Bone marrow mesenchymal stem cell transplantation improves radiation-induced heart injury through DNA damage repair in rat model

Radiotherapy is an effective form of therapy for most thoracic malignant tumors. However, myocardial injury resulting from the high doses of radiation is a severe complication. Here we aimed to study the possibility of reducing radiation-induced myocardial injury with mesenchymal stem cell (MSC) transplantation. We used MSCs extracted from bone marrow (BMSCs) to transplant via the tail vein into a radiation-induced heart injury (RIHI) rat model. The rats were divided into six groups: a Sham group, an IRR (irradiation) group, and four IRR + BMSCs transplantation groups obtained at different time points. After irradiation, BMSC transplantation significantly enhanced the cardiac function in rats. By analyzing the expression of PPAR-α, PPAR-γ, TGF-β, IL-6, and IL-8, we found that BMSC transplantation alleviated radiation-induced myocardial fibrosis and decreased the inflammatory reaction. Furthermore, we found that expression of γ-H2AX, XRCC4, DNA ligase4, and TP53BP1, which are associated with DNA repair, was up-regulated, along with increased secretion of growth factors SDF-1, CXCR4, VEGF, and IGF in rat myocardium in the IRR + BMSCs transplantation groups compared with the IRR group. Thus, BMSC transplantation has the potential to improve RIHI via DNA repair and be a new therapeutic approach for patients with myocardial injury.     

Association between circulating inflammatory molecules and alcoholic liver disease in men

The association between alcoholic liver disease (ALD) and the inflammatory response remains controversial. The aim of this study was to explore this association between ALD and inflammation. We enrolled 214 male participants, who were divided into three age-matched groups: ALD (n?=?135), chronic alcohol ingestion without ALD (non-ALD; n?=?42), and control (n?=?37). The BMI was significantly higher in the ALD group than in the non-ALD and control groups (all P?=?0.000). Further, the constituent ratio of the liver inflammatory level was significantly higher in the ALD group than in the non-ALD and control groups (P?=?0.002 and P?=?0.000, respectively). In addition, the median serum ALT, AST, and GGT levels were significantly higher in the ALD group than in the control group (P?=?0.023, P?=?0.008, and P?=?0.000, respectively); these levels were also significantly higher in the ALD group than in the non-ALD group (P?=?0.013, P?=?0.010, and P?=?0.000, respectively). The median serum CRP level was significantly higher in the ALD group than in the non-ALD and control groups (P?=?0.006 and P?=?0.000, respectively). Further, the median serum TNF-α level was significantly lower in the ALD group than in the non-ALD and control groups (P?=?0.004 and P?=?0.000, respectively). The median serum sOX40L and HSP70 levels were significantly lower in the ALD group than in the control group (P?=?0.008 and P?=?0.018, respectively). In addition, the ALT, AST, and GGT levels were positively correlated with the CRP level (r?=?0.211, P?=?0.002; r?=?0.220, P?=?0.001 and r?=?0.295, P?=?0.000, respectively), and the GGT level was negatively correlated with the TNF-α (r?=??0.225, P?=?0.001), sOX40L (r?=??0.165, P?=?0.016), and HSP70 levels (r?=??0.178, P?=?0.009). Further, the Cr level was negatively correlated with the IL-10 level (r?=??0.166, P?=?0.015). Logistic regression analysis verified that the BMI (OR??=??1.637, 95%CI: 1.374–1.951, P??=??0.000) and GGT level were significantly higher (OR??=??1.039, 95%CI: 1.020–1.059, P??=??0.000) and that the TNF-α (OR??=??0.998, 95%CI: 0.996–1.000, P??=??0.030) and HSP70 levels were significantly lower (OR??=??1.017, 95%CI: 1.003–1.031, P??=??0.029) in the ALD group than in the non-ALD group. Further, the moderate-to-severe ALD patients had a significantly higher serum CRP level (Or?=???1.349, 95%CI: 1.066–1.702, P??=??0.013) and significantly lower HSP60 (OR??=??0.965, 95%CI: 0.938–0.993, P??=??0.014) and HSP70 levels (OR??=??0.978, 95%CI: 0.962–0.995, P??=??0.010) than the mild ALD patients. These results suggest that ALD patients may present with obesity, liver damage, and an imbalanced inflammatory immune response, mainly manifesting as decreased levels of immune inflammatory cytokines. In addition, they suggest that certain liver and kidney function parameters and ALD severity are either positively or negatively correlated with certain inflammatory cytokines. Hence, ALD patients may be at increased risks of obesity- and inflammation-related diseases. Accordingly, to control the inflammatory response, preventative measures for patients with this disease should include weight control and protection of liver and kidney function.     

Phylogenetic study of clavicipitaceous fungi using acetaldehyde dehydrogenase gene sequences

Aciculosporium and Heteroepichloë (Clavicipitaceae) are characteristic bambusicolous fungi in east Asia. In this study, we examined their intergeneric relationships based on the ALDH1-1 gene, which encodes a member of the aldehyde dehydrogenase family. In the clavicipitaceous fungi examined in this study, the nucleotide sequence of the third exon of ALDH1-1 (Exon-3) is 889 bp in length and has no insertion/deletion. A phylogenetic tree based on Exon-3 indicated that the clavicipitaceous fungi could be divided into two large groups: Cordyceps, Nomuraea, and Ustilaginoidea species formed a paraphyletic group, and the other grass biotrophic species formed a monophyletic group. This monophyletic group was further divided into three groups with high bootstrap support: i.e., species with Neotyphodium anamorphs (e.g., Epichloë), species with Ephelis anamorphs (e.g., Heteroepichloë), and Aciculosporium-Claviceps species. We discuss the relationships among Aciculosporium, Heteroepichloë, and other clavicipitaceous fungi.     

Assessment of genetic diversity and structure in cocoa trees (<Emphasis Type="Italic">Theobroma cacao</Emphasis> L.) in Côte d’Ivoire with reference to their susceptibility to Cocoa swollen shoot virus disease (CSSVD)

Resistance to Cocoa Swollen Shoot Virus disease (CSSVD) is becoming an increasingly important criterion for selection of new cocoa cultivars in Côte-d’Ivoire, where the disease resurfaced since 2003. This virus can seriously affect the yield of trees with a loss of 25%, 1 year after infection, to around 100% 3 years after. In order to find tolerant plant material, 337 farm accessions have been collected on fields affected by CSSVD, according to the status of accessions potentially tolerant (APT) or susceptible (APS). Both phenotypic groups were genotyped using 30 microsatellite markers (SSR) in the presence of representative clones of the ten genetic groups of cocoa. This study revealed 214 alleles with the set of primer pairs used. The number of alleles per locus was between 3 and 16 with an average of 7.13 alleles per locus. The results showed a high contribution of genetic diversity within population (H_s?=?0.51) to the total genetic diversity (H_t?=?0.53) for the two studied groups. There was no significant difference between tolerant and susceptible groups (Fst?=?0.05). These results suggest that APT could be a potential genetic reservoir for other traits of interest associated with virus resistance. The phylogenetic tree, as the STRUCTURE analysis of Ivorian cocoa population, showed a distribution of individuals following four groups marked by a high contribution of group 4 (Nanay, Maranon, Guiana) followed by group 2 (Criollo), and group 1 (Amelonado), and a lower contribution of group 3 (Iquitos, Purus, Nacional, Curaray, Contamana).     

Phylogeographic structure of <Emphasis Type="Italic">Spondias tuberosa</Emphasis> Arruda Câmara (Anacardiaceae): seasonally dry tropical forest as a large and continuous refuge

Spondias tuberosa occurs in the Caatinga domain (seasonally dry tropical forest biome) of north-eastern Brazil, a large biome with ecogeographic regions that may have modelled the population structure of the species. Here we studied the phylogeographic pattern of S. tuberosa using sequences of the accD-psaI plastid region and six SSR markers in individuals distributed across 20 localities. The results for accD-psaI demonstrated nine haplotypes: some of which were exclusive to Caatinga ecoregions, whereas others were found in all localities. Spatial analysis of molecular variance revealed two groups (F_ct?=?0.34, P?<?0.0039) with 33.91% variation between them. The SSR analyses displayed 2–5 alleles at each locus, some of which were unique to certain localities. As in the accD-psaI region, the population structure obtained using SSR markers fell into two groups: (1) a large group containing the majority of the geographic region of Caatinga and (2) a small group near the Atlantic forest. We demonstrate the population structure of S. tuberosa, identifying the Caatinga as large, continuous refuge and the region near the interface between the Caatinga and the Atlantic forest as second refuge.     

Genetic associations between ADHD and dopaminergic genes (<Emphasis Type="Italic">DAT1</Emphasis> and <Emphasis Type="Italic">DRD4</Emphasis>) VNTRs in Korean children

It is well known that dopaminergic genes affect the development of attention deficit hyperactivity disorder (ADHD) in various populations. Many studies have shown that variable number tandem repeats (VNTRs) located within the 3′-untranslated region of DAT1 and in exon 3 of DRD4 are associated with ADHD development; however, these results were inconsistent. Therefore, we investigated the genetic association between two VNTRs and ADHD in Korean children. We determined the VNTRs using PCR. We examined genotype and allele frequency differences between the experimental and control groups, along with the odds ratios, using Chi square and exact tests. We observed a significant association between the children with ADHD and the control group in the 10R/10R genotype of DAT1 VNTRs (p?=?0.025). In addition, the 11R allele of DAT1 VNTRs showed a higher frequency in the control group than in the ADHD group (p?=?0.023). Also, the short repeat (without 11R) and long repeat alleles (including 11R) were associated with ADHD (p?<?0.05). The analysis of DRD4 VNTRs revealed that the 2R allele is associated with ADHD (p?=?0.025). A significant result was also observed in long and short repeats (p?<?0.05). Additionally, ADHD subtypes showed that the DRD4 VNTRs are associated with combined and hyperactive-impulsive subtype groups (p?<?0.05). Therefore, our results suggest that DAT1 VNTRs and DRD4 VNTRs play a role in the genetic etiology of ADHD in Korean children.     

<Emphasis Type="Italic">Cortinarius</Emphasis> sect. <Emphasis Type="Italic">Riederi</Emphasis>: taxonomy and phylogeny of the new section with European and North American distribution

Cortinarius is one of the most species-rich genera of mushroom-forming fungi. Based on phylogenetic and morphological evidence, Cortinarius, sect. Riederi, is introduced at sectional level (= subsect. Riederi sensu Brandrud & Melot). The taxonomy, phylogeny, ecology and distribution of not only mainly European but also including some North American taxa of this section are treated, which includes nine species and two varieties. Of these, three taxa are described as new (C. burlinghamiae, C. pallidoriederi and C. argenteolilacinus var. dovrensis). The sect. Riederi species possess morphological features similar to Phlegmacium group(s) and forms a phylogenetically isolated lineage, with no supported affinity to other phlegmacioid groups. Three taxa are known from both Europe and North America, two species are known only from North America and five only from Europe. Altogether, eight of the ten taxa are associated with conifers or northern (boreal-subalpine) deciduous trees (Betula spp.). Only two species occur in more temperate forests (Fagus forests), and no species have so far been found in thermophilous Quercus forests     

Assessment of right atrium dysfunction in patients with obstructive sleep apnea syndrome using velocity vector imaging

Background and Objectives

This study aimed to assess the changes of RA function in patients with obstructive sleep apnea syndrome (OSAS) using velocity vector imaging (VVI) and to evaluate the application of VVI technology.

Methods

According to the apnea–hypopnea index (AHI), 71 patients with OSAS were divided into three groups: mild, moderate, and severe. A total of 30 cases of healthy subjects were enrolled as the control group. Digital images of apex four-chamber views were acquired to measure the right atrium (RA) linear dimensions and volume parameters including RA longitudinal diameter (RAL), transverse diameter (RAT), RA maximum volume (Vmax), RA minimum volume (Vmin), right atrial volume before contraction (Vpre). Right atrial volume parameters were corrected by body surface area (VImax, VImin, VIpre). The total right atrial emptying fraction (RATEF), right atrial passive emptying fraction (RAPEF), right atrial active contraction emptying fraction (RAAEF) were calculated. The VVI data measuring right atrial global strain (RA-GLS), right atrial strain rate in ventricular systolic phase (RA-SRs), right atrial strain rate in ventricular early diastolic phase (RA-SRe), right atrial strain rate in ventricular late diastolic phase (RA-SRa).

Results

1. 1.
   RA linear dimensions and volume parameters in severe OSAS were higher than those of control group. RAPEF in severe group was lower than control group and mild OSAS group (t?= 2.681, P?=?0.021; t?= 2.985, P?=?0.011; respectively). RAAEF in OSAS moderate group was higher than that of control group (t?= 3.006, P?=?0.02), and without statistical difference (P?>?0.05) in the severe OSAS group and the control group.
    
2. 2.
   RA-GLS in moderate OSAS group was significantly lower than that of control group (t?= 2.333, P?=?0.040) and reduced more obvious in the severe OSAS group (vs control, t?= 3.25, P?=?0.008, vs mild; t?= 3.011, P?=?0.012; respectively). RA-SRe in moderate and severe OSAS groups were lower than control group (t?= 2.466, P?=?0.031; t?= 3.547, P?=?0.005; respectively). RA-SRs of OSAS in severe group was lower than that of control and mild groups (t?= 3.665, P?=?0.004; t?= 3.204, P?=?0.008; respectively). RA-SRa in severe OSAS group was lower than that of control group (t?= 2.425, P?=?0.034).
    
3. 3.
   Multivariate regression analysis showed that RA-GLS and RA-SRe were independently correlated with AHI (t?=???2.738, P?=?0.010; t?=???2.191, P?=?0.036; respectively).
    

Conclusion

RA function was impaired in patients with OSAS. On hemodynamics, the change of RA function performed increased of reserve function, reduced pipeline function and increased of contraction function. However, the strain and strain rate reduced in different degree. RA-GLS and RA-SRe decreased the earliest, which suggested that strain and strain rate were the parameters which can reflect myocardial function damage earliest. VVI can more earlier and accurately detect myocardial dysfunction of right atrium in patients with OSAS, which is expected to be a worthy technique for early clinical therapy in patients with OSAS.

     

Factors Influencing Non-<Emphasis Type="Italic">albicans</Emphasis> Candidemia: A Case–Case–Control Study

The study identified factors predisposing to non-albicans candidemia with special interest to prior antimicrobial treatment. A retrospective, case–case–control study was performed at the University Hospital of Heraklion, Greece, from November 2007 through September 2011 including adult patients. The study had three groups. The first included 58 patients with non-albicans candidemia, the second 48 with C. albicans candidemia, while the third (control) 104 without candidemia. Each of the two candidemia groups was compared with the control using multivariate logistic regression model. The mean (SD) age of the non-albicans, the albicans and the control patients was 67 (12), 67 (18) and 59 (19) years, respectively. The most common non-albicans Candida spp. isolated were C. parapsilosis in 19 patients (33%), C. glabrata in 17 (29%) and C. tropicalis in 15 (26%). Independent risk factors for non-albicans candidemia were prior treatment with quinolones (p < 0.001), b-lactam-b-lactamase inhibitors (p = 0.011) and presence of central venous catheter (p = 0.05), while for C. albicans candidemia were prior treatment with quinolones (p < 0.001), carbapenems (p = 0.003) along with cardiac disease (p < 0.001). Neither duration of hospitalization nor in-hospital mortality [41% for the non-albicans vs 29% for C. albicans group (p = 0.192)] was significantly different between the two candidemia groups. The study reveals the role of antimicrobial exposure as a risk factor for candidemia caused by different species. Prior treatment with b-lactam-b-lactamase inhibitors was associated with non-albicans, while with carbapenems with C. albicans candidemia. Prior use of quinolones was associated with candidemia in general.     

New species of the buprestid genus <Emphasis Type="Italic">Endelus</Emphasis> Deyrolle (Coleoptera,Buprestidae) from China,India, and Laos

Endelus (Kubaniellus) indicus sp. n. from India, E. (K.) lao sp. n. and E. (K.) khnzoriani sp. n. from Laos, E. (s. str.) sausai sp. n. from China, and E. (s. str.) dembickyi sp. n. from India are described, the two latter species are included in the Endelus bicarinatus Théry, 1932 species-group recently established by the author. E. collinus Obenberger, 1922 is included in this group; lectotype of this species is designated. Keys to species of the subgenus Kubaniellus and of the E. collinus group are provided. E. (K.) kareni Kalashian is for the first time recorded for Shaanxi Prov., E. pacholatkoi Kalashian, E. smaragdinus Desc. et Vill., and E collinus Obenb., for Laos (the latter species, also for Myanmar).     

<Emphasis Type="Italic">Sporidiobolus johnsonii</Emphasis> and <Emphasis Type="Italic">Sporidiobolus salmonicolor</Emphasis> revisited

The relationship between Sporidiobolus johnsonii and S. salmonicolor was investigated using rDNA sequence data. Two statistically well-supported clades were obtained. One clade included the type strain of S. johnsonii and the other included the type strain of S. salmonicolor. However, some mating strains of S. salmonicolor were found in the S. johnsonii group. These strains belonged to mating type A2 and were sexually compatible with mating type A1 strains from the S. salmonicolor group. DNA–DNA reassociation values were high within each clade and moderate between the two clades. In the re-investigation of teliospore germination, we observed that the basidia of S. salmonicolor were two-celled. In S. johnsonii, basidia were not formed and teliospore germination resulted in direct formation of yeast cells. We hypothesize that the S. johnsonii clade is becoming genetically isolated from the S. salmonicolor group and that a speciation process is presently going on. We suspect that the observed sexual compatibility between strains of the S. johnsonii and S. salmonicolor groups and the possible genetic flow between the two species has little biological relevance because distinct phenotypes have been fixed in the two taxa and intermediate (hybrid) sequences for LSU and ITS rDNAs have not been detected.     

Effects of neutrophils peptide-1 transgenic <Emphasis Type="Italic">Chlorella ellipsoidea</Emphasis> on the gut microbiota of male Sprague–Dawley rats,as revealed by high-throughput 16S rRNA sequencing

Rabbit neutrophils peptide-1 (NP-1) is a type of defensin that possesses a broad spectrum of antimicrobial activity. Chlorella ellipsoidea is a new eukaryotic expression system for exogenously producing NP-1. The NP-1 transgenic C. ellipsoidea can be directly added into feed as antimicrobial agent without any purification procedure for the NP-1 peptide. However, the effects of C. ellipsoidea and NP-1 on the host gut microbiota should be explored before application. In this study, diets containing different concentrations (1.25, 2.5, and 5 %) of C. ellipsoidea and NP-1 transgenic C. ellipsoidea were administered to male Sprague–Dawley rats. Compared with the chow diet control group, none of the experimental groups showed any significant differences in their growth indices, and no histopathological damage was observed. The phylotypes of gut microbiota in the control group, the 5 % C. ellipsoidea diet group and the 5 % NP-1 transgenic C. ellipsoidea diet group were determined by 16S rRNA sequencing. The results showed that both 5 % experimental groups had shifted community memberships of gut microbiota. In particular, the 5 % NP-1 transgenic C. ellipsoidea diet exhibited an increased abundance of most Gram-positive bacterial taxa and a reduced abundance of most Gram-negative bacterial taxa, and it promoted the growth of some lactic acid bacterial genera. Lactic acid bacteria, especially the Bifidobacterium and Lactobacillus, have been widely reported to be benefic effects on the host. Thus NP-1 transgenic C. ellipsoidea is promising feed additive and gut regulator, as it have the potential to increase the abundance of Bifidobacterium and Lactobacillus in gut microbiota of animal.     

Ectomycorrhizae of <Emphasis Type="Italic">Tuber huidongense</Emphasis> and <Emphasis Type="Italic">T. liyuanum</Emphasis> with <Emphasis Type="Italic">Castanea mollissima</Emphasis> and <Emphasis Type="Italic">Pinus armandii</Emphasis>

Tuber huidongense and T. liyuanum are common commercial white truffles in China that belong to the Rufum and Puberulum groups of the genus Tuber, respectively. Their mycorrhizae were successfully synthesized with two native trees—Castanea mollissima and Pinus armandii—under greenhouse conditions. The identities of the mycorrhizae were confirmed through internal transcribed spacer (ITS) sequence analyses, and their morphological characteristics were described. All of the obtained mycorrhizae have an interlocking pseudoparenchymatous mantle, which is a typical feature of truffle mycorrhizae. The mycorrhizae of T. huidongense on the two trees have hyaline branched emanating hyphae, similar to the documented mycorrhizae of the Rufum group. The unramified, spiky, and hyaline cystidia on the mycorrhizae of T. liyuanum with both C. mollissima and P. armandii further confirmed that this characteristic is constant for the mycorrhizae of the Puberulum group. The successful mycorrhizal syntheses on the two nut-producing trees will be of economic importance in the cultivation of the two truffles.     

Effects of <Emphasis Type="Italic">Lactobacillus</Emphasis>-fermented ginger stem on <Emphasis Type="Italic">Salmonella</Emphasis>-infected broiler chicks

Broiler salmonellosis is a major problem for poultry industry. Here, we supplemented broiler feed with 1% of ginger stems (GS) fermented with Lactobacillus paracasei and analyzed the effects on the resistance to Salmonella gallinarum. The chickens were divided into four dietary groups. The control group (C) received the basal diet, and the other chickens received the basal diet supplemented with 0.1% w/w L. paracasei ML-7 (L group), 0.1% ginger stem powder (GS group), or 0.2% fermented ginger stem (FGS group) for 21 days. The dietary groups were further split into two subgroups: one challenged with 1 × 105 CFU/mL S. gallinarum orally administered in 1 mL of saline from days 7 and 14, and one that received 1 mL of saline without bacteria. Both uninfected and S. gallinarum-infected broilers fed with fermented GS (FGS) significantly increased body weight and feed intake, and had lower mortality compared to relative control groups. Furthermore, dietary FGS decreased cecal, Salmonella spp. counts and serum IgA and IgG levels. These results indicate that FGS prevented S. gallinarum colonization and promoted weight gain in broilers, suggesting that FGS supplementation can be effectively used as a replacement of antibiotic growth promoters to prevent Salmonella infection.     

Contributions of <Emphasis Type="Italic">TaSUTs</Emphasis> to grain weight in wheat under drought

Key message

The homologous genes to OsSUT1-5 in wheat were identified and detailed analysed. TaSUT1 was the predominant sucrose transporter group and it illustrated the genotypic variations towards drought during grain filling.

Abstract

Sucrose transporters (SUT) play crucial roles in wheat stem water soluble carbohydrate (WSC) remobilization to grain. To determine the major functional SUT gene groups in shoot parts of wheat during grain development, drought tolerant varieties, Westonia and Kauz, were investigated in field drought experiments. Fourteen homologous genes to OsSUT1-5 were identified on five homeologous groups, namely TaSUT1_4A, TaSUT1_4B, TaSUT1_4D; TaSUT2_5A, TaSUT2_5B, TaSUT2_5D; TaSUT3_1A, TaSUT3_1D; TaSUT4_6A, TaSUT4_6B, TaSUT4_6D; TaSUT5_2A, TaSUT5_2B, and TaSUT5_2D, and their gene structures were analysed. Wheat plants above the ground were harvested from pre-anthesis to grain maturity and the stem, leaf sheath, rachis, lemma and developing grain were used for analysing TaSUT gene expression. Grain weight, thousand grain weight, kernel number per spike, biomass and stem WSC were characterized. The study showed that among the five TaSUT groups, TaSUT1 was the predominant sucrose transporting group in all organs sampled, and the expression was particularly high in the developing grain. In contrast to TaSUT1, the gene expression levels of TaSUT2, TaSUT3 and TaSUT4 were lower, except for TaSUT3 which showed preferential expression in the lemma before anthesis. The TaSUT5 gene group was very weakly expressed in all tissues. The upregulated gene expression of TaSUT1 Westonia type in stem and grain reveal a crucial role in stem WSC remobilization to grain under drought. The high TaSUT1 gene expression and the significant correlations with thousand grain weight (TGW) and kernel number per spike demonstrated the contribution in Kauz’s high grain yield in an irrigated environment and high TGW in Westonia under drought stress. Further molecular level identification is required for gene marker development.

     

Characterization of the complete mitochondrial genome of flower-breeding <Emphasis Type="Italic">Drosophila incompta</Emphasis> (Diptera,Drosophilidae)

Drosophila incompta belongs to the flavopilosa group of Drosophila, and has a restricted ecology, being adapted to flowers of Cestrum as feeding and oviposition sites. We sequenced, assembled, and characterized the complete mitochondrial genome (mtDNA) of D. incompta. In addition, we performed phylogenomic and polymorphism analyses to assess evolutionary diversification of this species. Our results suggest that this genome is syntenic with the other published mtDNA of Drosophila. This molecule contains 15,641 bp and encompasses two rRNA, 22 tRNA and 13 protein-coding genes. Regarding nucleotide composition, we found a high A?T bias (76.6 %). The recovered phylogenies indicate D. incompta in the virilis–repleta radiation, as sister to the virilis or repleta groups. The most interesting result is the high degree of polymorphism found throughout the D. incompta mitogenome, revealing pronounced intrapopulational variation. Furthermore, intraspecific nucleotide diversity levels varied between different regions of the genome, thus allowing the use of different mitochondrial molecular markers for analysis of population structure of this species.     

Connection between proliferation rate and temozolomide sensitivity of primary glioblastoma cell culture and expression of <Emphasis Type="Italic">YB-1</Emphasis> and <Emphasis Type="Italic">LRP/MVP</Emphasis>

Glioblastomas (GBL) are the most common and aggressive brain tumors. They are distinguished by high resistance to radiation and chemotherapy. To find novel approaches for GBL classification, we obtained 16 primary GBL cell cultures and tested them with real-time PCR for mRNA expression of several genes (YB-1, MGMT, MELK, MVP, MDR1, BCRP) involved in controlling cell proliferation and drug resistance. The primary GBL cultures differed in terms of proliferation rate, wherein a group of GBL cell cultures with low proliferation rate demonstrated higher resistance to temozolomide. We found that GBL primary cell cultures characterized by high proliferation rate and lower resistance to temozolomide expressed higher mRNA level of the YB-1 and MDR1 genes, whereas upregulated expression of MVP/LRP mRNA was a marker in the group of GBL with low proliferation rate and high resistance. A moderate correlation between expression of YB-1 and MELK as well as YB-1 and MDR1 was found. In the case of YB-1 and MGMT expression, no correlation was found. A significant negative correlation was revealed between mRNA expression of MVP/LRP and MELK, MDR1, and BCRP. No correlation in expression of YB-1 and MVP/LRP genes was observed. It seems that mRNA expression of YB-1 and MVP/LRP may serve as a marker for GBL cell cultures belonging to distinct groups, each of which is characterized by a unique pattern of gene activity.     

Double-check: validation of diagnostic statistics for PLS-DA models in metabolomics studies

Partial Least Squares-Discriminant Analysis (PLS-DA) is a PLS regression method with a special binary ‘dummy’ y-variable and it is commonly used for classification purposes and biomarker selection in metabolomics studies. Several statistical approaches are currently in use to validate outcomes of PLS-DA analyses e.g. double cross validation procedures or permutation testing. However, there is a great inconsistency in the optimization and the assessment of performance of PLS-DA models due to many different diagnostic statistics currently employed in metabolomics data analyses. In this paper, properties of four diagnostic statistics of PLS-DA, namely the number of misclassifications (NMC), the Area Under the Receiver Operating Characteristic (AUROC), Q ² and Discriminant Q ² (DQ ²) are discussed. All four diagnostic statistics are used in the optimization and the performance assessment of PLS-DA models of three different-size metabolomics data sets obtained with two different types of analytical platforms and with different levels of known differences between two groups: control and case groups. Statistical significance of obtained PLS-DA models was evaluated with permutation testing. PLS-DA models obtained with NMC and AUROC are more powerful in detecting very small differences between groups than models obtained with Q ² and Discriminant Q ² (DQ ²). Reproducibility of obtained PLS-DA models outcomes, models complexity and permutation test distributions are also investigated to explain this phenomenon. DQ ² and Q ² (in contrary to NMC and AUROC) prefer PLS-DA models with lower complexity and require higher number of permutation tests and submodels to accurately estimate statistical significance of the model performance. NMC and AUROC seem more efficient and more reliable diagnostic statistics and should be recommended in two group discrimination metabolomic studies.     

Characterization of phosphate solubilizing rhizobacteria associated with pea (<Emphasis Type="Italic">Pisum sativum</Emphasis> L.) isolated from two agricultural soils

Phosphorous (P) availability is a major concern in European agriculture where reserves are limited. In the case of pea (Pisum sativum L.), one of the most important legumes in the human diet, P has specific effects on nodulation and N₂ fixation. Therefore, when biofertilization schemes are considered for pea cropping, it is very important to include symbiotic dinitrogen-fixing bacteria as well as phosphate-solubilizing bacteria (PSB). In this study sixteen PSB were isolated from the rhizosphere of two pea cultivars in two French soils with different characteristics. They were phenotypically and genotypically diverse displaying 9 different Two Primers-Random Amplified Polymorphic DNA (TP-RAPD) patterns. The 16S rRNA gene analysis of representative strains showed that they belong to four highly divergent phylogenetic groups. Most of the PSB strains belonged to the genus Pseudomonas and were closely related to Pseudomonas baetica, P. lutea, P. azotoformans, P. jessenii and P. frederiksbergensis. Other strains from the genus Burkholderia were closely related to B. caledonica and those from the genus Rhizobium to R. grahamii. The single strain of genus Bacillus was close to Bacillus toyonensis. Some phylogenetic groups to which our PSB strains belong are widely distributed in plant rhizospheres in different countries and continents. This is particularly interesting in the case of strains from the phylogenetic group of P. fluorescens which includes PSB strains with high ability to solubilize phosphate indicating that they may be used as biofertilizers in many soils.