Encapsulation of ZnO and Ho:ZnO Nanoparticles in the Core of Wrinkled Mesoporous Silica.

Wrinkled mesoporous silica (WMS) has a flower- or dendritic-like morphology, tunable pore size, and highly ordered and accessible three-dimensional (3D) pore structures. In this research, a method to encapsulate semiconductor nanoparticles in the core of the wrinkled mesoporous silica during synthesis is described. Highly uniform zinc oxide and holmium-doped zinc oxide nanoparticles have been synthesized by a sonochemical method. Zinc oxide and holmium-doped zinc oxide nanoparticles have been encapsulated in wrinkled mesoporous silica during synthesis. The ZnO@WMS and Ho:ZnO@WMS particles have been characterized by transmission electron microscopy (TEM), scanning electron microscopy (SEM), UV-vis spectroscopy, fluorescence, dynamic light scattering (DLS), confocal microscopy, and X-ray diffraction (XRD).

Dysbiosis of Oral and Gut Microbiomes in SARS-CoV-2 Infected Patients in Bangladesh: Elucidating the Role of Opportunistic Gut Microbes.

Coronavirus disease-2019 (COVID-19) is an infectious disease caused by SARS-CoV-2 virus. The microbes inhabiting the oral cavity and gut might play crucial roles in maintaining a favorable gut environment, and their relationship with SARS-CoV-2 infection susceptibility and severity is yet to be fully explored. This study investigates the diversity and species richness of gut and oral microbiota of patients with COVID-19, and their possible implications toward the severity of the patient's illness and clinical outcomes. Seventy-four (n = 74) clinical samples (gut and oral) were collected from 22 hospitalized patients with COVID-19 with various clinical conditions and 15 apparently healthy people (served as controls). This amplicon-based metagenomic sequencing study yielded 1,866,306 paired-end reads that were mapped to 21 phyla and 231 classified genera of bacteria. Alpha and beta diversity analyses revealed a distinct dysbiosis of the gut and oral microbial communities in patients with COVID-19, compared to healthy controls. We report that SARS-CoV-2 infection significantly reduced richness and evenness in the gut and oral microbiomes despite showing higher unique operational taxonomic units in the gut. The gut samples of the patients with COVID-19 included 46 opportunistic bacterial genera. Escherichia, Shigella, and Bacteroides were detected as the signature genera in the gut of patients with COVID-19 with diarrhea, whereas a relatively higher abundance of Streptococcus was found in patients with COVID-19 having breathing difficulties and sore throat (BDST). The patients with COVID-19 had a significantly lower abundance of Prevotella in the oral cavity, compared to healthy controls and patients with COVID-19 without diabetes, respectively. The altered metabolic pathways, including a reduction in biosynthesis capabilities of the gut and oral microbial consortia after SARS-CoV-2 infection, were also observed. The present study may, therefore, shed light on interactions of SARS-CoV-2 with resilient oral and gut microbes which might contribute toward developing microbiome-based diagnostics and therapeutics for this deadly pandemic disease.

Insights into the nutritional properties and microbiome diversity in sweet and sour yogurt manufactured in Bangladesh.

Yogurt is one of the most frequently consumed dairy products for nutritional benefits. Although yogurt is enriched with probiotics, it is susceptible to spoilage because of the presence of pathogenic microbes. Spoiled yogurt if consumed can cause food-borne diseases. This study aimed to assess the nutritional composition and microbiome diversity in yogurt manufactured in Bangladesh. Microbial diversity was analyzed through high-throughput sequencing of bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) region. From nutritional analysis, significantly (P < 0.05) higher pH, fat, moisture, total solid and solid-non-fat contents (%) were observed in sweet yogurt. Following the classification of Illumina sequences, 84.86% and 72.14% of reads were assigned to bacterial and fungal genera, respectively, with significantly higher taxonomic richness in sour yogurt prepared from buffalo. A significant difference in bacterial (Ppermanova = 0.001) and fungal (Ppermanova = 0.013) diversity between sweet and sour yogurt was recorded. A total of 76 bacterial and 70 fungal genera were detected across these samples which were mostly represented by Firmicutes (92.89%) and Ascomycota (98%) phyla, respectively. This is the first study that accentuates nutritional profiles and microbiome diversity of Bangladeshi yogurt which are crucial in determining both active and passive health effects of yogurt consumption in individuals.

Transcriptome of nasopharyngeal samples from COVID-19 patients and a comparative analysis with other SARS-CoV-2 infection models reveal disparate host responses against SARS-CoV-2.

BACKGROUND: Although it is becoming evident that individual's immune system has a decisive influence on SARS-CoV-2 disease progression, pathogenesis is largely unknown. In this study, we aimed to profile the host transcriptome of COVID-19 patients from nasopharyngeal samples along with virus genomic features isolated from respective host, and a comparative analyses of differential host responses in various SARS-CoV-2 infection systems. RESULTS: Unique and rare missense mutations in 3C-like protease observed in all of our reported isolates. Functional enrichment analyses exhibited that the host induced responses are mediated by innate immunity, interferon, and cytokine stimulation. Surprisingly, induction of apoptosis, phagosome, antigen presentation, hypoxia response was lacking within these patients. Upregulation of immune and cytokine signaling genes such as CCL4, TNFA, IL6, IL1A, CCL2, CXCL2, IFN, and CCR1 were observed in lungs. Lungs lacked the overexpression of ACE2 as suspected, however, high ACE2 but low DPP4 expression was observed in nasopharyngeal cells. Interestingly, directly or indirectly, viral proteins specially non-structural protein mediated overexpression of integrins such as ITGAV, ITGA6, ITGB7, ITGB3, ITGA2B, ITGA5, ITGA6, ITGA9, ITGA4, ITGAE, and ITGA8 in lungs compared to nasopharyngeal samples suggesting the possible way of enhanced invasion. Furthermore, we found comparatively highly expressed transcription factors such as CBP, CEBP, NFAT, ATF3, GATA6, HDAC2, TCF12 which have pivotal roles in lung injury. CONCLUSIONS: Even though this study incorporates a limited number of cases, our data will provide valuable insights in developing potential studies to elucidate the differential host responses on the viral pathogenesis in COVID-19, and incorporation of further data will enrich the search of an effective therapeutics.

Host range projection of SARS-CoV-2: South Asia perspective.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causing agent of Coronavirus Disease-2019 (COVID-19), is likely to be originated from bat and transmitted through intermediate hosts. However, the immediate source species of SARS-CoV-2 have not yet been confirmed. Here, we used diversity analysis of the angiotensin I converting enzyme 2 (ACE2) that serves as cellular receptor for SARS-CoV-2 and transmembrane protease serine 2 (TMPRSS2), which has been proved to be utilized by SARS-CoV-2 for spike protein priming. We also simulated the structure of receptor-binding domain of SARS-CoV-2 spike protein (SARS-CoV-2S RBD) with the ACE2s to investigate their binding affinity to determine the potential intermediate animal hosts that could spread the SARS-CoV-2 to humans in South Asia. We identified cow, buffalo, goat and sheep, which are predominant species in the household farming system in South Asia that can potentially be infected by SARS-CoV-2. All the bird species studied along with rat and mouse were considered less potential to interact with SARS-CoV-2. The interaction interfaces of SARS-CoV-2S RBD and ACE2 protein complex suggests pangolin as a potential intermediate host in SARS-CoV-2. Our results provide a valuable resource for the identification of potential hosts for SARS-CoV-2 in South Asia and henceforth reduce the opportunity for a future outbreak of COVID-19.

Microbiome dynamics and genomic determinants of bovine mastitis.

The milk of lactating cows presents a complex ecosystem of interconnected microbial communities which can influence the pathophysiology of mastitis. We hypothesized possible dynamic shifts of microbiome composition and genomic features with different pathological conditions of mastitis (Clinical Mastitis; CM, Recurrent CM; RCM, Subclinical Mastitis; SCM). To evaluate this hypothesis, we employed whole metagenome sequencing (WMS) in 20 milk samples (CM, 5; RCM, 6; SCM, 4; H, 5) to unravel the microbiome dynamics, interrelation, and relevant metabolic functions. The WMS data mapped to 442 bacterial, 58 archaeal and 48 viral genomes with distinct variation in microbiome composition (CM > H > RCM > SCM). Furthermore, we identified a number of microbial genomic features, including 333, 304, 183 and 50 virulence factors-associated genes (VFGs) and 48, 31, 11 and 6 antibiotic resistance genes (ARGs) in CM, RCM, SCM, and H-microbiomes, respectively. We also detected different metabolic pathway and functional genes associated with mastitis pathogenesis. Therefore, profiling microbiome dynamics in different conditions of mastitis and associated microbial genomic features contributes to developing microbiome-based diagnostics and therapeutics for bovine mastitis.

Goat Genomic Resources: The Search for Genes Associated with Its Economic Traits.

Goat plays a crucial role in human livelihoods, being a major source of meat, milk, fiber, and hides, particularly under adverse climatic conditions. The goat genomics related to the candidate gene approach is now being used to recognize molecular mechanisms that have different expressions of growth, reproductive, milk, wool, and disease resistance. The appropriate literature on this topic has been reviewed in this article. Several genetic characterization attempts of different goats have reported the existence of genotypic and morphological variations between different goat populations. As a result, different whole-genome sequences along with annotated gene sequences, gene function, and other genomic information of different goats are available in different databases. The main objective of this review is to search the genes associated with economic traits in goats. More than 271 candidate genes have been discovered in goats. Candidate genes influence the physiological pathway, metabolism, and expression of phenotypes. These genes have different functions on economically important traits. Some genes have pleiotropic effect for expression of phenotypic traits. Hence, recognizing candidate genes and their mutations that cause variations in gene expression and phenotype of an economic trait can help breeders look for genetic markers for specific economic traits. The availability of reference whole-genome assembly of goats, annotated genes, and transcriptomics makes comparative genomics a useful tool for systemic genetic upgradation. Identification and characterization of trait-associated sequence variations and gene will provide powerful means to give positive influences for future goat breeding program.

Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach.

The newly identified SARS-CoV-2 has now been reported from around 185 countries with more than a million confirmed human cases including more than 120,000 deaths. The genomes of SARS-COV-2 strains isolated from different parts of the world are now available and the unique features of constituent genes and proteins need to be explored to understand the biology of the virus. Spike glycoprotein is one of the major targets to be explored because of its role during the entry of coronaviruses into host cells. We analyzed 320 whole-genome sequences and 320 spike protein sequences of SARS-CoV-2 using multiple sequence alignment. In this study, 483 unique variations have been identified among the genomes of SARS-CoV-2 including 25 nonsynonymous mutations and one deletion in the spike (S) protein. Among the 26 variations detected in S, 12 variations were located at the N-terminal domain (NTD) and 6 variations at the receptor-binding domain (RBD) which might alter the interaction of S protein with the host receptor angiotensin-converting enzyme 2 (ACE2). Besides, 22 amino acid insertions were identified in the spike protein of SARS-CoV-2 in comparison with that of SARS-CoV. Phylogenetic analyses of spike protein revealed that Bat coronavirus have a close evolutionary relationship with circulating SARS-CoV-2. The genetic variation analysis data presented in this study can help a better understanding of SARS-CoV-2 pathogenesis. Based on results reported herein, potential inhibitors against S protein can be designed by considering these variations and their impact on protein structure.

Biphenyl Wrinkled Mesoporous Silica Nanoparticles for pH-Responsive Doxorubicin Drug Delivery.

Biphenyl wrinkled mesoporous silica nanoparticles with controlled particle size and high surface area were evaluated for the storage and delivery of doxorubicin. The average particle size and surface area were ~70 nm and ~1100 m2/g. The doxorubicin loading efficiency was 38.2 ± 1.5 (w/w)% and the release was pH dependent. The breast cancer cell line, MCF-7 (Michigan Cancer Foundation-7) was used for the in vitro drug release study. The cytotoxicity of doxorubicin-loaded nanoparticles was significantly higher than free doxorubicin. Fluorescence images showed biphenyl wrinkled mesoporous silica (BPWS) uptake by the MCF-7 cells. The biphenyl bridged wrinkled silica nanoparticles appear promising for hydrophobic drug loading and delivery.

Identification of non-cerebral cyst: Zoonotic Taenia multiceps in domestic goat in Bangladesh.

AIM: This study was performed to identify the non-cerebral Taenia multiceps cyst through molecular phylogeny of the 12S rRNA gene. MATERIALS AND METHODS: Eight cyst samples were collected from 385 examined slaughtered goats during October 2015-September 2016 from three slaughterhouses in Chittagong City Corporation. Cysts were removed from the thigh muscle, and scolices were collected for light microscopic examination and molecular identification. The DNA was extracted and analyzed by polymerase chain reaction using 12S rRNA gene primers. Cyst samples were also preserved in 10% buffered formalin for histopathological study. RESULTS: T. multiceps non-cerebral cyst is 2.1% prevalent in goat in this area. Under light microscopic examination, scolex was found with four suckers and a rostellum with the double crown of 32 hooks and hooklets. Molecularly, all the samples were amplified with 12S rRNA gene fragments yielded 270 base pair amplicon. Zenker's necrosis with focal to diffuse infiltration of lymphocytes and eosinophil was also found around the cyst wall in histopathological examination. CONCLUSION: Although the non-cerebral form of the cysts produced by T. multiceps is genetically identical with the cerebral cyst, previously published data indicated that cerebral T. multiceps cyst is predominant in other parts of the world as well as in Bangladesh. This study showed that non-cerebral cyst is also prevalent in this country which is very important for public health concern. This study depicts an idea of non-cerebral form of zoonotic T. multiceps cyst which will be helpful in taenia cyst control and prevention.

The local nature of incompressibility of quantum Hall effect.

Since the experimental realization of the integer quantum Hall effect in a two-dimensional electron system, the interrelation between the conductance quantization and the topological properties of the system has been investigated. Assuming that the two-dimensional electron system is described by a Bloch Hamiltonian, system is insulating in the bulk of sample throughout the quantum Hall plateau due to a magnetic field induced energy gap. Meanwhile, the system is conducting at the edges resembling a 2+1 dimensional topological insulator without time-reversal symmetry. Here, by our magneto-transport measurements performed on GaAs/AlGaAs high purity Hall bars with two inner contacts we show that incompressible strips formed at the edges result in Hall quantization, even if the bulk is compressible. Consequently, the relationship between the quantum Hall effect and topological bulk insulator breaks for specific field intervals within the plateaus. The measurement of conducting bulk, strongly challenges all existing single-particle theories.

Identification and molecular characterization of Echinococcus granulosus from domestic goat in Chittagong, Bangladesh.

The tapeworm Echinococcus granulosus causes cystic echinococcosis (CE) in human and many domestic animals worldwide including Bangladesh. The parasite has significant public health importance in the country and no in-depth study has been conducted to determine this cestode in either human or animals. The aim of present study was to evaluate genotype of E. granulosus isolated from domestic goats reared in Chittagong, Bangladesh using DNA based tools. Partial gene fragment of 12S rRNA gene and Cytochrome oxidase 1 gene were accomplished by PCR followed by sequencing and phylogenetic analyses. A total of 19 hydatid cyst samples were collected from 385 goats from several local slaughterhouses located in Chittagong. The rates of fertile hydatid cysts were found as high as 57.89% while remaining cysts were found non-viable and sterile. Genomic DNA was extracted from germinal membrane and/or protoscolices for PCR assay. Sequence similarity based on BLAST search revealed variable prevalence of E. granulosus genotypes such as G1 (68.42%) and G1/G3 complex (31.58%) which is reported for the first time in the country. This result indicates common sheep strain G1 is the dominant subtype of E. granulosus in this region. The study generated six sequences of which four were aligned with G1 common sheep strain and two were aligned with G3 strain (commonly referred as Buffalo strain). Phylogenetic analysis of 12S rRNA gene and Cytochrome oxidase 1 gene also indicated that common sheep strain (G1) and Buffalo strain (G3) are circulating among domestic goats in Chittagong region of Bangladesh.

A realistic quantum capacitance model for quantum Hall edge state based Fabry-Pérot interferometers.

In this work, the classical and the quantum capacitances are calculated for a Fabry-Pérot interferometer operating in the integer quantized Hall regime. We first consider a rotationally symmetric electrostatic confinement potential and obtain the widths and the spatial distribution of the insulating (incompressible) circular strips using a charge density profile stemming from self-consistent calculations. Modelling the electrical circuit of capacitors composed of metallic gates and incompressible/compressible strips, we investigate the conditions to observe Aharonov-Bohm (quantum mechanical phase dependent) and Coulomb blockade (capacitive coupling dependent) effects reflected in conductance oscillations. In a last step, we solve the Schrödinger and the Poisson equations self-consistently in a numerical manner taking into account realistic experimental geometries. We find that, describing the conductance oscillations either by Aharanov-Bohm or Coulomb blockade strongly depends on sample properties also other than size, therefore, determining the origin of these oscillations requires further experimental and theoretical investigation.

Anomalous resistance overshoot in the integer quantum Hall effect.

In this work we report on experiments performed on smooth edge-narrow Hall bars. The magneto-transport properties of intermediate mobility two-dimensional electron systems are investigated and analyzed within the screening theory of the integer quantized Hall effect. We observe a non-monotonic increase of Hall resistance at the low magnetic field ends of the quantized plateaus, known as the overshoot effect. Unexpectedly, for Hall bars that are defined by shallow chemical etching the overshoot effect becomes more pronounced at elevated temperatures. We observe the overshoot effect at odd and even integer plateaus, which favor a spin independent explanation, in contrast to discussion in the literature. In a second set of the experiments, we investigate the overshoot effect in gate defined Hall bar and explicitly show that the amplitude of the overshoot effect can be directly controlled by gate voltages. We offer a comprehensive explanation based on scattering between evanescent incompressible channels.

Stability of spin droplets in realistic quantum Hall devices.

We study the formation and characteristics of 'spin droplets', i.e. compact spin-polarized configurations in the highest occupied Landau level, in an etched quantum Hall device at filling factors 2 ≤ ν ≤ 3. The confining potential for electrons is obtained with self-consistent electrostatic calculations on a GaAs/AlGaAs heterostructure with experimental system parameters. Real-space spin-density-functional calculations for electrons confined in the obtained potential show the appearance of stable spin droplets at ν ~ 5/2. The qualitative features of the spin droplet are similar to those in idealized (parabolic) quantum-dot systems. The universal stability of the state against geometric deformations underlines the applicability of spin droplets in, for example, spin-transport through quantum point contacts.

Charting the proteome of Cryptosporidium parvum sporozoites using sequence similarity-based BLAST searching.

Cryptosporidium (C.) spp. are important zoonotic parasites causing widespread diarrhoeal disease in man and animals. The recent release of the complete genome sequences for C. parvum and C. hominis has facilitated the comprehensive global proteome analysis of these opportunistic pathogens. The well-known approach for mass spectrometry (MS) based data analysis using the BLAST tool (MS BLAST) is a database search protocol for identifying unknown proteins by sequence similarity to homologous proteins using peptide sequences produced by mass spectrometry. We have used several complementary approaches to explore the global sporozoite proteome of C. parvum with available proteomic tools. To optimize the output of the MS data, a sequence similarity-based MS BLAST strategy was employed for bioinformatic analysis. Most significantly, almost all the constituents of glycolysis and several mitochondrion-related proteins were identified. In addition, many hypothetical Cryptosporidium proteins were validated by the identification of their constituent peptides. The MS BLAST approach was found to be useful during the study and could provide valuable information towards a complete understanding of the unique biology of Cryptosporidium.