Journal of Biological Research-Thessaloniki最新文献

Background: Anthocyanins are plant secondary metabolites with key roles in attracting insect pollinators and protecting against biotic and abiotic stresses. They have potential health-promoting effects as part of the human diet. Anthocyanin biosynthesis has been elucidated in many species, enabling the development of anthocyanin-enriched fruits, vegetables, and grains; however, few studies have investigated Brassica napus anthocyanin biosynthesis.

Results: We developed a high-anthocyanin resynthesized B. napus line, Rs035, by crossing anthocyanin-rich B. rapa (A genome) and B. oleracea (C genome) lines, followed by chromosome doubling. We identified and characterized 73 and 58 anthocyanin biosynthesis genes in silico in the A and C genomes, respectively; these genes showed syntenic relationships with 41 genes in Arabidopsis thaliana and B. napus. Among the syntenic genes, twelve biosynthetic and six regulatory genes showed transgressively higher expression in Rs035, and eight structural genes and one regulatory gene showed additive expression. We identified three early-, four late-biosynthesis pathways, three transcriptional regulator genes, and one transporter as putative candidates enhancing anthocyanin accumulation in Rs035. Principal component analysis and Pearson's correlation coefficients corroborated the contribution of these genes to anthocyanin accumulation.

Conclusions: Our study lays the foundation for producing high-anthocyanin B. napus cultivars. The resynthesized lines and the differentially expressed genes we have identified could be used to transfer the anthocyanin traits to other commercial rapeseed lines using molecular and conventional breeding.

Modern biology is experiencing a deep transformation by the expansion of molecular-level measurements at all scales, using omics technologies. A key element in this transformation is the field of bioinformatics, that has-in the meanwhile-permeated pretty much all of biological and biomedical research and is now emerging as a key inter-disciplinary area that connects the natural sciences, chemical and electrical engineering, science education and science policy, on a number of science and technology fronts. The strong tradition of open access for large volumes of raw data, collections of complex results and high-quality algorithm implementations in bioinformatics makes the field a unique, special case of open science. We report on our recent research activities, the development of training initiatives in the wider region during the past years, and the lessons learned regarding our efforts away from major epicenters, within the general context of open science.

Background: Doxorubicin is a widely used anticancer drug due to its broad spectrum of antitumor activity. Various mechanisms have been proposed for its cytostatic activity, including DNA intercalation, topoisomerase II inhibition, generation of free radicals and apoptosis. The present study aims to further clarify the cytostatic activity of doxorubicin by its specific effect on (a) DNA damage, (b) micronucleation and (c) apoptosis, using a combination of different methods and cell systems such as human lymphocytes and HL-60 human leukemic cells. DNA lesions were analyzed by the alkaline comet assay in combination with formamidopyrimidine (Fpg) and human 8-oxoguanine (hOGG1) repair enzymes. Micronucleation was investigated by the Cytokinesis-Block Micronucleus assay (CBMN) in combination with Fluorescence In Situ Hybridization analysis. Impairment on mitotic apparatus was investigated by double immunofluorescence of β- and γ-tubulin. Apoptotic cell frequency was determined by the CBMN cytome assay. Complementary to the above, caspase-3 level was investigated by Western blot.

Results: It was found that doxorubicin generates DNA breakage induced by oxidative damage in DNA bases, which can be repaired by the Fpg and hOGG1 enzymes. Increased micronucleus frequency was identified mainly through chromosome breakage and, at a lesser extent, through chromosome delay. Analysis of mitotic spindle showed disturbance of chromosome orientation and centrosome duplication and/or separation, leading to aneuploidy. Enhanced frequency of apoptotic leukemic cells was also observed. Caspase-3 seems to be involved in the generation of apoptosis.

Conclusions: The aforementioned findings derived from different treatment schedules, doses and time of exposure on primary versus transformed cells extend our knowledge about doxorubicin genotoxicity and contribute to the better understanding of the mechanisms by which doxorubicin induces genotoxic effects on human cells.

Background: Type IV lupus nephritis (LNIV) is a severe disease characterized by diffuse proliferative lesions, and its prognosis is worse with cellular crescent (LNIV-CC) involvement. Urinary exosomes have been shown to reflect the degree of kidney injury. This study was aimed to identify non-invasive diagnostic markers for LNIV-CC. We analysed the expression profile of microRNAs (miRNAs) isolated from urinary exosomes in patients with LNIV-CC and LNIV, and healthy individuals using high-throughput sequencing.

Results: A total of 66 differentially expressed miRNAs were identified, which were significantly enriched in 15 signalling pathways. Bioinformatic analysis revealed a co-expression network of miRNAs, predicted transcription factors and target mRNAs. Expression of three miRNAs including miR-3135b, miR-654-5p, and miR-146a-5p were further analysed and validated by reverse transcription-quantitative polymerase chain reaction. ROC analysis suggested these as candidate biomarkers for LNIV-CC.

Conclusions: LNIV-CC has a unique miRNA expression profile of urinary exosome and complex regulatory network. miR-3135b, miR-654-5p and miR-146a-5p in urinary exosomes could be used as novel non-invasive diagnostic markers for LNIV-CC.

Background: The insect-trapping leaves of Dionaea muscipula provide a model for studying the secretory pathway of an inducible plant secretory system. The leaf glands were induced with bovine serum albumin to secrete proteases that were characterized via zymogram activity gels over a 6-day period. The accompanying morphological changes of the endoplasmic reticulum (ER) and Golgi were analyzed using 3D electron tomography of glands preserved by high-pressure freezing/freeze substitution methods.

Results: Secretion of multiple cysteine and aspartic proteases occurred biphasically. The majority of the Golgi was organized in clusters consisting of 3-6 stacks surrounded by a cage-like system of ER cisternae. In these clusters, all Golgi stacks were oriented with their cis-most C1 cisterna facing an ER export site. The C1 Golgi cisternae varied in size and shape consistent with the hypothesis that they form de novo. Following induction, the number of ER-bound polysomes doubled, but no increase in COPII vesicles was observed. Golgi changes included a reduction in the number of cisternae per stack and a doubling of cisternal volume without increased surface area. Polysaccharide molecules that form the sticky slime cause swelling of the trans and trans Golgi network (TGN) cisternae. Peeling of the trans-most cisternae gives rise to free TGN cisternae. One day after gland stimulation, the free TGNs were frequently associated with loose groups of oriented actin-like filaments which were not seen in any other samples.

Conclusions: These findings suggest that the secretory apparatus of resting gland cells is "overbuilt" to enable the cells to rapidly up-regulate lytic enzyme production and secretion in response to prey trapping.

Background: The Raphitomidae family in the Mediterranean Sea is under revision. Accordingly, new data are of taxonomic and comparative relevance. In this study, new material from the Hellenic Seas is presented.

Results: The Raphitomidae fauna of Greece was collected and investigated during the period from October 2008 to February 2018. Thirty-five (35) species were identified and their status was compared with existing checklists and other collections. This effort revealed two new Raphitoma species, and one new record for the Mediterranean Sea. Also from the present collection, four species are new records for the East Mediterranean, 10 for the Hellenic fauna and six are reported for second time. The main identification characteristics and baseline ecological information are given and discussed.

Conclusions: By this report, the Hellenic Raphitomidae biodiversity is enriched by 10 new records, out of which, two are new species, one is new record for the Mediterranean Sea, and four for the East basin.

Background: Estuaries are primary habitats that serve as feeding and nursery grounds for most juvenile marine fish. However, estuaries have been used as fishing grounds by the artisanal fishers in Tanzania. The slow-growing predatory fish at juvenile and sub-adult stages are among the most frequently caught species that functionally enhance multiple linkages of energy pathways within the food web. Stomach contents and stable isotopes (δ¹³C and δ¹⁵N) were used to describe the nutritional sources and trophic niches between the co-existing benthic, predatory species, Carangoides chrysophrys and Epinephelus malabaricus in the Pangani estuary, Tanzania.

Results: The findings indicated significant inter-specific variations in dietary composition (PERMANOVA, p = 0.001, pseudo-F = 15.81). The prey-specific index of relative importance (%PSIRI) indicated that juvenile shrimps (%PSIRI = 51.4) and Teleostei (%PSIRI = 26.5) were the main diets of C. chrysophrys while brachyura (%PSIRI = 38.8), juvenile shrimps (%PSIRI = 25.6) and Teleostei (%PSIRI = 23.3) were important diets of E. malabaricus. The isotope mixing models indicated that the predatory fish species accumulate nutrients derived from similar autotrophic sources, microphytobenthos, seagrass and macro-algae via consumption of small fish, including clupeids and mugilids. Yet, they significantly showed different isotopic niche width with varying degree of niche overlap across the longitudinal estuary gradient. This situation was justified by the presence of basal food sources among the estuarine zones that isotopically were different.

Conclusion: The reliance of both predators on clupeids and mugilid preys that are trophically linked with estuarine and marine basal food sources, is an indication of low estuarine food webs' connectivity to the fresh water related food web. This situation is most likely threatening the stability of the estuarine food web structure. Management strategies and plans in place should be cautiously implemented to ensure the balanced anthropogenic freshwater use in the catchment and fishing activities, for the maintenance of the Pangani estuarine ecosystem health.

Background: Transverse cortical microtubule orientation, critical for anisotropic cell expansion, is established in the meristematic root zone. Intending to elucidate the possible prerequisites for this establishment and factors that are involved, microtubule organization was studied in roots of Arabidopsis thaliana, wild-type and the p60-katanin mutants fra2, ktn1-2 and lue1. Transverse cortical microtubule orientation in the meristematic root zone has proven to persist under several regimes inhibiting root elongation. This persistence was attributed to the constant moderate elongation of meristematic cells, prior to mitotic division. Therefore, A. thaliana wild-type seedlings were treated with aphidicolin, in order to prevent mitosis and inhibit premitotic cell elongation.

Results: In roots treated with aphidicolin for 12 h, cell divisions still occurred and microtubules were transverse. After 24 and 48 h of treatment, meristematic cell divisions and the prerequisite elongation ceased, while microtubule orientation became random. In meristematic cells of the p60-katanin mutants, apart from a general transverse microtubule pattern, cortical microtubules with random orientation were observed, also converging at several cortical sites, in contrast to the uniform transverse pattern of wild-type cells.

Conclusion: Taken together, these observations reveal that transverse cortical microtubule orientation in the meristematic zone of A. thaliana root is cell division-dependent and requires severing by katanin.

Background: MicroRNAs (miRNAs) are small, non-coding RNA molecules that play a key role in gene regulation in both plants and animals. MicroRNA biogenesis involves the enzymatic processing of a primary RNA transcript. The final step is the production of a duplex molecule, often designated as miRNA:miRNA*, that will yield a functional miRNA by separation of the two strands. This miRNA will be incorporated into the RNA-induced silencing complex, which subsequently will bind to its target mRNA in order to suppress its expression. The analysis of miRNAs is still a developing area for computational biology with many open questions regarding the structure and function of this important class of molecules. Here, we present StarSeeker, a simple tool that outputs the putative miRNA* sequence given the precursor and the mature sequences.

Results: We evaluated StarSeeker using a dataset consisting of all plant sequences available in miRBase (6992 precursor sequences and 8496 mature sequences). The program returned a total of 15,468 predicted miRNA* sequences. Of these, 2650 sequences were matched to annotated miRNAs (~ 90% of the miRBase-annotated sequences). The remaining predictions could not be verified, mainly because they do not comply with the rule requiring the two overhanging nucleotides in the duplex molecule.

Conclusions: The expression pattern of some miRNAs in plants can be altered under various abiotic stress conditions. Potential miRNA* molecules that do not degrade can thus be detected and also discovered in high-throughput sequencing data, helping us to understand their role in gene regulation.

[This corrects the article DOI: 10.1186/s40709-018-0074-6.].