bluuebunny/crossref_metadata_2025 huggingface dataset:
In BRCA1 and BRCA2 breast cancers, chromosome breaks occur near herpes tumor virus sequences
Authors: Friedenson Bernard
Published: April 2021

Inherited mutations in BRCA1 and BRCA2 genes increase risks for breast, ovarian, and other cancers. Both genes encode proteins for accurately repairing chromosome breaks. If mutations inactivate this function, broken chromosome fragments get lost or reattach indiscriminately. These mistakes are characteristic of hereditary breast cancer. We tested the hypothesis that mistakes in reattaching broken chromosomes preferentially occur near viral sequences on human chromosomes. We tested millions of DNA bases around breast cancer breakpoints for similarities to all known viral DNA. DNA around breakpoints often closely matched the Epstein-Barr virus (EBV) tumor variants HKHD40 and HKNPC60. Almost all breakpoints were near EBV anchor sites, EBV tumor variant homologies, and EBV-associated regulatory marks. On chromosome 2, EBV binding sites accounted for 90% of breakpoints (p<0.0001). On chromosome 4, 51/52 inter-chromosomal breakpoints were close to EBV variant sequences. Five viral anchor sites at critical genes were near breast cancer breakpoints. Twenty-five breast cancer breakpoints were within 1.25% of breakpoints in model EBV cancers. EBV-like sequence patterns around breast cancer breakpoints resemble gene fusion breakpoints in model EBV cancers. All BRCA1 and BRCA2 breast cancers had mutated genes essential for immune responses. Because of this immune compromise, herpes viruses can attach and produce nucleases that break chromosomes. Alternatively, anchored viruses can retard break repairs, whatever the causes. The results imply proactive treatment and prevention of herpes viral infections may benefit BRCA mutation carriers.
Axes of inter-sample variability among transcriptional neighborhoods reveal disease-associated cell states in single-cell data
Authors: Reshef Yakir , Rumker Laurie , Kang Joyce B. , Nathan Aparna , Korsunsky Ilya , Asgari Samira , Murray Megan B. , Moody D. Branch , Raychaudhuri Soumya
Published: April 2021

As single-cell datasets grow in sample size, there is a critical need to characterize cell states that vary across samples and associate with sample attributes like clinical phenotypes. Current statistical approaches typically map cells to cell-type clusters and examine sample differences through that lens alone. Here we present covarying neighborhood analysis (CNA), an unbiased method to identify cell populations of interest with greater flexibility and granularity. CNA characterizes dominant axes of variation across samples by identifying groups of very small regions in transcriptional space—termed neighborhoods—that covary in abundance across samples, suggesting shared function or regulation. CNA can then rigorously test for associations between any sample-level attribute and the abundances of these covarying neighborhood groups. We show in simulation that CNA enables more powerful and accurate identification of disease-associated cell states than a cluster-based approach. When applied to published datasets, CNA captures a Notch activation signature in rheumatoid arthritis, redefines monocyte populations expanded in sepsis, and identifies a previously undiscovered T-cell population associated with progression to active tuberculosis.
Improving the phylogenetic resolution of Malaysian and Javan mahseer (Cyprinidae),Tor tambroidesandTor tambra: Whole mitogenomes sequencing, phylogeny and potential mitogenome markers
Authors: Kit Lim Leonard Whye , Chung Hung Hui , Lin Lau Melinda Mei , Aziz Fazimah , Gan Han Ming
Published: April 2021

The true mahseer (Torspp.) is one of the highest valued fish in the world due to its high nutritional value and great unique taste. Nevertheless, its morphological characterization and single mitochondrial gene phylogeny in the past had yet to resolve the ambiguity in its taxonomical classification. In this study, we sequenced and assembled 11 complete mahseer mitogenomes collected from Java of Indonesia, Pahang and Terengganu of Peninsular Malaysia as well as Sarawak of East Malaysia. The mitogenome evolutionary relationships among closely relatedTorspp. samples were investigated based on maximum likelihood phylogenetic tree construction. Compared to the commonly used COX1 gene fragment, the complete COX1, Cytb, ND2, ND4 and ND5 genes appear to be better phylogenetic markers for genetic differentiation at the population level. In addition, a total of six population-specific mitolineage haplotypes were identified among the mahseer samples analyzed, which this offers hints towards its taxonomical landscape.
Oncogenic signaling inhibits c-FLIP expression and promotes cancer cell survival during ECM-detachment
Authors: Tsegaye Matyas Abel , He Jianping , McGeehan Kyle , Murphy Ireland M. , Nemera Mati , Schafer Zachary T.
Published: April 2021

Inhibition of programmed cell death pathways is frequently observed in cancer cells where it functions to facilitate tumor progression. However, some proteins involved in the regulation of cell death function dichotomously to both promote and inhibit cell death depending on the cellular context. As such, understanding how cell death proteins are regulated in a context-dependent fashion in cancer cells is of utmost importance. We have uncovered evidence that cellular FLICE-like Inhibitory Protein (c-FLIP), a well-known anti-apoptotic protein, is often downregulated in tumor tissue when compared to adjacent normal tissue. These data argue that c-FLIP may have activity distinct from its canonical role in antagonizing cell death. Interestingly, we have discovered that detachment from extracellular matrix (ECM) serves as a signal to elevate c-FLIP transcription and that oncogenic signaling blocks ECM-detachment-induced c-FLIP elevation. In addition, our data reveal that downregulation of c-FLIP promotes the survival of ECM-detached cells and that c-FLIP overexpression in cancer cells restricts the viability of cancer cells grown in anchorage-independent conditions. Taken together, our study reveals an unexpected role for c-FLIP in constraining the viability of cancer cells during ECM-detachment and raises the idea that c-FLIP may have context-dependent pro- and anti-cell death roles during tumorigenesis.
Mutant alleles differentially shape cattle complex traits and fitness
Authors: Xiang Ruidong , Breen Ed J. , Bolormaa Sunduimijid , Vander Jagt Christy J. , Chamberlain Amanda J. , Macleod Iona M. , Goddard Michael E.
Published: April 2021

Classical mutant alleles (MAs), with large effects on phenotype, tend to be deleterious to traits and fitness. Is this the case for mutations with small effects? We infer MAs for 8 million sequence variants in 113k cattle and quantify the effects of MA on 37 complex traits. Heterozygosity for variants at genomic sites conserved across 100 vertebrates increase fertility, stature, and milk production, positively associating these traits with fitness. MAs decrease stature and fat and protein concentration in milk, but increase gestation length and somatic cell count in milk (the latter indicative of mastitis). However, the allele frequency of MAs that decrease fat and protein concentration and stature and increase gestation length and somatic cell count is lower than the allele frequency of MAs with the opposite effect. These results suggest bias in the direction of effect of mutation (e.g. towards reduced protein in milk), but selection operating to reduce the frequency of these MAs. Taken together, our results imply two classes of genomic sites subject to long-term selection: sites conserved across vertebrates show hybrid vigour while sites subject to less long-term selection show a bias in mutation towards alleles that are selected against.
The Impact of a Dynamic Working Environment on Human Gut Microbiota
Authors: Ling Lu , Zhou Jun , Meng Qianlong , Zhang Ziran , Li Wenkun , Cui Zilu , Liu Kuiliang , Zeng Fanxin , Wu Jing , Wang Jing
Published: April 2021

Gut microbiota dysbiosis is associated with a variety of diseases, such as inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS), metabolic diseases, allergic diseases, neurodevelopmental disorders and cancer. The human gut microbiota can be influenced by a variety of factors, including geography, dietary habits, living environment, age and altered lifestyle etc. This study was conducted to explore the gut microbiota compositions in officials who are in a stable working environment and train drivers who are in a dynamic working environment. Microbiota communities in the feces of 80 officials and 88 train drivers were analyzed using Illumina MiSeq sequencing targeting the V3-V4 region of 16S ribosomal RNA (rRNA) gene and ITS1 region of fungi. There were significant differences between the two groups in diversity and richness of gut microbiota, while the microbial community compositions of the two groups were similar. The relationship between gut microbiota and clinical characteristics was investigated. We found that more bacteria and fungi were positively correlated with clinical characteristics. Functional prediction analysis of the gut microbiota between the two groups by PICRUSt2 revealed significant differences between the official group and the train driver group. Elucidating these differences of the microbiome between the two groups will provide a foundation understanding of the impact of a dynamic environment on gut microbiota.
Novel MAPK/AKT-impairing germline NRAS variant identified in a melanoma-prone family
Authors: Brown Kevin M. , Xu Mai , Sargen Michael , Jang Hyunbum , Zhang Mingzhen , Zhang Tongwu , Zhu Bin , Jones Kristie , Kim Jung , Mendoza Laura , Hayward Nicholas K. , Tucker Margaret A. , Goldstein Alisa M. , Yang Xiaohong Rose , Stewart Douglas R. , Hicks Belynda , Consonni Dario , Pesatori Angela C. , Fargnoli Maria Concetta , Peris Ketty , Stratigos Alex , Menin Chiara , Ghiorzo Paola , Puig Susana , Nagore Eduardo ,   MelaNostrum Consortium, Andresson Thorkell , Nussinov Ruth , Calista Donato , Landi Maria Teresa
Published: April 2021

While several high-penetrance melanoma risk genes are known, variation in these genes fail to explain melanoma susceptibility in a large proportion of high-risk families. As part of a melanoma family sequencing study, including 435 families from Mediterranean populations, we identified a novel NRAS variant (c.170A>C, p.D57A) in a melanoma-prone family. This variant is absent in exomes in gnomAD, ESP, UKBiobank, and the 1000 Genomes Project, as well as in 11 273 Mediterranean individuals and 109 melanoma-prone families from the US and Australia. This variant occurs in the GTP-binding pocket of NRAS. Differently from other RAS activating alterations, NRAS D57A expression is unable to activate MAPK-pathway both constitutively and after stimulation but enhances EGF-induced PI3K-pathway signaling in serum starved conditions in vitro. Consistent with in vitro data demonstrating that NRAS D57A does not enrich GTP binding, molecular modeling suggests that the D57A substitution would be expected to impair Mg2+ binding and decrease nucleotide-binding and GTPase activity of NRAS. While we cannot firmly establish NRAS c.170A>C (p.D57A) as a melanoma susceptibility variant, further investigation of NRAS as a familial melanoma gene is warranted.
Effectiveness of the BNT162b2 vaccine in preventing COVID-19 in the working age population – first results from a cohort study in Southern Sweden
Authors: Björk Jonas , Inghammar Malin , Moghaddassi Mahnaz , Rasmussen Magnus , Malmqvist Ulf , Kahn Fredrik
Published: April 2021

Background

Vaccine effectiveness against COVID-19 needs to be assessed in diverse real-world population settings.

Methods

A cohort study of 805 741 residents in Skåne county, Southern Sweden, aged 18-64 years, of whom 26 587 received at least one dose of the BNT162b2 vaccine. Incidence rates of COVID-19 were estimated in sex- and age-adjusted analysis and stratified in two-week periods with substantial community spread of the disease.

Results

The estimated vaccine effectiveness in preventing infection ≥7 days after second dose was 86% (95% CI 72-94%) but only 42% (95% CI 14-63%) ≥14 days after a single dose. No difference in vaccine effectiveness was observed between females and males. Having a prior positive test was associated with 91% (95% CI 85 to 94%) effectiveness against new infection among the unvaccinated.

Conclusion

A satisfactory effectiveness of BNT162b2 after the second dose was suggested, but with possibly substantially lower effect before the second dose.
Children have similar RT-PCR cycle threshold for SARS-CoV-2 in comparison with adults
Authors: Polese-Bonatto Márcia , Sartor Ivaine Tais Sauthier , Varela Fernanda Hammes , Gianinni Gabriela Luchiari Tumioto , Azevedo Thaís Raupp , Kern Luciane Beatriz , Fernandes Ingrid Rodrigues , Zavaglia Gabriela Oliveira , de David Caroline Nespolo , de Almeida Walquiria Aparecida Ferreira , Porto Victor Bertollo Gomes , Scotta Marcelo Comerlato , Stein Renato T. ,   COVIDa study group
Published: April 2021

Background

The viral dynamics and the role of children in the spread of SARS-CoV-2 are not completely understood. Our aim was to evaluate RT-PCR Ct values among children with confirmed SARS-CoV-2 compared with that of adult subjects.

Methods

Patients (aged from 2 months to ≤18 years, and adults) with signs and symptoms of acute SARS-CoV-2 infection for less than 7 days, were prospectively enrolled in the study from May to November 2020. All participants performed RT-PCR assay for SARS-CoV-2 detection; Ct values of ORF1ab, N, and S gene-targets, and the average of all the three probes were used as surrogates of viral load.

Results

There were 21 infants, 62 children and 293 adults of 376 participants with confirmed SARS-CoV-2 infections. RT-PCR Ct values of children under 18 were not significantly different from that of adults after adjusting for days of illness, as observed by the analyzed probes (namely ORF1ab, N, and S), and by the mean of all 3 gene-targets.

Conclusions

Ct values for children were comparable to that of adults. Days of illness are a major confounder for SARS-CoV-2 viral load and must be adjusted in any comparison. Although viral load is not the only determinant of SARS-CoV-2 transmission, children may play a significant role in the spread of in the community.
When can we safely return to normal? A novel method for identifying safe levels of NPIs in the context of COVID-19 vaccinations
Authors: Bianchin Gianluca , Dall’Anese Emiliano , Poveda Jorge I. , Buchwald Andrea G.
Published: April 2021

Over the course of the COVID-19 pandemic, governing bodies and individuals have relied on a variety of non-pharmaceutical interventions (NPIs) to control the transmission of SARS-CoV-2, which posed an acute threat to individuals’ well-being and consistently impacted economic activities in many countries worldwide. NPIs have been implemented at varying levels of severity and in response to widely-divergent perspectives of risk tolerance. Now, concurrently with the introduction of multiple SARS-CoV-2 vaccines, the world looks optimistically to a “return to normality”. In this work, we propose a multi-disciplinary approach, combining transmission modeling with control and optimization theory, to examine how risk tolerance and vaccination rates will impact the safe return to normal behavior over the next few months. To this end, we consider a version of the Susceptible-Exposed-Infected-Recovered transmission model that accounts for hospitalizations, vaccinations, and loss of immunity. We then propose a novel control approach to calibrate the necessary level of NPIs at various geographical levels to guarantee that the number of hospitalizations does not exceed a given risk tolerance (i.e., a maximum allowable threshold). Our model and control objectives are calibrated and tailored for the state of Colorado, USA. Our results suggest that: (i) increasing risk tolerance can decrease the number of days required to discontinue all NPIs; (ii) increasing risk tolerance inherently increases COVID-19 deaths even in the context of vaccination; (iii) if the vaccination uptake in the population is 70% or less, then return to normal behavior within the next year may newly stress the healthcare system. Furthermore, by using a multi-region model accounting for travel, our simulations predict that: (iv) relaxation should take into account regional heterogeneity in transmission and travel; and (v) premature relaxation of NPIs, even if restricted only to low-density regions, will lead to exceeding hospitalization limits even when highly-populated regions implement full-closures. Although the simulations are performed for the state of Colorado, the proposed model of transmission and control methods are applicable to any area worldwide and can be utilized at any geographical granularity.
Loss-of-function variants in the KCNQ5 gene are associated with genetic generalized epilepsies
Authors: Krüger Johanna , Schubert Julian , Kegele Josua , Labalme Audrey , Mao Miaomiao , Heighway Jacqueline , Seebohm Guiscard , Yan Pu , Koko Mahmoud , Aslan Kezban , Caglayan Hande , Steinhoff Bernhard J. , Weber Yvonne G. , Keo-Kosal Pascale , Berkovic Samuel F. , Hildebrand Michael S. , Petrou Steven , Krause Roland , May Patrick , Lesca Gaetan , Maljevic Snezana , Lerche Holger
Published: April 2021

Objective

De novo missense variants in KCNQ5, encoding the voltage-gated K+ channel KV7.5, have been described as a cause of developmental and epileptic encephalopathy (DEE) or intellectual disability (ID). We set out to identify disease-related KCNQ5 variants in genetic generalized epilepsy (GGE) and their underlying mechanisms.

Methods

1292 families with GGE were studied by next-generation sequencing. Whole-cell patch-clamp recordings, biotinylation and phospholipid overlay assays were performed in mammalian cells combined with docking and homology modeling.

Results

We identified three deleterious heterozygous missense variants, one truncation and one splice site alteration in five independent families with GGE with predominant absence seizures, two variants were also associated with mild to moderate ID. All three missense variants displayed a strongly decreased current density indicating a loss-of-function (LOF). When mutant channels were co-expressed with wild-type (WT) KV7.5 or KV7.5 and KV7.3 channels, three variants also revealed a significant dominant-negative effect on WT channels. Other gating parameters were unchanged. Biotinylation assays indicated a normal surface expression of the variants. The p.Arg359Cys variant altered PI(4,5)P2- interaction, presumably in the non-conducting preopen-closed state.

Interpretation

Our study indicates that specific deleterious KCNQ5 variants are associated with GGE, partially combined with mild to moderate ID. The disease mechanism is a LOF partially with dominant-negative effects through functional, rather than trafficking deficits. LOF of KV7.5 channels will reduce the M-current, likely resulting in increased excitability of KV7.5- expressing neurons. Further studies on a network level are necessary to understand which circuits are affected and how the variants induce generalized seizures.
Is it time to ACT? A qualitative study of the acceptability and feasibility
of Acceptance and Commitment Therapy for adolescents with Chronic Fatigue
Syndrome
Authors: Clery Philippa , Starbuck Jennifer , Laffan Amanda , Parslow Roxanne , Linney Catherine , Leveret Jamie , Crawley Esther
Published: April 2021

Background

Paediatric Chronic Fatigue Syndrome/Myalgic Encephalomyelitis (CFS/ME)
is disabling and relatively common. Although evidenced based treatments are
available, at least 15% of children remain symptomatic after one year of
treatment. Acceptance and Commitment Therapy (ACT) is an alternative therapy
option; however, little is known about whether it is an acceptable treatment
approach. Our aim was to find out if children who are still disabled by
CFS/ME after 12 months of treatment would find ACT acceptable, to inform a
randomised controlled trial (RCT) of ACT.

Methods

We recruited children (diagnosed with CFS/ME; not recovered after one
year of treatment; aged 11-17 years), their parent/carer, and healthcare
professionals (HCPs) from one specialist UK paediatric CFS/ME service. We
conducted semi-structured interviews to explore barriers to recovery; views
on current treatments; acceptability of ACT; and feasibility of using an RCT
to test effectiveness. Thematic analysis was used to identify patterns in
data.

Results

Twelve adolescents, eleven parents, and seven HCPs were interviewed. All
participants thought ACT was acceptable. Participants identified reasons why
ACT might be efficacious: pragmatism, acceptance and compassion are valued
in chronic illness; values-focussed treatment provides motivation and
direction; psychological and physical needs are addressed; normalising
difficulties is a useful life-skill. Some adolescents preferred ACT to
Cognitive Behavioural Therapy as it encouraged accepting (rather than
challenging) thoughts. Most adolescents would consent to an RCT of ACT but a
barrier to recruitment was reluctance to randomisation. All HCPs deemed ACT
feasible to deliver. Some were concerned patients might confuse ‘acceptance’
with ‘giving up’ and called for clear explanations. All participants thought
the timing of ACT should be individualised.

Conclusions

All adolescents with CFS/ME, parents, and HCPs thought ACT was
acceptable, and most adolescents were willing to try ACT. An RCT needs to
solve issues around randomisation and timing of the intervention.

BOX

What is known about the subject?

Not all young people with CFS/ME recover.

ACT is a possible alternative therapy for CFS/ME, which
focuses on improving functioning and quality of life rather
than symptom reduction.

ACT is efficacious in paediatric chronic pain, and
preliminary results show promising effects in adults with
CFS/ME.

What this study adds?

ACT is an acceptable therapy for young people with
CFS/ME.

Participants thought the ‘pragmatic’, ‘compassionate’
and ‘values-based’ focus of ACT would be helpful.

Adolescents, parents and healthcare professionals
support a randomised controlled trial of ACT.
DNA-based data storage via combinatorial assembly
Authors: Roquet Nathaniel , Bhatia Swapnil P , Flickinger Sarah A , Mihm Sean , Norsworthy Michael W , Leake Devin , Park Hyunjun
Published: April 2021

Persistent data storage is the basis of all modern information systems. The long-term value and volume of data are growing at an accelerating rate and pushing extant storage systems to their limits. DNA offers exciting potential as a storage medium, but no practical scheme has been proposed to date that can scale beyond narrow-band write rates. Here, we demonstrate a combinatorial DNA data encoding scheme capable of megabits per second write speeds. The system relies on rapid, combinatorial assembly of multiple smaller DNA parts that are dispensed through inkjet printing. To demonstrate this approach, we wrote approximately 25 kB of information into DNA using our system and read the information back out with commercially available nanopore sequencing. Moreover, we demonstrate the ability to replicate and selectively access the information while it is in DNA, opening up the possibility of more sophisticated DNA computation.
High efficiency excitation energy transfer in biohybrid quantum dot–bacterial reaction center nanoconjugates
Authors: Amoruso Giordano , Liu Juntai , Polak Daniel W. , Tiwari Kavita , Jones Michael R. , Oliver Thomas A. A.
Published: April 2021

Reaction centers (RCs) are the pivotal component of natural photosystems, converting solar energy into the potential difference between separated electrons and holes that is used to power much of biology. RCs from anoxygenic purple photosynthetic bacteria such asRhodobacter sphaeroidesonly weakly absorb much of the visible region of the solar spectrum which limits their overall light-harvesting capacity. Forin vitroapplications such as bio-hybrid photodevices this deficiency can be addressed by effectively coupling RCs with synthetic lightharvesting materials. Here, we studied the time scale and efficiency of Förster resonance energy transfer (FRET) in a nanoconjugate assembled from a synthetic quantum dot (QD) antenna and a tailored RC engineered to be fluorescent. Time-correlated single photon counting spectroscopy of biohybrid conjugates enabled the direct determination of FRET from QDs to attached RCs on a time scale of 26.6 ± 0.1 ns and with a high efficiency of 0.75 ± 0.01.
Effects of CO2and RuBisCO concentration on cyanobacterial growth and carbon isotope fractionation
Authors: Garcia Amanda , Kedzior Mateusz , Taton Arnaud , Li Meng , Young Jodi , Kaçar Betül
Published: April 2021

Carbon isotope biosignatures preserved in the Precambrian geologic record are primarily interpreted to reflect ancient cyanobacterial carbon fixation catalyzed by Form I RuBisCO enzymes. The average range of isotopic biosignatures generally follows that produced by extant cyanobacteria. However, this observation is difficult to reconcile with several environmental (e.g., temperature, pH, and CO2concentrations), molecular, and physiological factors that likely would have differed during the Precambrian and can produce fractionation variability in contemporary organisms that meets or exceeds that observed in the geologic record. To test a range of genetic and environmental factors that may have impacted ancient carbon isotope biosignatures, we engineered a mutant strain of the model cyanobacteriumSynechococcus elongatusPCC 7942 that overexpresses RuBisCO and characterized the resultant physiological and isotope fractionation effects. We specifically investigated how both increased atmospheric CO2concentrations and RuBisCO regulation influence cell growth, oxygen evolution rate, and carbon isotope fractionation in cyanobacteria. We found that elevated CO2increases the growth rate of wild-type and mutant strains, and that the pool of active RuBisCO enzyme increases with increased expression. RuBisCO overexpression in our engineered strain does not significantly affect isotopic discrimination at all tested CO2concentrations, yielding cellular13C/12C isotope discrimination (εp) of ∼24‰ for both wild-type and mutant strains at elevated CO2. Understanding the environmental factors that impact gene regulation, physiology, and evolution is crucial for reconciling microbially driven carbon isotope fractionation with the geologic record carbon biosignatures.
Ultrastructure Expansion Microscopy inTrypanosoma brucei
Authors: Kalichava Ana , Ochsenreiter Torsten
Published: April 2021

Abstract-Introduction

The recently developed ultrastructure expansion microscopy (U-ExM) technique allows to increase the spatial resolution within a cell or tissue for microscopic imaging through the physical expansion of the sample. In this study we validate the use of U-ExM inTrypanosoma bruceiby visualizing the nucleus and kDNA as well as proteins of the cytoskeleton, the basal body, the mitochondrion and the ER.T. bruceiis a unicellular flagellated protozoan parasite and the causative agent of human African sleeping sickness and Nagana in cattle.The highly polarized parasite cell body is about 25 μm in length and is shaped by the subpellicular microtubule corset. Its single flagellum emanates from the posterior part of the cell and is attached along the entire cell body.T. bruceiThe cell contains all typical organelles of eukaryotic cells including ER, Golgi and mitochondrion. Interestingly, Golgi and mitochondrion are single unit organelles in this protozoan parasite. The signature feature of trypanosomes is the single unit mitochondrial genome, the kinetoplast DNA (kDNA) that is organized in a complex structure of interlocked mini- and maxicircles. The kDNA is segregated during cell division by the tripartite attachment complex (TAC) that connects it via the mitochondrial membranes to the base of the flagellum.
The Functional Nanopore Screen: A Versatile High-throughput Assay to Study and Engineer Protein Nanopores inEscherichia coli
Authors: Weber Wadim , Roeder Markus , Probanowski Tobias , Yang Jie , Abujubara Helal , Koeppl Heinz , Tietze Alesia , Stein Viktor
Published: April 2021

Nanopores comprise a versatile class of membrane proteins that carry out a range of key physiological functions and are increasingly developed for different biotechnological applications. Yet, a capacity to study and engineer protein nanopores by combinatorial means has so far been hampered by a lack of suitable assays that combine sufficient experimental resolution with throughput. Addressing this technological gap, the Functional Nanopore (FuN) screen now provides a quantitative and dynamic read-out of nanopore assembly and function inE. coli. The assay is based on genetically-encoded fluorescent protein sensors that resolve the nanopore-dependent influx of Ca2+across the inner membrane ofE. coli. Illustrating its versatile capacity, the FuN screen is first applied to dissect the molecular features that underlie the assembly and stability of nanopores formed by the S2168 holin. In a subsequent step, nanopores are engineered by recombining the transmembrane module of S2168 with different ring-shaped oligomeric protein structures that feature defined hexa-, hepta- and octameric geometries. Library screening highlights substantial plasticity in the ability of the S2168 transmembrane module to oligomerize in alternative geometries while the functional properties of the resultant nanopores can be fine-tuned through the identity of the connecting linkers. Overall, the FuN screen is anticipated to facilitate both fundamental studies and complex nanopore engineering endeavors with many potential applications in biomedicine, biotechnology and synthetic biology.
A shuttle-vector system allows heterologous gene expression in the thermophilic methanogenMethanothermobacter thermautotrophicusΔH
Authors: Fink Christian , Beblawy Sebastian , Enkerlin Andreas M. , Mühling Lucas , Angenent Largus T. , Molitor Bastian
Published: April 2021

ThermophilicMethanothermobacterspp. are used as model microbes to study the physiology and biochemistry of the conversion of hydrogen and carbon dioxide into methane (i.e., hydrogenotrophic methanogenesis), because of their short doubling times and robust growth with high growth yields. Yet, a genetic system for these model microbes was missing despite intense work for four decades. Here, we report the establishment of tools for genetic modification ofM. thermautotrophicus. We developed the modularMethanothermobactervector system, which provided shuttle-vector plasmids (pMVS) with exchangeable selectable markers and replicons for bothEscherichia coliandM. thermautotrophicus. ForM. thermautotrophicus, a thermostable neomycin-resistance cassette served as the selectable marker for positive selection with neomycin, and the cryptic plasmid pME2001 fromMethanothermobacter marburgensisserved as the replicon. The pMVS-plasmid DNA was transferred fromE. coliintoM. thermautotrophicus viainterdomain conjugation. After the successful validation of DNA transfer and positive selection inM. thermautotrophicus, we demonstrated heterologous gene expression of a thermostable β-galactosidase-encoding gene (bgaB) fromGeobacillus stearothermophilusunder the expression control of four distinct synthetic and native promoters. In quantitativein-vitroenzyme activity assays, we found significantly different β-galactosidase activity with these distinct promoters. With a formate dehydrogenase operon-encoding shuttle vector, we allowed growth ofM. thermautotrophicuson formate as the sole growth substrate, while this was not possible for the empty vector control. These genetic tools provide the basis to investigate hypotheses from four decades of research on the physiology and biochemistry ofMethanothermobacterspp. on a genetic level.

Significance Statement

The world economies are facing permanently increasing energy demands. At the same time, carbon emissions from fossil sources need to be circumvented to minimize harmful effects from climate change. The power-to-gas platform is utilized to store renewable electric power and decarbonize the natural gas grid. The microbeMethanothermobacter thermautotrophicusis already applied as the industrial biocatalyst for the biological methanation step in large-scale power-to-gas processes. To improve the biocatalyst in a targeted fashion, genetic engineering is required. With our shuttle-vector system for heterologous gene expression inM. thermautotrophicus, we set the cornerstone to engineer the microbe for optimized methane production, but also for production of high-value platform chemicals in power-to-x processes.
Wolbachia cifBinduces cytoplasmic incompatibility in the malaria mosquito
Authors: Adams Kelsey L. , Abernathy Daniel G. , Willett Bailey C. , Selland Emily K. , Itoe Maurice A. , Catteruccia Flaminia
Published: April 2021

Wolbachiainfections are a fascinating example of reproductive parasitism with strong potential to combat vector-borne diseases, due to their combined ability to spread in insect populations and block pathogen replication. Though theWolbachiafactors mediating the notable reproductive manipulation cytoplasmic incompatibility (CI) have now been identified as prophage WO genescifAandcifB, the relative role of these genes is still intensely debated, with different models claiming that CI requires either both factors orcifBalone. Here we investigated whethercifAandcifBare sufficient to induce conditional sterility in the major malaria vectorAnopheles gambiae, a species that appears to have limited susceptibility to invasion byWolbachia. We report that CI can be fully recapitulated in these mosquitoes, and thatcifBis sufficient to cause this reproductive manipulation.cifB-induced sterility is fully rescued by high levels ofcifAexpression in females. Surprisingly, however, whencifAis highly expressed in males alongsidecifB, the CI phenotype is attenuated.cifBstrongly impairs fertility also when expressed in the female germline, again mitigated bycifA. These data support a system wherebycifBandcifAmust be fine-tuned to exercise CI and rescue, respectively, possibly explaining the limited success ofWolbachiaat invadingAnopheles. Our findings pave the way towards facilitatingWolbachiainfections in anopheline vectors, for use in malaria control strategies.
Multifactorial seroprofiling dissects the contribution of pre-existing human coronaviruses responses to SARS-CoV-2 immunity
Authors: Abela Irene A. , Pasin Chloé , Schwarzmüller Magdalena , Epp Selina , Sickmann Michèle E. , Schanz Merle M. , Rusert Peter , Weber Jacqueline , Schmutz Stefan , Audigé Annette , Maliqi Liridona , Hunziker Annika , Hesselman Maria C. , Niklaus Cyrille R. , Gottschalk Jochen , Schindler Eméry , Wepf Alexander , Karrer Urs , Wolfensberger Aline , Rampini Silvana K. , Meyer Sauteur Patrick M. , Berger Christoph , Huber Michael , Böni Jürg , Braun Dominique L. , Marconato Maddalena , Manz Markus G. , Frey Beat M. , Günthard Huldrych F. , Kouyos Roger D. , Trkola Alexandra
Published: April 2021

Determination of SARS-CoV-2 antibody responses in the context of pre-existing immunity to circulating human coronavirus (HCoV) is critical to understanding protective immunity. Here we perform a multifactorial analysis of SARS-CoV-2 and HCoV antibody responses in pre-pandemic (N=825) and SARS-CoV-2-infected donors (N=389) using a custom-designed multiplex ABCORA assay. ABCORA seroprofiling, when combined with computational modeling, enables accurate definition of SARS-CoV-2 seroconversion and prediction of neutralization activity, and reveals intriguing interrelations with HCoV immunity. Specifically, higher HCoV antibody levels in SARS-CoV-2-negative donors suggest that preexisting HCoV immunity may provide protection against SARS-CoV-2 acquisition. In those infected, higher HCoV activity is associated with elevated SARS-CoV-2 responses, indicating cross-stimulation. Most importantly, HCoV immunity may impact disease severity, as patients with high HCoV reactivity are less likely to require hospitalization. Collectively, this evidence points to HCoV immunity promoting the rapid development of SARS-CoV-2-specific immunity, underscoring the importance of exploring cross-protective responses for comprehensive coronavirus prevention.
Clinical evaluation of the SD Biosensor saliva antigen rapid test with symptomatic and asymptomatic, non-hospitalized patients
Authors: Igloi Zsofia , Velzing Jans , Huisman Robin , Geurtsvankessel Corine , Comvalius Anoushka , van Beek Janko , Ensing Roel , Boelsums Timo , Koopmans Marion , Molenkamp Richard
Published: April 2021

Performance of saliva antigen rapid test was evaluated in non-hospitalized patients, with or without symptoms. Overall sensitivity was 66.1% compared to RT-PCR in saliva. Using cycle threshold <30 cutoff or virus culture as reference, sensitivity increased to 88.6% or 96.7% respectively. Specificity was 99.6%.
Clinical profile of cutaneous adverse events of immune checkpoint inhibitors in a single tertiary center
Authors: Park Ji‐Hye , Yoon Dokyoung , Lee Jeeyun , Oh Se Jin , Kim Hyun Je , Lee Jong Hee , Lee Dong‐Youn
Published: April 2021

Programmed death 1 (PD‐1)/programmed death ligand 1 (PD‐L1) inhibitors have demonstrated their efficacy in the treatment of various malignancies. Despite their benefits, their immunomodulatory activities can cause unpredictable cutaneous adverse events (CAE). This study aimed to identify characteristics of CAE in patients treated with PD‐1/PD‐L1 inhibitors through the medical records, photographs, and pathology reports. Fifty CAE occurred in 47 (2.75%) of 1711 patients treated with PD‐1/PD‐L1 inhibitors. Pruritic, psoriasiform, urticarial, and acneiform eruptions were the four most common types. Melanoma patients showed CAE more frequently than other malignancies. Acneiform eruption occurred more often at ages under 60 years. Urticarial eruption appeared earlier, while keratoacanthoma appeared later after immunotherapy. The overall survival times were not significantly different between the two groups with and without CAE by Kaplan–Meier analysis (p = 0.055). Studies on CAE may provide more information to understand these drugs and to help manage the patients.
Improving performance of species distribution model in mountainous areas with complex topography
Authors: Liao Chi‐Cheng , Chen Yi‐Huey
Published: April 2021

This study aims to improve performance of species distribution model in mountainous areas with complex topography. Random Forest algorithm was used to evaluate distribution ranges ofTrochodendron aralioidesSiebold & Zucc. in northern Taiwan to identify the determinants of the plant distributions and to assess the effects of data collections on the spatial bias of model predictions. Gridded climate dataset with spatial resolution of 50 × 50 m2for the study area was generated from daily data of 18 meteorological stations and environmental variables were interpolated by inverse distance weighted method and altitudinal adjusted by linear regression model using empirical lapse rates varied among slope inclinations. Model performances were much better when model was run with larger sizes of training datasets generated by randomized resample of presence/absence data records. Surprisingly, distribution ranges of the plant were drastically affected by marginal individuals that is likely to have reached its geographical border as well as climatic limits. Wind speed in winter and temperature differences between warmest and coldest months contributed noticeably to the model predictions. In contrast, index of cloud occurrence contributed little to the model predictions, despiteT. aralioideswas a characteristic species of cloud zone. The interpolated bioclimatic predictors had precisely reflected the habitat differentiation among topographical positions and accurately captured habitat requirements of plant species at fine scale. Our results presented practical and applicable example of novel interpolation method to generate gridded climate dataset that is useful to improve performance of model predictions in mountainous areas with complex topography.
Increased variation in sex organ positions can increase reciprocity and pollination success in heterostylous plant populations
Authors: Ganguly Shatarupa , Shreenidhi PM , Barua Deepak
Published: April 2021

The reciprocal position of sexual organs in complementary floral morphs is central to our understanding of heterostyly. Reciprocity indices are used to quantify the spatial match between complementary sex organs, but previous indices fail to appropriately account for intra‐population variation in sex organ positions. In this study, we examine how an increase in intra‐population variation in sex organ heights affects reciprocity and consequently reproductive success. We formulated a reciprocity index that incorporates this variation and asked if estimates of reciprocity can predict reproductive success in naturally occurring heterostylous populations. We developed a reciprocity index that assumed pollen transfer success equalled one for a perfectly matched stigma–anther pair, and decreased to zero with increasing mismatch. We examined the relationship between intra‐population variation in organ position and reciprocity, compared previously proposed indices using simulated populations and empirical data from natural populations, and tested the ability of the indices to predict reproductive success. We observed that when differences between mean complementary sex‐organ heights are small, increasing intra‐population variation in heights resulted in a decrease in reciprocity. However, when this difference is larger, reciprocity increased, reached a peak, and then decreased with increasing variation. Previous indices failed to capture this behavior. Seed set was positively related to reciprocity for our index. These results challenge the current understanding that increasing variation in sex‐organ heights will always decrease reciprocity in heterostylous populations. This may help explain why heterostylous systems exhibit and tolerate high amounts of intra‐population variation in sex organ heights.
Nanoliposomes for encapsulation and calcium delivery of egg white peptide–calcium complex
Authors: Zhang Penglin , Bao Zhijie , Jiang Pengfei , Zhang Simin , Zhang Xiumin , Lin Songyi , Sun Na
Published: April 2021

Nanoliposomes and crude liposomes loaded with egg white peptide–calcium complex (EWP–Ca) were fabricated by thin‐film dispersion with or without dynamic high‐pressure microfluidization. Their physiochemical properties, in vitro stability, and calcium release profiles were investigated in this study. Results showed that the EWP–Ca‐loaded nanoliposomes exhibited spherical structures with a lower particle size and polydispersity index as well as a higher thermal stability as compared to the corresponding crude liposomes. Further investigations revealed that EWP–Ca was embedded into the liposomes mainly through hydrogen bonding and present in an amorphous form within the liposomes. Additionally, the EWP–Ca‐loaded nanoliposomes effectively slowed the release of calcium in gastric digestion, allowing more soluble calcium to enter the intestinal tract; in the subsequent intestinal digestion, the EWP–Ca‐loaded nanoliposomes were more electrically and physically stable than the crude liposomes. Therefore, the EWP–Ca‐loaded nanoliposomes could be used as a favorable dietary calcium delivery system to promote calcium bioavailability.

Practical Application

Nanoliposomes were fabricated in this study to encapsulate the egg white peptide–calcium complex (EWP–Ca) for calcium delivery. The EWP–Ca‐loaded nanoliposomes effectively slowed the release of calcium in gastric digestion, allowing more soluble calcium to enter the intestinal tract, and were more electrically and physically stable in the subsequent intestinal digestion. Therefore, the EWP–Ca‐loaded nanoliposomes may be incorporated in calcium‐fortified food to enhance calcium delivery for maintaining bone health.
General anaesthesia in end‐of‐life care: extending the indications for anaesthesia beyond surgery
Authors: Takla A. , Savulescu J. , Wilkinson D. J. C. , Pandit J. J.
Published: April 2021

In this article, we describe an extension of general anaesthesia – beyond facilitating surgery – to the relief of suffering during dying. Some refractory symptoms at the end of life (pain, delirium, distress, dyspnoea) might be managed by analgesia, but in high doses, adverse effects (e.g. respiratory depression) can hasten death. Sedation may be needed for agitation or distress and can be administered as continuous deep sedation (also referred to as terminal or palliative sedation) generally using benzodiazepines. However, for some patients these interventions are not enough, and others may express a clear desire to be completely unconscious as they die. We summarise the historical background of an established practice that we refer to as ‘general anaesthesia in end‐of‐life care’. We discuss its contexts and some ethical and legal issues that it raises, arguing that these are largely similar issues to those already raised by continuous deep sedation. To be a valid option, general anaesthesia in end‐of‐life care will require a clear multidisciplinary framework and consensus practice guidelines. We see these as an impending development for which the specialty should prepare. General anaesthesia in end‐of‐life care raises an important debate about the possible role of anaesthesia in the relief of suffering beyond the context of surgical/diagnostic interventions.
The Energetic Brain Club in Life and Death
Authors: Hames Aaron
Published: April 2021

Japan’s aging society leaves many of its eldest residents to encounter loneliness and social isolation. However, the elderly in Japan and elsewhere are rarely passive vessels to fate and often use available tools to meet their needs. Exploring loneliness and its remedy, this essay presents an ethnographic account of a single Energetic Brain Club meeting in the Tokyo sprawl. While, on paper, the club is aimed at preventing dementia, cognitive declines frequently remain a peripheral topic. Elderly members partake in hospitality rituals and engage in long, meandering conversations about family, memories, struggles, and politics. In the process, they find commiseration, connection, and a salve for loneliness.