bluuebunny/crossref_metadata_2025 huggingface dataset:
Using ultraviolet absorption spectroscopy to study nanoswitches based on non-canonical DNA structures
Authors: McCarte Blair , Yeung Owen T. , Speakman Alexander J. , Elfick Alistair , Dunn Katherine E.
Published: August 2021

Non-canonical forms of DNA are attracting increasing interest for applications in nanotechnology. It is frequently convenient to characterize DNA molecules using a label-free approach such as ultraviolet absorption spectroscopy. In this paper we present the results of our investigation into the use of this technique to probe the folding of quadruplex and triplex nanoswitches. We confirmed that four G-quartets were necessary for folding at sub-mM concentrations of potassium and found that the wrong choice of sequence for the linker between G-tracts could dramatically disrupt folding, presumably due to the presence of kinetic traps in the folding landscape. In the case of the triplex nanoswitch we examined, we found that the UV spectrum showed a small change in absorbance when a triplex was formed. We anticipate that our results will be of interest to researchers seeking to design DNA nanoswitches based on quadruplexes and triplexes.

Highlights

Ultraviolet absorption spectroscopy can probe non-canonical DNA structures.

Absorbance at 295nm tends to increase as G-quadruplexes form.

Four G-quartets are needed to form a quadruplex with less than 1mM potassium.

Formation of DNA triplexes can also yield a small change in UV spectra.

UV absorption is a cheap label-free method for studying DNA nanoswitches.
Widespread cell stress and mitochondrial dysfunction in early Alzheimer’s Disease
Authors: Venkataraman Ashwin V , Mansur Ayla , Rizzo Gaia , Bishop Courtney , Lewis Yvonne , Kocagoncu Ece , Lingford-Hughes Anne , Huiban Mickael , Passchier Jan , Rowe James B , Tsukada Hideo , Brooks David J. , Martarello Laurent , Comley Robert A. , Chen Laigao , Schwarz Adam J. , Hargreaves Richard , Gunn Roger N. , Rabiner Eugenii A. , Matthews Paul M
Published: August 2021

Cell stress and impaired oxidative phosphorylation are central to mechanisms of synaptic loss and neurodegeneration in the cellular pathology of Alzheimer’s disease (AD). We quantified the in vivo density of the endoplasmic reticulum stress marker, the sigma 1 receptor (S1R) using [11C]SA4503 PET, as well as that of mitochondrial complex I (MC1) with [18F]BCPP-EF and the pre-synaptic vesicular protein SV2A with [11C]UCB-J in 12 patients with early AD and in 16 cognitively normal controls. We integrated these molecular measures with assessments of regional brain volumes and brain perfusion (CBF) measured with MRI arterial spin labelling. 8 AD patients were followed longitudinally to estimate rates of change with disease progression over 12-18 months. The AD patients showed widespread increases in S1R (≤ 27%) and regional decreases in MC1 (≥ -28%), SV2A (≥ -25%), brain volume (≥ -23%), and CBF (≥ -26%). [18F]BCPP-EF PET MC1 density (≥ -12%) and brain volumes (≥ -5%) were further reduced at follow up in brain regions consistent with the differences between AD patients and controls at baseline. Exploratory analyses showing associations of MC1, SV2A and S1R density with cognitive changes at baseline and longitudinally with AD, but not in controls, suggested a loss of metabolic functional reserve with disease. Our study thus provides novel in vivo evidence for widespread cellular stress and bioenergetic abnormalities in early AD and that they may be clinically meaningful.
CD19+IgD+CD27- naïve B Cells as predictors of humoral response to COVID-19 mRNA vaccination in immunocompromised patients
Authors: Schulz Eduard , Hodl Isabel , Forstner Patrick , Hatzl Stefan , Sareban Nazanin , Moritz Martina , Fessler Johannes , Dreo Barbara , Uhl Barbara , Url Claudia , Grisold Andrea , Khalil Michael , Kleinhappl Barbara , Enzinger Christian , Stradner Martin H. , Greinix Hildegard , Schlenke Peter , Steinmetz Ivo
Published: August 2021

Immunocompromised patients are considered high-risk and prioritized for vaccination against COVID-19. We aimed to analyze B-cell subsets in these patients to identify potential predictors of humoral vaccination response. Patients (n=120) suffering from hematologic malignancies or other causes of immunodeficiency and healthy controls (n=79) received a full vaccination series with an mRNA vaccine. B-cell subsets were analyzed prior to vaccination. Two independent anti-SARS-CoV-2 immunoassays targeting the receptor-binding domain (RBD) or trimeric S protein (TSP) were performed three to four weeks after the second vaccination. Seroconversion occurred in 100% of healthy controls, in contrast to 67% (RBD) and 82% (TSP) of immunocompromised patients, while only 32% (RBD) and 22% (TSP) achieved antibody levels comparable to those of healthy controls. The number of circulating CD19+IgD+CD27- naïve B cells was strongly associated with antibody levels (ρ=0.761, P<0.001) and the only independent predictor for achieving antibody levels comparable to healthy controls (OR 1.07 per 10-µl increase, 95%CI 1.02–1.12, P=0.009). Receiver operating characteristic analysis identified a cut-off at ≥61 naïve B cells per µl to discriminate between patients with and without an optimal antibody response. Consequently, measuring naïve B cells in immunocompromised hematologic patients could be useful in predicting their humoral vaccination response.
The fomite contribution to the transmission of COVID-19 in the UK: an evolutionary population estimate
Authors: Meiksin A.
Published: August 2021

A SEIR model with an added fomite term is used to constrain the contribution of fomites to the spread of COVID-19 under the Spring 2020 lockdown in the UK. Assuming uniform priors on the reproduction number in lockdown and the fomite transmission rate, an upper limit is found on the fomite transmission rate of less than 1 contaminated object in 7 per day per infectious person (95% CL). Basing the prior on the reproduction rate during lockdown instead on the CoMix study results for the reduction in social contacts under lockdown, and assuming the reproduction number scales with the number of social contacts, provides a much more restrictive upper limit on the transmission rate by contaminated objects of fewer than 1 in 30 per day per infectious person (95% CL). Applied to postal deliveries and groceries, the upper limit on the fomite transmission rate corresponds to a probability below 1 in 70 (95% CL) that a contaminated object transmits the infection. Fewer than about half (95% CL) of the total number of deaths during the lockdown are found to arise from fomites, and most likely fewer than a quarter. These findings apply only to fomites with a transmission rate that is unaffected by a lockdown.
Hepatitis B and D: a forecast on actions needed to reduce incidence and achieve elimination
Authors: Greenhalgh Scott , Klug Andrew
Published: August 2021

Background

Viral hepatitis negatively affects the health of millions, with the worst health outcomes associated with the hepatitis D virus (HDV). Fortunately, HDV is rare and requires prior infection with the hepatitis B virus (HBV) before it can establish infection and transmit. As such, public health officials have opted to indirectly control HDV by reducing HBV incidence, primarily through hepatitis B vaccination, which has dramatically reduced HBV incidence since its rollout in the 1980s. However, investigations into the consequences of hepatitis B vaccination on both the control and evolution of HDV remain limited.

Methods

We developed a mathematical model of HBV and HDV transmission to investigate the effects of hepatitis B vaccination on both HBV and HDV. We calibrated our model to the HBV and HDV transmission scenarios occurring in Sub-Saharan Africa, and estimate HBV vaccination thresholds that cause HBV and HDV elimination, inhibit the spread of virulent HDV strains, and achieve the targets set by public health authorities for reducing all viral hepatitis incidence by 90%.

Results

Our findings illustrate hepatitis B vaccination rates above 0.0096 year−1and 0.018 year−1will likely achieve HDV and HBV elimination, respectively. Furthermore, in the majority of transmission settings, scaling-up vaccination rates to at least 0.009 year−1or 0.02136 year−1will achieve the 90% reduction in hepatitis D and B, respectively, called for by health authorities.

Conclusion

Our results suggest a scale-up of hepatitis B vaccination is required to achieve the targets set by public health officials for reducing all viral hepatitis by 90%. Furthermore, the scale-up required to achieve such targets would bring HBV and HDV to the brink of the vaccination threshold required for their elimination. Thus, with sufficient investments to scale up global hepatitis vaccination, prevention, testing, and treatment services, the eradication of both HBV and HDV are likely feasible endeavors, especially once the 90% reduction goal is reached.
Cardiovascular diseases associated with influenza infection: protocol for a systematic review and meta-analysis
Authors: del Carmen Caycho Torres María , Yamahuchi Johnny Clavo , Cornejo Ramos Cory Ximena , Diaz Gomez Katherine Ada , Gayoso Liviac Oscar Alonso , Zanoni Ramos Omar Fabricio , Zambrano Victor Vega , Ugarte-Gil Cesar
Published: August 2021

Background

Cardiovascular diseases represent important diagnoses that can become fatal if an early and adequate management is not carried out. Since 1930, a possible relationship between these events and influenza virus infection has been proposed.

Objectives

To determine the association between cardiovascular diseases and previous infection by influenza virus.

Materials and methods

We propose to do a systematic review and meta-analysis according to PRISMA. In order to do so, we will perform an electronic search in the databases of EMBASE, PubMed, Global Index Medicus, Google Scholar and Cochrane Library. Articles will first be selected according to their respective titles and abstracts; and subsequently, the full text of each article will be evaluated. Both phases will be executed by 4 authors. The extracted data will include study details, study methodology and results. The quality of the studies will be verified using standardized tools according to the study design and we will evaluate possible biases. In addition, a meta-analysis of the association measures will be performed using Cochrane’s Software Review Manager 5.4.1 and we will use the GRADE tool to assess the certainty of the results obtained from the analyzed studies.

Results

We will publish the results of this systematic review and meta-analysis in a peer-reviewed journal.

Conclusions

This systematic review will provide more up-to-date evidence compared to previous work on the association between laboratory-confirmed influenza and cardiovascular diseases.
Agent-based modeling of DFNB1A prevalence with regard to intensity of selection pressure in isolated human population: will cochlear implantation increase the cases of hereditary deafness?
Authors: Romanov Georgii P. , Smirnova Anna A. , Zamyatin Vladimir I. , Mukhin Aleksey M. , Kazantsev Fedor V. , Pshennikova Vera G. , Teryutin Fedor M. , Solovyev Aisen V. , Fedorova Sardana A. , Posukh Olga L. , Lashin Sergey A. , Barashkov Nikolay A.
Published: August 2021

It was evidenced, that the increase in the prevalence of autosomal recessive deafness 1A (DFNB1A) in populations of European descent was promoted by assortative marriages among deaf people. Assortative marriages become possible with a widespread introduction of sign language resulting in increased the genetic fitness of deaf individuals, thus relaxing selection against deafness. Currently, cochlear implantation is becoming a common method of rehabilitation for deaf patients, restoring their hearing ability and promoting the acquirement of spoken language. Whether the mass cochlear implantation could affect the spread of hereditary deafness is unknown. We have developed an agent-based computer model for analysis of the spread of DFNB1A. Using the model, we tested impact of different intensity of selection pressure on an isolated human population for 400 years. The modeling of the “purifying” selection pressure on deafness resulted in decrease of the proportion of deaf individuals and the pathogenic allele frequency. The modeling of relaxed selection resulted in increase of the proportion of deaf individuals and the decrease of the pathogenic allele frequency. The results of neutral selection pressure modeling showed no significant changes in both the proportion of deaf individuals and the pathogenic allele frequency after 400 years. Thus, initially low genetic fitness of deaf people can be significantly increased in the presence of assortative mating by deafness, resulting in a higher prevalence of DFNB1A. Contrary, frequency of pathogenic allele and the incidence of hereditary hearing loss will not increase in a population where all deaf individuals undergo cochlear implantation.
A Novel Convolutional Neural Network for COVID-19 detection and classification using Chest X-Ray images
Authors: Nafees Muhammad Talha , Irshadullah  , Rizwan Muhammad , Maazullah  , Khan Muhammad Irfanullah , Farhan Muhammad
Published: August 2021

The early and rapid diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), the main cause of fatal pandemic coronavirus disease 2019 (COVID-19), with the analysis of patients chest X-ray (CXR) images has life-saving importance for both patients and medical professionals. In this research a very simple novel and robust deep-learning convolutional neural network (CNN) model with less number of trainable-parameters is proposed to assist the radiologists and physicians in the early detection of COVID-19 patients. It also helps to classify patients into COVID-19, pneumonia and normal on the bases of analysis of augmented X-ray images. This augmented dataset contains 4803 COVID-19 from 686 publicly available chest X-ray images along with 5000 normal and 5000 pneumonia samples. These images are divided into 80% training and 20 % validation. The proposed CNN model is trained on training dataset and then tested on validation dataset. This model has a promising performance with a mean accuracy of 92.29%, precision of 99.96%, Specificity of 99.85% along with Sensitivity value of 85.92%. The result can further be improved if more data of expert radiologist is publically available.
Diversification by CofC and control by CofD govern biosynthesis and evolution of coenzyme F420 and its derivative 3PG-F420
Authors: Hasan Mahmudul , Schulze Sabrina , Berndt Leona , Palm Gottfried J. , Braga Daniel , Richter Ingrid , Last Daniel , Lammers Michael , Lackner Gerald
Published: August 2021

Coenzyme F420 is a microbial redox cofactor that is increasingly used for biocatalytic applications. Recently, diversified biosynthetic routes to F420 and the discovery of a derivative, 3PG-F420, were reported. 3PG-F420 is formed via activation of 3-phospho-D-glycerate (3-PG) by CofC, but the structural basis of substrate binding, its evolution, as well as the role of CofD in substrate selection remained elusive.

Here, we present a crystal structure of the 3-PG-activating CofC from Mycetohabitans sp. B3 and define amino acids governing substrate specificity. Site-directed mutagenesis enabled bidirectional switching of specificity and thereby revealed the short evolutionary trajectory to 3PG-F420 formation. Furthermore, CofC stabilized its product, thus confirming the structure of the unstable molecule, revealing its binding mode and suggesting a substrate channeling mechanism to CofD. The latter enzyme was shown to significantly contribute to the selection of related intermediates to control the specificity of the combined biosynthetic CofC/D step. Taken together, this work closes important knowledge gaps and opens up perspectives for the discovery, enhanced biotechnological production, and engineering of coenzyme F420 derivatives in the future.

Importance

The microbial cofactor F420 is crucial for processes like methanogenesis, antibiotics biosynthesis, drug resistance, and biocatalysis. Recently, a novel derivative of F420 (3PG-F420) was discovered, enabling the production and use of F420 in heterologous hosts.

By analyzing the crystal structure of a CofC homolog whose substrate choice leads to formation of 3PG-F420, we defined amino acid residues governing the special substrate selectivity. A diagnostic residue enabled reprogramming of the substrate specificity, thus mimicking the evolution of the novel cofactor derivative and successfully guiding the identification of further 3-PG-activating enzymes.

Furthermore, a labile reaction product of CofC was revealed that has not been directly detected so far and CofD was shown to provide as another layer of specificity of the combined CofC/D reaction, thus controlling the initial substrate choice of CofC. The latter finding resolves a current debate in the literature about the starting point of F420 biosynthesis in various organisms.
Genetic study of late-onset neonatal sepsis reveals significant differences by sex
Authors: Ciesielski Timothy H. , Zhang Xueyi , Tacconelli Alessandra , Lutsar Irja , de Cabre Vincent Meiffredy , Roilides Emmanuel , Ciccacci Cinzia , Borgiani Paola , Scott William K. ,   NeoMero Consortium, Williams Scott M. , Sirugo Giorgio
Published: August 2021

Late-Onset Neonatal Sepsis (LOS) is a rare, but life-threatening condition, involving widespread infection, immune disruption, organ dysfunction, and often death. Because exposure to pathogens is not 100% preventable, identifying susceptibility factors is critical to defining neonates at greater risk. Prior studies demonstrated that both genetics and infant sex influence susceptibility. We, therefore, performed a genome wide association study (GWAS) with 224 cases and 273 controls from six European countries to identify genetic risk factors. We tested for association with both autosomal and X-chromosome variants in the total sample and in the samples stratified by sex. In total 71 SNPs associated with neonatal sepsis at p<1×10−4in at least one analysis. Most importantly, the sex stratified analyses revealed associations with multiple SNPs (28 SNPs in males and 16 in females), but none of 44 SNPs from single-sex analyses associated with sepsis in the other sex at p<0.05, and the vast majority showed significant SNP X sex interactions (17 of 28 from the male-only analyses and all 16 from the female-only study). Pathway analyses showed that NOTCH signaling is over-represented among loci identified by the analyses. Our results indicate that susceptibility to LOS is genetically sexually dimorphic, and suggest that NOTCH signaling is likely to play a role in it.
Harmony COVID-19: a ready-to-use kit, low-cost detector, and smartphone app for point-of-care SARS-CoV-2 RNA detection
Authors: Panpradist Nuttada , Atkinson Robert G. , Roller Michael , Kline Enos , Wang Qin , Hull Ian T. , Kotnik Jack H. , Oreskovic Amy K. , Bennett Crissa , Leon Daniel , Lyon Victoria , Han Peter D. , Starita Lea M. , Thompson Matthew J. , Lutz Barry R.
Published: August 2021

RNA amplification tests allow sensitive detection of SARS-CoV-2 infection, but their complexity and cost are prohibitive for expanding COVID-19 testing. We developed “Harmony COVID-19”, a point-of-care test using inexpensive consumables, ready-to-use reagents, and a simple device that processes up to 4 samples simultaneously. Our lyophilized reverse-transcription, loop-mediated isothermal amplification (RT-LAMP) can detect as little as 15 SARS-CoV-2 RNA copies per reaction, and it can report as early as 17 min for samples with high viral load (2 x 105 RNA copies per reaction). Analysis of RNA extracted from clinical nasal specimens (n = 101) showed 95% concordance with RT-PCR, including 100% specificity in specimens positive for other viruses and bacteria. Analysis of contrived samples in the nasal matrix showed detection of 92% or 100% in samples with ≥20 or ≥100 particles per reaction, respectively. Usability testing showed 95% accuracy by healthcare workers operating the test for the first time.

ONE SENTENCE SUMMARY

Harmony COVID-19: point-of-care SARS-CoV-2 RNA detection
COVID-19 vaccine uptake among older people in relation to sociodemographic factors –cohort results from southern Sweden
Authors: Inghammar Malin , Moghaddassi Mahnaz , Rasmussen Magnus , Malmqvist Ulf , Kahn Fredrik , Björk Jonas
Published: August 2021

The aim of this cohort study was to investigate sociodemographic determinants of COVID-19 vaccine uptake in the 70+ age group in Skåne county, Sweden (n = 216 243 at baseline). Uptake of the first dose was high (91.9%) overall, but markedly lower (75.3%) among persons born outside the Nordic countries. Vaccine uptake was generally satisfactory among native Swedes also in areas with lower socioeconomic status, but dropped substantially among non-Nordic born in those areas. The identified clusters of unvaccinated older people, mainly representing ethnic minorities in disadvantaged areas, warrants intensified efforts regarding tailored communication, easier vaccine access and local engagement.

Key points

COVID-19 vaccine uptake in the 70+ age group in Skåne county, Sweden, was high (91.9%) overall, but markedly lower (75.3%) within the group born outside the Nordic countries

Inverse associations between indicators of neighbourhood deprivation and vaccine uptake were observed, which lowered the uptake among persons born outside the Nordic countries further

The identified clusters of unvaccinated older people, mainly representing ethnic minorities in disadvantaged areas, warrants intensified efforts regarding tailored communication, easier vaccine access and local engagement
Plasmodium falciparummalaria during pregnancy: the impact of parasitaemia and anaemia on birthweight
Authors: Abbas Dawood Ackom , Mutala Abdul-Hakim , Agordzo Samuel Kekeli , Owusu Christian Kwasi , Lawson Bernard Walter Lartekwei , Badu Kingsley
Published: August 2021

Malaria in pregnancy remains a major problem of public health concern in Sub-Saharan Africa due to its endemicity and the diverse consequences on both the mother and the baby. Much attention, therefore, is needed to fully understand the epidemiology of the disease and to mitigate the devastating outcomes. The present study aimed at investigating malaria in pregnancy, its adverse effects on pregnant women and the impact on birthweight of babies. A total of 222 pregnant women gave their consent and were recruited into the study during their routine Antenatal care visits. This study employed a combination of cross-sectional and longitudinal cohort study designs. For 122 women in the cross-sectional arm, blood samples and data were obtained once, whilst 100 women in the longitudinal cohort arm were followed up from recruitment until delivery. Demographic information, obstetric history and risk factors were obtained by administering questionnaires. About 1.0 ml of venous blood was drawn to determine malaria parasitaemia and anaemia status of the participants. The birthweights of the babies were also taken at delivery. The prevalence of malaria and anaemia was 19.8% and 27.0% respectively at registration for all 222 participants. All infections wereP. falciparummalaria. One hundred and forty-six (65.8%) of participants had ITN but only 72 (32.4%) used it the previous night. Young age and rural settings were risk factors for malaria. Young age and malaria positive pregnant women had increased risk of anaemia. In the follow-up group which ended with 54 participants, the overall prevalence of malaria and anaemia were 18.7% and 32.4% respectively. Fifty-two (96.3%) of pregnant women attended ANC ≥ 4 times and 55.6% took ≥ 3 doses of SP. There were two cases of miscarriage. Low birthweight occurred in 5.6% of babies. Both malaria and anaemia during pregnancy had no significant impact on birthweight of the babies. Although few of the babies had low birthweight, this number can be further reduced when pregnant women attend ANC and take SP at the recommended number of times.
Characterising the persistence of RT-PCR positivity and incidence in a community survey of SARS-CoV-2
Authors: Eales Oliver , Walters Caroline E. , Wang Haowei , Haw David , Ainslie Kylie E. C. , Atchison Christina , Page Andrew J. , Prosolek Sophie J. , Trotter Alexander J. , Le Viet Thanh , Alikhan Nabil-Fareed , Jackson Leigh M , Ludden Catherine ,   The COVID-19 Genomics UK (COG-UK) Consortium, Ashby Deborah , Donnelly Christl A. , Cooke Graham , Barclay Wendy , Ward Helen , Darzi Ara , Elliott Paul , Riley Steven
Published: August 2021

Background

Community surveys of SARS-CoV-2 RT-PCR swab-positivity provide prevalence estimates largely unaffected by biases from who presents for routine case testing. The REal-time Assessment of Community Transmission-1 (REACT-1) has estimated swab-positivity approximately monthly since May 2020 in England from RT-PCR testing of self-administered throat and nose swabs in random non-overlapping cross-sectional community samples. Estimating infection incidence from swab-positivity requires an understanding of the persistence of RT-PCR swab positivity in the community.

Methods

During round 8 of REACT-1 from 6 January to 22 January 2021, of the 2,282 participants who tested RT-PCR positive, we recruited 896 (39%) from whom we collected up to two additional swabs for RT-PCR approximately 6 and 9 days after the initial swab. We estimated sensitivity and duration of positivity using an exponential model of positivity decay, for all participants and for subsets by initial N-gene cycle threshold (Ct) value, symptom status, lineage and age. Estimates of infection incidence were obtained for the entire duration of the REACT-1 study using P-splines.

Results

We estimated the overall sensitivity of REACT-1 to detect virus on a single swab as 0.79 (0.77, 0.81) and median duration of positivity following a positive test as 9.7 (8.9, 10.6) days. We found greater median duration of positivity where there was a low N-gene Ct value, in those exhibiting symptoms, or for infection with the Alpha variant. The estimated proportion of positive individuals detected on first swab,P0, was found to be higher for those with an initially low N-gene Ct value and those who were pre-symptomatic. When compared to swab-positivity, estimates of infection incidence over the duration of REACT-1 included sharper features with evident transient increases around the time of key changes in social distancing measures.

Discussion

Home self-swabbing for RT-PCR based on a single swab, as implemented in REACT-1, has high overall sensitivity. However, participants’ time-since-infection, symptom status and viral lineage affect the probability of detection and the duration of positivity. These results validate previous efforts to estimate incidence of SARS-CoV-2 from swab-positivity data, and provide a reliable means to obtain community infection estimates to inform policy response.
Matrix stiffness controls ciliogenesis and centriole position
Authors: Williantarra Ivanna , Leung Sophia , Choi Yu Suk , Channa Ashika , McGlashan Sue R
Published: August 2021

Mechanical stress and the stiffness of the extracellular matrix are key drivers of tissue development and homeostasis. Aberrant mechanosensation is associated with a wide range of pathologies, including diseases such as osteoarthritis. Substrate stiffness is one of the well-known mechanical properties of the matrix that enabled establishing the central dogma of an integrin-mediated mechanotransduction using stem cells. However, how specific cells ‘feel’ or sense substrate stiffness requires further study. The primary cilium is an essential cellular organelle that senses and integrates mechanical and chemical signals from the extracellular environment. We hypothesised that the primary cilium dynamically alters its length and position to fine-tune cell mechanosignalling based on substrate stiffness alone. We used a hydrogel system of varying substrate stiffness to examine the role of substrate stiffness on cilia frequency, length and centriole position as well as cell and nuclei area over time. Contrary to other cell types, we show that chondrocyte primary cilia shorten on softer substrates demonstrating tissue-specific mechanosensing which is aligned with the tissue stiffness the cells originate from. We further show that stiffness alone determines centriole positioning to either the basal or apical membrane during attachment and spreading, with centriole positioned towards the basal membrane on stiffer substrates. These phenomena are mediated by force generation actin-myosin stress fibres in a time-dependent manner. Based on these findings, we propose that substrate stiffness plays a central role in cilia positioning, regulating cellular response to external forces, and may be a key driver of mechanosignalling-associated diseases.

Significance Statement

The primary cilium has been thrust into the limelight owing to its role as a cellular sensor in embryonic development and adult tissue maintenance. How the primary cilium interacts with the mechanical environment still remains unclear. We show that substrate stiffness dynamically regulates primary cilium length and position through integrin-mediated traction forces, the cilia are a key determinant of cell shape on certain stiffnesses. Our data support the promising potential of primary cilia as a novel target in mechanotherapy for improved clinical outcomes in cartilage pathobiology.
Limitations of composability of cis-regulatory elements in messenger RNA
Authors: Haynes Samuel , Auxillos Jamie , Danecka Weronika , Jain Abhishek , Alibert Clemence , Wallace Edward
Published: August 2021

Genes are commonly abstracted into a coding sequence and cis-regulatory elements (CREs), such as promoters and terminators, and short sequence motifs within these regions. Modern cloning techniques allow easy assembly of synthetic genetic constructs from discrete cis-regulatory modules. However, it is unclear how much the contributions of CREs to gene expression depend on other CREs in the host gene. Using budding yeast, we probe the extent of composability, or independent effects, of distinct CREs. We confirm that the quantitative effect of a terminator on gene expression depends on both promoter and coding sequence. We then explore whether individual cisregulatory motifs within terminator regions display similar context dependence, using transcriptomewide datasets of mRNA decay. To test the extent of composability, we construct reporter genes consisting of combinations of motifs within various terminator contexts, paired with different promoters. Our results show that the effect of a motif on RNA abundance depends both on its host terminator, and also on the associated promoter sequence. This emphasises the need for improved motif inference that includes both local and global context effects, which in turn could aid in the accurate use of CREs for the engineering of synthetic genetic constructs.
Peripheral sTREM2-related inflammatory activity alterations in early stage Alzheimer’s disease
Authors: Weber Grace E. , Khrestian Maria , Tuason Elizabeth D. , Shao Yvonne , Pillai Jagan , Rao Stephen , Feng Hao , Zhou Yadi , Cheng Feixiong , DeSilva Tara M. , Stauffer Shaun , Leverenz James B. , Bekris Lynn M.
Published: August 2021

Alzheimer’s disease (AD) has been linked to multiple immune system genetic variants, implicating potential broad alterations in inflammatory profiles in the disease. Triggering receptor expressed on myeloid cells 2 (TREM2) genetic variants are risk factors for AD and other neurodegenerative diseases. A soluble TREM2 isoform (sTREM2) is elevated in cerebrospinal fluid in the early stages of AD suggesting it may be a biomarker of progressive alterations in immune response to AD-related pathology. Multiple studies have reported an altered peripheral immune response in AD. However, less is known about the relationship between plasma sTREM2 and the altered peripheral immune response in AD. The objective of this exploratory study was to examine the relationship between sTREM2 and inflammatory activity in human participants defined by clinically characterized cognitive symptoms and groups defined by the cerebrospinal fluid biomarkersamyloid beta, phosphorylatedtau, andneurodegeneration (NIA-AA Research Framework: “ATN continuum”.) The hypothesis of this exploratory study was that sTREM2 related inflammatory activity differs by AD stage. We observed different patterns of inflammatory activity across disease groups and ATN categories that implicates peripheral sTREM2 related inflammatory activity as altered in the early stages of AD. Notably, fractalkine showed a significant relationship with sTREM2 across different analyses in the control groups that was lost as disease progressed, and fractalkine, IL-5 and IL-17A were decreased in AD. These preliminary data provide important support to the hypothesis that sTREM2-related inflammatory activity is a stage-specific biomarker of AD progression, providing the groundwork for future studies and therapeutic strategies.
Sciviewer enables interactive visual interrogation of single-cell RNA-Seq data from the Python programming environment
Authors: Kotliar Dylan , Colubri Andres
Published: August 2021

Visualizing two-dimensional (2D) embeddings (e.g. UMAP or tSNE) is a key step in interrogating single-cell RNA sequencing (scRNA-Seq) data. Subsequently, users typically iterate between programmatic analyses (e.g. clustering and differential expression) and visual exploration (e.g. coloring cells by interesting features) to uncover biological signals in the data. Interactive tools exist to facilitate visual exploration of embeddings such as performing differential expression on user-selected cells. However, the practical utility of these tools is limited because they don’t support rapid movement of data and results to and from the programming environments where the bulk of data analysis takes place, interrupting the iterative process. Here, we present the Single-cell Interactive Viewer (Sciviewer), a tool that overcomes this limitation by allowing interactive visual interrogation of embeddings from within Python. Beyond differential expression analysis of user-selected cells, Sciviewer implements a novel method to identify genes varying locally along any user-specified direction on the embedding. Sciviewer enables rapid and flexible iteration between interactive and programmatic modes of scRNA-Seq exploration, illustrating a useful approach for analyzing high-dimensional data.

Availability and implementation

Code and examples are provided at https://github.com/colabobio/sciviewer
Next generation restoration metrics: Using soil eDNA bacterial community data to measure trajectories towards rehabilitation targets
Authors: Liddicoat Craig , Krauss Siegfried L. , Bissett Andrew , Borrett Ryan J. , Ducki Luisa C. , Peddle Shawn D. , Bullock Paul , Dobrowolski Mark P. , Grigg Andrew , Tibbett Mark , Breed Martin F.
Published: August 2021

In post-mining rehabilitation, successful mine closure planning requires specific, measurable, achievable, relevant and time-bound (SMART) completion criteria, such as returning ecological communities to match a target level of similarity to reference sites. Soil microbiota are fundamentally linked to the restoration of degraded ecosystems, helping to underpin ecological functions and plant communities. High-throughput sequencing of soil eDNA to characterise these communities offers promise to help monitor and predict ecological progress towards reference states. Here we demonstrate a novel methodology for monitoring and evaluating ecological restoration using three long-term (> 25 year) case study post-mining rehabilitation soil eDNA-based bacterial community datasets. Specifically, we developed rehabilitation trajectory assessments based on similarity to reference data from restoration chronosequence datasets. Recognising that many alternative options for microbiota data processing have potential to influence these assessments, we comprehensively examined the influence of standard versus compositional data analyses, different ecological distance measures, sequence grouping approaches, eliminating rare taxa, and the potential for excessive spatial autocorrelation to impact on results. Our approach reduces the complexity of information that often overwhelms ecologically-relevant patterns in microbiota studies, and enables prediction of recovery time, with explicit inclusion of uncertainty in assessments. We offer a step change in the development of quantitative microbiota-based SMART metrics for measuring rehabilitation success. Our approach may also have wider applications where restorative processes facilitate the shift of microbiota towards reference states.
Autophagy cargo receptors are secreted via extracellular vesicles and particles in response to endolysosomal inhibition or impaired autophagosome maturation
Authors: Solvik Tina A. , Nguyen Tan A. , Lin Yu-Hsiu Tony , Marsh Timothy , Huang Eric J. , Wiita Arun P. , Debnath Jayanta , Leidal Andrew M.
Published: August 2021

The endosome-lysosome (endolysosome) system plays central roles in both autophagic degradation and secretory pathways, including the exocytic release of extracellular vesicles and particles (EVPs). Although previous work has revealed important interconnections between autophagy and EVP-mediated secretion, our molecular understanding of these secretory events during endolysosome inhibition remains incomplete. Here, we delineate a secretory autophagy pathway upregulated in response to endolysosomal inhibition that mediates the EVP-associated extracellular release of autophagic cargo receptors, including p62/SQSTM1. This extracellular secretion is highly regulated and critically dependent on multiple ATGs required for the progressive steps of early autophagosome formation as well as Rab27a-dependent exocytosis. Furthermore, the disruption of autophagosome maturation, either due to genetic inhibition of the autophagosome-to-autolyosome fusion machinery or blockade via the SARS-CoV2 viral protein ORF3a, is sufficient to induce robust EVP-associated secretion of autophagy cargo receptors. Finally, we demonstrate that this ATG-dependent, EVP-mediated secretion pathway buffers against the intracellular accumulation of autophagy cargo receptors when classical autophagic degradation is impaired. Based on these results, we propose that secretory autophagy via EVPs functions as an alternate route to clear sequestered material and maintain proteostasis in response to endolysosomal dysfunction or impaired autophagosome maturation.
Escaping from multiple visual threats: Modulation of escape responses in Pacific staghorn sculpin (Leptocottus armatus)
Authors: Kimura Hibiki , Pfalzgraff Tilo , Levet Marie , Kawabata Yuuki , Steffensen John F. , Johansen Jacob L. , Domenici Paolo
Published: August 2021

Fish perform rapid escape responses to avoid sudden predatory attacks. During escape responses, fish bend their bodies into a C-shape and quickly turn away from the predator and accelerate. The escape trajectory is determined by the initial turn (Stage 1) and a contralateral bend (Stage 2). Previous studies have used a single threat or model predator as a stimulus. In nature, however, multiple predators may attack from different directions simultaneously or in close succession. It is unknown whether fish are able to change the course of their escape response when startled by multiple stimuli at various time intervals. Pacific staghorn sculpin (Leptocottus armatus) were startled with a left and right visual stimulus in close succession. By varying the timing of the second stimulus, we were able to determine when and how a second stimulus could affect the escape response direction. Four treatments were used: a single visual stimulus (control); or two stimuli coming from opposite sides separated by a 0 ms (simultaneous treatment); a 33 ms; or a 83 ms time interval. The 33 ms and 83 ms time intervals were chosen to occur shortly before and after a predicted 60 ms visual escape latency (i.e. during Stage 1). The 0 ms and 33 ms treatments influenced both the escape trajectory and the Stage 1 turning angle, compared to a single stimulation, whereas the 83 ms treatment had no effect on the escape response. We conclude that Pacific staghorn sculpin can modulate their escape response only between stimulation and the onset of the response, but that escape responses are ballistic after the body motion has started.

SUMMARY STATEMENT

Using double stimulation from opposite sides at different time intervals to simulate coordinated predatory attacks, Pacific staghorn sculpin escape away from the first stimulus, but were unable to turn away from the second stimulus while the escape response was in progress.
Sleep spindles, ripples, and interictal epileptiform discharges in the human anterior and mediodorsal thalamus
Authors: Szalárdy Orsolya , Simor Péter , Ujma Péter , Jordán Zsófia , Halász László , Erőss Loránd , Fabó Dániel , Bódizs Róbert
Published: August 2021

Sleep spindles are major oscillatory components of Non-Rapid Eye Movement (NREM) sleep, reflecting hyperpolarization-rebound sequences of thalamocortical neurons, the inhibition of which is caused by the NREM-dependent activation of GABAergic neurons in the reticular thalamic nucleus. Reports suggest a link between sleep spindles and several forms of interictal epileptic discharges (IEDs) which are considered as expressions of pathological off-line neural plasticity in the central nervous system. Here we investigated the relationship between thalamic sleep spindles, IEDs and ripples in the anterior and mediodorsal nuclei (ANT and MD) of epilepsy patients. Whole-night LFP from the ANT and MD were co-registered with scalp EEG/polysomnography by using externalized leads in 15 epilepsy patients undergoing Deep Brain Stimulation protocol. Slow (∼12 Hz) and fast (∼14 Hz) sleep spindles were present in the human ANT and MD. Roughly, one third of thalamic sleep spindles were associated with IEDs or ripples. Both IED- and ripple-associated spindles were longer than pure spindles. IED-associated thalamic sleep spindles were characterized by broadband increase in thalamic and cortical activity, both below and above the spindle frequency range, whereas ripple-associated thalamic spindles exceeded pure spindles in terms of 80–200 Hz thalamic, but not cortical activity as indicated by time-frequency analysis. These result show that thalamic spindles coupled with IEDs are reflected at the scalp slow and beta-gamma oscillation as well. IED density during sleep spindles in the MD, but not in the ANT was identified as correlates of years spent with epilepsy, whereas no signs of pathological processes were correlated with measures of ripple and spindle association. Furthermore, the density of ripple-associated sleep spindles in the ANT showed a positive correlation with general intelligence. Our findings indicate the complex and multifaceted role of the human thalamus in sleep spindle-related physiological and pathological neural plasticity.
Efficient identification of trait-associated loss-of-function variants in the UK Biobank cohort by exome-sequencing based genotype imputation
Authors: Zhang Lei , Yan Shan-Shan , Ni Jing-Jing , Pei Yu-Fang
Published: August 2021

The large-scale open access whole-exome sequencing (WES) data of the UK Biobank ~200,000 participants is accelerating a new wave of genetic association studies aiming to identify rare and functional loss-of-function (LoF) variants associated with a broad range of complex traits and diseases, however the community is in short of stringent replication of new associations. In this study, we proposed to merge the WES genotypes and the genome-wide genotyping (GWAS) genotypes of 167,000 UKB Caucasian participants into a combined reference panel, and then to impute 241,911 UKB Caucasian participants who had the GWAS genotypes only. We then proposed to use the imputed data to replicate association identified in the discovery WES sample. Using a leave-100-out imputation strategy in the reference panel, we showed that average imputation accuracy measure r2is modest to high at LoF variants of all minor allele frequency (MAF) intervals including ultra-rare ones: 0.942 at MAF interval [1%, 50%], 0.807 at [0.1%, 1.0%), 0.805 at [0.01%, 0.1%), 0.664 at [0.001%, 0.01%) and 0.410 at (0, 0.001%). As applications, we studied single variant level and gene level associations of LoF variants with estimated heel BMD (eBMD) and 4 lipid traits: high-density-lipoprotein cholesterol (HDL-C), low-density-lipoprotein cholesterol (LDL-C), triglycerides (TG) and total cholesterol (TC). In addition to replicating dozens of previously reported genes such asMEPEfor eBMD andPCSK9for more than one lipid trait, the results also identified 2 novel gene-level associations:PLIN1(cumulative MAF=0.10%, discovery BETA=0.38, P=1.20×10−13; replication BETA=0.25, P=1.03×10−6) andANGPTL3(cumulative MAF=0.10%, discovery BETA=−0.36, P=4.70×10−11; replication BETA=−0.30, P=6.60×10−11) for HDL-C, as well as one novel single variant level association (11:14843853:C:T, MAF=0.11%, discovery BETA=−0.31, P=2.70×10−9; replication BETA=−0.31, P=8.80×10−14,PDE3B) for TG. Our results highlighted the strength of WES based genotype imputation as well as provided useful imputed data within the UKB cohort.
Microtubule deacetylation reduces cell stiffness to allow the onset of collective cell migrationin vivo
Authors: Marchant CL , Malmi-Kakkada AN , Espina JA , Barriga EH
Published: August 2021

Embryogenesis, tissue repair and cancer metastasis rely on collective cell migration (CCM).In vitrostudies propose that migrating cells are stiffer when exposed to stiff substrates, known to allow CCM, but softer when plated in compliant non-permissive surfaces. Here, by combiningin vivoatomic force microscopy (iAFM) and modelling we reveal that to collectively migratein vivo, cells require to dynamically decrease their stiffness in response to the temporal stiffening of their native substrate. Moreover, molecular and mechanical perturbations of embryonic tissues uncover that this unexpected cell mechanical response is achieved by a new mechanosensitive pathway involving Piezo1-mediated microtubule deacetylation. Finally, lowering microtubule acetylation and consequently cell stiffness was sufficient to allow CCM in soft non-permissive substrates, suggesting that a fixed value of substrate stiffness is not as essential for CCM as it is reaching an optimal cell-to-substrate stiffness value. Thesein vivoinsights on cell-to-substrate mechanical interplay have major implications to our re-interpretation of physiological and pathological contexts.
Virulence determinant, PTP7, controls vesicle budding from the Maurer’s clefts, adhesin protein trafficking and host cell remodeling inPlasmodium falciparum
Authors: Carmo Olivia M. S. , Shami Gerald J. , Cox Dezerae , Liu Boyin , Blanch Adam J. , Tiash Snigdha , Tilley Leann , Dixon Matthew W.A.
Published: August 2021

Presentation of the variant antigen,Plasmodium falciparumerythrocyte membrane protein 1 (EMP1), at knob-like protrusions on the surface of infected red blood cells, underpinsP. falciparummalaria pathogenicity. Here we describe a protein PF3D7_0301700 (PTP7), that functions at the nexus between the intermediate trafficking organelle, the Maurer’s cleft, and the infected red blood cell surface. Genetic disruption of PTP7 leads to accumulation of vesicles at the Maurer’s clefts, grossly aberrant knob morphology, and failure to deliver EMP1 to the red blood cell surface. We show that an expanded low complexity sequence in the C-terminal region of PTP7, found only in theLaveraniaclade ofPlasmodium, is critical for efficient virulence protein trafficking.

Author Summary

We describe a malaria parasite protein involved in virulence factor trafficking (PTP7) that moves between different compartments in the host red blood cell cytoplasm in a stage-dependent manner. Upon disruption of the PTP7 locus, the Maurer’s cleft trafficking compartments become decorated with vesicles; the knobby protrusions on the host red blood cell surface are depleted and distorted; and trafficking of the virulence protein, EMP1, to the host red blood cell surface is ablated. We provide evidence that a region of PTP7 with low sequence complexity plays an important role in driving fission of vesicles from the Maurer’s clefts.