bluuebunny/crossref_metadata_2025 huggingface dataset:
Long-Term Comparison of the Aesthetic Outcomes between Nasoalveolar Molding– and Non–Nasoalveolar Molding–Treated Patients with Unilateral Cleft Lip and Palate
Authors: Nayak Tulasi , Bonanthaya Krishnamurthy , Parmar Renu , Shetty Pritham N.
Published: October 2021

Background:

The cleft lip-nose deformity in unilateral cleft lip and palate is one of the most challenging problem for surgeons to correct. Although nasoalveolar molding has been shown to be effective in improving presurgical symmetry in patients with complete unilateral cleft lip and palate, there is need for better evidence regarding the long-term nasolabial aesthetics of patients who have received this therapy.

Methods:

Thirty-eight patients treated with nasoalveolar molding and 48 patients not treated with nasoalveolar molding (but otherwise treated similarly) with unilateral cleft lip and palate were studied to assess and compare the nasolabial aesthetics. The objective evaluation of the nasal symmetry was performed on the basal view of two-dimensional photographs and the subjective nasolabial aesthetic evaluation was performed using the Asher-McDade scale.

Results:

At 5-year postoperative follow-up, nasoalveolar molding group patients had better mean values on the objective scores; however, these were not statically significant. The nasoalveolar molding group of patients had a statistically significant improvement in the subjective evaluation in comparison to the non–nasoalveolar molding–treated patients. The number of lip revisions was also statistically higher in the non–nasoalveolar molding–treated group of patients.

Conclusions:

In this retrospective, single-center study, the authors found that at 5-year postoperative follow-up, nasoalveolar molding–treated patients had improved nasolabial aesthetics and fewer revision operations. These are, however, preliminary results and the patients will be followed up until the end of growth to assess the longer term effects of nasoalveolar molding on the nasolabial aesthetics in unilateral cleft lip and palate.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, III.
MERS-CoV infection causes brain damage in human DPP4-transgenic mice through complement-mediated inflammation
Authors: Jiang Yuting , Chen Yuehong , Sun Hong , Zhang Xiaolu , He Lei , Li Jiangfan , Zhao Guangyu , Sun Shihui
Published: October 2021

The highly pathogenic Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is a severe respiratory virus. Recent reports indicate additional central nervous system (CNS) involvement. In this study, human DPP4 transgenic mice were infected with MERS-CoV, and viral antigens were first detected in the midbrain-hindbrain 4 days post-infection, suggesting the virus may enter the brainstem via peripheral nerves. Neurons and astrocytes throughout the brain were infected, followed by damage of the blood brain barrier (BBB), as well as microglial activation and inflammatory cell infiltration, which may be caused by complement activation based on the observation of deposition of complement activation product C3 and high expression of C3a receptor (C3aR) and C5a receptor (C5aR1) in neurons and glial cells. It may be concluded that these effects were mediated by complement activation in the brain, because of their reduction resulted from the treatment with mouse C5aR1-specific mAb. Such mAb significantly reduced nucleoprotein expression, suppressed microglial activation and decreased activation of caspase-3 in neurons and p38 phosphorylation in the brain. Collectively, these results suggest that MERS-CoV infection of CNS triggers complement activation, leading to inflammation-mediated damage of brain tissue, and regulating of complement activation could be a promising intervention and adjunctive treatment for CNS injury by MERS-CoV and other coronaviruses.
Relationship between systolic blood pressure and decision-making during emotional processing
Authors: Betka Sophie , Watson David , Garfinkel Sarah , Pfeifer Gaby , Sequeira Henrique , Duka Theodora , Critchley Hugo
Published: October 2021

Objective

Emotional states are expressed in body and mind through subjective experience of physiological changes. In previous work, subliminal priming of anger prior to lexical decisions increased systolic blood pressure (SBP). This increase predicted the slowing of response times (RT), suggesting that baroreflex-related autonomic changes and their interoceptive (feedback) representations, influence cognition. Alexithymia is a subclinical affective dysfunction characterized by difficulty in identifying emotions. Atypical autonomic and interoceptive profiles are observed in alexithymia. Therefore, we sought to identify mechanisms through which SBP fluctuations during emotional processing might influence decision-making, including whether alexithymia contributes to this relationship.

Methods

Thirty-two male participants performed an affect priming paradigm and completed the Toronto Alexithymia Scale. Emotional faces were briefly presented (20ms) prior a short-term memory task. RT, accuracy and SBP were recorded on a trial-by-trial basis. Generalized mixed-effects linear models were used to evaluate the impact of emotion, physiological changes, alexithymia score, and their interactions, on performances.

Results

A main effect of emotion was observed on accuracy. Participants were more accurate on trials with anger primes, compared to neutral priming. Greater accuracy was related to increased SBP. An interaction between SBP and emotion was observed on RT: Increased SBP was associated with RT prolongation in the anger priming condition, yet this relationship was absent under the sadness priming. Alexithymia did not significantly moderate the above relationships.

Conclusions

Our data suggest that peripheral autonomic responses during affective challenges guide cognitive processes. We discuss our findings in the theoretical framework proposed by Lacey and Lacey (1970).
Nucleocapsid antibody positivity as a marker of past SARS-CoV-2 infection in population serosurveillance studies: impact of variant, vaccination, and choice of assay cut-off
Authors: Whitaker Heather J , Gower Charlotte , Otter Ashley D , Simmons Ruth , Kirsebom Freja , Letley Louise , Quinot Catherine , Ireland Georgina , Linley Ezra , Ribeiro Sonia , Ladhani Shamez , Lopez-Bernal Jamie , Amirthalingam Gayatri , Ramsay Mary E , Brown Kevin E
Published: October 2021

Serological surveillance studies sometimes use presence of anti-nucleocapsid antibody as a marker of natural SARS-CoV-2 infection. We explore seroconversion rates and antibody levels following Alpha and Delta variant infections, and vaccine breakthrough infections. We find lower seroconversion rates particularly following Alpha-variant vaccine breakthrough infections. We re-evaluate assay performance with a mix of past waned infections and recent breakthrough infections, that is relevant to current serological surveillance.
Increased interhemispheric asymmetry of cerebral blood flow in comatose adult patients on extracorporeal membrane oxygenation
Authors: Johnson Thomas W. , Dar Irfaan , Donohue Kelly , Xu Yama Y. , Santiago Esmeralda , Selioutski Olga , Marinescu Mark A. , Maddox Ross K. , Wu Tong Tong , Schifitto Giovanni , Gosev Igor , Choe Regine , Khan Imad
Published: October 2021

Extracorporeal membrane oxygenation (ECMO) is a mechanical circulatory support method that is associated with a high burden of neurologic injury, but neurologic examination and imaging of this population presents prohibitive medical and logistical challenges. Diffuse correlation spectroscopy (DCS) can measure relative cerebral blood flow (rBF) non-invasively at the bedside. In this study we observed interhemispheric differences in rBF in response to mean arterial pressure (MAP) changes in adult ECMO recipients. Thirteen patients were recruited (ages 21-78, 7 with cardiac arrest, 4 with acute heart failure, 2 with acute respiratory distress syndrome). They were dichotomized via Glasgow Coma Scale Motor score (GCS-M) into comatose (GCS-M ≤ 4; n=4) and non-comatose (GCS-M > 4; n=9) groups. Comatose patients had more interhemispheric rBF asymmetry (ASYMrBF) vs. non-comatose patients over a range of MAP values (29% [IQR 23-34%] vs. 11% [IQR 8-13%], p=0.009). ASYMrBFin comatose patients resolved near a MAP range of 70-80 mm Hg, while rBF remained symmetric through a wider MAP range in non-comatose patients. Associations between post-oxygenator pCO2or pH vs. ASYMrBFindividually did not meet significance, though the linear model slopes were different between comatose and non-comatose subgroups. Here we have demonstrated asymmetric cerebral autoregulation in comatose ECMO patients.
Cost-effective epigenetic age profiling in shallow methylation sequencing data
Authors: Trapp Alexandre , Gladyshev Vadim N.
Published: October 2021

There is a critical need for robust, high-throughput assays of biological aging trajectories. Among various approaches, epigenetic aging clocks emerged as reliable molecular trackers of the aging process. However, current methods for epigenetic age profiling are inherently costly and lack throughput. Here, we leverage the scAge framework for accurate prediction of biological age from very few bisulfite sequencing reads in bulk samples, thereby enabling drastic (100-1,000-fold) reduction in sequencing costs per sample. Our approach permits age assessment based on distinct assortments of CpG sites in different samples, without the need for targeted site enrichment or specialized reagents. We demonstrate the efficacy of this method to quantify the age of mouse blood samples across independent cohorts, identify the effect of calorie restriction as an attenuator of the aging process, and discern rejuvenation upon cellular reprogramming. We propose that this framework may be used for epigenetic age prediction in extremely high-throughput applications, enabling robust, large-scale and inexpensive interventions testing and age profiling.
Detection of SARS-CoV-2 RNA Throughout Wastewater Treatment Plants and A Modeling Approach to Understand COVID-19 Infection Dynamics in Winnipeg, Canada
Authors: Yanaç Kadir , Adegoke Adeola , Wang Liqun , Yuan Qiuyan , Uyaguari Miguel
Published: October 2021

Although numerous studies have detected SARS-CoV-2 in wastewater and attempted to find correlations between the concentration of SARS-CoV-2 and the number of cases, no consensus has been reached on sample collection and processing, and data analysis. Moreover, the fate of SARS-CoV-2 in wastewater treatment plants is another issue, specifically regarding the discharge of the virus into environmental settings and the water cycle. The current study monitored SARS-CoV-2 in influent and effluent wastewater samples with three different concentration methods and sludge samples over six months (July to December 2020) to compare different virus concentration methods, assess the fate of SARS-CoV-2 in wastewater treatment plants, and describe the potential relationship between SARS-CoV-2 concentrations in influent and infection dynamics. Skimmed milk flocculation (SMF) resulted in higher recoveries (15.27% ± 3.32%) of an internal positive control, Armored RNA, and higher positivity rate of SARS-CoV-2 in samples compared to ultrafiltration methods employing a prefiltration step to eliminate solids. Our results suggested that SARS-CoV-2 may predominate in solids and therefore, concentration methods focusing on both supernatant and solid fractions may result in better recovery. SARS-CoV-2 was detected in influent and primary sludge samples but not in secondary and final effluent samples, indicating a significant reduction during primary and secondary treatments. SARS-CoV-2 was first detected in influent on September 30th, 2020. A decay-rate formula was applied to estimate initial concentrations of late-processed samples with SMF. A model based on shedding rate and new cases was applied to estimate SARS-CoV-2 concentrations and the number of active shedders. Inferred sensitivity of observed and modeled concentrations to the fluctuations in new cases and test-positivity rates indicated a potential contribution of newly infected individuals to SARS-CoV-2 loads in wastewater.
Single-cell profiling of transcriptome and histone modifications with EpiDamID
Authors: Rang Franka J. , de Luca Kim L. , de Vries Sandra S. , Valdes-Quezada Christian , Boele Ellen , Nguyen Phong D. , Guerreiro Isabel , Sato Yuko , Kimura Hiroshi , Bakkers Jeroen , Kind Jop
Published: October 2021

Recent advances in single-cell sequencing technologies have enabled simultaneous measurement of multiple cellular modalities, including various combinations of transcriptome, genome and epigenome. However, comprehensive profiling of the histone post-translational modifications that influence gene expression at single-cell resolution has remained limited. Here, we introduce EpiDamID, an experimental approach to target a diverse set of chromatin types by leveraging the binding specificities of genetically engineered proteins. By fusing Dam to single-chain variable fragment antibodies, engineered chromatin reader domains, or endogenous chromatin-binding proteins, we render the DamID technology and all its implementations compatible with the genome-wide identification of histone post-translational modifications. Importantly, this enables the joint analysis of chromatin marks and transcriptome in a variety of biological systems at the single-cell level. In this study, we use EpiDamID to profile single-cell Polycomb occupancy in mouse embryoid bodies and provide evidence for hierarchical gene regulatory networks. We further demonstrate the applicability of this method to in vivo systems by mapping H3K9me3 in early zebrafish embryogenesis, and detect striking heterochromatic regions specifically in the notochord. Overall, EpiDamID is a new addition to a vast existing toolbox for obtaining systematic insights into the role of chromatin states during dynamic cellular processes.
Increased alcohol self-administration following repeated Toll-like receptor 3 agonist treatment in male and female rats
Authors: Lovelock Dennis F. , Randall Patrick A. , Van Voorhies Kalynn , Vetreno Ryan P. , Crews Fulton T. , Besheer J.
Published: October 2021

Toll-like receptor (TLR) signaling may play an important role in the neuroimmune system’s involvement in the development and maintenance of alcohol use disorder. In the present study we administered TLR3 agonist poly(I:C) in male and female Long-Evans rats to determine whether TLR3 agonism can increase alcohol consumption in a daily 15% alcohol operant self-administration paradigm. We found few effects when poly(I:C) was given every-other-day at 0.3 or 1.0 mg/kg, however when instead 1.0 mg/kg was given on consecutive days alcohol intake increased in the days following injections specifically in females. Furthermore, in a second experiment we found that this effect only emerged when rats had a history of multiple poly(I:C) injections. In the final experiment the dose was increased to 3.0 mg/kg on consecutive days which resulted in significant reductions on injection days in females that were not accompanied by subsequent increases. The dose was increased to 9 mg/kg for one final pair of injections which led to reductions in intake in both males and females but only increased subsequent alcohol consumption in males. Overall, poly(I:C) was able to increase subsequent alcohol consumption in both sexes, with females being sensitive to lower doses than males both in terms of changes in alcohol consumption and general locomotor reduction. These findings show that TLR3 agonism may be involved in driving increased alcohol consumption and add to the body of work identifying the neuroimmune system as a potential therapeutic target for AUD.
On stability of the Darwinian dynamics
Authors: Satouri Mohammadreza , Rezaei Jafar , Staňková Kateřina
Published: October 2021

Here we analyze Darwinian dynamics of cancer introduced in [1], extended by including a competition matrix, and evaluate (i) when the eco-evolutionary equilibrium is positive and (ii) when the eco-evolutionary equilibrium is asymptotically stable.
Effects of Superhydrophobic Sand Mulching on Evapotranspiration and Phenotypic Responses in Tomatoes (Solanum lycopersicum) under Normal and Reduced Irrigation
Authors: Odokonyero Kennedy , Gallo Adair , Santos Vinicius Dos , Mishra Himanshu
Published: October 2021

Irrigated agriculture in arid and semi-arid regions is a vital contributor to the global food supply; however, these regions endure massive evaporative losses that are compensated by unsustainable freshwater withdrawals. Plastic mulches have been used to curtail evaporation, improve water-use efficiency, and ensure food–water security, but they are non-biodegradable and their disposal is unsustainable. We recently developed superhydrophobic sand (SHS), which comprises sand grains with a nanoscale wax coating that could offer a more sustainable mulching solution. Here, the effects of adding a 1.0 cm-thick layer of SHS mulch on the evapotranspiration and phenotypic responses of tomato (Solanum lycopersicum) plants are studied under normal and reduced irrigation. Under both irrigation regimes, SHS mulching suppressed evaporation and enhanced transpiration by 78% and 17%, respectively relative to the bare soil. Overall, SHS mulching enhanced root xylem vessel diameter, stomatal aperture, stomatal conductance, and chlorophyll content index by 21%, 25%, 28%, and 23%, respectively. Total fruit yields, total dry mass, and harvest index increased in SHS-mulched plants by 33%, 20%, and 16%, respectively than in bare soil. These findings demonstrate the potential of SHS to boost irrigation efficiency in water-limited environments and provide mechanistic insights behind yield enhancement by SHS mulching.
Upregulated PD-1 Signaling is an Important Antagonist to Glomerular Health in Aged Kidneys
Authors: Pippin Jeffrey W. , Kaverina Natalya , Wang Yuliang , Eng Diana G. , Zeng Yuting , Tran Uyen , Loretz Carol J. , Chang Anthony , O’Connor Christopher , Bitzer Markus , Wessely Oliver , Shankland Stuart J.
Published: October 2021

Kidney aging and its contribution to disease and its underlying mechanisms are not well understood. With an aging population, kidney health becomes an important medical and socioeconomic factor. We previously showed that podocytes isolated from aged mice exhibit increased expression of Programed Cell Death Protein 1 (PD-1) surface receptor and its two ligands (PD-L1, PD-L2).PDCD1transcript increases with age in micro-dissected human glomeruli, which correlates with lower eGFR, and higher segmental glomerulosclerosis and vascular arterial intima to lumen ratio.In vitrostudies in podocytes demonstrate a critical role for PD-1 signaling in cell survival and induction of a Senescence-Associated Secretory Phenotype (SASP). To prove PD-1 signaling is critical to podocyte aging, aged mice were injected with anti-PD-1 antibody (aPD-1ab). Treatment significantly improved the aging phenotype in both kidney and liver. In the glomerulus, it increased the life-span of podocytes, but not parietal epithelial, mesangial or endothelial cells. Transcriptomic and immunohistochemistry studies demonstrate that anti-PD-1 treatment improved the health-span of podocytes. It restored the expression of canonical podocyte genes, transcription factors and gene regulatory networks, increased cellular metabolism signatures and lessened SASPs. These results suggest a critical contribution for increased PD-1 signaling towards both kidney and liver aging.
seqr : a web-based analysis and collaboration tool for rare disease genomics
Authors: Pais Lynn S. , Snow Hana , Weisburd Ben , Zhang Shifa , Baxter Samantha , DiTroia Stephanie , O’Heir Emily , England Eleina , Chao Katherine , Lemire Gabrielle , Osei-Owusu Ikeoluwa , VanNoy Grace E. , Wilson Michael , Nguyen Kevin , Arachchi Harindra , Phu William , Solomonson Matthew , Mano Stacy , O’Leary Melanie , Lovgren Alysia , Babb Lawrence , Austin-Tse Christina , Rehm Heidi L. , MacArthur Daniel G. , O’Donnell-Luria Anne
Published: October 2021

Exome and genome sequencing have become the tools of choice for rare disease diagnosis, leading to large amounts of data available for analyses. To identify causal variants in these datasets, powerful filtering and decision support tools that can be efficiently used by clinicians and researchers are required. To address this need, we developed seqr - an open source, web-based tool for family-based monogenic disease analysis that allows researchers to work collaboratively to search and annotate genomic callsets. To date, seqr is being used in several research pipelines and one clinical diagnostic lab. In our own experience through the Broad Institute Center for Mendelian Genomics, seqr has enabled analyses of over 10,000 families, supporting the diagnosis of more than 3,800 individuals with rare disease and discovery of over 300 novel disease genes. Here we describe a framework for genomic analysis in rare disease that leverages seqr’s capabilities for variant filtration, annotation, and causal variant identification, as well as support for research collaboration and data sharing. The seqr platform is available as open source software, allowing low-cost participation in rare disease research, and a community effort to support diagnosis and gene discovery in rare disease.
The association between lymphocyte mitochondrial DNA abundance and Stroke: a combination of multivariable-adjusted survival and mendelian randomization analyses
Authors: Martens Leon G , Luo Jiao , Wermer Marieke J H , van Dijk Ko Willems , Hägg Sara , Grassmann Felix , Noordam Raymond , van Heemst Diana
Published: October 2021

Background and Purpose

Mitochondrial dysfunction is associated with increased Reactive Oxygen Species that are thought to drive risk of disease, including stroke. We investigated the association between mtDNA abundance, as a proxy for mitochondrial function, and incident stroke using multivariable-adjusted survival and Mendelian Randomization (MR) analyses.

Methods

Cox-proportional hazard model analyses were conducted to assess the association between lymphocyte mtDNA abundance, and incident ischemic and hemorrhagic stroke over a maximum of 14-years follow-up in unrelated European-ancestry participants from UK Biobank. MR was conducted using independent (R2<0.001) lead variants for lymphocyte mtDNA abundance (p < 5×10-8) as instrumental variables. Single-Nucleotide Polymorphism (SNP)- ischemic stroke associations were derived from three published open source European-ancestry results databases (cases/controls): MEGASTROKE (60,341/454,450), UK Biobank (2,404/368,771) and FinnGen (10,551/202,223). MR was performed per study, and results were subsequently meta-analyzed.

Results

A total of 288,572 unrelated participants (46% men) with mean (SD) age of 57 (8) years were included in the cox-proportional hazard analyses. After correction for considered confounders (BMI, hypertension, cholesterol, T2D), no association was found between mtDNA abundance and ischemic or hemorrhagic stroke (lowest 20% versus highest 20%: ischemic stroke, hazard ratio, 1.06 [95% confidence interval 0.95, 1.18]; hemorrhagic stroke, hazard ratio 0.97 [95% confidence interval, 0.82, 1.15]). In line, in the MR analyses, we found no evidence for an association between genetically-influenced mtDNA abundance and ischemic stroke (odds ratio, 1.04; confidence interval, 0.95, 1.15).

Conclusions

From the multivariable-adjusted survival analyses and the MR analyses, we did not find support for low lymphocyte mtDNA abundance as a causal risk factor in the development of stroke.
Boosting of Cross-Reactive Antibodies to Endemic Coronaviruses by SARS-CoV-2 Infection but not Vaccination with Stabilized Spike
Authors: Crowley Andrew R. , Natarajan Harini , Hederman Andrew P. , Bobak Carly A. , Weiner Joshua A. , Wieland-Alter Wendy , Lee Jiwon , Bloch Evan M. , Tobian Aaron A.R. , Redd Andrew D. , Blankson Joel N. , Wolf Dana , Goetghebuer Tessa , Marchant Arnaud , Connor Ruth I. , Wright Peter F. , Ackerman Margaret E.
Published: October 2021

Pre-existing antibodies to endemic coronaviruses (CoV) that cross-react with SARS-CoV-2 have the potential to influence the antibody response to COVID-19 vaccination and infection for better or worse. In this observational study of mucosal and systemic humoral immunity in acutely infected, convalescent, and vaccinated subjects, we tested for cross reactivity against endemic CoV spike (S) protein at subdomain resolution. Elevated responses, particularly to the β-CoV OC43, were observed in all natural infection cohorts tested and were correlated with the response to SARS-CoV-2. The kinetics of this response and isotypes involved suggest that infection boosts preexisting antibody lineages raised against prior endemic CoV exposure that cross react. While further research is needed to discern whether this recalled response is desirable or detrimental, the boosted antibodies principally targeted the better conserved S2 subdomain of the viral spike and were not associated with neutralization activity. In contrast, vaccination with a stabilized spike mRNA vaccine did not robustly boost cross-reactive antibodies, suggesting differing antigenicity and immunogenicity. In sum, this study provides evidence that antibodies targeting endemic CoV are robustly boosted in response to SARS-CoV-2 infection but not to vaccination with stabilized S, and that depending on conformation or other factors, the S2 subdomain of the spike protein triggers a rapidly recalled, IgG-dominated response that lacks neutralization activity.

Graphical Abstract

Graphical Abstract

Antibody responses to SARS-CoV-2 and endemic CoV spike proteins were measured in diverse cohorts. While antibodies to SARS-CoV-2 were induced across all isotypes, only IgA and IgG responses to endemic CoV were robustly boosted, and only among naturally-infected but not vaccinated individuals. These recalled, cross-reactive responses to endemic CoV primarily recognized the better conserved S2 domain and were non-neutralizing. While other antiviral activities of broadly cross-reactive S2-specifc antibodies are not known, the differing antigenicity of natural infection and vaccination with stabilized pre-fusion spike has potential implications for the breadth and level of protection afforded by each.
Chlamydomonas State Transition Is Quiet Around Pyrenoid and Independent from Thylakoid Deformation
Authors: Zhang XianJun , Fujita Yuki , Kaneda Naoya , Tokutsu Ryutaro , Ye Shen , Minagawa Jun , Shibata Yutaka
Published: October 2021

Photosynthetic organisms have developed a rapid regulation mechanism called state transition (ST) to rapidly adjust the excitation balance between two photosystems by light-harvesting complex II (LHCII) movement. Though many researchers have assumed coupling of the ultrastructural dynamics of the thylakoid membrane to the ST mechanism, how ST is related to the ultrastructural dynamic of the thylakoid in Chlamydomonas remains elusive. To clarify the above-mentioned relation, here we used two specialized microscope techniques, observation via the excitation-spectral microscope (ESM) developed recently by us and the super-resolution imaging based on structured illumination microscopy (SIM). The ESM observation revealed a highly reversible rearrangement of LHCII-related fluorescence. More importantly, it clarified lower ST activity in the region surrounding the pyrenoid, which is the specific subcellular compartment associated with the carbon-fixation reaction. On the other hand, the SIM observation resolved partially irreversible fine thylakoid transformations induced by the ST-inducing illumination. Fine irreversible thylakoid transformation was also observed for the Stt7-kinase-lacking mutant. This result, together with the nearly equal structural changes in the less active ST regions around the pyrenoid, suggested the independence of the observed fine structural changes from the LHCII phosphorylation.
Universal features shaping organelle gene retention
Authors: Giannakis Konstantinos , Arrowsmith Samuel J. , Richards Luke , Gasparini Sara , Chustecki Joanna M. , Røyrvik Ellen C. , Johnston Iain G.
Published: October 2021

Mitochondria and plastids power complex life, and retain their own organelle DNA (oDNA) genomes, with highly reduced gene contents compared to their endosymbiont ancestors. Why some protein-coding genes are retained in oDNA and some lost remains a debated question. Here we harness over 15k oDNA sequences and over 300 whole genome sequences with tools from structural biology, bioinformatics, machine learning, and Bayesian model selection to reveal the properties of genes, and associated underlying mechanisms, that shape oDNA evolution. Striking symmetry exists between the two organelle types: gene retention patterns in both are predicted by the hydrophobicity of a protein product and its energetic centrality within its protein complex, with additional influences of nucleic acid and amino acid biochemistry. Remarkably, retention principles from one organelle type successfully and quantitatively predict retention in the other, supporting this universality; these principles also distinguish gene profiles in independent endosymbiotic relationships. The identification of these features shaping organelle gene retention both provides quantitative support for several existing evolutionary hypotheses, and suggests new biochemical and biophysical mechanisms influencing organelle genome evolution.
Human pluripotent stem cell-derived kidney organoids for personalized congenital and idiopathic nephrotic syndrome modeling
Authors: Jansen Jitske , van den Berge Bartholomeus T , van den Broek Martijn , Maas Rutger J , Willemsen Brigith , Kuppe Christoph , Reimer Katharina C , Giovanni Gianluca Di , Mooren Fieke , Nlandu Quincy , Mudde Helmer , Wetzels Roy , den Braanker Dirk , Parr Naomi , Nagai James S , Drenic Vedran , Costa Ivan G , Steenbergen Eric , Nijenhuis Tom , Endlich Nicole , van de Kar Nicole CAJ , Schneider Rebekka K , Wetzels Jack FM , van der Vlag Johan , Kramann Rafael , Schreuder Michiel F , Smeets Bart
Published: October 2021

Nephrotic syndrome (NS) is characterized by severe proteinuria as a consequence of kidney glomerular injury due to podocyte damage. In vitro models mimicking in vivo podocyte characteristics are a prerequisite to resolve NS pathogenesis. Here, we report human induced pluripotent stem cell derived kidney organoids containing a podocyte population that heads towards adult podocytes and were superior compared to 2D counterparts, based on scRNA sequencing, super-resolution imaging and electron microscopy. In this study, these next-generation podocytes in kidney organoids enabled personalized idiopathic nephrotic syndrome modeling as shown by activated slit diaphragm signaling and podocyte injury following protamine sulfate treatment and exposure to NS plasma containing pathogenic permeability factors. Organoids cultured from cells of a patient with heterozygous NPHS2 mutations showed poor NPHS2 expression and aberrant NPHS1 localization, which was reversible after genetic correction. Repaired organoids displayed increased VEGFA pathway activity and transcription factor activity known to be essential for podocyte physiology, as shown by RNA sequencing. This study shows that organoids are the preferred model of choice to study idiopathic and congenital podocytopathies.

Summary Statement

Kidney organoid podocytes allow personalized nephrotic sydrome modeling,
Investigating Biases Associated with Dietary Starch Incorporation and Retention with an Oral Biofilm Model
Authors: Bartholdy Bjørn Peare , Henry Amanda G.
Published: October 2021

Dental calculus has proven to contain a wealth of information on the dietary habits of past populations. These insights have, to a large extent, been obtained by the extraction and identification of starch granules contained within the mineralised dental plaque from a wide range of regions and time periods. The scope of previous studies have been limited to microfossil extraction and identification to reconstruct dietary preferences from the archaeological record, and few studies have attempted to address the biases of starch retention in dental calculus. Those that have considered this problem have been limited toin vivostudies on modern humans and non-human primates. Here, we present a multispecies oral biofilm model, which allows experimental research on starch incorporation and retention to be conducted onin vitrodental calculus in a controlled laboratory setting. The biofilms were exposed to treatment solutions with known quantities of dietary starches (wheat and potato) during the 25-day growth period. After this, the starch granules were extracted from the mature biofilm (by dissolution in EDTA), and counted. We show that the granule counts extracted from the model dental calculus represented a low proportion (ranging from 0.06% to 0.16%) of the total number of granules exposed to the biofilms throughout the experiment. Additionally, we found that the ratios of granule sizes from the extracted starch granules differed from the original treatment solutions, with large granules (>20μm) consistently being under-represented. We also found a correlation between the absolute granule counts and dry-weight of the biofilm (r= 0.66, 90%CI[0.46,0.79]), as well as between the concentration (count per mg) of granules and dry-weight (r= 0.30, 90%CI[0.06,0.51]).

Our results reinforce previousin vivostudies suggesting that dental calculus presents a very small, and partly biased picture of the original dietary intake of starches, with an over-representation of plants producing granules smaller than 20μm in size. The experimental model presented here is well-suited to address the need for further validation of methods and biases associated with dietary research on dental calculus.
Syrbactin-class dual constitutive- and immuno-proteasome inhibitor TIR-199 impedes myeloma-mediated bone degenerationin vivo
Authors: Tandon Vasudha , Vala Ruturajsinh M , Chen Albert , Sah Robert L , Patel Hitendra M , Pirrung Michael C , Banerjee Sourav
Published: October 2021

Proteasome-addicted neoplastic malignancies present a considerable refractory and relapsed phenotype with patients exhibiting drug-resistance and high mortality rates. To counter this global problem, novel proteasome-based therapies are being developed. In the current study we extensively characterize TIR-199, a syrbactin-class proteasome inhibitor derived from a plant virulence factor of bacteriumPseudomonas syringae pv syringae.We report that TIR-199 is a potent constitutive and immunoproteasome inhibitor, capable of inducing cell death in multiple myeloma, triple-negative breast cancer and non-small cell lung cancer lines, effectively inhibit proteasome in primary myeloma cells of refractory patients, and bypass the PSMB5 A49T+A50V bortezomib-resistant mutant. TIR-199 treatment leads to accumulation of canonical proteasome substrates in cells, it is specific, and does not inhibit 50 other enzymes tested in vitro. The drug exhibits synergistic cytotoxicity in combination with proteasome-activating-kinase DYRK2 inhibitor LDN192960. Furthermore, low dose TIR-199 exhibits in vivo activity in delaying myeloma-mediated bone degeneration in a mouse xenograft model. Together, our data indicates that proteasome inhibitor TIR-199 could indeed be a next generation drug within the repertoire of proteasome-based therapeutics with a potential to target relapsed and refractory proteasome-addicted neoplasia.
Spatial Probabilistic Mapping of Metabolite Ensembles in Mass Spectrometry Imaging
Authors: Sammour Denis Abu , Cairns James L. , Boskamp Tobias , Kessler Tobias , Guevara Carina Ramallo , Panitz Verena , Sadik Ahmed , Cordes Jonas , Marsching Christian , Friedrich Mirco , Platten Michael , Wolf Ivo , von Deimling Andreas , Opitz Christiane A. , Wick Wolfgang , Hopf Carsten
Published: October 2021

Mass spectrometry imaging (MSI) vows to enable simultaneous spatially-resolved investigation of hundreds of metabolites in tissue sections, but it still relies on poorly defined ion images for data interpretation. Here, we outline moleculaR, a computational framework (https://github.com/CeMOS-Mannheim/moleculaR) that introduces probabilistic mapping and point-for-point statistical testing of metabolites in tissue. It enables collective molecular projections and consequently spatially-resolved investigation of ion milieus, lipid pathways or user-defined biomolecular ensembles within the same image.
Ultra-deep sequencing reveals no evidence of oncogenic mutations or enrichment by ex vivo CRISPR/Cas9 genome editing in human hematopoietic stem and progenitor cells
Authors: Cromer M. Kyle , Barsan Valentin V. , Jaeger Erich , Wang Mengchi , Hampton Jessica P. , Chen Feng , Kennedy Drew , Khrebtukova Irina , Granat Ana , Truong Tiffany , Porteus Matthew H.
Published: October 2021

As CRISPR-based therapies enter the clinic, evaluation of the safety remains a critical and still active area of study. While whole genome sequencing is an unbiased method for identifying somatic mutations introduced by ex vivo culture and genome editing, this methodology is unable to attain sufficient read depth to detect extremely low frequency events that could result in clonal expansion. As a solution, we utilized an exon capture panel to facilitate ultra-deep sequencing of >500 tumor suppressors and oncogenes most frequently altered in human cancer. We used this panel to investigate whether transient delivery of high-fidelity Cas9 protein targeted to three different loci (using guide RNAs (gRNAs) corresponding to sites at AAVS1, HBB, and ZFPM2) at day 4 and day 10 timepoints post-editing resulted in the introduction or enrichment of oncogenic mutations. In three separate primary human HSPC donors, we identified a mean of 1,488 variants per Cas9 treatment (at <0.07% limit of detection). After filtering to remove germline and/or synonymous changes, a mean of 3.3 variants remained per condition, which were further reduced to six total mutations after removing variants in unedited treatments. Of these, four variants resided at the predicted off-target site in the myelodysplasia-associated EZH2 gene that were subject to ZFPM2 gRNA targeting in Donors 2 and 3 at day 4 and day 10 timepoints. While Donor 1 displayed on-target cleavage at ZFPM2, we found no off-target activity at EZH2. Sanger sequencing revealed a homozygous single nucleotide polymorphism (SNP) at position 14bp distal from the Cas9 protospacer adjacent motif in EZH2 that eliminated any detectable off-target activity. We found no evidence of exonic off-target INDELs with either of the AAVS1 or HBB gRNAs. These findings indicate that clinically relevant delivery of high-fidelity Cas9 to primary HSPCs and ex vivo culture up to 10 days does not introduce or enrich for tumorigenic variants and that even a single SNP outside the seed region of the gRNA protospacer is sufficient to eliminate Cas9 off-target activity with this method of delivery into primary, repair competent human HSPCs.
Auditory Brainstem Responses in the C57BL/6J Fragile X Syndrome Knockout Mouse Model
Authors: Chawla Amita , McCullagh Elizabeth A
Published: October 2021

Sensory hypersensitivity, especially in the auditory system, is a common symptom in Fragile X Syndrome (FXS), the most common monogenic form of intellectual disability. However, linking phenotypes across genetic background strains of mouse models has been a challenge and could underly some of the issues with translatability of drug studies to the human condition. This study is the first to characterize the auditory brainstem response (ABR), a minimally invasive physiological readout of early auditory processing that is also used in humans, in a commonly used mouse background strain model of FXS, C57BL/6J. We measured morphological features of pinna and head and used ABR to measure hearing range, monaural and binaural auditory responses in hemizygous males, homozygous females and heterozygous females compared to wildtype mice. Consistent with previous work we showed no difference in morphological parameters across genotypes or sexes. Male FXS mice had increased threshold for high frequency hearing at 64 kHz compared to wildtype males, while females had no difference in hearing range between genotypes. In contrast, female homozygous FXS mice had decreased amplitude of wave IV of the monaural ABR, while there was no difference in males for amplitudes and no change in latency of ABR waveforms across sexes and genotypes. Lastly, FXS males had increased latency of the binaural interaction component (BIC) at 0 ITD compared to wildtype males. These findings further clarify auditory brainstem processing in FXS by adding more information across genetic background strains allowing for a better understanding of shared phenotypes.
Coccolith Sr/Ca is a Robust Temperature and Growth Rate Indicator that Withstands Dynamic Microbial Interactions
Authors: Eliason Or , Segev Einat
Published: October 2021

Coccolithophores are a diverse group of calcifying microalgae that have left a prominent fossil record on Earth. Various coccolithophore relics, both organic and inorganic, serve as proxies for reconstruction of past oceanic conditions.

Emiliania huxleyi is the most widely distributed representative of the coccolithophores in modern oceans, and is known to engage in dynamic interactions with bacteria. Algal-bacterial interactions influence various aspects of algal physiology and alter algal alkenone unsaturation (UK’37), a frequently used organic coccolithophore-derived paleotemperature proxy. Whether algal-bacterial interactions influence inorganic coccolithophore-derived paleo-proxies, is yet unknown.

A commonly used inorganic proxy for past productivity and sea surface temperature is the Sr/Ca ratio of the coccolith calcite. Interestingly, during interactions between bacteria and a population of calcifying algae, bacteria were shown to physically attach only to non-calcified algal cells, suggesting an influence on algal calcification.

In this study we explore the effects of algal-bacterial interactions on calcification and coccolith Sr/Ca ratios. We find that while bacteria attach only to non-calcified algal cells, coccolith cell coverage and overall calcite production in algal populations with and without bacteria, is similar. Furthermore, we find that Sr/Ca values are impacted only by water temperature and algal growth rate, regardless of bacterial influences on algal physiology. Our observations reinforce the robustness of coccolith Sr/Ca ratios as a paleo-proxy independent of microbial interactions, and highlight a fundamental difference between organic and inorganic paleo-proxies.

Summary Statement

The current research investigates the effect of microbial interactions on coccolith Sr/Ca ratio and overall calcification in the coccolithophore Emiliania huxleyi. We co-cultured E. huxleyi with the marine bacterium Phaeobacter inhibens and compared coccolith Sr/Ca between different growth stages in a range of temperatures. Our results indicate that coccolith Sr/Ca depends on temperature and algal growth rate, and remains robust despite significant bacterial influences on algal physiology.
A remark on ab initio indexing of electron backscatter diffraction patterns
Authors: Morawiec Adam
Published: October 2021

There is a growing interest in ab initio indexing of electron backscatter diffraction (EBSD) patterns. The methods of solving the problem are presented as innovative. The purpose of this note is to point out that ab initio EBSD indexing belongs to the field of indexing single-crystal diffraction data, and it is solved on the same principles as indexing of patterns of other types. It is shown that reasonably accurate EBSD-based data can be indexed by programs designed for X-ray data.
Synthesis, structural, characterization and Hirshfeld analysis of a bisselenide and a zinc complex of a new hemilabile ferrocenylbisphosphane, [Fe{C5H4P(C6H4CH2NMe2-o)2}2]
Authors: Kunchur Harish S. , Mondal Dipanjan , Rao Sowmya , Mague Joel T. , Balakrishna Maravanji S.
Published: October 2021

The novel hemilabile ferrocenylbisphosphane 1,1′-bis(bis{2-[(dimethylamino)methyl]phenyl}phosphanyl)ferrocene, [Fe{C5H4P(C6H4CH2NMe2-o)2}2] (1), was synthesized by reacting bis(dichlorophosphanyl)ferrocene, [Fe{C5H4(PCl2)}2] with LiC6H4CH2NMe2-o. Treatment of 1 with gray selenium and anhydrous ZnCl2 yielded, respectively, the bisselenide (ferrocene-1,1′-diyl)bis(bis{2-[(dimethylamino)methyl]phenyl}phosphine selenide), [Fe(C23H28N2PSe)2] (2), and the dizinc complex [μ-1,1′-bis(bis{2-[(dimethylamino)methyl]phenyl}phosphanyl)ferrocene-κ2
N,P:κ2
N′,P′]bis[dichloridozinc(II)] dichloromethane monosolvate, [FeZn2Cl4(C23H28N2P)2]·CH2Cl2 (3), and both have been structurally characterized. Both compounds crystallized with the asymmetric unit containing half a molecule and with the Fe atom on an inversion centre. A Hirshfeld surface analysis indicated that the most significant contributions to the crystal packing of 2 are from H...H (76.7%), C...H/H...C (13.2%) and Se...H/H...Se (7.1%) contacts, while those for 3 are from H...H (62.3%), Cl...H/H...Cl (24.4%) and C...H/H...C (10.9%) contacts.
Corrosion protection of some Cu-based alloys by polyacrylate-alumina nanocomposite coatings
Authors: Attia Adel , Khorshed Lobna , Morsi Samir , Ashour Elsayed
Published: October 2021

Purpose

The purpose of this study was to investigate the polyacrylic polymer/Al2O3 as a new nanocomposite coating to protect brass and Al-bronze in 3.5% NaCl and the role of alumina formulation on their protection efficiency

Design/methodology/approach

The corrosion efficiency of the nanocomposite coating (NCC) was evaluated by open circuit potential and electrochemical impedance spectroscopy (EIS).

Findings

The protection efficiency was more in the case of Al-bronze even for the same formulation of alumina NCC indicated the Cu substrate contribution. The Cu oxides in alloys and Al2O3 from the NCC and Al-bronze were responsible for this protection.

Originality/value

All the techniques supported each other, the presence of alumina was responsible for the corrosion protection efficiency.
Evaluation of the corrosion behavior of AZ31 magnesium alloy with different protein concentrations
Authors: Ma Yucong , Talha Mohd , Wang Qi , Li Zhonghui , Lin Yuanhua
Published: October 2021

Purpose

The purpose of this paper is to study systematically the corrosion behavior of AZ31 magnesium (Mg) alloy with different concentrations of bovine serum albumin (BSA) (0, 0.5, 1.0, 1.5, 2.0 and 5.0 g/L).

Design/methodology/approach

Electrochemical impedance spectroscopy and potential dynamic polarization tests were performed to obtain corrosion parameters. Scanning electrochemical microscopy (SECM) was used to analyze the local electrochemical activity of the surface film. Atomic force microscope (AFM), Scanning electron microscope-Energy dispersive spectrometer and Fourier transform infrared spectroscopy were used to determine the surface morphology and chemical composition of the surface film.

Findings

Experimental results showed the presence of BSA in a certain concentration range (0 to 2.0 g/L) has a greater inhibitory effect on the corrosion of AZ31, however, the presence of high-concentration BSA (5.0 g/L) would sharply reduce the corrosion resistance.

Originality/value

When the concentration of BSA is less than 2.0 g/L, the corrosion resistance of AZ31 enhances with the concentration. The adsorption BSA layer will come into being a physical barrier to inhibit the corrosion process. However, high-concentration BSA (5.0 g/L) will chelate with dissolved metal ions (such as Mg and Ni) to form soluble complexes, which increases the roughness of the surface and accelerates the corrosion process.