bluuebunny/crossref_metadata_2025 huggingface dataset:
In utero delivery of miRNA induces epigenetic alterations and corrects pulmonary pathology in congenital diaphragmatic hernia
Authors: Ullrich Sarah J , Yung Nicholas K , Bauer-Pisani Tory J , Maassel Nathan L , Guerra Mary Elizabeth , Freedman-Weiss Mollie , Ahle Samantha L , Ricciardi Adele S , Sauler Maor , Saltzman W Mark , Piotrowski-Daspit Alexandra S , Stitelman David H.
Published: March 2022

Structural fetal diseases, such as congenital diaphragmatic hernia (CDH) can be diagnosed prenatally. Neonates with CDH are healthy in utero as gas exchange is managed by the placenta, but impaired lung function results in critical illness from the time a baby takes its first breath. During fetal development, lungs are capable of remarkable growth and the fetus does not yet require lung function for gas exchange. MicroRNA (miR) 200b and its downstream targets in the TGFβ pathway are critically involved lung branching morphogenesis. Here we characterize the expression of miR200b and the TGFβ pathway at different gestational times using a rat model of CDH. Fetal rats with CDH are deficient in miR200b at gestational day 18. We demonstrate that NPs loaded with miR200b given systemically to fetal rats result in changes in the TGFβ pathway; these epigenetic changes improve lung size, lung morphology, and lung vascularization. This is the first demonstration of in utero epigenetic therapy to improve lung growth and development in a pre-clinical model. With refinement, this technique could be applied to fetal cases of CDH or other forms of impaired lung development in a minimally invasive fashion.

eTOC Synopsis

In utero treatment with NPs loaded with miR200b improves lung development in a rat model of CDH. miR200b treatment epigenetic changes in the TGFβ, leads to larger lungs with more airspace and favorable pulmonary vascular remodeling.
Traditional treatment of HIV and the role of family members as barriers to access to HIV care service or antiretroviral therapy among people living with HIV
Authors: Fauk Nelsensius Klau , Mwanri Lillian , Hawke Karen , Ward Paul Russell
Published: March 2022

Access to HIV care service or antiretroviral therapy (ART) is essential for the improvement of health outcomes of people living with HIV (PLHIV) and in reducing HIV transmission and HIV-related deaths. As a part of a qualitative study in Belu, this paper describes the use of traditional treatment and the role of families in determining traditional treatment for their HIV-positive family member as barriers to access to HIV care service or ART among PLHIV. One-on-one in-depth interviews were employed to collect data from 46 PLHIV (26 women and 20 men) and 10 healthcare professionals recruited using the snowball sampling technique. Data analysis was performed using NVivo 12 software and guided by a qualitative data analysis framework. The findings showed that the use of traditional treatment, a well-known cultural practice in Belu, was a barrier to access to HIV care service or ART among PLHIV. The role of family in determining traditional treatment for HIV, supported by the lack of knowledge of ART, effectiveness of traditional medicines in treating other health issues, and social influence of families, neighbours and friends, were also significant barriers to PLHIV’s access to HIV care service or ART. The findings indicate the need for dissemination of HIV care-related information for PLHIV, family and community members to increase their knowledge on the service, ART and its function, and to support and improve access to ART by PLHIV.
A compartmental Mathematical model of COVID-19 intervention scenarios for Mumbai
Authors: Singh Avaneesh , Bajpai Manish Kumar
Published: March 2022

A new mathematical method with an outstanding potential to predict the incidence of COVID-19 diseases has been proposed. The model proposed is an improvement to the SEIR model. In order to improve the basic understanding of disease spread and outcomes, four compartments included presymptomatic, asymptomatic, quarantine hospitalized and hospitalized. We have studied COVID-19 cases in the city of Mumbai. We first gather clinical details and fit it on death cases using the Lavenberg-Marquardt model to approximate the various parameters. The model uses logistic regression to calculate the basic reproduction number over time and the case fatality rate based on the age-category scenario of the city of Mumbai. Two types of case fatality rate are calculated by the model: one is CFR daily, and the other is total CFR. The total case fatality rate is 4.2, which is almost the same as the actual scenario. The proposed model predicts the approximate time when the disease is at its worst and the approximate time when death cases barely arise and determines how many hospital beds in the peak days of infection would be expected. The proposed model outperforms the classic ARX, SARIMAX and the ARIMA model. And It also outperforms the deep learning models LSTM and Seq2Seq model. To validate results, RMSE, MAPE and R squared matrices are used and are represented using Taylor diagrams graphically.
Delirium due to hip fracture is associated with activated immune-inflammatory pathways and a reduction in negative immunoregulatory mechanisms
Authors: Thisayakorn Paul , Thipakorn Yanin , Tantavisut Saran , Sirivichayakul Sunee , Maes Michael
Published: March 2022

The objectives of this study were to delineate whether delirium is associated with activation of the immune-inflammatory response system (IRS) as indicated by activation of M1, Thelper (Th)1, and Th17 profiles, and/or by reduced activities of the compensatory immunoregulatory system (CIRS), including Th2 and Tregulatory profiles. We recruited 65 elderly patients with a low energy impact hip fracture who underwent hip fracture operation. The CAM-ICU and the Delirium Rating Scale, Revised-98-Thai version (DRS-R-98) were assessed pre-operatively and 1, 2 and 3 days after surgery. Blood samples (day 1 and 2) post-surgery were assayed for cytokines/chemokines using a MultiPlex assay and the neutrophil/lymphocyte ratio. We found that delirium and/or the DRS-R-98 score were associated with IRS activation as indicated by activated M1, Th1, Th17 and T cell growth profiles and by attenuated CIRS functions. The most important IRS biomarkers were CXCL8, interleukin (IL)-6, and tumor necrosis factor-α, and the most important CIRS biomarkers were IL-4 and soluble IL-1 receptor antagonist. We found that 42.5% of the variance in the actual changes in the DRS-R-98 score (averaged from day 1 to day 3) was explained by T cell growth factors, baseline DRS-R-98 scores and age. The pain scores during delirium were significantly and positively associated with CXCL8 and CCL3 and negatively with IL-4 and sIL-1RA. An increase in the NLR reflects overall IRS, M1, Th1, Th17, and Th2 activation. In conclusion, post-hip surgery delirium is associated with activated IRS pathways and appears especially in patients with lowered CIRS functions.
The CTP-binding domain is disengaged from the DNA-binding domain in a co-crystal structure of Bacillus subtilis Noc-DNA complex
Authors: Sukhoverkov Kirill V. , Jalal Adam S. B. , Lawson David M. , Le Tung B. K.
Published: March 2022

In Bacillus subtilis, a ParB-like nucleoid occlusion protein (Noc) binds specifically to Noc-binding sites (NBS) around the chromosome to help coordinate chromosome segregation and cell division. Noc does so by binding to cytidine triphosphate (CTP) to form large membrane-associated nucleoprotein complexes to physically inhibit the assembly of the cell division machinery. The site-specific binding of Noc to NBS DNA is a prerequisite for CTP-binding and the subsequent formation of a membrane-active DNA-entrapped protein complex. Here, we solve the structure of a truncated B. subtilis Noc bound to NBS DNA to reveal the conformation of Noc at this crucial step. Our structure reveals the disengagement between the N-terminal CTP-binding domain and the NBS-binding domain of each DNA-bound Noc subunit, this is driven, in part, by the swapping of helices 4 and 5 at the interface of the two domains. Site-specific crosslinking data suggest that this conformation of Noc-NBS exists in solution. Overall, our results lend support to the recent proposal that parS/NBS-binding catalyzes CTP-binding and DNA-entrapment by preventing the re-engagement of the NTD and DBD from the same ParB/Noc subunit.
Separability of Human Motor Memories during Reaching Adaptation with Force Cues
Authors: Crevecoeur F. , Mathew J. , Lefèvre P
Published: March 2022

Judging by the breadth of our motor repertoire during daily activities, it is clear that acquiring multiple motor skills is a hallmark of the human motor system. However, for reaching movements the different planning conditions under which this is possible in laboratory settings have remained a challenging question. Considering the sensitivity of limb afferent feedback relative to externally applied forces, we hypothesised that independent cues delivered by means of background loads could support simultaneous formation of different motor memories of various velocity-dependent force fields. We demonstrate in a series of experiments that indeed healthy adults can form internal priors about opposite force fields, independently of the direction of the background force cue. However, when the cue and force field were only related by their magnitude, a separation was still observed but the associated mechanism was subject to interference. Finally, we highlight that this paradigm allows dissociating trial-by-trial acquisition of internal representations from within-trial feedback adaptation, as these two adaptation mechanisms are associated with different time scales that can be measured reliably.

Significance Statement

The conditions under which humans can adapt to different contexts in parallel remain the subject of active debates. Mounting evidence highlights that contextual factors linked to movement planning are necessary to form different motor memories. Here we show that background forces indicative of the direction of a force field could play the role of contextual factors, and enable dual adaptation to different force fields. However, we uncovered that when the cue and the force field were in the same direction but of different magnitudes, the motor memories were still distinct but subject to interference. We further show that different timescales of adaptation observed can be explained by offline and online mechanisms in a model of reaching adaptation and control.
A single episode of CMV reactivation initiates long-term expansion and differentiation of the NK cell repertoire
Authors: Hassan Norfarazieda , Eldershaw Suzy , Stephens Christine , Kinsella Francesca , Craddock Charles , Malladi Ram , Zuo Jianmin , Moss Paul
Published: March 2022

NK cells play an important role in suppression of viral replication and are critical for effective control of persistent infections such as herpesviruses. Cytomegalovirus infection is associated with expansion of ‘adaptive-memory’ NK cells with a characteristic CD16brightCD56dimNKG2C+ phenotype but the mechanisms by which this population is maintained remain uncertain. We studied NK cell reconstitution in patients undergoing haemopoietic stem cell transplantation and related this to CMV reactivation. NK cells expanded in the early post-transplant period but then remained stable in the absence of viral reactivation. However, a single episode of CMV reactivation led to a rapid and sustained 10-fold increase in NK cell number. NKG2C expression was increased on all NK subsets although the kinetics of expansion peaked at 6 months on immature CD56brightcells whilst continuing to rise on the mature CD56dimpool. Phenotypic maturation was observed by acquisition of CD57 and KIR expression. Transplantation from CMV-seropositive donors was associated with more rapid NK expansion and superior control of viral reactivation. Effective control of viral reactivation was seen when the peripheral NK cell count reached 20,000/ml. These data show that a single episode of CMV reactivation acts to reprogramme hemopoiesis to drive a sustained modulation and expansion of the NK cell pool and reveal further insight into long term regulation of the innate immune repertoire by infectious challenge.

Author Summary

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Innate immune cells respond rapidly to infectious challenge and it has previously been thought that they were unable to ‘learn’ from specific infecitons but provided only short term control. However, in recent years it has become apparent that some subsets of innate cells, termed adaptive natural killer (NK) cells, are permanently increased in people who have become infected with cytomegalovirus. The mechanism by which this is maintained is not known. We studied the kinetics of adaptive NK cell expansion in patients who had recently undergone stem cell (bone marrow) transplantation as CMV very often ‘reactivates’ in this setting and allows study of how this affects the immune system. We find that one short term episode of viral replication led to a large and prolonged expansion of adaptive NK cells. Indeed, their levls increasd 11-fold over 10 months.
In-vivo phase-dependent enhancement and suppression of brain oscillations by transcranial alternating current stimulation (tACS)
Authors: Haslacher David , Narang Asmita , Cavallo Alessia , Nasr Khaled , Santarnecchi Emiliano , Soekadar Surjo R.
Published: March 2022

Transcranial alternating current stimulation (tACS) can influence human perception and behavior, with recent evidence also suggesting its potential impact in clinical settings, but the underlying mechanisms are poorly understood. Behavioral and indirect physiological evidence indicates that phase-dependent constructive and destructive interference between the tACS electric field and ongoing brain oscillations may play an important role, but direct in-vivo validation was infeasible because stimulation artifacts impeded such assessment. Using stimulation artifact source separation (SASS), a real-time compatible artifact suppression approach, we overcame this limitation and provide direct evidence for millisecond-by-millisecond phase-dependent enhancement and suppression of ongoing brain oscillations during amplitude-modulated tACS (AM-tACS) across 29 healthy human volunteers. We found that AM-tACS enhanced and suppressed targeted brain oscillations by 11.7 ± 5.14% and 10.1 ± 4.07% respectively. Millisecond-precise modulation of oscillations predicted modulation of behavior (r = 0.65, p < 0.001). These results not only provide direct evidence for constructive and destructive interference as a key mechanism of AM-tACS but suggest superiority of phase-locked (closed-loop) AM-tACS over conventional (open-loop) AM-tACS to purposefully enhance or suppress brain oscillations.

Significance

The presented data provide direct evidence for a key mechanism underlying neurophysiological and behavioral effects of transcranial alternating current stimulation (tACS), a broadly used neuromodulation approach that yields promising clinical results but also raised controversies because of its variable effects. Our findings not only elucidate the underlying mechanisms of tACS, but also provide the rationale for closed-loop tACS protocols that will enable targeted enhancement and suppression of brain oscillations related to various brain functions such perception, memory or cognition. Towards this end, we introduce the technical prerequisites to establish millisecond-to-millisecond precise closed-loop tACS protocols that will be important to advance tACS as a neuroscientific and clinical tool, for example in the treatment of neuropsychiatric disorders.
The extracellular matrix fibulin 7 maintains epidermal stem cell heterogeneity during skin aging
Authors: Raja Erna , Changarathil Gopakumar , Oinam Lalhaba , Ngo Yen Xuan , Tsunezumi Jun , Ishii Ryutaro , Sasaki Takako , Imanaka-Yoshida Kyoko , Yanagisawa Hiromi , Sada Aiko
Published: March 2022

Tissue stem cells divide infrequently as a protective mechanism against internal and external stresses associated with aging. Here, we demonstrate that slow- and fast-cycling interfollicular epidermal stem cells in mouse skin undergo distinct aging processes. Two years of lineage tracing reveals that Dlx1+ slow-cycling clones expanded into the fast-cycling stem cell territory, while the number of Slc1a3+ fast-cycling clones gradually declined. Transcriptome analysis further indicated that the molecular properties of each stem cell population are altered with age. Mice lacking fibulin 7, an extracellular matrix (ECM), show early impairments resembling epidermal stem cell aging, such as the loss of fast-cycling clones, delayed wound healing, and increased expression of inflammation- and differentiation-related genes. Fibulin 7 interacts with structural ECM and matricellular proteins, and the overexpression of fibulin 7 in primary keratinocytes results in slower proliferation in the absence or presence of inflammatory cytokine IL-6. Thus, these results suggest that fibulin 7 plays a crucial role in maintaining tissue resilience and epidermal stem cell heterogeneity during skin aging.
HIF-1α induces glycolytic reprogramming in tissue-resident alveolar macrophages to promote survival during acute lung injury
Authors: Woods Parker S. , Kimmig Lucas M. , Sun Kaitlyn A. , Meliton Angelo Y. , Shamaa Obada R. , Tian Yufeng , Cetin-Atalay Rengül , Sharp Willard W. , Hamanaka Robert B. , Mutlu Gökhan M.
Published: March 2022

Cellular metabolism is a critical regulator of macrophage effector function. Tissue-resident alveolar macrophages (TR-AMs) inhabit a unique niche marked by high oxygen and low glucose. We have recently shown that in contrast to bone marrow-derived macrophages (BMDMs), TR-AMs cannot utilize glycolysis and predominantly rely on mitochondrial function for their effector response. It is not known how changes in local oxygen concentration that occur during conditions such as acute respiratory distress syndrome (ARDS) might affect TR-AM metabolism and function; however, ARDS is associated with progressive loss of TR-AMs, which correlates with the severity of disease and mortality. Here, we demonstrate that hypoxia robustly stabilizes HIF-1α in TR-AMs to promote a glycolytic phenotype. Hypoxia altered TR-AM metabolite signatures, cytokine production, and decreased their sensitivity to the inhibition of mitochondrial function. By contrast, hypoxia had minimal effects on BMDM metabolism. The effects of hypoxia on TR-AMs were mimicked by FG-4592, a HIF-1α stabilizer. Treatment with FG-4592 decreased TR-AM death and attenuated acute lung injury in mice. These findings reveal the importance of microenvironment in determining macrophage metabolic phenotype, and highlight the therapeutic potential in targeting cellular metabolism to improve outcomes in diseases characterized by acute inflammation.
Combining genetic constraint with predictions of alternative splicing to prioritize deleterious splicing in rare disease studies
Authors: Cormier Michael J. , Pedersen Brent S. , Bayrak-Toydemir Pinar , Quinlan Aaron R.
Published: March 2022

Background

Despite numerous molecular and computational advances, roughly half of patients with a rare disease remain undiagnosed after exome or genome sequencing. A particularly challenging barrier to diagnosis is identifying variants that cause deleterious alternative splicing at intronic or exonic loci outside of canonical donor or acceptor splice sites.

Results

Several existing tools predict the likelihood that a genetic variant causes alternative splicing. We sought to extend such methods by developing a new metric that aids in discerning whether a genetic variant leads to deleterious alternative splicing. Our metric combines genetic variation in the Genome Aggregate Database with alternative splicing predictions from SpliceAI to compare observed and expected levels of splice-altering genetic variation. We infer genic regions with significantly less splice-altering variation than expected to be constrained. The resulting model of regional splicing constraint captures differential splicing constraint across gene and exon categories, and the most constrained genic regions are enriched for pathogenic splice-altering variants. Building from this model, we developed ConSpliceML. This ensemble machine learning approach combines regional splicing constraint with multiple per-nucleotide alternative splicing scores to guide the prediction of deleterious splicing variants in protein-coding genes. ConSpliceML more accurately distinguishes deleterious and benign splicing variants than state-of-the-art splicing prediction methods, especially in “cryptic” splicing regions beyond canonical donor or acceptor splice sites.

Conclusion

Integrating a model of genetic constraint with annotations from existing alternative splicing tools allows ConSpliceML to prioritize potentially deleterious splice-altering variants in studies of rare human diseases.
Metabolome and transcriptome analysis reveals components regulating triterpenoid saponin biosynthesis of soapberry
Authors: Xu Yuanyuan , Zhao Guochun , Ji Xiangqin , Liu Jiming , Zhao Tianyun , Gao Yuan , Gao Shilun , Hao Yingying , Gao Yuhan , Wang Lixian , Weng Xuehuang , Chen Zhong , Jia Liming
Published: March 2022

Soapberry (Sapindus mukorossi Gaertn.) pericarps are rich in valuable bioactive triterpenoid saponins. However, the saponin content dynamics and the molecular regulatory network of saponin biosynthesis in soapberry pericarps remain largely unclear. Here, we performed combined metabolite profiling and transcriptome analysis to identify saponin accumulation kinetic patterns, investigate gene networks, and characterize key candidate genes and transcription factors involved in saponin biosynthesis in soapberry pericarps. A total of 54 saponins were tentatively identified, including 25 that were differentially accumulated. Furthermore, 49 genes putatively involved in sapogenin backbone biosynthesis and some candidate genes assumed to be responsible for the backbone modification, including 41 cytochrome P450s and 45 glycosyltransferases, were identified. Saponin-specific clusters/modules were identified by Mfuzz clustering and weighted gene co-expression network analysis, and one TF–gene regulatory network underlying saponin biosynthesis was proposed. The results of yeast one-hybrid assay and electrophoretic mobility shift assay suggested that SmbHLH2, SmTCP4, and SmWRKY27 may play important roles in the triterpenoid saponin biosynthesis by directly regulating the transcription of SmCYP71D-3 in soapberry pericarp. Overall, these findings provide valuable information for understanding the molecular regulatory mechanism of saponin biosynthesis, enriching the gene resources, and guiding further research on triterpenoid saponin accumulation in soapberry pericarps.

One–sentence summary

Combining metabolome and transcriptome analysis to identify saponin kinetic patterns, gene networks, and key candidate genes and transcription factors involved in saponin biosynthesis of soapberry.
RK-33, a small molecule inhibitor of host RNA helicase DDX3, suppresses multiple variants of SARS-CoV-2
Authors: Vesuna Farhad , Akhrymuk Ivan , Smith Amy , Winnard Paul T. , Lin Shih-Chao , Scharpf Robert , Kehn-Hall Kylene , Raman Venu
Published: March 2022

SARS-CoV-2, the virus behind the deadly COVID-19 pandemic, continues to spread globally even as vaccine strategies are proving effective in preventing hospitalizations and deaths. However, evolving variants of the virus appear to be more transmissive and vaccine efficacy towards them is waning. As a result, SARS-CoV-2 will continue to have a deadly impact on public health into the foreseeable future. One strategy to bypass the continuing problem of newer variants is to target host proteins required for viral replication. We have used this host-targeted antiviral (HTA) strategy that targets DDX3, a host DEAD-box RNA helicase that is usurped by SARS-CoV-2 for virus production. We demonstrated that targeting DDX3 with RK-33, a small molecule inhibitor, reduced the viral load in four isolates of SARS-CoV-2 (Lineage A, and Lineage B Alpha, Beta, and Delta variants) by one to three log orders in Calu-3 cells. Furthermore, proteomics and RNA-seq analyses indicated that most SARS-CoV-2 genes were downregulated by RK-33 treatment. Also, we show that the use of RK-33 decreases TMPRSS2 expression, which may be due to DDX3s ability to unwind G-quadraplex structures present in the TMPRSS2 promoter. The data presented supports the use of RK-33 as an HTA strategy to control SARS-CoV-2 infection, irrespective of its mutational status, in humans.
Temporal and environmental factors interact with rootstock genotype to shape leaf elemental composition in grafted grapevines
Authors: Harris Zachary N , Pratt Julia E , Bhakta Niyati , Frawley Emma , Klein Laura L. , Kwasniewski Misha T , Migicovsky Zoë , Miller Allison J
Published: March 2022

Plants take up elements through their roots and transport them to their shoot systems for use in numerous biochemical, physiological, and structural functions. Elemental composition of above-ground plant tissues, such as leaves, reflects both above- and below-ground activities of the plant genotype, as well the local environment. Perennial, grafted plants, where the root system of one individual is fused to the shoot system of a genetically distinct individual, offer a powerful experimental system in which to study the role of the root system in the elemental composition of the shoot system. We measured elemental composition of over 7000 leaves in the grapevine cultivar ‘Chambourcin’ growing ungrafted and grafted to three rootstock genotypes. Leaves were collected over multiple years and phenological stages (across the season) and along a developmental time series. Temporal components of this study had the largest effect on leaf elemental composition; and rootstock genotype interacted with year, phenological stage, and leaf age to differentially modulate leaf elemental composition. Further, the local, above-ground environment affected leaf elemental composition, an effect influenced by rootstock genotype. This work highlights the dynamic nature by which root systems interact with shoot systems to respond to temporal and environmental variation.
A BALB/c IGHV Reference Set, defined by haplotype analysis of long-read VDJ-C sequences from F1 (BALB/c / C57BL/6) mice
Authors: Jackson Katherine JL , Kos Justin T , Lees William , Gibson William S , Smith Melissa Laird , Peres Ayelet , Yaari Gur , Corcoran Martin , Busse Christian E. , Ohlin Mats , Watson Corey T , Collins Andrew M
Published: March 2022

The immunoglobulin genes of inbred mouse strains that are commonly used in models of antibody-mediated human diseases are poorly characterized. This compromises data analysis. To infer the immunoglobulin genes of BALB/c mice, we used long-read SMRT sequencing to amplify VDJ-C sequences from F1 (BALB/c x C57BL/6) hybrid animals. Previously unreported strain variations were identified in theIghmandIghg2bgenes, and analysis of VDJ rearrangements led to the inference of 278 germline IGHV alleles. 169 alleles are not present in the C57BL/6 genome reference sequence. To establish a set of expressed BALB/c IGHV germline gene sequences, we computationally retrieved IGHV haplotypes from the IgM dataset. Haplotyping led to the confirmation of 162 BALB/c IGHV gene sequences. A musIGHV398 pseudogene variant also appears to be present in the BALB/cByJ substrain, while a functional musIGHV398 gene is highly expressed in the BALB/cJ substrain. Only four of the BALB/c alleles were also observed in the C57BL/6 haplotype. The full set of inferred BALB/c sequences has been used to establish a BALB/c IGHV reference set, hosted athttps://ogrdb.airr-community.org. We assessed whether assemblies from the Mouse Genome Project (MGP) are suitable for the determination of the genes of the IGH loci. Only 37 (43.5%) of the 85 confirmed IMGT-named BALB/c IGHV and 33 (42.9%) of the 77 confirmed non-IMGT IGHV were found in a search of the MGP BALB/cJ genome assembly. This suggests that Adaptive Immune Receptor Repertoire sequencing (AIRR-Seq) data, but not currently-available genome assemblies, are suited to the documentation of germline IGHV genes.
ATM modulates nuclear mechanics by regulating lamin A levels
Authors: Shah Pragya , McGuigan Connor W. , Cheng Svea , Vanpouille-Box Claire , Demaria Sandra , Weiss Robert S. , Lammerding Jan
Published: March 2022

Ataxia-telangiectasia mutated (ATM) is one of the three main apical kinases at the crux of DNA damage response and repair in mammalian cells. ATM activates a cascade of downstream effector proteins to regulate DNA repair and cell cycle checkpoints in response to DNA double-strand breaks. While ATM is predominantly known for its role in DNA damage response and repair, new roles of ATM have recently begun to emerge, such as in regulating oxidative stress or metabolic pathways. Here, we report the surprising discovery that ATM inhibition and deletion lead to reduced expression of the nuclear envelope protein lamin A. Lamins are nuclear intermediate filaments that modulate nuclear shape, structure, and stiffness. Accordingly, inhibition or deletion of ATM resulted in increased nuclear deformability and enhanced cell migration through confined spaces, which requires substantial nuclear deformation. These findings point to a novel connection between ATM and lamin A and may have broad implications for cells with ATM mutations—as found in patients suffering from Ataxia Telangiectasia and many human cancers—which could lead to enhanced cell migration and increased metastatic potential.
Novel QTLs for cucumber resistance to two Colletotrichum orbiculare strains of different pathogenic races
Authors: Matsuo Hiroki , Isobe Sachiko , Shirasawa Kenta , Yoshioka Yosuke
Published: March 2022

Colletotrichum orbiculare is a hemibiotrophic fungal pathogen that causes anthracnose disease in cucumber (Cucumis sativus L.) and other cucurbit crops. The cucumber accession Ban Kyuri (G100) has a high level of resistance to anthracnose and is considered to be promising breeding material. Here, we report genetic mapping of loci from this cultivar that confer resistance to 104-T and CcM-1 of C. orbiculare that belong to pathogenic races 0 and 1, respectively. Quantitative trait locus (QTL) analysis based on phenotypic data from 196 F2:3 families detected one major QTL, An5, and one minor QTL, An6.2, for resistance to race 0, and one major QTL, An2, and three minor QTLs (An1.1, An1.2 and An6.1) for resistance to race 1. We identified lysM domain receptor-like kinase 3 (CsaV3_5G036150) and wall-associated receptor kinase-like (CsaV3_6G048820) as candidate genes for An5 and An6.2, respectively. Multiple genes encoding pattern recognition receptors were located in the regions of the QTLs conferring resistance to race 1. Thus, we identified potential sources of genetic resistance to different pathogenic races of C. orbiculare in the Ban Kyuri cultivar of cucumber.

Key message

Quantitative trait locus analysis identified independent novel loci in cucumber responsible for resistance to races 0 and 1 of the anthracnose fungal pathogen Colletotrichum orbiculare.
Isolation of a potently neutralizing and protective human monoclonal antibody targeting yellow fever virus
Authors: Doyle Michael P. , Genualdi Joseph R. , Bailey Adam L. , Kose Nurgun , Gainza Christopher , Rodriguez Jessica , Reeder Kristen M. , Nelson Christopher A. , Jethva Prashant N. , Sutton Rachel E. , Bombardi Robin G. , Gross Michael L. , Julander Justin G. , Fremont Daved H. , Diamond Michael S. , Crowe James E.
Published: March 2022

Yellow fever virus (YFV) causes sporadic outbreaks of infection in South America and sub-Saharan Africa. While live-attenuated yellow fever virus vaccines based on three substrains of 17D are considered some of the most effective vaccines in use, problems with production and distribution have created large populations of unvaccinated, vulnerable individuals in endemic areas. To date, specific antiviral therapeutics have not been licensed for human use against YFV or any other related flavivirus. Recent advances in monoclonal antibody (mAb) technology have allowed for identification of numerous candidate therapeutics targeting highly pathogenic viruses, including many flaviviruses. Here, we sought to identify a highly neutralizing antibody targeting YFV envelope (E) protein as a therapeutic candidate. We used human B cell hybridoma technology to isolate mAbs from the circulating memory B cells from human YFV vaccine recipients. These antibodies bound to recombinant YFV E protein and recognized at least five major antigenic sites on E. Two mAbs (designated YFV-136 and YFV-121) recognized a shared antigenic site and neutralized the YFV 17D vaccine strainin vitro. YFV-136 also potently inhibited infection by multiple wild-type YFV strains, in part, at a post-attachment step in the virus replication cycle. YFV-136 showed therapeutic protection in two animal models of YFV challenge including hamsters and immunocompromised mice engrafted with human hepatocytes. These studies define features of the antigenic landscape on YFV E protein recognized by the human B cell response and identify a therapeutic antibody candidate that inhibits infection and disease caused by highly virulent strains of YFV.
Assessing the transportability of clinical prediction models for cognitive impairment using causal models
Authors: Fehr Jana , Piccininni Marco , Kurth Tobias , Konigorski Stefan ,   the Alzheimer’s Disease Neuroimaging Initiative
Published: March 2022

Background

Machine learning models promise to support diagnostic predictions, but may not perform well in new settings. Selecting the best model for a new setting without available data is challenging. We aimed to investigate the transportability by calibration and discrimination of prediction models for cognitive impairment in simulated external settings with different distributions of demographic and clinical characteristics.

Methods

We mapped and quantified relationships between variables associated with cognitive impairment using causal graphs, structural equation models, and data from the ADNI study. These estimates were then used to generate datasets and evaluate prediction models with different sets of predictors. We measured transportability to external settings under guided interventions on age, APOE ε4, and tau-protein, using differences between internal and external settings measured by calibration metrics and area under the receiver operating curve (AUC).

Results

Calibration differences indicated that models predicting with causes of the outcome were more transportable than those predicting with consequences. AUC differences indicated inconsistent trends of transportability between the different external settings. Models predicting with consequences tended to show higher AUC in the external settings compared to internal settings, while models with parents or all variables showed similar AUC.

Conclusions

We demonstrated with a practical prediction task example that predicting with causes of the outcome results in better transportability compared to anti-causal predictions measured by calibration differences. We conclude that calibration differences are more suitable than AUC differences to assess model transportability to external settings.
In vitro Characterization of SARS-CoV-2 Protein Translated from the Moderna mRNA-1273 Vaccine
Authors: Veenstra Timothy D. , Pauley Brad , Injeti Elisha , Rotello Rocco J.
Published: March 2022

Extensive research around mRNA vaccines and their proposed utility during the current COVID-19 pandemic resulted in many publications concerning the SARS-Cov-2 spike protein and angiotensin converting enzyme-2 receptor-binding domain of the virus, but none describe the characteristics of the full-length protein obtained from the modified/synthetic mRNA that is part of the Moderna and Pfizer-BioNTech vaccines. In this paper, we provide the first data characterizing the actual proteins produced by mouse and human cells in culture that had been incubated up to 30 minutes with the commercial vaccine produced by Moderna (i.e., Spikevax). The mRNA vaccine continues to produce proteins up to 12-14 days after introduction to the cells. The molecular weight of the SARS-CoV-2 encoded protein ranges from 135-200 kilodaltons depending on the extent of glycosylation.
Fine-scale variation in the effect of national border on COVID-19 spread: A case study of the Saxon-Czech border region
Authors: Mertel Adam , Vyskočil Jiří , Schüler Lennart , Schlechte-Wełnicz Weronika , Calabrese Justin M.
Published: March 2022

The global extent and temporally asynchronous pattern of COVID-19 spread have repeatedly highlighted the role of international borders in the fight against the pandemic. Additionally, the deluge of high resolution, spatially referenced epidemiological data generated by the pandemic provides new opportunities to study disease transmission at heretofore inaccessible scales. Existing studies of cross-border infection fluxes, for both COVID-19 and other diseases, have largely focused on characterizing overall border effects. Here, we couple fine-scale incidence data with localized regression models to quantify spatial variation in the inhibitory effect of an international border. We take as a case study the border region between the German state of Saxony and the neighboring regions in northwestern Czechia, where municipality-level COVID-19 incidence data are available on both sides of the border. Consistent with past studies, we find an overall inhibitory effect of the border, but with a clear asymmetry, where the inhibitory effect is stronger from Saxony to Czechia than vice versa. Furthermore, we identify marked spatial variation along the border in the degree to which disease spread was inhibited. In particular, the area around Löbau in Saxony appears to have been a hotspot for cross-border disease transmission. The ability to identify infection flux hotspots along international borders may help to tailor monitoring programs and response measures to more effectively limit disease spread.
Dual Guidance in Regional Anesthesia – Influence of Needle Electrode Configuration on Stimulation Success at Sciatic Nerve; A Randomized, Controlled Pilot Trial
Authors: Wegner Julia , Ertmer Martin , Tafelski Sascha , Klotz Edda , Birnbaum Jürgen
Published: March 2022

Introduction

In contrast to ultrasound technology (US), peripheral nerve stimulation (PNS) for regional anesthesia was little improved in recent years. When using the combination of both techniques, PNS can give additional information for nerve localization to improve safety and success of regional anesthesia. There are influencing factors on the success rate of stimulation in PNS remaining uninvestigated in a clinical setting to date. This randomized controlled pilot trial evaluates the impact of shape and size of stimulation needles electrodes under dual guidance conditions.

Methods

In a randomized controlled clinical trial 35 participants undergoing lower limb surgery received a preoperative proximal sciatic nerve block in dual guidance technique. Use of facet needles with point shaped electrodes (N=19, facet group) were compared with tuohy needles with large electroconductive tips (N=16, touhy group). Stimulation success at minimal distance between needle tip and nerve was recorded. Block success and complications of regional anesthesia were assessed.

Results

In 87% of successful stimulation (20 of 23) an ultrasound-proven contact of needle tip and sciatic nerve was necessary to elicit a motor response. More successful stimulations could performed using facet needles (84%, 16/19) compared to tuohy needles (44%, 7/16, p=0.03). If stimulation was successful the number of successful sensory blockades was increased (78%, 18/23, p=0.02). No serious complications of regional anesthesia were recorded.

Discussion

This pilot trial suggests that stimulation needles with small electrodes may be more reliable in indicating a contact of needle and nerve, which may improve safety and success of proximal sciatic nerve blocks.
No impact of sex on surgical site infections in abdominal surgery: A multi-center study
Authors: Zwicky Simone Nora , Gloor Severin , Tschan Franziska , Candinas Daniel , Demartines Nicolas , Weber Markus , Beldi Guido
Published: March 2022

Objective

Male sex is controversially discussed as a risk factor for surgical site infections (SSI). The aim of the present study was to evaluate the impact of sex on SSI in abdominal surgery under elimination of relevant confounders.

Methods

Clinicopathological data of 6603 patients undergoing abdominal surgery from a multi-center prospective database of four Swiss hospitals including patients between 2015 and 2018 were assessed. Patients were stratified according to postoperative SSI and risk factors for SSI were assessed using univariate and multivariate analysis.

Results

In 649 of 6603 patients SSI was reported (9.8%). SSI was significantly associated with reoperation (22.7% vs. 3.4%, p <0.001), higher mortality rate (4.6% vs. 0.9%, p <0.001) and higher rate of length of hospital stay over the 75th percentile (57.0 % vs. 17.9 %, p <0.001). In univariate analysis male sex was a significant risk factor for SSI (p = 0.01). In multivariate analysis including multiple confounders ‘ such as comorbidities and perioperative factors there was no association between male sex and risk of SSI (odds ratio (OR) 1.1 [CI 0.8 – 1.4]). Independent risk factors for SSI in multivariate analysis were BMI ≥ 30 kg/m2 (OR 1.8 [CI 1.3 - 2.3]), duration of surgery > 75th percentile (OR 2.3 [1.8 - 2.9]), high contamination level (OR 1.3 [1.0 – 1.6]), laparotomy (OR 1.3 [1.0 – 1.7]), pervious laparotomy (OR 1.4 [1.1 – 1.7]), blood transfusion (OR 1.7 [1.2 – 2.4]), cancer (OR 1.3 [1.0-1.8], malnutrition (OR 2.5 [1.8 – 3.4]).

Conclusion

Under elimination of relevant confounders there is no significant correlation between sex and risk of SSI after abdominal surgery.
Comparing Waves of COVID-19 in the US: Scale of response changes over time
Authors: Richards Robert L. , Foster Grant , Elderd Bret D. , Dallas Tad A.
Published: March 2022

Local response to the SARS-CoV-2 pandemic differed spatially across the United States but the drivers of this spatial variation remain unclear. We approach this open question by studying the relationship between the growth rate of subsequent waves of the pandemic at the county level during the first year of the pandemic, asking whether state or county demographics better explain variation in this relationship. We found clear spatiotemporal patterns in the relationship between the slopes of subsequent waves in a given county. Generally the standardized difference between the growth rates of waves 1 and 2 and waves 2 and 3 were strongly positively correlated over short distances and shifted to a weak negative correlation at intermediate distances. We also found that peer county health group (a categorization of counties by demographic information relevant to public health) explained variation in response better between wave 1 and 2, while state identity was most important between wave 2 and 3. Taken together, we suggest that there are identifiable spatial patterns in pandemic response across the US but that the nature of these patterns change over the course of the pandemic.
MemBrain: A Deep Learning-aided Pipeline for Automated Detection of Membrane Proteins in Cryo-electron Tomograms
Authors: Lamm Lorenz , Righetto Ricardo D. , Wietrzynski Wojciech , Pöge Matthias , Martinez-Sanchez Antonio , Peng Tingying , Engel Benjamin D.
Published: March 2022

Background and Objective

Cryo-electron tomography (cryo-ET) is an imaging technique that enables 3D visualization of the native cellular environment at sub-nanometer resolution, providing unpreceded insights into the molecular organization of cells. However, cryo-electron tomograms suffer from low signal-to-noise ratios and anisotropic resolution, which makes subsequent image analysis challenging. In particular, the automated detection of membrane-embedded proteins is a problem still lacking satisfactory solutions.

Methods

We present MemBrain – a new deep learning-based pipeline that automatically detects membrane-bound protein complexes in cryo-electron tomograms. After subvolumes are sampled along a segmented membrane, each subvolume is assigned a score using a convolutional neural network (CNN), and protein positions are extracted by a clustering algorithm. Incorporating rotational subvolume normalization and using a tiny receptive field simplify the task of protein detection and thus facilitate the network training.

Results

MemBrain requires only a small quantity of training labels and achieves excellent performance with only a single annotated membrane (F1 score: 0.88). A detailed evaluation shows that our fully trained pipeline outperforms existing classical computer vision-based and CNN-based approaches by a large margin (F1 score: 0.92 vs. max. 0.63). Furthermore, in addition to protein center positions, MemBrain can determine protein orientations, which has not been implemented by any existing CNN-based method to date. We also show that a pre-trained MemBrain program generalizes to tomograms acquired using different cryo-ET methods and depicting different types of cells.

Conclusions

MemBrain is a powerful and label-efficient tool for the detection of membrane protein complexes in cryo-ET data, with the potential to be used in a wide range of biological studies. It is generalizable to various kinds of tomograms, making it possible to use pretrained models for different tasks. Its efficiency in terms of required annotations also allows rapid training and fine-tuning of models. The corresponding code, pretrained models, and instructions for operating the MemBrain program can be found at: https://github.com/CellArchLab/MemBrain
Two Interaction Surfaces between XPA and RPA Organize the Preincision Complex in Nucleotide Excision Repair
Authors: Kim Mihyun , Kim Hyun Suk , D’Souza Areetha , Gallagher Kaitlyn , Jeong Eunwoo , Topolska-Wos Agnieszka , Le Meur Kateryna Ogorodnik , Tsai Chi-Lin , Tsai Miaw-Sheue , Kee Minyong , Tainer John A. , Yeo Jung-Eun , Chazin Walter J. , Schärer Orlando D.
Published: March 2022

The XPA and RPA proteins fulfill essential roles in the assembly of the preincision complex in the nucleotide excision repair pathway. We have previously characterized the two interaction surfaces between XPA and RPA, with the RPA32 and RPA70AB subunits. Here we show that the mutations in the two individual interaction surfaces reduce NER activity in biochemical and cellular systems, and that combining mutations in two domains leads to an additive inhibition of NER, suggesting that they fulfill distinct roles. Our data suggest that the interaction between XPA and RPA32 is important for the initial association of XPA with NER complexes, while the interaction between XPA and RPA70 is needed for structural organization of the complex to license the dual incision reaction. SAXS analysis of complexes of XPA and RPA bound to ss/dsDNA junction substrates reveals the architecture of XPA and RPA in the preincision complex and shows that the two interaction domains between RPA and XPA are located at opposite sides of the two molecules. We propose a structure for the overall NER preincision complex that shows that the two strands of the NER bubble assume a U-shape with the two ss/dsDNA junctions localized in close proximity, with the interaction between XPA and RPA70 as one of the key organizing elements.