Phylogenetic and Drug-Resistance Analysis of HIV-1 Sequences From an Extensive Paediatric HIV-1 Outbreak in Larkana, Pakistan.

INTRODUCTION: In April 2019, an HIV-1 outbreak among children occurred in Larkana, Pakistan, affecting more than a thousand children. It was assumed that the outbreak originated from a single source, namely a doctor at a private health facility. In this study, we performed subtype distribution, phylogenetic and drug-resistance analysis of HIV-1 sequences from 2019 outbreak in Larkana, Pakistan. METHODS: A total of 401 blood samples were collected between April-June 2019, from children infected with HIV-1 aged 0-15 years recruited into a case-control study to investigate the risk factors for HIV-1 transmission. Partial HIV-1 pol sequences were generated from 344 blood plasma samples to determine HIV-1 subtype and drug resistance mutations (DRM). Maximum-likelihood phylogenetics based on outbreak and reference sequences was used to identify transmission clusters and assess the relationship between outbreak and key population sequences between and within the determined clusters. Bayesian analysis was employed to identify the time to the most recent common recent ancestor (tMRCA) of the main Pakistani clusters. RESULTS: The HIV-1 circulating recombinant form (CRF) 02_AG and subtype A1 were most common among the outbreak sequences. Of the treatment-naïve participants, the two most common mutations were RT: E138A (8%) and RT: K219Q (8%). Four supported clusters within the outbreak were identified, and the median tMRCAs of the Larkana outbreak sequences were estimated to 2016 for both the CRF02_AG and the subtype A1 clusters. Furthermore, outbreak sequences exhibited no phylogenetic mixing with sequences from other high-risk groups of Pakistan. CONCLUSION: The presence of multiple clusters indicated a multi-source outbreak, rather than a single source outbreak from a single health practitioner as previously suggested. The multiple introductions were likely a consequence of ongoing transmission within the high-risk groups of Larkana, and it is possible that the so-called Larkana strain was introduced into the general population through poor infection prevention control practices in healthcare settings. The study highlights the need to scale up HIV-1 prevention programmes among key population groups and improving infection prevention control in Pakistan

FIGURE 1. A in The genus Microhyla (Anura: Microhylidae) in Pakistan: species status and origins

FIGURE 1. A: Median-joining haplotype network inferred from a 16S rRNA showing the intraspecific relationships of Microhyla nilphamariensis with regards to Pakistani populations. B (inset): the haplotype network of BDNF gene representing relationships in M. ornata group according to Garg et al. (2019). C: map displaying the localities of genetically investigated (16S rRNA) population of the species with an expected range highlighted in grey (sensu Garg et al. 2018, 2019). GenBank accession numbers of analysed sequences are associated with a particular detected haplotype/locality. The type locality of M. nilphamariensis is marked with a star. The populations investigated using both genes are marked by arrows in the map. Question marks suggest unclear species presence. The pictured specimens originate from two investigated localities of Pakistan, Margalla Hills National Park, Islamabad (DJ7915) and Parera, Chakwal district, Punjab (DJ7882).Published as part of Jablonski, Daniel, Khan, Muazzam Ali & Masroor, Rafaqat, 2020, The genus Microhyla (Anura: Microhylidae) in Pakistan: species status and origins, pp. 293-296 in Zootaxa 4845 (2) on page 294, DOI: 10.11646/zootaxa.4845.2.11, http://zenodo.org/record/449423

The genus Microhyla (Anura: Microhylidae) in Pakistan: species status and origins

Jablonski, Daniel, Khan, Muazzam Ali, Masroor, Rafaqat (2020): The genus Microhyla (Anura: Microhylidae) in Pakistan: species status and origins. Zootaxa 4845 (2): 293-296, DOI: 10.11646/zootaxa.4845.2.1

A new species of Microgecko Nikolsky, 1907 (Squamata: Gekkonidae) from Pakistan

Masroor, Rafaqat, Khisroon, Muhammad, Khan, Muazzam Ali, Jablonski, Daniel (2020): A new species of Microgecko Nikolsky, 1907 (Squamata: Gekkonidae) from Pakistan. Zootaxa 4780 (1): 147-164, DOI: https://doi.org/10.11646/zootaxa.4780.1.

An Intelligent and Secure Air Quality Monitoring System Using Neural Network Algorithm and Blockchain

Indoor air pollution is more dangerous for residents. So, it is necessary to monitor the quality of indoor air and take some preventive steps to reduce the possible dangers to the health of the inhabitants. The cost and maintenance factors of air quality (AQI) systems lead the researchers to model, design, and implement low-cost indoor AQI monitoring systems. In this research, we proposed an indoor AQI monitoring system with a data-driven model to predict the AQI through the Neural Network Algorithm and Block-chain. The Internet of Things (IoT) connects and processes data, and low-cost sensors collect the data from the environment. The Indoor Air Quality system consists of temperature, humidity, Carbon Di Oxide, Particulate Matter, Carbon Mono Oxide, and LPG. The data are collected from five different sensors, and the NN decision-making model is used to predict the AQI to prevent harmful situations. The suggested IoT-based smart block-chain technology plays a vital role by imparting scalability, privacy, and reliability. This study will work effectively with ease of use, cost-effectiveness, and maintenance of the entire system.Taif University - grant No. TURSP-2020/55

Appearances often deceive in racerunners: integrative approach reveals two new species of Eremias (Squamata: Lacertidae) from Pakistan

Masroor, Rafaqat, Khan, Muazzam Ali, Nadeem, Muhammad Sajid, Amir, Shabir Ali, Khisroon, Muhammad, Jablonski, Daniel (2022): Appearances often deceive in racerunners: integrative approach reveals two new species of Eremias (Squamata: Lacertidae) from Pakistan. Zootaxa 5175 (1): 55-87, DOI: 10.11646/zootaxa.5175.1.

Water treatment by photodegradation on orthorhombic antimony sulfide powder and effect of key operational parameters using methyl orange as a model pollutant

Photocatalytic treatment of colored wastewaters containing methyl orange was achieved using visible light active Sb2S3 photocatalyst powder. Antimony chloride and sodium sulfide were used as antimony and sulfur precursors, respectively, for the synthesis of Sb2S3 powder by the hydrothermal method. The temperature of the Teflon lined autoclave was maintained at 105, 150 and 200 °C for varying times of 4, 6 and 12 h and corresponding phase evolution was studied by X-ray diffraction. XRD showed well crystalline single phase orthorhombic Sb2S3 powder synthesized at the different temperatures of autoclave maintained for different times. From the view point of time and temperature efficiency, Sb2S3 powder synthesized at 105 °C/4 h was selected for further characterization and photocatalytic studies. Well grown spherical particles were observed under scanning electron microscope. Material was found to be thermally stable in temperature range of 25–1000 °C. Vibrational modes of metal-sulfur bonds were observed at wave numbers below 1000 cm−1 in the Fourier transform infrared spectrum at room temperature. BET surface area of the material was 65 m2/g as obtained through N2 adsorption experiments. The well characterized material was used for the degradation studies of methyl orange and the effect of various factors such as, pH, concentration of the solution, time, temperature and quantity of catalyst was investigated. Lower MO concentrations were degraded better and lower pH favored the degradation. The catalyst dosage had direct relationship with the degradation rate up to a certain limit. Pseudo first rate constant of 0.0012 min−1 was calculated from the fitting of kinetic data. Degradation rate increased with the increase in reaction temperature. Degradation mechanism was designed based on the characterization and photocatalytic studies. Keywords: Chalcogenides, Chemical preparation, X-ray diffraction, Photocatalysi

Influence of Fe2+ and Ni2+ contents on the optical and electrical properties of ZnS quantum dots

The work reports a well controlled synthesis of un-doped and Fe2+ and Ni2+ doped ZnS quantum dots (QDs) based highly luminescent of pure cubic zinc blende structure. The samples were characterized for structural, morphological, optical and electrical parameters and great care has been made in correlating all these properties. The optimum concentrations of Zn1-xFexS and Zn1-xNixS dopants were found to be x = 0.2 for superior optical and electrical properties. Incorporation of Fe2+ or Ni2+ into ZnS lattice have generated acceptor level as an isolated state just above the valence band of ZnS, and hence electron requiring less excitation energy for transferring from the acceptor level to the conduction band. Moreover, it was found that the PL emission intensity of Fe2+ doped ZnS QDs is higher than that of Ni2+ doped. The results indicated that the active luminescent centers created by dopants and localized surface plasmon resonance energy transfer of ZnS QDs significantly increased with Fe2+ ions into the ZnS lattice. Over all in light of the results obtained during the study, the doped samples can have potential for function in vast variety of applications.</p

Synthesis, biological evaluation and molecular docking study of pyrimidine based thiazolidinone derivatives as potential anti-urease and anti-cancer agents

Hybrid analogs containing molecules are always the choice of different synthetic researcher due to their diverse biological applications and significantly more efficient. Heterocyclic being a good inhibitors against varied disease are most commonly used in drug designing and development. The current study also addressed the synthesis of pyrimidine-based thiazolidinone derivatives (1–13) using stepwise processes and their structure was confirmed using various characterization techniques such as 1HNMR, 13CNMR, and HREI-MS. Furthermore, the biological significances of the synthesized scaffolds were also explored and proved to be as anti-urease and anti-cancer moieties. Their inhibitory potentials were determined using the minimum inhibitory concentration (MIC) in the presence of their standard drugs, Thiourea (IC50 = 8.20 ± 0.20 µM) and Tetrandrineb (IC50 = 12.30 ± 0.10 µM) respectively. Structure activity relationship (SAR) was established for all the synthesized scaffolds and compared their inhibitory potentials in which scaffolds 3 (IC50 = 2.30 ± 0.30 and 3.20 ± 0.50 µM), 6 (IC50 = 3.10 ± 0.20 and 6.20 ± 0.10 µM), 7 (IC50 = 3.20 ± 0.20 and 3.80 ± 0.30 µM) and 10 (IC50 = 4.20 ± 0.20 and 5.10 ± 0.30 µM) exhibited the most influential activity. These compounds were subsequently examined using molecular docking experiments, which evaluate the binding interaction of ligands with enzyme active sites

The Role of Membrane Transporters in Plant Growth and Development, and Abiotic Stress Tolerance

The proteins of membrane transporters (MTs) are embedded within membrane-bounded organelles and are the prime targets for improvements in the efficiency of water and nutrient transportation. Their function is to maintain cellular homeostasis by controlling ionic movements across cellular channels from roots to upper plant parts, xylem loading and remobilization of sugar molecules from photosynthesis tissues in the leaf (source) to roots, stem and seeds (sink) via phloem loading. The plant’s entire source-to-sink relationship is regulated by multiple transporting proteins in a highly sophisticated manner and driven based on different stages of plant growth and development (PG&D) and environmental changes. The MTs play a pivotal role in PG&D in terms of increased plant height, branches/tiller numbers, enhanced numbers, length and filled panicles per plant, seed yield and grain quality. Dynamic climatic changes disturbed ionic balance (salt, drought and heavy metals) and sugar supply (cold and heat stress) in plants. Due to poor selectivity, some of the MTs also uptake toxic elements in roots negatively impact PG&D and are later on also exported to upper parts where they deteriorate grain quality. As an adaptive strategy, in response to salt and heavy metals, plants activate plasma membranes and vacuolar membrane-localized MTs that export toxic elements into vacuole and also translocate in the root’s tips and shoot. However, in case of drought, cold and heat stresses, MTs increased water and sugar supplies to all organs. In this review, we mainly review recent literature from Arabidopsis, halophytes and major field crops such as rice, wheat, maize and oilseed rape in order to argue the global role of MTs in PG&D, and abiotic stress tolerance. We also discussed gene expression level changes and genomic variations within a species as well as within a family in response to developmental and environmental cues