Macroalgal susceptibility to grazing by herbivore fish Siganus spp. at Gulf of Mannar reef,Indian Ocean

Environmental Biology of Fishes - Enhancing the herbivore fish stock is envisaged as a mitigation tool to reverse the macroalgal dominance in a coral reef environment. However, identifying the key...     

Efficient secretion of three fungal laccases from Saccharomyces cerevisiae and their potential for decolorization of textile industry effluent—A comparative study

Laccases are enzymes with a broad range of biotechnological applications and have, for example, the ability to oxidize many xenobiotics including synthetic dyes. In order to obtain an efficient laccase for the decolorization of dyes which spoil wastewater from the textile industry, genes encoding three various laccase enzymes were expressed in Saccharomyces cerevisiae. The expression of laccases from ascomycete Myceliophthora thermophila (MtL), and two basidiomycetes Trametes versicolor (TvL) and Trametes trogii (TtL) was optimized via selection of plasmids, promoters, media composition, and cultivation conditions. For the first time, the activity of the three secreted laccases was directly compared with the use of various substrates, including different dyes and a wastewater sample. A strong constitutive ADH1 promoter, minimal growth medium, optimized combination of copper and organic nitrogen source, and low cultivation temperature were shown to significantly increase the yields and relative activities of secreted laccases. Heterologous expression of three fungal laccases was successfully achieved in S. cerevisiae being the highest for MtL and the lowest for TvL. MtL, and particularly TtL, showed the decolorization capacity. This is the first report which compared decolorization of synthetic dyes and wastewater by several recombinant laccases and suggested MtL and TtL to be applicable in the ecofriendly enzymatic treatment of colored industry effluent. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:69–80, 2018     

Human Serum Promotes Osteogenic Differentiation of Human Dental Pulp Stem Cells In Vitro and In Vivo

Human dental pulp is a promising alternative source of stem cells for cell-based tissue engineering in regenerative medicine, for the easily recruitment with low invasivity for the patient and for the self-renewal and differentiation potential of cells. So far, in vitro culture of mesenchymal stem cells is usually based on supplementing culture and differentiation media with foetal calf serum (FCS). FCS is known to contain a great quantity of growth factors, and thus to promote cell attachment on plastic surface as well as expansion and differentiation. Nevertheless, FCS as an animal origin supplement may represent a potential means for disease transmission besides leading to a xenogenic immune response. Therefore, a significant interest is focused on investigating alternative supplements, in order to obtain a sufficient cell number for clinical application, avoiding the inconvenients of FCS use. In our study we have demonstrated that human serum (HS) is a suitable alternative to FCS, indeed its addition to culture medium induces a high hDPSCs proliferation rate and improves the in vitro osteogenic differentiation. Furthermore, hDPSCs-collagen constructs, pre-differentiated with HS-medium in vitro for 10 days, when implanted in immunocompromised rats, are able to restore critical size parietal bone defects. Therefore these data indicate that HS is a valid substitute for FCS to culture and differentiate in vitro hDPSCs in order to obtain a successful bone regeneration in vivo.     

A 10-year experience in the treatment of intraabdominal cerebrospinal fluid pseudocysts

The aim of this retrospective study was to assess a ten-year experience in the treatment of rare complications of ventriculoperitoneal shunting--intraabdominal cerebrospinal fluid pseudocysts. At this time there are no data about incidence, clinical course and treatment of these complications in Croatia. Cerebrospinal fluid (CSF) abdominal pseudocyst is an uncommon but important complication of ventriculoperitoneal shunts. Retrospective data were obtained from 5 children with abdominal CSF pseudocysts, treated between 1996 and 2007. The incidence of intraabdominal CSF pseudocysts in our study is 2.9%. All patients were girls ranged in age from 4 to 12 years old (mean 8.8 years). In most cases etiology of hydrocephalus was congenital, idiopathic. Abdominal pain and distension were the most frequent clinical finding (4/5). Although infection has been reported as responsible for pseudocyst formation, we did not found it in our series. Laparotomy with cyst wall excision and catheter replacement was performed in 2/5 cases, and only cyst fluid aspiration with catheter replacement in 3/5 cases. Recurrence of the abdominal cyst was observed in one girl who was in terminal stadium of anaplastic ependymoma. It is our opinion that only catheter replacement and cyst fluid evacuation, as one of the treatment modalities, may be successful, even in large CSF intraperitoneal pseudocysts.     

Human amniotic fluid stem cells: neural differentiation in vitro and in vivo

The successful integration of stem cells after their implantation into the brain has become a central issue in modern neuroscience. In this study, we test the neural differentiation potential of c-Kit⁺/Oct-4⁺ human amniotic fluid stem cells (hAFSCs) in vitro and their survival and integration in vivo. hAFSCs were induced towards neural differentiation and specific markers (GFAP, β-III tubulin, CNPase, MAP2, NeuN, synapsines, S100, PMP22) were detected by immunofluorescence and Western blot analysis. Glial proteins were expressed as early as 2 weeks after the initial differentiation stimulus, whereas neuronal markers started to appear from the third week of differentiation under culturing conditions of high cell density. This timeline suggested that glial cells possessed a promoting role in the differentiation of hAFSCs towards a neuronal fate. hAFSCs were then implanted into the lateral ventricle of the brain of 1-day-old rats, since neuronal development occurs up to 1 month after birth in this animal model. Our data showed that hAFSCs survived for up to 6 weeks post-implantation, were integrated into various areas of the central nervous system and migrated away from the graft giving rise to mature neurons and oligodendrocytes. We conclude that hAFSCs are able to differentiate and integrate into nervous tissue during development in vivo.     

The carbon dioxide laser: an alternative surgery technique for the treatment of common cutaneous tumors in dogs

Background

Tumors of the skin and subcutaneous tissue are the largest group of canine neoplasms. Total excision is still the most effective method for treatment of these skin tumors. For its universal properties the carbon dioxide (CO₂) laser appears to be an excellent surgical instrument in veterinary surgery. Laser techniques are alternatives to traditional methods for the surgical management of tumors. The aim of this study was to compare various types of laser techniques in skin oncologic surgery: excision, ablation and mixed technique and to suggest which technique of CO₂ laser procedure is the most useful in particular case of tumors in dogs.

Findings

The study was performed on 38 privately-owned dogs with total number of 40 skin tumors of different type removed by various CO₂ laser operation techniques from 2010–2013. The treatment effect was based on the surgical wound evaluation, the relative time of healing and possible local recurrence of the tumor after 3 months post surgery. Local recurrence was observed in two cases. The study showed that in 30 cases time needed for complete resection of lesions was less than 10 minutes. Time of healing was longer than 12 days in 6 cases (42.8%) with tumor excision and in 14 cases (87.5%) where excision with ablation technique was performed.

Conclusions

The advantages of the CO₂ laser surgery were better hemostasis, precision of working, non-contact dissection, less instruments at the site of operation and minimum traumatization of the surrounding tissues.     

Experimental validation of methods for differential gene expression analysis and sample pooling in RNA-seq

Background

Massively parallel cDNA sequencing (RNA-seq) experiments are gradually superseding microarrays in quantitative gene expression profiling. However, many biologists are uncertain about the choice of differentially expressed gene (DEG) analysis methods and the validity of cost-saving sample pooling strategies for their RNA-seq experiments. Hence, we performed experimental validation of DEGs identified by Cuffdiff2, edgeR, DESeq2 and Two-stage Poisson Model (TSPM) in a RNA-seq experiment involving mice amygdalae micro-punches, using high-throughput qPCR on independent biological replicate samples. Moreover, we sequenced RNA-pools and compared their results with sequencing corresponding individual RNA samples.

Results

False-positivity rate of Cuffdiff2 and false-negativity rates of DESeq2 and TSPM were high. Among the four investigated DEG analysis methods, sensitivity and specificity of edgeR was relatively high. We documented the pooling bias and that the DEGs identified in pooled samples suffered low positive predictive values.

Conclusions

Our results highlighted the need for combined use of more sensitive DEG analysis methods and high-throughput validation of identified DEGs in future RNA-seq experiments. They indicated limited utility of sample pooling strategies for RNA-seq in similar setups and supported increasing the number of biological replicate samples.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1767-y) contains supplementary material, which is available to authorized users.     

The highly modified microcin peptide plantazolicin is associated with nematicidal activity of Bacillus amyloliquefaciens FZB42

Bacillus amyloliquefaciens FZB42 has been shown to stimulate plant growth and to suppress the growth of plant pathogenic organisms including nematodes. However, the mechanism underlying its effect against nematodes remains unknown. In this study, we screened a random mutant library of B. amyloliquefaciens FZB42 generated by the mariner transposon TnYLB-1 and identified a mutant strain F5 with attenuated nematicidal activity. Reversible polymerase chain reaction revealed that three candidate genes RAMB_007470, yhdY, and prkA that were disrupted by the transposon in strain F5 potentially contributed to its decreased nematicidal activity. Bioassay of mutants impaired in the three candidate genes demonstrated that directed deletion of gene RBAM_007470 resulted in loss of nematicidal activity comparable with that of the F5 triple mutant. RBAM_007470 has been reported as being involved in biosynthesis of plantazolicin, a thiazole/oxazole-modified microcin with hitherto unknown function. Electrospray ionization time-of-flight mass spectrometry (ESI-TOF-MS) analyses of surface extracts revealed that plantazolicin bearing a molecular weight of 1,354 Da was present in wild-type B. amyloliquefaciens FZB42, but absent in the ΔRABM_007470 mutant. Furthermore, bioassay of the organic extract containing plantazolicin also showed a moderate nematicidal activity. We conclude that a novel gene RBAM_007470 and its related metabolite are involved in the antagonistic effect exerted by B. amyloliquefaciens FZB42 against nematodes.     

Relating the ontogeny of functional morphology and prey selection with larval mortality in Amphiprion frenatus

Survival during the pelagic larval phase of marine fish is highly variable and is subject to numerous factors. A sharp decline in the number of surviving larvae usually occurs during the transition from endogenous to exogenous feeding known as the first feeding stage in fish larvae. The present study was designed to evaluate the link between functional morphology and prey selection in an attempt to understand how the relationship influences mortality of a marine fish larva, Amphiprion frenatus, through ontogeny. Larvae were reared from hatch to 14 days post hatch (DPH) with one of four diets [rotifers and newly hatched Artemia sp. nauplii (RA); rotifers and wild plankton (RP); rotifers, wild plankton, and newly hatched Artemia nauplii (RPA); wild plankton and newly hatched Artemia nauplii (PA)]. Survival did not differ among diets. Larvae from all diets experienced mass mortality from 1 to 5 DPH followed by decreased mortality from 6 to 14 DPH; individuals fed RA were the exception, exhibiting continuous mortality from 6 to 14 DPH. Larvae consumed progressively larger prey with growth and age, likely due to age related increase in gape. During the mass mortality event, larvae selected small prey items and exhibited few ossified elements. Cessation of mass mortality coincided with consumption of large prey and ossification of key elements of the feeding apparatus. Mass mortality did not appear to be solely influenced by inability to establish first feeding. We hypothesize the interaction of reduced feeding capacities (i.e., complexity of the feeding apparatus) and larval physiology such as digestion or absorption efficiency contributed to the mortality event during the first feeding period. J. Morphol., 2010. © 2010 Wiley‐Liss, Inc.