bluuebunny/crossref_metadata_2025 huggingface dataset:
A Mixed-chimerism Protocol Utilizing Thymoglobulin and Belatacept Did Not Induce Lung Allograft Tolerance, Despite Previous Success in Renal Allotransplantation
Authors: Sommer Wiebke , O Jane M. , Pruner Kurt B. , Dehnadi Abbas , Ha Huh Kyu , Robinson Kortney A. , Hanekamp Isabel , Rosales Ivy , Bean Alison S. , Paster Josh , Oura Tetsu , Neal Smith Rex , Colvin Robert , Benichou Gilles , Kawai Tatsuo , Madsen Joren C. , Allan James S.
Published: May 2021

Background.

In kidney transplantation, long-term allograft acceptance in cynomolgus macaques was achieved using a mixed-chimerism protocol based on the clinically available reagents, rabbit anti-thymocyte globulin (ATG), and belatacept. Here, we have tested the same protocol in cynomolgus macaques transplanted with fully allogeneic lung grafts.

Methods.

Five cynomolgus macaques underwent left orthotopic lung transplantation. Initial immunosuppression included equine ATG and anti-IL6RmAb induction, followed by triple-drug immunosuppression for 4 mo. Post-transplant, a nonmyeloablative conditioning regimen was applied, including total body and thymic irradiation. Rabbit ATG, belatacept, anti-IL6RmAb, and donor bone marrow transplantation (DBMT) were given, in addition to a 28-d course of cyclosporine. All immunosuppressant drugs were stopped on day 29 after DBMT.

Results.

One monkey rejected its lung before DBMT due to AMR, after developing donor-specific antibodies. Two monkeys developed fatal post-transplant lymphoproliferative disorder, and both monkeys had signs of cellular rejection in their allografts upon autopsy. The remaining 2 monkeys showed severe cellular rejection on days 42 and 70 post-DBMT. Cytokine analysis suggested higher levels of pro-inflammatory markers in the lung transplant cohort, as compared to kidney recipients.

Conclusion.

Although the clinically applicable protocol showed success in kidney transplantation, the study did not show long-term survival in a lung transplant model, highlighting the organ-specific differences in tolerance induction.
The practice of note-taking in Taylor White's natural history collection
Authors: Greenfield Emilienne
Published: May 2021

Between the 1750s and 1770s Taylor White compiled over 750 manuscript notes to accompany his collection of animal portraits. These notes are written on individual unbound sheets of paper, and offer descriptions of the birds, mammals and fish that he commissioned to be painted. Examination of the structure and content of White's notes reveals that he chose and edited information from published sources while supplementing this with his own personal observations, that he wrote in both Latin and English, and that he obtained the help of an assistant to copy out many of his drafts in a more refined hand. This article discusses what White's purpose might have been in compiling these notes, what relationship they held to his collection of images, and how his note-taking practices aligned with the contemporary eighteenth-century culture of note-taking and information management in natural history.
David Gregory's manuscript ‘Isaaci Neutoni Methodus fluxionum’ (1694): A study on the early publication of Newton's discoveries on calculus
Authors: Guicciardini Niccolò
Published: May 2021

David Gregory's manuscript ‘Isaaci Neutoni methodus fluxionum’ is the first systematic presentation of the method of fluxions written by somebody other than Newton. It was penned in 1694, when Gregory was the Savilian Professor of Astronomy at Oxford. I provide information about its content, sources and circulation. This short treatise reveals what Newton allowed to be known about his method in the mid-1690s. Further, it sheds light upon Gregory's views on how Newton's mathematical innovations related to the work of other mathematicians, both British and Continental. This paper demonstrates two things. First, it proves that Newton, far from being—as often stated—wholly isolated and reluctant to publish the method of fluxions, belonged to a network of mathematicians who were made aware of his discoveries. Second, it shows that Gregory—very much as other Scottish mathematicians such as George Cheyne and John Craig—received Newton's fluxional method within a tradition that was independent from England and that, before getting in touch with Newton, had assimilated elements of the calculi developed on the Continent.
The Bacillus virulome in endophthalmitis
Authors: Coburn Phillip S. , Miller Frederick C. , Enty Morgan A. , Land Craig , LaGrow Austin L. , Mursalin Md Huzzatul , Callegan Michelle C.
Published: May 2021

Bacillus cereus

is recognized as a causative agent of gastrointestinal syndromes, but can also cause a devastating form of intraocular infection known as endophthalmitis. We have previously reported that the PlcR/PapR master virulence factor regulator system regulates intraocular virulence, and that the S-layer protein (SlpA) contributes to the severity of

B. cereus

endophthalmitis. To better understand the role of other

B. cereus

virulence genes in endophthalmitis, expression of a subset of factors was measured at the midpoint of disease progression in a murine model of endophthalmitis by RNA-Seq. Several cytolytic toxins were expressed at significantly higher levels in vivo than in BHI. The virulence regulators codY, gntR, and nprR were also expressed in vivo. However, at this timepoint, plcR/papR was not detectable, although we previously reported that a

B. cereus

mutant deficient in PlcR was attenuated in the eye. The motility-related genes fla, fliF, and motB, and the chemotaxis-related gene cheA were detected during infection. We have shown previously that motility and chemotaxis phenotypes are important in

B. cereus

endophthalmitis. The sodA2 variant of manganese superoxide dismutase was the most highly expressed gene in vivo. Expression of the surface layer protein gene, slpA, an activator of Toll-like receptors (TLR)−2 and −4, was also detected during infection, albeit at low levels. Genes expressed in a mouse model of

Bacillus

endophthalmitis might play crucial roles in the unique virulence of

B. cereus

endophthalmitis, and serve as candidates for novel therapies designed to attenuate the severity of this often blinding infection.
Characterization of mitochondrial DNA quantity and quality in the human aged and Alzheimer’s disease brain
Authors: Klein Hans-Ulrich , Trumpff Caroline , Yang Hyun-Sik , Lee Annie J. , Picard Martin , Bennett David A. , De Jager Philip L.
Published: May 2021

Mitochondrial dysfunction is a feature of neurodegenerative diseases, including Alzheimer’s disease (AD). Using whole-genome sequencing, we assessed mitochondrial DNA (mtDNA) heteroplasmy levels and mtDNA copy number (mtDNAcn) in 1,361 human brain samples of five brain regions from three studies. Multivariable analysis of ten common brain pathologies identified tau pathology in the dorsolateral prefrontal cortex and TDP-43 pathology in the posterior cingulate cortex as primary drivers of reduced mtDNAcn in the aged human brain. Amyloid-β pathology, age, and sex were not associated with mtDNAcn. Further, there is evidence for a direct effect of mitochondrial health on cognition. In contrast, while mtDNA heteroplasmy levels increase by about 1.5% per year of life in the cortical regions, we found little evidence for an association with brain pathologies or cognitive functioning. Thus, our data indicates that mtDNA heteroplasmy burden is unlikely to be involved in the pathogenesis of late-onset neurodegenerative diseases.
A feasibility study to test a novel approach to dietary weight loss with a focus on assisting informed decision making in food selection
Authors: Lee Mindy H. , Applegate Catherine C. , Shaffer Annabelle L. , Emamaddin Abrar , Erdman John W. , Nakamura Manabu T.
Published: May 2021

Obesity is a significant contributor to the development of chronic diseases, some of which can be prevented or reversed by weight loss. However, dietary weight loss programs have shortcomings in the success rate, magnitude, or sustainability of weight loss. The Individualized Diet Improvement Program’s (iDip) objective was to test the feasibility of a novel approach that helps individuals self-select a sustainable diet for weight loss and maintenance instead of providing weight loss products or rigid diet instructions to follow.

The iDip study consisted of 22 dietary improvement sessions over 12 months with six months of follow-up. Daily weights were collected, and a chart summarizing progress was provided weekly. Six 24-hour dietary records were collected, and dietary feedback was provided in the form of a protein-fiber plot, in which protein/energy and fiber/energy of foods were plotted two-dimensionally together with a target box specific to weight loss or maintenance. An exit survey was conducted at 12 months.

Twelve (nine female, 46.3±3.1 years (mean±SE)) of the initial 14 participants (BMI>28 kg/m2) completed all sessions. Mean percent weight loss (n=12) at six and 12 months was -4.9%±1.1 (p=0.001) and -5.4%±1.7 (p=0.007), respectively. Weight loss varied among individuals at 12 months; top and bottom halves (n=6 each) achieved - 9.7%±1.7 (p=0.0008) and -1.0%±1.4 weight loss, respectively. The 24-hour records showed a significant increase in protein density from baseline to final (4.1g/100kcal±0.3 vs. 5.7g/100kcal±0.5; p=0.008). Although mean fiber density showed no significant change from the first month (1.3g/100kcal±0.1), the top half had significantly higher fiber/energy intake than the bottom half group. The survey suggested that all participants valued the program and its self-guided diet approach.

In conclusion, half of the participants successfully lost >5% and maintained the lost weight for 12 months without strict diet instructions, showing the feasibility of the informed decision-making approach.
COVID-19 vaccination hesitancy model: The impact of vaccine education on controlling the outbreak in the United States
Authors: Oduro Bismark , Miloua Attou , Apenteng Ofosuhene O. , Osei Prince P.
Published: May 2021

The coronavirus outbreak continues to pose a significant challenge to human lives globally. Many efforts have been made to develop vaccines to combat this virus. However, with the arrival of the COVID-19 vaccine, there is hesitancy and a mixed reaction toward getting the vaccine. We develop a mathematical model to analyze and investigate the impacts of education on individuals hesitant to get vaccinated. The findings indicate that vaccine education can substantially minimize the daily cumulative cases and deaths of COVID-19 in the United States. The results also show that vaccine education significantly increases the number of willing susceptible individuals, and with a high vaccination rate and vaccine effectiveness, the outbreak can be controlled in the US.
Transdiagnostic connectome-based prediction of craving
Authors: Garrison Kathleen A , Sinha Rajita , Potenza Marc N. , Gao Siyuan , Liang Qinghao , Lacadie Cheryl , Scheinost Dustin
Published: May 2021

Craving is a central construct in the study of motivation and human behavior and is also a clinical symptom of substance and non-substance-related addictive disorders. Thus, craving represents a target for transdiagnostic modeling. We applied connectome-based predictive modeling (CPM) to functional connectivity data in a large (N=274) transdiagnostic sample of individuals with and without substance-use-related conditions, to predict self-reported craving. CPM is a machine-learning approach used to identify neural ‘signatures’ in functional connectivity data related to a specific phenotype. Functional connectomes were derived from three guided imagery conditions of personalized appetitive, stress, and neutral-relaxing experiences. Craving was rated before and after each imagery condition. CPM successfully predicted craving, thereby identifying a transdiagnostic ‘craving network’ comprised primarily of the posterior cingulate cortex, hippocampus, visual cortex, and primary sensory areas. Findings suggest that craving may be associated with difficulties directing attention away from internal self-related processing, represented in the default mode network.
Detecting COVID-19 Related Pneumonia on CT Scans using Hyperdimensional Computing
Authors: Watkinson Neftali , Givargis Tony , Joe Victor , Nicolau Alexandru , Veidenbaum Alexander
Published: May 2021

Pneumonia is a common complication associated with COVID-19 infections. Unlike common versions of pneumonia spread quickly through large lung regions, COVID-19 related pneumonia starts in small localized pockets before spreading over the course of several days. This makes the infection more resilient and with a high probability of developing acute respiratory distress syndrome. Because of the peculiar spread pattern, the use of pulmonary computerized tomography (CT) scans was key in identifying COVID-19 infections. Identifying uncommon pulmonary diseases could be a strong line of defense in early detection of new respiratory infection-causing viruses. In this paper we describe a classification algorithm based on hyperdimensional computing for the detection of COVID-19 pneumonia in CT scans. We test our algorithm using three different datasets. The highest reported accuracy is 95.2% with an F1 score of 0.90, and all three models had a precision of 1 (0 false positives).
Machine Learning Prediction of Food Processing
Authors: Menichetti Giulia , Ravandi Babak , Mozaffarian Dariush , Barabási Albert-László
Published: May 2021

Despite the accumulating evidence that increased consumption of ultra-processed food has adverse health implications, it remains difficult to decide what constitutes processed food. Indeed, the current processing-based classification of food has limited coverage and does not differentiate between degrees of processing, hindering consumer choices and slowing research on the health implications of processed food. Here we introduce a machine learning algorithm that accurately predicts the degree of processing for any food, indicating that over 73% of the U.S. food supply is ultra-processed. We show that the increased reliance of an individual’s diet on ultra-processed food correlates with higher risk of metabolic syndrome, diabetes, angina, elevated blood pressure and biological age, and reduces the bio-availability of vitamins. Finally, we find that replacing foods with less processed alternatives can significantly reduce the health implications of ultra-processed food, suggesting that access to information on the degree of processing, currently unavailable to consumers, could improve population health.
Protein structure prediction using AI and quantum computers
Authors: Geoffrey A S Ben
Published: May 2021

This work seeks to combine the combined advantage of leveraging these emerging areas of Artificial Intelligence and quantum computing in applying it to solve the specific biological problem of protein structure prediction using Quantum Machine Learning algorithms. The CASP dataset from ProteinNet was downloaded which is a standardized data set for machine learning of protein structure. Its large and standardized dataset of PDB entries contains the coordinates of the backbone atoms, corresponding to the sequential chain of N, C_alpha, and C’ atoms. This dataset was used to train a quantum-classical hybrid Keras deep neural network model to predict the structure of the proteins. To visually qualify the quality of the predicted versus the actual protein structure, protein contact maps were generated with the experimental and predicted protein structure data and qualified. Therefore this model is recommended for the use of protein structure prediction using AI leveraging the power of quantum computers.
A defined medium based on R2A for cultivation and exometabolite profiling of soil bacteria
Authors: de Raad Markus , Li Yifan , Andeer Peter , Kosina Suzanne M. , Saichek Nicholas R. , Golini Amber , Han La Zhen , Wang Ying , Bowen Benjamin P. , Chakraborty Romy , Northen Trent R.
Published: May 2021

Exometabolomics is an approach to assess how microorganisms alter their environments through the depletion and secretion of chemical compounds. Comparisons of inoculated with uninoculated media can be used to provide direct biochemical observations on depleted and secreted metabolites which can be used to predict resource competition, cross-feeding and secondary metabolite production in microbial isolates and communities. This approach is most powerful when used with defined media that enable tracking of all depleted metabolites. However, microbial growth media have traditionally been developed for the isolation and growth of microorganisms but not metabolite utilization profiling through LC-MS/MS. Here, we describe the construction of a defined medium, the Northen Lab Defined Medium (NLDM), that not only supports the growth of diverse bacteria but is defined and therefore suited for exometabolomic experiments. Metabolites included in NLDM were selected based on their presence in R2A medium and soil, elemental stoichiometry requirements, as well as knowledge of metabolite usage by different bacteria. We found that NLDM supported the growth of 53 phylogenetically diverse soil bacterial isolates and all of its metabolites were trackable through LC–MS/MS analysis. These results demonstrate the viability and utility of the constructed NLDM medium for cultivating and characterizing diverse microbial isolates and communities.

Originality-Significance Statement

We build a defined medium based on the metabolite composition of R2A medium and soil, elemental stoichiometry requirements, and knowledge of metabolite usage by different bacteria. The newly formulated defined medium was evaluated on its ability to support the growth of soil isolates and its application for metabolite utilization profiling. We found that of 53 phylogenetically diverse soil bacterial isolates grew on the defined medium and all of its metabolites were trackable through LC–MS/MS analysis. This demonstrates the viability and utility of the constructed defined medium for cultivating and characterizing diverse microbial isolates and communities.
Preliminary genetic assessment of three goatfish species in the Mediterranean Sea
Authors: Soliman Taha , DiBattista Joseph D. , Fahim Reda M. , Reimer James D.
Published: May 2021

We examined genetic diversity and connectivity of two indigenous Mediterranean goatfish species (Mullus barbatusandM. surmuletus), and a Lessepsian migrant species (Upeneus moluccensis), across the Nile Delta outflow using two mitochondrial DNA markers (COI and cyt b). Genetic diversity was high for the two Mediterranean species but relatively lower for the migrant species, suggesting founder effects after invasion from the Red Sea. Confirmation of this hypothesis, however, would require comparison with populations of origin in the Red Sea and the Indo-West Pacific. AMOVA and network analyses revealed no genetic partitioning for all species, indicating the Nile outflow does not currently, and may not have historically, posed a significant barrier to larval dispersal in these goatfish despite a present-day temperature and salinity gradient along the Mediterranean coastline of Egypt.
Using kinematics to re-define the pull test as a quantitative biomarker of the postural response
Authors: Daly Samuel , Hanson Jacob T. , Mavanji Vibha , Gravely Amy , Lewis Scott , Ashe James , Looft John M. , McGovern Robert A.
Published: May 2021

Background

Quantitative biomarkers are needed for the diagnosis, monitoring and therapeutic assessment of postural instability.

Objective

Create a practical and objective measure of postural instability using kinematic measurement of the pull test to incorporate into clinical practice.

Methods

Twenty patients evaluated and treated for normal pressure hydrocephalus were tested over a number of sessions. Patients were fitted with 15 inertial measurement units during each session. At each session, the patient underwent 10-20 pull tests performed by a trained clinician. The clinician purposefully induced a range of perturbations during each session to assess the patient’s step response. Kinematic data was extracted for each pull test and aggregated.

Results

Patients participated in 57 sessions for a total of 860 trials and were separated into groups by pull test score. The center of mass velocity profile easily distinguished between groups such that score increases correlated with decreases in peak velocity and later peak velocity onset. All patients except those scored as “3” demonstrated an increase in step length and decrease in reaction time with increasing pull intensity. Groups were distinguished by differences in overall step length or reaction time regardless of pull intensity (y-intercept). A logistic regression model including only kinematic variables identified three kinematic factors that could be used to identify trials in which patients needed to be caught (i.e. “fell”).

Conclusion

An instrumented, purposefully varied pull test produces kinematic metrics useful for distinguishing clinically meaningful differences between and within NPH patients. These metrics should be followed prospectively to examine fall risk.
Investigating the possible origin and transmission routes of SARS-CoV-2 genomes and variants of concern in Bangladesh
Authors: Nahid Abdullah Al , Ghosh Ajit
Published: May 2021

The COVID-19 pandemic induced by the SARS-CoV-2 virus and its variants has ravaged most countries around the world including Bangladesh. We have analyzed publicly available genomic data to understand the current COVID-19 outbreak scenario as well as the evolutionary origin and transmission routes of SARS-CoV-2 isolates in Bangladesh. All the early isolates as well as recent B.1.1.7 and B.1.351 variants had already spread across the major divisional cities of Bangladesh. A sex biasness towards male COVID-19 patient samples sequencing has observed over female in all age-group, that could be the trend in infection rate. Phylogenetic analysis indicated a total of 13 estimated countries, including Italy, India, United Kingdom, Saudi Arabia, United Arab Emirates, Germany, Australia, New Zealand, South Africa, Democratic Republic of the Congo, United States, Russia, and Denmark, could be the possible origin introduced SARS-CoV-2 isolates in Bangladesh due to regional and intercontinental travel. Recent, B.1.1.7 variant could be imported from a total of 7 estimated countries including UK, India, Nigeria, Spain, Ireland, Australia, and Indonesia, while South Africa and the United States are the most likely sources of B.1351 variant in Bangladesh. Based on these findings, public health strategies could be designed and implemented to reduce the local transmission of the virus.
Distinct changes in mature root and growing root tip proteomes underlie physiological responses of bread wheat to salinity stress
Authors: Dissanayake Bhagya M. , Staudinger Christiana , Munns Rana , Taylor Nicolas L. , Millar A. Harvey
Published: May 2021

The impact of salinity on wheat plants is often studied by analysis of shoot responses, even though the main mechanism of tolerance is shoot Na+ exclusion. There is a need to understand the molecular responses of root tissues that directly experience rising NaCl concentrations. We have combined analysis of root growth, ion content and respiration with proteome responses in wheat root tip and mature root tissues under saline conditions. We find significant changes in translation and protein synthesis, energy metabolism and amino acid metabolism in a root tissue specific manner. Translation and protein synthesis related proteins showed significant decreases in abundance only in root tips, as did most of the glycolytic enzymes and selected TCA cycle enzymes and ATP synthase subunits. This selective root tip proteome response indicates protein synthesis capacity and energy production were impaired under salt stress, correlating with the anatomical response of roots and reduced root tip respiration rate. Wheat roots respond directly to soil salinity, therefore shoot responses such as reduction in shoot growth and photosynthetic capacity need to be considered in light of these effects.
Undivided attention: The temporal effects of attention dissociated from decision, memory, and expectation
Authors: Moerel Denise , Grootswagers Tijl , Robinson Amanda K. , Shatek Sophia M. , Woolgar Alexandra , Carlson Thomas A. , Rich Anina N.
Published: May 2021

Selective attention prioritises relevant information amongst competing sensory input. Time-resolved electrophysiological studies have shown stronger representation of attended compared to unattended stimuli, which has been interpreted as an effect of attention on information coding. However, because attention is often manipulated by making only the attended stimulus a target to be remembered and/or responded to, many reported attention effects have been confounded with target-related processes such as visual short-term memory or decision-making. In addition, the effects of attention could be influenced by temporal expectation. The aim of this study was to investigate the dynamic effect of attention on visual processing using multivariate pattern analysis of electroencephalography (EEG) data, while 1) controlling for target-related confounds, and 2) directly investigating the influence of temporal expectation. Participants viewed rapid sequences of overlaid oriented grating pairs at fixation while detecting a “target” grating of a particular orientation. We manipulated attention, one grating was attended and the other ignored, and temporal expectation, with stimulus onset timing either predictable or not. We controlled for target-related processing confounds by only analysing non-target trials. Both attended and ignored gratings were initially coded equally in the pattern of responses across EEG sensors. An effect of attention, with preferential coding of the attended stimulus, emerged approximately 230ms after stimulus onset. This attention effect occurred even when controlling for target-related processing confounds, and regardless of stimulus onset predictability. These results provide insight into the effect of attention on the dynamic processing of competing visual information, presented at the same time and location.
The mechanism underlying the organization of Borna disease virus inclusion bodies is unique among mononegaviruses
Authors: Hirai Yuya , Tomonaga Keizo , Horie Masayuki
Published: May 2021

Inclusion bodies (IBs) are characteristic biomolecular condensates organized by mononegaviruses. Here, we characterize the IBs of Borna disease virus 1 (BoDV-1), a unique mononegavirus that forms IBs in the nucleus, in terms of liquid-liquid phase separation (LLPS). The BoDV-1 phosphoprotein (P) alone induces LLPS and the nucleoprotein (N) is incorporated into the P droplet in vitro. In contrast, co-expression of N and P is required for the formation of IB-like structure in cells. Furthermore, while BoDV-1 P binds to RNA, an excess amount of RNA dissolves the liquid droplets formed by N and P. Notably, the N-terminal intrinsically disordered region of BoDV-1 P is essential to drive LLPS and bind to RNA, suggesting that both abilities could compete with one another. These features are unique among mononegaviruses, and thus this study will contribute to a deeper understanding of LLPS-driven organization and RNA-mediated regulation of biomolecular condensates.
Systemic gene therapy with thymosin β4 alleviates glomerular injury in mice
Authors: Mason William J , Jafree Daniyal J , Pomeranz Gideon , Kolatsi-Joannou Maria , Pacheco Sabrina , Moulding Dale A , Wolf Anja , Kupatt Christian , Peppiatt-Wildman Claire , Papakrivopoulou Eugenia , Riley Paul R , Long David A , Vasilopoulou Elisavet
Published: May 2021

Plasma ultrafiltration in the kidney occurs across glomerular capillaries, which are surrounded by epithelial cells called podocytes. Podocytes have a unique shape maintained by a complex cytoskeleton, which becomes disrupted in glomerular disease resulting in defective filtration and albuminuria. Lack of endogenous thymosin β4 (TB4), an actin sequestering peptide, exacerbates glomerular injury and disrupts the organisation of the podocyte actin cytoskeleton, however, the effect of exogenous TB4 therapy on podocytopathy is unknown. Here, through interrogating single-cell RNA-sequencing data of isolated glomeruli we demonstrate that Adriamycin, a toxin which injures podocytes and leads to leakage of albumin in the urine of mice, results in reduced levels of podocyte TB4. Systemic administration of an adeno-associated virus vector encoding TB4 prevented Adriamycin-induced podocyte loss and albuminuria. Adriamycin injury was associated with disorganisation of the actin cytoskeleton in vitro, which was ameliorated by exogenous TB4. Furthermore, Adriamycin administration in mice was associated with increased prevalence of podocyte vesicles, a mechanism by which albumin may leak into the urine, which was also prevented by TB4. Collectively, we propose that TB4 gene therapy prevents podocyte injury and maintains glomerular filtration via modulation of the podocyte cytoskeleton thus presenting a novel treatment strategy for glomerular disease.
Standard Sample Storage Conditions Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns
Authors: Poulsen Casper Sahl , Kaas Rolf Sommer , Aarestrup Frank M. , Pamp Sünje Johanna
Published: May 2021

Storage of biological specimens is crucial in the life and medical sciences. The storage conditions for samples can be different for a number of reasons, and it is unclear which effect this can have on the inferred microbiome composition in metagenomics analyses. Here, we assess the effect of common storage temperatures (deep freezer: -80°C, freezer: -20°C, fridge: 5°C, room temperature: 22°C) and storage times, (immediate sample processing: 0h, next day: 16h, over weekend: 64h, and longer term: 4, 8, 12 months), as well as repeated sample freezing and thawing (2-4 freeze-thaw cycles). We examine two different pig feces and sewage samples, unspiked and spiked with a mock community, and in triplicates, respectively, amounting to a total of 438 samples (777 Gbp; 5.1 billion reads). Storage conditions had a significant and systematic effect on the taxonomic and functional composition of microbiomes. Distinct microbial taxa and antimicrobial resistance classes were in some situations similarly effected across samples, while others were not, suggesting an impact of individual inherent sample characteristics. With an increasing number of freeze-thaw cycles, an increasing abundance of Firmicutes, Actinobacteria, and eukaryotic microorganisms was observed. We include recommendations for sample storage, and strongly suggest including more detailed information in the metadata together with the DNA sequencing data in public repositories to better facilitate meta-analyses and reproducibility of findings.

IMPORTANCE

Previous research has reported effects of DNA isolation, library preparation, and sequencing technology on metagenomics-based microbiome composition; however, the effect of biospecimen storage conditions has not been thoroughly assessed. We examined the effect of common sample storage conditions on metagenomics-based microbiome composition and find significant and, in part, systematic effects. Repeated freeze-thaw cycles could be used to improve the detection of microorganisms with more rigid cell walls, including parasites. We provide a dataset that could also be used for benchmarking algorithms to identify and correct for batch effects. Overall, the findings suggest that all samples of a microbiome study should be stored in the same way. Furthermore, there is a need to mandate more detailed information about sample storage and processing published together with the DNA sequencing data at INSDC (ENA/EBI, NCBI, DDBJ) or other repositories.
In vivo complex haploinsufficiency-based genetic analysis identifies a transcription factor circuit regulating Candida albicans oropharyngeal infection and epithelial cell endocytosis
Authors: Solis Norma V. , Wakade Rohan S. , Ollinger Tomye L. , Wellington Melanie , Mitchell Aaron P. , Filler Scott G. , Krysan Damian J.
Published: May 2021

Oropharyngeal candidiasis (OPC) is a common infection that complicates a wide range of medical conditions which can cause either mild or severe disease depending on the patient. The pathobiology of OPC shares many features with candidal biofilms of abiotic surfaces. The transcriptional regulation of C. albicans formation of biofilms on abiotic surfaces has been extensively characterized and involves six key transcription factors (Efg1, Ndt80, Rob1, Bcr1, Brg1, and Tec1). To determine whether this same in vitro biofilm transcriptional regulatory network played a role in OPC, we have carried out the first systematic genetic interaction analysis in a mouse model of C. albicans infection. Whereas all six transcription factors are required for in vitro biofilm formation, only three homozygous deletion mutants (tec1ΔΔ, bcr1ΔΔ, and rob1ΔΔ) and one heterozygous mutant (tec1Δ/TEC1) have reduced infectivity in a mouse model of OPC, indicating the network is more robust in vivo than in vitro. Although single mutants (heterozygous or homozygous) of BRG1 and EFG1 have no effect on fungal burden, the double heterozygous and homozygous mutants have dramatically reduced infectivity, indicating a critical genetic interaction between these two transcription factors. Using epistasis analysis, we have formulated a genetic circuit [EFG1+BRG1]→TEC1→BCR1 that is required for OPC infectivity and oral epithelial cell endocytosis. Surprisingly, we also found transcription factor mutants with in vitro defects in filamentation such as efg1ΔΔ and brg1ΔΔ filament during oral infection and that decreased filamentation did not correlate with decreased infectivity. Taken together, these data indicate that key in vitro biofilm transcription factors are involved in OPC but that the network characteristics and functional connections are remodeled significantly during interactions with tissues.

Author Summary

The pathology of oral candidiasis has features of biofilm formation, a well-studied process in vitro. Based on that analogy, we hypothesized that network of transcription factors that regulates in vitro biofilm formation might have similarities and differences in during oral infection. To test this, we employed the first systematic genetic interaction analysis of C. albicans in a mouse model of oropharyngeal infection. This revealed that the six regulators involved in in vitro biofilm formation played roles in vivo but that the functional connections between factors were quite distinct. Surprisingly, we also found that, while many of the factors are required for filamentation in vitro, none of the transcription factor deletion mutants was deficient for this key virulence trait in vivo. These observations clearly demonstrate that C. albicans regulates key aspects of its biology differently in vitro and in vivo.
Improved HIV-1 drug resistance mutation prediction using quasispecies reconstruction supported analysis
Authors: Sutar Jyoti , Bhowmick Shilpa , Padwal Varsha , Nagar Vidya , Patil Priya , Patel Vainav , Bandivdekar Atmaram
Published: May 2021

Accurate and sensitive approaches to detect HIV-1 drug resistance mutations (DRMs) are indispensable for the paradigm of ‘treatment as prevention’. While HIV-1 proviral DNA allows sensitive high throughput sequencing (HTS)-based DRM detection, its applicability is limited by presence of defective genomes. This study demonstrates application of quasispecies reconstruction algorithms (QRAs) to improve DRM detection sensitivity from proviral DNA. A robust benchmarking of 5 QRAs was performed with 2 distinct experimental control-datasets including a stringent, novel control: DCPM, simulating in-vivo variant distribution (0.08%-86.5%). Selected QRA was further evaluated for its ability to differentiate DRMs from hypermutated sequences using an in-silico control. PredictHaplo outperformed all others in terms of precision and was selected for further analysis. Near full-genome HTS was performed on proviral DNA from 20 HIV-1C infected individuals, at different stages of ART, from Mumbai, India. DRM detection was performed through residue-wise variation analysis and implementation of QRAs. Both analyses were highly concordant for DRM frequencies >10% (spearman r=0.91, p<0.0001). Phylogenetic association in HTS datasets with shared transmission history could also be demonstrated by PredictHaplo. This study highlights utility of QRAs as an adjunct to traditional residue-wise variation-based DRM detection leading to optimal personalized ART as well as better disease management.
Rab3a regulates melanin exocytosis induced by keratinocyte-conditioned medium
Authors: Cabaço Luís C. , Bento-Lopes Liliana , Neto Matilde V. , Ramalho José S. , Seabra Miguel C. , Barral Duarte C.
Published: May 2021

Skin pigmentation relies on melanin and is crucial for photoprotection against ultraviolet radiation-induced toxicity. Melanin is synthesized and stored in melanosomes, within melanocytes and then transferred to keratinocytes. While the molecular players involved in melanogenesis have been extensively studied, those underlying melanin transfer remain poorly characterized. Previously, our group proposed that coupled exo/phagocytosis is the predominant mechanism of melanin transfer in human skin and showed an essential role for Rab11b and the exocyst tethering complex in this process. Using a fluorescence-based assay, we show here that keratinocyte-conditioned medium (KCM) specifically induces melanin exocytosis from melanocytes. Moreover, we found that Rab3a, but not Rab11b, regulates melanin exocytosis upon KCM stimulation. In fact, melanosomes accumulate in melanocyte dendrites upon KCM stimulation, co-localizing with Rab3a mainly in the vicinity of the plasma membrane. Additionally, Rab3a silencing does not affect melanin transfer in melanocyte/keratinocyte co-cultures, in contrast with Rab11b depletion, indicating that Rab11b regulates non-KCM-stimulated melanin exocytosis. Thus, our results suggest the existence of at least two distinct routes of melanin exocytosis: one controlled by Rab11b and another Rab3a-dependent, stimulated by KCM. Furthermore, these results provide evidence that soluble factors secreted by keratinocytes can control skin pigmentation via induction of melanocyte signaling pathways that promote peripheral transport of melanosomes and a Rab3a-mediated exocytosis mechanism.
ProteinBERT: A universal deep-learning model of protein sequence and function
Authors: Brandes Nadav , Ofer Dan , Peleg Yam , Rappoport Nadav , Linial Michal
Published: May 2021

Self-supervised deep language modeling has shown unprecedented success across natural language tasks, and has recently been repurposed to biological sequences. However, existing models and pretraining methods are designed and optimized for text analysis. We introduce ProteinBERT, a deep language model specifically designed for proteins. Our pretraining scheme consists of masked language modeling combined with a novel task of Gene Ontology (GO) annotation prediction. We introduce novel architectural elements that make the model highly efficient and flexible to very large sequence lengths. The architecture of ProteinBERT consists of both local and global representations, allowing end-to-end processing of these types of inputs and outputs. ProteinBERT obtains state-of-the-art performance on multiple benchmarks covering diverse protein properties (including protein structure, post translational modifications and biophysical attributes), despite using a far smaller model than competing deep-learning methods. Overall, ProteinBERT provides an efficient framework for rapidly training protein predictors, even with limited labeled data. Code and pretrained model weights are available at https://github.com/nadavbra/protein_bert.
Testing the maintenance of natural responses to survival-relevant calls in the conservation breeding population of a critically endangered corvid (Corvus hawaiiensis)
Authors: Sabol Anne C. , Greggor Alison L. , Masuda Bryce , Swaisgood Ronald R.
Published: May 2021

Vocal communication serves an important role in driving many animals’ social interactions and ultimately their survival. However, both the structure of and responses towards natural vocal behavior can be lost or subject to alteration under human care. Determining if animals in conservation breeding programs exhibit and respond appropriately to species-specific vocalizations is therefore important for ensuring their survival and persistence post-release. We tested whether endangered ‘alalā(Corvus hawaiiensis),which are extinct in nature, have retained their natural responses to vocal calls that were previously linked to survival and reproduction in the wild. We conducted our studies on breeding populations derived from a small number of founding ‘alalā maintained under human care since their extinction in the wild in 2002. We presented pairs of ‘alalā with alarm, territorial intrusion, and two types of control playback calls (a non-threatening territorial maintenance call and a novel heterospecific call). ‘Alalā were significantly more likely to approach the speaker following alarm call playback than other call types, and were more likely to respond to territorial intrusion calls with the same aggressive territorial calls. Males were more likely to make these aggressive calls than females, mirroring their roles in territory defense. We also found individual consistency in the level of vocal behavior response across all call types, indicating that some individuals are more vocal than others. These results are encouraging, showing that ‘alalā exhibit relevant, species-specific behaviors despite generations under human care. They do illustrate, however, that not all individuals respond appropriately, so animals’ responses to vocal stimuli may be an important factor to consider in determining the release suitability of individuals.

Significance Statement

Effective communication is crucial to the survival of many animals, but can erode without natural selection. Therefore, testing the flexibility and maintenance of communication and vocal responses in contexts where animals are isolated from conspecifics or from survival consequences, such as in conservation breeding centers, can help determine species’ susceptibility to communication loss. We used playbacks of survival-related conspecific calls to test if ‘alalā(Corvus hawaiiensis),retained species-specific responses to these calls after generations under human care. We found that birds maintained a species-level natural response, however these natural responses were not consistent across individuals, suggesting that some birds may not be well equipped to survive in the wild without additional training or care.
Precise visuomotor transformations underlying collective behavior in larval zebrafish
Authors: Harpaz Roy , Nguyen Minh Nguyet , Bahl Armin , Engert Florian
Published: May 2021

Complex schooling behaviors result from local interactions among individuals. Yet, how sensory signals from neighbors are analyzed in the visuomotor stream of animals is poorly understood. Here, we studied aggregation behavior in larval zebrafish and found that over development larvae transition from overdispersed groups to tight shoals. Using a virtual reality assay, we characterized the algorithms fish use to transform visual inputs from neighbors into movement decisions. We found that young larvae turn away from retinal “clutter” by integrating and averaging retina-wide visual inputs within each eye, and by using a winner-take-all strategy for binocular integration. As fish mature, their responses expand to include attraction to low retinal clutter, that is based on similar algorithms of visual integration. Using model simulations, we show that the observed algorithms accurately predict group structure over development. These findings allow us to make testable predictions regarding the neuronal circuits underlying collective behavior in zebrafish.
Comment on ‘Fruitless mutant male mosquitoes gain attraction to human odor’
Authors: Amos Brogan A. , Hoffmann Ary A. , Staunton Kyran M. , Lau Meng-Jia , Burkot Thomas R. , Ross Perran A.
Published: May 2021

Female Aedes aegypti mosquitoes integrate multiple sensory cues to locate human hosts for blood meals. While male mosquitoes do not blood feed, male Ae. aegypti swarm around and land on humans in nature. Basrur et al. (2020) generated male Ae. aegypti lacking the fruitless gene and discovered that they gained strong attraction to humans, similar to female mosquitoes. The authors assume that host-seeking is a female-specific trait. However, all experiments were performed under confined laboratory conditions which are unable to detect long-range attraction. We used semi-field experiments to demonstrate robust attraction of male Ae. aegypti to humans. Our observations refute a key assumption of Basrur et al. (2020) and raise questions around conditions under which fruitless prevents male host-seeking. Male mosquito attraction to humans is likely to be important for mating success in wild populations and its basis should be further explored.
The Phtheirospermum japonicum isopentenyltransferase PjIPT1a regulates host cytokinin responses in Arabidopsis
Authors: Greifenhagen Anne , Braunstein Isabell , Pfannstiel Jens , Yoshida Satoko , Shirasu Ken , Schaller Andreas , Spallek Thomas
Published: May 2021

The hemiparasitic plant Phtheirospermum japonicum is a nutritional specialist that supplements its nutrient requirements by parasitizing other plants through haustoria. During parasitism, the Phtheirospermum haustorium transfers hypertrophy-inducing cytokinins (CKs) to the infected host root. The CK biosynthesis genes required for haustorium-derived CKs and the induction of hypertrophy are still unknown. We searched for haustorium-expressed isopentenyltransferases (IPTs) that catalyse the first step of CK biosynthesis, confirmed the specific expression by in vivo imaging of a promoter-reporter, and further analysed the subcellular localization, the enzymatic function, and contribution to inducing hypertrophy by studying CRISPR-Cas9 induced Phtheirospermum mutants. PjIPT1a was expressed in intrusive cells of the haustorium close to the host vasculature. PjIPT1a and its closest homolog PjIPT1b located to the cytosol and showed isopentenyltransferases activity in vitro with differences in substrate specificity. Mutating PjIPT1a abolished parasite-induced CK responses in the host. A homolog of PjIPT1a with shared characteristics was also identified in the related weed Striga hermonthica. We propose that PjIPT1a exemplifies how parasitism-related functions evolve through gene duplications and neofunctionalization.
Fast photoswitchable molecular prosthetics control neuronal activity in the cochlea
Authors: Garrido-Charles Aida , Huet Antoine , Matera Carlo , Thirumalai Anupriya , Llebaria Amadeu , Moser Tobias , Gorostiza Pau
Published: May 2021

Artificial control of neuronal activity enables studies of neural circuits and restoration of neural function. Direct, rapid, and sustained photocontrol of intact neurons could overcome shortcomings of established electrical stimulation such as poor selectivity. We have developed fast photoswitchable ligands of glutamate receptors to establish such control in the auditory system. The new photoswitchable ligands produced photocurrents in untransfected neurons upon covalently tethering to endogenous glutamate receptors and activating them reversibly with visible light pulses of few milliseconds. As a proof of concept of these molecular prostheses, we apply them to the ultrafast synapses of auditory neurons of the cochlea that encode sound and provide auditory input to the brain. This drug-based method affords kilohertz rate stimulation of auditory neurons of adult gerbils without genetic manipulation that would be required for their optogenetic control. The new photoswitchable ligands are also broadly applicable to spatiotemporally control fast spiking interneurons in the brain.