Genomic sequencing and characterization of four human rhinovirus-c strains from Malaysian patients

Human rhinovirus (HRV) is one of the respiratory viruses responsible for acute respiratory tract infections (ARTI). HRVs infect both upper and lower respiratory tracts, especially in children. HRVs were initially classified into two clusters, HRV-A and HRV-B. A novel HRV strain, HRV-C was discovered in year 2006. There is a limited number of HRV-C complete genome in the GenBank. Hence, the objective of the present study is to sequence and characterize the Malaysian HRV-C complete genome. Four RNA samples were collected from children with respiratory signs and symptoms hospitalized in Universiti Malaya Medical Center (UMMC). These samples were previously confirmed as HRV-C by sequencing of VP4/VP2 region. Two steps reverse transcription polymerase chain reaction (RT-PCR) was performed. The complete genome was amplified using several sets of modified and redesigned primers. To understand the phylogenetic relationship of Malaysian HRV-Cs, MEGA6 software was used to construct phylogenetic trees. Characteristics of Malaysian HRV-C were determined and recombination was investigated using Recombination Detection Program (RDP) software. Approximately 7.1 kbp of four Malaysian HRV-Cs complete genome sequences were obtained. All the genes in Malaysian HRV-C coding region exhibited similar genomic features as other HRV-Cs. Malaysian HRV-C showed similar receptor utilization, immunogenic sites and antiviral sites with other HRV-Cs. Based on VP4/VP2 sequences, Malaysian HRV-Cs were classified as HRV-C6, C22, C23 and C42. Pairwise distance threshold further confirmed the classification based on VP4/VP2 sequences. Three Malaysian HRV-Cs (C22, C23 and C42) represent the first complete genome were successfully sequenced. No recombination was identified. Negative selective pressure was the dominant selective pressure exerted on Malaysian HRV-C and other HRV-Cs coding sequences. In conclusion, the present study provided four HRV-C complete genome sequences which will lead to a better understanding of functional sequences, predicted receptor usage, secondary structure and selective pressure in HRV-C

The Critical Studies of Fucoxanthin Research Trends from 1928 to June 2021: A Bibliometric Review

Fucoxanthin is a major carotenoid in brown macroalgae and diatoms that possesses a broad spectrum of health benefits. This review evaluated the research trends of the fucoxanthin field from 1928 to June 2021 using the bibliometric method. The present findings unraveled that the fucoxanthin field has grown quickly in recent years with a total of 2080 publications. Japan was the most active country in producing fucoxanthin publications. Three Japan institutes were listed in the top ten productive institutions, with Hokkaido University being the most prominent institutional contributor in publishing fucoxanthin articles. The most relevant subject area on fucoxanthin was the agricultural and biological sciences category, while most fucoxanthin articles were published in Marine Drugs. A total of four research concepts emerged based on the bibliometric keywords analysis: “bioactivities”, “photosynthesis”, “optimization of process’’, and “environment”. The “bioactivities” of fucoxanthin was identified as the priority in future research. The current analysis highlighted the importance of collaboration and suggested that global collaboration could be the key to valorizing and efficiently boosting the consumer acceptability of fucoxanthin. The present bibliometric analysis offers valuable insights into the research trends of fucoxanthin to construct a better future development of this treasurable carotenoid

A simple 18S rDNA approach for the identification of cultured eukaryotic microalgae with an emphasis on primers

Any forms of valorization of microorganisms would require accurate identity recognition to ensure repeatability, reproducibility and quality assurance. This study aimed to evaluate the effectiveness of different primers for identifying cultured eukaryotic microalgae using a simple 18S rDNA approach. A total of 34 isolated microalgae and one culture collection were utilized in the search for an effective molecular identification method for microalgae. Ammonium formate was applied to marine microalgae prior to DNA extraction. The microalgal DNA was extracted using a commercial kit and subjected directly to PCR amplification using four different published 18S rDNA primers. The DNA sequences were analysed using Basic Local Alignment Search Tool (BLAST) and phylogenetic trees to determine the microalgae identity. The identity was further validated with conventional morphological taxonomic identification, and the relationship of microalgal morphology and genetic materials was also determined. The microalgal DNA was successfully amplified, including marine species without prior cleaning. In addition, the ss5 + ss3 primer pair was found to be an ideal primer set among the tested primers for identifying microalgae. Overall, molecular identification showed relative matching with morphological identification (82.86%). This study is important because it serves as a platform to develop a standardized eukaryotic microalgae identification method. In addition, this method could help to ease the eukaryotic microalgae identification process and enrich the current reference databases such as GenBank

Comparative genetic analyses of Human Rhinovirus C (HRV-C) complete genome from Malaysia

Human rhinovirus-C (HRV-C) has been implicated in more severe illnesses than HRV-A and HRV-B, however, the limited number of HRV-C complete genomes (complete 5' and 3' non-coding region and open reading frame sequences) has hindered the in-depth genetic study of this virus. This study aimed to sequence seven complete HRV-C genomes from Malaysia and compare their genetic characteristics with the 18 published HRV-Cs. Seven Malaysian HRV-C complete genomes were obtained with newly redesigned primers. The seven genomes were classified as HRV-C6, C12, C22, C23, C26, C42, and pat16 based on the VP4/VP2 and VP1 pairwise distance threshold classification. Five of the seven Malaysian isolates, namely, 3430-MY-10/C22, 8713-MY-10/C23, 8097-MY-11/C26, 1570-MY-10/C42, and 7383-MY-10/pat16 are the first newly sequenced complete HRV-C genomes. All seven Malaysian isolates genomes displayed nucleotide similarity of 63-81% among themselves and 63-96% with other HRV-Cs. Malaysian HRV-Cs had similar putative immunogenic sites, putative receptor utilization and potential antiviral sites as other HRV-Cs. The genomic features of Malaysian isolates were similar to those of other HRV-Cs. Negative selections were frequently detected in HRV-Cs complete coding sequences indicating that these sequences were under functional constraint. The present study showed that HRV-Cs from Malaysia have diverse genetic sequences but share conserved genomic features with other HRV-Cs. This genetic information could provide further aid in the understanding of HRV-C infection

Uncovering Research Trends of Phycobiliproteins Using Bibliometric Approach

Phycobiliproteins are gaining popularity as long-term, high-value natural products which can be alternatives to synthetic products. This study analyzed research trends of phycobiliproteins from 1909 to 2020 using a bibliometric approach based on the Scopus database. The current findings showed that phycobiliprotein is a burgeoning field in terms of publications outputs with “biochemistry, genetics, and molecular biology” as the most related and focused subject. The Journal of Applied Phycology was the most productive journal in publishing articles on phycobiliproteins. Although the United States of America (U.S.A.) contributed the most publications on phycobiliproteins, the Chinese Academy of Sciences (China) is the institution with the largest number of publications. The most productive author on phycobiliproteins was Glazer, Alexander N. (U.S.A.). The U.S.A. and Germany were at the forefront of international collaboration in this field. According to the keyword analysis, the most explored theme was the optimization of microalgae culture parameters and phycobiliproteins extraction methods. The bioactivity properties and extraction of phycobiliproteins were identified as future research priorities. Synechococcus and Arthrospira were the most cited genera. This study serves as an initial step in fortifying the phycobiliproteins market, which is expected to exponentially expand in the future. Moreover, further research and global collaboration are necessary to commercialize phycobiliproteins and increase the consumer acceptability of the pigments and their products

Optimization of the freezing-thawing method for extracting phycobiliproteins from <i>arthrospira</i> sp.

The freezing&ndash;thawing method had been reported to be the best phycobiliprotein extraction technique. However, optimum parameters of this extraction method for Arthrospira sp. (one of the major phycobiliprotein sources) still remained unclear. Hence, this study aimed to optimize the freezing&ndash;thawing parameters of phycobiliprotein extraction in Arthrospira sp. (UPMC-A0087). The optimization of the freezing&ndash;thawing method was conducted using different solvents, biomass/solvent ratios, temperatures, time intervals and freezing&ndash;thawing cycles. The extracted phycobiliproteins were quantified using a spectrophotometric assay. Double distilled water (pH 7) with a 0.50% w/v biomass/solvent ratio was the most efficient solvent in extracting high concentrations and purity of phycobiliproteins from Arthrospira sp. In addition, the combination of freezing at &minus;80 &deg;C (2 h) and thawing at 25 &deg;C (24 h) appeared to be the optimum temperature and extraction time to obtain the highest amount of phycobiliproteins. A minimum of one cycle of freezing and thawing was sufficient for extracting high concentrations of phycobiliproteins. The findings from this study could reduce the cost and labor needed for extracting high quality phycobiliproteins. It also allowed the harvesting of large amounts of valuable phycobiliproteins

A Recommendation for a Pre-Standardized Marine Microalgal Dry Weight Determination Protocol for Laboratory Scale Culture Using Ammonium Formate as a Washing Agent

Microalgal biomass is one of the crucial criteria in microalgal studies. Many reported methods, even the well-established protocol on microalgal dry weight (DW) determination, vary greatly, and reliable comparative assessment amongst published results could be problematic. This study aimed to determine the best condition of critical parameters in marine microalgal DW determination for laboratory-scale culture using four different marine microalgal species. These parameters included the washing process, grades of glass microfiber filter (GMF), GMF pretreatment conditions, washing agent (ammonium formate) concentrations, culture: washing agent ratios (v:v) and washing cycles. GMF grade GF/A with precombustion at 450 °C provided the most satisfactory DW and the highest ash-free dry weight (AFDW)/DW ratio. Furthermore, 0.05 M ammonium formate with 1:2 culture: washing agent ratio and a minimum of two washing cycles appeared to be the best settings of microalgal DW determination. The present treatment increased the AFDW/DW ratio of the four respective microalgae by a minimum of 19%. The findings of this study could serve as a pivotal reference in developing a standardized protocol of marine microalgal DW determination to obtain veracious and reliable marine microalgal DW

A recommendation for a pre-standardized marine microalgal dry 3 weight determination protocol for laboratory scale culture using 4 ammonium formate as a washing agent

Microalgal biomass is one of the crucial criteria in microalgal studies. Many reported methods, even the well-established protocol on microalgal dry weight (DW) determination, vary greatly, and reliable comparative assessment amongst published results could be problematic. This study aimed to determine the best condition of critical parameters in marine microalgal DW determination for laboratory-scale culture using four different marine microalgal species. These parameters included the washing process, grades of glass microfiber filter (GMF), GMF pretreatment conditions, washing agent (ammonium formate) concentrations, culture: washing agent ratios (v:v) and washing cycles. GMF grade GF/A with precombustion at 450 °C provided the most satisfactory DW and the highest ash-free dry weight (AFDW)/DW ratio. Furthermore, 0.05 M ammonium formate with 1:2 culture: washing agent ratio and a minimum of two washing cycles appeared to be the best settings of microalgal DW determination. The present treatment increased the AFDW/DW ratio of the four respective microalgae by a minimum of 19%. The findings of this study could serve as a pivotal reference in developing a standardized protocol of marine microalgal DW determination to obtain veracious and reliable marine microalgal DW

Enhancing Diatom, Cyclotella meneghiniana Growth Using Growth-Promoting Bacteria Isolated From the Phycosphere of Chlorophytes and Chrysophytes

The relationship between microalgae and bacteria in a microenvironment, the phycosphere, has a significant role in enhancing the quality and quantity of microalgal production, which would in turn affect consumers' growth and nutritional quality, such as the zooplankton, which are important live feeds in aquaculture. Thus, selecting and characterising suitable microalgal growth-promoting bacteria (MGPB) for enhancing microalgal production is an important process since not all bacteria promote high growth. In this study, physcosphere bacteria associated with chlorophytes and chrysophytes were isolated, screened for their microalgae-promoting attributes (phosphorus solubilisation, indole-3-acetic acid (IAA) production, and nitrogen fixation) and re-inoculated into microalgal cultures. A total of seven bacterial isolates were recorded to have multiple growth promoting traits, with three strains (CY-2, CY-4, CY-5) showing the greatest (P < 0.05) link for those traits. These seven potential MGPB were molecularly characterised using 16S rRNA approach. The phylogenetic tree of the isolated bacteria demonstrated the dominant bacteria associated with the chlorophytes were in the class bacteroidetes, while the chrysophytes appeared to be associated with Firmicutes bacteria suggesting that the compositions were strictly species-specific to the microalgae host. Enhanced Cyclotella meneghiniana growth by the seven isolated bacterial strains was highly dependent on the growth-promoting traits; especially those demonstrated by Pseudomonas hibiscicola and Ochrobactrum haematophilum. These two bacteria showed the potential to enhance the quality of microalgae, and they could be bioencapsulated and used to improve the quality of zooplankton as one of the main live feeds in the aquaculture industry