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Home > Genomic and Proteomic Analysis of Indigenous Bacteria under the Stress of Selected Micropollutants

Genomic and Proteomic Analysis of Indigenous Bacteria under the Stress of Selected Micropollutants

Thesis Info

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Author

Basharat, Zarrin

Program

PhD

Institute

Fatima Jinnah Women University

City

Rawalpindi

Province

Punjab

Country

Pakistan

Thesis Completing Year

2018

Thesis Completion Status

Completed

Subject

Biotechnology

Language

English

Link

http://prr.hec.gov.pk/jspui/bitstream/123456789/10274/1/Zarrin%20Basharat_Biotech_2018_FJWU_PRR.pdf

Added

2021-02-17 19:49:13

Modified

2024-03-24 20:25:49

ARI ID

1676726331032

Similar


Micropollutants are harmful for human health, therefore, this study was undertaken to address the concerns of micropollutant contamination of the environment. Inadequate biological information or molecular understanding of the cellular responses underpinning bacterial bioremediation hampers site-specific mineralization. It is necessary to generate information related to pollutant attenuating microorganisms and biotransforming genes as well as related phenomenon which could impact remediation. This work is an attempt to provide information necessary for a reliable evaluation of the state of the internal cellular environment as well as baseline information for crafting bioremediation strategies. Autocthonous bacteria were screened for their ability to resist pollutants and two bacteria, belonging to phylum Proteobacteria were studied at genome scale. Democratization of genome sequencing has made bacterial genomics a mature and easy approach for researchers from interdisciplinary fields like environment, evolution and scientists working in the biomedical disciplines. Whole genome sequencing of two isolates Alcaligenes faecalis strain MB207 and Serratia nematodiphila MB307 was attempted to provide a genomic foundation for micropollutant attenuation by these organisms. Genome sizes were roughly 4.16 (with 3749 protein coding genes) and 5.16 MB (with 4794 protein coding genes) for Alcaligenes faecalis MB207 and Serratia nematodiphila MB307, respectively. Both isolates yielded numerous gene sequences (such as monooxyenases, dioxygenases, azoreductases, peroxidases, metal resistance, porins etc.) with bioremediation potential. Pathways for biodegradation were searched in the KEGG database and 225 genes in Serratia nematodiphila MB307 while 201 genes in Alcaligenes faecalis MB207 were linked with microbial metabolism in varied environments. Whole genome analysis marked Alcaligenes faecalis strain MB207 and Serratia nematodiphila MB307 as prospective eco-friendly bacteria, provided their nutritional and physiological requirements are met for proper functioning of biotransformation pathways. Occurrence of metal resistance genes with antibiotic and biocide resistance DNA segments depicted a co-selection and common regulatory mechanism of these genes, which needs to be further explored. Availability of the sequence data in public genome repository of NCBI is also useful for future researchers to explore enzymes and apparatus for sustainable environmental clean-up. One isolate, identified as Serratia nematodiphila was found to have remarkable attenuation properties and further exploited for metabolite production and functional genomic/proteomic analysis under pollutant stress. Some novel metabolites were obtained which depict new or xiv evolved pathways in Serratia nematodiphila MB307 for biotransformation. A global view of the proteins was obtained which complemented genomic information. Differential regulation of several proteins was observed in the whole cell as well as in the enriched membrane fraction when subjected to 100 μg/ml pollutant for 24 hours. Numerous ribosomal proteins and chaperones were 2-fold differentially regulated during pollutant stress. This depicted either a change in protein production required to combat stress or utilization of energy for survival at the cost of cell growth/division. Although there were some common proteins differentially regulated under different type of stresses, a common pattern for pollution resistance could not be deciphered, depicting different mechanisms of coping with each class of pollutant (i.e. metals, azo dyes and pharmaceutical). Comparison with other related studies led to several interesting findings and made the study concurrently deeper as well as diffused, warranting more research in this domain. Indigenous bacteria are physiologically and genetically acclimatized to their surroundings and help detoxify the polluted environment in an efficient manner. This study sheds light on molecular mechanism of their catabolic traits as well as proteome rewiring behind their adaptation to stressed surroundings and biotransformation of environmental contaminants. Obtained results pave way for further systematic investigation (such as linking time resolved metabolome with degradation genes/pathways). Evolution of co-resistance and stress signatures of these biotopes after intermittent and prolonged pollutant exposure also needs to be studied.
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امجدؔ حیدرآبادی

امجدؔ حیدرآبادی
افسوس ہے کہ پچھلے دنوں حضرت امجد حیدرآبادی کا۸۳ سال کی عمر میں انتقال ہوگیا۔مرحوم بڑے قادر الکلام اورنغز گوشاعر تھے۔نثراورنظم دونوں میں یدِ طولیٰ رکھتے تھے۔لیکن رباعی گوئی اُن کا خاص فن تھا۔اس میدان میں وہ اپنا کوئی حریف نہیں رکھتے تھے،اس اعتبار سے و ہ درحقیقت اردو زبان کے سرمد تھے۔ چنانچہ مولانا گرامی نے بجاطورپر کہاتھا:
امجد بہ رباعی ست فردا مجد
کلکِ امجد کلیدِ گنجِ سَرمد
گفتم کہ بودجوابِ سرمدؔ امروز
روحِ سَرمد بگفت امجد امجد
 بلند پایہ شاعرادیب اورمصنف ہونے کے علاوہ بڑے صاحب ِدل،صاحبِ معرفت،خوددار،غیور اورپابندِ وضع بزرگ تھے۔زندگی بالکل درویشانہ ا ورقلندانہ تھی۔عسرت وافلاس سے ہمیشہ سابقہ رہا مگراربابِ ثروت ووجاہت کے ساتھ نیازمندی کاتعلق رکھ کراپنے فن اورکمال کی توہین کبھی گوارا نہیں کی۔سیلاب رودِموسی کے واقعہ کے بعد جس میں اُن کے دیکھتے ہی دیکھتے بوڑھی ماں اورجوان بیوی بہہ گئیں اورغرق ہوگئیں تھیں وہ سوزوگداز مجسم اورپیکر عبرت ہوکررہ گئے تھے لیکن کیا مجال کہ تسلیم و رضا کی پیشانی پرکوئی بل بھی پڑا۔مولانا سید مناظر احسن گیلانی اورمرحوم میں بڑے مخلصانہ تعلقات تھے اوردونوں ایک دوسرے کی دل سے قدرومنزلت کرتے تھے۔مرحوم سے راقم الحروف کی پہلی ملاقات ۱۹۴۴ء میں حیدرآباد میں مولانا کے مکان پرہی ہوئی تھی۔یہ ملاقات اگرچہ سرسری تھی، لیکن مرحوم کے حافظہ کاکمال یہ تھا کہ ۱۹۵۸ء میں جب سفرحیدرآباد کے سلسلہ میں موصوف کے مکان پرحاضر ہوا تو اگرچہ ضعیفی اورحافظہ اورمسلسل علالت کی وجہ سے بہت کمزور ہورہے تھے اوربینائی بھی بہت کمزور ہوچکی تھی، مگر باایں ہمہ میری آواز سنتے ہی فوراً زنانخانہ سے مردانہ میں آگئے۔ بڑی شفقت ومحبت سے خاطر تواضع کی، دیر تک باتیں کرتے اوربرہان و ندوۃ المصنفین کی خدمات کاتذکرہ کرتے رہے۔چلنے لگا تواپنی تمام کتابوں کاسیٹ عطافرمایا،میں نے اُن کاہدیہ پیش کیا تومیرے سخت اصرار کے بعد بادل نخواستہ قبول فرمایا۔...

Computer Aided Instruction For Preschoolers In Mathematics

Computers are increasingly a part of pre-schoolers to professional lives. The use of multimedia in education has significantly changed people’s learning processes.  Computer technology holds promise for improving student performance and quality of teaching education program at all levels. Today, development has been rapid and technology has been acknowledged as an additional teaching tool. Results from a number of research studies indicate that appropriately designed multimedia instruction enhances students’ learning performance in mathematics, and literacy. The purpose of the present paper was to discuss research avenues employing computers as a learning tool and to analyse the results obtained by this method at the pre-schoolers learning level.

Synthesis of Some N4-Substituted Isatins-3-Thiosemicarbazones and Their Transition Metal Complexes As Potential Bioactive Agents.

The focus of this thesis is on the synthesis and in vitro biological testing of some target N4- substituted isatin-3-thiosemicarbazones and their transition metal complexes. Thus, three series of N4-benzyl substituted isatin-3-thiosemicarbazones (19-33), (34- 48) and (49-63) were synthesized by condensing isatin, 5-nitroisatin and 5-chloroisatin, respectively, with the appropriate N-substituted thiosemicarbazides. All the synthesized thiosemicarbazones (19-63) were characterized by means of their analytical (CHN) and spectral (IR, 1H-NMR, 13C-NMR, EIMS) data and tested for the selected biological properties i.e. antiurease, phytotoxic, cytotoxic, anticarbonic anhydrase and antiglycation activities. All the synthetic thiosemicarbazones (19-63) proved to be highly potent inhibitors of urease, displaying excellent inhibitory activity (IC50 = 0.87 ± 0.25 − 11.23 ± 0.19 µM) even better than the reference inhibitor, thiourea (IC50 = 22.3 ± 1.06 µM) used in the assay. In phytotoxicity assay, 33 out of 45 thiosemicarbazones tested i.e. (19-22), (25), (26), (28-30), (32), (33), (34-40), (42-44), (46-48), (51), (52), (56-61) and (63) appeared to be active, exhibiting weak or non-significant (5-100%) growth inhibition of Lemna aequinocitalis at 1000 or 500 µg/mL concentrations in comparison to paraquat (the standard herbicide), which showed 100% plant growth inhibition at 0.015 µg/mL concentration. In the brine shrimp (Artemia salina) lethality bioassay, only 4 compounds i.e. (20), (28), (33) and (42) were found to be active, demonstrating cytotoxic activity with LD50 values 3.63 × 10-5, 2.90 × 10-5, 2.31 × 10-4 and 2.55 × 10-5 M, respectively. The remaining compounds gave LD50 values greater than 2.36 × 10-4 − 3.22 × 10-4 M and were, therefore, considered to be almost inactive. On the other hand, in the carbonic anhydrase (CA-II) inhibition bioassay, all the trial compounds (19-63) showed less than 50% of enzymatic inhibition and thus were considered to be inactive. However, in the antiglycation activity assay, 21 out of 45 compounds tested i.e. (20-22), (24), (26), (28), (29), (34), (36), (39), (45), (47), (48), (50), (51), (56-59), (61) and (62) proved to be potent inhibitors of glycation, demonstrating inhibition with IC50 values ranging from 114.51 ± 1.08 to 643.80 ± 5.80 µM. Of these, (21), (22), (26), (28), (29), (34), (36), (51), (56-58) and (62) exhibited superb inhibitory activity (IC50 = 114.51 ± 1.08 – 241.90 ± 1.97 µM) even better than the reference inhibitor, rutin (294.50 ± 1.50 µM) and thus may act as convincing leads for further studies. The synthetic thiosemicarbazones (19), (21), (22), (24-31), (34-37), (39-42), (44-46) and (48) were used as ligands for synthesizing their Cu(II) complexes. All the synthesized metal complexes (64-86) were characterized by means of their analytical (CHN), spectral (IR, R (Raman), UV-Vis), magnetic moments, thermal and molar conductance data, and evaluated for the selected biological properties viz. antiurease, anticarbonic anhydrase and antiglycation activities. In antiurease assay, coordination of all the thiosemicarbazone ligands to metal ions was found to lead to decrement in the enzyme inhibitory activity that they possessed. Relatively, extensive decrease occurred in the cases of (65), (67), (68), (71), (73), (76-81) and (84). On the contrary, in CA inhibition bioassay, coordination of the ligands to metal ions was found to give rise to induction of enzyme inhibitory activity in certain cases. For example, the metal complexes (66), (72-76), (80) and (83-86) exhibited promising enzymatic inhibition with IC50 values 5.9 ± 0.00 − 21.26 ± 0.35 µM in contrast to the corresponding ligands (22), (29-31), (34), (35), (40), (44-46) and (48), which displayed less than 50% (i.e. from − 9.3 to 33.1%) inhibition of the enzyme and thus considered to be inactive. Similarly, the coordination of thiosemicarbazone ligands to metal ions was found to bring about either induction or enhancement of antiglycation activity. For example, the metal complexes (64), (68), (70), (73), (74), (76), (78), (80-83) and (85) showed excellent activity with IC50 values ranging from 105.74 ± 3.1 to 247.06 ± 1.75 µM as compared to the relevant ligands (19), (25), (27), (30), (31), (35), (37), (40-43) and (46), which demonstrated less than 50% (i.e. 10.32−40.98 %) inhibition of glycation. Similarly, the metal complexes (65-67), (69), (71), (72), (75), (77), (79) and (84) displayed markedly enhanced antiglycation activity in comparison to the respective ligands (21), (22), (24), (26), (28), (29), (34), (36), (39) and (45) (IC50 values 94.64 ± 0.99 − 135.20 ± 1.87 vs. 209.87 ± 0.37 − 522.68 ± 9.1 µM).