Biological characterization of D-lactate dehydrogenase responsible for high-yield production of D-phenyllactic acid in Sporolactobacillus inulinus

PLA (3-D-phenyllactic acid) is an ideal antimicrobial and immune regulatory compound present in honey and fermented foods. Sporolactobacillus inulinus is regarded as a potent D-PLA producer that reduces phenylpyruvate (PPA) with D-lactate dehydrogenases. In this study, PLA was produced by whole-cell bioconversion of S. inulinus ATCC 15538. Three genes encoding D-lactate dehydrogenase (d-ldh1, d-ldh2, and d-ldh3) were cloned and expressed in Escherichia coli BL21 (DE3), and their biochemical and structural properties were characterized. Consequently, a high concentration of pure D-PLA (47 mM) was produced with a high conversion yield of 88%. Among the three enzymes, D-LDH1 was responsible for the efficient conversion of PPA to PLA with kinetic parameters of Km (0.36 mM), k_cat (481.10 s⁻¹), and k_cat/Km (1336.39 mM⁻¹ s⁻¹). In silico structural analysis and site-directed mutagenesis revealed that the Ile307 in D-LDH1 is a key residue for excellent PPA reduction with low steric hindrance at the substrate entrance. This study highlights that S. inulinus ATCC 15538 is an excellent PLA producer, equipped with a highly specific and efficient D-LDH1 enzyme.     

A novel framework for evaluating in situ breeding management strategies in endangered populations

Conservation breeding management aims to reduce inbreeding and maximize the retention of genetic diversity in endangered populations. However, breeding management of wild populations is still rare, and there is a need for approaches that provide data-driven evidence of the likelihood of success of alternative in situ strategies. Here, we provide an analytical framework that uses in silico simulations to evaluate, for real wild populations, (i) the degree of population-level inbreeding avoidance, (ii) the genetic quality of mating pairs, and (iii) the potential genetic benefits of implementing two breeding management strategies. The proposed strategies aim to improve the genetic quality of breeding pairs by splitting detrimental pairs and allowing the members to re-pair in different ways. We apply the framework to the wild population of the Critically Endangered helmeted honeyeater by combining genomic data and field observations to estimate the inbreeding (i.e., pair-kinship) and genetic quality (i.e., Mate Suitability Index) of all mating pairs for seven consecutive breeding seasons. We found no evidence of population-level inbreeding avoidance and that ~91.6% of breeding pairs were detrimental to the genetic health of the population. Furthermore, the framework revealed that neither proposed management strategy would significantly improve the genetic quality or reduce inbreeding of the mating pairs in this population. Our results demonstrate the usefulness of our analytical framework for testing the efficacy of different in situ breeding management strategies and for making evidence-based management decisions.     

Chromosome-level genome assembly of Welwitschia mirabilis,a unique Namib Desert species

Welwitschia mirabilis, which is endemic to the Namib Desert, is the only living species within the family Welwitschiaceae. This species has an extremely long lifespan of up to 2,000 years and bears a single pair of opposite leaves that persist whilst alive. However, the underlying genetic mechanisms and evolution of the species remain poorly elucidated. Here, we report on a chromosome-level genome assembly for W. mirabilis, with a 6.30-Gb genome sequence and contig N50 of 27.50 Mb. In total, 39,019 protein-coding genes were predicted from the genome. Two brassinosteroid-related genes (BRI1 and CYCD3), key regulators of cell division and elongation, were strongly selected in W. mirabilis and may contribute to their long ever-growing leaves. Furthermore, 29 gene families in the mitogen-activated protein kinase signalling pathway showed significant expansion, which may contribute to the desert adaptations of the plant. Three positively selected genes (EHMT1, EIF4E, SOD2) may be involved in the mechanisms leading to long lifespan. Based on molecular clock dating and fossil calibrations, the divergence time of W. mirabilis and Gnetum montanum was estimated at ~123.5 million years ago. Reconstruction of population dynamics from genome data coincided well with the aridification of the Namib Desert. The genome sequence detailed in the current study provides insight into the evolution of W. mirabilis and should be an important resource for further study on gnetophyte and gymnosperm evolution.     

Genomic insights into the adaptation and evolution of the nautilus,an ancient but evolving “living fossil”

The nautilus, commonly known as a “living fossil,” is endangered and may be at risk of extinction. The lack of genomic information hinders a thorough understanding of its biology and evolution, which can shed light on the conservation of this endangered species. Here, we report the first high-quality chromosome-level genome assembly of Nautilus pompilius. The assembled genome size comprised 785.15 Mb. Comparative genomic analyses indicated that transposable elements (TEs) and large-scale genome reorganizations may have driven lineage-specific evolution in the cephalopods. Remarkably, evolving conserved genes and recent TE insertion activities were identified in N. pompilius, and we speculate that these findings reflect the strong adaptability and long-term survival of the nautilus. We also identified gene families that are potentially responsible for specific adaptation and evolution events. Our study provides unprecedented insights into the specialized biology and evolution of N. pompilius, and the results serve as an important resource for future conservation genomics of the nautilus and closely related species.     

The AMP-dependent kinase pathway is upregulated in BAP1 mutant uveal melanoma

Metastatic uveal melanoma (UM) responds poorly to targeted therapies and immune checkpoint inhibitors. Loss of BRCA1-associated protein 1 (BAP1) via inactivating mutations in the BAP1 gene is associated with UM progression. Thus, molecular alterations caused by BAP1 dysfunction may be novel therapeutic targets for metastatic UM. Here, we found that phosphorylation of AMP-dependent kinase (AMPK) was elevated in BAP1-altered (or mutant) compared to BAP1-unaltered (or wild-type [WT]) UM tumors. As a readout of AMPK pathway activation, phosphorylation of an AMPK downstream effector, acetyl-CoA-carboxylase (ACC), was also elevated. BAP1 re-expression in BAP1-null UM cell lines decreased phospho-AMPK (pAMPK) and phospho-ACC (pACC) levels. AMPK phosphorylation is mediated by calcium/calmodulin dependent protein kinase kinase 2 (CaMKK2) and potentially liver kinase B1 (LKB1) in BAP1 mutant UM cells. Knockdown of AMPKα1/2 reduced the viability of BAP1 mutant UM cells, indicating a survival function of AMPK in BAP1 mutant UM. Our data suggest that the AMPK pathway is an important mechanism mediating the survival of BAP1 mutant UM. Targeting the AMPK pathway may be a novel therapeutic strategy for metastatic UM.     

Collagen organization in canine myxomatous mitral valve disease: an x-ray diffraction study

Collagen fibrils, a major component of mitral valve leaflets, play an important role in defining shape and providing mechanical strength and flexibility. Histopathological studies show that collagen fibrils undergo dramatic changes in the course of myxomatous mitral valve disease in both dogs and humans. However, little is known about the detailed organization of collagen in this disease. This study was designed to analyze and compare collagen fibril organization in healthy and lesional areas of myxomatous mitral valves of dogs, using synchrotron small-angle x-ray diffraction. The orientation, density, and alignment of collagen fibrils were mapped across six different valves. The findings reveal a preferred collagen alignment in the main body of the leaflets between two commissures. Qualitative and quantitative analysis of the data showed significant differences between affected and lesion-free areas in terms of collagen content, fibril alignment, and total tissue volume. Regression analysis of the amount of collagen compared to the total tissue content at each point revealed a significant relationship between these two parameters in lesion-free but not in affected areas. This is the first time this technique has been used to map collagen fibrils in cardiac tissue; the findings have important applications to human cardiology.     

Antidiabetic potential of oleanolic acid from Ligustrum lucidum Ait

Ligustrum lucidum Ait. has been used in traditional Chinese medicine for over 1000 years because of its anti-tumor, antimutagenic, antidiabetic, and hepatoprotective properties. The aim of this study was to determine whether oleanolic acid (OA) is the principal active compound of L. lucidum responsible for its antidiabetic properties, and to examine its effect on the expression of thyroid hormones and insulin secretion, thus revealing the mechanism by which L. lucidum modulates insulin levels in diabetes. When rats with streptozotocin-induced diabetes were treated with OA (100 and 200 mg/kg body mass per day, for 40 days), the changes in blood glucose levels and in oral glucose tolerance tests showed that hypoglycemia was more pronounced in OA-treated groups than in the diabetic control rats, and that the levels of triglyceride, total cholesterol, and low-density lipoportein cholesterol in OA-treated rats were lower than those in the diabetic control rats, whose high-density lipoprotein cholesterol increased. OA-treated rats also gained weight, and exhibited increased serum insulin levels. In contrast, OA treatment did not effect the levels of thyroid hormone or TSH in rats with streptozotocin-induced diabetes. These results indicate that OA has hypoglycemic and hypolipidemic effects. OA treatment might stimulate insulin release, and consequently, results in the modulation of glucose levels and regulation of lipid metabolism.     

Gene cloning and heterologous expression of a serine protease from Streptomyces fradiae var.k11

The gene sfp1, which encodes a predicted serine proteinase designated SFP1, was isolated by the screening of a gene library of the feather-degrading strain Streptomyces fradiae var.k11. The open reading frame of sfp1 encodes a protein of 454 amino acids with a calculated molecular mass of 46.19 kDa. Sequence analysis reveals that SFP1 possesses a typical pre-pro-mature organization that consists of a signal sequence, an N-terminal propeptide region, and a mature proteinase domain. The pre-enzyme of SFP1 was expressed in Escherichia coli and consequently purified. The 25.6 kDa fraction with protease activity separated by gel filtration chromatography indicated that the mature enzyme of SFP1 was formed by autolysis of the propeptide after its expression. The purified SFP1 is active under a broad range of pH and temperature. SFP1 has pH and temperature optima of pH 8.5 and 65 degrees C for its caseinolytic activity and pH 9 and 62 degrees C for its keratinolytic activity. SFP1 was sharply inhibited by the serine proteinase inhibitor phenylmethyl sulfonyl fluoride and exhibited a good stability to solvents, detergents, and salts. Comparison of the protease activity of SFP1 with other commercial proteases indicates that SFP1 has a considerable caseinolytic and keratinolytic activity as does proteinase K.     

Freezability of rat epididymal sperm induced by raffinose in modified Krebs-Ringer bicarbonate (mKRB) based extender solution

The objective of this study was to develop an ideal freezing extender and method for rat epididymal sperm cryopreservation. Epididymal sperm collected from 30 Wistar males was frozen, and experiments were conducted to study its post-thaw characteristics when freezing with raffinose-free buffer or various concentrations of raffinose and egg yolk dissolved in distilled and deionised water, PBS, or modified Krebs–Ringer bicarbonate (mKRB)-based extender. Different concentrations of glycerol, Equex STM, or sodium dodecyl sulfate (SDS) dissolved in either PBS or mKRB containing egg yolk were also tested. Based on the data from these experiments, further experiments tested how different sugars such as raffinose, trehalose, lactose, fructose, and glucose dissolved in mKRB with Equex STM, SDS and egg yolk supplementation affected the post-thaw characteristics of cryopreserved sperm. Cryosurvival of frozen-thawed sperm were judged by microscopic assessment of the sperm motility index (SMI), and acrosome integrity was measured using FITC-PNA staining. Thawed sperm were subjected to 3 h of a thermal resistance test. Beneficial effects on the post-thaw survival of sperm were obtained when 0.1 M raffinose in mKRB was used with 0.75% Equex STM, 0.05% SDS, and 20% egg yolk. Sperm cryopreserved with this treatment exhibited a higher motility index and maintained greater SMI and acrosome integrity throughout incubation when compared to sperm frozen in various concentrations of other cryoprotectants and trehalose, lactose, fructose, glucose. In conclusion, cryopreservation in an extender solution of raffinose dissolved in mKRB containing Equex STM, SDS and egg yolk greatly enhances the freezability of rat epididymal sperm.     

Synthesis and anti-inflammatory activity of N-phthalimidomethyl 2,3-dideoxy- and 2,3-unsaturated glycosides

3,4,6-Tri-O-acetyl-D-galactal, 3,4,6-tri-O-acetyl-D-glucal and 3,6,2',3',4'6'-hexa-O-acetyl-D-lactal were reacted with N-hydroxymethylphthalimide and boron trifluoride etherate to produce the corresponding phthalimidomethyl unsaturated glycosides via Ferrier rearrangement. When the galactal derivative was used, a non-Ferrier rearrangement product was also isolated as a minor product under classical Ferrier conditions. Phthalimidomethyl deoxy glycosides were readily prepared by hydrogenation of the unsaturated glycosides. Following deacetylation, the anti-inflammatory activities of these compounds were tested on mice and three were found to possess potent activity compared to hydrocortisone sodium succinate (HSS).