Cahyo Budiman

Lignocellulases: a review of emerging and developing enzymes, systems, and practices

The highly acclaimed prospect of renewable lignocellulosic biocommodities as obvious replacement of their fossil-based counterparts is burgeoning within the last few years. However, the use of the abundant lignocellulosic biomass provided by nature to produce value-added products, especially bioethanol, still faces significant challenges. One of the crucial challenging factors is in association with the expression levels, stability, and cost-effectiveness of the cellulose-degrading enzymes (cellulases). Interestingly, several recommendable endeavors in the bid to curb these challenges are in pursuance. However, the existing body of literature has not well provided the updated roadmap of the advancement and key players spearheading the current success. Moreover, the description of enzyme systems and emerging paradigms with high prospects, for example, the cell-surface display system has been ill-captured in the literature. This review focuses on the lignocellulosic biocommodity pathway, with emphasis on cellulase and hemicellulase systems. The paradigm shift towards cell-surface display system and its emerging recommendable developments have also been discussed. The attempts in supplementing cellulase with other enzymes, accessory proteins, and chemical additives have also been discussed. Moreover, some of the prominent and influential discoveries in the cellulase fraternity have been discussed.Graphical abstractThe roadmap of cellulose-degrading enzymes

FRET spectroscopy—towards effective biomolecular probing

The advent of super-resolution microscopy has been a major breakthrough in bioscience research, allowing accurate molecular signaling analysis of cellular and biological materials. Forster resonance energy transfer (FRET) spectroscopy, for instance, has emerged to be significant over the past few decades, owing to its non-invasive spatiotemporal cellular and subcellular probing abilities. The success of FRET has been the resurgence of fluorescent proteins (FPs) and sophisticated imaging techniques. The developments in FP and FRET-based techniques have made FRET investigations possible in diverse biotechnological fields. However, the current literature suffers a dearth in terms of a review that explains the fundamental principles (with examples) of the major areas of FRET application. This article presents a retrospective overview of the salient exploits and advancements of FRET spectroscopy and discusses the current challenges with some options. Moreover, some of the much anticipated future applications have been highlighted.

Physicochemical Properties, Fatty Acid Profiles, and Sensory Characteristics of Fermented Beef Sausage by Probiotics Lactobacillus plantarum IIA-2C12 or Lactobacillus acidophilus IIA-2B4

Probiotics may be used to enhance the functionality and nutritional values of fermented sausages. This study aims to evaluate the physicochemical and sensory properties of beef sausages fermented by lactic acid bacteria of Lactobacillus plantarum IIA-2C12 and L. acidophilus IIA-2B4. These strains were isolated from beef cattle and have shown to display probiotic features. While the nutrient contents were not affected by the probiotics, the pH, texture, and color varied among the sausages. Further analysis on fatty acids showed different profiles of saturated (C14:0, C17:0, and C20:0) and unsaturated (C14:1, C18:1n9c, C18:2n6c, and C22:6n3) fatty acids in sausages with probiotics. Gas chromatography-mass spectrometry further revealed some flavor development compounds including acid, alcohols, aldehydes, aromatic, ketones, sulfur, hydrocarbons and terpenes, varied among the sausages. Hedonic test showed no difference in the preference toward aroma, texture, and color for untrained panelists.

Adaptive Strategies of Bacillus thuringiensis Isolated from Acid Mine Drainage Site in Sabah, Malaysia

The adaptive process in bacteria is driven by specific genetic elements which regulate phenotypic characteristics such as tolerance to high metal ion concentrations and the secretion of protective biofilms. Extreme environments such as those associated with heavy metal pollution and extremes of acidity offer opportunities to study the adaptive mechanisms of microorganisms. This study focused on the genome analysis of Bacillus thuringiensis (Bt MCMY1), a gram positive rod shaped bacterium isolated from an acid mine drainage site in Sabah, Malaysia by using a combination of Single Molecule Real Time DNA Sequencing, Scanning Electron Microscopy (SEM) and Fourier Transform Infrared Spectroscopy (FTIR). The genome size of Bt MCMY1 was determined to be 5,458,152 bases which was encoded on a single chromosome. Analysis of the genome revealed genes associated with resistance to Copper, Mercury, Arsenic, Cobalt, Zinc, Cadmium and Aluminum. Evidence from SEM and FTIR indicated that the bacterial colonies form distinct films which bear the signature of polyhydroxyalkanoates (PHA) and this finding was supported by the genome data indicating the presence of a genetic pathway associated with the biosynthesis of PHAs. This is the first report of a Bacillus sp. isolated from an acid mine drainage site in Sabah, Malaysia and the genome sequence will provide insights into the manner in which B. thuringiensis adapts to acid mine drainage.

Elucidating endotoxin-biomolecule interactions with FRET: extending the frontiers of their supramolecular complexation

Endotoxin has been one of the topical chemical contaminants of major concern to researchers, especially in the field of bioprocessing. This major concern of researchers stems from the fact that the presence of Gram-negative bacterial endotoxin in intracellular products is unavoidable and requires complex downstream purification steps. For instance, endotoxin interacts with recombinant proteins, peptides, antibodies and aptamers and these interactions have formed the foundation for most biosensors for endotoxin detection. It has become imperative for researchers to engineer reliable means/techniques to detect, separate and remove endotoxin, without compromising the quality and quantity of the end-product. However, the underlying mechanism involved during endotoxin-biomolecule interaction is still a gray area. The use of quantitative molecular microscopy that provides high resolution of biomolecules is highly promising, hence, may lead to the development of improved endotoxin detection strategies in biomolecule preparation. Förster resonance energy transfer (FRET) spectroscopy is one of the emerging most powerful tools compatible with most super-resolution techniques for the analysis of molecular interactions. However, the scope of FRET has not been well-exploited in the analysis of endotoxin-biomolecule interaction. This article reviews endotoxin, its pathophysiological consequences and the interaction with biomolecules. Herein, we outline the common potential ways of using FRET to extend the current understanding of endotoxin-biomolecule interaction with the inference that a detailed understanding of the interaction is a prerequisite for the design of strategies for endotoxin identification and removal from protein milieus.