Changes In Secondary Structure Research Articles

Resistance Is Not Futile: Widespread Convergent Evolution of Resistance to Alpha-Neurotoxic Snake Venoms in Caecilians (Amphibia: Gymnophiona).

Predatory innovations impose reciprocal selection pressures upon prey. The evolution of snake venom alpha-neurotoxins has triggered the corresponding evolution of resistance in the post-synaptic nicotinic acetylcholine receptors of prey in a complex chemical arms race. All other things being equal, animals like caecilians (an Order of legless amphibians) are quite vulnerable to predation by fossorial elapid snakes and their powerful alpha-neurotoxic venoms; thus, they are under strong selective pressure. Here, we sequenced the nicotinic acetylcholine receptor alpha-1 subunit of 37 caecilian species, representing all currently known families of caecilians from across the Americas, Africa, and Asia, including species endemic to the Seychelles. Three types of resistance were identified: (1) steric hindrance from N-glycosylated asparagines; (2) secondary structural changes due to the replacement of proline by another amino acid; and (3) electrostatic charge repulsion of the positively charged neurotoxins, through the introduction of a positively charged amino acid into the toxin-binding site. We demonstrated that resistance to alpha-neurotoxins convergently evolved at least fifteen times across the caecilian tree (three times in Africa, seven times in the Americas, and five times in Asia). Additionally, as several species were shown to possess multiple resistance modifications acting synergistically, caecilians must have undergone at least 20 separate events involving the origin of toxin resistance. On the other hand, resistance in non-caecilian amphibians was found to be limited to five origins. Together, the mutations underlying resistance in caecilians constitute a robust signature of positive selection which strongly correlates with elapid presence through both space (sympatry with caecilian-eating elapids) and time (Cenozoic radiation of elapids). Our study demonstrates the extent of convergent evolution that can be expected when a single widespread predatory adaptation triggers parallel evolutionary arms races at a global scale.

Para-Cresyl Sulfate and BSA Conjugation for Developing Aptasensor: Spectroscopic Methods and Molecular Simulation

Para-cresol sulfate (PCS), a protein-bound uremic toxin, is gut microbiota derived metabolite and known for its role in human physiology and pathology. After PCS formation, it goes to blood stream and interact with serum albumin with high affinity. Normally, PCS is cleared by the kidney but if it gets accumulated then leads to chronic kidney disease (CKD). Present study is an attempt to understand the nuances of interaction wherein bovine serum albumin (BSA) has been taken as model protein to understand this interaction. Absorption spectroscopy result indicated that in presence of PCS (ranging from 2 μM to 200 μM), the absorbance of BSA gradually decreased due to complex formation between them and obtained detection limit of 0.42 μM with a linearity of 0.95. Fourier transform infra-red and circular spectroscopy results demonstrated change in secondary structure of BSA upon interaction of PCS. These interaction studies reveal that PCS binds on two sites of BSA. Docking studies represent binding score of −5.6 Kcal mol−1, demarking that PCS is involved in interaction with BSA via amino acid residues, forming the stable complex. This study helps in PCS aptamers synthesis by using this conjugate, to fabricate apta-sensors for early detection of CKD.

Synthesis and characterization of bisacodyl loaded chitosan nanoparticles (BSL@CS NPs), multispectroscopic study of their interaction with bovine serum albumin (BSA)

The novel nanoparticles i.e., bisacodyl (BSL) drug loaded chitosan nanoparticles (BSL@CS NPs) have been synthesized by using the ionotropic gelation method. The obtained nanoparticles were then characterized using different characterization techniques (FTIR, PXRD, SEM and TEM), which showed presence of spherical shaped BSL@CS NPs. Further, the interaction between bovine serum albumin (BSA) and BSL@CS NPs (BSA-BSL@CS NPs system) have been evaluated through multispectroscopic (fluorescence spectroscopy, synchronous fluorescence spectroscopy, UV spectroscopy and CD spectroscopy) techniques. The spectroscopic results indicated presence of static quenching mechanism and induced conformational changes (increase in hydrophobicity) in BSA. The secondary structural content changes (decrease in α-helical content), but preserving of major α-helical content was also suggested from CD spectra of the BSA-BSL@CS NPs system.

Complex Inhibitory Mechanism of Glycomimetics with Heparanase.

Heparanase (HPSE) is the only mammalian endo-β-glucuronidase known to catalyze the degradation of heparan sulfate. Dysfunction of HPSE activity has been linked to several disease states, resulting in HPSE becoming the target of numerous therapeutic programs, yet no drug has passed clinical trials to date. Pentosan polysulfate sodium (PPS) is a heterogeneous, FDA-approved drug for the treatment of interstitial cystitis and a known HPSE inhibitor. However, due to its heterogeneity, characterization of its mechanism of HPSE inhibition is challenging. Here, we show that inhibition of HPSE by PPS is complex, involving multiple overlapping binding events, each influenced by factors such as oligosaccharide length and inhibitor-induced changes in the protein secondary structure. The present work advances our molecular understanding of the inhibition of HPSE and will aid in the development of therapeutics for the treatment of a broad range of pathologies associated with enzyme dysfunction, including cancer, inflammatory disease, and viral infections.

PH-Sensitive Poly(acrylic acid)-g-poly(L-lysine) Charge-Driven Self-Assembling Hydrogels with 3D-Printability and Self-Healing Properties.

We report the rheological behavior of aqueous solutions of a graft copolymer polyampholyte, constituted of polyacrylic acid (PAA) backbone grafted by Poly(L-lysine) (PAA-b-PLL). The graft copolymer self-assembles in aqueous media, forming a three-dimensional (3D) network through polyelectrolyte complexation of the oppositely charged PAA and PLL segments. Rheological investigations showed that the hydrogel exhibits interesting properties, namely, relatively low critical gel concentration, elastic response with slow dynamics, remarkable extended critical strain to flow, shear responsiveness, injectability, 3D printability and self-healing. Due to the weak nature of the involved polyelectrolyte segments, the hydrogel properties display pH-dependency, and they are affected by the presence of salt. Especially upon varying pH, the PLL secondary structure changes from random coil to α-helix, affecting the crosslinking structural mode and, in turn, the overall network structure as reflected in the rheological properties. Thanks to the biocompatibility of the copolymer constituents and the biodegradability of PLL, the designed gelator seems to exhibit potential for bioapplications.

Amino Acid Transporter as a Potential Carrier Protein for the Root-to-Shoot Translocation of Polybrominated Diphenyl Ethers in Rice.

As typical persistent organic pollutants, polybrominated diphenyl ethers (PBDEs) tend to accumulate in edible parts of rice, posing great ecological and health risks. The translocation of PBDEs from underground to aboveground parts of rice is a crucial procedure to determine the final bioaccumulation level. Herein, this study aimed to identify the transporter proteins for PBDEs in rice plants in order to strengthen our understanding of the bioaccumulation mechanism and the potential prevention strategy of the PBDE risk. Similar time-dependent patterns were observed among the root-to-shoot translocation factors (TFs) of PBDEs, the expression of lysine histidine transporter (LHT) protein, and the relative levels of LHT substrates (phenylalanine or tyrosine), implying the potential co-transport of PBDEs, phenylalanine, and tyrosine by the carrier LHT. Fluorescence spectra and circular dichroism showed that PBDE congeners interfered with LHT via static fluorescence quenching and changes in the protein's secondary structure. The in vitro sorption fraction of LHT to PBDEs, as revealed by sorption equilibrium analysis, was comparable to the in vivo TF values. Knockout of OsLHT1 in rice using CRISPR/Cas9 technology caused a 48.2-78.4% decrease in PBDE translocation. Molecular docking simulation suggested that PBDEs, phenylalanine, and tyrosine were inserted into the same ligand-binding cavity of LHT, substantiating the potential carrier role of LHT for PBDEs from a conformational perspective. Quantitative structure activity relationship analysis demonstrated that the ether-bond oxygen and the carbons at the site 4 and 4' of PBDE molecules are significant determinants of the binding affinity with the LHT protein and in vivo translocation of PBDEs. In summary, this study discovered that LHT acts as the cellular carrier for PBDEs and offered a comprehensive molecular explanation for the bioaccumulation and translocation of PBDEs in rice plants, covering both biological and chemical perspectives. These findings fill in a knowledge gap on the endogenous transporter proteins for exogenous organic pollutants.

Analysis of genetic variants in the exon 2 and 3 of autosomal DAZLA gene among infertile South Indian men

BackgroundBoule, DAZLA, and DAZ are members of the Deleted in Azoospermia family of genes, which play significant roles in gametogenesis and are important fertility factors in humans. In a few studies, deletion of the Y chromosomal DAZ cluster and single nucleotide polymorphisms in the DAZLA gene were reported to affect male fertility, although this is paradoxical because they were found in both control and fertile men. As a result, the goal of this study was to check if Y chromosomal DAZ cluster deletion and SNPs in the DAZLA gene on chromosome 3 of humans are associated to male infertility in the population. For computational analysis, different bioinformatics tools such as SIFT, PolyPhen2, Mutation Taster, FATHMM, and PROVEAN were used to analyse mutations.ResultsWithin the studied population, we found no association between DAZ deletion and the most prevalent DAZLA SNPs A260G (rs11710967) and A386G (rs1219183446). We also discovered two new deleterious genetic variations in exon 3 of the DAZLA gene, one nonsynonymous mutation that replaced Valine with Glutamate at the 66 codon position and the other a stop gain mutation at the 74 amino acid position. These genetic changes are found in the RRM domain of the DAZLA gene, which is confirmed by Motif scan analysis and results in a change in the DAZLA protein's secondary structure. The RRM domain is a highly conserved regulatory domain for mRNA transport and translation. Azoospermia and necrospermia infertility phenotypes were shown in infertile male samples with these genotypes.ConclusionWe can conclude that further investigation of the aforesaid new mutations in the DAZLA gene may be valuable in understanding their significance in male infertility in different populations due to the multifactorial nature of male infertility and arrays of gene expression required at every stage of spermatogenesis.

GM1 oligosaccharide efficacy against α-synuclein aggregation and toxicity in vitro

Fibrillary aggregated α-synuclein represents the neurologic hallmark of Parkinson's disease and is considered to play a causative role in the disease. Although the causes leading to α-synuclein aggregation are not clear, the GM1 ganglioside interaction is recognized to prevent this process. How GM1 exerts these functions is not completely clear, although a primary role of its soluble oligosaccharide (GM1-OS) is emerging. Indeed, we recently identified GM1-OS as the bioactive moiety responsible for GM1 neurotrophic and neuroprotective properties, specifically reverting the parkinsonian phenotype both in in vitro and in vivo models.Here, we report on GM1-OS efficacy against the α-synuclein aggregation and toxicity in vitro. By amyloid seeding aggregation assay and NMR spectroscopy, we demonstrated that GM1-OS was able to prevent both the spontaneous and the prion-like α-synuclein aggregation. Additionally, circular dichroism spectroscopy of recombinant monomeric α-synuclein showed that GM1-OS did not induce any change in α-synuclein secondary structure. Importantly, GM1-OS significantly increased neuronal survival and preserved neurite networks of dopaminergic neurons affected by α-synuclein oligomers, together with a reduction of microglia activation.These data further demonstrate that the ganglioside GM1 acts through its oligosaccharide also in preventing the α-synuclein pathogenic aggregation in Parkinson's disease, opening a perspective window for GM1-OS as drug candidate.

Thiazole-benzamide derivatives as α-glucosidase inhibitors: Synthesis, kinetics study, molecular docking, and in vivo evaluation

In this study, a series of thiazole-benzamide derivatives (6a-6o) was obtained by molecular hybridization and screened for their inhibitory study towards the α-glucosidase activity. The results showed that all compounds (6a-6o) showed α-glucosidase (from S. cerevisiae) inhibitory activity (IC50 = 12.18 ± 0.08 - 79.34 ± 1.30 μM) by comparison with standard acarbose (IC50 = 774.69 ± 11.65 μM). A study on the kinetics of compound 6c showed a competitive mode against α-glucosidase. In addition, the changes in fluorescence intensity, secondary structure, and possible binding sites in the interaction between 6c and α-glucosidase were studied using fluorescence spectrometry, circular dichroism, and molecular docking, respectively. Furthermore, in vivo experiment indicated that 6c can reduce the rise of blood sugar levels in the sucrose loading experiment. Moreover, compound 6c had low cytotoxic activity toward the human normal HEK 293 cell line.

Ultrasonic extraction of soy protein isolate: Characterization and comparison with microwave and enzymatic extraction methods.

Soy meal as an agro-industrial by-product produced by the soybean oil processing industry is rich in protein. To valorize soy meal, the present study was aimed at the optimization of soy protein isolate (SPI) extraction by ultrasound treatment, its characterization, and comparison with microwave, enzymatic, and conventionally extracted SPI. Maximum yield (24.17%±0.79%) and protein purity (91.6%±1.08%) of SPI were obtained at the optimized ultrasound extraction conditions of 15.38:1 (liquid-solid ratio), 51.85% (amplitude), 21.70°C (temperature), 3.49s (pulse), and 11.01min (time). The SPI extracted with ultrasound treatment showed a smaller particle size (27.24±0.33µm) as compared to that extracted with microwave, enzymatically, or conventional treatment. Functional characteristics, namely, water and oil binding capacity, emulsion properties, and foaming properties of ultrasonically extracted SPI were increased by 40%-50% as compared to SPI extracted with microwave treatment, enzymatically, or conventionally. Structural and thermal properties studied by Fourier-transform infrared spectroscopy, X-ray diffraction, and differential scanning colorimeter showed amorphous, secondary structural change, and high thermal resistance of ultrasonically extracted SPI. Increased functionality of ultrasonically obtained SPI can enhance its application in the development of various new food products. PRACTICAL APPLICATION: Soybean meal is one of the richest sources of protein and has huge potential to lessen protein-based malnutrition. Most of the studies on soy protein extraction were found to be based on the conventional methods that yield less quantity of protein. Hence, ultrasound treatment which is one of the novel nonthermal techniques has been selected for the present work and optimized for soy protein extraction. The ultrasound treatment showed significant improvement in extraction yield, proximate composition, amino acids profile, and improvement of functional properties of SPI as compared to the conventional, microwave, and enzymatic methods which proved the novelty of the work. Hence, the ultrasound technique could be used to increase the applications of SPI for developing a wide range of food products.

Extraction and modification of protein from sesame oil cake by the application of emerging technologies

Present work evaluated the extraction yield and quality of protein from defatted sesame meal (DSM) using ultrasound-assisted extraction (UAE), low-temperature microwave-assisted extraction (MAE), and moderate electric field-assisted extraction (MEFAE). It was observed that the application of emerging technologies as pre-treatments significantly increased protein yield from 26.4% (without pre-treatments) to 38.9% (with UAE 450 W–20 min), 36.05% for MAE (with 500 W–20 min) and 32.75% for MEFAE (with 100 V–30 min) and improved the functional properties of Sesame protein isolate (SPI). FTIR revealed Amide I to III bands in SPI, with characteristic changes in protein secondary structure. The treated sample showed higher thermal stability evident from the denaturation temperature increase from 203.41 to 221.40 °C. The protein's microstructure in this study was transformed using various extraction techniques into a compact structure with a wrinkled surface. MAE-SPI showed maximum Invitro protein digestibility as 94.44%. The molecular weight profile revealed that the SPI samples' protein bands had molecular weights between 6.5 and 200 kDa. SDS-PAGE results revealed a change in the intensity of protein bands, and all of the main allergen protein bands were degraded.

Inhibition of α-amylase and amyloglucosidase by cellulose nanofibrils with different surface charge and spectroscopic analysis of their interaction mechanism

We investigated the inhibition effect of carboxymethylated cellulose nanofibrils with four different surface chargeon α-amylase and amyloglucosidase via enzyme activity inhibition assay, fluorescence spectra and secondary structure change analysis. These results revealed that cellulose nanofibril with lowest surface charge displayed the greatest inhibition effects against α-amylase (9.81 mg/mL) and amyloglucosidase (13.16 mg/mL). All cellulose nanofibrils in starch model significantly (p < 0.05) inhibited the starch digestion, where the inhibition effect was negatively correlated with the magnitude of particle surface charge. Cellulose nanofibrils could bind α-amylase or amyloglucosidase to form new complex in the manner of static quenching. The thermodynamic parameters demonstrated that the cellulose nanofibrils-starch hydrolase (α-amylase or amyloglucosidase) complexes were formed spontaneously via hydrophobic effects. Additionally, Fourier transform Infrared spectra exhibited the changes in the fraction of secondary structures of starch hydrolase after the interactions with carboxymethylated cellulose nanofibrils. These data provide a convenient and simple method tailor gastrointestinal digestion of starch by changing cellulose surface charge, to control postprandial serum glucose upsurge.

Cyclodextrins and Their Polymers Affect Human Serum Albumin's Interaction with Drugs Used in the Treatment of Pulmonary Infections.

Respiratory infectious diseases have challenged medical communities and researchers. Ceftriaxone, meropenem and levofloxacin are widely used for bacterial infection treatment, although they possess severe side effects. To overcome this, we propose cyclodextrin (CD) and CD-based polymers as a drug delivery system for the drugs under consideration. CD polymers demonstrate higher binding affinity for levofloxacin (Ka ≈ 105 M) compared to drug-CD complexes. CDs slightly alter the drugs' affinity for human serum albumin (HSA), whereas CD polymers increase the drugs' binding affinity up to 100 times. The most significant effect was observed for more the hydrophilic drugs ceftriaxone and meropenem. The drug's encapsulation in CD carriers leads to a decrease in the degree of change in the protein's secondary structure. The drug-CD carrier-HSA complexes demonstrate satisfying antibacterial activity in vitro, and even a high binding affinity does not decrease the drug's microbiological properties after 24 h. The proposed carriers are promising for a drug form with a prolonged drug release.

Thermal properties of AlN (nano) filled LDPE composites

Abstract The thermal properties of aluminium nitride nano-particles (n-AlN) filled into low-density polyethylene (LDPE) are discussed. Cylindrical specimens were prepared using a melt mixing process. X-ray diffraction was performed to characterize the structural properties of the pellets under investigation. The X-ray diffraction analysis confirms the change in secondary structure, such as crystallinity, of the LDPE due to the dispersion of n-AlN powder. The thermal stability of pure and n-AlN filled LDPE was checked by performing thermo-gravimetric analysis. The analysis confirms an improvement in the thermal stability of LDPE due to n-AlN addition. The thermal conductivity of the samples was measured using a KD2 Pro device (based on the transient hot wire technique of thermal conductivity measurement) at room temperature. Our finding reveals ∼1.36 fold enhancement in the effective thermal conductivity of LDPE due to the addition of 15 vol.% of n-AlN. The room-temperature thermal conductivity data of the investigated pellets were analyzed as a function of n-AlN concentration in the light of available theoretical models and correlations. The variation in thermal conductivity data of LDPE with n-AlN concentration is well explained by the semi-empirical model proposed by Agari and Uno.

Broad-Spectrum Detection of Tetracyclines by Riboswitch-Based Cell-Free Expression Biosensing.

We describe a sensitive and selective method for the determination of tetracycline content in foods using a riboswitch sensor. The sensor is based on a cell-free expression system that can be lyophilized to produce paper-based sensors or tube-based sensors for long-term storage. The riboswitch constructed using artificially screened tetracycline RNA aptamers was cloned into the pET-28a(+) vector of Escherichia coli TOP 10. The expression of the green fluorescent protein was positively correlated with the concentration of tetracyclines. The binding of tetracyclines to the aptamer domain results in a conformational change in the riboswitch secondary structure, resulting in the exposure of the ribosome binding site thereby promoting expression. The detection limits of the prepared sensor for the detection of tetracycline, oxytetracycline, chlortetracycline, and doxycycline were 0.47, 0.079, 0.084, and 0.43 μM, respectively. Moreover, the 1 μM tetracyclines allow for qualitative detection in milk samples by the naked eye. The work provides a proof-of-principle for riboswitch design to address global health and food safety.

A facile strategy for plant protein fiber formation without extrusion or shear processing

Extrusion and shear cell processing were once considered the only techniques to create fibrous meat-like structures. Here, we show that zein, the prolamin from corn, can form fibers in situ when plasticized using acid and extended in a supporting matrix. Rapid-swelling starches and pea protein were explored as the particle-filled supporting matrix. Synchrotron computed tomography identified regions of linear fiber formation, separation of phases with elongated air capillaries, and network density increases. Molecular changes in secondary structure also aided in fiber formation which produced textural properties similar to cooked chicken and/or beef. The analysis demonstrated that extensive processing is not needed to create meat-like analogues. Instead, exploiting the inherent physical and molecular properties of each component and their interactions can aid in the creation of complex food structures.

Picloram binds to the h1 and h4 helices of HSA domain IIIA at drug binding site 2

Picloram (PC) is a systemic herbicide that controls herbaceous weeds and woody plants. HSA, the most abundant protein in human physiology, binds to all exogenic and endogenic ligands. PC is a stable molecule (t1/2∼157–513 days) and a potential threat to human health via the food chain. HSA and PC binding study has been done to decipher the location and thermodynamics of binding. It has been studied with prediction tools like autodocking and MD simulation and then confirmed with fluorescence spectroscopy. HSA fluorescence was quenched by PC at pH 7.4 (N state), pH 3.5 (F state), and pH 7.4 with 4.5 M urea (I state) at temperatures 283 K, 297 K, and 303 K. The location of binding was found to be interdomain between II and III which overlaps with drug binding site 2. The binding was spontaneous, and entropy-driven that show a noticeable increase in binding with the increase in temperature. No secondary structure change at the native state has been observed due to binding. The binding results are important to understand the physiological assimilation of PC. In silico predictions and the results of spectroscopic studies unambiguously indicate the locus and nature of the binding.

The effect of novel tyrosine-modified polyethyleneimines on human albumin structure – Thermodynamic and spectroscopic study

The interaction of proteins with nanoparticle components are crucial for the evaluation of nanoparticle function, toxicity and biodistribution. Polyethyleneimines (PEIs) with defined tyrosine modifications are a class of novel polymers designed for improved siRNA delivery. Their interactions with biomacromolecules are still poorly described. This paper analyzes the interaction of different tyrosine-modified PEIs with human serum albumin as the most abundant serum protein. The ability of tyrosine modified, linear or branched PEIs to bind human serum albumin (HSA) was analyzed and further characterized. The interaction with hydrophobic parts of protein were studied using 1- nilinonaphthalene-8-sulfonic acid (ANS) and changes in the HSA secondary structure were evaluated using circular dichroism (CD). Complex formation and sizes were studied by transmission electron microscopy (TEM) and dynamic light scattering methods (DLS). We demonstrate that tyrosine modified PEIs are able to bind human serum albumin. Based on thermodynamic studies, van der Waals interaction, H-bonding and hydrophobic interactions are determined as main molecular forces involved in complex formation. Analysis of secondary structures revealed that the polymers decreased α-helix content, while increasing levels of randomly folded structures. Complex formation was confirmed by TEM and DLS. These findings are crucial for understanding polymer-protein interactions and the properties of nanoparticles.

Overlapping neurological phenotypes in two extended consanguineous families with novel variants in the CNTNAP1 and ADGRG1 genes.

Population diversity is important and rare disease isolates can frequently reveal novel homozygous or biallelic mutations that lead to expanded clinical heterogeneity, with diverse clinical presentations. The present study describes two consanguineous families with a total of seven affected individuals suffering from a clinically similar severe syndromic neurological disorder, with abnormal development and central nervous system (CNS) and peripheral nervous system (PNS) abnormalities. Whole exome sequencing (WES) and Sanger sequencing followed by 3D protein modeling was performed to identify the disease-causing gene. RNA was extracted from the fresh blood of both families affected and healthy individuals. The families were clinically assessed in the field in different regions of Khyber Pakhtunkhwa. Magnetic resonance imagining was obtained in the probands and blood was collected for DNA extraction and WES was performed. Sanger sequencing confirmed a homozygous, likely pathogenic mutation (GRCh38: chr17:42684199G>C; (NM_003632.3): c.333G>C);(NP_003623.1): p.(Trp111Cys) in the CNTNAP1 gene in family A, previously associated with Congenital Hypo myelinating Neuropathy 3 (CHN3; OMIM # 618186) and a novel nonsense variant in family B, (GRCh38: chr16: 57654086C>T; NC_000016.10 (NM_001370440.1): c.721C>T); (NP_001357369.1): p.(Gln241Ter) in the ADGRG1 gene previously associated with bilateral frontoparietal polymicrogyria (OMIM # 606854); both families have extended CNS and PNS clinical manifestations. In addition, 3D protein modeling was performed for the missense variant, p.(Trp111Cys), identified in the CNTNAP1, suggesting extensive secondary structure changes that might lead to improper function or downstream signaling. No RNA expression was observed in both families affected and healthy individuals hence showing that these genes are not expressed in blood. In the present study, two novel biallelic variants in the CNTNAP1 and ADGRG1 genes in two different consanguineous families with a clinical overlap in the phenotype were identified. Thus, the clinical and mutation spectrum is expanded to provide further evidence that CNTNAP1 and ADGRG1 are very important for widespread neurological development.

Global Spread Dynamics and Intrinsic Evolutionary Dynamics of Apple Chlorotic Leaf Spot Virus Whole-Genome Sequences over the Last 30 Years

Apple chlorotic leaf spot virus (ACLSV; genus Trichovirus) is an economically important virus. Approximately 101 ACLSV whole-genome sequences were obtained from NCBI and used to explore the evolutionary dynamics of ACLSV. The time to the most recent common ancestor of ACLSV based on BEAST analysis appeared on an apple host from Canada in 1918 and then spread around the world in three ways concurrent with host spread. The maximum clade credibility tree of ACLSV shows that the mean evolution rate was 4.92 × 10-4 substitutions per site per year (subs/site/year), and we found that, during host evolution, the rate of evolution was mostly 2.31 × 10-4 to 2.72 × 10-4 subs/site/year. The rate of geographic evolution was 5.51 × 10-4 to 6.17 × 10-4 subs/site/year. To further explore the intrinsic changes in ACLSV during the process of geographic and host spread, we explored the secondary structural changes of the ACLSV coat protein (CP), which were mainly concentrated in four regions-20 to 40, 70 to 90, 120 to 140, and 180 to 193-which are related to the presence or absence and change in length of the β-turn, β strand, coil, and α helix, respectively. We then explored the codon usage preference within the CP across the migration pathways of ACLSV. These comprehensive analyses not only reveal the changes in ACLSV in the last 30 years but also further elucidate the intrinsic evolutionary dynamics of ACLSV. This is also the first report on the intrinsic evolutionary dynamics of ACLSV.