Role of Probiotics in the Management of COVID-19: A Computational Perspective

Coronavirus disease 2019 (COVID-19) was declared a pandemic at the beginning of 2020, causing millions of deaths worldwide. Millions of vaccine doses have been administered worldwide; however, outbreaks continue. Probiotics are known to restore a stable gut microbiota by regulating innate and adaptive immunity within the gut, demonstrating the possibility that they may be used to combat COVID-19 because of several pieces of evidence suggesting that COVID-19 has an adverse impact on gut microbiota dysbiosis. Thus, probiotics and their metabolites with known antiviral properties may be used as an adjunctive treatment to combat COVID-19. Several clinical trials have revealed the efficacy of probiotics and their metabolites in treating patients with SARS-CoV-2. However, its molecular mechanism has not been unraveled. The availability of abundant data resources and computational methods has significantly changed research finding molecular insights between probiotics and COVID-19. This review highlights computational approaches involving microbiome-based approaches and ensemble-driven docking approaches, as well as a case study proving the effects of probiotic metabolites on SARS-CoV-2.

Drug Discovery of Spinal Muscular Atrophy (SMA) from the Computational Perspective: A Comprehensive Review

Spinal muscular atrophy (SMA), one of the leading inherited causes of child mortality, is a rare neuromuscular disease arising from loss-of-function mutations of the survival motor neuron 1 (SMN1) gene, which encodes the SMN protein. When lacking the SMN protein in neurons, patients suffer from muscle weakness and atrophy, and in the severe cases, respiratory failure and death. Several therapeutic approaches show promise with human testing and three medications have been approved by the U.S. Food and Drug Administration (FDA) to date. Despite the shown promise of these approved therapies, there are some crucial limitations, one of the most important being the cost. The FDA-approved drugs are high-priced and are shortlisted among the most expensive treatments in the world. The price is still far beyond affordable and may serve as a burden for patients. The blooming of the biomedical data and advancement of computational approaches have opened new possibilities for SMA therapeutic development. This article highlights the present status of computationally aided approaches, including in silico drug repurposing, network driven drug discovery as well as artificial intelligence (AI)-assisted drug discovery, and discusses the future prospects.

Lactobacillus Strains Alleviated Hyperlipidemia and Liver Steatosis in Aging Rats via Activation of AMPK

In this study, we hypothesized that different strains of Lactobacillus can alleviate hyperlipidemia and liver steatosis via activation of 5′ adenosine monophosphate-activated protein kinase (AMPK), an enzyme that is involved in cellular energy homeostasis, in aged rats. Male rats were fed with a high-fat diet (HFD) and injected with D-galactose daily over 12 weeks to induce aging. Treatments included (n = 6) (i) normal diet (ND), (ii) HFD, (iii) HFD-statin (lovastatin 2 mg/kg/day), (iv) HFD-Lactobacillus fermentum DR9 (10 log CFU/day), (v) HFD-Lactobacillus plantarum DR7 (10 log CFU/day), and (vi) HFD-Lactobacillus reuteri 8513d (10 log CFU/day). Rats administered with statin, DR9, and 8513d reduced serum total cholesterol levels after eight weeks (p < 0.05), while the administration of DR7 reduced serum triglycerides level after 12 weeks (p < 0.05) as compared to the HFD control. A more prominent effect was observed from the administration of DR7, where positive effects were observed, ranging from hepatic gene expressions to liver histology as compared to the control (p < 0.05); downregulation of hepatic lipid synthesis and β-oxidation gene stearoyl-CoA desaturase 1 (SCD1), upregulation of hepatic sterol excretion genes of ATP-binding cassette subfamily G member 5 and 8 (ABCG5 and ABCG8), lesser degree of liver steatosis, and upregulation of hepatic energy metabolisms genes AMPKα1 and AMPKα2. Taken altogether, this study illustrated that the administration of selected Lactobacillus strains led to improved lipid profiles via activation of energy and lipid metabolisms, suggesting the potentials of Lactobacillus as a promising natural intervention for alleviation of cardiovascular and liver diseases.

Lactobacillus plantarum DR7 improved upper respiratory tract infections via enhancing immune and inflammatory parameters: A randomized, double-blind, placebo-controlled study

The aims of this study were to investigate the effects of Lactobacillus plantarum DR7 isolated from bovine milk against upper respiratory tract infections (URTI) and elucidate the possible mechanisms underlying immunomodulatory properties. The DR7 strain (9 log cfu/d) was administered for 12 wk in a randomized, double-blind, and placebo-controlled human study involving 109 adults (DR7, n = 56; placebo, n = 53). Subjects were assessed for health conditions monthly via questionnaires, and blood samples were evaluated for cytokine concentrations, peroxidation and oxidative stress, and gene expression in T cells and natural killer (NK) cells. The administration of DR7 reduced the duration of nasal symptoms (mean difference 5.09 d; 95% CI: 0.42-9.75) and the frequency of URTI (mean difference 0.32; 95% CI: 0.01-0.63) after 12 and 4 wk, respectively, compared with the placebo. The DR7 treatment suppressed plasma proinflammatory cytokines (IFN-γ, TNF-α) in middle-aged adults (30 to 60 yr old), while enhancing anti-inflammatory cytokines (IL-4, IL-10) in young adults (<30 yr old), accompanied by reduced plasma peroxidation and oxidative stress levels compared with the placebo. Young adults who received DR7 showed higher expression of plasma CD44 and CD117 by 4.50- and 2.22-fold, respectively, compared with the placebo. Meanwhile, middle-aged adults showed lower expression of plasma CD4 and CD8 by 11.26- and 1.80-fold, respectively, compared with the placebo, indicating less T-cell activation. In contrast, both young and middle-aged adults who received DR7 showed enhanced presence of nonresting and mature NK cells compared with those who received the placebo. We postulate that DR7 alleviated the symptoms of URTI by improving inflammatory parameters and enhancing immunomodulatory properties.

Lactobacillus Strains Alleviated Aging Symptoms and Aging-Induced Metabolic Disorders in Aged Rats

Aging is an inevitable and ubiquitous progress that affects all living organisms. A total of 18 strains of lactic acid bacteria (LAB) were evaluated on the activation of adenosine monophosphate-activated protein kinase (AMPK), an intracellular energy sensor mediating lifespan extension. The cell-free supernatant (CFS) of Lactobacillus fermentum DR9 (LF-DR9), Lactobacillus paracasei OFS 0291 (LP-0291), and Lactobacillus helveticus OFS 1515 (LH-1515) showed the highest activation of AMPK and was further evaluated. The phosphorylation of AMPK by these three LAB strains was more evident in U2OS and C2C12 cells, compared to the other cell lines and control (P < .05). Using premature senescent Sprague-Dawley rats induced by D-galactose (D-gal), the administration of LAB (10 log CFU/rat/day) for 12 weeks prevented the shortening of telomere length in D-gal-treated rats compared to the untreated control (P < .05). LF-DR9 lowered gene expression of p53, a known senescent biomarker, in gastrocnemius muscle and tibia compared to the control. The selected LAB strains also enhanced lipid, renal, and liver profile of rats, suggesting added potential of the strains in preventing aging-induced metabolic diseases. Strain LP-0291 and LH-1515 showed ability to adhere to mucin, no antibiotic resistance, tolerated and proliferated under gastric and intestinal simulated conditions, and inhibited the growth of pathogens Escherichia coli, Staphylococcus aureus, and Staphylococcus epidermidis, comparable to commercial probiotic LF-DR9 and Lactobacillus sakei Probio 65. This study provided an insight into the potential of LAB for exhibiting antisenescence effects, with potentials as new medicinal foods for targeted antiaging therapies.

Lactobacillus plantarum DR7 Reduces Cholesterol via Phosphorylation of AMPK That Down-regulated the mRNA Expression of HMG-CoA Reductase

Hypercholesterolemia is one of the primary risk factors for cardiovascular diseases. The use of lactobacilli probiotics to reduce blood cholesterol levels have been extensively reported. However, more information is needed to evaluate the possible mechanisms involved and to identify possible targets for further therapeutic development. In this study, strains of lactobacilli were screened based on the ability to assimilate cholesterol, and prevention of cholesterol accumulation in hepatic (HepG2) and intestinal (HT-29) cells. Cell free supernatant (CFS) from Lactobacillus plantarum DR7 showed a higher ability to assimilate cholesterol, reduction in cholesterol accumulation in both HepG2 and HT-29 cells, accompanied by reduced mRNA expression of HMG-CoA reductase (HMGCR) in HepG2 (p<0.05), compared to other lactobacilli. The reduction of HMGCR expression was also diminished in the presence of an AMPK inhibitor (Compound C), suggesting that L. plantarum DR7 exerted its effect via the AMPK pathway, typically via the phosphorylation of AMPK instead of the AMPK mRNA expression in HepG2 (p<0.05). Altogether, our present study illustrated that lactobacilli could exert cholesterol lowering properties along the AMPK pathway, specifically via phosphorylation of AMPK that led to reduced expression of HMGCR.

Aerothermoelastic-Acoustics Simulation of Flight Vehicles

This paper describes a novel computational-fluid-dynamics-based numerical solution procedure for effective simulation of aerothermoacoustics problems with application to aerospace vehicles. A finite element idealization is employed for both fluid and structure domains, which fully accounts for thermal effects. The accuracies of both the fluid and structure capabilities are verified with flight- and ground-test data. A time integration of the structural equations of motion, with the governing flow equations, is conducted for the computation of the unsteady aerodynamic forces, which uses a transpiration boundary condition at the surface nodal points in lieu of the updating of the fluid mesh. Two example problems are presented herein to that effect. The first one relates to a cantilever wing with a NACA 0012 airfoil. The solution results demonstrate the effect of temperature loading that causes a significant increase in acoustic response. A second example, the hypersonic X-43 vehicle, is also analyzed; and relevant results are presented. The common finite element-based aerothermoelastic-acoustics simulation process, its applicability to the efficient and routine solution of complex practical problems, the employment of the effective transpiration boundary condition in the computational fluid dynamics solution, and the development and public domain distribution of an associated code are unique features of this paper.

Probiotics and the BSH-related cholesterol lowering mechanism: a Jekyll and Hyde scenario

Probiotic microorganisms have been documented over the past two decades to play a role in cholesterol-lowering properties via various clinical trials. Several mechanisms have also been proposed and the ability of these microorganisms to deconjugate bile via production of bile salt hydrolase (BSH) has been widely associated with their cholesterol lowering potentials in prevention of hypercholesterolemia. Deconjugated bile salts are more hydrophobic than their conjugated counterparts, thus are less reabsorbed through the intestines resulting in higher excretion into the feces. Replacement of new bile salts from cholesterol as a precursor subsequently leads to decreased serum cholesterol levels. However, some controversies have risen attributed to the activities of deconjugated bile acids that repress the synthesis of bile acids from cholesterol. Deconjugated bile acids have higher binding affinity towards some orphan nuclear receptors namely the farsenoid X receptor (FXR), leading to a suppressed transcription of the enzyme cholesterol 7-alpha hydroxylase (7AH), which is responsible in bile acid synthesis from cholesterol. This notion was further corroborated by our current docking data, which indicated that deconjugated bile acids have higher propensities to bind with the FXR receptor as compared to conjugated bile acids. Bile acids-activated FXR also induces transcription of the IBABP gene, leading to enhanced recycling of bile acids from the intestine back to the liver, which subsequently reduces the need for new bile formation from cholesterol. Possible detrimental effects due to increased deconjugation of bile salts such as malabsorption of lipids, colon carcinogenesis, gallstones formation and altered gut microbial populations, which contribute to other varying gut diseases, were also included in this review. Our current findings and review substantiate the need to look beyond BSH deconjugation as a single factor/mechanism in strain selection for hypercholesterolemia, and/or as a sole mean to justify a cholesterol-lowering property of probiotic strains.

Incidental renal cell carcinoma originating from a native kidney after en-bloc resection for adrenal carcinoma in a kidney transplant recipient

BACKGROUND

Renal transplantation is the best treatment for patients with end-stage renal disease. Although there is significantly increased risk of malignancy after renal transplantation, carcinoma of the native kidney is very rare, and moreover, the risk of endocrinologic malignancy after renal transplantation is lower than in the general population and adrenal cortical carcinoma extremely rare. We report a case of incidental renal cell carcinoma originating from a native kidney after en-bloc resection for adrenal carcinoma in a kidney transplant recipient.

CASE REPORT

A 57 year-old male patient had undergone living-donor kidney transplantation for chronic renal failure from hypertension 15 years earlier and had a right adrenal tumor diagnosed on surveillance abdomen-pelvis computerized tomography. Based on 24-hour catecholamine laboratory findings, nonfunctioning tumor was suspected. The planned en-bloc resection of right adrenal gland and right native kidney combining the perirenal tissue and Gerota fascia was performed, because the tumor was suspicious for malignancy and could possibly invade the perirenal tissue or right kidney. On the final pathology, combined adrenal cortical carcinoma and incidental renal cell carcinoma was confirmed. Renal cell carcinoma was papillary, type I, and stage T1N0M0. Adrenal cortical carcinoma was 7.6 × 6.5 cm in size, had marked nuclear atypia, and was grade IV/IV. Mitotic counts were >10 per high-power field, but it had no capsular invasion or vascular invasion, and free resection margin was confirmed. In the preoperative period, he had taken immunosuppressants FK506 and mycophenolate sodium, but after combined carcinomas were confirmed, the regimen of combination of immunosuppressants was changed to sirolimus with low-dose FK506 and half-dose mycophenolate sodium.

Prenylated xanthones from mangosteen as promising cholinesterase inhibitors and their molecular docking studies

Garcinia mangostana is a well-known tropical plant found mostly in South East Asia. The present study investigated acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) inhibitory activities of G. mangostana extract and its chemical constituents using Ellman's colorimetric method. Cholinesterase inhibitory-guided approach led to identification of six bioactive prenylated xanthones showing moderate to potent cholinesterases inhibition with IC50 values of lower than 20.5 μM. The most potent inhibitor of AChE was garcinone C while γ-mangostin was the most potent inhibitor of BChE with IC50 values of 1.24 and 1.78 μM, respectively. Among the xanthones, mangostanol, 3-isomangostin, garcinone C and α-mangostin are AChE selective inhibitors, 8-deoxygartanin is a BChE selective inhibitor while γ-mangostin is a dual inhibitor. Preliminary structure-activity relationship suggests the importance of the C-8 prenyl and C-7 hydroxy groups for good AChE and BChE inhibitory activities. The enzyme kinetic studies indicate that both α-mangostin and garcinone C are mixed-mode inhibitors, while γ-mangostin is a non-competitive inhibitor of AChE. In contrast, both γ-mangostin and garcinone C are uncompetitive inhibitors, while α-mangostin is a mixed-mode inhibitor of BChE. Molecular docking studies revealed that α-mangostin, γ-mangostin and garcinone C interacts differently with the five important regions of AChE and BChE. The nature of protein-ligand interactions is mainly hydrophobic and hydrogen bonding. These bioactive prenylated xanthones are worthy for further investigations.

Does procurement technique affect posttransplant graft function in deceased donor liver transplantation?

INTRODUCTION

Various techniques have been described deceased donor liver transplantation (DDLT) procurement. One is a technique whereby almost total dissection is done in the porta hepatis and perihepatic detachment is carried out before cross-clamping the donor aorta. In another approach, after the donor aorta is cross-clamped, rapid and minimal en bloc dissection is performed with minimal manipulation. We evaluated early posttransplant graft function among liver procurement techniques.

METHOD

Between January 2008 and August 2012, we performed 45 consecutive adult DDLTs. One patient was excluded from this analysis due to early death from sepsis after transplantation. The 44 included patients were divided into two cohorts according to the procurement technique: A warm dissection (n = 23; 52%) and a cold dissection group (n = 21; 48%). We compared early posttransplant graft function using the aspartate aminotransferase (AST), alanine aminotransferase (ALT), total bilirubin (T-bil), and prothrombin time (PT) values of the two groups from the first to seventh postoperative day.

RESULT

The AST values in the warm group were significantly greater than those in the cold group on postoperative days 3 and 5. In addition, the ALT values in the warm group were greater than those in the cold group on postoperative days 4, 5, and 6. Moreover, the T-bil values in the warm group were greater than those in the cold group on postoperative days 2, 3, 4, 5, 6, and 7. However, there were no differences in PT values.

CONCLUSION

During liver procurement for DDLT, rapid en bloc procurement with minimal manipulation after clamping the donor aorta achieved better early graft function posttransplantation.

Eurycomanone, the major quassinoid in Eurycoma longifolia root extract increases spermatogenesis by inhibiting the activity of phosphodiesterase and aromatase in steroidogenesis

ETHNOPHARMACOLOGICAL RELEVANCE

Eurycoma longifolia Jack (Simaroubaceae family), known locally as 'Tongkat Ali' by the ethnic population, is popularly taken as a traditional remedy to improve the male libido, sexual prowess and fertility. Presently, many tea, coffee and carbonated beverages, pre-mixed with the root extract are available commercially for the improvement of general health and labido. Eurycomanone, the highest concentrated quassinoid in the root extract of E. longifolia improved fertility by increasing testosterone and spermatogenesis of rats through the hypothalamus-pituitary-gonadal axis, but the mechanisms underlying the effects are not totally clear.

AIM OF THE STUDY

To provide evidences on the plant ethnopharmacological use and the involvement of eurycomanone, the major indigenous plant quassinoid in testosterone steroidogenesis and spermatogenesis increase.

MATERIAL AND METHODS

The rat testicular Leydig cell-rich interstitial cells were isolated and incubated in the culture medium M199. The viability of the cells was determined with trypan blue staining and the concentration of the viable cells was counted with a haemocytometer. The 3β-hydroxysteroid dehydrogenase (HSD) staining method was used to measure the abundance of Leydig cells in the preparation. Eurycomanone and the standard steroidogenesis inhibitors were incubated with 1.0 × 10(5) cells, and after 2h, the testosterone and the oestrogen concentrations were determined by the ELISA method. Computational molecular docking was performed to determine the binding affinity of the compound at the respective steroidogenesis enzymes.

RESULTS

Eurycomanone (EN) significantly increased testosterone production dose-dependently at 0.1, 1.0 and 10.0 μM (P<0.05), but the two lower doses when combined with 3-isobutyl-1-methylxanthine (IBMX), the phosphodiesterase inhibitor were not significantly higher than EN or IBMX alone, except at a higher concentration. The molecular docking studies indicated EN and IBMX were binding at different sites of the enzyme. EN has no reversal of inhibition by aminoglutethimide, ketoconazole or nifedipine at the respective steroidogenesis enzyme. The quassinoid was also non-responsive to the inhibition of oestrogen receptor by tamoxifen, but displayed improved formestane inhibition of aromatase in reducing oestrogen production. The molecular docking studies further supported that EN and formestane bound to aromatase with similar orientations and free energy binding values.

CONCLUSION

Eurycomanone enhanced testosterone steroidogenesis at the Leydig cells by inhibiting aromatase conversion of testosterone to oestrogen, and at a high concentration may also involve phosphodiesterase inhibition. The quassinoid may be worthy for further development as a phytomedicine to treat testosterone-deficient idiopathic male infertility and sterility.

Surgical outcomes and prognostic factors for ampulla of Vater cancer

BACKGROUND AND AIMS

The prognosis for patients with ampulla of Vater cancer is better than other periampullary cancers. The aim of the present study is to determine the clinicopathologic factors predictive of survival and recurrence in patients with ampulla of Vater cancer.

MATERIAL AND METHODS

From 1991 to 2008, we identified and reviewed 78 patients with ampulla of Vater cancer retrospectively. Clinicopathologic factors possibly influencing survival and recurrence were statistically analyzed.

RESULTS

Pancreaticoduodenectomy was performed in 68 patients and 2 patients underwent transduodenal ampullectomy. Hospital mortality was 2.6%. The 5-year survival rates following resection were 59.9%. Univariate analysis for overall survival revealed that total bilirubin greater than 5 mg/dl, ulcerative tumors, differentiation, and pancreatic invasion were significant prognostic factors. Recurrence occurred in 31 patients. Univariate analysis for disease-free survival revealed that total bilirubin greater than 5mg/dl, preoperative biliary drainage, tumor differentiation, and stage were statistically significant. Multivariate analysis revealed that tumor differentiation was an independent prognostic factor for recurrence. The presence of lymph node metastasis did not affect overall survival significantly in this study. However, two or more metastatic lymph nodes significantly affect disease-free survival.

CONCLUSIONS

Pancreaticoduodenectomy is a safe surgical procedure with acceptable long-term survival for ampulla of Vater cancer. Pancreaticoduodenectomy with lymph node dissection might control lymph node spread and enhance survival outcome.

Electric field-induced coherent control in GaAs: polarization dependence and electrical measurement [Invited]

A static electric field enables coherent control of the photoexcited carrier density in a semiconductor through the interference of one- and two-photon absorption. An experiment using optical detection is described. The polarization dependence of the signal is consistent with a calculation using a 14-band k · p model for GaAs. We also describe an electrical measurement. A strong enhancement of the phase-dependent photocurrent through a metal-semiconductor-metal structure is observed when a bias of a few volts is applied. The dependence of the signal on bias and laser spot position is studied. The field-induced enhancement of the signal could increase the sensitivity of semiconductor-based carrier-envelope phase detectors, useful in stabilizing mode-locked lasers for use in frequency combs.

Optical coherent control induced by an electric field in a semiconductor: a new manifestation of the Franz-Keldysh effect

In (100)-oriented GaAs illuminated at normal incidence by a laser and its second harmonic, interference between one- and two-photon absorption results in ballistic current injection, but not modulation of the overall carrier injection rate. Results from a pump-probe experiment on a transversely biased sample show that a constant electric field enables coherent control of the carrier injection rate. We ascribe this to the nonlinear optical Franz-Keldysh effect and calculate it for a two-band parabolic model. The mechanism is relevant to centrosymmetric semiconductors as well.

Contactless photoconductive terahertz generation

We describe a pulsed terahertz (THz) emitter that uses a rapidly oscillating, high-voltage bias across electrodes insulated from a photoconductor. Because no carriers are injected from the electrodes, trap-enhanced electric fields do not form. The resulting uniform field allows excitation with a large laser spot, lowering the carrier density for a given pulse energy and increasing the efficiency of THz generation. Compared to a dc bias, less susceptibility to damage is observed.

Terahertz near-field enhancement in narrow rectangular apertures on metal film

We report huge field accumulations in rectangular aperture arrays on thin metal film by using shape resonance in THz frequency region. A huge far-field transmission enhancement is observed in samples of various widths ranging from 10 mum to 1.8 mum which correspond to only an order of lambda/100. Theoretical calculations based on vector diffraction theory indicates 230 times near-field enhancement in case of the 1.8 mum wide rectangular aperture. Transmission measurement through the single rectangular aperture shows that the shape resonance, not the periodicity, is mainly responsible for the transmission enhancement and the corresponding field enhancement.

Central bisectionectomy for centrally located hepatocellular carcinoma

BACKGROUND

Central bisectionectomy, which involves the removal of the central hepatic segments (IVA, IVB, V, VIII) for hepatocellular carcinoma (HCC), is performed to reduce the volume of resected liver and to overcome the problem of insufficient future residual volume.

METHODS

Twenty-seven patients with HCC underwent central bisectionectomy from January 1998 to April 2007 in one hospital. The surgical techniques, clinicopathological characteristics and outcomes were reviewed.

RESULTS

The median operating time was 330 min. Twelve patients developed postoperative complications and two died. The most common complication, occurring in five patients, was bile duct injury leading to biloma or bile leakage. Median follow-up was 19.1 (range 1.4-102.2) months and eight patients developed a recurrence. Twenty-four patients were alive at the time of writing.

CONCLUSION

Although biliary complications occur somewhat frequently, central bisectionectomy in centrally located HCC can be performed safely to preserve liver volume.

Effects of ultraviolet intensity and wavelength on the photolysis of triclosan

The effects of ultraviolet (UV) intensity and wavelength on triclosan (TCS) photodegradation kinetic, efficiency, mechanisms and pathway were studied. The TCS photodegradation followed the pseudo-first order kinetic model at all UV intensities examined at the wavelengths of 254 and 365 nm and the photodegradation rate increased with increasing UV intensity. TCS photodegradation efficiencies of 90 to 98% and 79 to 90% were obtained at the wavelengths of 254 and 365 nm, respectively. TCS was degraded mainly by photon induced hydroxyl radicals while the direct photon reaction with TCS played a subordinate role. Chlorophenol, dichlorophenol and phenol were the intermediates detected in all experiments conducted. Dibenzodichloro-p-dioxin and dibenzo-p-dioxin were observed as the intermediates only at lower UV intensities investigated at the wavelength of 365 nm. Based on these intermediates, a complete TCS photolysis pathway was proposed for the first time.

Lead biosorption by waste biomass of Corynebacterium glutamicum generated from lysine fermentation process

Biomass waste, mainly Corynebacterium glutamicum, is generated from large-scale lysine fermentation process. In this study, protonated C. glutamicum biomass was evaluated as a biosorbent for the removal of lead from synthetic wastewater. As Pb2+ were bound to the biomass, the solution pH deceased, indicating that protons in the biomass were exchanged with lead ions. The Corynebacterium biomass bound Pb2+ at up to 2.74 mmol g(-1) at pH 5, where lead does not precipitate. Compared with other biosorbents and conventional sorbents, such as natural zeolite, activated carbon and synthetic ion exchange resin, the protonated C. glutamicum biomass was considered to be a useful biomaterial for lead biosorption.

Increasing rice productivity and yield by manipulation of starch synthesis

Plant productivity and yield are dependent on source-sink relationships, i.e. the capacity of source leaves to fix CO2 and the capacity of developing sink tissues and organs to assimilate and convert this fixed carbon into dry matter. Studies from our laboratories as well as others have demonstrated that rice productivity and yield are mainly sink-limited during its development because of limited capacity to utilize the initial photosynthetic product (triose phosphate). This limitation in triose phosphate utilization, evident at both the vegetative and reproductive stages of rice development, may be associated with limited capacity for carbohydrate synthesis in rice leaves (which are poor accumulators of starch) or feedback due to limited sink strength of developing seeds. Strategies in improving triose phosphate utilization by enhancing starch production in leaves and developing seeds by the expression of engineered genes for ADP glucose pyrophosphorylase, a key regulatory enzyme of starch biosynthesis, are discussed.

Identification of a cytoskeleton-associated 120 kDa RNA-binding protein in developing rice seeds

During rice seed development, prolamine RNAs are localized to the surface of the prolamine storage protein bodies (PBs), organelles bounded by the endoplasmic reticulum (ER). The exact mechanism by which prolamine RNAs are enriched on this ER subdomain is not known but recent evidence indicates the directed transport and targeting of prolamine RNAs to the prolamine PBs. As such a process involves RNA signal determinants and cytoskeleton-interacting proteins that recognize these signals, we obtained an enriched cytoskeleton-PB fraction and identified a prominent RNA-binding activity, Rp120, by RNA-binding UV-cross-linking assay. Recombinant cDNA clones of Rp120 revealed that the primary sequence shared considerable structural homology to the human transcriptional coactivator p100 and possessed a modular organization, four nucleic acid-binding SN domains, a tudor domain and a coil-coil domain. Consistent with the presence of SN domains, Rp120 binds a variety of RNAs including prolamine RNA. Interaction with the latter RNA, however, was specific as binding activity was evident only to the prolamine 3' UTR and not to the 5' UTR or coding sequences. Rp120 is also able to interact with other proteins as its sedimentation behavior in sucrose density gradient suggests an association with the cytoskeleton. The presence of a tudor domain, suggested to have a role in RNA processing or transport, together with the SN and coiled-coil domains are consistent with the view that Rp120 may be involved in RNA sorting in rice endosperm.

Investigation of subunit function in ADP-glucose pyrophosphorylase

ADP-glucose pyrophosphorylase (AGPase), a key regulatory enzyme in higher plant starch biosynthesis, is composed of a pair of large and small subunits (alpha(2)beta(2)). Current evidence suggests that the large subunit has primarily a regulatory function, while the small subunit has both regulatory and catalytic roles. To define the structure-function relationship of the large subunit (LS), the LS of potato AGPase was subjected to chemical mutagenesis and coexpressed with the wild-type (WT) small subunit (SS) cDNA in an AGPase defective Escherichia coli strain. An LS mutant (M143) was isolated, which accumulated very low levels of glycogen compared to the WT recombinant AGPase, but maintained normal catalytic activity when assayed under saturating conditions. Sequence analysis revealed that M143 has a single amino acid change, V463I, which lies adjacent to the C-terminus. This single mutation had no effect on the Km for ATP and Mg(2+), which were similar to the WT enzyme. The K(m) for glucose 1-P, however, was sixfold higher than the WT enzyme. These results suggest that the LS plays a role in binding glucose 1-P through its interaction with the SS.

Transcriptional expression characteristics and subcellular localization of ADP-glucose pyrophosphorylase in the oil plant Perilla frutescens

Three ADP-glucose pyrophosphorylase clones were isolated from the cotyledon cDNA library of the oil plant, Perilla frutescens, and their intracellular localization investigated. Two of three cDNAs (PfagpS1 and PfagpS2) were homologous to the catalytic small subunit of AGPases found in other plants, while the third clone (PfagpL) was highly similar to the large subunit type. Transcripts for PfagpS1 and PfagpS2 were observed in both photosynthetic and non-photosynthetic tissue, showing the highest expression in the stem, while PfagpL transcripts were abundantly expressed in stem and cotyledon. To evaluate the subcellular localization of PfagpS2 and PfagpL as well as the maize BT2, N-terminus-GFP DNA fusion were constructed and transformed into tobacco plants. Immunoblot analysis showed that the expressed PfagpS2- and PfagpL-GFP fusions were targeted to the plastid in the heterologous tobacco system whereas the BT2-GFP remained intact, suggesting a cytoplasmic location. These intracellular assignments were confirmed by direct confocal microscopic examination. GFP signals were localized to the cytoplasm as well as in the nucleus in BT2-GFP plants, and to the plastids in PfagpS2- and PfagpL-GFP plants. Our results indicate that Perilla cotyledons contain multiple AGPase subunits, of which at least two isoforms and very likely the third, are plastidial in nature.

Messenger RNA targeting of rice seed storage proteins to specific ER subdomains

Rice seeds, a rich reserve of starch and protein, are a major food source in many countries. Unlike the seeds of other plants, which typically accumulate one major type of storage protein, rice seeds use two major classes, prolamines and globulin-like glutelins. Both storage proteins are synthesized on the endoplasmic reticulum (ER) and translocated to the ER lumen, but are then sorted into separate intracellular compartments. Prolamines are retained in the ER lumen as protein bodies whereas glutelins are transported and stored in protein storage vacuoles. Mechanisms responsible for the retention of prolamines within the ER lumen and their assembly into intracisternal inclusion granules are unknown, but the involvement of RNA localization has been suggested. Here we show that the storage protein RNAs are localized to distinct ER membranes and that prolamine RNAs are targeted to the prolamine protein bodies by a mechanism based on RNA signal(s), a process that also requires a translation initiation codon. Our results indicate that the ER may be composed of subdomains that specialize in the synthesis of proteins directed to different compartments of the plant endomembrane system.

Parameter estimates for direct and maternal genetic effects on yearling, eighteen-month, and slaughter weights of Korean native cattle

Data collected by the National Livestock Research Institute of the Rural Development Administration of Korea were used to estimate genetic parameters for yearling (YWT, n = 5,848), 18-mo (W18, n = 4,585), and slaughter (SWT, n = 2,279) weights for Korean Native cattle. Nine animal models were used to obtain REML estimates of genetic parameters: DP-2 included genetic, uncorrelated dam, and residual random effects; DQ-2 included genetic, sire x region x year-season interaction, and residual random effects; DPQ-2 was based on DQ-2 but included both interaction and dam effects; DMP-2 was based on DP-2 but with dam effect partitioned to include maternal genetic and permanent environmental effects; and DMPQ-2 was based on DMP-2 but also included sire interaction effects. Those five models included two fixed factors: region x year-season and age of dam x sex effects. Models DP-3, DQ-3, DPQ-3, and DMPQ-3 were based on DP-2, DQ-2, DPQ-2, and DMPQ-2 but included as a third fixed factor whether or not identification of the sire was known. Estimates of heritability with DMPQ-3 for YWT, with DPQ-3 for W18 and SWT when analyzed with single-trait analyses were .14, .11, and .17, respectively, and were nearly the same with bivariate analyses. Estimate of maternal heritability for YWT from single-trait analysis was .04, with estimates for other traits near zero. For bivariate analyses, the estimate for YWT was .01. With single trait analysis, estimate of the direct-maternal genetic correlation for YWT was negative (-.81). Estimates of direct genetic correlations between YWT and W18, YWT and SWT, and W18 and SWT were .99, 1.00, and .97, respectively. Estimates of environmental correlations varied from .60 to .81; the largest was between W18 and SWT. Including a fixed factor for whether sire identification was missing or not missing reduced the estimate of heritability for slaughter weight. The results suggest that the sire x region x year-season interaction is important for yearling weight and may be needed in a model for slaughter weight. Maternal effects may be of slight importance for yearling weight but of no importance for W18 and SWT. Models for national cattle evaluations for Korean Native cattle for YWT should be considered that include maternal genetic and permanent environmental as well as sire x region x year-season interaction effects, but those effects seem not to be needed for models for W18 and SWT. Not much reranking of sires occurred when ranked was based on the different models for W18 and SWT.

Parameter estimates for genetic effects on carcass traits of Korean native cattle

Data (n = 1,746) collected from 1985 through 1995 on Korean Native Cattle by the National Livestock Research Institute of Korea were used to estimate genetic parameters for marbling score, dressing percentage, and longissimus muscle area, with backfat thickness, slaughter age, or slaughter weight as covariates. Estimates were obtained with REML. Model 1 included animal genetic and residual random effects. Model 2 was extended to include an uncorrelated random effect of the dam. Model 3 was based on Model 1 but also included sire x region x year-season interaction effects. Model 4 combined Models 2 and 3. All models included fixed effects for region x year-season and age of dam x sex combinations. From single-trait analyses, estimates of heritability with covariates to adjust for backfat thickness, slaughter age, and slaughter weight from Model 4 were, respectively, .10, .08, and .01 for marbling score; .09, .12, and .16 for dressing percentage; and .18, .17, and .24 for longissimus muscle area. From three-trait analyses, estimates of genetic correlations between marbling score and dressing percentage, marbling score and longissimus muscle area, and dressing percentage and longissimus muscle area were, respectively, -.99, .20, and -.11 with backfat thickness as covariate; -.88, .47, and .01 with slaughter age as covariate; and -.03, .39, and .91 with slaughter weight as covariate. Results of this study suggest that choice of covariate (backfat thickness, slaughter age, or slaughter weight) for the model seems to be important for carcass traits for Korean Native Cattle. Including sire x region x year-season interaction effects in the model for marbling score and dressing percentage may be important because whether sire x region x year-season interaction effects were in the model affected estimates of other variance components for the three carcass traits. Whether the maternal effect was in the model had little effect on estimates of other parameters. With backfat thickness and slaughter age end points, selection for increasing marbling score would be expected to result in decreasing dressing percentage for Korean Native Cattle. With slaughter weight as a covariate for end point, increased longissimus muscle area would be associated with increased dressing percentage, and increased marbling score would be related to increased longissimus muscle area. The differences in estimates associated with choice of end point, however, need further study.

Synthesis and characterization of new cationic hexacoordinate silanes

The reaction of N,N,N',N"-pentamethyldiethylenetriamine (pmdeta) with HSiCl3 and H2SiCl2 in dry CH2Cl2 affords the novel cationic intermolecular hexacoordinate silanes [pmdeta.HSiCl2]+Cl- (1) and [pmdeta.H2SiCl]+Cl(2), respectively. The addition of N,N,N',N',N"-pentaethyldiethylenetriamine (pedeta) to a solution of HSiCl3 in dry CH2Cl2 gives the redistribution product formulated as the salt [pedeta.H2SiCl]+Cl- (3) and SiC4. Treatment of H2SiCl2 with pedeta and N,N,N',N',N",N"'-hexamethyltriethylenetetramine (hmteta) produces [pedeta.H2SiCl]+Cl(3) and [hmteta.H2SiCl]+C1- (HCl) (4). In 4, the fourth amine is not bonded to silicon. Reactions of 2, 3, and 4 with NaBPh4 give the ion exchange products [pmdeta.H2SiC1]+BPh4- (5), [pedeta.H2SiCl]+BPh4- (6), and [hmteta.H2SiCl]+BPh4- (HCl) (7), respectively. The salts 1, 5, 6, and 7 were characterized by single-crystal X-ray diffraction analysis. Most notable is that the cations in 1, 5, 6, and 7 are slightly distorted octahedra in which two hydrogen atoms are at the trans positions. The reactions of 3 with tmeda and pmdeta afford the intermolecular ligand exchange products tmeda.H2SiCl2 and 2, respectively.

Cloning of CTP:phosphocholine cytidylyltransferase cDNA from Arabidopsis thaliana

As one of the first steps to elucidate the relationship between the structure and function of CTP:phosphocholine cytidylytransferase (EC 2.7.7.15) in plants, the cytidylyltransferase cDNA of Arabidopsis thaliana was cloned and characterized. The A. thaliana cytidylyltransferase cDNA is 1447 bp long and contains an open reading frame of 993 bp coding for a protein of 331 amino acids. The deduced structure of the enzyme was composed of three main regions; the catalytic domain in the N-terminal half, the hydrophilic C-terminal region and the amphipathic domain in the middle. The catalytic domain region was relatively well conserved among different organisms, showing 76 and 72% homology with the rat and yeast protein sequences, respectively. The hydropathy profile revealed that the C-terminal non-catalytic portion of the protein was very hydrophilic, highly enriched in negatively charged aspartic acid and glutamic acid residues. In the region between the catalytic domain and the C-terminal region, there was an amphipathic alpha-helical domain, which was believed to bind the membrane surface in the active formation. Unlike animal counterparts, there was only one potential site of phosphorylation by protein kinase C and none by Ca2+/calmodulin protein kinase II in the C-terminal region. The identity of cytidylyltransferase cDNA was verified by successful transformation of a yeast mutant defective in the enzyme activity, using an expression vector inserted with the A. thaliana cytidylyltransferase cDNA. This was further confirmed by in vivo analysis of the enzyme reaction product after labeling the yeast transformants with radioactive phosphocholine. Southern analysis indicated the presence of a single copy of the citidylyltransferase gene in A. thaliana.

Gene cloning of the human cytomegalovirus (HCMV) antigen reactive with the serum from a HCMV-infected patient

The human cytomegalovirus(HCMV) gene encoding the protein reactive with the sera of HCMV-infected patient was cloned and characterized. A reactive phage clone was screened from a lambda gt11 expression library of cDNA of HCMV AD169 strain using HCMV-infected patient sera. The recombinant protein was expressed as 138 kDa-fusion protein with beta-galactosidase, which was reactive with IgM or IgG HCMV antibody-positive sera, but not with anti-HCMV antibody-negative sera. A homology search of the DNA sequence of the cloned gene with HCMV AD169 sequences revealed that it was composed of 709 base pairs spanning between 0.174 and 0.177 map units of the UL32 region of the HCMV AD169 strain genome. This position corresponded to a part of the gene encoding 150 kDa phosphoprotein-(pp150), a major tegument protein, which was reported as an immunogenic protein which evoked strong and longstanding antibody response and had no sequence homology with the proteins of other herpesviruses. These results suggested that pp150 was an immunogenic protein in natural HCMV infection and therefore this clone was regarded as a useful candidate for developing an antigen for the serodiagnosis of HCMV.

Analysis of antigenic characteristics of Rickettsia tsutsugamushi Boryong strain and antigenic heterogeneity of Rickettsia tsutsugamushi using monoclonal antibodies

Twenty-four monoclonal antibodies were produced by immunizing BALB/c mice with Rickettsia tsutsugamushi Boryong strain and used for the analysis of antigenic characteristics of R.tsutsugamushi Boryong strain and antigenic heterogeneity of R.tsutsugamushi by indirect immunofluorescent(IF) test. R. tsutsugamushi Kato, Karp, Gilliam, TA686, TA716, TA763, TC586, TH1817, and Boryong were used for the analysis of antigenic heterogeneity of R.tsutsugamushi. Five monoclonal antibodies were reactive with 27-kDa protein, four monoclonal antibodies were reactive with 47-kDa protein, and eight monoclonal antibodies were reactive with 56-kDa protein of R.tsutsugamushi Boryong strain. The reactive protein of seven monoclonal antibodies could not be identified by immunoblotting method. All monoclonal antibodies to 27-kDa protein and three monoclonal antibodies to 47-kDa protein, and five monoclonal antibodies to 56-kDa protein were reactive with three to eight strains among nine strains of R. tsutsugamushi tested. One monoclonal antibody reactive to 47-kDa protein(KI18) and two monoclonal antibodies reactive to 56-kDa protein(KI36, and KI37) reacted with all the strains of R. tsutsugamushi tested. Strain-specific monoclonal antibody(KI58) could be found among antibodies which were reactive with 56-kDa protein. There was no strain which showed same reactivity pattern to these 24 monoclonal antibodies among nine strains. From this results, it could be concluded that Boryong strain is antigenically different from other strains of R.tsutsugamushi and antigenic heterogeneity of R.tsutsugamushi is due to the antigenic diversity of several proteins of R. tsutsugamushi including 56-kDa protein.

Multiple metabolic effects of CGRP in conscious rats: role of glycogen synthase and phosphorylase

Calcitonin gene-related peptide (CGRP) is a neuropeptide that is released at the neuromuscular junction in response to nerve excitation. To examine the relationship between plasma CGRP concentration and intracellular glucose metabolism in conscious rats, we performed insulin (22 pmol.kg-1.min-1) clamp studies combined with the infusion of 0, 20, 50, 100, 200, and 500 pmol.kg-1.min-1 CGRP (plasma concentrations ranging from 2 x 10(-11) to 5 x 10(-9) M). CGRP antagonized insulin's suppression of hepatic glucose production at plasma concentrations (approximately 10(-10) M) that are only two- to fivefold its basal portal concentration. Insulin-mediated glucose disposal was decreased by 20-32% when CGRP was infused at 50 pmol.kg-1.min-1 (plasma concentration 3 x 10(-10) M) or more. The impairment in insulin-stimulated glycogen synthesis in skeletal muscle accounted for all of the CGRP-induced decrease in glucose disposal, while whole body glycolysis was increased despite the reduction in total glucose uptake. The muscle glucose 6-phosphate concentration progressively increased during the CGRP infusions. CGRP inhibited insulin-stimulated glycogen synthase in skeletal muscle with a 50% effective dose of 1.9 +/- 0.36 x 10(-10) M. This effect on glycogen synthase was due to a reduction in enzyme affinity for UDP-glucose, with no changes in the maximal velocity. In vitro CGRP stimulated both hepatic and skeletal muscle adenylate cyclase in a dose-dependent manner. These data suggest that 1) CGRP is a potent antagonist of insulin at the level of muscle glycogen synthesis and hepatic glucose production; 2) inhibition of glycogen synthase is its major biochemical action in skeletal muscle; and 3) these effects are present at concentrations of the peptide that may be in the physiological range for portal vein and skeletal muscle. These data underscore the potential role of CGRP in the physiological modulation of intracellular glucose metabolism.

In vivo insulin resistance induced by amylin primarily through inhibition of insulin-stimulated glycogen synthesis in skeletal muscle

We examined the in vivo mechanisms of amylin-induced resistance in concious rats (n = 18). During 180-min euglycemic insulin-clamp (21.5 pmol.kg-1.min-1) studies, amylin (50, 200, or 500 pmol.kg-1.min-1; plasma concentration from 3 x 10(-10) to 9 x 10(-9) M) infusion determined a 19-27% reduction in glucose uptake (117.8 +/- 7.0 vs. 145.8 +/- 11.0, 107.1 +/- 9.2 vs. 145.1 +/- 6.7, and 105.0 +/- 7.2 vs. 144.4 +/- 7.0 mumol.kg-1.min-1 at 50, 200, or 500 pmol.kg-1.min-1, respectively, P less than 0.01) versus insulin alone, whereas 10-pmol.kg-1.min-1 amylin infusion (plasma concn 5 x 10(-11) M) failed to affect insulin-mediated glucose disposal. After amylin infusion, the contribution of whole-body glycolysis to overall glucose disposal increased from 43-48 to 62-79%, whereas muscle glycogen synthesis decreased significantly at all peptide concentrations greater than 3 x 10(-10) M, completely accounting for the decrease in glucose uptake. Skeletal muscle glucose-6-phosphate concentration rose from 0.219 +/- 0.038 mumol/g (insulin alone) to 0.350 +/- 0.018, 0.440 +/- 0.020, and 0.505 +/- 0.035 mumol/g (insulin plus amylin at 50, 200, or 500 pmol.kg-1.min-1, P less than 0.01). Suppression of hepatic glucose production by insulin was unaffected by a 50-pmol.kg-1.min-1 amylin infusion (18.5 +/- 4.3 vs. 21.7 +/- 2.9 mumol.kg-1.min-1), whereas it was slightly but significantly impaired by amylin infusion at 200 pmol.kg-1.min-1 (17.8 +/- 3.9 vs. 24.7 +/- 4.5 mumol.kg-1.min-1, P less than 0.05).(ABSTRACT TRUNCATED AT 250 WORDS)

Mechanism by which calcitonin gene-related peptide antagonizes insulin action in vivo

Calcitonin gene-related peptide (CGRP) is a peptide with structural homology to amylin, which is present in nerve terminals of skeletal muscle and intestine. The effect of this peptide on in vivo insulin action was studied in conscious rats. All rats received 180 min euglycemic (5.6 mM) insulin (21.5 pmol.kg-1.min-1) clamp study in combination with [3-3H]- and [U-14C]glucose infusions. In the basal state, the plasma CGRP concentration was 36 +/- 5 pM, and the skeletal muscle CGRP concentration was 376 +/- 88 pmol/kg wet wt. CGRP was infused at 100 pmol.kg-1.min-1 during the last 90 min of the insulin clamp study and determined a rise in plasma concentration to 781 +/- 34 pM. Hepatic glucose production was stimulated by the infusion of CGRP (35.6 +/- 6.1 vs. 24.4 +/- 4.4 mumol.kg-1.min-1). During infusion in insulin alone, glucose uptake was 133.3 +/- 8.9 mumol.kg-1.min-1 and decreased to 105.5 +/- 12.2 mumol.kg-1.min-1 with CGRP. However, the whole body rates of glycolysis (3H2O generation) were higher during the infusion of CGRP (83.9 +/- 6.1 mumol.kg-1.min-1) compared with insulin alone (72.2 +/- 7.8 mumol.kg-1.min-1). By contrast, CGRP determined a severe impairment in muscle glycogen synthesis (11.7 +/- 3.9 vs. 47.8 +/- 5.0 mumol.kg-1.min-1). Skeletal muscle glucose 6-phosphate concentration was significantly increased after CGRP infusion compared with insulin alone (0.540 +/- 0.052 vs. 0.219 +/- 0.038 mumol/g wet wt; P less than 0.01).(ABSTRACT TRUNCATED AT 250 WORDS)

Analyses of RBC insulin receptor bindings in chronic liver disease

¹²⁵I-insulin binding to erythrocytes was measured to evaluate the role of insulin receptors in the mechanism of insulin resistance in partients with chronic liver disease (CLD). Patients with CLD were divided into two groups by the fasting plasma glucose level (FBS) and the glucose disappearance rate (k-glucose) during intravenous glucose tolerance tests: one with normal FBS and normal k-glucose (group I), and the other with higher FBS and lower k-glucose (group II). Insulin receptor bindings were reduced in group I patients compared with those of normal controls, but were not reduced in group II patients. Fasting insulin levels were significantly higher in group I patients than those in normal subjects, and down-regulation by hyperinsulinemia might be the cause of reduced insulin receptor bindings in these patients. However down-regulation of insulin receptors was not associated with glucose intolerance. So it is suggested that insulin resistance in CLD is not due to a primary defect of insulin receptors in peripheral tissues, and down-regulation of insulin receptors is an epiphenomenon of hyperinsulinemia.