bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrated 18F-FDG PET/CT parameter defines metabolic oligometastatic non-small cell lung cancer
Authors: Ma Rong , Zhao Qian , Zhao Ren , Li Juan , Wang Yan-Yang
Published: June 2022

Aims

The purpose of this study was to define metabolic oligometastatic non-small cell lung cancer (NSCLC) by using the number of metastatic lesions and 18F-FDG PET/CT parameters.

Methods

One hundred twenty-four newly diagnosed stage IV NSCLC patients who received pretreatment 18F-FDG PET/CT examination were retrospectively analyzed. The maximum standardized uptake value (SUVmax) of primary and metastatic lesions and the collected clinical parameters were fed into the univariate and multivariate Cox proportional hazard model. Survival analysis was performed using Kaplan–Meier and log-rank test.

Results

In univariate analysis, the results revealed that histology, metastatic organ numbers, adrenal gland metastasis, SUVmax of both primary and metastatic lesions, lactate dehydrogenase, systemic treatment, and local treatment were significantly correlated with overall survival of stage IV NSCLC patients. Multivariate analysis demonstrated that SUVmax of primary lesions and systemic treatment were independent risk factors of stage IV NSCLC patients. The addition of primary lung cancer SUVmax to traditional method (only count the numbers of metastasis lesions) enhanced the identification of oligometastatic NSCLC and the C-index increased from 0.601 to 0.693.

Conclusion

We developed a method for the definition of metabolic oligometastatic NSCLC, which combined the number of organs involved, the number of metastatic lesions, and the SUVmax of primary lung cancer.
Clinical effect of pulmonary rehabilitation combined with diaphragm pacemaker therapy in the treatment of severely ill patients with mechanical ventilation
Authors: Liu Zi-Bo , Wang Lu-yi , Zhao Long , Pang Ya-Tao , Liu Yan-song , Xu Wei , Li Hong-Ling
Published: June 2022

To investigate the effect of pulmonary rehabilitation combined with diaphragm pacemaker therapy on the diaphragm function of severely ill patients on mechanical ventilation. Forty patients were randomly divided into the control group (CG; n = 20) and experimental group (EG; n = 20). The CG was given basic ICU nursing and conventional rehabilitation treatment. The EG added a diaphragm pacemaker and pulmonary rehabilitation therapies along with basic ICU nursing and conventional rehabilitation treatment. The relevant indexes were compared at baseline and postintervention, including the Glasgow Coma Scale (GCS), Acute Physiology, Chronic Health Evaluation II (APACHE II) scores, diaphragm mobility and thickness. The indexes of mechanical ventilation time, ICU and total hospital stays were compared between the two groups. There was no difference in the GCS and APACHE II scores, and diaphragm mobility and thickness between the two groups before treatment (P > 0.05). After 30 days of treatment, the GCS scores increased in both groups, the APACHE II scores decreased significantly, and diaphragm mobility and thickness decreased compared with before treatment (P < 0.05), but the improvement of each index in the EG was more evident than in the CG. Compared with the CG, the indexes of the EG, including offline, ICU and total hospitalization times, were significantly shorter (P < 0.05). Additionally, there were no adverse events such as accidental tube detachment or falling out of bed during treatment. Pulmonary rehabilitation combined with a diaphragm pacemaker is safe and effective in treating severely ill mechanically ventilated patients.
Comparison of plantar pressure distribution in underweight, normal, overweight, and obese adolescents: A cross-sectional study evaluation of plantar pressure in adolescents
Authors: Yıldırım Şahan Tezel , Türker Duygu , Söyler Osman
Published: June 2022

Background:

Repeated overload by body weight in the adolescents affects the foot structure.

Objective:

This study aimed to evaluate plantar pressure distribution in adolescents with different body mass indices during gait and standing.

Study design:

This is a randomized, cross-sectional study.

Methods:

One hundred eighty-six adolescents between the ages of 8 and 15 years were included. The individuals were divided into groups according to body mass index (BMI). Plantar pressure distributions were examined during gait and standing. Surface areas, plantar pressures, forefoot-hindfoot load, surface amounts, and foot angles of the individuals were determined during gait and standing.

Results:

Significant differences were detected in left-right surfaces, maximum load quantities, average pressures, forefoot-hindfoot surface areas between static and dynamic plantar pressure distributions of underweight, normal, overweight, and obese adolescents (P < 001). Maximum, average pressure, right forefoot foot load, and foot angles increased in the obese group during standing as BMI increased; total surface areas, and loads in forefoot, hindfoot surface areas in right and left feet also increased in maximum and average pressures during gait (P < .05). No differences were detected between groups in foot angles during standing and gait (P > .05).

Conclusions:

This study show that increased BMI causes increased plantar pressures during gait and standing, and weight gain would cause problems in adolescents.
Assessment of Fat Fractions in the Tongue, Soft Palate, Pharyngeal Wall, and Parapharyngeal Fat Pad by the GOOSE and DIXON Methods
Authors: Song Ruitian , Hwang Scott N. , Goode Chris , Storment Diana , Scoggins Matthew , Abramson Zachary , Hillenbrand Claudia M. , Mandrell Belinda , Krull Kevin , Reddick Wilburn E.
Published: June 2022

Objective

The 2-point DIXON method is widely used to assess fat fractions (FFs) in magnetic resonance images (MRIs) of the tongue, pharyngeal wall, and surrounding tissues in patients with obstructive sleep apnea (OSA). However, the method is semiquantitative and is susceptible to B0 field inhomogeneities and R2* confounding factors. Using the method, although several studies have shown that patients with OSA have increased fat deposition around the pharyngeal cavity, conflicting findings was also reported in 1 study. This discrepancy necessitates that we examine the FF estimation method used in the earlier studies and seek a more accurate method to measure FFs.

Materials and Methods

We examined the advantages of using the GOOSE (globally optimal surface estimation) method to replace the 2-point DIXON method for quantifying fat in the tongue and surrounding tissues on MRIs. We first used phantoms with known FFs (true FFs) to validate the GOOSE method and examine the errors in the DIXON method. Then, we compared the 2 methods in the tongue, soft palate, pharyngeal wall, and parapharyngeal fat pad of 63 healthy participants to further assess the errors caused by the DIXON method. Six participants were excluded from the comparison of the tongue FFs because of technical failures. Paired Student t tests were performed on FFs to detect significant differences between the 2 methods. All measures were obtained using 3 T Siemens MRI scanners.

Results

In the phantoms, the FFs measured by GOOSE agreed with the true FF, with only a 1.2% mean absolute error. However, the same measure by DIXON had a 10.5% mean absolute error. The FFs obtained by DIXON were significantly lower than those obtained by GOOSE (P < 0.0001) in the human participants. We found strong correlations between GOOSE and DIXON in the tongue (R
2 = 0.90), soft palate (R
2 = 0.66), and parapharyngeal fat pad (R
2 = 0.88), but the correlation was weaker in the posterior pharyngeal walls (R
2 = 0.32) in participants.

Conclusions

The widely used 2-point DIXON underestimated FFs, relative to GOOSE, in phantom measurements and tissues studied in vivo. Thus, an advanced method, such as GOOSE, that uses multiecho complex data is preferred for estimating FF.
Blastococcus tunisiensis sp. nov., isolated from limestone collected in Tunisia
Authors: Louati Moussa , Hezbri Karima , Montero-Calasanz Maria del Carmen , Rohde Manfred , Göker Markus , Ghodhbane-Gtari Faten , Klenk Hans-Peter , Nouioui Imen , Gtari Maher
Published: June 2022

A new actinobacterium strain, designated BMG 823T, was isolated from a limestone sample collected in Tunisia. Its taxonomic position was scrutinized using a polyphasic approach. Colonies of strain BMG 823T were pink orange-coloured, regular and had a moist surface. Cells are Gram-stain-positive, catalase-negative and oxidase-negative. The strain grew at pH 5.5–9, 10–40 °C and in presence of up to 4 % NaCl (w/v). Chemotaxonomically, strain BMG 823T was characterized by cell-wall type III containing meso-diaminopimelic acid as diamino acid, glucose, ribose and rhamnose as whole-cell sugars, MK-9(H4) as predominant menaquinone, and phosphatidylcholine, diphosphadidylglycerol, phosphatidethanolamine, phosphatidylcholine, phosphatidylinositol, unidentified glycolipid, unidentified aminophospholipids and unidentified glycophospholipid as major polar lipids. The fatty acid profile consisted of iso-C16 : 0 and iso-C17 : 1
 ω9. Phylogenetic trees based on 16S rRNA gene and genome sequences placed strain BMG 823T within the genus

Blastococcus

and separated it from all type strains of validly published species. Comparison of 16S rRNA gene sequence similarity, digital DNA–DNA hybridization and average nucleotide identity indicated that strain BMG 823T was most closely related to

Blastococcus litoris

DSM 106127T and

Blastococcus colisei

BMG 822T with pairwise values well below the species differentiation thresholds. The distinct phenotypic and genotypic features of strain BMG 823T (=DSM 46838T=CECT 8881T) within the genus

Blastococcus

warrant its recognition as the type strain for the new species for which we propose the name Blastococcus tunisiensis sp. nov.
On the biological constraints that limit the productivity of rain-fed annual crops
Authors: Kan Iddo , Tsur Yacov , Moshelion Menachem
Published: June 2022

Efforts to cope with hunger by breeding highly productive annual crops for rain-fed agriculture in stochastic-rainfall environments have had only minor success, which we attribute to biological constraints that limit the crops’ yields. We use optimization modelling to interpret experimentally measured transpiration trajectories of wild barley plants following a rain event: the plants first maximized biomass accumulation by employing their maximal transpiration rate, then switched to their minimal transpiration rate to ensure survival until maturity. Thus, breeding plants with lower minimal transpiration rates combined with higher water-use efficiency and maximal transpiration rates could increase expected yields. However, our experimental results indicate that biological constraints impose tradeoffs among maximal and minimal transpiration rates and water-use efficiency. A proposed breeding methodology identifies less biologically constrained cultivar candidates.
A Highly Selective Response to Food in Human Visual Cortex Revealed by Hypothesis-Free Voxel Decomposition
Authors: Khosla Meenakshi , Murty N Apurva Ratan , Kanwisher Nancy
Published: June 2022

Prior work has identified cortical regions selectively responsive to specific categories of visual stimuli. However, this hypothesis-driven work cannot reveal how prominent these category selectivities are in the overall functional organization of visual cortex, or what others might exist that scientists have not thought to look for. Further, standard voxel-wise tests cannot detect distinct neural selectivities that coexist within voxels. To overcome these limitations, we used data-driven voxel decomposition methods to identify the main components underlying fMRI responses to thousands of complex photographic images (Allen et al 2021). Our hypothesis-neutral analysis rediscovered components selective for faces, places, bodies, and words, validating our method and showing that these selectivities are dominant features of the ventral visual pathway. The analysis also revealed an unexpected component with a distinct anatomical distribution that responded highly selectively to images of food. Alternative accounts based on low to mid-level visual features like color, shape or texture failed to account for the food selectivity of this component. High-throughput testing and control experiments with matched stimuli on a highly accurate computational model of this component confirm its selectivity for food. We registered our methods and hypotheses before replicating them on held-out participants and in a novel dataset. These findings demonstrate the power of data-driven methods, and show that the dominant neural responses of the ventral visual pathway include not only selectivities for faces, scenes, bodies, and words, but also the visually heterogeneous category of food, thus constraining accounts of when and why functional specialization arises in the cortex.
The effects of conscious movement processing on the neuromuscular control of posture
Authors: Jie Li-Juan , Kal Elmar , Ellmers Toby J. , Rosier Joëlle , Meijer Kenneth , Boonstra Tjeerd
Published: June 2022

Maintaining balance is thought to primarily occur sub-consciously. Occasionally, however, individuals will direct conscious attention towards balance, e.g., in response to a threat to balance. Such conscious movement processing (CMP) increases the reliance on attentional resources and may disrupt balance performance. However, the underlying changes in neuromuscular control remain poorly understood. We investigated the effects of CMP (manipulated using verbal instructions) on neural control of posture in twenty-five adults (11 females, mean age = 23.9, range = 18–33). Participants performed 90-second, bipedal stance balance trials in high- and low-CMP conditions, during both stable (solid surface) and unstable (foam) task conditions. Postural sway amplitude, frequency and complexity were used to assess postural control. Surface EMG was recorded bilaterally from lower leg muscles (Soleus, Tibialis Anterior, Gastrocnemius Medialis, Peroneus Longus) and intermuscular coherence (IMC) was assessed for 12 muscle pairs across four frequency bands. We observed significantly increased sway amplitude, and decreased sway frequency and complexity in the high- compared to the low-CMP conditions. All sway variables increased in the unstable compared to the stable conditions. We observed reduced beta band IMC between several muscle pairs during high- compared to low-CMP, but these findings did not remain significant after controlling for multiple comparisons. Finally, IMC significantly increased in the unstable conditions for most muscle combinations and frequency bands. In all, results tentatively suggest that CMP-induced changes in sway outcomes may be facilitated by reduced beta-band IMC, but these findings need to be replicated before they can be interpreted more conclusively.
An α-π transition in S6 shapes the conformational cycle of the bacterial sodium channel NavAb
Authors: Choudhury Koushik , Howard Rebecca J , Delemotte Lucie
Published: June 2022

Voltage gated sodium channels play an important role in electrical signaling in excitable cells. In response to changes in membrane potential, they cycle between nonconducting and conducting conformations. With recent advances in structural biology, structures of sodium channels have been captured in several distinct conformations, thought to represent different functional states. However, it has been difficult to capture the intrinsically transient open state. We recently showed that a proposed open state of the bacterial sodium channel NavMs was not conductive, and that a conformational change involving a transition to aπhelix in the pore-lining S6 helix converted this structure into a conducting state. However, the relevance of this structural feature in other sodium channels, and its implications for the broader gating cycle, remained unclear. Here, we propose a comparable open state of another class of bacterial channel fromAliarcobacter butzleri(NavAb), with characteristic pore hydration, ion permeation and drug binding properties. Furthermore, we show that aπ-helix transition can lead to pore opening, and that such a conformational change blocks fenestrations in the inner helix bundle. We also discover that a region in the C-terminal domain can undergo a disordering transition proposed to be important for pore opening. These results support a role for aπ-helix transition in the opening of NavAb, enabling new proposals for the structural annotation and drug modulation mechanisms in this important model sodium channel.
Predictive model of transcriptional elongation control identifies trans regulatory factors from chromatin signatures
Authors: Akcan Toray S. , Heinig Matthias
Published: June 2022

Promoter-proximal Polymerase II (Pol II) pausing is a key rate limiting step for gene expression. DNA and RNA-binding trans-acting factors regulating the extent of pausing have been identified. However, we lack a quantitative model of how interactions of these factors determine pausing, therefore the relative importance of implicated factors is unknown. Moreover, previously unknown regulators might exist. Here we address this gap with a machine learning model that accurately predicts the extent of promoter proximal Pol II pausing from large scale genome and transcriptome binding maps, as well as gene annotation and sequence composition features. We demonstrate high accuracy and generalizability of the model by validation on an independent cell line which reveals the model’s cell line agnostic character. Model interpretation in light of prior knowledge about molecular functions of regulatory factors confirms the interconnection of pausing with other RNA processing steps. Harnessing underlying feature contributions we assess the relative importance of each factor, quantify their predictive effects and systematically identify previously unknown regulators of pausing. We additionally identify 16 previously unknown 7SK ncRNA interacting RNA-binding proteins predictive of pausing. Our work provides a framework to further our understanding of the regulation of the critical early steps in transcriptional elongation.

Key Points: Please provide 3 bullet points summarizing the manuscript’s contribution to the field

-

ML model that accurately predicts promoter proximal Pol II pausing from ChIP and eClip-seq data

-

Quantification of the interconnection of pausing and other steps of gene regulation

-

Identification of novel putative trans regulators of pausing

GRAPHICAL ABSTRACT
Metabolic traits and the niche of bulk soil bacteria in a Mediterranean grassland
Authors: Zhalnina Kateryna , White Richard Allen , de Raad Markus , Deng Kai , Nicora Carrie D. , Karaoz Ulas , Pett-Ridge Jennifer , Firestone Mary K. , Lipton Mary S. , Northen Trent R. , Brodie Eoin L.
Published: June 2022

Soil microorganisms have adapted to compete and exploit different metabolic niches in their physically and chemically diverse environment via evolution and acquisition of distinct physiological and biochemical traits. As the interface for most carbon and nutrient exchange between plants and microorganisms, the rhizosphere has received substantial attention. By comparison, what is commonly termed bulk-soil (soil free of living roots) represents a far greater volume and surface area throughout the season, and substantially higher taxonomic and phylogenetic diversity; the traits and activity of its inhabitants may also have a significant impact on overall soil function. We used a combination of comparative genomics and exoproteomics to identify metabolic traits of bacteria adapted to life in bulk soil and compared these with traits of bacteria living in the rhizosphere of wild oat, Avena barbata. In bulk soil bacteria, we observed: (i) greater investment in extracellular polymer-degrading enzyme production; (ii) greater potential for secretion (presence of signal peptides) of polymer-degrading enzymes; (iii) production of accessory proteins (carbohydrate binding modules) fused with glycoside hydrolases that enhance substrate affinity, stabilize, and increase reaction rates of polymer degrading enzymes; and (iv) organization of polymer degradation machinery within gene clusters that facilitate co-transcription of enzymes, transcription factors and transporters for polymer depolymerization products. Together, these findings suggest that unlike rhizosphere-adapted bacteria—which specialize on small molecules released primarily as root exudates—bulk soil-adapted bacteria have evolved to exploit plant polymers. This biochemically costly strategy may be mitigated by protein-level adaptations that enhance the efficiency of extracellular enzyme-mediated substrate acquisition.

IMPORTANCE

Plant-soil-microbe interactions are dynamic and complex, with significant implications for ecosystem functioning. Microbial traits, such as nutrient acquisition and growth yield, combined with soil and climate parameters, impact major biogeochemical processes and can define the future fate of soil carbon. Diverse soil microorganisms occupy different physical habitats within soil and exploit distinct niches by expressing different metabolic traits. Identifying and quantifying traits that underlie their fitness and function is key for understanding and predicting how soil carbon transformation and stabilization will change in the future or can be managed through intervention.
Supercharged Protein Nanosheets for Cell Expansion on Bioemulsions
Authors: Chrysanthou Alexandra , Kanso Hassan , Zhong Wencheng , Shang Li , Gautrot Julien E.
Published: June 2022

Cell culture at liquid-liquid interfaces, for example at the surface of oil microdroplets, is an attractive strategy to scale up adherent cell manufacturing whilst replacing the use of microplastics. Such process requires the adhesion of cells at interfaces stabilized and reinforced by protein nanosheets displaying high elasticity, but also presenting cell adhesive ligands able to bind integrin receptors. In this report, supercharged albumins are found to form strong elastic protein nanosheets and mediate extracellular matrix (ECM) protein adsorption and cell adhesion. The interfacial mechanical properties and elasticity of supercharged nanosheets is characterized by interfacial rheology and behaviors are compared to those of native bovine serum albumin, human serum albumin and α-lactalbumin. ECM protein adsorption to resulting supercharged nanosheets is then quantified via surface plasmon resonance and fluorescence microscopy, demonstrating the dual role supercharged albumins are proposed to play, as scaffold proteins structuring liquid-liquid interfaces and substrates for the capture of ECM molecules. Finally, the adhesion and proliferation of primary human epidermal stem cells is investigated, at pinned droplets, as well as on bioemulsions stabilized by corresponding supercharged nanosheets. This study demonstrates the potential of supercharged proteins for the engineering of biointerfaces for stem cell manufacturing, and draws structure-property relationships that will guide further engineering of associated systems.
New, fast, and precise method of COVID-19 detection in nasopharyngeal and tracheal aspirate samples combining optical spectroscopy and machine learning
Authors: Ceccon Denny M. , Amaral Paulo Henrique R. , Lídia M. Andrade , da Silva Maria I. N. , Andrade Luis A. F. , Moraes Thais F.S. , Bagno Flavia F , Rocha Raissa P. , de Almeida Marques Daisymara Priscila , Ferreira Geovane Marques , Lourenço Alice Aparecida , Ribeiro Ágata Lopes , Coelho-dos-Reis Jordana G. A. , da Fonseca Flavio G. , Gonzalez J. C.
Published: June 2022

Fast, precise, and low-cost diagnostic testing to identify persons infected with SARS– CoV-2 virus is pivotal to control the global pandemic of COVID-19 that began in late 2019. The gold standard method of diagnostic recommended is the RT-qPCR test. However, this method is not universally available, and is time-consuming and requires specialized personnel, as well as sophisticated laboratories. Currently, machine learning is a useful predictive tool for biomedical applications, being able to classify data from diverse nature. Relying on the artificial intelligence learning process, spectroscopic data from nasopharyngeal swab and tracheal aspirate samples can be used to leverage characteristic patterns and nuances in healthy and infected body fluids, which allows to identify infection regardless of symptoms or any other clinical or laboratorial tests. Hence, when new measurements are performed on samples of unknown status and the corresponding data is submitted to such an algorithm, it will be possible to predict whether the source individual is infected or not. This work presents a new methodology for rapid and precise label-free diagnosing of SARS-CoV-2 infection in clinical samples, which combines spectroscopic data acquisition and analysis via artificial intelligence algorithms. Our results show an accuracy of 85% for detection of SARS-CoV-2 in nasopharyngeal swab samples collected from asymptomatic patients or with mild symptoms, as well as an accuracy of 97% in tracheal aspirate samples collected from critically ill COVID-19 patients under mechanical ventilation. Moreover, the acquisition and processing of the information is fast, simple, and cheaper than traditional approaches, suggesting this methodology as a promising tool for biomedical diagnosis vis-à-vis the emerging and re-emerging viral SARS-CoV-2 variant threats in the future.
What Do Child Abuse and Neglect Medical Evaluation Consultation Notes Tell Us?
Authors: Golonka Megan , Liu Yuerong , Rohrs Rosie , Copeland Jennie , Byrd Jessalyn , Stilwell Laura , Crew Carter , Kuehn Molly , Snyder-Fickler Elizabeth , Hurst Jillian , Evans Kelly , Terrell Lindsay , Gifford Elizabeth
Published: June 2022

Child abuse and neglect (CAN) medical experts provide specialized multidisciplinary care to children when there is concern for maltreatment. Their clinical notes contain valuable information on child- and family-level factors, clinical concerns, and service placements that may inform the needed supports for the family. We created and implemented a coding system for data abstraction from these notes. Participants were 1,397 children ages 0-17 years referred for a consultation with a CAN medical provider at an urban teaching and research hospital between March 2013 and December 2017. Coding themes were developed using an interdisciplinary team-based approach to qualitative analysis, and descriptive results are presented using a developmental-contextual framework. This study demonstrates the potential value of developing a coding system to assess characteristics and patterns from CAN medical provider notes, which could be helpful in improving quality of care and prevention and detection of child abuse.
A cross-sectional study of the neuropsychiatric phenotype of CACNA1C-related disorder
Authors: Levy Rebecca J. , Timothy Katherine W. , Underwood Jack F. G. , Hall Jeremy , Bernstein Jonathan A. , Paşca Sergiu P.
Published: June 2022

CACNA1C encodes the voltage gated L-type calcium channel CaV1.2. A specific gain of function pathogenic variant in CACNA1C causes Timothy syndrome type 1 (TS1) with cardiac long QT syndrome, syndactyly, and neuropsychiatric symptoms. Recent case series highlighted a broader spectrum of CACNA1C-related disorder (CRD) that includes isolated cardiac disease, isolated neurologic deficits, and TS, but it is unknown how the clinical presentation of other CRD variants relate to neural defects. We surveyed individuals with CRD to define the neuropsychiatric and developmental phenotype in an effort to guide future research into the role of calcium channels in neural development. Among 24 participants the most common neuropsychiatric symptoms and/or diagnoses were developmental delay in 92%, incoordination in 71%, hypotonia in 67%, autism spectrum disorder in 50% (autistic features in 92%), seizures in 38%, and attention deficit hyperactivity disorder in 21% of participants. There were no significant differences in symptoms between participants with and without long QT syndrome. These findings indicate the key role of CaV1.2 in brain development and the clinical importance of screening and therapeutically addressing neuropsychiatric symptoms in all individuals with CRD.
Germline Transmission of a Circular Human Artificial Chromosome in the Mouse
Authors: Wudzinska Aleksandra , Mitchell Leslie A. , Brosh Ran , Bosco Nazario , Boccalatte Francesco , Aifantis Ioannis , Kim Sang Y. , Davoli Teresa , Boeke Jef D.
Published: June 2022

Although the structure and function of the alphoid-tetO Human Artificial Chromosome (tetO-HAC) has been previously described in cell culture models and somatically in the mouse, in vivo persistence and stability throughout meiosis and across generations were not evaluated. Here we report germline transmission of a circular tetO-HAC across three mouse generations without observable health or reproductive deficiencies. Furthermore, we show that the tetO-HAC is maintained without selection as an episome and can be efficiently transmitted by both ova and sperm.
A database of accurate electrophoretic migration patterns for human proteins in cell lines
Authors: Mylonas Roman , Potts Alexandra , Waridel Patrice , Barblan Jachen , del Carmen Conde Rubio Maria , Widmann Christian , Quadroni Manfredo
Published: June 2022

Native molecular weight (MW) is one of the defining features of proteins. Denaturing gel electrophoresis (SDS-PAGE) is a very popular technique for separating proteins and determining their MW. Coupled with antibody-based detection, SDS-PAGE is widely applied for protein identification and quantitation. Yet, electrophoresis is poorly reproducible and the MWs obtained are often inaccurate. This hampers antibody validation and negatively impacts the reliability of western blot data, resulting worldwide in a considerable waste of reagents and labour. To alleviate these problems there is a need to establish a database of reference MWs measured by SDS-PAGE. Using mass spectrometry as an orthogonal detection method, we acquired electrophoretic migration patterns for approximately 10’000 human proteins in five commonly used cell lines. We applied a robust internal calibration of migration to determine accurate and reproducible molecular weights. This in turn allows merging replicates to increase accuracy, but also enables comparing different cell lines. Mining of the data obtained highlights structural factors that affect migration of distinct classes of proteins. We also show that the information produced recapitulates known post-translational modifications and differential splicing and can be used to formulate hypotheses on new or poorly known processing events. The full information is freely accessible as a web resource through a user friendly graphical interface (https://pumba.dcsr.unil.ch/). We anticipate that this database will be useful to investigators worldwide for troubleshooting western blot experiments, but could also contribute to the characterization of human proteoforms.
Did circular DNA shape the evolution of mammalian genomes?
Authors: Holt Sylvester , Tané Gerard Arrey , Regenberg Birgitte
Published: June 2022

Extrachromosomal circular DNA of chromosomal origin (eccDNA) can rapidly shape the evolution and adaptation of mitotically dividing cells such as tumor cells. However, whether eccDNA has a permanent impact on genome evolution through the germline is largely unexplored. Here, we propose that a large fraction of the syntenic changes that are found between mammalian species are caused by germline transposition of eccDNA. We have previously shown the existence of eccDNA in mammalian meiotic cells. By reanalysis of available synteny maps, we now find that up to 6% of mammalian genomes might have rearranged via a circular DNA intermediate. Hence, eccDNA in the germline is expected to have large effects on evolution of gene order.

Highlights

Extrachromosomal circular DNA (eccDNA) is present in mammalian germline cells showing that eccDNAs are not excluded, repressed or eliminated during meiosis

Large eccDNA reinsertions into the genome can change gene synteny in a recognizable pattern based on its circular junction and integration breakpoint.

By reanalyzing synteny maps form 8 mammalian species, we show that 6% of genome of the ungulates cow and sheep can be explained by eccDNA insertions.

We propose that reinsertion of large eccDNA that are fixed in germline cells may have contributed to speciation barriers and evolution of new species
The role of histone acetyltransferases Gcn5 and Esa1 in recruiting the RSC complex and maintaining nucleosome-depleted regions genome-wide in Saccharomyces cerevisiae
Authors: Biernat Emily , Verma Mansi , Werick Matthew , Khan Uzair , Joseph Sama , Govind Chhabi K.
Published: June 2022

Chromatin remodelers are essential for the maintenance of chromatin structure and gene regulation. In this study, we examined the role of histone acetyltransferases (HATs) Gcn5 and Esa1 in regulating RSC and histone occupancies and their effects on transcription genome-wide. We identified contrasting roles of HATs in modulating RSC occupancies in promoters and ORFs. In HAT mutants, RSC accumulated in nucleosome depleted regions (NDRs) with “fragile nucleosomes (FNs)” more than those with stable -1 nucleosomes. Moreover, the accumulation was more significant in the Esa1 mutant than in the Gcn5 mutant. However, RSC NDR accumulation was not observed in cells lacking H3 or H4 tails. Furthermore, we observed marked increases in histone occupancies in NDRs in the HAT mutants genome-wide. Overall, these data suggest that FNs use hypoacetylated tails to recruit RSC to NDRs, and subsequent acetylation of the tails promote histone eviction. In contrast to the promoters, RSC occupancies were significantly reduced in transcribed ORFs in the HAT mutants. Additionally, the HAT mutants showed reduced TBP and Pol II binding at promoters. Thus, our data implicate HATs and RSC in maintaining NDRs, regulating chromatin structure, and promoting transcription.
Time-kill kinetics reveal heterogeneous tolerance to disinfectants
Authors: Nordholt Niclas , Lewerenz Dominique , Schreiber Frank
Published: June 2022

Disinfection is an important strategy to limit the spread of infections. Failure of disinfection may facilitate evolution of resistance against disinfectants and antibiotics through the processes of cross-resistance and co-resistance. The best possible outcome of disinfection minimizes the number of surviving bacteria and the chance for resistance evolution. Resistance describes the ability to grow in previously inhibitory concentrations of an antimicrobial, whereas tolerance is associated with enhanced survival of lethal doses. Individual bacteria from the same population can display considerable heterogeneity in their ability to survive treatment (i.e. tolerance) with antimicrobials, which can result in unexpected treatment failure. Here, we investigated how phenotypic heterogeneity affects the ability of E. coli to survive treatment with six different substances commonly used as active substances in disinfectants, preservatives and antiseptics. A mathematical model which assumes that phenotypic heterogeneity underlies the observed disinfection kinetics was used to infer whether time-kill kinetics were caused by a tolerant subpopulation. The analysis identified bimodal kill kinetics for benzalkonium chloride (BAC), didecyldimethylammonium chloride (DDAC), and isopropanol (Iso). In contrast, kill kinetics by chlorhexidine (CHX), glutaraldehyde (GTA), and hydrogen peroxide (H2O2) were best explained by unimodal kill kinetics underpinned by a broad distribution of tolerance times for CHX as opposed to a narrow distribution of tolerance times for GTA and H2O2. These findings have implications for the risk of disinfection failure, with potential consequences for the evolution of antimicrobial resistance and tolerance.
Evidence for the digital programming of cellular differentiation: characterization of binary switches in lineage-determining transcription factors
Authors: Li Hongchuan , Rahman Md Ahasanur , Wright Paul W , Cao Jennie , Ratnayake Shashikala , Chen Qingrong , Yan Chunhua , Meerzaman Daoud , Freud Aharon G , Anderson Stephen K
Published: June 2022

Previous studies of the murine Ly49 and human KIR gene clusters have revealed a role for bidirectional promoters in the control of variegated gene expression. Whether or not competing promoters control other instances of cell fate determination remains an outstanding question. Although divergent transcripts within 300 bp are found in ~6% of human genes, an analysis of human transcription factor (TF) genes (1640) revealed that 33% possess stable divergent transcripts with a transcription start site (TSS) less than 300 bp upstream, with many separated by less than 30 bp, indicating an enrichment for potential binary switches in TFs. We have performed a detailed examination of putative bidirectional promoter switches in three lineage-determining TF genes: AHR, GATA3, and RORγT. These genes also contain additional pairs of opposing promoters that would prevent simultaneous transcription of sense and antisense, and thus may represent simple on/off switches rather than probabilistic switches. In situ RNA hybridization of human tissues revealed mutually exclusive expression of sense versus antisense transcription, indicating switching between stable sense or antisense transcriptional states. Single-cell RNAseq confirmed the separate sense/antisense states, and revealed the identity of cells with active switch elements. Differential gene expression analysis of cells with antisense switch transcripts revealed an enrichment for genes found in immature/stem cells and a lack of genes associated with terminally differentiated cells. Taken together, these data indicate that there is a digital component to the differentiation program mediated by binary promoter switches in lineage-determining transcription factors.
Targeted cortical stimulation reveals principles of cortical contextual interactions
Authors: Wang Shen , Palmigiano Agostina , Miller Kenneth D. , Van Hooser Stephen D.
Published: June 2022

Cross-orientation suppression is a classic form of contextual normalization in visual cortex, yet the degree to which cortical circuits participate in the normalization computation is unclear. We visualized orientation maps of individual ferrets, and provided patterned optogenetic stimulation to both excitatory and inhibitory cells in orientation columns that either matched or were orthogonal to the preferred visual orientation of neurons recorded with electrodes. When visual or optogenetic stimulation of columns preferring one orientation was combined with optogenetic stimulation of columns preferring the orthogonal orientation, we observed less suppression than when orthogonal stimulation was provided visually, suggesting that cortical circuits do not provide a large fraction of visual cross-orientation suppression. Integration of visual and optogenetic signals was linear when neurons exhibited low firing rates and became sublinear when neurons exhibited higher firing rates. We probed the nature of sublinearities in cortex by examining the influence of optogenetic stimulation of cortical interneurons. We observed a range of responses, including evidence for paradoxical responses in which interneuron stimulation caused a decrease in inhibitory firing rate, presumably due to the withdrawal of recurrent excitation. These results are compatible with cortical circuits that exhibit strong recurrent excitation with stabilizing inhibition that provides normalization, albeit normalization that is too weak across columns to account for cross-orientation suppression.
Ancient origin of Jingchuvirales derived glycoproteins integrated in arthropod genomes
Authors: Dezordi Filipe Zimmer , Coutinho Gutembergmann Batista , Dias Yago José Mariz , Wallau Gabriel Luz
Published: June 2022

Endogenous virus elements (EVEs) are viral-derived sequences integrated into their host genomes. EVEs of the Jingchuvirales order were detected in a wide range of insect genomes covering several distantly related families and Jingchuvirales-derived glycoproteins were recently associated by our group with the origin of a putative new retrovirus based on a glycoprotein captured by a mosquito retrotransposon. But, except for mosquitoes, there is a lack of a more detailed understanding of the endogenization mechanism, timing and frequency per viral lineages. Here we screened Jingchuvirales glycoprotein-derived EVEs (Jg-EVEs) in eukaryotic genomes. We found six distinct endogenization events of Jg-EVEs, that belong to two out of five known Jingchuvirales families (Chuviridae and Natareviridae). For seven arthropod families bearing Jg-EVEs there is no register of bona fide circulating chuvirus infection. Hence, our results show that Jingchuvirales viruses infected or still infect these host families, expanding their known host range. We estimated that two endogenization events occurred in the ancestors of the Myrmicinae-Ponerinae subfamilies (Pteromalidae - Hymenoptera order) around 155∼54.8 MyA and Bombus genus (Hemiptera order) around (36∼2 MyA). Although we found abundant evidence of LTR-Gypsy retrotransposons fragments associated with the glycoprotein in Hymenoptera and other insect orders, there is no evidence of potential functional glycoprotein capture. Our results show that the widespread distribution of Jingchuvirales glycoproteins in extant Arhtropods is a result of multiple ancient endogenization events and that these viruses’ fossils are being vertically inherited for millions of years through the Arthropods evolutionary tree.

Graphical Abstract
Carbon isotope fractionation by an ancestral rubisco suggests biological proxies for CO2through geologic time should be re-evaluated
Authors: Wang Renée Z. , Nichols Robert J. , Liu Albert K. , Flamholz Avi I. , Artier Juliana , Banda Doug M. , Savage David F. , Eiler John M. , Shih Patrick M. , Fischer Woodward W.
Published: June 2022

The history of Earth’s carbon cycle reflects trends in atmospheric composition convolved with the evolution of photosynthesis. Fortunately, key parts of the carbon cycle have been recorded in the carbon isotope ratios of sedimentary rocks. The dominant model used to interpret this record as a proxy for ancient atmospheric CO2is based on carbon isotope fractionations of modern photoautotrophs, and longstanding questions remain about how their evolution might have impacted the record. We tested the intersection of environment and evolution by measuring both biomass (εp) and enzymatic (εRubisco) carbon isotope fractionations of a cyanobacterial strain (Synechococcus elongatusPCC 7942) solely expressing a putative ancestral Form 1B rubisco dating to ≫1 Ga. This strain, nicknamed ANC, grows in ambient pCO2and displays larger εpvalues than WT, despite having a much smaller εRubisco(17.23 ± 0.61‰ vs. 25.18 ± 0.31‰ respectively). Measuring both enzymatic and biomass fractionation revealed a surprising result—ANC εpexceeded ANC εRubiscoin all conditions tested, contradicting prevailing models of cyanobacterial carbon isotope fractionation. However, these models were corrected by accounting for cyanobacterial physiology, notably the CO2concentrating mechanism (CCM). Our model suggested that additional fractionating processes like powered inorganic carbon uptake systems contribute to εp, and this effect is exacerbated in ANC. Understanding the evolution of rubisco and the CCM is therefore critical for interpreting the carbon isotope record. Large fluctuations in that record may reflect the evolving efficiency of carbon fixing metabolisms in addition to changes in atmospheric CO2.

Significance Statement

Earth scientists rely on chemical fossils like the carbon isotope record to derive ancient atmospheric CO2concentrations, but interpretation of this record is calibrated using modern organisms. We tested this assumption by measuring the carbon isotope fractionation of a reconstructed ancestral rubisco enzyme (>1 billion years old)in vivoandin vitro. Our results contradicted prevailing models of carbon flow in Cyanobacteria, but our data could be rationalized if light-driven uptake of CO2is taken into account. Our study showed that the carbon isotope record tracks both the evolution of photosynthesis physiology as well as changes in atmospheric CO2, highlighting the value of considering both evolution and physiology for comparative biological approaches to understanding Earth’s history.
Molecular Mechanism of Active Cas7-11 in Processing CRISPR RNA and Interfering Target RNA
Authors: Gowswami Hemant , Rai Jay , Das Anuska , Li Hong
Published: June 2022

Cas7-11 is a Type III-E CRISPR Cas effector that confers programmable RNA cleavage and has potential applications in RNA interference. Cas7-11 encodes a single polypeptide containing four Cas7- and one Cas11-like segments that obscures the distinction between the multi-subunit Class 1 and the single-subunit Class-2 CRISPR-Cas systems. We report a cryo-EM structure of the active Cas7-11 from Desulfonema ishimotonii (DiCas7-11) that reveals the molecular basis for RNA processing and interference activities. DiCas7-11 arranges its Cas7- and Cas11-like domains in an extended form that resembles the backbone made up by four Cas7 and one Cas11 subunits in the multi-subunit enzymes. Unlike the multi-subunit enzymes, however, the backbone of DiCas7-11 contains evolutionarily different Cas7 and Cas11 domains, giving rise to their unique functionality. The first Cas7-like domain nearly engulfs the last 15 direct repeat nucleotides and is responsible for processing and recognition of the CRISPR RNA. Whereas both the second and the third Cas7-like domains mediate target RNA cleavage, they differ in metal requirement for catalysis. The long variable insertion to the fourth Cas7-like domain has little impact to RNA processing or targeting, suggesting the possibility for engineering a compact and programmable RNA interference tool.

One Sentence Summary

Structures of Cas7-11 reveal the molecular basis for processing CRISPR RNA and for cleaving target RNA.
Prevalence of Hepatitis B viral infection and associated factors among adults in Moyo district, North-Western Uganda
Authors: Lulu Patrick Madrama , Alege John Bosco
Published: June 2022

Background

Hepatitis B viral infection is a public health problem and estimates show that about 30% of the world’s population is infected with the virus, with about 350 to 400 million of them remaining chronically infected. Northern Uganda has the highest prevalence of HBV in Uganda. In this study, we sought to establish factors influencing the prevalence of Hepatitis B viral infection among adults in Moyo district, North-Western Uganda.

Methods

We used a descriptive cross-sectional study where quantitative data collection methods and analysis was employed. Self-reported HBV infection by respondents who had test result forms diagnosed with HBV within the last one year was reviewed by the researchers to confirm whether the respondent was negative or positive with Hepatitis B. 384 samples were determined using Cochran (1963:75) and a multi-stage sampling technique was used. Bivariate and multivariate analyses were done using SPSS (20.0).

Results

Out of the 384 respondents interviewed, 29 (7.6%, 95%CI: 5.1-10.7) had HBV. Factors influencing the prevalence of HBV were; level of education (p=0.047*), ever having had STIs (aOR=18.090, 95%CI=5.699-57.426, p=0.000*), Health facilities have equipment for screening HEP B viral infection ANC (aOR=10.762, 95%CI=1.316-88.027, p=0.027*) were statically significant in influencing the prevalence of HBV, while the number of sexual partners ever had (p=0.984) was not statistically significant in influencing the prevalence of Hepatitis B viral infection.

Conclusion

We found a high prevalence of HBV among adults in Moyo district in North-Western Uganda compared to the national prevalence. Key influences of HBV prevalence included education level, ever being infected with any other STIs (HIV, Syphilis, gonorrhoea), multiple sexual partners and presence of HBV screening equipment at the health facilities. Need for more emphasis on HBV childhood immunization, screening, vaccination of adults, other preventive measures and treatment of those already infected.