The complete mitochondrial genome of Penicillium expansum: Insights into the fungal evolution and phylogeny

Penicillium expansum is an important phytopathogenic fungus that causes blue mold disease. In this study, the novel mitochondrial genome of P. expansum was sequenced, assembled, annotated, and compared with the previously published Penicillium mitogenomes. P. expansum mitogenome is composed of circular DNA molecules with a genome size of 25,496 bp. It encodes 16 protein-encoding genes (PCGs), two rRNA genes, and 25 tRNA genes. Comparative analysis with six other Penicillium species revealed that gene length, GC content, AT skew, and GC skew were variable among the core protein-coding genes. The Penicillium species' gene synteny analysis identified several gene rearrangements. Among the core 15 PCGs, atp8 had the lowest K2P genetic distance, which shows that this gene is highly conserved. The Ka/Ks value of most PCGs was less than 1, which shows that these genes have undergone purifying selection. Phylogenetic analysis based on 14 concatenated core mitochondrial genes revealed that P. expansum shares a close relationship with P. solitum. This study served as a first report on the complete mitochondrial genome of P. expansum and its comparative analysis that will contribute to population genetics and rapid evolutionary studies among Penicillium species.

Plants used against liver disorders by autochthonous practitioners of Multan, Pakistan

The research work was commenced with an aim to document plant based drug recipes used by autochthonous practitioners against liver diseases in Multan region. The data was collected by interviews and semi-structured questionnaire from 43 traditional herbal practitioners. Recorded data was evaluated using the use value, relative frequency of citation (RFC), family importance value (FIV) and family use value (FUV). Total of 69 plant species belonging to 38 families were reported to be utilized to treat various liver disorders. The most important species regarding their use value were 3.0 for Polygonum bistorta, Citrus limon. It means that highly cited plants are more important in traditional medicines but this does not mean the plants low-citation plants by respondents are less medicinal important. It may be due to unavailability of plants in the area or lack of knowledge. Most of plant parts used were leaves due to ease of collection as compared to underground parts. One the basis family use value Asteraceae as the dominating or prominent family. These plants can be further investigated for allied pharmacological studies that will affect the socio-economical condition of the local community.

ISSR-Based Genetic Diversity Assessment of Genus Jasminum L. (Oleaceae) from Pakistan

The genus Jasminum L., of the family Oleaceae, includes many species occurring in the wild, or cultivated worldwide. A preliminary investigation based on inter-simple sequence repeats (ISSR) was performed to assess the genetic diversity among 28 accessions, representing nine species of Jasminum from various regions, representing a range of altitudes in Pakistan. A total of 21 ISSR primers were used, which produced 570 amplified bands of different sizes, with a mean polymorphic band percentage of 98.26%. The maximum resolving power, polymorphism information content, and index values of the ISSR markers recorded for primers 6, 16, and 19 were 0.40, 12.32, and 24.21, respectively. Based on the data of the ISSR markers, the resulting UPGMA dendrogram with the Jaccard coefficient divided the 28 accessions into two main clades. At the species level, the highest values for Shannon's information index, polymorphism percentage, effective allele number, Nei's genetic variations, and genetic unbiased diversity were found in Jasminum sambac L. and J. humile L., while the lowest were observed in J. mesnyi Hance and J. nitidum Skan. Based on Nei's unbiased genetic identity pairwise population matrix, the maximum identity (0.804) was observed between J. elongatum Willd and J. multiflorum (Burm. f.) Andrews, and the lowest (0.566) between J. nitidum Skan. and J. azoricum L. Molecular variance analysis displayed a genetic variation of 79% among the nine populations. The study was aimed to established genetic diversity in Jasminum species using ISSR markers. With the help of this technique, we were able to establish immense intra- and interspecific diversity across the Jasminum species.

Evaluating the cleavage efficacy of CRISPR-Cas9 sgRNAs targeting ineffective regions of Arabidopsis thaliana genome

The CRISPR-Cas9 system has recently evolved as a powerful mutagenic tool for targeted genome editing. The impeccable functioning of the system depends on the optimal design of single guide RNAs (sgRNAs) that mainly involves sgRNA specificity and on-target cleavage efficacy. Several research groups have designed algorithms and models, trained on mammalian genomes, for predicting sgRNAs cleavage efficacy. These models are also implemented in most plant sgRNA design tools due to the lack of on-target cleavage efficacy studies in plants. However, one of the major drawbacks is that almost all of these models are biased for considering only coding regions of the DNA while excluding ineffective regions, which are of immense importance in functional genomics studies especially for plants, thus making prediction less reliable. In the present study, we evaluate the on-target cleavage efficacy of experimentally validated sgRNAs designed against diverse ineffective regions of Arabidopsis thaliana genome using various statistical tests. We show that nucleotide preference in protospacer adjacent motif (PAM) proximal region, GC content in the PAM proximal seed region, intact RAR and 3^rd stem loop structures, and free accessibility of nucleotides in seed and tracrRNA regions of sgRNAs are important determinants associated with their high on-target cleavage efficacy. Thus, our study describes the features important for plant sgRNAs high on-target cleavage efficacy against ineffective genomic regions previously shown to give rise to ineffective sgRNAs. Moreover, it suggests the need of developing an elaborative plant-specific sgRNA design model considering the entire genomic landscape including ineffective regions for enabling highly efficient genome editing without wasting time and experimental resources.

Comparative palynology and taxonomic implication of Jasminum L. (Oleaceae) species from Pakistan on the bases of scanning electron microscopy

Jasminum L. is the largest genus containing ~200 species found wild mostly in the tropical regions of the world. The comparative palynological study of nine Pakistani Jasminum species with SEM showed zonocolpus, trilobate, and tricolpus pollen types with simple endocolpus apertures which are plesiomorphic and conserved in the Jasminum species. The equatorial pollen view was prolate, subprolate, and perprolate with elliptic, lobate, subcircular whereas polar view was subtriangular in all species. Few characters were specific to some species like heteropolarity in Jasminum grandiflorum and foveolate exine ornamentation with rounded heterobrochate in Jasminum angulare whereas reticulate and angular homobrochate character was common in other species. The UPGMA dendrogram based on qualitative characters did not support the phylogenetic classification of the genus Jasminum as these are highly conserved. The quantitative data showed more variation in some characters whereas few characters showed little or no variation. A greater variation in pollen size was observed among the variants of same species, for example, Jasminum humile showed highly variable polar length and equatorial diameter as compared to other species. Minimum variation was observed in colpus length which divided all species in to two groups. The large lumina were specific to Jasminum nitidum and broader muri was the prominent characteristic of Jasminum angulare. Some species like Jasminum sambac and Jasminum azoricum were unable to develop true pollen due to structural or functional disabilities. So, the quantitative characters of pollen are only suitable for palynological based grouping of Jasminum species but less suitable to infer their evolutionary relationship.

Classification and Computational Analysis of Arabidopsis thaliana Sperm Cell-Specific F-Box Protein Gene 3p.AtFBP113

In plants, F-box proteins (FBPs) constitute one of the largest superfamilies of regulatory proteins. Most F-box proteins are shown to be an integral part of SCF complexes, which carry out the degradation of proteins and regulate diverse important biological processes. Anthers and pollen development have a huge importance in crop breeding. Despite the vast diversity of FBPs in Arabidopsis male reproductive organs, their role in anther and pollen development is not much explored. Moreover, a standard nomenclature for naming FBPs is also lacking. Here, we propose a standard nomenclature for naming the FBPs of Arabidopsis thaliana uniformly and carry out a systematic analysis of sperm cell-specific FBP gene, i.e., 3p.AtFBP113 due to its reported high and preferential expression, for detailed functional annotation. The results revealed that 3p.AtFBP113 is located on the small arm of chromosome and encodes 397 amino acid long soluble, stable, and hydrophilic protein with the possibility of localization in various cellular compartments. The presence of the C-terminal F-box associated domain (FBA) with immunoglobulin-like fold anticipated its role in protein binding. Gene ontology based functional annotation and tissue-specific gene co-expression analysis further strengthened its role in protein binding and ubiquitination. Moreover, various potential post/co-translational modifications were anticipated and the predicted tertiary structure also showed the presence of characteristic domains and fold. Thus, the outcomes of the study will be useful in developing a better understating of the function of 3p.AtFBP113 during the process of pollen development, which will be helpful for targeting the gene for manipulation of male fertility that has immense importance in hybrid breeding.

Timing and ecological priority shaped the diversification of sedges in the Himalayas

BACKGROUND

Diversification patterns in the Himalayas have been important to our understanding of global biodiversity. Despite recent broad-scale studies, the most diverse angiosperm genus of the temperate zone-Carex L. (Cyperaceae), with ca. 2100 species worldwide-has not yet been studied in the Himalayas, which contains 189 Carex species. Here the timing and phylogenetic pattern of lineage and ecological diversification were inferred in this ecologically significant genus. We particularly investigated whether priority, adaptation to ecological conditions, or both explain the highly successful radiation of the Kobresia clade (ca. 60 species, of which around 40 are present in the Himalayas) of Himalayan Carex.

METHODS

Phylogenetic relationships were inferred using maximum likelihood analysis of two nuclear ribosomal DNA (nrDNA) regions (ITS and ETS) and one plastid gene (matK); the resulting tree was time-calibrated using penalized likelihood and a fossil calibration at the root of the tree. Biogeographical reconstruction for estimation of historical events and ancestral ranges was performed using the dispersal-extinction-cladogenesis (DEC) model, and reciprocal effects between biogeography and diversification were inferred using the geographic state speciation and extinction (GeoSSE) model. Climatic envelopes for all species for which mapped specimen data available were estimated using climatic data from WORLDCLIM, and climatic niche evolution was inferred using a combination of Ornstein-Uhlenbeck models of shifting adaptive optima and maximum likelihood inference of ancestral character states under a Brownian motion model.

RESULTS

The Himalayan Carex flora represents three of the five major Carex clades, each represented by multiple origins within the Himalayas. The oldest Carex radiation in the region, dating to ca. 20 Ma, near the time of Himalayan orogeny, gave rise to the now abundant Kobresia clade via long-distance dispersal from the Nearctic. The Himalayan Carex flora comprises a heterogeneous sample of diversifications drawn from throughout the cosmopolitan, but mostly temperate, Carex radiation. Most radiations are relatively recent, but the widespread and diverse Himalayan Kobresia radiation arose at the early Miocene. The timing and predominance of Kobresia in high-elevation Himalayan meadows suggests that Kobresia may have excluded other Carex lineages: the success of Kobresia in the Himalayas, in other words, appears to be a consequence largely of priority, competitive exclusion and historical contingency.

Carbon-dot wrapped ZnO nanoparticle-based photoelectrochemical sensor for selective monitoring of H2O2 released from cancer cells

This study reports on a simple approach for the fabrication of an electrode modified with biocompatible C-dot wrapped ZnO nanoparticles for selective photoelectrochemical monitoring of H₂O₂ released from living cells. The biocompatibility of the ZnO nanoparticles was confirmed through in-vitro cellular testing using the MTT assay on Huh7 cell lines. The ZnO nanoparticles wrapped with dopamine-derived C-dots possess numerous catalytically active sites, excessive surface defects, good electrical conductivity, and efficient separation ability of photo-induced electrons and holes. These properties offer highly sensitive and selective non-enzymatic photo-electrochemical monitoring of H₂O₂ released from HeLa cells after stimulation with N-formylmethionyl-leucyl-phenylalanine. The sensor has a wide linear range (20-800 nM), low detection limit (2.4 nM), and reliable reproducibility, this implying its suitability for biological and biomedical applications. Graphical abstract Schematic of the fabrication of ZnO nanoparticles by using a plant extract as a reducing agent. Wrapping of ZnO with C-dots enhances the photoelectrocatalytic efficacy. Sensitive and selective photoelectrochemical monitoring of H₂O₂ released from cancer cells is demonstrated.

Biological and phytochemical studies on Capparis decidua (Forssk) Edgew from Cholistan desert

The present work deals with the biological and phytochemical studies on Capparis decidua (Forssk) Edgew from Cholistan desert of Pakistan. Aerial and floral parts of C. decidua were collected and dried under shade. Powdered materials of each part of C. decidua were extracted with methanol separately, followed by phytochemical studies. Hexane fraction of aerial parts of the C. decidua obtained after solvent-solvent extraction was purified through repeated column chromatography by increasing order of polarity. Four compounds were purified and identified as simiarenol (1), lupeol (2), taraxerol (3) and β-sitosterol (4). Simiarenol and lupeol were isolated for the first time from genus Capparis. The structures of these compounds were established by comparing the spectroscopic data (¹H NMR, ¹³C NMR, IR, UV & Mass spectrometry) reported in literature. The structure of 1 was further confirmed by XRD analysis. Anti-bacterial activities of crude methanolic extracts were determined against 13 bacterial strains (MIC 250-1000 μg/mL). α-Glucosidase and urease inhibitory activities of pure compounds were also determined. Compounds 1, 2 and 4 showed α-glucosidase inhibition with IC₅₀ at 96.12 ± 0.12, 65.28 ± 0.13 and 128.14 ± 0.17 μM, respectively.

5-HT1A Receptor Function Makes Wound Healing a Happier Process

Skin wound healing is a multistage phenomenon that is regulated by cell–cell interplay and various factors. Endogenous serotonin is an important neurotransmitter and cytokine. Its interaction with the serotonin 1A receptor (5-HTR1A) delivers downstream cellular effects. The role of serotonin (5-hydroxytryptamine, 5-HT) and the 5-HT1A receptor has been established in the regeneration of tissues such as the liver and spinal motor neurons, prompting the investigation of the role of 5-HT1A receptor in skin healing. This study assessed the role of 5-HT1A receptor in excisional wound healing by employing an excisional punch biopsy model on 5-Ht1a receptor knockout mice. Post-harvest analysis revealed 5-Ht1a receptor knockout mice showed impaired skin healing, accompanied by a greater number of F4/80 macrophages, which prolongs the inflammatory phase of wound healing. To further unravel this phenomenon, we employed the 5-HT1A receptor agonist [(R)-(+)-8-Hydroxy-DPAT hydrobromide] as a topical cream treatment in an excisional punch biopsy model. The 5-HT1A receptor agonist treated group showed a smaller wound area, scar size, and improved neovascularization, which contributed to improve healing outcomes as compared to the control. Collectively, these findings revealed that serotonin and 5-HT1A receptor play an important role during the healing process. These findings may open new lines of investigation for the potential treatment alternatives to improve skin healing with minimal scarring.

The Role of Serotonin during Skin Healing in Post-Thermal Injury

Post-burn trauma significantly raises tissue serotonin concentration at the initial stages of injury, which leads us to investigate its possible role in post burn wound healing. Therefore, we planned this study to examine the role of serotonin in wound healing through in vitro and in vivo models of burn injuries. Results from in vitro analysis revealed that serotonin decreased apoptosis and increased cell survival significantly in human fibroblasts and neonatal keratinocytes. Cellular proliferation also increased significantly in both cell types. Moreover, serotonin stimulation significantly accelerated the cell migration, resulting in narrowing of the scratch zone in human neonatal keratinocytes and fibroblasts cultures. Whereas, fluoxetine (a selective serotonin reuptake inhibitor) and ketanserin (serotonin receptor 2A inhibitor) reversed these effects. Scald burn mice model (20% total body surface area) showed that endogenous serotonin improved wound healing process in control group, whereas fluoxetine and ketanserin treatments (disruptors of endogenous serotonin stimulation), resulted in poor reepithelization, bigger wound size and high alpha smooth muscle actin (α-SMA) count. All of these signs refer a prolonged differentiation state, which ultimately exhibits poor wound healing outcomes. Collectively, data showed that the endogenous serotonin pathway contributes to regulating the skin wound healing process. Hence, the results of this study signify the importance of serotonin as a potential therapeutic candidate for enhancing skin healing in burn patients.

Application of the Triazolization Reaction to Afford Dihydroartemisinin Derivatives with Anti-HIV Activity

Artemisinin and synthetic derivatives of dihydroartemisinin are known to possess various biological activities. Post-functionalization of dihydroartemisinin with triazole heterocycles has been proven to lead to enhanced therapeutic potential. By using our newly developed triazolization strategy, a library of unexplored fused and 1,5-disubstituted 1,2,3-triazole derivatives of dihydroartemisinin were synthesized in a single step. All these newly synthesized compounds were characterized and evaluated for their anti-HIV (Human Immunodeficiency Virus) potential in MT-4 cells. Interestingly; three of the synthesized triazole derivatives of dihydroartemisinin showed activities with half maximal inhibitory concentration (IC₅₀) values ranging from 1.34 to 2.65 µM.

Identification of IgE- binding pollen protein from Cannabis sativa in pollen-hypersensitive patients from north Pakistan

Cannabis sativa (C.sativa) is well-known for its medicinal, industrial and recreational use. However, allergies in relation to Cannabis sativa (C.sativa) are rarely reported. C. sativa is one of the common weeds found in Pakistan and its pollen grains are common in spring and fall season. Although categorized as an aeroallergen, there are limited number of reports regarding allergenic potential in C. sativa. Therefore, the current study is aimed at exploring the IgE- binding potential among the C. sativa pollen in local pollen allergic patients. Initial screening of C. sativa sensitized individuals was carried out by dot blot from the sera of pollen allergic patients. Proteins from the pollen grains were extracted and resolved on 10% gel. Eight bands were visible on gel however only one protein fragment i.e. of 14KDa size was found to bind to IgE as analyzed through protein gel blot analysis. Strong IgE affinity of a 14 kDa protein fragment from C. sativa pollen extract suggests its allergenic potential. Further study is required to find the exact nature of this protein fragment.

Pharmacologically active flavonoids from the anticancer, antioxidant and antimicrobial extracts of Cassia angustifolia Vahl

BACKGROUND

Cassia angustifolia Vahl. (commonly known as senna makkai or cassia senna), native to Saudi Arabia, Egypt, Yemen and also extensively cultivated in Pakistan, is a medicinal herb used traditionally to cure number of diseases like liver diseases, constipation, typhoid, cholera etc. This study was conducted to evaluate the in-vitro antimicrobial, antioxidant and anticancer assays and phytochemical constituents of aqueous and organic extracts of C. angustifolia leaves.

METHODS

The antimicrobial activities of C. angustifolia aqueous and organic (methanol, ethanol, acetone, ethyl acetate) extracts were investigated by the disk diffusion method. These extracts were further evaluated for antioxidant potential by the DPPH radical scavenging assay. Anticancer activities of the extracts were determined by the MTT colorimetric assay. The total phenolic and flavonoid contents of C. angustifolia extracts were evaluated by the Folin-Ciocalteu method and aluminum chloride colorimetric assay, respectively. The structures of the bioactive compounds were elucidated by NMR and ESI-MS spectrometry.

RESULTS

Bioactivity-guided screening of C. angustifolia extracts, led to the isolation and identification of three flavonoids quercimeritrin (1), scutellarein (2), and rutin (3) reported for the first time from this plant, showed significant anticancer activity against MCF-7 (IC_50, 4.0 μg/μL), HeLa (IC_50, 5.45 μg/μL), Hep2 (IC_50, 7.28 μg/μL) and low cytotoxicity against HCEC (IC_50, 21.09 μg/μL). Significant antioxidant activity was observed with IC₅₀ 2.41 μg/mL against DPPH radical. Moreover, C. angustifolia extracts have the potential to inhibit microbial growth of E. cloacae, P. aeruginosa, S. mercescens and S. typhi.

CONCLUSION

C. angustifolia extracts revealed the presence of quercimeritrin (1), scutellarein (2), and rutin (3), all known to have useful bioactivities including antimicrobial, antioxidant and anticancer activities.

The Phylogeographic and Spatiotemporal Spread of HCV in Pakistani Population

Hepatitis C Virus (HCV) is the most prevalent human pathogen in Pakistan and is the major cause of liver cirrhosis and hepatocellular carcinoma in infected patients. It has shifted from being hypo-endemic to being hyper-endemic. There was no information about the origin and evolution of the local variants. Here we use newly developed phyloinformatic methods of sequence analysis to conduct the first comprehensive investigation of the evolutionary and biogeographic history in unprecedented detail and breadth. Considering evolutionary rate and molecular-clock hypothesis in context, we reconstructed the spatiotemporal spread of HCV in the whole territory of its circulation using a combination of Bayesian MCMC methods utilizing all sequences available in GenBank. Comparative analysis were performed and were addressed. Whole genome and individual gene analysis have shown that sub-types 1a, 1b and 3a are recognized as epidemic strains and are distributed globally. Here we confirm that the origin of HCV 3a genotypes is in South Asia and HCV has evolved in the region to become stably adapted to the host environment.

A comparative ethno-botanical study of Cholistan (an arid area) and Pothwar (a semi-arid area) of Pakistan for traditional medicines

BACKGROUND

The present study is intended to compare and document the therapeutic flora, their remedial use, and the traditional knowledge used frequently by the residents of the Cholistan desert and Pothwar (Potohar) Plateau of Punjab, Pakistan. The old endemic remedies of these areas are diminishing due to lack of qualitative and quantitative research.

METHODS

The data was generated by unstructured-interviews, informal meetings, open-ended conversations and group discussions with local people and traditional health healers of the study area. Reported literature was also utilized.

RESULTS

The study recorded a list of various medicinal plants used as traditional medicines by local people. Total 86 numbers of plant species belonging to 38 families and 67 plant species belonging to 29 families have been reported in the Pothwar and Cholistan respectively. Only 10.5% of similar plant species were present in the studied areas.

CONCLUSION

The investigation revealed that the local people of study areas inherit a rich traditional knowledge but there is great danger of losing this wealth of knowledge in the near future. Documentation of the knowledge exclusively from desert area of Cholistan, Pakistan is unique information in its nature. The study presents the undocumented knowledge worth recognition that will not only help in conservation of medicinal plant species but will highlight the pharmacological capacity for improved human healthcare regarding many common ailments.