillar-based assay quantifying the abnormal nuclear morphology in tumor cells at single-cell level.
Adaptive scans allow 3D-targeted laser-dissection to probe the mechanics of cell sheets
Authors: Meng Huicheng , Nuzhdin Dmitry , Sison Miguel , Galland Frédéric , LeGoff Loïc
Published: February 2022

The mechanical actuation of cells by active forces from the cytoskeleton drives tissue morphogenesis. To understand these forces, multicellular laser dissection has become an essential tool for severing tissue locally and inferring tension from the recoil of surrounding structures. However, conventional laser dissection is limited by 2D steering, which is inadequate for embryos and developing tissues that are intrinsically 3D structures. In this study, we introduce a flexible near-infrared (NIR) fs-pulsed laser dissection system that allows for dissection trajectories to proceed in 3D and adapt to the curved surfaces of cell sheets, which are prominent structures in embryos. Trajectories are computed through an unsupervised search for the surface of interest. Using this technique, we demonstrate sectioning of multicellular domains on curved tissue, which was not possible with regular NIR laser scanning.

We apply the developed strategy to map mechanical stresses in the imaginal disc of the developing Drosophila wing. Our targeted, adaptive scans can be used in other non-linear processes, such as two-photon fluorescence imaging or optogenetics. Overall, this new laser dissection system offers an innovative solution for studying complex 3D structures and their mechanical properties.
Effects of global change on animal biodiversity in boreal forest landscape: an assemblage dissimilarity analysis
Authors: Bouderbala Ilhem , Labadie Guillemette , Béland Jean-Michel , Boulanger Yan , Hébert Christian , Desrosiers Patrick , Allard Antoine , Fortin Daniel
Published: February 2022

Despite an increasing number of studies highlighting the impacts of climate change on boreal species, the main factors that will drive changes in species assemblages remain ambiguous. We quantify two climate-induced pathways based on direct and indirect effects on species occupancy and assemblage dis-similarity under different harvest management scenarios. The direct climate effects illustrate the impact of climate variables while the indirect effects are reflected through the changes in land cover composition. To understand the main causes in assemblage dissimilarity, we analyze the regional and the latitudinal species assemblage dissimilarity by decomposing it into balanced variation in species occupancy and occurrence and occupancy and occurrence gradient. We develop empirical models to predict the distribution of more than 100 bird and beetle species in the Côte-Nord region of Québec over the next century. Our results show that the two pathways are complementary and alter biodiversity, mainly caused by balanced variation in species occupancy and occurrence. At the regional scale, both effects have an impact on decreasing the number of winning species. Yet, responses are much larger in magnitude under mixed climate effects (a mixture of direct and indirect effects). Regional assemblage dissimilarity reached 0.77 and 0.69 under mixed effects versus 0.09 and 0.10 under indirect effects for beetles and birds, respectively, between RCP8.5 and baseline climate scenarios when considering harvesting. Therefore, inclusion of climatic variables considers aspects other than just those related to forest landscapes, such as life cycles of animal species. Latitudinally, assemblage dissimilarity increased following the climate conditions pattern. Our analysis contributes to the understanding of how climate change alters biodiversity by reshaping community composition and highlights the importance of climate variables in biodiversity prediction.
Bimodally oriented cellulose fibers and reticulated homogalacturonan networks - A direct visualization of Allium cepa primary cell walls
Authors: Nicolas William J , Fäßler Florian , Dutka Przemysław , Schur Florian KM , Jensen Grant , Meyerowitz Elliot
Published: February 2022

One hallmark of plant cells is their pecto-cellulosic cell walls. They protect cells against the environment and high turgor and mediate morphogenesis through the dynamics of their mechanical and chemical properties. The walls are a complex polysaccharidic structure. Although their biochemical composition is well known, how the different components organize in the volume of the cell wall and interact with each other is not well understood and yet is key to the wall’s mechanical properties. To investigate the ultrastructure of the plant cell wall, we imaged the walls of onion (Allium cepa) bulbs in a near-native state via cryo-Focused Ion Beam milling (cryo-FIB-milling) and cryo-Electron Tomography (cryo-ET). This allowed the high-resolution visualization of cellulose fibers in situ (in muro). We reveal the coexistence of dense fiber fields bathed in a reticulated matrix we termed “meshing,” which is more abundant at the inner surface of the cell wall. The fibers adopted a regular bimodal angular distribution at all depths in the cell wall and bundled according to their orientation, creating layers within the cell wall. Concomitantly, employing homogalacturonan (HG)-specific enzymatic digestion, we observed changes in the meshing, suggesting that it is at least in part composed of HG pectins. We propose the following model for the construction of the abaxial epidermal primary cell wall: The cell deposits successive layers of cellulose fibers at −45° and +45° relative to the cell’s long axis and secretes the surrounding HG-rich meshing proximal to the plasma membrane, which then migrates to more distal regions of the cell wall.
Whole-Genome Sequence of African Swine Fever Virus isolate from India provides insights into diversity and evolution
Authors: Mahajan Sonalika , Doley Juwar , Subramaniam Saravanan , Yadav Ajay K. , Pegu Seema Rani , Mohan Narayana H. , Chander Vishal , Mathesh Karikalan , Nandi Sukdeb , Singh Karam Pal , Gupta Vivek Kumar , Sharma Gaurav Kumar
Published: February 2022

African swine fever (ASF) was first reported in 1921, and since then has posed a major threat to the world pig industry and still remains a major challenge as there is no vaccine or therapy available. In May 2020, the first incidence of ASF was recorded in India, followed by a number of outbreaks in the north eastern part of India. In this study, we report the first whole genome of an Indian isolate of ASF virus (ASF/IND/20/CAD/543) using next generation sequencing and compared with the other ASFV complete genome. On phylogenetic analysis, the virus was assigned to genotype II on the basis of p72 genotyping. However, the whole genome based phylogeny distinguished it from other genotype II isolates of clade 1.1.1. This study adds to our understanding of ASFV’s genetic diversity and molecular evolution.
Revisiting degron motifs in human AURKA required for its targeting by APC/C-FZR1
Authors: Abdelbaki Ahmed , Ascanelli Camilla , Okoye Cynthia N. , Akman Begum , Janson Giacomo , Min Mingwei , Marcozzi Chiara , Hagting Anja , Grant Rhys , De Luca Maria , Asteriti Italia Anna , Guarguaglini Giulia , Paiardini Alessandro , Lindon Catherine
Published: February 2022

Mitotic kinase Aurora A (AURKA) diverges from other kinases in its multiple active conformations that may explain its interphase roles and association with cancer, and the limited efficacy of drugs targeting the kinase pocket. Regulation of AURKA activity by the cell is critically dependent on destruction mediated by the Anaphase-Promoting Complex (APC/CFZR1) during mitotic exit and G1 phase and requires an atypical N-terminal degron in AURKA called the ‘A-box’ in addition to a reported canonical D-box degron in the C-terminus. Here we find that the proposed C-terminal D-box of AURKA does not act as a degron and instead mediates essential structural features of the protein. In living cells, as previously reported in vitro, the N-terminal intrinsically disordered region (IDR) of AURKA containing the A-box is sufficient to confer FZR1-dependent mitotic degradation. Both in silico and in cellulo assays predict the QRVL Short Linear Interacting Motif (SLiM) of the A-box to be a phospho-regulated D-box. We propose that degradation of full-length AURKA additionally depends on an intact C-terminal domain because of critical conformational parameters permissive for both activity and mitotic degradation of AURKA.

Summary blurb

AURKA degron motifs are redefined to show that the so-called N-terminal ‘A-box’ is in fact a D-box, and the so-called ‘D-box’ in the C-terminus is not a degron but a motif critical for the active, degradable conformation of AURKA
A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition
Authors: Altınışık N. Ezgi , Kazancı Duygu Deniz , Aydoğan Ayça , Gemici Hasan Can , Erdal Ömür Dilek , Sarıaltun Savaş , Vural Kıvılcım Başak , Koptekin Dilek , Gürün Kanat , Sağlıcan Ekin , Çakan Gökhan , Koruyucu Meliha Melis , Lagerholm Vendela Kempe , Karamurat Cansu , Özkan Mustafa , Kılınç Gülşah Merve , Sevkar Arda , Sürer Elif , Götherström Anders , Atakuman Çiğdem , Erdal Yılmaz Selim , Özer Füsun , Erim Özdoğan Aslı , Somel Mehmet
Published: February 2022

Upper Mesopotamia played a key role in the Neolithic Transition in Southwest Asia through marked innovations in symbolism, technology, and foodways. We present thirteen ancient genomes (c.8500-7500 calBCE) from Pre-Pottery Neolithic Çayönü in the Tigris basin together with bioarchaeological and material culture data. Our findings reveal that Çayönü was a genetically diverse population, carrying a mixed ancestry from western and eastern Fertile Crescent, and that the community received immigrants. Our results further suggest that the community was organised along biological family lines. We document bodily interventions such as head-shaping and cauterization among the individuals examined, reflecting Çayönü’s cultural ingenuity. Finally, we identify Upper Mesopotamia as the likely source of eastern gene flow into Neolithic Anatolia, in line with material culture evidence. We hypothesise that Upper Mesopotamia’s cultural dynamism during the Neolithic Transition was the product not only of its fertile lands but also of its interregional demographic connections.
Non canonical scaffold-type ligase complex mediates protein UFMylation
Authors: Peter Joshua J. , Magnussen Helge M. , DaRosa Paul Anthony , Millrine David , Matthews Stephen P , Lamoliatte Frederic , Sundaramoorthy Ramasubramanian , Kopito Ron R , Kulathu Yogesh
Published: February 2022

Protein UFMylation is emerging as a posttranslational modification essential for endoplasmic reticulum and cellular homeostasis. Despite its biological importance, we have a poor understanding of how UFM1 is conjugated onto substrates. Here, we use a rebuilding approach to define the minimal requirements of protein UFMylation. We find that the reported E3 ligase UFL1 is inactive on its own and identify UFBP1 to bind UFL1 to form an active E3 ligase complex. While UFC1 is an intrinsically Cys-reactive E2, we do not identify any catalytic cysteines on UFL1/UFBP1, suggesting a scaffold-type E3 ligase mechanism. Interestingly, the E3 ligase complex consists of winged-helix (WH) domain repeats that activate UFC1 for aminolysis. We identify the adaptor protein CDK5RAP3 to bind to and regulate E3 ligase activity potentially by preventing off-target UFMylation. In summary, our work identifies the minimal requirements for UFMylation and reveals regulatory principles of this atypical E3 ligase complex.
Extracellular vesicle microRNA cargo engineering reveals critical mechanisms underlying therapeutic efficacy
Authors: Euscher Lindsey M. , Mentkowski Kyle I. , Tarvirdizadeh Touba , Julian Isabella , Bhatt Karan , Eagler Lisa , Lang Jennifer K.
Published: February 2022

Background

Extracellular vesicles (EVs) are key mediators of intercellular communication and function to transfer biological cargo, including microRNA (miR), from donor to recipient cells. EVs isolated from cardiosphere-derived cells (CDCs) have demonstrated therapeutic efficacy in pre-clinical models of ischemic heart disease, highlighting them as promising vectors for the treatment of CVD. Importantly, it has not yet been established whether miR cargo is necessary for the observed therapeutic benefit of CDC-EVs following acute MI (AMI).

Methods

CDCs were transfected with siRNA against Drosha, the initial endonuclease in the miRNA biogenesis pathway, to generate miR depleted DROSHA-EVs. EVs were characterized by size, morphology, and protein/miR expression. The role of EV miRNA on cardiac target cell apoptosis, proliferation and angiogenesis was examined using a series of in vitro assays. Mice with acute MI underwent delivery of human CDC EVs, DROSHA-EVs and placebo in a double-blind study. LVEF was assessed by echo at 1- and 28-days post-MI and tissue samples processed for assessment of histological endpoints. In vitro sufficiency assays were performed using a combinatorial approach with individual candidate miRs to identify clusters exhibiting synergistic efficacy.

Results

DROSHA-EVs exhibited global downregulation of miRNA cargo but were otherwise indistinguishable from wild-type CDC-EVs. miR cargo was responsible for mediating the beneficial effects of human CDC-EV treatment on cardiomyocyte apoptosis, fibroblast proliferation and angiogenesis in vitro. DROSHA-EVs were unable to promote recovery following AMI on a functional or histological level, highlighting the critical role of EV miRNAs in cardioprotection following ischemic injury. A potentially therapeutic miR cluster, miR-146a-370-126a, was identified which acted synergistically to reduce cardiomyocyte apoptosis and was sufficient to render inert EVs into therapeutic vectors.

Conclusions

These results demonstrate for the first time that miRNAs are required for the regenerative potential of CDC-EVs following AMI and identify a novel miR cluster with therapeutic implications.
LAG3 regulates antibody responses in a murine model of kidney transplantation
Authors: Nicosia Michael , Fan Ran , Lee Juyeun , Gorbacheva Victoria , Valenzuela José I. , Yamamoto Yosuke , Beavers Ashley , Dvorina Nina , Chuluyan Eduardo , Araki Motoo , Baldwin William M. , Fairchild Robert L. , Min Booki , Valujskikh Anna
Published: February 2022

Lymphocyte activation gene-3 (LAG3) is a coinhibitory receptor expressed by a range of immune cells. While immunomodulatory potential of LAG3 is being actively explored in cancer and autoimmunity fields, there is no information on how this pathway affects alloreactive immune responses following organ transplantation. The goal of this study was to investigate the functions of recipient LAG3 in a mouse model of renal allograft rejection. We found that mice deficient in LAG3 expression have elevated heterologous immunity against a panel of alloantigens prior to transplantation. Recipient LAG3 deficiency results in rapid rejection of MHC-mismatched renal allografts that are spontaneously accepted by WT recipients, with graft histology characteristic of antibody mediated rejection (ABMR). Depletion of recipient B cells but not CD8+T cells significantly extended kidney allograft survival in LAG3-/-recipients further supporting ABMR as the main mechanism of graft loss. Treatment of WT recipients with an antagonistic LAG3 antibody enhanced anti-donor immune responses and induced kidney damage associated with chronic rejection. The experiments using conditional LAG3 knockout recipients demonstrated that LAG3 expression on either T or B cells is sufficient to regulate anti-donor humoral immunity. These results are the first to identify LAG3 as a regulator of both T and B cell responses to kidney allografts and a potential therapeutic target for ABMR prevention and treatment.
Glia of C. elegans coordinate the heat shock response independent of the neuronal thermosensory circuit and serotonin
Authors: Gildea Holly K. , Frankino Phillip A. , Tronnes Sarah U. , Pender Corinne L. , Choi Hyun Ok , Hunter Tayla D. , Cheung Shannon S. , Frakes Ashley E , Sukarto Edward , Dillin Andrew
Published: February 2022

As organisms age, they lose the ability to induce appropriate stress responses, becoming vulnerable to protein toxicity and tissue damage. Neurons can signal to peripheral tissues to induce protective organelle-specific stress responses. Recent work has demonstrated a novel and independent role of glia in inducing such responses. Here, we show that overexpression of heat shock factor 1 (hsf-1) in the four astrocyte-like cephalic sheath cells of C. elegans is sufficient to induce a non-cell autonomous cytosolic unfolded protein response (UPR), also known as the heat shock response (HSR), in distal cells. These animals upregulate the HSR in peripheral cells and have increased lifespan and resistance to heat stress. This glial HSR regulation is independent of the canonical neuronal thermosensory circuit and of known neurotransmitters but is dependent on the small clear vesicle release protein UNC-13. Additionally, HSF-1 and the FOXO transcription factor DAF-16 are partially required in peripheral tissues for increase of non-autonomous HSR, lifespan, and thermotolerance. We find that cephalic sheath glial hsf-1 over-expression leads to increased pathogen resistance, which suggests a role for this signaling pathway in immune function.
Fungal community dynamics and carbon mineralization in coarse woody debris across decay stage, tree species, and stand development stage in northern boreal forests
Authors: Hart Saskia C. , Porter Teresita M. , Basiliko Nathan , Venier Lisa , Hajibabaei Mehrdad , Morris Dave
Published: February 2022

Fungi are primary agents of coarse woody debris (CWD) decay in forests, playing an essential role in nutrient cycling and carbon storage. Characterizing fungal communities within CWD will promote further understanding of the fungal controls on CWD decomposition. We compared fungal community assemblages using alpha and beta diversity metrics, carbon mineralization, and physical and chemical properties of CWD across 3 tree species (trembling aspen [Populus tremuloides], black spruce [Picea mariana], and jack pine [Pinus banksiana]), 5 decay classes, and 2 stand development stages, differing in time-since-stand replacing disturbance (i.e., young/self-thinning and mature/steady-state) in Ontario’s boreal forest region. In total, we sampled 180 individual CWD logs from 6 independent stands, with 3 replicates per each species × decay class combination at each site. We found that fungal community structure significantly differed across tree species, decay stage, and stand age. Higher proportions of white rot fungi were found in trembling aspen CWD, whereas higher proportions of brown rot fungi were found in black spruce and jack pine CWD. Proportions of specialized wood decay fungi increased with decay stage and were higher in CWD located in mature forest stands. Fungal diversity was highest in decay class 4 CWD. We found that Mn and K concentrations, total carbon, C/N ratio, carbon mineralization (mg CO2 g dry CWD-1 d-1), and moisture content were important predictors of fungal composition across CWD species and/or decay stage, though how CWD chemistry influences fungal species composition (and vice versa) is unknown. Carbon mineralization was highest in trembling aspen CWD and increased with decay stage, perhaps facilitated by increased N concentrations. This study suggests that forest management guidelines that consider both deadwood quantity and quality will support a broader range of fungal species and communities through post-disturbance stand development, thereby conserving biodiversity over the longer-term in our managed forest systems.
Rapid stem cell spreading induced by high affinity α5β1 integrin-selective bicyclic RGD peptide in biomimetic hydrogels
Authors: Liu Kaizheng , Vandaele Johannes , Bernhagen Dominik , van Erp Merijn , Oosterwijk Egbert , Timmerman Peter , Rocha Susana , Kouwer Paul H. J.
Published: February 2022

Cell-matrix interactions form a crucial parameter for the design of a synthetic extracellular matrix (ECM), as they ultimately dictate cell fate and functions. Universally, synthetic biomaterials are conjugated with a linear or cyclic Arg-Gly-Asp (RGD) peptide to establish a direct link of the ECM with the cell. These peptides, however, present low binding affinities and lack selectivity towards integrin subtypes presented on the cell membrane. Here, a highly biomimetic synthetic ECM based on polyisocyanides (PIC) that has been decorated with bicyclic peptides that show a high affinity towards specific integrin subtypes is presented. 3D cell studies show that human adipose-derived stem cells (hASCs) in matrices carrying the optimized bicyclic α5β1 -integrin binder, spread within 24 hours, which is much faster than in other PIC gels, including the default RGD-decorated gel, but also much faster than in the positive Matrigel control. YAP/TAZ staining shows that the rapid morphological change in the 3D microenvironments is YAP independent. The data highlights that the design of synthetic matrices with appropriate, optimized guiding signals is key to guide cells towards a predetermined outcome.
The ABA INSENSITIVE (ABI) 4 transcription factor is stabilized by stress, ABA and phosphorylation
Authors: Maymon Tzofia , Eisner Nadav , Bar-Zvi Dudy
Published: February 2022

The Arabidopsis transcription factor ABSCISIC ACID INSENSITIVE 4 (ABI4) is a key player in the plant hormone abscisic acid (ABA) signaling pathway. ABI4 is also involved in seed development and germination, the response to abiotic stresses such as drought and salinity, control of lipid reserve mobilization in the embryo, lateral root formation, and redox control. Expression of the ABI4 gene is tightly regulated and basal expression is low. Maximal transcript levels occur during seed maturation and in the early stages of seed germination and are markedly reduced in other developmental stages. ABI4 is an unstable lowly expressed protein, resulting from tight post-transcriptional regulation. Here, we studied factors affecting the stability of the ABI4 protein using transgenic Arabidopsis plants expressing 35S::HA-FLAG-ABI4-eGFP. Despite the expression of eGFP-tagged ABI4 being driven by the highly active 35S CaMV promoter the steady-state levels of ABI4 were extremely low in the roots of seedling grown in optimal conditions. These levels were markedly enhanced upon exposure of the seedlings to abiotic stress and ABA. ABI4 is degraded rapidly by the 26S proteasome and we report on the role of phosphorylation of ABI4-serine 114 in regulating ABI4 stability. Our results indicate that ABI4 is tightly regulated both post-transcriptionally and post-translationally. Moreover, abiotic factors and plant hormones have similar effects on ABI4 transcripts and ABI4 protein levels. This double-check mechanism for controlling ABI4 reflects on its central role in plant development and cellular metabolism.

SIGNIFICANCE STATEMENT

We show that stabilization of the ABI4 transcription factor by stress and hormones is mediated by phosphorylation of Serine 114 by MAP kinases. Transcription of ABI4 is also modulated by MAP kinases, suggesting that the same signals affect both transcript and protein levels, resulting in tight modulation of ABI4 activity.
Dot and Slot Hybridization of Purified RNA
Authors: Green Michael R. , Sambrook Joseph
Published: February 2022

Dot blotting and slot blotting are techniques for immobilizing several preparations of nucleic acids on the same solid support, usually a charged nylon membrane. The concentrations of the target sequence of interest can be estimated by hybridizing the immobilized samples to an appropriate probe. The amounts of target sequence are estimated by comparing the intensity of signals emitted by dots containing the test samples with standards containing known concentrations of the target sequence. This protocol describes the blotting and subsequent hybridization of RNA that has been purified from cells or tissues.