bluuebunny/crossref_metadata_2025 huggingface dataset:
Uracil-auxotrophic marker recycling system for multiple gene disruption in Pseudozyma antarctica
Authors: Sameshima-Yamashita Yuka , Yarimizu Tohru , Uenishi Hirohide , Tanaka Takumi , Kitamoto Hiroko
Published: May 2022

The basidiomycetous yeast Pseudozyma antarctica, which has multiple auxotrophic markers, was constructed, without inserting a foreign gene, as the host strain for the introduction of multiple useful genes. P. antarctica was more resistant to ultraviolet (UV) irradiation than the model yeast Saccharomyces cerevisiae, and a Paura3 mutant (C867T) was obtained after 3 min of UV exposure. A uracil-auxotrophic marker (URA3) recycling system developed in ascomycetous yeasts and fungi was applied to the P. antarctica Paura3 strain. The PaLYS12 and PaADE2 loci were disrupted via site-directed homologous recombination of PaURA3 (pop-in), followed by the removal of PaURA3 (pop-out). In the obtained double auxotrophic strain (Palys12Δ, Paura3), PaADE2 was further disrupted, and PaURA3 was removed to obtain the triple auxotrophic strain PGB800 (Paura3, Palys12Δ, Paade2Δ). The whole-genome sequence of the PGB800 strain did not contain foreign genes used for genetic manipulation and disrupted PaADE2 and PaLYS12 and removed PaURA3, as planned.
Does Down syndrome influence the outcomes of congenital cardiac surgery? A systematic review and meta-analysis
Authors: Wang Benjamen , Verrocchi Justin , Liew Danny , Zentner Dominica
Published: May 2022

Background

Congenital cardiac surgery for individuals with Down syndrome (DS) has historically occurred at a reduced frequency. Little data are available regarding long-term post-congenital cardiac surgical outcomes. Limited sample sizes and clinical heterogeneity require a pooled analysis approach.

Aims

To compare long-term outcomes post-congenital heart surgery between adults with and without DS.

Methods

Databases (Medline, Embase, and PubMed) were searched utilizing terms related to DS and congenital heart disease.

Studies that enrolled adults (>18 years) with operated congenital heart disease and compared long-term outcomes with respect to DS presence were included. All study designs were included, but those with limited/peri-operative follow-up, non-English texts, case studies, and literature reviews were excluded.

Blinded screening, data extraction, and quality assessment were independently conducted by two reviewers. QUIPS criteria were used for risk of bias analysis. Both random- and fixed-effects models were used for meta-analysis.

Results

A total of 23 studies (n = 10 466) were included. Risk of bias was frequently high due to unblinded retrospective study designs and analyses limited in adjustment for other prognostic factors.

Meta-analysis demonstrated no effect of DS on long-term mortality [hazard ratio (HR) 0.86, 95% confidence interval (95% CI) 0.6–1.23], to a maximum described follow-up of 38 years. Lower cardiac reoperation risk (HR 0.6, 95% CI 0.46–0.78) for individuals with DS was found on pooled analysis. Meta-analysis was limited by between-study variation.

Conclusion

DS does not affect post-congenital cardiac surgical survival in adulthood. Reduced reoperation may reflect challenges in assessing functional and symptomatic status and/or concerns regarding perceived reoperation difficulties or likely benefits.
Career Pressures and Organizational Evil: A Novel Perspective on the Study of Organized Violence
Authors: Scharpf Adam , Gläßel Christian
Published: May 2022

Dictators, rebel commanders, and mafia bosses frequently delegate gruesome and immoral tasks to their subordinates. However, most individuals want to avoid such work. This analytical essay proposes an institutional logic to understand how dictatorships, insurgent organizations, and criminal gangs get their evil work done nonetheless. We argue that common features of organizations produce mundane career pressures that incentivize subordinates to zealously execute reprehensible tasks. Subordinates may come under pressure for six distinct reasons: incompetence, misconduct, origin, isolation, organizational backlog, and shrinkage. Superiors, in turn, can exploit that pressured subordinates hope to improve their prospects for advancement by loyally executing the organization’s evil tasks. Empirically, we illustrate how Nazi Germany utilized each of the suggested career pressures to staff the units in charge of the Holocaust. We highlight that our logic might also apply to less extreme forms of organizational evil. Together, the essay offers a novel perspective to demystify radical behavior in state and non-state organizations with important implications for our understanding of transnational terrorist violence and underworld crimes.
Alignment of the central galaxies with the environment
Authors: Rodriguez Facundo , Merchán Manuel , Artale M Celeste
Published: May 2022

In this work, we combine ellipticity and major axis position angle measurements from the Sloan Digital Sky Server Data Release 16 with the group finder algorithm of Rodriguez & Merchán to determine the alignment of the central galaxies with the surrounding structures and satellite galaxies lying in their group. We use two independent methods: a modified version of the two-point cross-correlation function and the angle between the central galaxy orientation and the satellite galaxies relative position. The first method allows us to study the inner and outer regions of the cluster, while the second method provides information within the haloes. Our results show that central galaxies present anisotropy in the correlation function up to $\sim 10 \, h^{-1}~{\rm Mpc}$, which becomes ∼10 per cent stronger for the brightest ones (0.1Mr < −21.5). When we split the galaxy sample by colour, we find that red central galaxies are the main contributors to this anisotropy. We also show that this behaviour does not depend on the group mass or central galaxy ellipticity. Finally, our results are in agreement with previous findings, showing that the two-point cross-correlation function is a good tracer of the galaxy alignments using all galaxies and not only those of the group to which it belongs. In addition, this feature allows us to explore the behaviour of the alignment on larger scales.
On the effect of surface bipolar magnetic regions on the convection zone dynamo
Authors: Pipin V V
Published: May 2022

We investigate the effect of surface bipolar magnetic regions (BMRs) on the large-scale dynamo distributed in the bulk of the convection zone. The study employs the non-linear three-dimensional mean-field dynamo model. We model the emergence of the BMRs on the surface through the non-axisymmetric magnetic buoyancy effect, which acts on the large-scale toroidal magnetic field in the upper half of the convection zone. The non-axisymmetric magnetic field that results from this mechanism is shallow. On the surface, the effect of the BMRs on the magnetic field generation is dominant. However, because of the shallow distribution of BMRs, its effect on the global dynamo is less compared with the effect on the convective zone dynamo. We find that the mean-field α-effect, which acts on the non-axisymmetric magnetic field of the BMRs, provides the greater contribution to the dynamo process than the tilt of the BMRs. Even so, the fluctuations of the tilt of the BMRs lead to parity braking in the global dynamo. At the surface, the non-axisymmetric magnetic fields, which are generated because of the activity of the BMRs, show a tendency for the bihelical spectrum with positive sign for the low ℓ modes during the maximum of the magnetic activity cycle.
Narrative Assessments in Higher Education: A Scoping Review to Identify Evidence-Based Quality Indicators
Authors: Chakroun Molk , Dion Vincent R. , Ouellet Kathleen , Graillon Ann , Désilets Valérie , Xhignesse Marianne , St-Onge Christina
Published: May 2022

Purpose

Narrative comments are increasingly used in assessment to document trainees’ performance and to make important decisions about academic progress. However, little is known about how to document the quality of narrative comments, since traditional psychometric analysis cannot be applied. The authors aimed to generate a list of quality indicators for narrative comments, to identify recommendations for writing high-quality narrative comments, and to document factors that influence the quality of narrative comments used in assessments in higher education.

Method

The authors conducted a scoping review according to Arksey & O’Malley’s framework. The search strategy yielded 690 articles from 6 databases. Team members screened abstracts for inclusion and exclusion, then extracted numerical and qualitative data based on predetermined categories. Numerical data were used for descriptive analysis. The authors completed the thematic analysis of qualitative data with iterative discussions until they achieved consensus for the interpretation of the results.

Results

After the full-text review of 213 selected articles, 47 were included. Through the thematic analysis, the authors identified 7 quality indicators, 12 recommendations for writing quality narratives, and 3 factors that influence the quality of narrative comments used in assessment. The 7 quality indicators are (1) describes performance with a focus on particular elements (attitudes, knowledge, skills); (2) provides a balanced message between positive elements and elements needing improvement; (3) provides recommendations to learners on how to improve their performance; (4) compares the observed performance with an expected standard of performance; (5) provides justification for the mark/score given; (6) uses language that is clear and easily understood; and (7) uses a nonjudgmental style.

Conclusions

Assessors can use these quality indicators and recommendations to write high-quality narrative comments, thus reinforcing the appropriate documentation of trainees’ performance, facilitating solid decision making about trainees’ progression, and enhancing the impact of narrative feedback for both learners and programs.
Functional and Patient-reported Outcomes following Transmetatarsal Amputation in High-risk Limb Salvage Patients
Authors: Deldar Romina , Cach Gina , Sayyed Adaah A. , Truong Brian N. , Kim Emily , Atves Jayson N. , Steinberg John S. , Evans Karen K. , Attinger Christopher E.
Published: May 2022

Background:

Transmetatarsal amputation (TMA) is performed in patients with nonhealing wounds of the forefoot. Compared with below-knee amputations, healing after TMA is less reliable, and often leads to subsequent higher-level amputation. The aim of this study was to evaluate the functional and patient-reported outcomes of TMA.

Methods:

A retrospective review of patients who underwent TMA from 2013 to 2021 at our limb-salvage center was conducted. Primary outcomes included postoperative complications, secondary proximal lower extremity amputation, ambulatory status, and mortality. Univariate and multivariate analyses were performed to evaluate independent risk factors for higher-level amputation after TMA. Patient-reported outcome measures for functionality and pain were also obtained.

Results:

A total of 146 patients were identified. TMA success was achieved in 105 patients (72%), and 41 patients (28%) required higher-level amputation (Lisfranc: 31.7%, Chopart: 22.0%, below-knee amputations: 43.9%). There was a higher incidence of postoperative infection in patients who subsequently required proximal amputation (39.0 versus 9.5%, P < 0.001). At mean follow-up duration of 23.2 months (range, 0.7–97.6 months), limb salvage was achieved in 128 patients (87.7%) and 83% of patients (n = 121) were ambulatory. Patient-reported outcomes for functionality corresponded to a mean maximal function of 58.9%. Pain survey revealed that TMA failure patients had a significantly higher pain rating compared with TMA success patients (P = 0.016).

Conclusions:

TMA healing remains variable, and many patients will eventually require a secondary proximal amputation. Multi-institutional studies are warranted to identify perioperative risk factors for higher-level amputation and to further evaluate patient-reported outcomes.
Intravenous immunoglobulin and treatment in COVID-19 patients: case series
Authors: Mohtadi Negar , Ghaysouri Abas , Nazari Ali , Feizi Jalil , Tavan Hamed
Published: May 2022

Introduction:

Intravenous immunoglobulin (IVIG) is one of the drugs used to treat COVID-19. The aim of this study was to evaluate the role of IVIG in the treatment of COVID-19 in hospitalized patients.

Materials and methods:

The patients received IVIG before being intubated. The patients’ symptoms, disease severity, clinical features, and chest computed tomography findings were compared between before and after the treatment.

Results:

Out of 62 patients who received IVIG, 35 patients (56.5%) were male, and 27 patients (43.5%) were female. Overall, 13 (21%) patients died, and 49 (79%) recovered and were discharged from the hospital.

Conclusion:

IVIG can be used as an effective drug to save patients’ lives before they enter the intubation phase.
miR-155-3p: processing by-product or rising star in immunity and cancer?
Authors: Dawson Owen , Piccinini Anna Maria
Published: May 2022

MicroRNAs (miRNAs) are key players in gene regulation that target specific mRNAs for degradation or translational repression. Each miRNA is synthesized as a miRNA duplex comprising two strands (5p and 3p). However, only one of the two strands becomes active and is selectively incorporated into the RNA-induced silencing complex in a process known as miRNA strand selection. Recently, significant progress has been made in understanding the factors and processes involved in strand selection. Here, we explore the selection and functionality of the miRNA star strand (either 5p or 3p), which is generally present in the cell at low levels compared to its partner strand and, historically, has been thought to possess no biological activity. We also highlight the concepts of miRNA arm switching and miRNA isomerism. Finally, we offer insights into the impact of aberrant strand selection on immunity and cancer. Leading us through this journey is miR-155, a well-established regulator of immunity and cancer, and the increasing evidence that its 3p strand plays a role in these arenas. Interestingly, the miR-155-5p/-3p ratio appears to vary dependent on the timing of the immune response, and the 3p strand seems to play a regulatory role upon its partner 5p strand.
Revisiting causality using stochastics: 2. Applications
Authors: Koutsoyiannis Demetris , Onof Christian , Christofidis Antonis , Kundzewicz Zbigniew W.
Published: May 2022

In a companion paper, we develop the theoretical background of a stochastic approach to causality with the objective of formulating necessary conditions that are operationally useful in identifying or falsifying causality claims. Starting from the idea of stochastic causal systems, the approach extends it to the more general concept of hen-or-egg causality, which includes as special cases the classic causal, and the potentially causal and anti-causal systems. The framework developed is applicable to large-scale open systems, which are neither controllable nor repeatable. In this paper, we illustrate and showcase the proposed framework in a number of case studies. Some of them are controlled synthetic examples and are conducted as a proof of applicability of the theoretical concept, to test the methodology witha prioriknown system properties. Others are real-world studies on interesting scientific problems in geophysics, and in particular hydrology and climatology.
Shifts in gut microbiome across five decades of repeated guppy translocations in Trinidadian streams
Authors: Evans S. E. , Zandonà E. , Amaral J. Ribeiro , Fitzpatrick S. W.
Published: May 2022

An organism's gut microbiome can alter its fitness, yet we do not know how gut microbiomes change as their hosts evolve in the wild. We took advantage of a five-decade ‘chronosequence’ of translocated fish populations to examine associated changes in the gut microbiome. Populations of Trinidadian guppies have displayed parallel phenotypic convergence six times when moved from high predation (HP) to low predation (LP) environments. Across four drainages, we found microbiomes of fish translocated 5–6 years prior to sampling were already distinct from the microbiomes of their HP source populations. Changes in environmental conditions were most important in driving this shift, followed by phenotypic shifts in gut morphology. After 30–60 years in LP environments, microbiome composition was still distinct from native LP populations, but microbiome function was not. We found some evidence that nitrogen fixation enhanced gut nutrient absorption, but most functional shifts were not parallel across drainages. Stream-and drainage-specific signatures were present for both composition and function, despite our overall finding of consistent microbiome change across drainages. As we unravel the complexities of host–microbiome evolution in the wild, studies should consider environmental microbial colonization, host phenotypic plasticity in nature, and more realistic environmental conditions excluded from laboratory studies.
Diurnal dynamics of stress and mood during COVID-19 lockdown: a large multinational ecological momentary assessment study
Authors: Feneberg Anja C. , Forbes Paul A. G. , Piperno Giulio , Pronizius Ekaterina , Stijovic Ana , Skoluda Nadine , Lamm Claus , Nater Urs M. , Silani Giorgia
Published: May 2022

The COVID-19 pandemic resulted in severe disruption to people's lives as governments imposed national ‘lockdowns’. Several large surveys have underlined the detrimental short- and long-term mental health consequences resulting from this disruption, but survey findings are only informative of individuals' retrospectively reported psychological states. Furthermore, knowledge on psychobiological responses to lockdown restrictions is scarce. We used smartphone-based real-time assessments in 731 participants for 7 days and investigated how individuals’ self-reported stress and mood fluctuated diurnally during lockdown in spring 2020. We found that age, gender, financial security, depressive symptoms and trait loneliness modulated the diurnal dynamics of participants' momentary stress and mood. For example, younger and less financially secure individuals showed an attenuated decline in stress as the day progressed, and similarly, more lonely individuals showed a diminished increase in calmness throughout the day. Hair collected from a subsample (
n
= 140) indicated a decrease in cortisol concentrations following lockdown, but these changes were not related to any of the assessed person-related characteristics. Our findings provide novel insights into the psychobiological impact of lockdown and have implications for how, when and which individuals might benefit most from interventions during psychologically demanding periods.
Macroevolutionary dynamics of climatic niche space
Authors: Quintero Ignacio , Suchard Marc A. , Jetz Walter
Published: May 2022

How and why lineages evolve along with niche space as they diversify and adapt to different environments is fundamental to evolution. Progress has been hampered by the difficulties of linking a robust empirical characterization of species niches with flexible evolutionary models that describe their evolution. Consequently, the relative influence of abiotic and biotic factors remains poorly understood. Here, we characterize species' two-dimensional temperature and precipitation niche space occupied (i.e. species niche envelope) as complex geometries and assess their evolution across all Aves using a model that captures heterogeneous evolutionary rates on time-calibrated phylogenies. We find that extant birds coevolved from warm, mesic climatic niches into colder and drier environments and responded to the Cretaceous–Palaeogene (K–Pg) boundary with a dramatic increase in disparity. Contrary to expectations of subsiding rates of niche evolution, our results show that overall rates have increased steadily, with some lineages experiencing exceptionally high evolutionary rates, associated with the colonization of novel niche spaces, and others showing niche stasis. Both competition- and environmental change-driven niche evolution transpire and result in highly heterogeneous rates near the present. Our findings highlight the growing ecological and conservation insights arising from the model-based integration of comprehensive environmental and phylogenetic information.
Feather chemicals contain information about the major histocompatibility complex in a highly scented seabird
Authors: Jennings Sarah L. , Hoover Brian A. , Wa Sin Simon Yung , Ebeler Susan E.
Published: May 2022

Mate choice informed by the immune genes of the major histocompatibility complex (MHC) may provide fitness benefits including offspring with increased immunocompetence. Olfactory cues are considered the primary mechanism organisms use to evaluate the MHC of potential mates, yet this idea has received limited attention in birds. Motivated by a finding of MHC-dependent mate choice in the Leach's storm-petrel (Oceanodroma leucorhoa), we examined whether the chemical profiles of this highly scented seabird contain information about MHC genes. Whereas previous studies in birds examined non-volatile compounds, we used gas chromatography–mass spectrometry to measure the volatile compounds emitted from feathers that potentially serve as olfactory infochemicals about MHC and coupled this with locus-specific genotyping of MHC IIB genes. We found that feather chemicals reflected individual MHC diversity through interactions with sex and breeding status. Furthermore, similarity in MHC genotype was correlated with similarity in chemical profiles within female–female and male–female dyads. We provide the first evidence that volatile chemicals from bird feathers can encode information about the MHC. Our findings suggest that olfaction likely aids MHC-based mate choice in this species and highlight a role for chemicals in mediating genetic mate choice in birds where this mode of communication has been largely overlooked.
Non-typhoidal Salmonella bacteremia: comparison of adults and children in a single medical center
Authors: Megged Orli , Assous Marc V.
Published: May 2022

Introduction. Non-typhoidal

Salmonella

(NTS) bacteremia can cause significant morbidity and mortality. There is high incidence of Salmonellosis in the Middle East, including Israel, but there is a paucity of data on the clinical and epidemiological features of children in comparison to adults.

Hypothesis/Gap Statement. Previous studies describing the differences between paediatric and adult populations with

Salmonella

bacteremia are sparse.

Aim. This study’s aim was to describe the differences between adults and children with NTS bacteremia.

Methodology. All records of patients with NTS bacteremia between 1 January 1998 and 31 July 2020 were reviewed. Data regarding clinical manifestations and laboratory results were extracted from the medical records; records of children (aged <18 years) were compared with those of adults.

Results. Records for 137 cases of

Salmonella

bacteremia (69 adults and 68 children, aged 2 days to 98 years) were reviewed. Seventy nine (58 %) patients had concomitant gastrointestinal symptoms. Fifty-eight (84 %) adults and 13 (19 %) children had underlying conditions (P<0.001). Eighteen patients died, none of whom was a child. Over the study period, most of the children (n=46, 67 %) but only five adults were discharged from the emergency department on their first visit to the ED.

Conclusions. The main characteristics of NTS bacteremia in children compared to adults, are higher rates of prior discharge from emergency department, higher rate of gastrointestinal symptoms and better prognosis.
SARS-CoV-2 NSP3, NSP4 and NSP6 mutations and Epistasis during the pandemic in the world: Evolutionary Trends and Natural Selections in Six Continents
Authors: fooladinezhad Haniyeh , Shahidi Maryamsadat , Mahmanzar Mohammadamin , Mahdavi Bahar , Tokhanbigli Samaneh , Sisakht Mahsa Mollapour , Moradi Bahman , Ganjalikhany Mohamad Reza , Rahimian Karim , Ganjalikhani-Hakemi Mazdak
Published: May 2022

Background

The Coronavirus 2019 (COVID-19) was named by the World Health Organization (WHO) due to its rapid transmittable potential and high mortality rate. Based on the critical role of None Structural Proteins (NSP), NSP3, NSP4, and NSP6 in COVID-19, this study attempts to investigate the superior natural selection mutations and Epistasis among these none structural proteins.

Methods

Approximately 6.5 million SARS-CoV-2 protein sequences of each NSP3, NSP4, and NSP6 nonstructural protein were analyzed from January 2020 to January 2022. Python programming language was utilized to preprocess and apply inclusion criteria on the FASTA file to prepare a list of suitable samples. NSP3, NSP4, and NSP6 were aligned to the reference sequence to compare and identify mutation patterns categorized based on frequency, geographical zone distribution, and date. To discover epistasis situations, linear regression between mutation frequency and date among candidate genes was performed to determine correlations.

Results

The rate of NSP3, NSP4, and NSP6 mutations in divided geographical areas was different. Based on continental studies, P1228L (54.48%), P1469S (54.41%), and A488S (53.86%) mutations in NSP3, T492I (54.84%), and V167L (52.81%) in NSP4 and T77A (69.85%) mutation in NSP6 increased over time, especially in recent months. For NSP3, Europe had the highest P1228L, P1469S, and A488S mutations. For NSP4, Oceania had the highest T492I and V167L mutations, and for NSP6, Europe had the highest T77A mutation. Hot spot regions for NSP3, NSP4, and NSP6 were 1358 to 1552 AA, 150 to 200 AA, and 58 to 87 AA, respectively. Our results showed a significant correlation and co-occurrence between NSP3, NSP4, and NSP6 mutations.

Conclusion

We conclude that the effect of mutations on virus stability and replication can be predicted by examining the amino acid changes of P1228L, P1469S, A488S, T492I, V167L and T77A mutations. Also, these mutations can possibly be effective on the function of proteins and their targets in the host cell.
Unveiling the G4-PAMAM capacity to bind and protect Ang-(1-7) bioactive peptide
Authors: Chi L. América , Asgharpour Somayeh , Correa-Basurto José , Bandala Cindy Rodríguez , Martínez-Archundia Marlet
Published: May 2022

New therapies that allow natural healing processes are required. Such as the endogenous peptide called Angiotensin-(1-7), a safe and eff e drug, which is able to re-balance the Renin-Angiotensin system affected during several pathologies, including the new COVID-19; cardiovascular, renal, and pulmonary disease; diabetes; neuropathic pain; Alzheimer and cancer. However, one of the limiting factors for its application is its unfavorable pharmacokinetic profile. In this work, we propose the coupling of Angiotensin-(1-7) to PAMAM dendrimers in order to evaluate the capacity of the nanocarrier to improve isolated peptide features and to gain insight into the structural as well as the energetic basis of its molecular binding. The In Silico tests were performed in acidic and neutral pH conditions as well as amino-terminated and hydroxyl-terminated PAMAM dendrimers. High-rigor computational approaches, such as molecular dynamics and metadynamics simulations were used. We found that, at neutral pH, PAMAM dendrimers with both terminal types are able to interact stably with 3 Angioteinsin-(1-7) peptides through ASP1, TYR4 and PRO7 key aminoacids, however, there are some differences in the binding sites of the peptides. In general, they bind on the surface in the case of the hydroxyl-terminated compact dendrimer and in the internal zone in the case of the amino-terminated open dendrimer. At acidic pH, PAMAM dendrimers with both terminal groups are still able to interact with peptides either internalized or in its periphery, however, the number of contacts, the percentage of coverage and the number of HBs are lesser than at neutral pH, suggesting a state for peptide release. In summary, amino-terminated PAMAM dendrimer showed slightly better features to bind, load and protect Angiotensin-(1-7) peptides.
Detection of latent Epstein-Barr virus gene expression in single-cell sequencing of peripheral blood mononuclear cells
Authors: Bäckerholm Alan , Tian Yarong , Holmqvist Isak , Xie Guojiang , Vracar Diana , Abrahamsson Sanna , Guibentif Carolina , Tang Ka-Wei
Published: May 2022

Epstein-Barr virus (EBV) DNA is regularly found in the blood of patients with EBV associated diseases and occasionally in healthy individuals. However, EBV infected primary B-lymphocytes have not yet been detected using scRNA seq. Here, we screened the viral transcriptome in single cell RNA sequencing datasets from peripheral blood to identify virus infected cells. Whereas EBV RNA was detected in an immunocompromised patient, EBV associated nasopharyngeal carcinoma and multiple sclerosis samples did not display any levels of circulating EBV RNA. We further screened whole-blood samples from a cohort of immunosuppressed patients for viral transcripts using a custom enhanced RT-qPCR panel and detected latency programs dominated by noncoding RNAs (EBERs and RPMS1). To explore the interplay between the EBV and the host-cell transcriptome profile, we used enriched B-lymphocytes from a splenectomy patient with 30% EBER positivity estimated by in situ hybridization and performed 5’ single-cell RNA sequencing with paired VDJ profiling. The EBV expression pattern of the patients’ B-lymphocytes confirmed the RT-qPCR assay with RPMS1 and LMP-1/BNLF2a/b significantly dominating the sequenced EBV polyadenylated RNA. A comparison between the expression profile of EBV positive B-lymphocytes and healthy controls B-lymphocytes revealed the upregulation in genes involved in cell population proliferation when infected with EBV. This is further supported by a measurable polyclonal expansion in the patient, as compared to a control, emphasizing EBV’s role in a host-cell’s tendency for cellular expansion. However, when contrasting to cells that have undergone malignant transformation, the primary EBV infected cells display a rather dissimilar expression profile, even to cells that are supposed to simulate primary EBV infection (I.e. Lymphoblastoid Cell Lines). This implies that during primary infection of EBV, the host-cell enters a state of premalignancy rather than a complete oncogenic transformation at the initial time of infection
Gram-positive bacteria evade phage predation through endolysin-mediated L-form conversion
Authors: Wohlfarth Jan C. , Feldmüller Miki , Schneller Alissa , Kilcher Samuel , Burkolter Marco , Pilhofer Martin , Schuppler Markus , Loessner Martin J.
Published: May 2022

Bacteriophages kill bacteria by osmotic lysis towards the end of the lytic cycle. In the case of Gram-positive bacteria, peptidoglycan-degrading endolysins released at the end of infection cycle cause explosive cell lysis not only of the infected host, but can also attack non-infected bystander cells. Here, we show that in osmotically stabilized environments, Listeria monocytogenes can evade phage predation by transient conversion to a cell wall-deficient L-form state. This L-form escape is triggered by endolysins disintegrating the cell wall from without, leading to turgor-driven extrusion of wall-deficient, yet viable L-form cells. Remarkably, in absence of phage predation, we show that L-forms can quickly revert to the walled state. These findings suggest that L-form conversion represents a population-level persistence mechanism to evade complete eradication by phage attack. Importantly, we also demonstrate phage-mediated L-form switching of the urinary tract pathogen Enterococcus faecalis in human urine, which underscores that this escape route may be widespread and has important implications for phage- and endolysin-based therapeutic interventions.
The substrate scopes of enzymes: a general prediction model based on machine and deep learning
Authors: Kroll Alexander , Ranjan Sahasra , Engqvist Martin K. M. , Lercher Martin J.
Published: May 2022

For a comprehensive understanding of metabolism, it is necessary to know all potential substrates for each enzyme encoded in an organism’s genome. However, for most proteins annotated as enzymes, it is unknown which primary and/or secondary reactions they catalyze [1], as experimental characterizations are time-consuming and costly. Machine learning predictions could provide an efficient alternative, but are hampered by a lack of information regarding enzyme non-substrates, as available training data comprises mainly positive examples. Here, we present ESP, a general machine learning model for the prediction of enzyme-substrate pairs, with an accuracy of over 90% on independent and diverse test data. This accuracy was achieved by representing enzymes through a modified transformer model [2] with a trained, task-specific token, and by augmenting the positive training data by randomly sampling small molecules and assigning them as non-substrates. ESP can be applied successfully across widely different enzymes and a broad range of metabolites. It outperforms recently published models designed for individual, well-studied enzyme families, which use much more detailed input data [3, 4]. We implemented a user-friendly web server to predict the substrate scope of arbitrary enzymes, which may support not only basic science, but also the development of pharmaceuticals and bioengineering processes.
Characterization and genome analysis of a psychrophilic methanotroph representing a ubiquitousMethylobacterspp. cluster in boreal lake ecosystems
Authors: Khanongnuch Ramita , Mangayil Rahul , Svenning Mette Marianne , Rissanen Antti Juhani
Published: May 2022

Lakes and ponds are considered as a major natural source of CH4emissions, particularly during the ice-free period in boreal ecosystems. Aerobic methane oxidizing bacteria (MOB), which utilize CH4using oxygen as an electron acceptor, are one of dominant microorganisms in the CH4-rich water columns. The metagenome-assembled genomes (MAGs) have revealed the genetic potential of MOB from boreal aquatic ecosystems for various microaerobic/anaerobic metabolic functions; however, the experimental validation of the process has not been succeeded. Additionally, psychrophilic (i.e., cold loving) MOB isolates and their CH4oxidizing process have rarely been investigated. In this study, we isolated, provided taxonomic description, and analyzed the genome ofMethylobacter sp. S3L5C, a psychrophilic MOB, from a boreal lake in Finland. Based on phylogenomic comparisons to MAGs,Methylobactersp. S3L5C represented a ubiquitous cluster ofMethylobacterspp. in boreal aquatic ecosystems. At optimal temperatures (3–12 °C) and pH (6.8–8.3), the specific growth rates (μ) and CH4utilization rate were in the range of 0.018–0.022 h-1and 0.66–1.52 mmol l-1d-1, respectively. In batch cultivation, the isolate could produce organic acids and the concentrations were elevated after replenishing CH4and air into headspace. The highest concentrations of 4.1 mM acetate, 0.02 mM malate and 0.07 mM propionate were observed at the end of the cultivation period under the optimal operational conditions. The results herein highlight the key role ofMethylobacterspp. in regulating CH4emissions and their potential to provide CH4-derived organic carbon compounds to surrounding heterotrophic microorganisms in cold ecosystems.
Impact of Shelterin Complex on Telomere Accessibility
Authors: Shiekh Sajad , Jack Amanda , Mustafa Golam , Kodikara Sineth G. , Gyawali Prabesh , Hoque Mohammed Enamul , Yildiz Ahmet , Balci Hamza
Published: May 2022

Shelterin plays critical roles in maintaining and protecting telomeres by regulating access of various physiological agents to telomeric DNA. We present single molecule measurements investigating the impact of the POT1 and a four-component shelterin complex on the accessibility of human telomeric DNA overhangs with physiologically relevant lengths (28-150 nt), which to our knowledge is the first direct approach to measure this effect on such telomeric constructs. To quantify telomere accessibility, we monitored transient binding events of a short peptide nucleic acid (PNA) probe that is complementary to telomeric overhangs using FRET-PAINT. Although POT1 has a mild G-quadruplex unfolding activity, it reduced accessibility of the PNA probe by ∼2.5 fold, indicating that POT1 effectively binds to and protects otherwise exposed telomeric sequences. In comparison, a four-component shelterin reduced the accessibility of telomeric overhangs by ∼5-fold. This enhanced protection suggests shelterin restructures the region between single and double stranded telomere, which is otherwise the most accessible part of the overhang, by a synergistic cooperation of shelterin components located on single and double stranded telomere.
Fitm2 is required for ER homeostasis and normal function of murine liver
Authors: Bond Laura M. , Ibrahim Ayon , Lai Zon W. , Walzem Rosemary L. , Bronson Roderick T. , Ilkayeva Olga R. , Walther Tobias C. , Farese Robert V.
Published: May 2022

The ER-resident protein fat-inducing transcript 2 (FIT2) catalyzes acyl-CoA cleavage in vitro and is required for endoplasmic reticulum (ER) homeostasis and normal lipid storage in cells. The gene encoding FIT2 is essential for the viability of mice and worms. Whether FIT2 acts as an acyl-CoA diphosphatase in vivo and how this activity affects liver, where the protein was discovered, are unknown. Here, we report that hepatocyte-specific Fitm2 knockout (FIT2-LKO) mice exhibited elevated acyl-CoA levels, ER stress, and signs of liver injury. FIT2-LKO mice fed a chow diet had more triglycerides in their livers than control littermates due, in part, to impaired secretion of triglyceride-rich lipoproteins and reduced capacity for fatty acid oxidation. Challenging FIT2-LKO mice with a high-fat diet to increase FIT2 acyl-CoA substrates worsened hepatic ER stress and liver injury, but unexpectedly reversed the steatosis phenotype, similar to what is observed in FIT2-deficient cells loaded with fatty acids. Our findings support the model that FIT2 acts as an acyl-CoA diphosphatase in vivo and is crucial for normal hepatocyte function and ER homeostasis in murine liver.
Subcutaneous delivery of an antibody against SARS-CoV-2 from a supramolecular hydrogel depot
Authors: Kasse Catherine M. , Yu Anthony C. , Powell Abigail E. , Roth Gillie A. , Liong Celine S. , Jons Carolyn K. , Buahin Awua , Maikawa Caitlin L. , Youssef Sawsan , Glanville Jacob E. , Appel Eric A.
Published: May 2022

Prolonged maintenance of therapeutically-relevant levels of broadly neutralizing antibodies (bnAbs) is necessary to enable passive immunization against infectious disease. Unfortunately, protection only lasts for as long as these bnAbs remain present at a sufficiently high concentration in the body. Poor pharmacokinetics and burdensome administration are two challenges that need to be addressed in order to make pre- and post-exposure prophylaxis with bnAbs feasible and effective. In this work, we develop a supramolecular hydrogel as an injectable, subcutaneous depot to encapsulate and deliver antibody drug cargo. This polymer-nanoparticle (PNP) hydrogel exhibits shear-thinning and self-healing properties that are required for an injectable drug delivery vehicle. In vitro drug release assays and diffusion measurements indicate that the PNP hydrogels prevent burst release and slow the release of encapsulated antibodies. Delivery of bnAbs against SARS-CoV-2 from PNP hydrogels is compared to standard routes of administration in a preclinical mouse model. We develop a multi-compartment model to understand the ability of these subcutaneous depot materials to modulate the pharmacokinetics of released antibodies; the model is extrapolated to explore the requirements needed for novel materials to successfully deliver relevant antibody therapeutics with different pharmacokinetic characteristics.
Mycobacterium tuberculosis genetic features associated with pulmonary tuberculosis severity
Authors: Genestet Charlotte , Refrégier Guislaine , Hodille Elisabeth , Zein-Eddine Rima , Meur Adrien Le , Hak Fiona , Barbry Alexia , Westeel Emilie , Berland Jean-Luc , Engelmann Astrid , Verdier Isabelle , Lina Gérard , Ader Florence , Dray Stéphane , Jacob Laurent , Massol François , Venner Samuel , Dumitrescu Oana
Published: May 2022

Mycobacterium tuberculosis (Mtb) infections result in a wide spectrum of clinical presentations but without proven Mtb genetic determinants. Herein, 234 pulmonary tuberculosis (TB) patients were stratified according to TB disease severity and Mtb genetic features were explored using whole genome sequencing, including heterologous single nucleotide polymorphism (SNP) calling to explore micro-diversity. Clinical isolates from patients with mild TB carried mutations in genes associated with host-pathogen interaction, while those from patients with moderate/severe TB carried mutations associated with regulatory mechanisms. Genome-wide association study identified a SNP in the promoter of the gene coding for the virulence regulator EspR associated with moderate/severe disease. Structural equation modelling and model comparisons indicated that TB severity was associated with the detection of Mtb micro-diversity within clinical isolates and to the espR SNP. Taken together, these results provide a new insight to better understand TB pathophysiology and could provide new prognosis tool for pulmonary TB severity.
Structural phase transition in a charge-transfer compound: tropylium hexafluoridoantimonate(V)–1,4-dimethylnaphthalene (1/1)
Authors: Liao Rong-Meng , An Zhen , Ye Heng-Yun
Published: May 2022

Molecular motion in crystals has attracted much attention for the development of stimuli-responsive materials. The most studied are molecules with few atoms or highly symmetrical molecules. To develop molecules with new motion characteristics, we synthesized a charge-transfer compound, namely, tropylium hexafluoridoantimonate(V)–1,4-dimethylnaphthalene (1/1), (C7H7)[SbF6]·C12H12, and studied its structural phase transition. In this compound, the tropylium cation and the 1,4-dimethylnaphthalene molecule have planar geometry, but the latter has low symmetry. They are stacked as a one-dimensional chain structure through π–π charge-transfer interactions. Weak intermolecular interactions and planar molecular geometry result in a large degree of freedom of in-plane motion. Upon heating, due to the in-plane rotation of the molecules, the compound undergoes an order–disorder structural phase transition (phase-transition temperature = 334 K). The space group of the room-temperature phase is P21/m and the space group of the high-temperature phase is P4/mmm. This phase transition is accompanied by significant dielectric anomalies. The current investigation shows that the structural features of the title compound can be used to construct functional materials with phase transitions, such as molecular ferroelectrics.
Structural visualization of transient interactions between the cis-acting acyltransferase and acyl carrier protein of the salinomycin modular polyketide synthase
Authors: Feng Y. , Zhang F. , Huang S. , Deng Z. , Bai L. , Zheng J.
Published: May 2022

Transient protein–protein interactions between cis-acting acyltransferase (AT) and acyl carrier protein (ACP) domains are critical for the catalysis and processivity of modular polyketide synthases (mPKSs), but are challenging for structural characterization due to the intrinsically weak binding affinity. Here, a stable complex of cis-acting AT and ACP domains from the ninth module of the salinomycin mPKS was obtained using a maleimide cross-linker and the structure of the complex was determined at 2.6 Å resolution. The crystal structure shows that the AT in combination with the ketosynthase (KS)-to-AT linker forms a C-shaped architecture to embrace the ACP. The large hydrolase subdomain of the AT serves as a major binding platform for the ACP, while the small ferredoxin-like subdomain of the AT and the KS-to-AT linker cooperate with each other to constrain binding of the ACP. The importance of interface residues in cis-acting AT–ACP interactions was confirmed by mutagenesis assays. The interaction mode observed in the cis-acting AT–ACP complex is completely different from those observed in trans-acting AT–ACP complexes, where the ACP primarily contacts the small domain of the AT. The complex structure provides detailed mechanistic insights into AT–ACP recognition in cis-AT mPKSs.
Learner characteristics attributable to completion and duration of completion in engineering and science degree programmes of OUSL
Authors: Navaratna Chandanie Wijayalatha , Bandarage Gunadya , Rajapaksha Appuhamilage Dilsha Nimmi , Pasqual Hemali , Rajendra Joseph Calistus Nihal , Ranasinghe Menaka D.D. , Ratnayake Uditha W.
Published: May 2022

Purpose

The purpose of this study is to identify the learner characteristics attributable to the likelihood and the duration of programme completion in the Bachelor of Science (BSc) and Bachelor of Technology Honours in Engineering (BTech) degree programmes of the Open University of Sri Lanka (OUSL).

Design/methodology/approach

Data were gathered from the re-registrants for the degree programmes in the academic year 2020/2021, using a questionnaire developed as a Google form. The sample consisted of 301 and 516 re-registrants from the BTech and BSc programmes respectively. Influential factors were identified using Kruskal Wallis test (for duration of completion), binary logistic regression (for likelihood of completion) and Chi-squared test (associations between presage and process factors).

Findings

Entry qualification, age and time management skills at entry had significant effects on duration of completion. Attendance at academic activities, organizing time for self-studies and the competency in English at enrolment had significant effects on the likelihood of completion. Prior open and distance learning (ODL) experience had no significant effect on any of the product factors considered.

Research limitations/implications

Inaccessibility of dropouts and using only the responses from the first administration of the questionnaire are limitations. Active learners are more likely to respond, in the first administration and may bias the results.

Practical implications

Findings are useful for designing future studies to identify at-risk students and thereby enhance the programme completion and reduce prolonged time for completion.

Social implications

Effective strategies to control the identified factors will uplift programme completion and reduce drop-out rates.

Originality/value

Decision making using inferential techniques makes the study distinct among studies undertaken on the same population. The study enriches the limited current research on factors affecting programme completion in ODL mode.