bluuebunny/crossref_metadata_2025 huggingface dataset:
Complement C5 is not critical for the formation of sub-RPE deposits inEfemp1mutant mice
Authors: Garland Donita L. , Pierce Eric A. , Fernandez-Godino Rosario
Published: July 2021

The complement system plays a role in the formation of sub-retinal pigment epithelial (RPE) deposits in early stages of age-related macular degeneration (AMD). But the specific mechanisms that connect complement activation and deposit formation in AMD patients are unknown, which limits the development of efficient therapies to reduce or stop disease progression. We have previously demonstrated that C3 blockage prevents the formation of sub-RPE deposits in a mouse model ofEFEMP1-associated macular degeneration. In this study, we have used double mutantEfemp1R345W/R345W:C5-/-mice to investigate the role of C5 in the formation of sub-RPE depositsin vivoandin vitro. The data revealed that the genetic ablation of C5 does not eliminate the formation of sub-RPE depositsin vivoorin vitro. Contrarily, the absence of C5 in RPE cultures promotes complement dysregulation that results in increased activation of C3, which likely contributes to deposit formation even in the absence of EFEMP1-R345W mutant protein. The results also suggest that genetic ablation of C5 alters the extracellular matrix turnover through an effect on matrix metalloproteinases in RPE cell cultures. These results confirm that C3 rather than C5 could be an effective therapeutic target to treat early AMD.
Species associations and management intensity modulate the habitat niche breadth of forest birds
Authors: Basile Marco , Asbeck Thomas , Cordeiro Pereira João M. , Mikusiński Grzegorz , Storch Ilse
Published: July 2021

Species associations can have profound effects on the realized habitat niche of species, indicating that habitat structure alone cannot fully explain observed abundances. To account for this aspect of community organization in niche modelling, we developed multi-species abundance models, incorporating the local effect of potentially associated species, alongside with environmental ones, targeting mainly forest management intensity. We coupled it with a landscape-scale analysis to further examine the role of management intensity in modifying the habitat niche in connection with the landscape context. Using empirical data from the Black Forest in southern Germany, we focused on the forest bird assemblage and in particular on the cavity nester and canopy forager guilds. We included in the analysis species that co-occur and for which evidences suggest association is likely. Our findings show that the local effect of species associations can moderate the effects of management intensity. We also found that species express a larger habitat niche breadth in intensively managed forests, depending on the landscape context. Species associations may facilitate the utilization of a broader range of environmental conditions under intensive forest management, which benefits some species over others. Such network of associations may be a relevant factor in the effectiveness of conservation-oriented forest management.
Spatial frequency-based image reconstruction to improve image contrast in multi-offset adaptive optics ophthalmoscopy
Authors: Mecê Pedro , Gofas Elena , Rui Yuhua , Zhang Min , Sahel José-Alain , Rossi Ethan A.
Published: July 2021

Off-axis detection methods in adaptive optics (AO) ophthalmoscopy can enhance image contrast of translucent retinal structures such as cone inner segments and retinal ganglion cells layer neurons. Here, we propose a 2D optical model showing that the phase contrast produced by these methods depends on the offset orientation. While one axis provides an asymmetric light distribution, hence a high phase contrast, the perpendicular axis provides a symmetric one, thus a substantially lower contrast. We support this model within-vivohuman data acquired with a multi-offset AO scanning light ophthalmoscope. Then, using this finding, we provide a post-processing method, named Spatial frequency-based iMAge ReconsTruction (SMART), to optimally combine images from different off-axis detector orientations, significantly increasing the structural cellular contrast ofin-vivohuman retinal neurons such as conne inner segment, putative rods and retinal ganglion cells.
Mutation of the nuclear pore complex component,aladin1, disrupts asymmetric cell division inZea mays(maize)
Authors: Best Norman B. , Addo-Quaye Charles , Kim Bong-Suk , Weil Clifford F. , Schulz Burkhard , Johal Guri , Dilkes Brian P.
Published: July 2021

The nuclear pore complex (NPC) regulates the movement of macromolecules between the nucleus and cytoplasm. Dysfunction of many components of the NPC results in human genetic diseases, including triple A syndrome (AAAS) as a result of mutations in ALADIN. Here we report a nonsense mutation in the maize ortholog,aladin1(ali1-1), at the orthologous amino acid residue of an AAAS allele from humans, alters plant stature, tassel architecture, and asymmetric divisions of subsidiary mother cells (SMCs). Crosses with the stronger nonsense alleleali1-2identified complex allele interactions for plant height and aberrant SMC division. RNA-seq analysis of theali1-1mutant identified compensatory transcript accumulation for other NPC components as well as gene expression consequences consistent with conservation of ALADIN1 functions between humans and maize. These findings demonstrate that ALADIN1 is necessary for normal plant development, shoot architecture, and asymmetric cell division in maize.
A versatile automated high-throughput drug screening platform for zebrafish embryos
Authors: Lubin Alexandra , Otterstrom Jason , Hoade Yvette , Bjedov Ivana , Stead Eleanor , Whelan Matthew , Gestri Gaia , Paran Yael , Payne Elspeth
Published: July 2021

Zebrafish provide a unique opportunity for drug screening in living animals, with the fast developing, transparent embryos allowing for relatively high throughput, microscopy-based screens. However, the limited availability of rapid, flexible imaging and analysis platforms has limited the use of zebrafish in drug screens. We have developed a easy-to-use, customisable automated screening procedure suitable for high-throughput phenotype-based screens of live zebrafish. We utilised the WiScan®HermesHigh Content Imaging System to rapidly acquire brightfield and fluorescent images of embryos, and the WiSoft®Athena Zebrafish Applicationfor analysis, which harnesses an Artificial Intelligence-driven algorithm to automatically detect fish in brightfield images, identify anatomical structures, partition the animal into regions, and exclusively select the desired side-oriented fish. Our initial validation combined structural analysis with fluorescence images to enumerate GFP-tagged haematopoietic stem and progenitor cells in the tails of embryos, which correlated with manual counts. We further validated this system to assess the effects of genetic mutations and x-ray irradiation in high content using a wide range of assays. Further, we performed simultaneous analysis of multiple cell types using dual fluorophores in high throughput. In summary, we demonstrate a broadly applicable and rapidly customisable platform for high content screening in zebrafish.
Distribution and functional potential of photoautotrophic bacteria in alkaline hot springs
Authors: Bennett Annastacia C. , Murugapiran Senthil K. , Kees Eric D. , Hamilton Trinity L.
Published: July 2021

Alkaline hot springs in Yellowstone National Park (YNP) provide a framework to study the relationship between photoautotrophs and temperature. Previous work has focused on cyanobacteria (oxygenic phototrophs), but anoxygenic phototrophs are critical parts of the evolutionary history of life on Earth and and are abundant across temperature gradients in alkaline hot springs. However, many questions remain regarding the ecophysiology of anoxygenic photosynthesis due to the taxonomic and metabolic diversity of these taxa. Here, we examined the distribution of genes involved in phototrophy and carbon and nitrogen fixation in eight alkaline (pH 7.3-9.4) hot spring sites approaching the upper temperature limit of photosynthesis (~72°C) in YNP using metagenome sequencing. Genes associated with cyanobacteria are abundant throughout our data and more diverse at temperatures > 63°C, genes for autotrophic Chloroflexi are more abundant in sites > 63°C and genes associated with phototrophic Chloroflexi are abundant throughout. Additionally, we recovered deep branching nitrogen fixation genes from our metagenomes, which could inform the evolutionary history of nitrogen fixation. Lastly, we recovered 25 metagenome assembled genomes of Chloroflexi. We found distinct differences in carbon fixation genes inRoseiflexusandChloroflexusbins, in addition to several novel Chloroflexi bins. Our results highlight the physiological diversity and evolutionary history of the understudied, anoxygenic autotrophic Chloroflex. Furthermore, we provide evidence that genes involved in nitrogen fixation in Chloroflexi is more widespread than previously assumed.

IMPORTANCE

Photosynthetic bacteria in hot springs are of great importance to both microbial evolution and ecology because they are responsible for the rise of oxygen and are critical to nutrient cycling. While a large body of work has focused on the oxygenic photosynthesis in cyanobacteria, many questions remain regarding the metabolic potential of anoxygenic phototrophs but are further compounded by their metabolic and taxonomic diversity. Here, we have recovered several novel metagenome bins and quantified the distribution of key genes involved in carbon and nitrogen metabolism in both oxygenic and anoxygenic phototrophs. Together, our results add to the body of work focusing on photosynthetic bacteria in hot springs in Yellowstone National Park.
A midbrain - thalamus - cortex circuit reorganizes cortical dynamics to initiate planned movement
Authors: Inagaki Hidehiko K. , Chen Susu , Ridder Margreet C. , Sah Pankaj , Li Nuo , Yang Zidan , Hasanbegovic Hana , Gao Zhenyu , Gerfen Charles R. , Svoboda Karel
Published: July 2021

Motor behaviors are often planned long before execution, but only released after specific sensory events. Planning and execution are each associated with distinct patterns of motor cortex activity. Key questions are how these dynamic activity patterns are generated and how they relate to behavior. Here we investigate the multi-regional neural circuits that link an auditory ‘go cue’ and the transition from planning to execution of directional licking. Ascending glutamatergic neurons in the midbrain reticular and pedunculopontine nuclei show short-latency and phasic changes in spike rate that are selective for the go cue. This signal is transmitted via the thalamus to the motor cortex, where it triggers a rapid reorganization of motor cortex state from planning-related activity to a motor command, which in turn drives appropriate movement. Our studies show how brainstem structures can control cortical dynamics via the thalamus for rapid and precise motor behavior.
Quantifying social contact patterns in Minnesota during Stay-at-Home social distancing order
Authors: Dorélien Audrey M. , Venkateswaran Narmada , Deng Jiuchen , Searle Kelly , Enns Eva , Kulasingam Shalini
Published: July 2021

SARS-CoV-2 is primarily transmitted through person-to-person contacts. It is important to collect information on age-specific contact patterns because SARS-CoV-2 susceptibility, transmission, and morbidity vary by age. To reduce risk of infection, social distancing measures have been implemented. Social contact data, which identify who has contact with whom especially by age and place are needed to identify high-risk groups and serve to inform the design of non-pharmaceutical interventions.

We estimated and used negative binomial regression to compare the number of daily contacts during the first wave (April-May 2020) of the Minnesota Social Contact Study, based on respondents age, gender, race/ethnicity, region, and other demographic characteristics. We used information on age and location of contacts to generate age-structured contact matrices. Finally, we compared the age-structured contact matrices during the stay-at-home order to pre-pandemic matrices.

During the state-wide stay-home order, the mean daily number of contacts was 5.6. We found significant variation in contacts by age, gender, race, and region. Adults between 40 and 50 years had the highest number of contacts. Respondents in Black households had 2.1 more contacts than respondent in White households, while respondents in Asian or Pacific Islander households had approximately the same number of contacts as respondent in White households. Respondents in Hispanic households had approximately two fewer contacts compared to White households. Most contacts were with other individuals in the same age group. Compared to the pre-pandemic period, the biggest declines occurred in contacts between children, and contacts between those over 60 with those below 60.
COVID-19 Pandemic Analysis
Authors: van Lint Victor A.J.
Published: July 2021

The development of coronavirus disease (COVID-19) deaths in selected nations and states is compared to the result of calculations using a conventional SEIR model of pandemic development. The model is based on the infection multiplier, R0, defined as the number of people infected by each infectious person. The infection rate increases exponentially when R0 >1.0; it remains constant at R0 = 1.0 and decreases for R0 < 1.0. R0 is determined by population behavior (frequency and proximity of interactions) and the ease by which a victim is infected by an infectious person (virulence of the virus). It is reduced by herd immunity when a large fraction of the population acquires immunity by vaccination or by recovering from infection.

The daily death rates in the U.S. and northern Europe exhibited peaks in April/May 2020 and Dec. 2020/Jan. 2021 with more a modest rate during the summer of 2020 and a gradually decreasing rate since Jan. 2021. The model produces this type of oscillatory response if it assumes that the population’s R0 responds to information reported about the pandemic, but with a delay between infections and resulting behavioral adjustments. Oscillatory behavior is typical of a control loop with delay in its feedback.

The analysis concludes that

Given the history of R0 the model predicts the development of pandemic deaths. However, since R0 is determined by the population’s behavior, control of the pandemic in democracies depends primarily on preparation and the persuasive power of political and scientific authorities. Data for S. Korea and New Zealand demonstrate the effectiveness of such methods.

For each death in the U.S. about 169 persons were infected, but fewer than half of them were identified as cases.

The pandemic was prolonged in the U.S. because the population chose to keep R0 near 1.0 by relaxing restrictions once the death rate subsided.

Initial values of R0 as high as 5.0 were observed, leading to infections doubling about every 2 days. If unabated, the resulting exponential growth increases the infected population by a factor of about 5000 before the death from the first infections is recorded.

Arrival from Italy probably initiated the pandemic in the eastern U.S., but, by the time the first death was recorded the number of domestic infections exceeded by far those that were imported. Import restrictions beyond this point are ineffective except in delaying the arrival of more virulent mutations.

If no social restrictions had been adopted, approximately 1.6 million deaths would have resulted in the U.S. The vaccine, although developed and deployed at record speed, was too late to ameliorate this result.

A third peak in death rate in Sept. 2021 may be prevented if more than 80% of the population is vaccinated.
Factors associated with transmission in COVID-19 outbreaks in long-term care facilities
Authors: Vijh Rohit , Ng Carmen H. , Shirmaleki Mehdi , Bharmal Aamir
Published: July 2021

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had a disproportionate impact on residents in long-term care facilities (LTCFs). Through our experience and data from managing COVID-19 exposures and outbreaks in LTCFs in the Fraser Health region in British Columbia, Canada, we identified risk factors associated with outbreak severity to inform current outbreak management strategies and future pandemic preparedness planning efforts.

Methods

We used a retrospective cohort study design to evaluate the association between non-modifiable factors (facility building, organization level, and resident population characteristics), modifiable factors (assessments for infection prevention and control (IPC) and public health measures), and severity of COVID-19 outbreaks (attack rate) in LTCFs. We modelled the COVID-19 attack rates in LTCF outbreaks using negative binomial regression models.

Results

From March 1, 2020 to January 10, 2021, a total of 145 exposures to at least one confirmed case of COVID-19 in 82 LTCFs occurred. For every item not met in the assessment tool, a 22% increase in the attack rate was observed (rate ratio 1.2 [95% CI 1.1 – 1.4]) after adjusting for other risk factors such as age of the facility, index case type (resident vs. staff) and proportion of single bed rooms.

Conclusion

Our findings highlight the importance of assessing IPC and public health measures for outbreak management. They also demonstrate the important modifiable and non-modifiable risk factors associated with COVID-19 outbreaks in our jurisdiction. We hope these findings will inform ongoing outbreak management and future pandemic planning efforts.
Increase in SARS-CoV-2 seroprevalence in healthy blood donors after the second wave of COVID-19 pandemic in South-Eastern Italy: evidence for asymptomatic young individuals as potential virus spreaders
Authors: Antonucci Francescopaolo , Fiore Josè Ramòn , De Feo Lucia , Granato Tommaso , Di Stefano Mariantonietta , Faleo Giuseppina , Farhan Mohamed Ahmed Mohamed , Margaglione Maurizio , Centra Michele , Santantonio Teresa Antonia
Published: July 2021

Background

Italy has been the first among western countries to experience SARS-CoV-2 spread during which the southern regions were also heavily affected by the pandemic. To understand and monitor properly the evolution of COVID-19 pandemic, population based seroprevalence studies are a valid tool for the infection rates and effective prevalence of the SARS-CoV-2.

Aim

In this prospective study, we assessed the changes in SARS-CoV-2 seroprevalence rates among non-vaccinated blood donors in South-Eastern Italy over May 2020 to March 2021.

Methods

8,183 healthy blood donors referring to the Transfusion Center at the University Hospital “Riuniti” of Foggia (Italy) for blood donation in the period May 2020-March 2021 were tested for anti-SARS-CoV-2 antibodies by Ortho Clinical Diagnostics VITROS® 3600. None of the considered subjects had a diagnosed symptomatic COVID-19 infection.

Results

Overall, 516 resulted positive for anti-SARS-CoV-2 IgG antibodies (6.3%, 95% CI, 0.03-0.15%), 387 (4.7%) were male and 129 (1.7%) female. A statistically significant increase in the seropositive population was found from May 2020 to March 2021 (Fisher’s p<0.001). The difference of the seroprevalence was significant in terms of age but not sex (2-sided p<0.05 for age; 2-sided p>0.05 for sex) in both groups.

Conclusion

Our study shows a significant increase in the SARS-CoV-2 seroprevalence among blood donors and suggests a potential role of asymptomatic individuals in continuing the spread of the pandemic. These results may contribute to establishing containment measures and priorities in vaccine campaigns.
When time-dependence in disease outcome risk is not captured by impact evaluation modeling studies: a measles vaccination case study
Authors: Portnoy Allison , Hsieh Yuli Lily , Abbas Kaja , Klepac Petra , Santos Heather , Brenzel Logan , Jit Mark , Ferrari Matthew
Published: July 2021

Background

In modeling studies that evaluate the effects of health programs, the risk of secondary outcomes attributable to infection can vary with underlying disease incidence. Consequently, the impact of interventions on secondary outcomes would not be proportional to incidence reduction. Here we use a case study on measles vaccine program to demonstrate how failure to capture this non-linear relationship can lead to over- or under-estimation.

Methods

We used a published model of measles CFR that depends on incidence and vaccine coverage to illustrate the effects of: (1) assuming higher CFR in “no-vaccination” scenarios; (2) time-varying CFRs over the past; and (3) time-varying CFRs in future projections on measles impact estimation. We evaluated how different assumptions on vaccine coverage, measles incidence, and CFR levels in “no-vaccination” scenarios affect estimation of future deaths averted by measles vaccination.

Results

Compared to constant CFRs, aligning both “vaccination” and “no-vaccination” scenarios with time variant measles CFR estimates led to larger differences in mortality in historical years and lower in future years.

Conclusions

To assess consequences of interventions, impact estimates should consider the effect of “no-intervention” scenario assumptions on model parameters to project estimated impact for alternative scenarios according to intervention strategies and investment decisions.
Ethnic and sexual identities: inequalities in adolescent health and wellbeing in a national population-based study
Authors: Khanolkar Amal R. , Frost David M. , Tabor Evangeline , Redclift Victoria , Amos Rebekah , Patalay Praveetha
Published: July 2021

Purpose

This study employed an intersectional framework to examine impact of inequities related to sexual and ethnic minority identities in risk for health, wellbeing, and health-related behaviors in a nationally representative sample.

Methods

The study sample comprised 9,789 (51% female) adolescents aged 17 years from the UK-wide Millennium Cohort Study, with data on self-identified sexual- and ethnic-identities. Adolescents were grouped into White-Heterosexual, White sexual minority (White-SM), ethnic minority (EM)-heterosexual, and ethnic- and sexual minority (EM-SM) categories.

Mental health (e.g., self-reported psychological distress, doctor-diagnosed depression, attempted suicide, victimisation), general health (self-rated health, chronic illness, Body mass index) and a range of health-related behaviors (e.g., smoking, substance use) were assessed by questionnaires. Associations were analysed using logistic and linear regression (adjusted for sex and parental income).

Results

Sexual minority individuals (White:18% and ethnic minority:3%) had increased odds for mental ill-health and attempted suicide, with higher odds in White-SM than EM-SM. Compared to White-heterosexual individuals, White-SM and EM-SM had higher risk for psychological distress (Odds ratios [OR]3.47/2.24 for White-SM/EM-SM respectively), and emotional problems (OR3.17/1.65). They had higher odds for attempted suicide (OR2.78/2.02), self-harm (OR3.06/1.52), and poor sleep quality (OR1.88/1.67). In contrast, White-Heterosexual and White-SM groups had similarly high proportions reporting risky behaviors except for drug use (OR1.34) and risky sex (OR1.40) which are more common in White-SM individuals. EM-Heterosexual and EM-SM individuals had decreased odds for health-related behaviors.

Conclusions

Sexual minority (White and EM) individuals had substantially worse mental health compared to their heterosexual peers. Adverse health-related behaviors were more common in White sexual minority individuals. Investigation into the mechanisms leading to these differences is needed.
Xeno-nucleic Acid (XNA) 2’-Fluoro-Arabino Nucleic Acid (FANA) Aptamers to the Receptor Binding Domain of SARS-CoV-2 S Protein Block ACE2 Binding
Authors: Ferreira-Bravo Irani Alves , DeStefano Jeffrey J.
Published: July 2021

The causative agent of COVID-19, SARS-CoV-2, gains access to cells through interactions of the receptor binding domain (RBD) on the viral S protein with angiotensin converting enzyme 2 (ACE2) on the surface of human host cells. Systematic Evolution of Ligands by Exponential Enrichment (SELEX) was used to generate aptamers (nucleic acids selected for high binding affinity to a target) to the RBD made from 2’-fluoroarabinonucleic acid (FANA). The best selected ~ 79 nucleotide aptamers bound the RBD (Arg319-Phe541) and the larger S1 domain (Val16-Arg685) of the 1272 amino acid S protein with equilibrium dissociation constants (KD,app) of ~ 10-20 nM and a binding half-life for the RBD of 53 ± 18 minutes. Aptamers inhibited the binding of the RBD to ACE2 in an ELISA assay. Inhibition, on a per weight basis, was similar to neutralizing antibodies that were specific for RBD. Aptamers demonstrated high specificity, binding with about 10-fold lower affinity to the related S1 domain from the original SARS virus, which also binds to ACE2. Overall, FANA aptamers show affinities comparable to previous DNA aptamers to RBD and S protein and directly block receptor interactions while using an alternative Xeno-nucleic acid (XNA) platform.
The E3 ubiquitin ligase RNF115 regulates phagosome maturation and host response to bacterial infection
Authors: Bilkei-Gorzo Orsolya , Heunis Tiaan , Marín-Rubio José Luis , Cianfanelli Francesca Romana , Raymond Benjamin Bernard Armando , Inns Joseph , Fabrikova Daniela , Peltier Julien , Oakley Fiona , Schmid Ralf , Härtlova Anetta , Trost Matthias
Published: July 2021

Phagocytosis is a key process in innate immunity and homeostasis. After uptake, newly formed phagosomes mature by acquisition of endo-lysosomal enzymes. Macrophage activation by interferon-gamma (IFN-γ) increases microbicidal activity, but delays phagosomal maturation by an unknown mechanism. Using quantitative proteomics, we show that phagosomal proteins harbour high levels of typical and atypical ubiquitin chain types. Moreover, phagosomal ubiquitylation of vesicle trafficking proteins is substantially enhanced upon IFN-γ activation of macrophages, suggesting a role in regulating phagosomal functions. We identified the E3 ubiquitin ligase RNF115, which is enriched on phagosomes of IFN-γ activated macrophages, as an important regulator of phagosomal maturation. Loss of RNF115 protein or ligase activity enhanced phagosomal maturation and increased cytokine responses to bacterial infection, suggesting that both innate immune signalling from the phagosome and phagolysosomal trafficking are controlled through ubiquitylation. RNF115 knock-out mice show less tissue damage in response toS. aureusinfection, indicating a role of RNF115 in inflammatory responsesin vivo. In conclusion, RNF115 and phagosomal ubiquitylation are important regulators of innate immune functions during bacterial infections.
Mathematically and biologically consistent framework for presence-absence pairwise indices
Authors: Šizling Arnošt L. , Keil Petr , Tjørve Even , Tjørve Kathleen M.C. , Žárský Jakub D. , Storch David
Published: July 2021

A large number of indices for presence-absence data that compare two assemblages have been proposed or reinvented. Interpretation of these indices varies across the literature, despite efforts for clarification and unification. Most effort has focused on the mathematics behind the indices, their relationships with diversity, and with each other. At the same time, the following issues have been largely overlooked: (i) requirement that a small re-arrangement of assemblages should only cause a small change in an index, (ii) inferences from the indices about diversity patterns, (iii) inter-dependence of indices based on their information value, (iv) overlap of the ecological phenomena that the indices aim to capture, and (v) incomparability of measures of different phenomena. Neglecting these issues has resulted in the invention or reinvention of indices without increasing their information value, although this value is crucial for correct interpretation of the indices. We offer a framework for pairwise diversity indices that accounts for these issues. We differentiate between statistical and information dependence of indices and show mathematical links between all indices, even those that have not yet been developed. Using linear algebra, we show (1) which set of indices carries complete information on assemblage arrangement, (2) how to calculate any index from two presence-absence indices, which can be used to standardize and compare different indices across the literature, and (3) what can be inferred about diversity phenomena from different informationally independent indices. It is impossible to purify an index of a single biodiversity phenomenon from the effects of other phenomena, because these phenomena inevitably constrain each other. Consequently, many recently proposed indices do not measure the phenomena that they were intended to measure. In contrast, a proper inference can be made by combining classical indices from different, information independent families.
SvAnna: efficient and accurate pathogenicity prediction for coding and regulatory structural variants in long-read genome sequencing
Authors: Danis Daniel , Jacobsen Julius O.B. , Balachandran Parithi , Zhu Qihui , Yilmaz Feyza , Reese Justin , Haimel Matthias , Lyon Gholson J. , Helbig Ingo , Mungall Christopher J , Beck Christine , Lee Charles , Smedley Damian , Robinson Peter N
Published: July 2021

Structural variants (SVs) are implicated in the etiology of Mendelian diseases but have been systematically underascertained owing to limitations of existing technology. Recent technological advances such as long-read sequencing (LRS) enable more comprehensive detection of SVs, but approaches for clinical prioritization of candidate SVs are needed. Existing computational approaches do not specifically target LRS data, thereby missing a substantial proportion of candidate SVs, and do not provide a unified computational model for assessing all types of SVs. Structural Variant Annotation and Analysis (SvAnna) assesses all classes of SV and their intersection with transcripts and regulatory sequences in the context of topologically associating domains, relating predicted effects on gene function with clinical phenotype data. We show with a collection of 182 published case reports with pathogenic SVs that SvAnna places over 90% of pathogenic SVs in the top ten ranks. The interpretable prioritizations provided by SvAnna will facilitate the widespread adoption of LRS in diagnostic genomics.
PyLipID: A Python package for analysis of protein-lipid interactions from MD simulations
Authors: Song Wanling , Corey Robin A. , Ansell T. Bertie , Cassidy C. Keith , Horrell Michael R. , Duncan Anna L. , Stansfeld Phillip J. , Sansom Mark S.P.
Published: July 2021

Lipids play important modulatory and structural roles for membrane proteins. Molecular dynamics simulations are frequently used to provide insights into the nature of these proteinlipid interactions. Systematic comparative analysis requires tools that provide algorithms for objective assessment of such interactions. We introduce PyLipID, a python package for the identification and characterization of specific lipid interactions and binding sites on membrane proteins from molecular dynamics simulations. PyLipID uses a community analysis approach for binding site detection, calculating lipid residence times for both the individual protein residues and the detected binding sites. To assist structural analysis, PyLipID produces representative bound lipid poses from simulation data, using a density-based scoring function. To estimate residue contacts robustly, PyLipID uses a dual-cutoff scheme to differentiate between lipid conformational rearrangements whilst bound from full dissociation events. In addition to the characterization of protein-lipid interactions, PyLipID is applicable to analysis of the interactions of membrane proteins with other ligands. By combining automated analysis, efficient algorithms, and open-source distribution, PyLipID facilitates the systematic analysis of lipid interactions from large simulation datasets of multiple species of membrane proteins.

ToC Graphic
Poly(acrylamide-co-N,N’-methylene bisacrylamide) monoliths for high peak capacity hydrophilic interaction chromatography high-resolution mass spectrometry of intact proteins at low trifluoroacetic acid content
Authors: Passamonti Marta , de Roos Chiem , Schoenmakers Peter J. , Gargano Andrea F.G.
Published: July 2021

In this study, we optimized a polymerization mixture to synthesize polyacrylamide-co-N,N’-methylene bisacrylamide monolithic stationary phases for hydrophilic-interaction chromatography (HILIC) of intact proteins. Thermal polymerization was performed, and the effects of varying the amount of crosslinker and the porogen composition on the separation performance of the resulting columns were studied.

The homogeneity of the structure and the different porosities were examined through scanning electron microscopy. Further characterization of the monolithic structure revealed a permeable (Kf between 2.5 × 10−15 and 1.40 × 10−13 m2) and polar stationary phase suitable for HILIC. The HILIC separation performance of the different columns was assessed using gradient separation of a sample containing four intact proteins, with the best performing stationary phase exhibiting a peak capacity of 51 in a gradient of 25 min.

Polyacrylamide-based materials were compared with a silica-based particulate amide phase (2.7 μm core-shell particles). The monolith has no residual silanol sites and, therefore, fewer sites for ion-exchange interactions with proteins. Thus, it required lower concentrations of ion-pair reagent in HILIC of intact proteins. When using 0.1% of trifluoroacetic acid (TFA) the peak capacities of the two columns were similar (31 and 36 for the monolithic and packed column, respectively). However, when decreasing the concentration of TFA to 0.005%, the monolithic column maintained its separation performance and selectivity (peak capacity 26), whereas the packed column showed greatly reduced performance (peak capacity 7), lower selectivity, and inability to elute all four reference proteins. Finally, using a mobile phase containing 0.1% formic acid and 0.005% TFA the HILIC separation on the monolithic column was successfully hyphenated with high-resolution mass spectrometry. Detection sensitivity for protein and glycoproteins was increased and the amount of adducts formed was decreased in comparison with separations performed at 0.1% TFA.
Phenotype switching of the mutation rate as a strategy for crossing fitness valleys
Authors: Lobinska Gabriela , Pilpel Yitzhak , Ram Yoav
Published: July 2021

Mutation rate plays an important role in adaptive evolution due to its effect on the rate of appearance of both beneficial and deleterious mutations and is therefore subject to second-order selection. The mutation rate varies between and within species and populations, increases under some stresses, and can be modified by mutator and anti-mutator alleles. It may also vary among genetically identical individuals: empirical evidence from bacteria suggests that the mutation rate can be affected by translation errors and expression noise in various proteins. Importantly, this non-genetic variation may be heritable via a transgenerational epigenetic mode of inheritance, giving rise to mutator phenotype switching that is independent from mutator alleles. Here we investigate mathematically how the rate of adaptive evolution on rugged, complex fitness landscapes is affected by the rate of mutation rate phenotype switching. Motivated by recent experimental results of mutation rate variation, we model an asexual population with two mutation rate phenotypes, non-mutator and mutator. An offspring may switch from its parental phenotype to the other phenotype. Thus, the mutation rate can be interpreted as a genetically inherited trait when the switching rate is low, as an epigenetically inherited trait when the switching rate is intermediate, or as a randomly determined trait when the switching rate is high. We find that intermediate switching rates maximize the rate of adaptation on rugged fitness landscapes. This is because an intermediate switching rate can maintain within the same individuals both a mutator phenotype and pre-existing mutations, a combination that facilitates the crossing of fitness valleys. Further, intermediate switching rates allow the population to quickly revert to a low mutation rate after adaptation is achieved, avoiding the accumulation of deleterious mutations linked to mutator alleles. Our results rationalize recently observed noise in the expression of proteins that affect the mutation rate and suggest that non-genetic inheritance of this phenotype may facilitate evolutionary adaptive processes.
Modeling Allelic Diversity of Multi-parent Mapping Populations Affects Detection of Quantitative Trait Loci
Authors: Odell Sarah G. , Hudson Asher I. , Praud Sébastien , Dubreuil Pierre , Tixier Marie-Helene , Ross-Ibarra Jeffrey , Runcie Daniel E.
Published: July 2021

The search for quantitative trait loci (QTL) that explain complex traits such as yield and flowering time has been ongoing in all crops. Methods such as bi-parental QTL mapping and genome-wide association studies (GWAS) each have their own advantages and limitations. Multi-parent advanced generation intercross (MAGIC) populations contain more recombination events and genetic diversity than bi-parental mapping populations and reduce the confounding effect of population structure that is an issue in association mapping populations. Here we discuss the results of using a MAGIC population of doubled haploid (DH) maize lines created from 16 diverse founders to perform QTL mapping. We compare three models that assume bi-allelic, founder, and ancestral haplotype allelic states for QTL. The three methods have different power to detect QTL for a variety of agronomic traits. Although the founder approach finds the most QTL, there are also QTL unique to each method, suggesting that each model has advantages for traits with different genetic architectures. A closer look at a well-characterized flowering time QTL, qDTA8, which containsvgt1, suggests a potential epistatic interaction and highlights the strengths and weaknesses of each method. Overall, our results reinforce the importance of considering different approaches to analyzing genotypic datasets, and show the limitations of binary SNP data for identifying multi-allelic QTL.9
Comparing the appetitive learning performance of six European honeybee subspecies in a common apiary
Authors: Scheiner R , Lim K , Meixner MD , Gabel MS
Published: July 2021

The Western honeybee (Apis melliferaL.) is one of the most widespread insects with numerous subspecies in its native range. In how far adaptation to local habitats has affected the cognitive skills of the different subspecies is an intriguing question which we investigate in this study. Naturally mated queens of the following five subspecies from different parts of Europe were transferred to Southern Germany:A. m. iberiensisfrom Portugal,A. m. melliferafrom Belgium,A. m. macedonicafrom Greece,A.m. ligusticafrom Italy andA. m. ruttnerifrom Malta. We also included the local subspeciesA.m. carnicain our study. New colonies were built up in a common apiary where the respective queens were introduced. Worker offspring from the different subspecies was compared in classical olfactory learning performance using the proboscis extension response. Prior to conditioning we measured individual sucrose responsiveness to investigate whether possible differences in learning performances were due to a differential responsiveness to the sugar water reward. Most subspecies did not differ in their appetitive learning performance. However, foragers of the Iberian honeybee,A. m. iberiensis, performed significantly more poorly, despite having a similar sucrose responsiveness. We discuss possible causes for the low cognitive performance of the Iberian honeybees, which may have been shaped by adaptation to local habitat.

Summary statement

This study is the first to compare the associative learning performance of six honeybee subspecies from different European regions in a common apiary.
Prolonged partner separation erodes nucleus accumbens transcriptional signatures of pair bonding in male prairie voles
Authors: Sadino Julie M. , Bradeen Xander G. , Kelly Conor J. , Brusman Liza E. , Walker Deena M. , Donaldson Zoe R.
Published: July 2021

The loss of a spouse is often cited as the most traumatic event in a person’s life. However, for most people, the severity of grief and its maladaptive effects subside over time via an understudied adaptive process. Like humans, socially monogamous prairie voles (Microtus ochrogaster) form opposite-sex pair bonds, and upon partner separation, show stress phenotypes that diminish over time. We test the hypothesis that extended partner separation diminishes pair bond-associated behaviors and causes pair bond transcriptional signatures to erode. Pairs were cohoused for 2 weeks and then either remained paired or were separated for 48hrs or 4wks before collecting fresh nucleus accumbens tissue for RNAseq. In a separate cohort, we assessed partner preference and selective aggression at these time points, finding that these behaviors persist despite prolonged separation in both same-sex and opposite-sex paired voles. Opposite-sex pair bonding led to changes in accumbal transcription that were stably maintained while animals remained paired but eroded following prolonged partner separation. Eroded genes are associated with gliogenesis and myelination, suggesting a previously undescribed role for glia in pair bonding and loss. Further, we pioneered neuron-specific translating ribosomal affinity purification in voles. Neuronally-enriched transcriptional changes revealed dopaminergic-, mitochondrial-, and steroid hormone signaling-associated gene clusters sensitive to acute pair bond disruption and loss adaptation. Our results suggest that partner separation erodes transcriptomic signatures of pair bonding despite core behavioral features of the bond remaining intact, revealing potential molecular processes priming a vole to be able to form a new bond.
Exploring the metabolic landscape of pancreatic ductal adenocarcinoma cells using genome-scale metabolic modeling
Authors: Islam Mohammad Mazharul , Goertzen Andrea , Singh Pankaj K. , Saha Rajib
Published: July 2021

Pancreatic ductal adenocarcinoma (PDAC) is a major research focus due to its poor therapy response and dismal prognosis. PDAC cells adapt their metabolism efficiently to the environment to which they are exposed, often relying on diverse fuel sources depending on availability. Since traditional experimental techniques appear exhaustive in the search for a viable therapeutic strategy against PDAC, in this study, a highly curated and omics-informed genome-scale metabolic model of PDAC was reconstructed using patient-specific transcriptomic data. From the analysis of the model-predicted metabolic changes, several new metabolic functions were explored as potential therapeutic targets against PDAC in addition to the already known metabolic hallmarks of pancreatic cancer. Significant downregulation in the peroxisomal fatty acid beta oxidation pathway reactions, flux modulation in the carnitine shuttle system, and upregulation in the reactive oxygen species detoxification pathway reactions were observed. These unique metabolic traits of PDAC were then correlated with potential drug combinations that can be repurposed for targeting genes with poor prognosis in PDAC. Overall, these studies provide a better understanding of the metabolic vulnerabilities in PDAC and will lead to novel effective therapeutic strategies.

Author summary

Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer, with late diagnosis, early metastasis, insufficient therapy response, and very low survival rates. Due to these challenges associated with the diagnosis and treatment of PDAC, it has been a research area of interest. With the goal of understanding the metabolic reprogramming in proliferating PDAC cells, we reconstructed healthy and PDAC models by incorporating patient transcriptomic data into a genome-scale global human metabolic model. Comparing the metabolic flux space for the reactions in the two context-specific models, we identified significantly divergent pathways in PDAC. These results allowed us to further investigate growth-limiting genes in PDAC and identify potential drug combinations that can be repositioned for treatment of PDAC.
Predicting stable binding modes from simulated dimers of the D76N mutant ofβ2-microglobulin
Authors: Oliveira Nuno F. B. , Rodrigues Filipe E. P. , Vitorino João N. M. , Loureiro Rui J. S. , Faísca Patrícia F. N. , Machuqueiro Miguel
Published: July 2021

The D76N mutant of theβ2m protein is a biologically motivated model system to study protein aggregation. There is strong experimental evidence, supported by molecular simulations, that D76N populates a highly dynamic conformation (which we originally named I2) that exposes aggregation-prone patches as a result of the detachment of the two terminal regions. Here, we use Molecular Dynamics simulations to study the stability of an ensemble of dimers of I2generated via protein-protein docking. MM-PBSA calculations indicate that within the ensemble of investigated dimers the major contribution to interface stabilization at physiological pH comes from hydrophobic interactions between apolar residues. Our structural analysis also reveals that the interfacial region associated with the most stable binding modes are particularly rich in residues pertaining to both the N- and C-terminus, as well residues from the BC- and DE-loops. On the other hand, the less stable interfaces are stabilized by intermolecular interactions involving residues from the CD- and EF-loops. By focusing on the most stable binding modes, we used a simple geometric rule to propagate the corresponding dimer interfaces. We found that, in the absence of any kind of structural rearrangement occurring at an early stage of the oligomerization pathway, some interfaces drive a self-limited growth process, while others can be propagated indefinitely allowing the formation of long, polymerized chains. In particular, the interfacial region of the most stable binding mode reported here falls in the class of self-limited growth.

Graphical Abstract

Highlights

The D76N mutant of proteinβ2m populates an aggregation-prone monomer (I2) with unstructured terminal regions

Molecular Dynamics simulations and MM-PBSA calculations indicate that dimers of I2are stabilized by hydrophobic interactions

The N- and C-terminal regions, together with the BC- and DE-loops are prevalent in the most stable dimer interfaces, while the CD- and EF-loop appear in the less stable ones

The most stable dimer interface has a limited potential to oligomerize in the absence of structural rearrangement