Application of Biology to Cultural Heritage

This Special Issue of the Applied Sciences, entitled “Application of Biology to Cultural Heritage” aimed to cover all the latest outstanding progress of biological and biochemical methods developed and applied to cultural heritage [...]

Development of a new method for determining the degree of ripeness of tomato fruits with different colors of ripe fruits

The paper evaluates the most common sensory, physical, physicochemical and biochemical methods of determining the degree of ripeness of tomato fruits. On the example of small-fruit varieties with red, orange, yellow and brown colors of ripe fruits, an attempt was made to create a universal scale to assess the degree of ripeness of tomato fruits based on the physiological state of the fruits. The paper presents data on the quantitative content of endogenous ethylene in fruits with certain ripeness level.

IDENTIFICATION OF VIBRIOSIS FROM SEAWEED CULTURE IN LOMBOK, WEST NUSA TENGGARA

The aim of the study was to identify vibrio disease in Eucheuma cottonii samples which had the characteristics of ice-ice disease, namely the thallus was whitish and broken. The research was conducted at two locations in Lombok, namely in Ekas Bay and in the waters of Buwun Mas Village. The samples were identified as vibrio bacteria at the Sekotong Marine Aquaculture Center using biochemical methods. The results showed that vibrio bacteria were associated with ice-ice disease in the observed seaweeds. The types of vibrio bacteria that cause ice-ice disease in samples in Ekas Bay and Buwun Mas are Vibrio parahaemolyticus, Vibrio alginolyticus, and Vibrio damsela.

Performance of MALDI–TOF Mass Spectrometry in the Philippines

Identification of the causative pathogen in infectious diseases is important for surveillance and to guide treatment. In low- and middle-income countries (LMIC), conventional culture and identification methods, including biochemical methods, are reference-standard. Biochemical methods can lack sensitivity and specificity and have slow turnaround times, causing delays in definitive therapy. Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI–TOF MS) is a rapid and accurate diagnostic method. Most studies comparing MALDI–TOF MS and biochemical methods are from high-income countries, with few reports from LMIC with tropical climates. The aim of this study was to assess the performance of MALDI–TOF MS compared to conventional methods in the Philippines. Clinical bacterial or fungal isolates were identified by both MALDI–TOF MS and automated (VITEK2) or manual biochemical methods in the San Lazaro Hospital, Metro Manila, the Philippines. The concordance between MALDI­–TOF MS and automated (VITEK2) or manual biochemical methods was analyzed at the species and genus levels. In total, 3530 bacterial or fungal isolates were analyzed. The concordance rate between MALDI–TOF MS and biochemical methods was 96.2% at the species level and 99.9% at the genus level. Twenty-three isolates could not be identified by MALDI–TOF MS. In this setting, MALDI–TOF MS was accurate compared with biochemical methods, at both the genus and the species level. Additionally, MALDI–TOF MS improved the turnaround time for results. These advantages could lead to improved infection management and infection control in low- and middle-income countries, even though the initial cost is high.

Visualizing the Integrity of Chloroplast Envelope by Rhodamine and Nile Red Staining

Chloroplasts are essential organelles in plant cells with many important functions. Chloroplasts isolated by Percoll density gradient centrifugation are widely used in the study of chloroplasts. The intactness of isolated chloroplasts is necessary for many of the experiments. In the past, those isolated chloroplasts were either simply believed to be intact or had to be analyzed by indirect biochemical methods. Here we show a new method to check the intactness of isolated chloroplasts by staining their envelope with fluorescent dyes, Rhodamine or Nile red, and then observing them with a fluorescence microscope. With this method, broken chloroplasts and intact chloroplasts can be distinguished easily and their integrity can be checked in a few minutes. Results of this method agreed well with those of biochemical methods. Moreover, we have also found that sometimes the middle layer chloroplasts from the Percoll gradient centrifugation could be mostly broken, which could cause mistakes in the experiment. With our method, this problem can be easily found. This chloroplast envelope staining method can be used in the preparation of isolated chloroplasts to ensure the intactness.

Bacterial chaperone protein Hfq facilitates the annealing of sponge RNAs to small regulatory RNAs

ABSTRACTBacterial small RNAs (sRNAs) in association with the chaperone protein Hfq regulate the expression of many target mRNAs. Since sRNAs’ action is crucial to engender a response to changing environmental conditions, their activity needs to be regulated. One such mechanism occurs at posttranscriptional level and involves sponge RNAs (or anti-sRNAs) which sequester sRNAs affecting their regulatory output. Both types of RNAs were identified on Hfq, but it is not known how Hfq interacts with RNA sponges and stimulates their base-pairing with sRNAs. Here, we used biochemical methods to demonstrate that anti-sRNAs resemble sRNAs by their structure and their modes of Hfq binding. Hfq facilitates sponge RNA annealing to sRNA, and each surface of the protein plays a particular role in the process. Moreover, we found that the efficiency of sponge RNA interactions with sRNAs can be improved, therefore, we propose that natural RNA sponges might not sequester sRNAs optimally.

Urea as a By-Product of Ammonia Metabolism Can Be a Potential Serum Biomarker of Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is highly malignant; nearly half of the new cases and deaths are in China. The poor prognosis of HCC is mainly due to late diagnosis; many new biomarkers have been developed for HCC diagnosis. However, few markers are quickly translated into clinical practice; early and differential diagnosis of HCC from cirrhosis and/or hepatitis is still a clinical challenge. Metabolomics and biochemical methods were used to reveal specific serum biomarkers of HCC. Most of the elevated metabolites in HCC and HBV patients were overlapped compared with controls. Urea was the specifically elevated serum biomarker of HCC patients. Moreover, urea combined with AFP and CEA can improve the sensitivity of HCC diagnosis. The plasma ammonia of HCC patients was significantly higher than healthy controls. Co-culture cell model revealed normal liver cells cooperated with cancer cells to metabolize ammonia into urea. The urea metabolism in cancer cells marginally depended on the expression of CPS1. However, the expression of CPS1 did not change with ammonium chloride, which might regulate the urea cycle through enzyme activity. The urea cycle could detoxify high concentrations of ammonia to promote cancer cell proliferation. Therefore, urea was a by-product of ammonia metabolism and could be a potential serum biomarker for HCC. The combined application of metabolomics and biochemical methods can discover new biomarkers for the early diagnosis of HCC and be quickly applied to clinical diagnosis.

Isolation and Identification of Biosurfactant Producing Bacteria From Workshop Wastewater

Automotive workshop activities produce oil ills that may pollute waters around the workshop area. The oil-polluted water may inhabit biosurfactant producing bacteria that are able to degrade the oil. A study aimed to isolate and identify the bacteria has been conducted from July to September 2020. The bacteria samples were sampled from workshop wastewater at Kubang Raya street KM 2,5 Pekanbaru, Riau Province and sampling were conducted three times. The bacteria were isolated using TSB (Tryptone Soy Broth) and TSA (Tryptone Soy Agar) media and were identified by using biochemical methods. Results showed that there were seven types of bacteria, namely Providencia, Proteus, Acinetobacter, Bacillus, Aeromonas, Proteus and Serratia. The Emulsification index of Providencia was 38.8%, Proteus 50%, Acinetobacter 48.8%, Bacillus 52,1%, Aeromonas 47,6%, Proteus 54,7% and Serratia 48,8%. Data obtained from this study showed that all of the identified bacteria are able to produce biosurfactants.

A cell-based ribozyme reporter system employing a chromosomally-integrated 5′ exonuclease gene

Background Bioinformatic genome surveys indicate that self-cleaving ribonucleic acids (ribozymes) appear to be widespread among all domains of life, although the functions of only a small number have been validated by biochemical methods. Alternatively, cell-based reporter gene assays can be used to validate ribozyme function. However, reporter activity can be confounded by phenomena unrelated to ribozyme-mediated cleavage of RNA. Results We established a ribozyme reporter system in Escherichia coli in which a significant reduction of reporter activity is manifest when an active ribozyme sequence is fused to the reporter gene and the expression of a foreign Bacillus subtilis RNaseJ1 5′ exonuclease is induced from a chromosomally-integrated gene in the same cell. Conclusions The reporter system could be useful for validating ribozyme function in candidate sequences identified from bioinformatics.