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Fulltext l-2-Haloacid dehalogenase (DehL) from Rhizobium sp. RC1

Adamu A, Wahab RA, Huyop F

Springerplus, 2016;5(1):695.
PMID: 27347470 DOI: 10.1186/s40064-016-2328-9

l-2-Haloacid dehalogenase (DehL) from Rhizobium sp. RC1 is a stereospecific enzyme that acts exclusively on l-isomers of 2-chloropropionate and dichloroacetate. The amino acid sequence of this enzyme is substantially different from those of other l-specific dehalogenases produced by other organisms. DehL has not been crystallised, and hence its three-dimensional structure is unavailable. Herein, we review what is known concerning DehL and tentatively identify the amino acid residues important for catalysis based on a comparative structural and sequence analysis with well-characterised l-specific dehalogenases.
Effects of EBN on embryo implantation, plasma concentrations of reproductive hormones, and uterine expressions of genes of PCNA, steroids, growth factors and their receptors in rats

Albishtue AA, Yimer N, Zakaria MZA, Haron AW, Babji AS, Abubakar AA, et al.

Theriogenology, 2019 Mar 01;126:310-319.
PMID: 30605790 DOI: 10.1016/j.theriogenology.2018.12.026

This study was conducted to determine the effect of edible bird's nest (EBN) supplement on uterine function and embryo-implantation rate. A total of 24 adult female rats, divided equally into four groups, were treated with different doses of EBN for 8 weeks. In the last week of treatment, intact fertile male rats were introduced into each group (three per group) for overnight for mating. On day 7 post-mating (post-implantation), blood samples were collected from the hearts of anaesthetised rats that were later sacrificed. The uteri were removed for assessment of embryo implantation rate, histological and electron microscopic examination, and immunohistochemical analyses. Results showed that as the concentration of EBN supplemented increased, the pregnancy and embryo implantation rates were also increased in the treated groups; significantly at G3 and G4. Although histological evaluation did not show much difference among the groups, scanning electron microscopic examination showed enhanced development of elongated microvilli and pinopods in G4. Results also revealed up-regulated expressions of epidermal growth factor (EGF), EGF receptor (EGFR), vascular endothelial growth factor (VEGF), proliferating cell nulear antigen (PCNA), and progesterone and estrogen receptors (P4R, E2R) in the uteri of treated groups. Moreover, plasma E2, P4, growth hormone (GH) and prolactin (P) levels were higher (p 
Multi-template homology-based structural model of L-2-haloacid dehalogenase (DehL) from Rhizobium sp. RC1

Adamu A, Shamsir MS, Wahab RA, Parvizpour S, Huyop F

J Biomol Struct Dyn, 2017 Nov;35(15):3285-3296.
PMID: 27800712 DOI: 10.1080/07391102.2016.1254115

Dehalogenases are of high interest due to their potential applications in bioremediation and in synthesis of various industrial products. DehL is an L-2-haloacid dehalogenase (EC 3.8.1.2) that catalyses the cleavage of halide ion from L-2-halocarboxylic acid to produce D-2-hydroxycarboxylic acid. Although DehL utilises the same substrates as the other L-2-haloacid dehalogenases, its deduced amino acid sequence is substantially different (<25%) from those of the rest L-2-haloacid dehalogenases. To date, the 3D structure of DehL is not available. This limits the detailed understanding of the enzyme's reaction mechanism. The present work predicted the first homology-based model of DehL and defined its active site. The monomeric unit of the DehL constitutes α/β structure that is organised into two distinct structural domains: main and subdomains. Despite the sequence disparity between the DehL and other L-2-haloacid dehalogenases, its structural model share similar fold as the experimentally solved L-DEX and DehlB structures. The findings of the present work will play a crucial role in elucidating the molecular details of the DehL functional mechanism.
Deciphering the catalytic amino acid residues of l-2-haloacid dehalogenase (DehL) from Rhizobium sp. RC1: An in silico analysis

Adamu A, Wahab RA, Shamsir MS, Aliyu F, Huyop F

Comput Biol Chem, 2017 Oct;70:125-132.
PMID: 28873365 DOI: 10.1016/j.compbiolchem.2017.08.007

The l-2-haloacid dehalogenases (EC 3.8.1.2) specifically cleave carbon-halogen bonds in the L-isomers of halogenated organic acids. These enzymes have potential applications for the bioremediation and synthesis of various industrial products. One such enzyme is DehL, the l-2-haloacid dehalogenase from Rhizobium sp. RC1, which converts the L-isomers of 2-halocarboxylic acids into the corresponding D-hydroxycarboxylic acids. However, its catalytic mechanism has not been delineated, and to enhance its efficiency and utility for environmental and industrial applications, knowledge of its catalytic mechanism, which includes identification of its catalytic residues, is required. Using ab initio fragment molecular orbital calculations, molecular mechanics Poisson-Boltzmann surface area calculations, and classical molecular dynamic simulation of a three-dimensional model of DehL-l-2-chloropropionic acid complex, we predicted the catalytic residues of DehL and propose its catalytic mechanism. We found that when Asp13, Thr17, Met48, Arg51, and His184 were individually replaced with an alanine in silico, a significant decrease in the free energy of binding for the DehL-l-2-chloropropionic acid model complex was seen, indicating the involvement of these residues in catalysis and/or structural integrity of the active site. Furthermore, strong inter-fragment interaction energies calculated for Asp13 and L-2-chloropropionic acid, and for a water molecule and His184, and maintenance of the distances between atoms in the aforementioned pairs during the molecular dynamics run suggest that Asp13 acts as the nucleophile and His184 activates the water involved in DehL catalysis. The results of this study should be important for the rational design of a DehL mutant with improved catalytic efficiency.
Genome-scale metabolic models as platforms for identification of novel genes as antimicrobial drug targets

Mienda BS, Salihu R, Adamu A, Idris S

Future Microbiol, 2018 03;13:455-467.
PMID: 29469596 DOI: 10.2217/fmb-2017-0195

The growing number of multidrug-resistant pathogenic bacteria is becoming a world leading challenge for the scientific community and for public health. However, advances in high-throughput technologies and whole-genome sequencing of bacterial pathogens make the construction of bacterial genome-scale metabolic models (GEMs) increasingly realistic. The use of GEMs as an alternative platforms will expedite identification of novel unconditionally essential genes and enzymes of target organisms with existing and forthcoming GEMs. This approach will follow the existing protocol for construction of high-quality GEMs, which could ultimately reduce the time, cost and labor-intensive processes involved in identification of novel antimicrobial drug targets in drug discovery pipelines. We discuss the current impact of existing GEMs of selected multidrug-resistant pathogenic bacteria for identification of novel antimicrobial drug targets and the challenges of closing the gap between genome-scale metabolic modeling and conventional experimental trial-and-error approaches in drug discovery pipelines.
Fulltext The role of edible bird's nest and mechanism of averting lead acetate toxicity effect on rat uterus

Albishtue AA, Yimer N, Zakaria MZA, Haron AW, Babji AS, Abubakar AA, et al.

Vet World, 2019 Jul;12(7):1013-1021.
PMID: 31528026 DOI: 10.14202/vetworld.2019.1013-1021

Aim: This study aimed to evaluate the protective effect of edible bird's nest (EBN) supplement on the uteri of rats exposed to lead acetate (LA) toxicity.
Materials and Methods: Five treatment groups were established as follows: Group 1 (C), which was given distilled water; Group 2 (T0), which was administered with LA (10 mg/kg body weight [BW]); and Groups 3 (T1), 4 (T2), and 5 (T3), which were given LA (10 mg/kg BW) plus graded concentrations of 30, 60, and 120 mg/kg BW of EBN, respectively. Rats were euthanized at week 5 to collect blood for superoxide dismutase (SOD) assay, and uterus for histomorphological study and expression analyses of epidermal growth factor (EGF), vascular endothelial growth factor (VEGF), and proliferating cell nuclear antigen (PCNA).
Results: Results revealed that LA causes destruction of uterine lining cells and necrosis of uterine glands of exposed rats without EBN supplement while the degree of damage decreased among EBN treated groups; T3 showed the highest ameliorating effect against LA toxicity, as well as an increased number of uterine glands. Increased levels of SOD were also achieved in EBN supplemented groups than the controls. Results of immunohistochemistry showed significantly higher expressions of EGF, VEGF, and PCNA levels (p<0.05) in T3 compared to other treatments. EBN maintained upregulation of antioxidant - reactive oxygen species balance.
Conclusion: The findings showed that EBN could ameliorate the detrimental effects of LA toxicity on the uterus possibly by enhancing enzymatic antioxidant (SOD) activity as well as expressions of EGF, VEGF, and PCNA with cell proliferation roles.
Theoretical analyses on enantiospecificity of L-2-haloacid dehalogenase (DehL) from Rhizobium sp. RC1 towards 2-chloropropionic acid

Adamu A, Abdul Wahab R, Aliyu F, Abdul Razak FI, Mienda BS, Shamsir MS, et al.

J Mol Graph Model, 2019 11;92:131-139.
PMID: 31352207 DOI: 10.1016/j.jmgm.2019.07.012

Dehalogenases continue to garner interest of the scientific community due to their potential applications in bioremediation of halogen-contaminated environment and in synthesis of various industrially relevant products. Example of such enzymes is DehL, an L-2-haloacid dehalogenase (EC 3.8.1.2) from Rhizobium sp. RC1 that catalyses the specific cleavage of halide ion from L-2-halocarboxylic acids to produce the corresponding D-2-hydroxycarboxylic acids. Recently, the catalytic residues of DehL have been identified and its catalytic mechanism has been fully elucidated. However, the enantiospecificity determinants of the enzyme remain unclear. This information alongside a well-defined catalytic mechanism are required for rational engineering of DehL for substrate enantiospecificity. Therefore, using quantum mechanics/molecular mechanics and molecular mechanics Poisson-Boltzmann surface area calculations, the current study theoretically investigated the molecular basis of DehL enantiospecificity. The study found that R51L mutation cancelled out the dehalogenation activity of DehL towards it natural substrate, L-2-chloropropionate. The M48R mutation, however introduced a new activity towards D-2-chloropropionate, conveying the possibility of inverting the enantiospecificity of DehL from L-to d-enantiomer with a minimum of two simultaneous mutations. The findings presented here will play important role in the rational design of DehL dehalogenase for improving substrate utility.
Fulltext Pre-grafting histological studies of skin grafts cryopreserved in α helix antarctic yeast oriented antifreeze peptide (Afp1m)

Khan MS, Ibrahim SM, Adamu AA, Rahman MBA, Bakar MZA, Noordin MM, et al.

Cryobiology, 2020 02 01;92:26-33.
PMID: 31580830 DOI: 10.1016/j.cryobiol.2019.09.012

A number of living creatures in the Antarctic region have developed characteristic adaptation of cold weather by producing antifreeze proteins (AFP). Antifreeze peptide (Afp1m) fragment have been designed in the sequence of strings from native proteins. The objectives of this study were to assess the properties of Afp1m to cryopreserve skin graft at the temperature of -10 °C and -20 °C and to assess sub-zero injuries in Afp1m cryopreserved skin graft using light microscopic techniques. In the present study, a process was developed to cryopreserve Sprague-Dawley (SD) rat skin grafts with antifreeze peptide, Afp1m, α-helix peptide fragment derived from Glaciozyma antractica yeast. Its viability assessed by different microscopic techniques. This study also described the damages caused by subzero temperatures (-10 and -20 °C) on tissue cryopreserved in different concentrations of Afp1m (0.5, 1, 2, 5 and 10 mg/mL) for 72 h. Histological scores of epidermis, dermis and hypodermis of cryopreserved skin grafts showed highly significant difference (p 
Fulltext Histological and mechanical evaluation of antifreeze peptide (Afp1m) cryopreserved skin grafts post transplantation in a rat model

Ibrahim SM, Kareem OH, Saffanah KM, Adamu AA, Khan MS, Rahman MBA, et al.

Cryobiology, 2018 06;82:27-36.
PMID: 29679551 DOI: 10.1016/j.cryobiol.2018.04.012

The objective of this study was to evaluate the use of Afp1m as a cryopreservative agent for skin by examining the transplanted skin histological architecture and mechanical properties following subzero cryopreservation. Thirty four (34) rats with an average weight of 208 ± 31 g (mean ± SD), were used. Twenty four (n = 24) rats were equally divided into four groups: (i) immediate non-cryopreserved skin autografts (onto same site), (ii) immediate non-cryopreserved skin autografts (onto different sites), (iii) skin autografts cryopreserved with glycerol for 72 h and (iv) skin autografts cryopreserved with Afp1m for 72 h at -4 °C. Rounded shaped full-thickness 1.5-2.5 cm in diameter skin was excised from backs of rats for the autograft transplantation. Non-cryopreserved or cryopreserved auto skin graft were positioned onto the wound defects and stitched. Non-transplanted cryopreserved and non-cryopreserved skin strips from other ten rats (n = 10) were allowed for comparative biomechanical test. All skin grafts were subjected to histological and mechanical examinations at the end of day 21. Histological results revealed that tissue architecture especially the epidermal integrity and dermal-epidermal junction of the Afp1m cryopreserved skin grafts exhibited better histological appearance, good preservation of tissue architecture and structural integrity than glycerolized skin. However, there was no significant difference among these groups in other histological criteria. There were no significant differences among the 4 groups in skin graft mechanical properties namely maximum load. In conclusion, Afp1m were found to be able to preserve the microstructure as well as the viability and function of the skin destined for skin transplantation when was kept at -4 °C for 72 h.
Fulltext Ginger Essential Oils-Loaded Nanoemulsions: Potential Strategy to Manage Bacterial Leaf Blight Disease and Enhanced Rice Yield

Adamu A, Ahmad K, Siddiqui Y, Ismail IS, Asib N, Bashir Kutawa A, et al.

Molecules, 2021 Jun 25;26(13).
PMID: 34202405 DOI: 10.3390/molecules26133902

The bacterial leaf blight (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious rice diseases, causing huge yield losses worldwide. Several technologies and approaches have been opted to reduce the damage; however, these have had limited success. Recently, scientists have been focusing their efforts on developing efficient and environmentally friendly nanobactericides for controlling bacterial diseases in rice fields. In the present study, a scanning electron microscope (SEM), transmission electron microscope (TEM), and a confocal laser scanning microscope (CLSM) were utilized to investigate the mode of actions of ginger EOs on the cell structure of Xoo. The ginger EOs caused the cells to grow abnormally, resulting in an irregular form with hollow layers, whereas the dimethylsulfoxide (DMSO) treatment showed a typical rod shape for the Xoo cell. Ginger EOs restricted the growth and production of biofilms by reducing the number of biofilms generated as indicated by CLSM. Due to the instability, poor solubility, and durability of ginger EOs, a nanoemulsions approach was used, and a glasshouse trial was performed to assess their efficacy on BLB disease control. The in vitro antibacterial activity of the developed nanobactericides was promising at different concentration (50-125 µL/mL) tested. The efficacy was concentration-dependent. There was significant antibacterial activity recorded at higher concentrations. A glasshouse trial revealed that developed nanobactericides managed to suppress BLB disease severity effectively. Treatment at a concentration of 125 μL/mL was the best based on the suppression of disease severity index, AUDPC value, disease reduction (DR), and protection index (PI). Furthermore, findings on plant growth, physiological features, and yield parameters were significantly enhanced compared to the positive control treatment. In conclusion, the results indicated that ginger essential oils loaded-nanoemulsions are a promising alternative to synthetic antibiotics in suppressing Xoo growth, regulating the BLB disease, and enhancing rice yield under a glasshouse trial.
Fulltext Trends in Nanotechnology and Its Potentialities to Control Plant Pathogenic Fungi: A Review

Kutawa AB, Ahmad K, Ali A, Hussein MZ, Abdul Wahab MA, Adamu A, et al.

Biology (Basel), 2021 Sep 08;10(9).
PMID: 34571758 DOI: 10.3390/biology10090881

Approximately 15-18% of crops losses occur as a result of animal pests, while weeds and microbial diseases cause 34 and 16% losses, respectively. Fungal pathogens cause about 70-80% losses in yield. The present strategies for plant disease control depend transcendently on agrochemicals that cause negative effects on the environment and humans. Nanotechnology can help by reducing the negative impact of the fungicides, such as enhancing the solubility of low water-soluble fungicides, increasing the shelf-life, and reducing toxicity, in a sustainable and eco-friendly manner. Despite many advantages of the utilization of nanoparticles, very few nanoparticle-based products have so far been produced in commercial quantities for agricultural purposes. The shortage of commercial uses may be associated with many factors, for example, a lack of pest crop host systems usage and the insufficient number of field trials. In some areas, nanotechnology has been advanced, and the best way to be in touch with the advances in nanotechnology in agriculture is to understand the major aspect of the research and to address the scientific gaps in order to facilitate the development which can provide a rationale of different nanoproducts in commercial quantity. In this review, we, therefore, described the properties and synthesis of nanoparticles, their utilization for plant pathogenic fungal disease control (either in the form of (a) nanoparticles alone, that act as a protectant or (b) in the form of a nanocarrier for different fungicides), nano-formulations of agro-nanofungicides, Zataria multiflora, and ginger essential oils to control plant pathogenic fungi, as well as the biosafety and limitations of the nanoparticles applications.
Fulltext Two decades of neuroscience publication trends in Africa

Maina MB, Ahmad U, Ibrahim HA, Hamidu SK, Nasr FE, Salihu AT, et al.

Nat Commun, 2021 Jun 08;12(1):3429.
PMID: 34103514 DOI: 10.1038/s41467-021-23784-8

Neuroscience research in Africa remains sparse. Devising new policies to boost Africa's neuroscience landscape is imperative, but these must be based on accurate data on research outputs which is largely lacking. Such data must reflect the heterogeneity of research environments across the continent's 54 countries. Here, we analyse neuroscience publications affiliated with African institutions between 1996 and 2017. Of 12,326 PubMed indexed publications, 5,219 show clear evidence that the work was performed in Africa and led by African-based researchers - on average ~5 per country and year. From here, we extract information on journals and citations, funding, international coauthorships and techniques used. For reference, we also extract the same metrics from 220 randomly selected publications each from the UK, USA, Australia, Japan and Brazil. Our dataset provides insights into the current state of African neuroscience research in a global context.

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