Effect of plant extracts and citric acid on phytoremediation of metal-contaminated soil.

Application of activating agents can significantly improve efficiency of plants for remediation of soils contaminated by heavy metals, however, damage to soil and plants limits application of traditional activating agents. The aim of our experiments is to select an efficient,green and low-cost activating agent to improve efficiency of plant extraction technology. In this study, contaminated soil was remediated by Sedum alfredii. The effects of two plant extracts (i.e., Oxalis corniculata,OX and Medicago sativaextract, ME) in addition to citric acid (CA) were studied in oscillatory activation experiment and pot experiment. The oscillation activation experiment revealed that extraction quantity of heavy metals in the soil was enhanced significantly with concentration of plant extract. The extraction quantity of Zn from 100% OX extract and ME extract were significantly higher than 10 mmol/L CA (54.04% and 33.09%, respectively). The 10 mmol/L CA has best extraction efficiency for Cd, up to 41.36 µg/kg, which is significantly higher than CK (control) (p < 0.05). The pot experiment exhibited that application of CA has significantly reduced soil pH and organic matter content by 8.63% and 28.21%, respectively, however the two extracts have no significant effect on soil properties. The study indicated that application of CA has negative effects on root morphological parameters and chlorophyll fluorescence parameters of Sedum alfredii.The addition of extracts of two plants have not caused any harm to Sedum alfredii. The application of three activating agents was beneficial for purification of Cd and Zn in soils, and its repairing efficiency was improved by 3.92, 3.37, 3.33 times and 0.44, 0.20, 0.86 times, respectively. The combination of plant extracts and hyperaccumulators can effectively remove heavy metals from contaminated soils, which provided a theoretical basis for mitigation of pollution in soils.

Bioavailability and Speciation of Heavy Metals in Polluted Soil as Alleviated by Different Types of Biochars.

Biochar is an important material for remediation of contaminated soils, however, different biochars have variable effects on bioavailability of heavy metals. This experiment revealed that peanut shell biochar (PSB) has highest reduction of 78% concentration of Pb in plant roots. The maize straw biochar (MSB) has significantly decreased Zn and Cd concentration (mg/kg dry weight) in Chinese cabbage than other treatments of biochars. The plants of Chinese cabbage have exhibited an efficient transport capability for Zn and Cd. The biochars have reduced exchangeable form of Cd/Zn, enhanced residual heavy metals, and consequently diminished accumulation of heavy metals in plants. The straw block biochar (SBB), PSB and MSB have efficiently relieved the stresses of heavy metals in plants.

Whole exome sequencing identified two novel homozygous missense variants in the same codon of CLCN7 underlying autosomal recessive infantile malignant osteopetrosis in a Pakistani family.

Autosomal recessive osteopetrosis is a severe fatal disorder with an average incidence of around 1:250,000. It is diagnosed soon after birth or within the 1st year of life with severe symptoms of abnormal bone remodelling. This study was aimed to identify the underlying genetic cause of the disease in a Pakistani family segregating infantile malignant osteopetrosis in autosomal recessive pattern. Whole exome sequencing of the proband was performed using the 51 Mb SureSelect V4 library kit and sequenced using the Illumina HiSeq2500 sequencing system. The reads were analysed using standard bioinformatic data analysis pipeline. The genotype of candidate variants was confirmed in the proband and his normal parents by Sanger sequencing. Two novel homozygous missense variants were found in the same codon 204 of CLCN7 NM_001287.5:c.[610A>T;612C>G] predicting p.(Ser204Trp) variant in the protein. Sanger sequencing and RFLP assay verified that both these variants were heterozygous in the unaffected parents. Moreover, these variants were not detected in the unrelated healthy Pakistani subjects (200 chromosomes), ExAC, dbSNP, or the 1000 Genomes Project data. Multiple bioinformatics tools unanimously predicted the p.(Ser204Trp) variant as deleterious. CLCN7 mutation p.(Ser204Trp) is the likely cause of the osteopetrosis disease in the Pakistani family. This study expands the restricted spectrum of CLCN7 mutations associated with infantile malignant osteopetrosis and indicates clinical significance of whole exome sequencing in the diagnosis of clinically and genetically heterogenous osteopetrosis phenotype. These data should be helpful in the improved genetic counselling, carrier identification and prenatal diagnosis of the affected family.

Identification of two novel variants in GNPTAB underlying mucolipidosis II in a Pakistani family.

Background Mucolipidosis II is a rare inherited metabolic disorder characterized by multiple pathologies including coarse facial features, thickened skin, dysostosis multiplex, and skeletal abnormalities. The disorder results due to variants in GNPTAB leading to reduced activity of the enzyme GlcNAc-1-phosphotransferase (GlcNAc-PT). Methods In the present study, a consanguineous Pakistani family was diagnosed with MLII based on clinical and biochemical examination. Peripheral blood samples were collected and subjected to DNA sequencing of all coding exons along with exon-intron boundaries of GNPTAB. Results Molecular investigation of the family identified two novel variants c.25C > T: p.Gln9* (maternal allele) in exon 1 and c.1160C > T: p.Ala387Val (paternal allele) in exon 10 segregating in compound heterozygous form in the affected individuals. Conclusions The GNPTAB variant c.25C > T variant is highly plausible to undergo nonsense-mediated mRNA decay, while the GNPTAB variant c.1160C > T is located in a highly conserved domain, thus both the variants predict to lead to affect the enzyme activity. Two novel variants have been identified in GNPTAB as the underlying cause of ML-II in a Pakistani family. The study thus expands the available GNPTAB mutation spectrum.

Nickel toxicity in plants: reasons, toxic effects, tolerance mechanisms, and remediation possibilities-a review.

Nickel (Ni) is a naturally occurring metal, but anthropogenic activities such as industrialization, use of fertilizers, chemicals, and sewage sludge have increased its concentration in the environment up to undesirable levels. Ni is considered to be essential for plant growth at low concentration; however, Ni pollution is increasing in the environment, and therefore, it is important to understand its functional roles and toxic effects on plants. This review emphasizes the environmental sources of Ni, its essentiality, effects, tolerance mechanisms, possible remediation approaches, and research direction that may help in interdisciplinary studies to assess the significance of Ni toxicity. Briefly, Ni affects plant growth both positively and negatively, depending on the concentration present in the growth medium. On the positive side, Ni is essential for normal growth, enzymatic activities (e.g., urease), nitrogen metabolism, iron uptake, and specific metabolic reactions. On the negative side, Ni reduces seed germination, root and shoot growth, biomass accumulation, and final production. Moreover, Ni toxicity also causes chlorosis and necrosis and inhibits various physiological processes (photosynthesis, transpiration) and cause oxidative damage in plants. The threat associated with Ni is increased as Ni concentration increases day by day in the environment, particularly in soils; therefore, it would be hazardous for crop production in the near future. Additionally, the lack of information regarding the mechanisms of Ni tolerance in plants further intensifies this situation. Therefore, future research should be focused on approachable and prominent solutions in order to minimize the entry of Ni into our ecosystems.

Genetic Testing of a Large Consanguineous Pakistani Family Affected with Mucolipidosis III Gamma Through Next-Generation Sequencing.

BACKGROUND: Mucolipidosis III gamma (MLIIIγ) is a rare autosomal recessive disorder characterized by radiographic evidence of mild-to-moderate dysostosis multiplex, progressive joint stiffness and pain, scoliosis, and normal to mildly impaired cognitive development. Cardiac valve involvement and respiratory complications can be significant. MLIIIγ is caused by mutations in the GNPTG, which encodes the γ subunit of the enzyme N-acetylglucosamine-1-phosphotransferase. OBJECTIVE: Clinical and genetic study of seven individuals of a consanguineous Pakistani family affected with mucolipidosis phenotype who never pursued medical care. METHODS: Genome-wide homozygosity mapping was performed using Affymetrix Human SNP Array 6.0 followed by whole exome and Sanger sequencing. RESULTS: The affected individuals showed characteristic clinical features of MLIIIγ. Whole-genome single nucleotide polymorphism genotyping identified a region of homozygosity shared by affected individuals of the family on chromosome 16p13.3. Whole exome sequencing identified a novel 4-bp deletion in the GNPTG segregating in the family in agreement with autosomal recessive pattern. CONCLUSIONS: We identified a novel mutation in the GNPTG gene as the underlying cause of MLIIIγ in a Pakistani family. This study supports the role of next-generation sequencing technologies for the molecular diagnosis of rare inherited disorders.

Deletion mutation in BSCL2 gene underlies congenital generalized lipodystrophy in a Pakistani family.

BACKGROUND: Congenital generalized lipodystrophy (CGL) also known as Berardinelli-Seip Congenital Lipodystrophy (BSCL) is a genetically heterogeneous disorder characterized by loss of adipose tissues, Acanthosis nigricans, diabetes mellitus, muscular hypertrophy, hepatomegaly and hypertriglyceridemia. There are four subclinical phenotypes of CGL (CGL1-4) and mutations in four genes AGPAT2, BSCL2, CAV1 and PTRF have been assigned to each type. METHODS: The study included clinical and molecular investigations of CGL disease in a consanguineous Pakistani family. For mutation screening all the coding exons including splice junctions of AGPAT2, BSCL2, CAV1 and PTRF genes were PCR amplified and sequenced directly using an automated DNA sequencer ABI3730. RESULTS: Sequence analysis revealed a single base pair deletion mutation (c.636delC; p.Tyr213ThrfsX20) in exon 5 of BSCL2 gene causing a frame shift and premature termination codon. CONCLUSION: Mutation identified here in BSCL2 gene causing congenital generalized lipodystrophy is the first report in Pakistani population. The patients exhibited characteristic features of generalized lipodystrophy, Acanthosis nigricans, diabetes mellitus and hypertrophic cardiomyopathy. VIRTUAL SLIDES: The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1913913076864247.