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Fulltext Functional analysis of down-regulated miRNA-221-5p in HeLa cell treated with polyphenol-rich Polyalthia longifolia as regulators of apoptotic HeLa cell death

Shanmugapriya, Sasidharan S

3 Biotech, 2020 May;10(5):206.
PMID: 32346497 DOI: 10.1007/s13205-020-02193-6

MicroRNAs are endogenous small non-coding-RNAs that control gene expression and cancer development. Previous studies reported that Polyalthia longifolia treatment induced apoptotic cell death in HeLa cells by down-regulation of miR-221-5p. Hence, the current study was conducted to validate the down-regulated miR-221-5p in HeLa cells. Functional analysis of miR-221-5p was conducted through the gain-of-function, and loss-of-function approach and the miRNA expression was quantified by a real-time polymerase chain reaction. The P. longifolia treatment significantly (p
Colorimetric detection of mercury (Hg2+) using UV-vis spectroscopy and digital image analysis based on gold nanoparticles functionalized with bromelain enzyme

Suhaidi NA, Halmi MIE, Rashidi AA, Anuar MFM, Mahmud K, Kusnin N, et al.

3 Biotech, 2023 May;13(5):121.
PMID: 37033387 DOI: 10.1007/s13205-023-03532-z

A very sensitive and selective colorimetric biosensor for the measurement of mercury ion (Hg2+) in environmental samples has been developed using functionalized gold nanoparticles with bromelain enzyme (brn-AuNPs). This work has shown that Hg2+ measurement based on spectrophotometer and digital image analysis is a very innovative and successful method for providing an effective preliminary system and has promise for the future of water quality biomonitoring. Response Surface Methodology (RSM), a Box-Behnken design-based technique, was used to identify the optimum levels of functionalization of bromelain to AuNPs. The created model's validity was confirmed, and statistical analysis revealed that the ideal functionalize conditions were 1 mM of AuNPs, functionalize with 0.59 mM bromelain concentration on 14 ℃ temperature and 72 h incubation time. The lowest colorimetric detection concentration (LOD) of brn-AuNPs of Hg2+ was 0.0092 ppm and 0.011 ppm for spectrophotometer and digital image analysis. As shown, digital image analysis had advantages based on the LOD result comparable to UV-VIS spectrophotometer. The practical application of the brn-AuNPs sensing was proven with mercury determination in water samples. The present study developed a robust sensor, which successfully implemented in a compact portable sensor kit, turning this sensor into a very potent tool for the development water quality biomonitoring system of Hg2+ application.
Gut microbiota of healthy Asians and their discriminative features revealed by metagenomics approach

Taha SFM, Bhassu S, Omar H, Raju CS, Rajamanikam A, Govind SKP, et al.

3 Biotech, 2023 Aug;13(8):275.
PMID: 37457869 DOI: 10.1007/s13205-023-03671-3

This study is conducted to identify the microbial architecture and its functional capacity in the Asian population via the whole metagenomics approach. A brief comparison of the Asian countries namely Malaysia, India, China, and Thailand, was conducted, giving a total of 916 taxa under observation. Results show a close representation of the taxonomic diversity in the gut microbiota of Malaysia, India, and China, where Bacteroidetes, Firmicutes, and Actinobacteria were more predominant compared to other phyla. Mainly due to the multi-racial population in Malaysia, which also consists of Malays, Indian, and Chinese, the population tend to share similar dietary preferences, culture, and lifestyle, which are major influences that shapes the structure of the gut microbiota. Moreover, Thailand showed a more distinct diversity in the gut microbiota which was highly dominated by Firmicutes. Meanwhile, functional profiles show 1034 gene families that are common between the four countries. The Malaysia samples are having the most unique gene families with a total of 67,517 gene families, and 51 unique KEGG Orthologs, mainly dominated by the metabolic pathways, followed by microbial metabolism in diverse environments. In conclusion, this study provides some general overview on the structure of the Asian gut microbiota, with some additional highlights on the Malaysian population.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-023-03671-3.
Extractive purification of recombinant thermostable lipase from fermentation broth of Escherichia coli using an aqueous polyethylene glycol impregnated resin system

Tan JS, Abbasiliasi S, Ariff AB, Ng HS, Bakar MHA, Chow YH

3 Biotech, 2018 Jun;8(6):288.
PMID: 29938157 DOI: 10.1007/s13205-018-1295-y

This study aimed at recovery of thermostable lipase from Escherichia coli BL21 using porous glass beads grafted with polyethylene glycol (PEG) in aqueous impregnated resins system (AIRS). The influencing parameters such as concentration and pH of extraction solution, concentration of NaCl, size of the beads, and pH of the desorption solution on the partition behaviour of lipase were evaluated. Smaller adsorbent (4 mm) had a 65.5% of recovery yield with approximately two-fold higher purification factor compared to that obtained with the larger adsorbent. Recombinant lipase was purified successfully using AIRS with a purification factor of 7.6 and yield of 78.4% under optimum conditions of 18% (w/w) PEG 4000, 10% (w/w) of potassium citrate at pH 9 with 3% (w/w) of NaCl. Optimum desorption was obtained with 4.0 mm of porous glass beads at pH 9.
Isolation and functional characterization of 5-enolpyruvylshikimate 3-phosphate synthase gene from glyphosate-tolerant Pseudomonas nitroreducens strains FY43 and FY47

Tan XL, Othman RY, Teo CH

3 Biotech, 2020 Apr;10(4):183.
PMID: 32257739 DOI: 10.1007/s13205-020-02176-7

5-Enolpyruvylshikimate 3-phosphate synthase (EPSPS) is the primary target for the broad-spectrum herbicide, glyphosate. Improvement of EPSPS gene for high level of glyphosate tolerance is important to generate glyphosate-tolerant crops. In this study, we report the isolation and characterization of EPSPS genes of glyphosate-tolerant Pseudomonas nitroreducens strains FY43 and FY47. Both P. nitroreducens strains FY43 and FY47, which showed glyphosate tolerance up to 8.768% (518.4 mM, 32 × higher than field application), were isolated from soil samples collected from oil palm plantation with a long history of glyphosate application. The glyphosate tolerance property of EPSPS genes of strains FY43 and FY47 was functionally characterized by expressing the genes in Escherichia coli strain BL21(DE3). Error-prone PCR was performed to mutagenize native EPSPS gene of strains FY43 and FY47. Ten mutagenized EPSPS with amino acid changes (R21C, N265S, A329T, P71L, T258A, L184F, G292C, G292S, L35F and A242V) were generated through error-prone PCR. Both native and mutated EPSPS genes of strains FY43 and FY47 were introduced into Escherichia coli strain BL21(DE3) and transformants were selected on basal salt medium supplemented with 8.768% (518.4 mM) glyphosate. Mutants with mutations (R21C, N265S, A329T, P71L, T258A, L35F, A242V, L184F and G292C) showed sensitivity to 8.768% glyphosate, whereas glyphosate tolerance for mutant with G292S mutation was not affected by the mutation.
Microalgae for freshwater arsenic bioremediation: examining cellular toxicity, bioconcentration factor and eluding an alternative arsenic detoxification pathway

Tang WW, Foo SC

3 Biotech, 2024 May;14(5):130.
PMID: 38605865 DOI: 10.1007/s13205-024-03977-w

Microalgae are photoautotrophic organisms in freshwater systems known to uptake and bioremediate arsenic, a heavy metal. In this study, we compared the growth and arsenic uptake of two microalgae strains, Nostoc and Chlorella, to determine their suitability for arsenic bioremediation. As compared to the control, our results showed that treatment with As (III) enhanced the Nostoc growth by approximately 15% when grown in the absence of phosphate. The highest bioconcentration factor of Nostoc at this treatment was 1463.6, whereas 0.10 mg L-1 As (V) treatment improved the Chlorella growth by 25%, in the presence of phosphate. However, arsenic uptake reduced from 175.7 to 32.3 throughout the cultivation period for Chlorella. This suggests that Nostoc has an upper advantage in the bioremediation of arsenic as compared to the Chlorella strain. To gain insights into the potential of Nostoc in arsenic bioremediation, we further conducted SEM analysis on the vegetative cell surface. The SEM results showed that As (III) disrupted the Nostoc vegetative cell surface and structure. Further to this, pathway analysis and polymerase chain reaction (PCR) were conducted to identify the potential arsenic pathway regulated by Nostoc. The primary As (III)-related pathways elucidated include the arsA transporter and arsD complex that require ATP and As (III) methylation to S-adenosylmethionine. The phosphate deficiency condition resulting in the inability to generate ATP caused As (III) could not be excreted from the Nostoc cells, potentially contributing to the high arsenic concentration accumulated under phosphate-depleted conditions. These insights contribute to understanding the efficacy of microalgae strains in freshwater arsenic bioremediation.
Fulltext Proteome of rice roots treated with exogenous proline

Teh CY, Ho CL, Shaharuddin NA, Lai KS, Mahmood M

3 Biotech, 2019 Mar;9(3):101.
PMID: 30800612 DOI: 10.1007/s13205-019-1615-x

Proteomic analysis was conducted to identify the rice root proteins induced by exogenous proline and their involvement in root growth. Proteins were extracted from the root tissues grown under two conditions, T1 (control) and T2 (10 mM proline), and profiled by two-dimensional polyacrylamide gel electrophoresis. Seventeen of 30 differentially expressed proteins were identified by mass spectrometry. Proline-treated rice roots showed up-regulation and down-regulation of nine and eight proteins, respectively, when compared to those in the control. Among the differentially expressed proteins, the down-regulation of glutathione reductase and peroxidase could be involved in the regulation of cellular hydrogen peroxide and reactive oxygen species levels that modulate the root cell wall structure. Differentially expressed proteins identified as pathogenesis-related proteins might be related to stress adaptive mechanisms in response to exogenous proline treatment. In addition, differentially expressed protein identified as the fructose-bisphosphate aldolases and cytochrome c oxidase might be associated with energy metabolism, which is needed during root developmental process. This is the first attempt to study the changes in rice root proteome treated with proline. The acquired information could open new avenues for further functional studies on the involvement of proline in modulating root development and its relation to stress adaptation of plants.
Characterization of Thiomonas delicata arsenite oxidase expressed in Escherichia coli

Teoh WK, Salleh FM, Shahir S

3 Biotech, 2017 Jun;7(2):97.
PMID: 28560637 DOI: 10.1007/s13205-017-0740-7

Microbial arsenite oxidation is an essential biogeochemical process whereby more toxic arsenite is oxidized to the less toxic arsenate. Thiomonas strains represent an important arsenite oxidizer found ubiquitous in acid mine drainage. In the present study, the arsenite oxidase gene (aioBA) was cloned from Thiomonas delicata DSM 16361, expressed heterologously in E. coli and purified to homogeneity. The purified recombinant Aio consisted of two subunits with the respective molecular weights of 91 and 21 kDa according to SDS-PAGE. Aio catalysis was optimum at pH 5.5 and 50-55 °C. Aio exhibited stability under acidic conditions (pH 2.5-6). The V max and K m values of the enzyme were found to be 4 µmol min(-1) mg(-1) and 14.2 µM, respectively. SDS and Triton X-100 were found to inhibit the enzyme activity. The homology model of Aio showed correlation with the acidophilic adaptation of the enzyme. This is the first characterization studies of Aio from a species belonging to the Thiomonas genus. The arsenite oxidase was found to be among the acid-tolerant Aio reported to date and has the potential to be used for biosensor and bioremediation applications in acidic environments.
Nanomaterials in food industry for the protection from mycotoxins: an update

Thirugnanasambandan T, Gopinath SCB

3 Biotech, 2023 Feb;13(2):64.
PMID: 36718411 DOI: 10.1007/s13205-023-03478-2

The storage of food grains against the fungal infection has been a great challenge to the farmers, but nanotechnology provides a solution to address this problem. The application of nanotechnology for the storage of food grains replaces synthetic fungicides in agriculture. Inorganic nanoparticles such as silver and zinc oxide are well-known for their antifungal activity. Green synthesized nanoparticles show enhanced antimicrobial activity than the chemically synthesized nanoparticles. Extracts and essential oils derived from plants exhibit very good antifungal properties. The synthesized nanoparticles can be impregnated in packaging materials, which are used to store food grains. Natural materials are having advantages like non-toxicity and easier to degrade and are suitable for food safety. This overview discusses the nanomaterials-mediated protection of food materials from mycotoxin and its releases into the open environment.
Fulltext Bacterial and eukaryotic microbial communities in urban water systems profiled via Illumina MiSeq platform

Ting ASY, Zoqratt MZHM, Tan HS, Hermawan AA, Talei A, Khu ST

3 Biotech, 2021 Feb;11(2):40.
PMID: 33479595 DOI: 10.1007/s13205-020-02617-3

Microbial communities from a lake and river flowing through a highly dense urbanized township in Malaysia were profiled by sequencing amplicons of the 16S V3-V4 and 18S V9 hypervariable rRNA gene regions via Illumina MiSeq. Results revealed that Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes were the dominant prokaryotic phyla; whereas, eukaryotic communities were predominantly of the SAR clade and Opisthokonta. The abundance of Pseudomonas and Flavobacterium in all sites suggested the possible presence of pathogens in the urban water systems, supported by the most probable number (MPN) values of more than 1600 per 100 mL. Urbanization could have impacted the microbial communities as transient communities (clinical, water-borne and opportunistic pathogens) coexisted with common indigenous aquatic communities (Cyanobacteria). It was concluded that in urban water systems, microbial communities vary in their abundance of microbial phyla detected along the water systems. The influences of urban land use and anthropogenic activities influenced the physicochemical properties and the microbial dynamics in the water systems.
Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-020-02617-3.
DNA barcode identification of cultivated and wild tropical fruit species

Tnah LH, Lee SL, Lee CT, Ng KKS, Ng CH, Zawiah N

3 Biotech, 2024 Jan;14(1):7.
PMID: 38074292 DOI: 10.1007/s13205-023-03848-w

With the rapid growth of the fruit industry worldwide, it is important to assess adulteration to ensure the authenticity and the safety of fruit products. The DNA barcoding approach offers a quick and accurate way of identifying and authenticating species. In this study, we developed reference DNA barcodes (rbcL, ITS2, and trnH-psbA) for 70 cultivated and wild tropical fruit species, representing 43 genera and 26 families. In terms of species recoverability, rbcL has a greater recoverability (100%) than ITS2 (95.7%) and trnH-psbA (88.6%). We evaluated the performance of these barcodes in species discrimination using similarity BLAST, phylogenetic tree, and barcoding gap analyses. The efficiency of rbcL, ITS2, and trnH-psbA in discriminating species was 80%, 100%, and 93.6%, respectively. We employed a multigene-tiered approach for species identification, with the rbcL region used for primary differentiation and ITS2 or trnH-psbA used for secondary differentiation. The two-locus barcodes rbcL + ITS2 and rbcL + trnH-psbA demonstrated robustness, achieving species discrimination rates of 100% and 94.3% respectively. Beyond the conventional species identification method based on plant morphology, the developed reference barcodes will aid the fruit agroindustry and trade, by making fruit-based product authentication possible.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-023-03848-w.
Development of constitutive and IPTG-inducible integron promoter-based expression systems for Escherichia coli and Agrobacterium tumefaciens

Toh WK, Teo YL, Tor XY, Loh PC, Wong HL

3 Biotech, 2023 Mar;13(3):91.
PMID: 36825259 DOI: 10.1007/s13205-023-03507-0

Broad host range (BHR) expression vector is a vital tool in molecular biology research and application. Currently, most of the plasmid vectors used in Agrobacterium spp. are binary vectors that are designed for plant transformation, and very few are designed for expressing transgenes in Agrobacterium spp. Class 1 integrons are common genetic elements that allow for the efficient capture and expression of antibiotic resistance genes, especially in Gram-negative bacteria. One of its compound promoters, PcS + P2, was used in this study and has been reported to be the strongest class 1 integron constitutive promoter; it is referred to as "integron promoter" (P int) henceforth. Herein, we created two versions of isopropyl-d-thiogalactopyranoside (IPTG)-inducible promoters by substituting and/or inserting lacO sequence(s) into P int. These inducible promoters, which possess different degrees of stringency and inducibility, were used to construct two broad host range expression vectors (pWK102 and pWK103) based on the versatile pGREEN system. This allows them to be stably maintained and replicated in both Escherichia coli and Agrobacterium tumefaciens. Functional validation of these vectors was performed by the expression of the reporter gene, superfolder green fluorescent protein (sfGFP), which was cloned downstream of these promoters. Due to the strong induction and tunable expression of a transgene located downstream to the inducible integron promoter, these vectors may be useful for heterologous gene expression in both E. coli and A. tumefaciens, thus facilitating recombinant protein production and genetic studies in Gram-negative bacteria.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-023-03507-0.
Production and characterization of graphene from carbonaceous rice straw by cost-effect extraction

Uda MNA, Gopinath SCB, Hashim U, Halim NH, Parmin NA, Uda MNA, et al.

3 Biotech, 2021 May;11(5):205.
PMID: 33868892 DOI: 10.1007/s13205-021-02740-9

This paper describes the synthesis of graphene-based activated carbon from carbonaceous rice straw fly ash in an electrical furnace and the subsequent potassium hydroxide extraction. The produced graphene has a proper morphological structure; flakes and a rough surface can be observed. The average size of the graphene was defined as up to 2000 nm and clarification was provided by high-resolution microscopes (FESEM and FETEM). Crystallinity was confirmed by surface area electron diffraction. The chemical bonding from the graphene was clearly observed, with -C=C- and O-H stretching at peaks of 1644 cm-1 and 3435 cm-1, respectively. Impurities in the graphene were found using X-ray photoelectron spectroscopy and energy dispersive X-ray spectroscopy. The measured size, according to zeta-potential analysis, was 8722.2 ± 25 nm, and the average polydispersity index was 0.576. The stability of the mass reduction was analyzed by a thermogravimetric at 100 °C, with a final reduction of ~ 11%.
Prevention of aspirin-mediated secondary toxicity by combined treatment of carotenoids in macrophages

Vijay K, Ambedkar R, Sowmya PR, Ramaiah S, Ranga Rao A, Gundamaraju R, et al.

3 Biotech, 2023 Jul;13(7):223.
PMID: 37292139 DOI: 10.1007/s13205-023-03632-w

Upon understanding the boosting role of carotenoids on the endogenous anti-inflammatory system, it is vital to explore their role in reducing the use of high doses of non-steroidal anti-inflammatory drug (NSAIDs), and their mediated secondary toxicity during the treatment of chronic diseases. The current study investigates the carotenoids potential on inhibition of secondary complications induced by NSAIDs, aspirin (ASA) against lipopolysaccharide (LPS) stimulated inflammation. Initially, this study evaluated a minimal cytotoxic dose of ASA and carotenoids (β-carotene, BC/lutein, LUT/astaxanthin, AST/fucoxanthin FUCO) in Raw 264.7, U937, and peripheral blood mononuclear cells (PBMCs). In all three cells, carotenoids + ASA treatment reduced the LDH release, NO, and PGE2 efficiently than an equivalent dose of carotenoid or ASA treated alone. Based on cytotoxicity and sensitivity results, RAW 264.7 cells were selected for further cell-based assay. Among carotenoids, FUCO + ASA exhibited an efficient reduction of LDH release, NO, and PGE2 than the other carotenoids (BC + ASA, LUT + ASA, and AST + ASA) treatment. FUCO + ASA combination decreased LPS/ASA induced oxidative stress, pro-inflammatory mediators (iNOS, COX-2, and NF-κB), and cytokines (IL-6, TNF-α, and IL-1β) efficiently. Further, apoptosis was inhibited by 69.2% in FUCO + ASA, and 46.7% in ASA than LPS treated cells. A drastic decrease in intracellular ROS generation with the increase in GSH was observed in FUCO + ASA compared to LPS/ASA groups. The results documented on the low dose of ASA with a relative physiological concentration of FUCO suggested greater importance for alleviating secondary complications and optimize prolonged chronic disease treatments with NSAID's associated side effects.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-023-03632-w.
Fulltext Anxiety determination by antibody-conjugated nanoparticles on an interdigitated electrode sensor

Wang X, Gopinath SCB, Li J

3 Biotech, 2020 Sep;10(9):377.
PMID: 32802719 DOI: 10.1007/s13205-020-02370-7

This work focused on the detection of cortisol on an interdigitated electrode sensor surface using an anti-cortisol antibody. To improve immobilization, antibodies were conjugated with silver nanoparticles and attached to the surface of the sensor. Cortisol interacted in a dose-dependent manner on the antibody-immobilized sensor surface, and current changes were observed. Linear regression analysis was performed by a 3σ calculation, and the limit of detection fell into the range of 0.01 and 0.1 ng/mL. The sensitivity of cortisol was calculated to be 0.01 ng/mL and the sensor discriminated against other hormones, namely norepinephrine and progesterone, with higher selectivity for cortisol. This result represented the selective detection of cortisol with high performance, which can help to determine anxiety disorders.
Fulltext Targeted DNA complementation on a 1,1'-carbonyldiimidazole-functionalized surface for identifying Mycobacterium tuberculosis

Xu S, Xue Y, Guo F, Xu M, Gopinath SCB, Mao X

3 Biotech, 2020 May;10(5):227.
PMID: 32373419 DOI: 10.1007/s13205-020-02216-2

Herein, a rapid and sensitive current-volt measurement was developed for identifying the IS6110 DNA sequence to diagnose Mycobacterium tuberculosis (TB). An aminated capture probe was immobilized on a 1,1'-carbonyldiimidazole-functionalized interdigitated electrode (IDE) silica substrate, and the target sequence was detected by complementation. It was found that all tested concentrations displayed a higher response in current changes than the control, and the limit of detection was 10 fM. The sensitivity ranged from 1 to 10 fM. The control sequences with single-, triple-mismatch and noncomplementary sequences showed great discrimination. This rapid and easy DNA detection method helps to identify M. tuberculosis for early-stage diagnosis of TB.
Fulltext Bamboo: an overview on its genetic diversity and characterization

Yeasmin L, Ali MN, Gantait S, Chakraborty S

3 Biotech, 2015 Feb;5(1):1-11.
PMID: 28324361 DOI: 10.1007/s13205-014-0201-5

Genetic diversity represents the heritable variation both within and among populations of organisms, and in the context of this paper, among bamboo species. Bamboo is an economically important member of the grass family Poaceae, under the subfamily Bambusoideae. India has the second largest bamboo reserve in Asia after China. It is commonly known as "poor man's timber", keeping in mind the variety of its end use from cradle to coffin. There is a wide genetic diversity of bamboo around the globe and this pool of genetic variation serves as the base for selection as well as for plant improvement. Thus, the identification, characterization and documentation of genetic diversity of bamboo are essential for this purpose. During recent years, multiple endeavors have been undertaken for characterization of bamboo species with the aid of molecular markers for sustainable utilization of genetic diversity, its conservation and future studies. Genetic diversity assessments among the identified bamboo species, carried out based on the DNA fingerprinting profiles, either independently or in combination with morphological traits by several researchers, are documented in the present review. This review will pave the way to prepare the database of prevalent bamboo species based on their molecular characterization.
Fulltext A simple and inexpensive physical lysis method for DNA and RNA extraction from freshwater microalgae

Yee W, Abdul-Kadir R, Lee LM, Koh B, Lee YS, Chan HY

3 Biotech, 2018 Aug;8(8):354.
PMID: 30105179 DOI: 10.1007/s13205-018-1381-1

In this work, a simple and inexpensive physical lysis method using a cordless drill fitted with a plastic pellet pestle and 150 mg of sterile sea sand was established for the extraction of DNA from six strains of freshwater microalgae. This lysis method was also tested for RNA extraction from two microalgal strains. Lysis duration between 15 and 120 s using the cetyltrimethyl ammonium bromide (CTAB) buffer significantly increased the yield of DNA from four microalgalstrains (Monoraphidium griffithii NS16, Scenedesmus sp. NS6, Scenedesmus sp. DPBC1 and Acutodesmus sp. DPBB10) compared to control. It was also found that grinding was not required to obtain DNA from two strains of microalgae (Choricystis sp. NPA14 and Chlamydomonas sp. BM3). The average DNA yield obtained using this lysis method was between 62.5 and 78.9 ng/mg for M. griffithii NS16, 42.2-247.0 ng/mg for Scenedesmus sp. NS6, 70.2-110.9 ng/mg for Scenedesmus sp. DPBC1 and 142.8-164.8 ng/mg for Acutodesmus sp. DPBB10. DNA obtained using this method was sufficiently pure for PCR amplification. Extraction of total RNA from M. griffithii NS16 and Mychonastes sp. NPD7 using this lysis method yielded high-quality RNA suitable for RT-PCR. This lysis method is simple, cheap and would enable rapid nucleic acid extraction from freshwater microalgae without requiring costly materials and equipment such as liquid nitrogen or beadbeaters, and would facilitate molecular studies on microalgae in general.
Physiological and metabolic responses of Scenedesmus quadricauda (Chlorophyceae) to nickel toxicity and warming

Yong WK, Sim KS, Poong SW, Wei D, Phang SM, Lim PE

3 Biotech, 2019 Aug;9(8):315.
PMID: 31406637 DOI: 10.1007/s13205-019-1848-8

An ecologically important tropical freshwater microalga, Scenedesmus quadricauda, was exposed to Ni toxicity under two temperature regimes, 25 and 35 °C to investigate the interactive effects of warming and different Ni concentrations (0.1, 1.0 and 10.0 ppm). The stress responses were assessed from the growth, photosynthesis, reactive oxygen species (ROS) generation and metabolomics aspects to understand the effects at both the physiological and biochemical levels. The results showed that the cell densities of the cultures were higher at 35 °C compared to 25 °C, but decreased with increasing Ni concentrations at 35 °C. In terms of photosynthetic efficiency, the maximum quantum yield of photosystem II (Fv/Fm) of S. quadricauda remained consistent across different conditions. Nickel concentration at 10.0 ppm affected the maximum rate of relative electron transport (rETRm) and saturation irradiance for electron transport (Ek) in photosynthesis. At 25 °C, the increase of non-photochemical quenching (NPQ) values in cells exposed to 10.0 ppm Ni might indicate the onset of thermal dissipation process as a self-protection mechanism against Ni toxicity. The combination of warming and Ni toxicity induced a strong oxidative stress response in the cells. The ROS level increased significantly by 40% after exposure to 10.0 ppm of Ni at 35 °C. The amount of Ni accumulated in the biomass was higher at 25 °C compared to 35 °C. Based on the metabolic profile, temperature contributed the most significant differentiation among the samples compared to Ni treatment and the interaction between the two factors. Amino acids, sugars and organic acids were significantly regulated by the combined factors to restore homeostasis. The most affected pathways include sulphur, amino acids, and nitrogen metabolisms. Overall, the results suggest that the inhibitory effect of Ni was lower at 35 °C compared to 25 °C probably due to lower metal uptake and primary metabolism restructuring. The ability of S. quadricauda to accumulate substantial amount of Ni and thrive at 35 °C suggests the potential use of this strain for phycoremediation and outdoor wastewater treatment.
Enhancing yeast growth with carboxylates under multiple nutrient limitations

Yusof TY, Lian MQ, Ong EBB, Teh AH

3 Biotech, 2021 Sep;11(9):409.
PMID: 34471591 DOI: 10.1007/s13205-021-02955-w

Yeast cell death is triggered when essential nutrients such as potassium and lipid are limited but ammonium is in excess. When ammonium and glucose were maintained at 100% of the normal concentration while all the other essential nutrients in yeast nitrogen base (YNB) were reduced to 2%, yeast growth was halted by ammonium toxicity. Yeast started to grow again when either ammonium was also reduced to 2% or gluconate was added, but simultaneously adding gluconate as well as reducing all the nutrients except glucose 50-fold revived yeast growth to a greater extent, i.e. a quarter of the normal growth. Gluconate, as well as formate and alginate, stimulated yeast growth by buffering the drop in pH. Yeast cells were seemingly more susceptible to low pH under the nutrient-limited conditions, entering the stationary phase at pH higher than that of the normal condition. Carboxylate salts may prove a cost-efficient replacement for large proportions of the essential nutrients as yeast cells, in the presence of 2 mg ml-1 gluconate, could still achieve nearly 90% of the normal growth when cultured in only 10% of the normal YNB concentration.

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