Engineering a recombinant chitinase from the marine bacterium Bacillus aryabhattai with targeted activity on insoluble crystalline chitin for chitin oligomer production

Chitin, an abundant polysaccharide in India, is primary by-product of the seafood industry. Efficiently converting chitin into valuable products is crucial. Chitinase, transforms chitin into chitin oligomers, holds significant industrial potential. However, the crystalline and insoluble nature of chitin makes the conversion process challenging. In this study, a recombinant chitinase from marine bacteria Bacillus aryabhattai was developed. This enzyme exhibits activity against insoluble chitin substrates, chitin powder and flakes. The chitinase gene was cloned into the pET 23a plasmid and transformed into E. coli Rosetta pLysS. IPTG induction was employed to express chitinase, and purification using Ni-NTA affinity chromatography. Optimal chitinase activity against colloidal chitin was observed in Tris buffer at pH 8, temperature 55°C, with the presence of 400 mM sodium chloride. Enzyme kinetics studies revealed a Vmax of 2000 μmole min-1 and a Km of 4.6 mg mL-1. The highest chitinase activity against insoluble chitin powder and flakes reached 875 U mg-1 and 625 U mg-1, respectively. The chitinase demonstrated inhibition of Candida albicans, Fusarium solani, and Penicillium chrysogenum growth. Thin Layer Chromatography (TLC) and LC-MS analysis confirmed the production of chitin oligomers, chitin trimer, tetramer, pentamer, and hexamer, from chitin powder and flakes using recombinant chitinase.

Identification and characterization of chitinase producing marine microorganism: Unleashing the potential of chitooligosaccharides for bioethanol synthesis

The dwindling supply of the petroleum product and its carbon footprint has initiated search for a sustainable fuel and alternate feed-stocks. One such underexplored feedstock is chitin, a waste derived from sea food processing. The limitation of insolubility and crystallinity inherent in chitin is addressed with the chitin hydrolysates. In the present study, a chitinases producing marine isolate was isolated from the sediments of Arabian Sea from a depth of 20 m. In order to increase the expression of the chitinases, sequential optimisation using one factor at a time and Taguchi experimental designs were employed which resulted in a yield of 13.46 U/mL which was 2.62 fold higher than the initial bioprocess condition values. In a two-step refinery protocol, Candida albicans was evolved towards chitooligosaccharides using chemically synthesized hydrolysates. In a fed -batch fermentation design the Candida yielded a 12.8 % conversion of these commercial chitin oligosaccharides into bioethanol in a run time of 48 h. This is the first report demonstrating the potential of Candida to utilise chitin oligosaccharides for the production of bioethanol.

Experimentally Induced Hyperglycemia in Prepubertal Phase Impairs Oocyte Quality and Functionality in Adult Mice

Reproductive abnormalities in women with a history of childhood diabetes are believed to be partially attributed to hyperglycemia. Prolonged hyperglycemia can negatively affect ovarian function and fertility during reproductive life. To address this in an experimental setting, the present study used streptozotocin-induced hyperglycemic prepubertal mouse model. The impact of prolonged hyperglycemic exposure during prepubertal life on ovarian function, oocyte quality, and functional competence was assessed in adult mice. The ovarian reserve was not significantly altered; however, the in vitro maturation potential (P < 0.001), mitochondrial integrity (P < 0.01), and meiotic spindle assembly (P < 0.05-0.001) in oocytes were significantly affected in hyperglycemic animals in comparison to control groups. The results from the study suggest that prepubertal hyperglycemia can have adverse effects on the oocyte functional competence and spindle integrity during the reproductive phase of life. Because these changes can have a significant impact on the genetic integrity and developmental potential of the embryos and fetus, the observation warrants further research both in experimental and clinical settings.

Duration of dry and humidified incubation of single-step embryo culture medium and oxygen tension during sham culture do not alter medium composition

Background: The extended embryo culture using single-step medium gained popularity in clinical in vitro fertilisation (IVF). However, there are concerns about the degradation of unstable medium components and their negative effects on the developing embryos. Further, dry-incubation can increase osmolality, which can in-turn enhance the concentration of constituents of the media and their stability. Hence, this study was conducted to understand the immediate changes in the culture media constituents in relation to clinically comparable situations such as single-step extended embryo culture and use of dry and humidified-incubation in two-different gaseous conditions. Methods: Commercially available single-step medium was sham-cultured in droplets under oil in two different conditions viz. dry (37°C; 6%CO 2; 5%O 2) and humidified (37°C; 6% CO 2; atmospheric O 2) for 0h, 72h, and 120h intervals. Droplets were subjected to the sensitivity-enhanced nuclear magnetic resonance (NMR)-based profiling using 800 MHz NMR equipped with a cryogenically cooled micro-coil (1.7mm) probe. NMR profile of the embryo culture medium between the two groups were comprehensively assessed. Results: A total of ten amino acids and four energy substrates were identified from the culture medium. The medium constituents identified showed a non-significant increase in the dry-incubation group at 72h and then declined at 120h. Humidified incubation had no effects on the level of the identified medium constituents until 120h. No significant differences in the levels of medium constituents identified were observed between the dry and humidified-groups at various time-points tested. Conclusions: A non-significant variation in the levels of medium constituents observed in the dry-incubation of single-step medium most unlikely to influence a clinical outcome. However, the impact of these subtle changes on the (epi)genetic integrity of the embryos in a clinical set-up to be addressed.

A marine chitinase from Bacillus aryabhattai with antifungal activity and broad specificity toward crystalline chitin degradation

Chitinases convert chitin into chitin oligomers and are also known antifungal agents. Chitin oligomers have numerous industrial applications. However, chitin's crystalline nature requires pretreatment before breakdown into oligomers. In the study, a novel marine bacterium Bacillus aryabhattai is isolated from the Arabian Sea. Bacterial growth in different crystalline chitin substrates like chitin powder, chitin flakes, and colloidal chitin confirmed the chitinase presence in bacterium could act upon insoluble crystalline chitin with the fractional release of oligomers. The domain architecture analysis of the chitinase confirmed the presence of two N-terminal LysM domains which help enzyme action on crystalline chitin. Statistical optimization of media and Process parameters revealed glycerol, yeast extract, magnesium chloride, and manganese sulfate as significant media components along with colloidal chitin. The optimum process parameters such as pH 7, temperature 40 °C, inoculum size 12.5% (v/v), and inoculum age 20 hours enhanced the specific enzyme activity to ±146.2 U/mL, ±114.9 U/mL and ±175.4 U/mL against chitin powder, chitin flakes and colloidal chitin respectively, which is five to six times higher than basal level activity. The antifungal activity of chitinase against plant pathogenic fungi like Candida albicans and Fusarium oxysporum revealed a zone of inhibition with 14 mm diameter.

Cloning, expression, purification and characterization of chitin deacetylase extremozyme from halophilic Bacillus aryabhattai B8W22

Chitin deacetylase (CDA) (EC 3.5.1.41) is a hydrolytic enzyme that belongs to carbohydrate esterase family 4 as per the CAZY database. The CDA enzyme deacetylates chitin into chitosan. As the marine ecosystem is a rich source of chitin, it would also hold the unexplored extremophiles. In this study, an organism was isolated from 40 m sea sediment under halophilic condition and identified as Bacillus aryabhattai B8W22 by 16S rRNA sequencing. The CDA gene from the isolate was cloned and overexpressed in E. coli Rosetta pLysS and purified using a Ni-NTA affinity chromatography. The enzyme was found active on both ethylene glycol chitin (EGC) and chitooligosaccharides (COS). The enzyme characterization study revealed, maximum enzyme velocity at one hour, optimum pH at 7 with 50 mM Tris-HCl buffer, optimum reaction temperature of 30 ºC in standard assay conditions. The co-factor screening affirmed enhancement in the enzyme activity by 142.43 ± 7.13% and 146.88 ± 4.09% with substrate EGC and COS, respectively, in the presence of 2 mM Mg2+. This activity was decreased with the inclusion of EDTA and acetate in the assay solutions. The enzyme was found to be halotolerant; the relative activity increased to 116.98 ± 3.87% and 118.70 ± 0.98% with EGC and COS as substrates in the presence of 1 M NaCl. The enzyme also demonstrated thermo-stability, retaining 87.27 ± 2.85% and 94.08 ± 0.92% activity with substrate EGC and COS, respectively, upon treatment at 50 ºC for 24 h. The kinetic parameters K m, V max, and K cat were 3.06E-05 µg mL-1, 3.06E + 01 µM mg-1 min-1 and 3.27E + 04 s-1, respectively, with EGC as the substrate and 7.14E-07 µg mL-1, 7.14E + 01 µM mg-1 min-1 and 1.40E + 06 s-1, respectively, with COS as the substrate. The enzyme was found to be following Michaelis-Menten kinetics with both the polymeric and oligomeric substrates. In recent years, enzymatic conversion of chitosan is gaining importance due to its known pattern of deacetylation and reproducibility. Thus, this BaCDA extremozyme could be used for industrial production of chitosan polymer as well as chitosan oligosaccharides for biomedical application.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03073-3.

Quality Improvement Project Demonstrate that Prolonged Pre-Analytical Time Does Not Lead to False Negative Blood Cultures

Introduction/Objective

Bacterial infection is a significant cause of morbidity and mortality. Prompt identification of microorganisms and their susceptibilities to antimicrobial therapies is critical in the management of patients with bloodstream infections. Blood cultures are collected in paired aerobic and anaerobic bottles. However, transport delays might allow some organisms to grow extensively prior to incubation in the blood culture instruments, leading to false-negative culture results. The Detroit Medical Center utilizes the BD Bactec™ instruments for blood culture incubation and the Verigene DNA-based molecular assay for the identification of bacteria and major resistance genes. It has a core microbiology lab that serves 6 hospitals, however, 2 of the hospitals are remotely located.

The aim of this project was to determine if transportation delays led to significant false-negative culture results. If significant false negativity occurred, additional Bactec™ instruments would need to be purchased.

Methods

For one month, we tracked the collection of blood cultures to incubation time at one of the remote hospitals. All blood cultures that remain negative after 164 hours of incubation are routinely discarded. However, in this case, they were subcultured to a Petri plate containing chocolate agar for 30 days. Any organisms that grew were identified by standard lab techniques.

Results

Of the 547 negative culture bottles that were subcultured for possible false-negative results, only 3 (0.5%) bottles grew bacteria. All three were isolated from different patients. The mean time from blood collection to incubation in the instrument was 4-8 hours. The isolates either met criteria for contaminated cultures, or they grew the same pathogen that had previously been identified in the paired bottle from the same culture. The organisms isolated include coagulase negative Staphylococcus species, Staphylococcus pettenkoferi, and Pseudomonas aeruginosa. No unexpected pathogenic organisms were detected.

Conclusion

Our results demonstrate that prolonged pre-analytical time does not lead to false-negative blood culture results. The patients’ diagnoses were not changed, therefore, the purchase of additional blood culture instruments was not necessary. However, transportation time from the patient floors to the main microbiology lab needs to be improved to meet the recommended 2 hours pre-analytical time.

Batch and continuous studies on the removal of heavy metals from aqueous solution using biosynthesised melanin-coated PVDF membranes

Heavy metals like mercury, chromium, lead and copper present in groundwater at lower concentrations cause severe health issues and can even be fatal when consumed. The biopigment/biopolymer melanin can be reaped from different sources like bacterium, fungus, and human hair. It has excellent heavy metal ion scavenging property and can be exploited for non-biological applications, substantially including water purification. In this work, melanin nanoparticles were derived from the marine bacterium Pseudomonas stutzeri and were coated onto hydrophobic polyvinylidene fluoride (PVDF) membrane as a support, for batch and continuous removal of heavy metal studies. Batch studies on the effect of pH, temperature and adsorbate dose and continuous adsorption studies on the effect of flow rate, adsorbate and adsorbent mass loadings were carried out by using biosynthesised melanin-coated PVDF membranes for the removal of Hg(II), Cr(VI), Pb(II) and Cu(II). Scanning electron microscope (SEM) images revealed the surface morphology, Fourier-transform infrared spectroscopy (FTIR) and energy-dispersive X-ray spectroscopy (EDS) deciphered the chemical characteristics of melanin-coated PVDF membranes before and after adsorption. Contact angle measurement confirmed the improvement in hydrophilicity of PVDF membrane upon coating with melanin. The maximum removal percentages of heavy metals achieved by melanin-coated PVDF membranes under batch mode operation were 87.6%, 88.45%, 91.8% and 95.8% for mercury, chromium, lead and copper, respectively optimised at 318 K and pH of 3 for chromium and 5 for other metals. However, the continuous mode of operation with a flow rate of 0.5 mL/min having 1 mg/L of heavy metal solution concentration exposed to 50 mg of melanin loading with a working volume of 200 mL showed better removal efficiencies compared with batch mode. The dynamic studies using Thomas and Yoon-Nelson models described the transient stage of the breakthrough curve and the model constants were calculated for column design and scale-up.

Residence Time Distribution Studies in a Modified Rotating Packed Disc Contactor: Mathematical Modeling and Validation

A modified rotating packed disc contactor (RPDC) with the maximum working volume of 65 liter is designed for biological waste water treatment. A hollow disc with radial vanes mounted on the disc was a modified design of this contactor. Stimulus-response experiments were conducted in the contactor to understand liquid mixing behavior under different operating conditions. The recycle stream was also used in the operation of the contactor. Experiments were conducted for different number of discs, rotational speeds and recycle ratios. The disc design and recycle ratio had marked influence on the mixing behavior. An increase in disc rotation and recycle ratio produced a well-mixed flow behavior. Moreover, the surface area available in the RPDC was about 4 times more than the surface area available in a standard rotating biological contactor (RBC) operating at similar conditions. A mathematical model was developed for the flow behavior under recycle and a good agreement was found between the model and experimental results.

Adsorptive removal of trivalent and pentavalent arsenic from aqueous solutions using iron and copper impregnated melanin extracted from the marine bacterium Pseudomonas stutzeri

The metalloid arsenic is one of the most conspicuous groundwater contaminants in the Indian subcontinent and its removal from aqueous medium is the main focus of this study. The study aims at functionalising melanin using iron and copper for the efficient removal of arsenic and rendering water fit for consumption. Melanin obtained from the marine bacteria Pseudomonas stutzeri was functionalised by iron impregnation (Fe-melanin) and copper impregnation (Cu-melanin). Morphological studies using FESEM portrayed the impregnated iron and copper granules on the surface of melanin, while XRD analysis confirmed the presence of Fe₂O₃ and CuO on melanin. Adsorption studies on As (V) and As (III) were conducted using Fe-melanin and Cu-melanin for different operating variables like pH, temperature and contact time. More than 99% per cent of As (III) and As (V) from water was removed at a pH range between 4 and 6 within 50 min in the case of Fe-melanin and 80 min for Cu-melanin. Adsorption equilibrium studies showed better fit with Langmuir adsorption isotherm and had good agreement with Redlich-Peterson's three-parameter model. The maximum adsorption capacities of Fe-melanin and Cu-melanin obtained from Langmuir adsorption model are 50.12 and 20.39 mg/g, respectively, for As (V) and similarly 39.98 and 19.52 mg/g, respectively, for As (III). Arsenic-binding to the functionalised melanin was confirmed using FT-IR and the XPS analysis. Reuse of the adsorbent was effectively done by desorbing the iron and copper together with the bound As (III) and As (V) and further re-impregnation of iron and copper in melanin. Re-functionalised melanin showed 99% adsorption efficiency up to four cycles of adsorption/desorption.

Screening of chitin deacetylase producing microbes from marine source using a novel receptor on agar plate

Chitosan is a deacetylated form of naturally occurring polymer; chitin. On an industrial scale, the deacetylation of chitin to chitosan is performed using harsh chemicals like sodium hydroxide. This not only adds to the environmental pollution but the product is also random in terms of its deacetylation. This shortcoming can be addressed by using enzymes like chitin deacetylase (CDA). The screening of these organisms would require a reliable, fast and sensitive screening method. The deacetylation of chitin into chitosan, releases acetate as the byproduct of the reaction. A receptor which specifically binds to the acetate ion was synthesized chemically. The receptor upon binding with the acetate ion emitted a fluorescence which could be viewed using the gel documentation unit. The receptor was optimized for the screening of CDA producing microbes with the positive fungal control as Penicillium sp. and bacterial control as Bacillus megaterium. A parallel study with the 4-Nitroacetanilide, the reported screening indicator for CDA was performed. The results obtained with the receptor in the present study were concordant with the 4-Nitroacetanilide. Upon standardization, the protocol was extended for the screening of CDA producing microbes from the marine crustacean dumped soil and water samples. The CDA activity of these microbes was further confirmed using spectrophotometric MBTH assay. This is the first report using this receptor for the screening of CDA producers. The method is not only sensitive but also reproducible and can be extended for a high throughput screening of CDA producers.

Data on the removal of heavy metals from aqueous solution by adsorption using melanin nanopigment obtained from marine source: Pseudomonas stutzeri

Heavy metals are one of deadly contaminants in ground water across the globe. Thus, herein, this data set comprises experimental and modelled data on the removal of heavy metals from ground water using melanin synthesized by the marine bacteria Pseudomonas stutzeri. Characterization of biosynthesized melanin and modelling of the kinetic and the thermodynamic study on adsorption of heavy metals such as mercury (Hg(II)), lead (Pb(II)), chromium (Cr(VI)), and copper (Cu(II)) are included in this article. Apart from the study of parameters involved in adsorption such as pH, temperature, concentration and time; the data from these studies are modelled to analyze the nature and characteristic of heavy metals adsorbing to melanin nanoparticles. The figures from models, results from models as tables, characterization and analytical figures are depicted in this work.

Kinetic and thermodynamic studies on the adsorption of heavy metals from aqueous solution by melanin nanopigment obtained from marine source: Pseudomonas stutzeri

The difficulty in removal of heavy metals at concentrations below 10 mg/L has led to the exploration of efficient adsorbents for removal of heavy metals. The adsorption capacity of biosynthesized melanin for Mercury (Hg(II)), Chromium (Cr(VI)), Lead (Pb(II)) and Copper (Cu(II)) was investigated at different operating conditions like pH, time, initial concentration and temperature. The heavy metals adsorption process was well illustrated by the Lagergren's pseudo-second-order kinetic model and the equilibrium data fitted excellently to Langmuir isotherm. Maximum adsorption capacity obtained from Langmuir isotherm for Hg(II) was 82.4 mg/g, Cr(VI) was 126.9 mg/g, Pb(II) was 147.5 mg/g and Cu(II) was 167.8 mg/g. The thermodynamic parameters revealed that the adsorption of heavy metals on melanin is favorable, spontaneous and endothermic in nature. Binding of heavy metals on melanin surface was proved by Fourier Transform Infrared Spectroscopy (FT-IR) and X-ray Photoelectron Spectroscopy (XPS). Contemplating the results, biosynthesized melanin can be a potential adsorbent for efficient removal of Hg(II), Cr(VI), Pb(II) and Cu(II) ions from aqueous solution.

Laser assisted zona hatching does not lead to immediate impairment in human embryo quality and metabolism

Laser assisted zona hatching (LAH) is a routinely used therapeutic intervention in assisted reproductive technology for patients with poor prognosis. However, results are not conclusive in demonstrating the benefits of zona hatching in improving the pregnancy rate. Recent observations on LAH induced genetic instability in animal embryos prompted us to look into the effects of laser assisted zona hatching on the human preimplantation embryo quality and metabolic uptake using high resolution nuclear magnetic resonance (NMR) technology. This experimental prospective study included fifty embryos from twenty-five patients undergoing intra cytoplasmic sperm injection. Embryo quality assessment followed by profiling of spent media for the non-invasive evaluation of metabolites was performed using NMR spectroscopy 24 hours after laser treatment and compared with that of non-treated sibling embryos. Both cell number and embryo quality on day 3 of development did not vary significantly between the two groups at 24 hours post laser treatment interval. Time lapse monitoring of the embryos for 24 hours did not reveal blastomere fragmentation adjacent to the point of laser treatment. Similarly, principal component analysis of metabolites did not demonstrate any variation across the groups. These results suggest that laser assisted zona hatching does not affect human preimplantation embryo morphology and metabolism at least until 24 hours post laser assisted zona hatching. However, studies are required to elucidate laser induced metabolic and developmental changes at extended time periods.

ABBREVIATIONS

AH: assisted hatching; ART: assisted reproductive technology; DNA: deoxy-ribo nucleic acid; LAH: laser assisted hatching; MHz: megahertz; NMR: nuclear magnetic resonance; PCA: principal component analysis; PGD: preimplantation genetic diagnosis; TLM: time lapse monitoring.

Scale-up of naringinase production process based on the constant oxygen transfer rate for a novel strain of Bacillus methylotrophicus

Naringinase bioprocess based on Bacillus methylotrophicus was successfully scaled up based on constant oxygen transfer rate (OTR) as the scale-up criterion from 5-L bioreactor to 20-L bioreactor. OTR was measured in 5 and 20-L bioreactor under various operating conditions using dynamic method. The operating conditions, where complete dispersion was observed were identified. The highest OTR of 0.035 and 0.04 mMol/L/s was observed in 5 and 20-L bioreactor, respectively. Critical dissolved oxygen concentration of novel isolated strain B. methylotrophicus was found to be 20% of oxygen saturation in optimized medium. The B. methylotrophicus cells grown on sucrose had maximum oxygen uptake rate of 0.14 mMol/L/s in optimized growth medium. The cells produced the maximum naringinase activity of 751 and 778 U/L at 34 hr in 5 and 20-L bioreactors, respectively. The maximum specific growth rate of about 0.178/hr was observed at both the scales of operations. The maximum naringinase yield of 160 and 164 U/g biomass was observed in 5 and 20-L bioreactors, respectively. The growth and production profiles at both scales were similar indicating successful scale-up strategy for B. methylotrophicus culture.

Enhancement of a novel extracellular uricase production by media optimization and partial purification by aqueous three-phase system

Uricase (urate: oxygen oxidoreductase, EC 1.7.3.3), an enzyme belonging to the class of oxidoreductases, catalyzes the enzymatic oxidation of uric acid to allantoin and finds a wide variety of application as therapeutic and clinical reagent. In this study, uricase production ability of the bacterial strains isolated from deep litter poultry soil is investigated. The strain with maximum extracellular uricase production capability was identified as Xanthomonas fuscans subsp. aurantifolii based on 16S rRNA sequencing. Effect of various carbon and nitrogen sources on uricase productivity was investigated. The uricase production for this strain was optimized using statistically based experimental designs and resulted in uricase activity of 306 U/L, which is 2 times higher than initial uricase activity. Two-step purification, such as ammonium sulfate precipitation and aqueous two-phase system, was carried out and a twofold increase in yield and specific activity was observed.