Accurate structure prediction of biomolecular interactions with AlphaFold 3.

The introduction of AlphaFold 21 has spurred a revolution in modelling the structure of proteins and their interactions, enabling a huge range of applications in protein modelling and design2-6. Here we describe our AlphaFold 3 model with a substantially updated diffusion-based architecture that is capable of predicting the joint structure of complexes including proteins, nucleic acids, small molecules, ions and modified residues. The new AlphaFold model demonstrates substantially improved accuracy over many previous specialized tools: far greater accuracy for protein-ligand interactions compared with state-of-the-art docking tools, much higher accuracy for protein-nucleic acid interactions compared with nucleic-acid-specific predictors and substantially higher antibody-antigen prediction accuracy compared with AlphaFold-Multimer v.2.37,8. Together, these results show that high-accuracy modelling across biomolecular space is possible within a single unified deep-learning framework.

Understanding the Droplet Diffusion in Ionic Liquid Microemulsions.

Ionic liquids (ILs) as polar components in nonaqueous microemulsions are complex formulations that have interesting transport and structural properties, and offer broader applicability of ILs in areas such as drug delivery and cleaning technology. The phase behavior, electrical conductivity, and nanostructures of these formulations have been investigated for quite some time, but the characteristics of the diffusion of nanodroplets were rarely explored─ and hence little understood. This work investigates the droplet diffusion processes in a series of IL-microemulsions containing 1-butyl-3-methylimidazolium tetrafluoroborate ([C4mim]BF4) by means of viscosity and depolarized dynamic light scattering (DDLS) measurements. The intensity correlation functions are strikingly similar to polymeric solutions in nonaqueous media and aqueous microemulsions containing block copolymers─having bimodal relaxations that are separated by three to four decades of correlation delay times. The "faster" diffusion process is likely a collective process characterizing the correlated motions of droplets in droplet clusters. The collective diffusion coefficient Dcol values are quite comparable to aqueous microemulsions. The "slower" diffusion is likely due to the "caging" effect caused by nearby clusters and/or bulk solvent─this mode may be linked to the microemulsion bulk viscosity. Interestingly, the Dcol variations on increasing [C4mim]BF4 concentration are strongly correlated to the microemulsion viscosity changes as well as locations of these compositions on the microemulsion phase diagram.

Dynamics of the wetland ecosystem health in urban and rural settings in high altitude ecoregion.

The focus of the present study was to assess the dynamics of wetland ecosystem health in both urban and rural settings situated in the high-altitude Kashmir Himalayan ecoregion. The basic aim was to identify the drivers responsible for wetland degradation in order to sustain ecosystem services effectively. To achieve this, we examined water quality, trophic status, fish species diversity and human disturbances by analyzing changes in land use and land cover (LULC) since 1980. For the limnological characterization of the two wetlands, we evaluated a total of 21 physico-chemical parameters at 24 sites. Two-way analysis of variance revealed significant (p < 0.05) spatial and temporal variability in the water quality parameters. The trophic state index values of 67.7 and 76.7 indicated that the rural and urban wetlands were in eutrophic and hypertrophic status, respectively, signifying potential environmental stress. The data on fish fauna indicated a decline in fish species over the past 40 years, particularly the schizothoracine species. Urban wetlands showed a more significant decrease in species (06) compared to rural wetlands (01). LULC mapping and change analysis employing the visual interpretation technique showed significant transformations in the immediate catchment of wetlands. Substantial growth in the built-up (433.2 % and 2620 %) and decrease in aquatic vegetation (-83.4 % and - 97.5 %) in the immediate catchment was recorded in both the urban and rural wetlands respectively from 1980 to 2020. Our findings demonstrated a relationship between LULC classes and water quality parameters, with an increase in built-up and road areas showing a significant positive correlation with the rise in decadal mean values of total phosphorus, orthophosphorus, nitrate nitrogen, ammonical nitrogen, and calcium content. Based on these observations, we concluded that changes in land use and land cover within the immediate catchment areas of the wetlands were the primary drivers responsible for the deterioration of wetland ecosystem health.

Intrafamilial and interfamilial heterogeneity of PINK1-associated Parkinson's disease in Sudan.

PINK1 is the second most predominant gene associated with autosomal recessive Parkinson's disease. Homozygous mutations in this gene are associated with an early onset of symptoms. Bradykinesia, tremors, and rigidity are common features, while dystonia, motor fluctuation, and non-motor symptoms occur in a lower percentage of cases and usually respond well to levodopa. We investigated 14 individuals with parkinsonism and eleven symptom-free siblings from three consanguineous Sudanese families, two of them multigenerational, using a custom gene panel screening 34 genes, 27 risk variants, and 8 candidate genes associated with parkinsonism. We found a known pathogenic nonsense PINK1 variant (NM_032409.3:c.1366C>T; p.(Gln456*)), a novel pathogenic single base duplication (NM_032409.3:c.1597dup; p.(Gln533Profs*29)), and another novel pathogenic insertion (NM_032409.3:c.1448_1449ins[1429_1443; TTGAG]; p.(Arg483Serfs*7)). All variants were homozygous and co-segregated in all affected family members. We also identified intrafamilial and interfamilial phenotypic heterogeneity associated with PINK1 mutations in these Sudanese cases, possibly reflecting the nature of the Sudanese population that has a large effective population size, which suggests a higher possibility of novel findings in monogenic and polygenic diseases in Sudan.

Sensory deficit screen identifies nsf mutation that differentially affects SNARE recycling and quality control.

The AAA+ NSF complex is responsible for SNARE complex disassembly both before and after membrane fusion. Loss of NSF function results in pronounced developmental and degenerative defects. In a genetic screen for sensory deficits in zebrafish, we identified a mutation in nsf, I209N, that impairs hearing and balance in a dosage-dependent manner without accompanying defects in motility, myelination, and innervation. In vitro experiments demonstrate that while the I209N NSF protein recognizes SNARE complexes, the effects on disassembly are dependent upon the type of SNARE complex and I209N concentration. Higher levels of I209N protein produce a modest decrease in binary (syntaxin-SNAP-25) SNARE complex disassembly and residual ternary (syntaxin-1A-SNAP-25-synaptobrevin-2) disassembly, whereas at lower concentrations binary disassembly activity is strongly reduced and ternary disassembly activity is absent. Our study suggests that the differential effect on disassembly of SNARE complexes leads to selective effects on NSF-mediated membrane trafficking and auditory/vestibular function.

Lack of evidence for ribosomal frameshifting in ATP7B mRNA decoding.

The research article describing the discovery of ribosomal frameshifting in the bacterial CopA gene also reported the occurrence of frameshifting in the expression of the human ortholog ATP7B based on assays using dual luciferase reporters. An examination of the publicly available ribosome profiling data and the phylogenetic analysis of the proposed frameshifting site cast doubt on the validity of this claim and prompted us to reexamine the evidence. We observed similar apparent frameshifting efficiencies as the original authors using the same type of vector that synthesizes both luciferases as a single polyprotein. However, we noticed anomalously low absolute luciferase activities from the N-terminal reporter that suggests interference of reporter activity or levels by the ATP7B test cassette. When we tested the same proposed ATP7B frameshifting cassette in a more recently developed reporter system in which the reporters are released without being included in a polyprotein, no frameshifting was detected above background levels.

Methylation of alpha-synuclein in a Sudanese cohort.

BACKGROUND: Several studies suggested a significant role of epigenetic changes, including alterations in miRNA, histone modifications, and DNA methylation of α-synuclein (SNCA) in Parkinson's disease (PD) pathogenicity. As of yet, only very few studies have been carried out in this field in Africa and none in Sudan. MATERIALS AND METHODS: We collected DNA from 172 Sudanese individuals (90 cases, 82 controls) who donated saliva for DNA extraction (mean age of onset: 40.6 ± 22.4 years). A family history of PD was evident in 64 patients. DNA preparation and bisulfite sequencing of SNCAintron1 was performed as described earlier. RESULTS: Of the fourteen analyzed CpGs of SNCAintron1, CpGs 16-23 were hypomethylated in PD (P-value ranged from 0.023 to 0.003). P-values improved, when sporadic cases were excluded from the analysis. CONCLUSION: We identified the presence of a specific pattern of DNA methylation in a young Sudanese cohort of familial PD, which confirms the importance of the methylation of SNCAintron1 for PD. This phenomenon appears to be independent of ethnicity, the impact of environmental factors, drug history, or familial clustering.

Cryo-EM, Protein Engineering, and Simulation Enable the Development of Peptide Therapeutics against Acute Myeloid Leukemia.

Cryogenic electron microscopy (cryo-EM) has emerged as a viable structural tool for molecular therapeutics development against human diseases. However, it remains a challenge to determine structures of proteins that are flexible and smaller than 30 kDa. The 11 kDa KIX domain of CREB-binding protein (CBP), a potential therapeutic target for acute myeloid leukemia and other cancers, is a protein which has defied structure-based inhibitor design. Here, we develop an experimental approach to overcome the size limitation by engineering a protein double-shell to sandwich the KIX domain between apoferritin as the inner shell and maltose-binding protein as the outer shell. To assist homogeneous orientations of the target, disulfide bonds are introduced at the target-apoferritin interface, resulting in a cryo-EM structure at 2.6 Å resolution. We used molecular dynamics simulations to design peptides that block the interaction of the KIX domain of CBP with the intrinsically disordered pKID domain of CREB. The double-shell design allows for fluorescence polarization assays confirming the binding between the KIX domain in the double-shell and these interacting peptides. Further cryo-EM analysis reveals a helix-helix interaction between a single KIX helix and the best peptide, providing a possible strategy for developments of next-generation inhibitors.

The AAA+ superfamily: a review of the structural and mechanistic principles of these molecular machines.

ATPases associated with diverse cellular activities (AAA+ proteins) are a superfamily of proteins found throughout all domains of life. The hallmark of this family is a conserved AAA+ domain responsible for a diverse range of cellular activities. Typically, AAA+ proteins transduce chemical energy from the hydrolysis of ATP into mechanical energy through conformational change, which can drive a variety of biological processes. AAA+ proteins operate in a variety of cellular contexts with diverse functions including disassembly of SNARE proteins, protein quality control, DNA replication, ribosome assembly, and viral replication. This breadth of function illustrates both the importance of AAA+ proteins in health and disease and emphasizes the importance of understanding conserved mechanisms of chemo-mechanical energy transduction. This review is divided into three major portions. First, the core AAA+ fold is presented. Next, the seven different clades of AAA+ proteins and structural details and reclassification pertaining to proteins in each clade are described. Finally, two well-known AAA+ proteins, NSF and its close relative p97, are reviewed in detail.

Exposure pathways and ecological risk assessment of common veterinary antibiotics in the environment through poultry litter in Bangladesh.

Veterinary antibiotics (VAs) have entered the ecosystem principally through the application of organic fertilizer. However, factors influencing the contributions made by the prescribers and users thereof with respect to VAs in poultry manure have not been investigated. The purpose of this paper, therefore, is to identify factors associated with the VA prescription and usage as well as to measure the residual concentration along with the ecological risk of common VAs in poultry litter in Bangladesh. Structured questionnaire surveys were conducted so as to provide an understanding the perspective of prescribers and farmers. Ciprofloxacin (CIP), enrofloxacin (ENR), oxytetracycline (OTC), and doxycycline (DOX) were screened through the use of thin-layer chromatography (TLC) and quantified through high-performance liquid chromatography (HPLC). Also, methods of risk quotient (RQ) were applied to assess ecotoxicity. Most VAs were prescribed without a confirmatory diagnosis. The residue of CIP was dominant with a high concentration, followed by OTC but with a low concentration. A high ecological risk was associated with the use of OTC and DOX whereas the risk associated with the use of CIP and ENR was insignificant to low. The study highlights prescriber and user factors along with the variable ecological risk of VAs in litter.

Exploiting Citrus aurantium seeds and their secondary metabolites in the management of Alzheimer disease.

Fruit by-products are considered nature's golden gift for human health and a good starting point to discover new drugs depending on the fact that they contain millions of bio-active compounds that are responsible for therapeutic activities. In this context, the main goal of this study is to recycle Citrus aurantium (C. aurantium) seeds to produce pharmaceutical molecules to be used in the prevention of the progressive neurological damage associated with Alzheimer disease (AD). Donepezil (0.75 mg/kg), hesperidin (125 and 250 mg/kg) and limonoids (50 and 100 mg/kg) were used for treatment of rats for 2 weeks prior to concomitant administration of AlCl3 for three successive weeks. Protection against cognitive deterioration was observed among study group with insignificant difference from normal control group and significant difference from positive control group in the Y-Maze test. On the other hand, treatment with both doses of hesperidin (125 and 250 mg/kg) and high dose of limonoids only (100 mg/kg) produced improvement in psychological state, observed by significant increase in ambulation frequency in comparison to positive control group, however it was not as frequent as normal group, as it was significantly less than normal group in the open field test. Regarding acetylcholine esterase (AChE) and beta-amyloid (ß amyloid) levels, the effect of limonoids low dose was the best as it didn't have a significant effect when compared to normal control, also hesperidin in both doses showed insignificant effects on ß amyloid levels when compared to normal control group. Our results encourage the use of C. aurantium seeds which are wasted in huge amounts, as Alzheimer prophylactic food additives.

Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon.

BACKGROUND: POLG, located on nuclear chromosome 15, encodes the DNA polymerase γ(Pol γ). Pol γ is responsible for the replication and repair of mitochondrial DNA (mtDNA). Pol γ is the only DNA polymerase found in mitochondria for most animal cells. Mutations in POLG are the most common single-gene cause of diseases of mitochondria and have been mapped over the coding region of the POLG ORF. RESULTS: Using PhyloCSF to survey alternative reading frames, we found a conserved coding signature in an alternative frame in exons 2 and 3 of POLG, herein referred to as ORF-Y that arose de novo in placental mammals. Using the synplot2 program, synonymous site conservation was found among mammals in the region of the POLG ORF that is overlapped by ORF-Y. Ribosome profiling data revealed that ORF-Y is translated and that initiation likely occurs at a CUG codon. Inspection of an alignment of mammalian sequences containing ORF-Y revealed that the CUG codon has a strong initiation context and that a well-conserved predicted RNA stem-loop begins 14 nucleotides downstream. Such features are associated with enhanced initiation at near-cognate non-AUG codons. Reanalysis of the Kim et al. (2014) draft human proteome dataset yielded two unique peptides that map unambiguously to ORF-Y. An additional conserved uORF, herein referred to as ORF-Z, was also found in exon 2 of POLG. Lastly, we surveyed Clinvar variants that are synonymous with respect to the POLG ORF and found that most of these variants cause amino acid changes in ORF-Y or ORF-Z. CONCLUSIONS: We provide evidence for a novel coding sequence, ORF-Y, that overlaps the POLG ORF. Ribosome profiling and mass spectrometry data show that ORF-Y is expressed. PhyloCSF and synplot2 analysis show that ORF-Y is subject to strong purifying selection. An abundance of disease-correlated mutations that map to exons 2 and 3 of POLG but also affect ORF-Y provides potential clinical significance to this finding.

Tailored Engineering of Bimetallic Plasmonic Au@Ag Core@Shell Nanoparticles.

A distinctive synthetic method for the efficient synthesis of multifunctional bimetallic plasmonic Au@Ag core@shell nanoparticles (NPs) with tunable size, morphology, and localized surface plasmon resonance (LSPR) using Triton X-100/hexanol-1/deionized water/cyclohexane-based water-in-oil (W/O) microemulsion (ME) is described. The W/O ME acted as a "true nanoreactor" for the synthesis of Au@Ag core@shell NPs by providing a confined and controlled environment and suppressing the nucleation, growth, agglomeration, and aggregation of the NPs. High-resolution transmission electron microscopic analysis of the synthesized Au@Ag core@shell NPs revealed an "unusual core@shell" contrast, and the selected area electron diffraction and Moiré patterns showed that Au layers are paralleled to Ag layers, thus indicating the formation of Au@Ag core@shell NPs. Interestingly, the UV-visible spectrum of the Au@Ag core@shell NPs exhibited enthralling plasmonic properties by introducing a high-frequency quadrupolar LSPR mode originated from the isolated Au@Ag NPs along with a low-frequency dipolar LSPR mode originated from the coupled Au@Ag NPs. The effective plasmonic enhancement of the Au@Ag core@shell NPs is attributed to the extreme enhancement of the localized electromagnetic field by coupling of the localized surface plasmons of the Au core and Ag shell. The mechanisms for the nucleation and growth of Au@Ag core@shell NPs in W/O ME have been proposed. A unique electron transfer phenomenon between the Au core and Ag shell is elucidated for better understanding and manipulation of the electronic properties, which evinced the development of Au@Ag core@shell NPs through suppression of the galvanic replacement reaction.

Ultraslow Relaxation in Aprotic Double Salt Ionic Liquids.

A mixture of two pure ionic liquids (ILs) or double salt ILs (DSILs) can push the limits of ILs in terms of unraveling their unique physicochemical properties and potential in clean technology. While the correlated ion dynamics and heterogeneity in the bulk of pure ILs have been reported, such a phenomenon at longer timescales in DSILs has never been elucidated. Here, a combination of temperature-dependent polarized dynamic light scattering and rheological measurements has been employed to reveal the presence of structural and ultraslow relaxation in three DSILs, each containing a 1-ethyl-3-methylimidazolium cation and two different anions. The slow relaxation caused by Brownian diffusion of cluster-like arrangements occurs at a timescale of a few to several hundred milliseconds; both the relaxation processes, nevertheless, are Arrhenius in nature. Notably, slow relaxation in the DSILs is much different compared to that in the pure ILs. The decay of intensity correlation functions (ICFs) and average hydrodynamic correlation length of the clusters and their response to temperature markedly vary with the nature of the two anions present in the DSILs. Stretched exponential analyses of the ICFs disclose the cluster-to-cluster transfer of ionic species as well as percolation dynamics among clusters. The identity of anions also governs whether the DSILs follow or violate the Stokes-Einstein relationship or not.

Unusual occurrence reporting system: Sharing a ten years experience from a tertiary care JCIA accredited university hospital.

PURPOSE: Identifying a true measure of safety is challenging in radiation oncology. A culture of unusual reporting may however be used as an indirect measure for it. The purpose of this study is to share our experience of unusual occurrence reporting system, established in the Radiation Oncology section since 2006, the first of this nature in Pakistan. MATERIALS AND METHODS: Data is collected over the last ten years. An in-house online reporting system has been developed for reporting unusual events. All the reported events are evaluated retrospectively. The stage of unusual occurrence along the radiation therapy process, possible causes, severity and preventive measures taken are discussed. RESULTS: Analysis of the 501 unusual occurrences reported over the last ten years has shown a substantial decrease in the number of significant mistakes observed. Of the total, 57 % unusual occurrences have been reported by radiation therapy technologists, including treatment preparation processes. Oversight is supposed to be the most common cause for unusual occurrences. CONCLUSIONS: The ten years experience with reporting and documenting of unusual occurrences resulted in a safety culture where every individual is willing to share any type of incident with a free well. Our experience at the Aga Khan University Hospital (AKUH) shows that the major reason for the occurrence of incidents was oversight. The majority of unusual occurrences were reported by radiation therapy technologists, as expected, since they handle the bulk of the treatment planning process.

Quantification of Intracellular Growth Inside Macrophages is a Fast and Reliable Method for Assessing the Virulence of Leishmania Parasites.

The lifecycle of Leishmania, the causative agent of leishmaniasis, alternates between promastigote and amastigote stages inside the insect and vertebrate hosts, respectively. While pathogenic symptoms of leishmaniasis can vary widely, from benign cutaneous lesions to highly fatal visceral disease forms depending on the infective species, all Leishmania species reside inside host macrophages during the vertebrate stage of their lifecycle. Leishmania infectivity is therefore directly related to its ability to invade, survive and replicate within parasitophorous vacuoles (PVs) inside macrophages. Thus, assessing the parasite's ability to replicate intracellularly serves as a dependable method for determining virulence. Studying leishmaniasis development using animal models is time-consuming, tedious and often difficult, particularly with the pathogenically important visceral forms. We describe here a methodology to follow the intracellular development of Leishmania in bone marrow-derived macrophages (BMMs). Intracellular parasite numbers are determined at 24 h intervals for 72 - 96 h following infection. This method allows for a reliable determination of the effects of various genetic factors on Leishmania virulence. As an example, we show how a single allele deletion of the Leishmania Mitochondrial Iron Transporter gene (LMIT1) impairs the ability of the Leishmania amazonensis mutant strain LMIT1/ΔLmit1 to grow inside BMMs, reflecting a drastic reduction in virulence compared to wild-type. This assay also allows precise control of experimental conditions, which can be individually manipulated to analyze the influence of various factors (nutrients, reactive oxygen species, etc.) on the host-pathogen interaction. Therefore, the appropriate execution and quantification of BMM infection studies provide a non-invasive, rapid, economical, safe and reliable alternative to conventional animal model studies.

Silver/poly(vinyl alcohol) nanocomposite film prepared using water in oil microemulsion for antibacterial applications.

HYPOTHESIS: Water in oil microemulsion (w/o) is a simple preparative route for nanoparticles where water droplets (dispersed in continuous oil medium and stabilized by surfactants and cosurfactants) act as nanoreactors to carry out chemical reactions. If polymeric matrix is incorporated inside the core of the microemulsions, it should prevent the agglomeration of nanoparticles after separation from microemulsions. Thus polymer nanocomposite films prepared from w/o microemulsions are expected to give narrow and homogeneous size distribution of nanoparticles throughout the polymer host. EXPERIMENTS: Silver/poly(vinyl alcohol) (Ag/PVA) nanocomposite film was successfully prepared, for the first time, using Triton X-100 (TX-100)/1-butanol/cyclohexane/water microemulsion. Reduction of the metal salt was carried out in the core of w/o microemulsion droplets containing PVA polymeric matrix. After separation from the microemulsion, Ag/PVA nanocomposite film was then prepared by solution casting method. The antibacterial activity of the nanocomposites was tested against Gram-negative, Escherichia coli and Gram-positive, Staphylococcus aureus by agar diffusion method. FINDINGS: Ag nanoparticles with an average diameter of 105 nm could be synthesized using PVA, whereas in the absence of PVA the nanoparticles agglomerated. The distribution of Ag nanoparticles on PVA surface of the nanocomposite film prepared using microemulsion was uniform, whereas the film prepared through in situ generation of Ag nanoparticles by chemical reduction process on PVA host showed non-uniform, coagulated, bunches of Ag nanoparticles. The film synthesized using microemulsion exhibited enhanced antibacterial efficacy compared to that prepared through in situ synthesis under the same test condition.