The flip-flop configuration of the PABP-dimer leads to switching of the translation function.

Poly(A)-binding protein (PABP) is a translation initiation factor that interacts with the poly(A) tail of mRNAs. PABP bound to poly(A) stimulates translation by interacting with the eukaryotic initiation factor 4G (eIF4G), which brings the 3' end of an mRNA close to its 5' m7G cap structure through consecutive interactions of the 3'-poly(A)-PABP-eIF4G-eIF4E-5' m7G cap. PABP is a highly abundant translation factor present in considerably larger quantities than mRNA and eIF4G in cells. However, it has not been elucidated how eIF4G, present in limited cellular concentrations, is not sequestered by mRNA-free PABP, present at high cellular concentrations, but associates with PABP complexed with the poly(A) tail of an mRNA. Here, we report that RNA-free PABPs dimerize with a head-to-head type configuration of PABP, which interferes in the interaction between PABP and eIF4G. We identified the domains of PABP responsible for PABP-PABP interaction. Poly(A) RNA was shown to convert the PABP-PABP complex into a poly(A)-PABP complex, with a head-to-tail-type configuration of PABP that facilitates the interaction between PABP and eIF4G. Lastly, we showed that the transition from the PABP dimer to the poly(A)-PABP complex is necessary for the translational activation function.

Structure-Guided Development of Bivalent Aptamers Blocking SARS-CoV-2 Infection.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused devastation to human society through its high virulence, infectivity, and genomic mutations, which reduced the efficacy of vaccines. Here, we report the development of aptamers that effectively interfere with SARS-CoV-2 infection by targeting its spike protein, which plays a pivotal role in host cell entry of the virus through interaction with the viral receptor angiotensin-converting enzyme 2 (ACE2). To develop highly effective aptamers and to understand their mechanism in inhibiting viral infection, we determined the three-dimensional (3D) structures of aptamer/receptor-binding domain (RBD) complexes using cryogenic electron microscopy (cryo-EM). Moreover, we developed bivalent aptamers targeting two distinct regions of the RBD in the spike protein that directly interact with ACE2. One aptamer interferes with the binding of ACE2 by blocking the ACE2-binding site in RBD, and the other aptamer allosterically inhibits ACE2 by binding to a distinct face of RBD. Using the 3D structures of aptamer-RBD complexes, we minimized and optimized these aptamers. By combining the optimized aptamers, we developed a bivalent aptamer that showed a stronger inhibitory effect on virus infection than the component aptamers. This study confirms that the structure-based aptamer-design approach has a high potential in developing antiviral drugs against SARS-CoV-2 and other viruses.

Brønsted acid-catalysed desilylative heterocyclisation to form substituted furans.

Heterocyclisation of tert-butyldimethylsilyl (TBS) protected γ-hydroxy-α,ß-unsaturated ketones catalysed by para-toluenesulfonic acid (p-TSA) to form substituted furans is reported. The reaction proceeds under mild conditions at room temperature in methanol to give a range of furan products (21 examples, up to 98% yield). Mechanistic experiments suggest the reaction proceeds via in situ deprotection followed by catalytic dehydrative heterocyclisation.

Genome-wide association study identifies RNF123 locus as associated with chronic widespread musculoskeletal pain.

BACKGROUND AND OBJECTIVES: Chronic widespread musculoskeletal pain (CWP) is a symptom of fibromyalgia and a complex trait with poorly understood pathogenesis. CWP is heritable (48%-54%), but its genetic architecture is unknown and candidate gene studies have produced inconsistent results. We conducted a genome-wide association study to get insight into the genetic background of CWP. METHODS: Northern Europeans from UK Biobank comprising 6914 cases reporting pain all over the body lasting >3 months and 242 929 controls were studied. Replication of three independent genome-wide significant single nucleotide polymorphisms was attempted in six independent European cohorts (n=43 080; cases=14 177). Genetic correlations with risk factors, tissue specificity and colocalisation were examined. RESULTS: Three genome-wide significant loci were identified (rs1491985, rs10490825, rs165599) residing within the genes Ring Finger Protein 123 (RNF123), ATPase secretory pathway Ca2+transporting 1 (ATP2C1) and catechol-O-methyltransferase (COMT). The RNF123 locus was replicated (meta-analysis p=0.0002), the ATP2C1 locus showed suggestive association (p=0.0227) and the COMT locus was not replicated. Partial genetic correlation between CWP and depressive symptoms, body mass index, age of first birth and years of schooling were identified. Tissue specificity and colocalisation analysis highlight the relevance of skeletal muscle in CWP. CONCLUSIONS: We report a novel association of RNF123 locus and a suggestive association of ATP2C1 locus with CWP. Both loci are consistent with a role of calcium regulation in CWP. The association with COMT, one of the most studied genes in chronic pain field, was not confirmed in the replication analysis.

RACK1 mediates rewiring of intracellular networks induced by hepatitis C virus infection.

Hepatitis C virus (HCV) is a positive-strand RNA virus replicating in a membranous replication organelle composed primarily of double-membrane vesicles (DMVs) having morphological resemblance to autophagosomes. To define the mechanism of DMV formation and the possible link to autophagy, we conducted a yeast two-hybrid screening revealing 32 cellular proteins potentially interacting with HCV proteins. Among these was the Receptor for Activated Protein C Kinase 1 (RACK1), a scaffolding protein involved in many cellular processes, including autophagy. Depletion of RACK1 strongly inhibits HCV RNA replication without affecting HCV internal ribosome entry site (IRES) activity. RACK1 is required for the rewiring of subcellular membranous structures and for the induction of autophagy. RACK1 binds to HCV nonstructural protein 5A (NS5A), which induces DMV formation. NS5A interacts with ATG14L in a RACK1 dependent manner, and with the ATG14L-Beclin1-Vps34-Vps15 complex that is required for autophagosome formation. Both RACK1 and ATG14L are required for HCV DMV formation and viral RNA replication. These results indicate that NS5A participates in the formation of the HCV replication organelle through interactions with RACK1 and ATG14L.

New insights in pectinase production development and industrial applications.

Pectinase, a group of pectin degrading enzymes, is one of the most influential industrial enzymes, helpful in producing a wide variety of products with good qualities. These enzymes are biocatalysts and are highly specific, non-toxic, sustainable, and eco-friendly. Consequently, both pectin and pectinase are crucially essential biomolecules with extensive applicatory perception in the biotechnological sector. The market demand and application of pectinases in new sectors are continuously increasing. However, due to the high cost of the substrate used for the growth of microbes, the production of pectinase using microorganisms is limited. Therefore, low-cost or no-cost substrates, such as various agricultural biomasses, are emphasized in producing pectinases. The importance and implications of pectinases are rising in diverse areas, including bioethanol production, extraction of DNA, and protoplast isolation from a plant. Therefore, this review briefly describes the structure of pectin, types and source of pectinases, substrates and strategies used for pectinases production, and emphasizes diverse potential applications of pectinases. The review also has included a list of pectinases producing microbes and alternative substrates for commercial production of pectinase applicable in pectinase-based industrial technology.Key points• Pectinase applications are continuously expanding.• Organic wastes can be used as low-cost sources of pectin.• Utilization of wastes helps to reduce pollution.

Cobalt/Lewis Acid Catalysis for Hydrocarbofunctionalization of Alkynes via Cooperative C-H Activation.

A catalytic system comprising a cobalt-diphosphine complex and a Lewis acid (LA) such as AlMe3 has been found to promote hydrocarbofunctionalization reactions of alkynes with Lewis basic and electron-deficient substrates such as formamides, pyridones, pyridines and related azines, imidazo[1,2-a]pyridines, and azole derivatives through site-selective C-H activation. Compared with known Ni/LA catalytic systems for analogous transformations, the present catalytic systems not only feature convenient setup using inexpensive and bench-stable precatalyst and ligand such as Co(acac)3 and 1,3-bis(diphenylphosphino)propane (dppp) but also display distinct site-selectivity toward C-H activation of pyridone and pyridine derivatives. In particular, a completely C4-selective alkenylation of pyridine has been achieved for the first time. Meanwhile, the present catalytic system proved to promote exclusively C5-selective alkenylation of imidazo[1,2-a]pyridine derivatives. Mechanistic studies including DFT calculations on the Co/Al-catalyzed addition of formamide to alkyne have suggested that the reaction involves cleavage of the carbamoyl C-H bond as the rate-limiting step, which proceeds through a ligand-to-ligand hydrogen transfer (LLHT) mechanism leading to an alkenyl(carbamoyl)cobalt intermediate.

Synthesis of triphenylene-fused phosphole oxides via C-H functionalizations.

The synthesis of triphenylene-fused phosphole oxides has been achieved through two distinct C-H functionalization reactions as key steps. The phosphole ring was constructed by a three-component coupling of 3-(methoxymethoxy)phenylzinc chloride, an alkyne, and dichlorophenylphosphine, involving the regioselective C-H activation of the C2 position of the arylzinc intermediate via 1,4-cobalt migration. The resulting 7-hydroxybenzo[b]phosphole derivative was used for further π-extension through Suzuki-Miyaura couplings and a Scholl reaction, the latter closing the triphenylene ring. The absorption and emission spectra of the thus-synthesized compounds illustrated their nature as hybrids of triphenylene and benzo[b]phosphole.

Pd-Catalyzed Annulation of 1-Halo-8-arylnaphthalenes and Alkynes Leading to Heptagon-Embedded Aromatic Systems.

A palladium-catalyzed heptagon-forming annulation reaction between 1-halo-8-arylnaphthalene and diarylacetylene is reported. The reaction is promoted using a catalytic system comprised of Pd(OAc)2 , moderately electron-deficient triarylphosphine P(4-ClC6 H4 )3 , and Ag2 CO3 to afford benzo[4,5]cyclohepta[1,2,3-de]naphthalene derivatives in moderate to good yields, in preference to fluoranthene as a competing byproduct. Twofold annulation can also be achieved to access a novel heptagon-embedded polycyclic aromatic hydrocarbon compound.

Dynamics of cognitive variability with age and its genetic underpinning in NIHR BioResource Genes and Cognition cohort participants.

A leading explanation for translational failure in neurodegenerative disease is that new drugs are evaluated late in the disease course when clinical features have become irreversible. Here, to address this gap, we cognitively profiled 21,051 people aged 17-85 years as part of the Genes and Cognition cohort within the National Institute for Health and Care Research BioResource across England. We describe the cohort, present cognitive trajectories and show the potential utility. Surprisingly, when studied at scale, the APOE genotype had negligible impact on cognitive performance. Different cognitive domains had distinct genetic architectures, with one indicating brain region-specific activation of microglia and another with glycogen metabolism. Thus, the molecular and cellular mechanisms underpinning cognition are distinct from dementia risk loci, presenting different targets to slow down age-related cognitive decline. Participants can now be recalled stratified by genotype and cognitive phenotype for natural history and interventional studies of neurodegenerative and other disorders.

Construction and functionalization of pyranone ring fused with pyran moiety: design and synthesis of novel pyrano[4,3-b]pyran-5(4H)-ones as potential inhibitors of sirtuins.

Novel pyrano[4,3-b]pyran-5(4H)-one based small molecules were designed as potential inhibitors of sirtuins (i.e., yeast sir2, a homolog of human SIRT1). Elegant synthesis of these compounds was performed via a multi-step sequence consisting of MCR, Sandmeyer type iodination, Sonogashira type coupling followed by iodocyclization and then Pd-mediated various C-C bond forming reactions. The overall strategy involved the construction of a pyran ring followed by the fused pyranone moiety and subsequent functionalization at C-8 position of the resultant core pyrano[4,3-b]pyran-5(4H)-one framework. The crystal structure analysis of a representative iodolactonized product (6d) is presented. Some of the synthesized compounds showed promising inhibitory activities when tested against yeast sir2 in vitro. The compound 6g showed dose dependent inhibition (IC50=78.05µM) of yeast sir2 and good interactions with this protein in silico.

Amberlite IR-120H catalyzed MCR: design, synthesis and crystal structure analysis of 1,8-dioxodecahydroacridines as potential inhibitors of sirtuins.

A rapid, inexpensive and high yielding method has been developed for the synthesis of 1,8-dioxodecahydroacridines using Amberlite IR-120H as a reusable catalyst under open air. These compounds were designed as potential inhibitors of sirtuins and prepared via the MCR of 5,5-dimethyl-1,3-cyclohexanedione, (hetero)aryl aldehydes and (hetero)aromatic amines under mild conditions. Further structure elaboration of a representative compound was performed via Pd catalyzed C-C bond forming reactions. The crystal structure analysis and H-bonding patterns along with in vitro inhibitory activity against yeast Sir2 of the same compound is presented. Docking studies indicated that the compound interacts well with the yeast Sir2.

Transition metal free hydrolysis/cyclization strategy in a single pot: synthesis of fused furo N-heterocycles of pharmacological interest.

A transition metal free tandem two-step strategy has been developed involving hydrolysis of 2-chloro-3-alkynyl quinoxalines/pyrazines followed by in situ cyclization of the corresponding 2-hydroxy-3-alkynyl intermediates in a single pot leading to fused furo N-heterocycles as potential inhibitors of sirtuins. A representative compound showed promising pharmacological properties in vitro and in vivo.

Urethral rhinosporidiosis: Prolapsing mass from urethra in a Bangladeshi farmer.

Rhinosporidiosis is a chronic granulomatous fungal infection caused by Rhinosporidium seeberi. Usual site of infection is the nasal mucosa & nasopharynx. Male urethra is extremely rare site involving this disease. Here we are reporting a rare case where rhinosporidiosis presented as a prolapsing mass from urethra during voiding.

Distribution and treatment needs of soil-transmitted helminthiasis in Bangladesh: A Bayesian geostatistical analysis of 2017-2020 national survey data.

BACKGROUND: In Bangladesh, preventive chemotherapy targeting soil-transmitted helminth (STH) infections in school-age children has been implemented since 2008. To evaluate the success of this strategy, surveys were conducted between 2017 and 2020 in 10 out of 64 districts. We estimate the geographic distribution of STH infections by species at high spatial resolution, identify risk factors, and estimate treatment needs at different population subgroups. METHODOLOGY: Bayesian geostatistical models were fitted to prevalence data of each STH species. Climatic, environmental, and socioeconomic predictors were extracted from satellite images, open-access, model-based databases, and demographic household surveys, and used to predict the prevalence of infection over a gridded surface at 1 x 1 km spatial resolution across the country, via Bayesian kriging. These estimates were combined with gridded population data to estimate the number of required treatments for different risk groups. PRINCIPAL FINDINGS: The population-adjusted prevalence of Ascaris lumbricoides, Trichuris trichiura, and hookworm across all ages is estimated at 9.9% (95% Bayesian credible interval: 8.0-13.0%), 4.3% (3.0-7.3%), and 0.6% (0.4-0.9%), respectively. There were 24 out of 64 districts with an estimated population-adjusted STH infection prevalence above 20%. The proportion of households with improved sanitation showed a statistically important, protective association for both, A. lumbricoides and T. trichiura prevalence. Precipitation in the driest month of the year was negatively associated with A. lumbricoides prevalence. High organic carbon concentration in the soil's fine earth fraction was related to a high hookworm prevalence. Furthermore, we estimated that 30.5 (27.2; 36.0) million dosages of anthelmintic treatments for school-age children were required per year in Bangladesh. CONCLUSIONS/SIGNIFICANCE: For each of the STH species, the prevalence was reduced by at least 80% since treatment was scaled up more than a decade ago. The current number of deworming dosages could be reduced by up to 61% if the treatment strategy was adapted to the local prevalence.

Pyrrolo[2,3-b]quinoxalines as inhibitors of firefly luciferase: their Cu-mediated synthesis and evaluation as false positives in a reporter gene assay.

2-Substituted pyrrolo[2,3-b]quinoxalines having free NH were prepared directly from 3-alkynyl-2-chloroquinoxalines in a single pot by using readily available and inexpensive methane sulfonamide (or p-toluene sulfonamide) as an ammonia surrogate. The reaction proceeded in the presence of Cu(OAc)(2) affording the desired product in moderate yield. The crystal structure analysis of a representative compound and its supramolecular interactions are presented. Some of the compounds synthesized exhibited inhibitory activities against luciferase that was supported by the predictive binding mode of these compounds with luciferase enzyme through molecular docking studies. The key observations disclosed here can alert users of luciferase reporter gene assays for possible false positive results due to the direct inhibition of luciferase.

Cellulase activity of a novel bacterial strain Arthrobacter woluwensis TDS9: its application on bioconversion of paper mill sludge.

BACKGROUND: Lignocellulosic biomasses produced from agriculture and forest-based industries are the cheapest or negative-cost biomass with a great potential for biotransformation to value-added bioproducts. Paper mill sludge, an important lignocellulosic biomass creates an environmental threat, which requires financial input for disposal. Thus, this study was aimed to isolate a novel bacterial strain capable of degrading cellulosic biomass including paper mill sludge to produce reducing sugar and other value-added bioproducts. RESULTS: A novel bacterial strain Arthrobacter woluwensis TDS9 isolated from the soil was screened for its cellulolytic activity using carboxymethyl cellulose (CMC) as the sole carbon source. The incubation period, temperature, pH, carbon, and nitrogen sources are the most important factors ruling the CMCase and sugar productions of the strain A. woluwensis TDS9, and an alkaline pH (pH 8.0) led to enhanced sugar production up to 1100.09 µg/mL after 72 h of incubation at 25°C in a medium containing 1.5% CMC and 1.25% beef extract. The optimal conditions for maximum CMCase activity were defined, and the potassium ion boosted the CMCase activity up to 1.06 U/mL when the enzymatic reaction was performed for 30 min at 50°C and pH 8 using CMC as a substrate. Moreover, the strain A. woluwensis TDS9 produced 433.33 µg/mL reducing sugar from 1% pretreated paper mill sludge. Significant alterations in the structural arrangement of cellulosic fiber of paper mill sludge observed under microscope after each step of chemical treatment process helped for loosening the cellulose fibers and increased the saccharification for enzymatic hydrolysis. Endoglucanase IV (33 KDa) and beta-glucosidase II (53 KDa) were identified in crude enzyme based on the zymogram analysis and substrate specificity. CONCLUSIONS: The research has for the first time proved that this A. woluwensis TDS9 strain can efficiently convert cellulose. Therefore, the strain TDS9 could be a potential candidate for cellulase production in an industrial biotransformation process of paper mill sludge to produce reducing sugar. This sugar stream can be further used as a substrate to produce biofuels and other organic acids using another microorganism, which represents a greener alternative to add value to the paper production helping paper mill industries.

Biological pretreatment of corn stover for enhancing enzymatic hydrolysis using Bacillus sp. P3.

The biological pretreatment for the enzymatic hydrolysis of lignocellulosic biomasses depends exclusively on the effective pretreatment process. Herein, we report a significant enhancement of enzymatic saccharification obtained with corn stover using a bacterial strain Bacillus sp. P3. The hemicellulose removal from corn stover by the strain Bacillus sp. P3 was evaluated for enhancing subsequent enzymatic hydrolysis. Therefore, our study revealed that an alkaline-resistant xylanase as well as other enzymes produced by Bacillus sp. P3 in fermentation broth led to a substantially enhanced hemicellulose removal rate from corn stover within pH 9.36-9.68. However, after a 20-day pretreatment of corn stover by the strain P3, the glucan content was increased by 51% and the xylan content was decreased by 35%. After 72 h of saccharification using 20 U/g of commercial cellulase, the yield of reducing sugar released from 20-day pretreated corn stover was increased by 56% in comparison to the untreated corn stover. Therefore, the use of the strain P3 could be a promising approach to pretreat corn stover for enhancing the enzymatic hydrolysis process of industrial bioenergy productions. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40643-021-00445-8.

Assessment of food safety knowledge, attitudes and practices of fish farmers and restaurants food handlers in Bangladesh.

The study was conducted to assess the present status of knowledge, attitudes and practices (KAP) concerning the food safety and hygiene issues among fish farmers and food handlers in Noakhali, Bangladesh. Data were collected from 100 respondents (50 fish farmers and 50 food handlers) through face to face interviews. All the respondents agreed that training on hygiene practices was necessary and they were interested to attend training in their spare time. Food handlers (88%) agreed that raw foods must be kept separate from prepared foods and 68% of them believed that improper preservation of foods is harmful to health. About 52% of farmers used a face mask when spreading insecticides, fertilizers, and chemicals. Food handlers were wearing protective clothing (32%) and masks (12%) when touching and distributing unwrapped foods, however no handlers used a cap. A significant strong correlation coefficient (rs) was found between knowledge with attitudes, knowledge with practices and attitudes with practices of 0.73-0.99 among the three domains for fish farmers and food handlers. The correlation among the three levels was satisfactory, however, some food safety concepts and practices regarding hygiene were still insufficient. Therefore, an effective and appropriate training program on food safety and hygiene should be launched in a holistic approach for all fish farmers and food handlers to increase awareness and ensure safe food for consumers with a view to reducing the possibility of disease outbreak.