Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape

Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human diseases remains unexplored. Using isogenic cell lines, patient samples, and a mutant mouse model, we investigated how cancer-associated mutations in SF3B1 alter transcription. We found that these mutations reduce the elongation rate of RNA polymerase II (RNAPII) along gene bodies and its density at promoters. The elongation defect results from disrupted pre-spliceosome assembly due to impaired protein-protein interactions of mutant SF3B1. The decreased promoter-proximal RNAPII density reduces both chromatin accessibility and H3K4me3 marks at promoters. Through an unbiased screen, we identified epigenetic factors in the Sin3/HDAC/H3K4me pathway, which, when modulated, reverse both transcription and chromatin changes. Our findings reveal how splicing factor mutant states behave functionally as epigenetic disorders through impaired transcription-related changes to the chromatin landscape. We also present a rationale for targeting the Sin3/HDAC complex as a therapeutic strategy.

Light-induced electronic polarization in antiferromagnetic Cr2O3

In a solid, the electronic subsystem can exhibit incipient order with lower point group symmetry than the crystal lattice. Ultrafast external fields that couple exclusively to electronic order parameters have rarely been investigated, however, despite their potential importance in inducing exotic effects. Here we show that when inversion symmetry is broken by the antiferromagnetic order in Cr2O3, transmitting a linearly polarized light pulse through the crystal gives rise to an in-plane rotational symmetry-breaking (from C3 to C1) via optical rectification. Using interferometric time-resolved second harmonic generation, we show that the ultrafast timescale of the symmetry reduction is indicative of a purely electronic response; the underlying spin and crystal structures remain unaffected. The symmetry-broken state exhibits a dipole moment, and its polar axis can be controlled with the incident light. Our results establish a coherent nonlinear optical protocol by which to break electronic symmetries and produce unconventional electronic effects in solids.

Rapid detection of Mucorales in human blood and urine samples by functionalized Heusler magnetic nanoparticle assisted customized loop-mediated isothermal amplification

Mucormycosis is a rare disease with scarce diagnostic methods for early intervention. Available strategies employing direct microscopy using calcofluor white-KOH, culture, radiologic, and histopathologic testing often are time-intensive and demand intricate protocols. Nucleic Acid Amplification Test holds promise due to its high sensitivity combined with rapid detection. Loop-mediated isothermal amplification (LAMP) based detection offers an ultrasensitive technique that does not require complicated thermocyclers like in polymerase chain reaction, offering a straightforward means for improving diagnoses as a near-point-of-care test. The study introduces a novel magnetic nanoparticle-based LAMP assay for carryover contaminant capture to reduce false positives. Solving the main drawback of LAMP-based diagnosis techniques. The assay targets the cotH gene, which is invariably specific to Mucorales. The assay was tested with various species of Mucorales, and the limit of detections for Rhizopus microsporus, Lichtheimia corymbifera, Rhizopus arrhizus, Rhizopus homothallicus, and Cunninghamella bertholletiae were 1 fg, 1 fg, 0.1 pg, 0.1 pg, and 0.01 ng, respectively. This was followed by a clinical blindfolded study using whole blood and urine samples from 30 patients diagnosed with Mucormycosis. The assay has a high degree of repeatability and had an overall sensitivity of > 83%. Early Mucormycosis detection is crucial, as current lab tests from blood and urine lack sensitivity and take days for confirmation despite rapid progression and severe complications. Our developed technique enables the confirmation of Mucormycosis infection in < 45 min, focusing specifically on the RT-LAMP process. Consequently, this research offers a viable technique for quickly identifying Mucormycosis from isolated DNA of blood and urine samples instead of invasive tissue samples.

Asthma and clinical outcomes of COVID-19 in a community setting

OBJECTIVES

The association between asthma and COVID-19 mortality remains inconclusive. We examined the association between asthma and clinical outcomes of patients with COVID-19.

STUDY DESIGN

A case-control study based on a surveillance cohort in Harris County, Texas.

METHODS

Using the data of 21,765 patients who reported having at least one chronic health condition, we investigated the association between asthma and COVID-19 severity, characterized primarily by hospitalization and death. Unconditional logistic regression models were used to estimate the multivariable odds ratio (mOR) and its 95 % confidence interval (CI) of COVID-19 severity associated with asthma and other chronic lung diseases, adjusting for demographic and other comorbidities. A P-value < 0.005 was considered statistically significant after correcting multiple testing.

RESULTS

In total, 3034 patients (13.9 %) had asthma, and 774 (3.56 %) had other chronic lung diseases. The case death rate among patients with asthma and other chronic lung diseases was 0.75 % and 19.0 %, respectively. Compared to patients without the respective conditions, patients with asthma had lower odds of death (mOR = 0.44, 95 % CI: 0.27-0.69), while patients with other chronic lung diseases had higher odds of hospitalization (mOR = 2.02, 95 % CI: 1.68-2.42) and death (mOR = 1.95, 95 % CI: 1.52-2.49) (P-values < 0.005). Risk factors for COVID-19 mortality included older age, male gender, diabetes, obesity, hypertension, cardiovascular disease, active cancer, and chronic kidney disease.

CONCLUSIONS

The public health surveillance data suggested that preexisting asthma was inversely associated with COVID-19 mortality.

Sperm intrusion into the implantation-stage blastocyst and its potential biological significance

The human embryo derives from fusion of oocyte and sperm, undergoes growth and differentiation, resulting in a blastocyst. To initiate implantation, the blastocyst hatches from the zona pellucida, allowing access from external inputs. Modelling of uterine sperm distribution indicates that 200-5000 sperm cells may reach the implantation-stage blastocyst following natural coitus. We show ultrastructural evidence of sperm cells intruding into trophectoderm cells of zona-free blastocysts obtained from the uterus of rhesus monkeys. Interaction between additional sperm and zona-free blastocyst could be an evolutionary feature yielding adaptive processes influencing the developmental fate of embryos. This process bears potential implications in pregnancy success, sperm competition and human health.

131I dose coefficients for a reference population using age-specific models

Age-specific dose coefficients are required to assess internal exposure to the general public. This study utilizes reference age-specific biokinetic models of iodine to estimate the total number of nuclear disintegrations ã(rS,τ) occurring in source regions (rS) during the commitment time (τ). Age-specific S values are estimated for 35 target regions due to131I present in 22rSusing data from 10 paediatric reference computational phantoms (representing five ages for both sexes) published recently by the International Commission of Radiation Protection (ICRP). Monte Carlo transport simulations are performed in FLUKA code. The estimated ã(rS,τ) and S values are then used to compute the committed tissue equivalent dose HT(τ) for 27 radiosensitive tissues and dose coefficients e(τ) for all five ages due to inhalation and ingestion of131I. The derived ã(rS,τ) values in the thyroid source are observed to increase with age due to the increased retention of iodine in the thyroid. S values are found to decrease with age, mainly due to an increase in target masses. Generally, HT(τ) values are observed to decrease with age, indicating the predominant behaviour of S values over ã(rS,τ). On average, ingestion dose coefficients are 63% higher than for inhalation in all ages. The maximum contribution to dose coefficients is from the thyroid, accounting for 96% in the case of newborns and 98%-99% for all other ages. Furthermore, the estimated e(τ) values for the reference population are observed to be lower than previously published reference values from the ICRP. The estimated S, HT(τ) and e(τ) values can be used to improve estimations of internal doses to organs/whole body for members of the public in cases of131I exposure. The estimated dose coefficients can also be interpolated for other ages to accurately evaluate the doses received by the general public during131I therapy or during a radiological emergency.

3D Cyclophane for the Selective Conversion of Epoxide to Cyclic Carbonate

A novel three-dimensional (3D) cyclophane molecule 1 was synthesized and fully characterized. Cyclophane 1, which can form a N heterocyclic carbene, was tested for conversion of certain epoxides (3-6) [scheme 2] to cyclic carbonates in the presence of CO2. Propylene oxide (3) was found to have more reactivity with cyclophane 1 compared to the other epoxides. The theoretical calculations based on N,N'-disubstituted imidazol(in)ium-2-carboxylates derived from N,N' disubstituted imidazole as the source of N-heterocyclic carbene show lower activation energy in the case of the reactivity of epoxides 5 and 6 as compared to 3 and 4. However, cyclophane 1, which possesses a 3D geometry, can form the open intermediate with CO2 and propylene oxide more feasibly than the other three epoxides, which have larger sizes as compared to propylene oxide. Hence, the reaction of propylene oxide, CO2, and cyclophane 1 can follow the mechanistic path 1, whereas the epoxides 4-6 can follow a different mechanistic path 2. Cyclophane 1 is the first example of a cyclophane to act as an organocatalyst for the conversion of CO2 and epoxide to cyclic carbonate via the N heterocyclic carbene pathway.

Cholesterol catalyzes unfolding in membrane-inserted motifs of the pore forming protein cytolysin A

Plasma membrane-induced protein folding and conformational transitions play a central role in cellular homeostasis. Several transmembrane proteins are folded in the complex lipid milieu to acquire a specific structure and function. Bacterial pore forming toxins (PFTs) are proteins expressed by a large class of pathogenic bacteria that exploit the plasma membrane environment to efficiently undergo secondary structure changes, oligomerize, and form transmembrane pores. Unregulated pore formation causes ion imbalance, leading to cell death and infection. Determining the free energy landscape of these membrane-driven-driven transitions remains a challenging problem. Although cholesterol recognition is required for lytic activity of several proteins in the PFT family of toxins, the regulatory role of cholesterol for the α-PFT, cytolysin A expressed by Escherichia coli remains unexplained. In a recent free energy computation, we showed that the β tongue, a critical membrane-inserted motif of the ClyA toxin, has an on-pathway partially unfolded intermediate that refolds into the helix-turn-helix motif of the pore state. To understand the molecular role played by cholesterol, we carry out string-method-based computations in membranes devoid of cholesterol, which reveals an increase of ∼30 times in the free energy barrier for the loss of β sheet secondary structure when compared with membranes containing cholesterol. Specifically, the tyrosine-cholesterol interaction was found to be critical to creating the unfolded intermediate. Cholesterol also increases the packing and hydrophobicity of the bilayer, resulting in enhanced interactions of the bound protein before complete membrane insertion. Our study illustrates that cholesterol is critical to catalyzing and stabilizing the membrane-inserted unfolded state of the β tongue motif of ClyA, opening up fresh insights into cholesterol-assisted unfolding of membrane proteins.

Droplet-on-chip electro-spectroscopy detects the ultra-short relaxation time of a dilute polymer solution

We report an electrode-embedded on-chip platform technology for the precise determination of ultra-short (of the order of a few nanoseconds) relaxation times of dilute polymer solutions, by deploying time-alternating electrical voltages. Our methodology delves into the sensitive dependence of the contact line dynamics of a droplet of the polymer solution atop a hydrophobic interface in response to the actuation voltage, resulting in a non-trivial interplay between the time-evolving electrical, capillary, and viscous forces. This culminates into a time-decaying dynamic response that mimics the features of a damped oscillator having its 'stiffness' mapped with the polymeric content of the droplet. The observed electro-spreading characteristics of the droplet are thus shown to correlate explicitly with the relaxation time of the polymer solution, drawing analogies with a damped electro-mechanical oscillator. By corroborating well with the reported values of the relaxation times as obtained from more elaborate and sophisticated laboratory set-ups. Our findings provide perspectives for a unique and simple approach towards electrically-modulated on-chip-spectroscopy for deriving ultra-short relaxation times of a broad class of viscoelastic fluids that could not be realized thus far.

Evidence for Bootstrap Percolation Dynamics in a Photoinduced Phase Transition

Upon intense femtosecond photoexcitation, a many-body system can undergo a phase transition through a nonequilibrium route, but understanding these pathways remains an outstanding challenge. Here, we use time-resolved second harmonic generation to investigate a photoinduced phase transition in Ca_{3}Ru_{2}O_{7} and show that mesoscale inhomogeneity profoundly influences the transition dynamics. We observe a marked slowing down of the characteristic time τ that quantifies the transition between two structures. τ evolves nonmonotonically as a function of photoexcitation fluence, rising from below 200 fs to ∼1.4  ps, then falling again to below 200 fs. To account for the observed behavior, we perform a bootstrap percolation simulation that demonstrates how local structural interactions govern the transition kinetics. Our work highlights the importance of percolating mesoscale inhomogeneity in the dynamics of photoinduced phase transitions and provides a model that may be useful for understanding such transitions more broadly.

Evolutionary dynamics of dengue virus in India

More than a hundred thousand dengue cases are diagnosed in India annually, and about half of the country's population carries dengue virus-specific antibodies. Dengue propagates and adapts to the selection pressures imposed by a multitude of factors that can lead to the emergence of new variants. Yet, there has been no systematic analysis of the evolution of the dengue virus in the country. Here, we present a comprehensive analysis of all DENV gene sequences collected between 1956 and 2018 from India. We examine the spatio-temporal dynamics of India-specific genotypes, their evolutionary relationship with global and local dengue virus strains, interserotype dynamics and their divergence from the vaccine strains. Our analysis highlights the co-circulation of all DENV serotypes in India with cyclical outbreaks every 3-4 years. Since 2000, genotype III of DENV-1, cosmopolitan genotype of DENV-2, genotype III of DENV-3 and genotype I of DENV-4 have been dominating across the country. Substitution rates are comparable across the serotypes, suggesting a lack of serotype-specific evolutionary divergence. Yet, the envelope (E) protein displays strong signatures of evolution under immune selection. Apart from drifting away from its ancestors and other contemporary serotypes in general, we find evidence for recurring interserotype drift towards each other, suggesting selection via cross-reactive antibody-dependent enhancement. We identify the emergence of the highly divergent DENV-4-Id lineage in South India, which has acquired half of all E gene mutations in the antigenic sites. Moreover, the DENV-4-Id is drifting towards DENV-1 and DENV-3 clades, suggesting the role of cross-reactive antibodies in its evolution. Due to the regional restriction of the Indian genotypes and immunity-driven virus evolution in the country, ~50% of all E gene differences with the current vaccines are focused on the antigenic sites. Our study shows how the dengue virus evolution in India is being shaped in complex ways.

Post-secretory synthesis of a natural analog of iron-gall ink in the black nectar of Melianthus spp

The black nectar produced by Melianthus flowers is thought to serve as a visual attractant to bird pollinators, but the chemical identity and synthesis of the black pigment are unknown. A combination of analytical biochemistry, transcriptomics, proteomics, and enzyme assays was used to identify the pigment that gives Melianthus nectar its black color and how it is synthesized. Visual modeling of pollinators was also used to infer a potential function of the black coloration. High concentrations of ellagic acid and iron give the nectar its dark black color, which can be recapitulated through synthetic solutions containing only ellagic acid and iron(iii). The nectar also contains a peroxidase that oxidizes gallic acid to form ellagic acid. In vitro reactions containing the nectar peroxidase, gallic acid, hydrogen peroxide, and iron(iii) fully recreate the black color of the nectar. Visual modeling indicates that the black color is highly conspicuous to avian pollinators within the context of the flower. Melianthus nectar contains a natural analog of iron-gall ink, which humans have used since at least medieval times. This pigment is derived from an ellagic acid-Fe complex synthesized in the nectar and is likely involved in the attraction of passerine pollinators endemic to southern Africa.

VPS45 is required for both diffuse and tip growth of Arabidopsis thaliana cells

INTRODUCTION

VPS45 belongs to the Sec1/Munc18 family of proteins, which interact with and regulate Qa-SNARE function during membrane fusion. We have shown previously that Arabidopsis thaliana VPS45 interacts with the SYP61/SYP41/VTI12 SNARE complex, which locates on the trans-Golgi network (TGN). It is required for SYP41 stability, and it functions in cargo trafficking to the vacuole and in cell expansion. It is also required for correct auxin distribution during gravitropism and lateral root growth.

RESULTS

As vps45 knockout mutation is lethal in Arabidopsis, we identified a mutant, vps45-3, with a point mutation in the VPS45 gene causing a serine 284-to-phenylalanine substitution. The VPS45-3 protein is stable and maintains interaction with SYP61 and SYP41. However, vps45-3 plants display severe growth defects with significantly reduced organ and cell size, similar to vps45 RNAi transgenic lines that have reduced VPS45 protein levels. Root hair and pollen tube elongation, both processes of tip growth, are highly compromised in vps45-3. Mutant root hairs are shorter and thicker than those of wild-type plants, and are wavy. These root hairs have vacuolar defects, containing many small vacuoles, compared with WT root hairs with a single large vacuole occupying much of the cell volume. Pollen tubes were also significantly shorter in vps45-3 compared to WT.

DISCUSSION

We thus show that VPS45 is essential for proper tip growth and propose that the observed vacuolar defects lead to loss of the turgor pressure needed for tip growth.

Transcription elongation defects link oncogenic splicing factor mutations to targetable alterations in chromatin landscape

Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human disease remains unexplored. Here, we investigated the impact of non-synonymous mutations in SF3B1 and U2AF1, two commonly mutated splicing factors in cancer, on transcription. We find that the mutations impair RNA Polymerase II (RNAPII) transcription elongation along gene bodies leading to transcription-replication conflicts, replication stress and altered chromatin organization. This elongation defect is linked to disrupted pre-spliceosome assembly due to impaired association of HTATSF1 with mutant SF3B1. Through an unbiased screen, we identified epigenetic factors in the Sin3/HDAC complex, which, when modulated, normalize transcription defects and their downstream effects. Our findings shed light on the mechanisms by which oncogenic mutant spliceosomes impact chromatin organization through their effects on RNAPII transcription elongation and present a rationale for targeting the Sin3/HDAC complex as a potential therapeutic strategy.

GRAPHICAL ABSTRACT

HIGHLIGHTS

Oncogenic mutations of SF3B1 and U2AF1 cause a gene-body RNAPII elongation defectRNAPII transcription elongation defect leads to transcription replication conflicts, DNA damage response, and changes to chromatin organization and H3K4me3 marksThe transcription elongation defect is linked to disruption of the early spliceosome formation through impaired interaction of HTATSF1 with mutant SF3B1.Changes to chromatin organization reveal potential therapeutic strategies by targeting the Sin3/HDAC pathway.

Conformational Flexibility Is a Key Determinant for the Lytic Activity of the Pore-Forming Protein, Cytolysin A

Several bacterial infections are mediated by pore-forming toxins (PFTs), a subclass of proteins that oligomerize on mammalian cell membranes forming lytic nanopores. Cytolysin A (ClyA), an α-PFT, undergoes a dramatic conformational change restructuring its two membrane-binding motifs (the β-tongue and the N-terminus helix), during pore formation. A complete molecular picture for this key transition and the driving force behind the secondary structure change upon membrane binding remain elusive. Using all-atom molecular dynamics (MD) simulations of the ClyA monomer and string method based free energy computations with path collective variables, we illustrate that an unfolded β-tongue motif is an on-pathway intermediate during the transition to the helix-turn-helix motif of the protomer. An aggregate of 28 μs of all-atom thermal unfolding MD simulations of wild-type ClyA and its single point mutants reveal that the membrane-binding motifs of the ClyA protein display high structural flexibility in water. However, point mutations in these motifs lead to a distinct reduction in the flexibility, especially in the β-tongue, thereby stabilizing the pretransition secondary structure. Resistance to unfolding was further corroborated by MD simulations of the β-tongue mutant motif in the membrane. Combined with the thermal unfolding simulations, we posit that the β-tongue as well as N-terminal mutants that lower the tendency to unfold and disorder the β-tongue are detrimental to pore formation by ClyA and its lytic activity. Erythrocyte turbidity and vesicle leakage assays indeed reveal a loss of activity for the β-tongue mutant, and delayed kinetics for the N-terminus mutants. On the other hand, a point mutation in the extracellular domain that did not abrogate lytic activity displayed similar unfolding characteristics as the wild type. Thus, attenuation of conformational flexibility in membrane-binding motifs correlates with reduced lytic and leakage activity. Combined with secondary structure changes observed in the membrane bound states, our study shows that the tendency to unfold in the β-tongue region is a critical step in the conformational transition and bistability of the ClyA protein and mutants that disrupt this tendency reduced pore formation. Overall, our finding suggests that inherent flexibility in the protein could play a wider and hitherto unrecognized role in membrane-mediated conformational transitions of PFTs and other membrane protein transformations.

A Versatile Suspended Lipid Membrane System for Probing Membrane Remodeling and Disruption

Artificial membrane systems can serve as models to investigate molecular mechanisms of different cellular processes, including transport, pore formation, and viral fusion. However, the current, such as SUVs, GUVs, and the supported lipid bilayers suffer from issues, namely high curvature, heterogeneity, and surface artefacts, respectively. Freestanding membranes provide a facile solution to these issues, but current systems developed by various groups use silicon or aluminum oxide wafers for fabrication that involves access to a dedicated nanolithography facility and high cost while conferring poor membrane stability. Here, we report the development, characterization and applications of an easy-to-fabricate suspended lipid bilayer (SULB) membrane platform leveraging commercial track-etched porous filters (PCTE) with defined microwell size. Our SULB system offers a platform to study the lipid composition-dependent structural and functional properties of membranes with exceptional stability. With dye entrapped in PCTE microwells by SULB, we show that sphingomyelin significantly augments the activity of pore-forming toxin, Cytolysin A (ClyA) and the pore formation induces lipid exchange between the bilayer leaflets. Further, we demonstrate high efficiency and rapid kinetics of membrane fusion by dengue virus in our SULB platform. Our suspended bilayer membrane mimetic offers a novel platform to investigate a large class of biomembrane interactions and processes.

Accuracy of ICD-10 codes for patients with acute myocarditis: a retrospective study at a large tertiary centre in London, UK

Background

Acute myocarditis (AM) is an inflammatory disease of the myocardium that is associated with heterogenous clinical presentations, which may be non-specific. Furthermore, several cardiac diseases can mimic its clinical phenotype. Research in AM frequently utilises ICD-10 codes from hospital admissions for case identification. We retrospectively confirmed or refuted a diagnosis of AM according to ESC Position Statement criteria in patients with an ICD-10 code for AM.

Methods

We performed a single-centre retrospective analysis of all unique admissions with ICD-10 codes corresponding to myocarditis or myopericarditis in the first three coding positions at King's College Hospital, London, United Kingdom. The diagnosis was classified as “confirmed” if proven by cardiac magnetic resonance imaging (CMR) or endomyocardial biopsy (EMB) or “suspected” in the absence of CMR or EMB if other ESC Position Statement criteria were met. To identify additional cases, we used an open-source retrieval system for unstructured clinical data (CogStack). We searched hospital and Intensive Care Unit (ICU) discharge summaries for inpatients discharged alive containing the keywords “myocarditis” or “myopericarditis”. We also searched for patients who died during the study period where the keywords “myocarditis” or “myopericarditis” were included on the death notification.

Results

We identified 308 unique admissions with an ICD-10 code for myocarditis or myopericarditis in this study, presenting between 2008 and 2020 (Figure 1). Overall, 26.0% of patients (n=80/308) could be excluded from a diagnosis of AM on review of the clinical summary. A total of 16.2% of patients (n=50/308) had insufficient evidence of AM, 1.9% (n=6/308) had not had coronary artery disease excluded as a culprit for the presentation, and 10.1% (n=31/308) had an alternative diagnosis. Only 45.8% (n=141/308) of all patients met criteria for suspected or confirmed AM. Of those, 86.5% (n=122/141) of cases were confirmed by CMR. Overall, 39.6% of patients with an ICD-10 code indicating AM had a confirmed diagnosis. An additional 46 suspected and 197 confirmed cases were identified using open-source retrieval from unstructured clinical data.

Conclusion

AM has heterogenous and sometimes non-specific clinical presentations, which may be compounded by limited access to CMR and EMB. We identified significant misclassification using ICD-10 codes. It is crucial to ensure that studies investigating AM include only patients meeting appropriate diagnostic criteria, thereby ensuring a high-quality evidence base in this disease.

Funding Acknowledgement

Type of funding sources: None.

Nucleic Acid Quantification with Amplicon Yield in Recombinase Polymerase Amplification

Amplification-based quantitative polymerase chain reaction (qPCR) provides accurate and sensitive nucleic acid quantification. However, the requirement of temperature cycling and real-time monitoring limits its translation to many settings. Quantitative isothermal amplification methods alleviate the need for thermal cyclers; however, they still require continuous monitoring of the nucleic acid amplification on sophisticated readers. Here, we adapted an isothermal recombinase polymerase amplification (RPA) reaction to develop a semiquantitative method that relies on the final amplicon yield to estimate the initial target nucleic acid copy number. To achieve this, we developed a phenomenological model that captures the essential RPA dynamics. We identified reaction conditions that constrained the reaction yield corresponding to the starting DNA template concentration. We validated these predictions experimentally and showed that the amplicon yields at the end of the RPA reaction correlated well with the starting DNA concentration while reducing nonspecific amplification robustly. We demonstrate this approach, termed quantitative endpoint RPA (qeRPA), to detect DNA over five log orders with a detection limit of 100 molecules. Using a linear regression model of the normalized endpoint intensity (NEI) standard curve, we estimate the viral load from the serum of dengue virus-infected patients with comparable performance to qPCR. Unlike the conventional isothermal quantitative methods, qeRPA can be employed for robust and sensitive nucleic acid estimation at close to room temperature without real-time monitoring and can be beneficial for field deployment in resource-limited settings.

A Literature Review of Diagnostic Applicability of ICD 11 Classification of Personality Disorders in Comparison with ICD 10

Introduction

Personality disorders are frequently encountered by all healthcare professionals and can often pose a diagnostic dilemma due to the crossover of different traits amongst the various subtypes. The ICD 10 classification comprised of succinct parameters of the 10 subtypes of personality disorders but lacked a global approach to address the complexity of the disease. The ICD 11 classification provides a more structural approach to aid in clinical diagnosis.

Objectives

A literature review of the diagnostic applicability of ICD 11 classification of personality disorders is presented in comparison with the ICD 10 classification.

Methods

A retrospective analysis of the literature outlining the ICD 10 and 11 classifications of personality disorders, exploring the differences in evidence-based applications of both.

Results

The ICD 11 classification of personality disorders supersedes the ICD 10 classification in describing the severity of the personality dysfunction in conjunction with a wide range of trait domain qualifiers, thus enabling the clinician to portray the disease dynamically. The current evidence available on the utility of the ICD 11 classification gives a promising outlook for its application in clinical settings.

Conclusions

The ICD 11 has transformed the classification of personality disorders by projecting a dimensional description of personality functioning, aiming to overcome the diagnostic deficiencies in the ICD 10 classification. The versatility offered by the application of the ICD 11 classification can be pivotal in reshaping the focus and intensity of clinical management of the disease.

Disclosure

No significant relationships.

Tumor tissue-specific bacterial biomarker panel for colorectal cancer: Bacteroides massiliensis, Alistipes species, Alistipes onderdonkii, Bifidobacterium pseudocatenulatum, Corynebacterium appendicis

Human microbiome studies have shown diversity to exist among different ethnic populations. However, studies pertaining to the microbial composition of CRC among the Indian population have not been well explored. We aimed to decipher the microbial signature in tumor tissues from North Indian CRC patients. Next-generation sequencing of tumor and adjacent tissue-derived bacterial 16S rRNA V3-V4 hypervariable regions was performed to investigate the abundance of specific microbes. The expression profile analysis deciphered a decreased diversity among the tumor-associated microbial communities. At the phyla level, Proteobacteria was differentially expressed in CRC tissues than adjacent normal. Further, DeSeq2 normalization identified 4 out of 79 distinct species (p < 0.005) only in CRC, Bacteroides massiliensis, Alistipes onderdonkii, Bifidobacterium pseudocatenulatum, and Corynebacterium appendicis. Thus, the findings suggest that microbial signatures can be used as putative biomarkers in diagnosis, prognosis and treatment management of CRC.

Immune profile and responses of a novel dengue DNA vaccine encoding an EDIII-NS1 consensus design based on Indo-African sequences

The ongoing COVID-19 pandemic highlights the need to tackle viral variants, expand the number of antigens, and assess diverse delivery systems for vaccines against emerging viruses. In the present study, a DNA vaccine candidate was generated by combining in tandem envelope protein domain III (EDIII) of dengue virus serotypes 1-4 and a dengue virus (DENV)-2 non-structural protein 1 (NS1) protein-coding region. Each domain was designed as a serotype-specific consensus coding sequence derived from different genotypes based on the whole genome sequencing of clinical isolates in India and complemented with data from Africa. This sequence was further optimized for protein expression. In silico structural analysis of the EDIII consensus sequence revealed that epitopes are structurally conserved and immunogenic. The vaccination of mice with this construct induced pan-serotype neutralizing antibodies and antigen-specific T cell responses. Assaying intracellular interferon (IFN)-γ staining, immunoglobulin IgG2(a/c)/IgG1 ratios, and immune gene profiling suggests a strong Th1-dominant immune response. Finally, the passive transfer of immune sera protected AG129 mice challenged with a virulent, non-mouse-adapted DENV-2 strain. Our findings collectively suggest an alternative strategy for dengue vaccine design by offering a novel vaccine candidate with a possible broad-spectrum protection and a successful clinical translation either as a stand alone or in a mix and match strategy.

Posttranslational regulation of transporters important for symbiotic interactions

Coordinated sharing of nutritional resources is a central feature of symbiotic interactions, and, despite the importance of this topic, many questions remain concerning the identification, activity, and regulation of transporter proteins involved. Recent progress in obtaining genome and transcriptome sequences for symbiotic organisms provides a wealth of information on plant, fungal, and bacterial transporters that can be applied to these questions. In this update, we focus on legume-rhizobia and mycorrhizal symbioses and how transporters at the symbiotic interfaces can be regulated at the protein level. We point out areas where more research is needed and ways that an understanding of transporter mechanism and energetics can focus hypotheses. Protein phosphorylation is a predominant mechanism of posttranslational regulation of transporters in general and at the symbiotic interface specifically. Other mechanisms of transporter regulation, such as protein-protein interaction, including transporter multimerization, polar localization, and regulation by pH and membrane potential are also important at the symbiotic interface. Most of the transporters that function in the symbiotic interface are members of transporter families; we bring in relevant information on posttranslational regulation within transporter families to help generate hypotheses for transporter regulation at the symbiotic interface.

Discovery of potential competitive inhibitors against With-No-Lysine kinase 1 for treating hypertension by virtual screening, inverse pharmacophore-based lead optimization, and molecular dynamics simulations

The With-No-Lysine (WNK) has received attention because of its involvement in hypertension. Genetic mutation in the genes of WNK, leading to its overexpression, has been reported in Familial Hyperkalaemic Hypertension, and thus WNK is considered a potential drug target. Herein, we have performed a high-throughput virtual screening of ~11,000 compounds, mainly the natural phytochemical compounds and kinase inhibitory libraries, to find potential competitive inhibitors against WNK1. Initially, candidates with a docking score of ~ -10.0 kcal/mol or less were selected to further screen their good pharmacological properties by applying absorption, distribution, metabolism, excretion, and toxicity (ADMET). Finally, six docked compounds bearing appreciable binding affinities and WNK1 selectivity were complimented with 500 ns long all-atom molecular dynamic simulations. Subsequently, the MMPBSA scheme (Molecular Mechanics Poisson Boltzmann Surface Area) suggested three phytochemical compounds, C00000947, C00020451, and C00005031, with favourable binding affinity against WNK1. Among them, C00000947 acts as the most potent competitive inhibitor of WNK1. Further, inverse pharmacophore-based lead optimization of the C00000947 leads to one potential compound, meciadanol, which shows better binding affinity and specificity than C00000947 towards WNK1, which may be further exploited to develop effective therapeutics against WNK1-associated hypertension after in vitro and in vivo validation.

Life cycle process dependencies of positive-sense RNA viruses suggest strategies for inhibiting productive cellular infection

Life cycle processes of positive-strand (+)RNA viruses are broadly conserved across families, yet they employ different strategies to grow in the cell. Using a generalized dynamical model for intracellular (+)RNA virus growth, we decipher these life cycle determinants and their dependencies for several viruses and parse the effects of viral mutations, drugs and host cell permissivity. We show that poliovirus employs rapid replication and virus assembly, whereas the Japanese encephalitis virus leverages its higher rate of translation and efficient cellular reorganization compared to the hepatitis C virus. Stochastic simulations demonstrate infection extinction if all seeding (inoculating) viral RNA degrade before establishing robust replication critical for infection. The probability of this productive cellular infection, 'cellular infectivity', is affected by virus-host processes and defined by early life cycle events and viral seeding. An increase in cytoplasmic RNA degradation and delay in vesicular compartment formation reduces infectivity, more so when combined. Synergy among these parameters in limiting (+)RNA virus infection as predicted by our model suggests new avenues for inhibiting infections by targeting the early life cycle bottlenecks.

Investigating potency of TMC-126 against wild-type and mutant variants of HIV-1 protease: a molecular dynamics and free energy study

A detailed computational study was performed to investigate the conformational changes of flap region and the mechanism underlying the binding of the inhibitor TMC-126 to HIV-1 protease (PR1) and its mutant variants through molecular dynamics simulations in conjunction with the molecular mechanics Poisson-Boltzmann (MM-PBSA) free energy calculation. Further, we have studied the effectiveness of the inhibitor against HIV-2 protease (PR2). The MM-PBSA calculation suggests that TMC-126 loses its potency against mutant variants and PR2 compared to wild-type PR1 mainly due to the loss in intermolecular electrostatic interactions. The potency of the inhibitor decreases in the order: wild type PR1 > M46L > MDR20 > I50V > PR2 > V32I > A28S. Our study reveals that the flap of PR1 adopts a semi-open conformation due to the mutation I50V or MDR20. The dissimilar nature of the movement of the flap tip of both monomers is evident from the dynamic cross-correlation map. The protein structural network analysis displays that mutation causes structural rearrangements and changes the communication path between residues. Overall, we believe our study may help explore and accelerate the development of novel HIV-1/HIV-2 protease inhibitors with better potency.

Evaluation of spike protein antigens for SARS-CoV-2 serology

BACKGROUND

Spike protein domains are being used in various serology-based assays to detect prior exposure to SARS-CoV-2 virus. However, there has been limited comparison of antibody titers against various spike protein antigens among COVID-19 infected patients.

METHODS

We compared four spike proteins (RBD, S1, S2 and a stabilized spike trimer (ST)) representing commonly used antigens for their reactivity to human IgG antibodies using indirect ELISA in serum from COVID-19 patients and pre-2020 samples. ST ELISA was also compared against the EUROIMMUN IgG ELISA test. Further, we estimated time appropriate IgG and IgA seropositivity rates in COVID-19 patients using a panel of sera samples collected longitudinally from the day of onset of symptoms (DOS).

RESULTS

Among the four spike antigens tested, the ST demonstrated the highest sensitivity (86.2 %; 95 % CI: 77.8-91.7 %), while all four antigens showed high specificity to COVID-19 sera (94.7-96.8 %). 13.8 % (13/94) of the samples did not show seroconversion in any of the four antigen-based assays. In a double-blinded head-to-head comparison, ST based IgG ELISA displayed a better sensitivity (87.5 %, 95 % CI: 76.4-93.8 %) than the EUROIMMUN IgG ELISA (67.9 %, 95 % CI: 54.8-78.6 %). Further, in ST-based assays, we found 48 % and 50 % seroconversion in the first six days (from DOS) for IgG and IgA antibodies, respectively, which increased to 84 % (IgG) and 85 % (IgA) for samples collected ≥22 days from DOS.

CONCLUSIONS

Comparison of spike antigens demonstrates that spike trimer protein is a superior option as an ELISA antigen for COVID-19 serology.

Nectar biosynthesis is conserved among floral and extrafloral nectaries

Nectar is a primary reward mediating plant-animal mutualisms to improve plant fitness and reproductive success. Four distinct trichomatic nectaries develop in cotton (Gossypium hirsutum), one floral and three extrafloral, and the nectars they secrete serve different purposes. Floral nectar attracts bees for promoting pollination, while extrafloral nectar attracts predatory insects as a means of indirect protection from herbivores. Cotton therefore provides an ideal system for contrasting mechanisms of nectar production and nectar composition between different nectary types. Here, we report the transcriptome and ultrastructure of the four cotton nectary types throughout development and compare these with the metabolomes of secreted nectars. Integration of these datasets supports specialization among nectary types to fulfill their ecological niche, while conserving parallel coordination of the merocrine-based and eccrine-based models of nectar biosynthesis. Nectary ultrastructures indicate an abundance of rough endoplasmic reticulum positioned parallel to the cell walls and a profusion of vesicles fusing to the plasma membranes, supporting the merocrine model of nectar biosynthesis. The eccrine-based model of nectar biosynthesis is supported by global transcriptomics data, which indicate a progression from starch biosynthesis to starch degradation and sucrose biosynthesis and secretion. Moreover, our nectary global transcriptomics data provide evidence for novel metabolic processes supporting de novo biosynthesis of amino acids secreted in trace quantities in nectars. Collectively, these data demonstrate the conservation of nectar-producing models among trichomatic and extrafloral nectaries.

Nectar antimicrobial compounds and their potential effects on pollinators

Nectar is a sugary, aqueous solution that plants offer as a reward to animal mutualists for visitation. Since nectars are so nutrient-rich, they often harbor significant microbial communities, which can be pathogenic, benign, or even sometimes beneficial to plant fitness. Through recent advances, it is now clear that these microbes alter nectar chemistry, which in turn influences mutualist behavior (e.g. pollinator visitation). To counteract unwanted microbial growth, nectars often contain antimicrobial compounds, especially in the form of proteins, specialized (secondary) metabolites, and metals. This review covers our current understanding of nectar antimicrobials, as well as their interplay with both microbes and insect visitors.

Genetic diversity and population structure of Jamunapari goat in India using pedigree analysis

Pedigree records of 6821 Jamunapari goats of India were collected from 1980 to 2011 and used to evaluate the population structure and genetic diversity in this flock. Animals born between 2009 and 2011 represented the current reference population. The average pedigree completeness index (PCI) and numbers of equivalent complete generations (EqG) were estimated for the entire (PCI = 0.18, EqG = 2.24) and reference (PCI = 0.31, EqG = 3.45) populations. The average generation interval was 3.33 years. The average inbreeding coefficient and the average relatedness were 0.46 and 1.06%, respectively, for the entire population and 0.77 and 3.87% for the reference population. The rate of inbreeding was 0.06% per generation. The effective population size (N_e), estimated from increases in inbreeding coefficients between the first and third equivalent complete generations, was 52.65, but periodic introductions of unrelated breeding males resulted in average inbreeding levels in the reference population that were lower than those predicted from the estimate of N_e. Effective numbers of founders (f_e), ancestors (f_a), founder genomes equivalents (f_g), and non-founder genomes (f_ng) were 51, 39, 25.8, and 48.2, respectively. The f_e/f_a ratio in the reference population was 1.31 and indicated that occasional bottlenecks had occurred in the population. The 14 most influential ancestors contributed 50% of the genetic variability in the reference population, with a maximum individual contribution of 9.25%. Approximately 1.9% of the initial heterozygosity had been lost from the population, indicating that substantial genetic diversity still exists in this flock.

The role of alanine synthesis and nitrate-induced nitric oxide production during hypoxia stress in Cucurbita pepo nectaries

Floral nectar is a sugary solution produced by nectaries to attract and reward pollinators. Nectar metabolites, such as sugars, are synthesized within the nectary during secretion from both pre-stored and direct phloem-derived precursors. In addition to sugars, nectars contain nitrogenous compounds such as amino acids; however, little is known about the role(s) of nitrogen (N) compounds in nectary function. In this study, we investigated N metabolism in Cucurbita pepo (squash) floral nectaries in order to understand how various N-containing compounds are produced and determine the role of N metabolism in nectar secretion. The expression and activity of key enzymes involved in primary N assimilation, including nitrate reductase (NR) and alanine aminotransferase (AlaAT), were induced during secretion in C. pepo nectaries. Alanine (Ala) accumulated to about 35% of total amino acids in nectaries and nectar during peak secretion; however, alteration of vascular nitrate supply had no impact on Ala accumulation during secretion, suggesting that nectar(y) amino acids are produced by precursors other than nitrate. In addition, nitric oxide (NO) is produced from nitrate and nitrite, at least partially by NR, in nectaries and nectar. Hypoxia-related processes are induced in nectaries during secretion, including lactic acid and ethanolic fermentation. Finally, treatments that alter nitrate supply affect levels of hypoxic metabolites, nectar volume and nectar sugar composition. The induction of N metabolism in C. pepo nectaries thus plays an important role in the synthesis and secretion of nectar sugar.

Increased paediatric presentations of severe diabetic ketoacidosis in an Australian tertiary centre during the COVID-19 pandemic

AIMS

To determine if the frequency of severe diabetic ketoacidosis at presentation of new-onset type 1 diabetes to an Australian tertiary centre increased during the initial period of restrictions resulting from the COVID-19 pandemic (March to May 2020).

METHODS

Data were collected on presentations of newly diagnosed type 1 diabetes as well as on all paediatric presentations to the emergency department of a tertiary centre between 2015 and 2020. Data from the period of initial COVID restrictions in Australia (March to May 2020) were compared to the period March to May of the previous 5 years (pre-pandemic periods).

RESULTS

The number of new diagnoses of type 1 diabetes was comparable in the pandemic period and pre-pandemic periods (11 in 2020 vs range 6-10 in 2015-2019). The frequency of severe diabetic ketoacidosis was significantly higher in the pandemic period compared to the pre-pandemic periods (45% vs 5%; P <0.003), odds ratio 16.7 (95% CI 2.0, 194.7). The overall frequency of diabetic ketoacidosis was also significantly higher during the pandemic period (73% vs 26%; P <0.007), odds ratio 7.5 (95% CI 1.7, 33.5). None of the individuals tested positive for COVID-19. Presentations of people aged <18 years to the emergency department decreased by 27% in the pandemic period compared to the average of the pre-pandemic periods (4799 vs 6550; range 6268 to 7131).

CONCLUSIONS

A significant increase in the frequency of severe diabetic ketoacidosis at presentation of type 1 diabetes was observed during the initial period of COVID-19 restrictions. We hypothesize that concern about presenting to hospital during a pandemic led to a delay in diagnosis. These data have important implications for advocacy of seeking healthcare for non-pandemic-related conditions during a global pandemic.

Hepatocellular carcinoma with atrial tumor thrombus presenting as myxoma: Resection under cardiopulmonary bypass

Surgical resection for Hepatocellular carcinoma (HCC) with atrial tumor thrombus is a rare life saving procedure. A case of left lateral segment liver tumor (HCC) with atrial tumor thrombus resected with use of cardio-pulmonary bypass is presented.

Protamine composition of koala and wombat spermatozoa provides new insights into DNA stability following cryopreservation

To investigate differences in the post-thaw DNA stability of koala and wombat spermatozoa, protamine amino acid sequences were compared and it was found that there were three more arginine residues for the wombat. Koala and wombat spermatozoa, cryopreserved using identical protocols, were examined for changes in sperm DNA fragmentation (SDF) dynamics over 24h of post-thaw incubation. Following validation of a wombat sperm chromatin dispersion test, wombat DNA showed a rate of SDF that was 6-fold higher than for koala spermatozoa (P=0.038). Finally, we examined whether expected differences in chromatin compactness, associated with protamine sequence, had an effect on restriction site accessibility of sperm DNA. Thawed spermatozoa were exposed to Alu I and EcoR1 endonuclease restriction enzymes and the SDF dynamics were observed. Koala spermatozoa exposed to Alu I showed a greater rate of SDF (P=0.01), whereas wombat spermatozoa exposed to EcoR1 showed a greater rate of SDF (P=0.032). We conclude that restriction sites in these species are differentially present or exposed and potentially account for differences in SDF dynamics. Although differences in the arginine composition of protamine may explain relative differences in SDF following cryopreservation, they do not support the hypothesis that increased arginine composition increases DNA stability; rather, increased arginine composition in the wombat may reduce post-thaw chromatin swelling.

Streaming potential in bio-mimetic microvessels mediated by capillary glycocalyx

Implantable medical devices and biosensors are pivotal in revolutionizing the field of medical technology by opening new dimensions in the field of disease detection and cure. These devices need to harness a biocompatible and physiologically sustainable safe power source instead of relying on external stimuli, overcoming the constraints on their applicability in-vivo. Here, by appealing to the interplay of electromechanics and hydrodynamics in physiologically relevant microvessels, we bring out the role of charged endothelial glycocalyx layer (EGL) towards establishing a streaming potential across physiological fluidic conduits. We account for the complex rheology of blood-mimicking fluid by appealing to Newtonian fluid model representing the blood plasma and a viscoelastic fluid model representing the whole blood. We model the EGL as a poroelastic layer with volumetric charge distribution. Our results reveal that for physiologically relevant micro-flows, the streaming potential induced is typically of the order of 0.1 V/mm, which may turn out to be substantial towards energizing biosensors and implantable medical devices whose power requirements are typically in the range of micro to milliwatts. We also bring out the specific implications of the relevant physiological parameters towards establishment of the streaming potential, with a vision of augmenting the same within plausible functional limits. We further unveil that the dependence of streaming potential on EGL thickness might be one of the key aspects in unlocking the mystery behind the angiogenesis pattern. Our results may open up novel bio-sensing and actuating possibilities in medical diagnostics as well as may provide a possible alternative regarding the development of physiologically safe and biocompatible power sources within the human body.

Clinical ultrasound image standardization using histogram specification

This article presents a novel ultrasound image standardization approach. This method aims to preserve the non-linear relationship in the echo-textures while ensuring the endurance in the transformed image. This is achieved by utilizing the concept of histogram specification. A reference cumulative distribution function (CDF) of a considered distribution is used to process the test images. Initially, the shape and scale parameter of the distribution are estimated for each type of echo-texture from the reference ultrasound images of a particular organ. These parameters are used to estimate the prototype parameter set. The obtained prototype parameter set, along with a distribution function, is then used to construct a reference CDF. This CDF, in turn, is used as a transfer function in the histogram specification technique for standardizing the given input image. The efficiency and stability of the proposed approach are investigated and compared with the linear scaling technique. Four measures are used to evaluate the algorithms on three data sets. The results show that the proposed approach provides better standardization of images and is invariant to the gain of the scanning device as opposed to linear scaling.

Understanding transport processes in lichen, Azolla-cyanobacteria, ectomycorrhiza, endomycorrhiza, and rhizobia-legume symbiotic interactions

Intimate interactions between photosynthetic and non-photosynthetic organisms require the orchestrated transfer of ions and metabolites between species. We review recent progress in identifying and characterizing the transport proteins involved in five mutualistic symbiotic interactions: lichens, Azolla–cyanobacteria, ectomycorrhiza, endomycorrhiza, and rhizobia–legumes. This review focuses on transporters for nitrogen and carbon and other solutes exchanged in the interactions. Their predicted functions are evaluated on the basis of their transport mechanism and prevailing transmembrane gradients of H ⁺ and transported substrates. The symbiotic interactions are presented in the assumed order from oldest to most recently evolved.