Using amplicon sequencing of rpoB for identification of inoculant rhizobia from peanut nodules

To improve the nitrogen fixation, legume crops are often inoculated with selected effective rhizobia. However, there is large variation in how well the inoculant strains compete with the indigenous microflora in soil. To assess the success of the inoculant, it is necessary to distinguish it from other, closely related strains. Methods used until now have generally been based either on fingerprinting methods or on the use of reporter genes. Nevertheless, these methods have their shortcomings, either because they do not provide sufficiently specific information on the identity of the inoculant strain, or because they use genetically modified organisms that need prior authorization to be applied in the field or other uncontained environments. Another possibility is to target a gene that is naturally present in the bacterial genomes. Here we have developed a method that is based on amplicon sequencing of the bacterial housekeeping gene rpoB, encoding the beta-subunit of the RNA polymerase, which has been proposed as an alternative to the 16S rRNA gene to study the diversity of rhizobial populations in soils. We evaluated the method under laboratory and field conditions. Peanut seeds were inoculated with various Bradyrhizobium strains. After nodule development, DNA was extracted from selected nodules and the nodulating rhizobia were analysed by amplicon sequencing of the rpoB gene. The analyses of the sequence data showed that the method reliably identified bradyrhizobial strains in nodules, at least at the species level, and could be used to assess the competitiveness of the inoculant compared to other bradyrhizobia.

Modification of porous polyetherimide hollow fiber membrane by dip-coating of Zonyl® BA for membrane distillation of dyeing wastewater

Wetting and fouling have significantly affected the application of membrane distillation (MD). In this work, a dip-coating method was used for improving surface hydrophobicity of the polyetherimide (PEI) hollow fiber membrane. An air gap membrane distillation (AGMD) process was applied for treatment of the methylene blue (MB) solution. The porous PEI membrane was fabricated by a dry-wet spinning process and the hydrophobic 2-(Perfluoroalkyl) ethanol (Zonyl^® BA) was used as the coating material. From FESEM, the modified PEI-Zonyl membrane showed an open structure with large finger-like cavities. The modified membrane displayed a narrow pore size distribution with mean pore size of 0.028 μm. The outer surface contact angle of the PEI-Zonyl membrane increased from 81.3° to 100.4° due to the formation of an ultra-thin coated layer. The pure water flux of the PEI-Zonyl membrane was slightly reduced compared to the pristine PEI membrane. A permeate flux of 6.5 kg/m² h and MB rejection of 98% were found for the PEI-Zonyl membrane during 76 h of the AGMD operation. Adsorption of MB on the membrane surface was confirmed based on the Langmuir isotherm evaluation, AFM and FESEM analysis. The modified PEI-Zonyl membrane can be a favorable alternative for AGMD of dyeing wastewaters.

Alteration of gene expression profile in mouse embryonic stem cells and neural differentiation deficits by ethephon

Ethephon, a member of the organophosphorus compounds, is one of the most widely used plant growth regulators for artificial ripening. Although million pounds of this chemical is being used annually, the knowledge regarding its molecular toxicity is yet not sufficient. The purpose of this study was to evaluate the potential developmental toxicity of ethephon using embryonic stem cell model. The mouse embryonic stem cells (mESCs) were exposed to various concentrations of ethephon and the viability, cell cycle alteration and changes in the gene expression profile were evaluated using high-throughput RNA sequencing. Further, the effect of ethephon on neural differentiation potential was examined. The results showed that ethephon at noncytotoxic doses induced cell cycle arrest in mESCs. Gene ontology enrichment analysis showed that terms related to cell fate and organismal development, including neuron fate commitment, embryo development and cardiac cell differentiation, were markedly enriched in ethephon-treated cells. Neural induction of mESCs in the presence of ethephon was inhibited and the expression of neural genes was decreased in differentiated cells. Results obtained from this work clearly demonstrate that ethephon affects the gene expression profile of undifferentiated mESCs and prevents neural differentiation. Therefore, more caution against the frequent application of ethephon is advised.

Sonication-assisted synthesis of a new cationic zinc nitrate complex with a tetradentate Schiff base ligand: Crystal structure, Hirshfeld surface analysis and investigation of different parameters influence on morphological properties

A nanostructured cationic zinc nitrate complex with a formula of [ZnLNO₃]NO₃ (where L = (N²E,N^2'E)-N¹,N^1'-(ethane-1,2-diyl)bis(N²-((E)-3-phenylallylidene)ethane-1,2-diamine)) was prepared by sonochemical process and characterized by single crystal X-ray crystallography, scanning electron microscopy (SEM), FT-IR and NMR spectroscopy and X-ray powder diffraction (XRPD). The X-ray analysis demonstrates the formation of a cationic complex that metal center is five-coordinated by four nitrogen atom from Schiff base ligand and one oxygen atom from nitrate group. The crystal packing analysis demonstrates the essential role of the nitrate groups in the organization of supramolecular structure. The morphology and size of ultrasound-assisted synthesized zinc nitrate complex have been investigated using scanning electron microscopy (SEM) by changing parameters such as the concentration of initial reactants, the sonication power and reaction temperature. In addition the calcination of zinc nitrate complex in air atmosphere led to production of zinc oxide nanoparticles.

The association between interval from acceptance to first-time donation, missed first appointment and future donation behaviour

BACKGROUND AND OBJECTIVES

We examined the association of the interval between the date an individual is accepted for blood donation and the date of first donation (IFD-interval, index-to-first-time donation interval) and missed first appointment with future donation behaviour among new donors. These two variables have not been analysed in previous studies of donation behaviour among new donors.

METHODS

Categories were generated for age (18-29 vs 30-65 years), missed-appointment status (no-show vs same-day cancellation) and the IFD-interval [short (≤median time) vs long (>median time)]. Accepted donors (n = 807) were followed for 19 months. Outcome measures were first-appointment attendance rates, return rates among first-time donors and the proportion of experienced donors, defined as those who gave ≥5 donations.

RESULTS

In logistic regression analyses, high no-show rates were significantly associated with decreased likelihood of first-time donation. Long IFD-intervals were significantly associated with decreased likelihood of returning for a second donation among first-time donors. Experienced donors, compared to novice donors, were more likely to be male than female, older than younger and with shorter vs longer IFD-intervals.

CONCLUSIONS

No-show and long IFD-intervals may be behavioural markers of low levels of motivation for making the first donation and for returning for a second donation, respectively.

The role of transforming growth factor beta 1 in communicating and non-communicating hydrocele

PURPOSE

Repair of inguinal hernia and hydrocele are one of the most common operations performed by surgeons. However, the exact biological mechanism responsible for the closure of processus vaginalis (PV) is not completely understood. Transforming growth factor beta 1 (TGF-β1) is a potent fibrogenic agent and probably stimulate fibrosis and disappearing of PV.

METHODS

From September 2012 to December 2014, all boys from 1 to 5 years who were referred for surgery of hydrocele were divided into two groups of communicating (HC) or non-communicating hydrocele (HNC). During surgery, the fluid in the sac was aspirated and sent for biochemical evaluation including calcium, phosphorus, total protein, and TGF-β1. Finally, a biopsy of the sac was sent to the pathology. The results obtained were considered statistically significant (P < 0.05).

RESULTS

The patients were categorized into two groups of non-communicating hydrocele, including 43 patients and communicating, including 33. The patients studied were aged 1-5 years (mean 33.6 months). Biochemical tests on hydrocele fluid showed no significant difference in the levels of calcium, phosphorus, total protein, and bilirubin between two groups. However, mean TGF-β1 in NHC was found to be 53.45-114.28 pg/ml in HC group. A statistically significant difference (P = 0.04) was obtained. Furthermore, the study showed higher amounts of muscles in NHC (P < 0.001).

CONCLUSION

The amount of TGF-β1 was higher in HC fluid than in non-communicating. To investigate the role of cytokine in the closure of PV, further studies will be required.

Poor appointment-keeping behaviour among repeat blood donors and its relationship to the intent to donate again

BACKGROUND AND OBJECTIVES

Anecdotal evidence suggests that missed donation appointments among repeat whole-blood donors are associated with decreased likelihood of future blood donation. This study sought to examine the relationship between missed donation appointments and intention to donate again among repeat whole-blood donors and to examine whether demographic variables are related to appointment-keeping behaviour.

METHODS

During the period February-June 2013, telephone interviews were conducted with repeat donors who either did not show up for or cancelled their donation appointments on the day of the appointment. We asked them whether or not they wanted to schedule appointments for subsequent donations.

RESULTS

Rates of missed donation appointments varied by age, but not gender. Although a statistically significant difference between male and female donors was not found with regard to willingness to donate again, female donors were more likely than male donors to call and cancel their appointment. Finally, compared with repeat donors who called and cancelled their appointment, no-show donors were 2.5 times less likely to schedule appointments for subsequent donations (P < 0.001).

CONCLUSION

The results demonstrate that poor appointment-keeping behaviour, and in particular no-show behaviour, is significantly associated with decreased likelihood of future blood donation among repeat whole-blood donors.

Increasing female preponderance of multiple sclerosis in Isfahan, Iran: a population-based study

There is an overall increase in the worldwide prevalence and incidence of multiple sclerosis (MS). Studies from several countries also demonstrated an increase of female/male ratio over time denoting an increase in the incidence of MS particularly in women. In this study we sought to assess the trends in MS incidence and prevalence in males and females over recent decades in Isfahan, Iran, which differs from other regions in terms of environmental and lifestyle changes. We determined female/male ratio by year of birth (YOB) in 1584 patients with MS registered with Isfahan Multiple Sclerosis Society (IMSS) from April 2003 to August 2007. A comparison of sex ratio of MS patients by YOB showed a significant, progressive, gradual increase, with an apparent interruption in the late 1960s. In this study year of birth is a significant predictor for sex ratio ( p < 0.001, χ2 = 17.130, Spearman’s rank correlation r = 0.893). Our findings show that there is a significant increase in the incidence of MS among females for the the last decades in the Isfahan province of Iran. This rapid increase may be related to changes in environmental interactions rather than genetic factors, and among them vitamin D insufficiency, enhanced diagnosis, and lifestyle changes appear to be more plausible causative factors.

The unique role of proprotein convertase subtilisin/kexin 9 in cholesterol homeostasis

The LDL receptor (LDLR) plays an essential role in the regulation of plasma (LDL) cholesterol concentrations by virtue of its ability to clear plasma LDL. Down-regulation of the LDLR by proprotein convertase subtilisin/kexin 9 (PCSK9) has recently emerged as a regulatory mechanism that controls plasma LDL cholesterol concentrations. Studies in which PCSK9 is over-expressed in mice, have demonstrated that PCSK9, by enhancing hepatic LDLR degradation, decreases the availability of the LDLR for LDL uptake, resulting in increased plasma LDL cholesterol levels. However, PCSK9 has also recently been shown to mediate down-regulation of surface receptors other than the LDLR, suggesting that it may have much broader roles than initially thought.

Prediction of response to splenectomy in patients with idiopathic thrombocytopenic purpura

BACKGROUND

Chronic immune thrombocytopenic purpura (ITP) is an autoimmune disorder characterized by destruction of opsonized platelets in the reticuloendothelial system, particularly the spleen, and by resulting low platelet counts. Splenectomy is the standard second-line treatment for patients with ITP who do not respond to corticosteroids. In the present study we determined predictive factors for the response of patients with ITP to splenectomy.

MATERIALS AND METHODS

For thirty-one patients with ITP referred from the Hematology Department of Shariati Hospital, open surgical splenectomy was performed between February 2002 and December 2004. All potentially important variables of response were collected and analyzed to determine predictive parameters.

RESULTS

Older patients (>52) responded less positively than younger patients (<52) to splenectomy (p<0.01). Likewise, patients with a sustained remission after splenectomy had a significantly shorter interval of diagnosis of ITP to splenectomy (p<0.05) and shorter duration of corticosteroid therapy before splenectomy (p<0.05).

CONCLUSIONS

This study confirms that splenectomy is an effective treatment for patients with ITP. Our findings highlight age as the major predictive factor of long-term response to splenectomy in patients with ITP.

Cerebral vein and dural sinus thrombosis in adults in Isfahan, Iran: frequency and seasonal variation

OBJECTIVE

To estimate the frequency of cerebral vein and dural sinus thrombosis (CVST) and its seasonal variation.

METHODS

A clinic-based prospective case-register study was conducted from 2001 to 2004. Hundred and twenty-two consecutive definite CVST patients (26 men and 96 women) treated in two major neurological centres of Isfahan, Iran, were included in the study. Part of examination included an assessment of CVST including conventional angiography and/or magnetic resonance imaging and self-reported medical history. Population data were obtained from the 1996 Iran Census. The mean (standard deviation) age of participants was 35.5 (11.9) years.

RESULTS

The annual frequency (95% confidence interval) of CVST was 12.3 (10.1, 14.5) per million in a population of 2,472,751, with higher rate in women than in men [19.9 (15.5, 23.9) women and 5.1 (3.2, 7.1) men] and with increasing age in women (up to 50 years), but not in men. The female/male ratio was 3.9 (2.5-6.0). The monthly frequency of CVST ranged from 0.6 per million (0.1, 1.1) in August to 2.1 (1.2, 3.0) in September. The seasonal CVST rate ranged from 2.2 per million (1.3, 3.2) in summer to 4.3 (3.1, 5.7) in autumn. The differences were statistically significant either for the months or season (P < 0.05).

CONCLUSION

The findings of this study show the CVST frequency in adults. More women than men are present with CVST and its frequency increased during autumn.

Fludarabine and busulfan as a myeloablative conditioning regimen for allogeneic stem cell transplantation in high- and standard-risk leukemic patients

Busulfan and cyclophosphamide (BuCy) are currently the most widely used myeloablative regimen to treat malignancies with allogeneic stem cell transplantation. Fludarabine has considerable efficacy in both immunosuppression and tumor cells killing with a minimal extramedullary toxicity. We evaluated the efficacy of 40 mg/m(2) fludarabine i.v. for 5 days and busulfan 4 mg/kg/day p.o. for 4 days as myeloablative conditioning regimen in 70 patients (median age 24 years) with acute leukemia or chronic phase of myelogenous leukemia. They all had human leukocyte antigen-matched sibling donors. The patients received 10 mug/kg granulocyte colony stimulating factor (GCSF), 24 h after stem cell infusion until engraftment occurred. Graft-versus-host disease (GVHD) prophylaxis included 3 mg/kg cyclosporine-A i.v. from day -2 to +6 followed by 12 mg/kg p.o. until day +60. The median time of neutrophil recovery (>0.5 x 109/l) and platelet recovery (>20 x 109/l) were 10 and 12 days, respectively. Mucositis (93%) and hepatic toxicity (16%) resolved with conservative therapy. The incidence of acute GVHD grade I-II and III-IV were 38.6 and 15.7% respectively. Overall survival and disease-free survival were 71 and 64% respectively with 17 months median follow-up for surviving patients. We conclude that FluBu may be used as a substitute for BuCy with almost the same efficacy and with a lower transplant adverse effect but to increase anti-leukemic effects, especially in acute lymphoblastic leukemia patients, it needs some modifications.

Characterization of an FcgammaRI-binding peptide selected by phage display

The high-affinity IgG receptor, Fcgamma receptor I (FcgammaRI), is expressed exclusively on myeloid cells, and there is a great interest in the targeting of vaccine antigens to FcgammaRI using anti-human FcgammaRI antibodies or fragments derived from such molecules. In order to reduce the size and complexity of the targeting reagent, we have searched for FcgammaRI binding peptides in peptide libraries displayed on phage. The human monocytic cell line U937 was used as target. Phages that displayed the consensus peptide CLRSGXGC were selected and revealed increased binding to IFN-gamma stimulated versus non-stimulated U937 cells as well as to FcgammaRI transfected versus non-transfected IIA1.6 cells. Furthermore, they bound the extracellular domains of soluble FcgammaRI, but neither FcgammaRIIA, FcgammaRIIB nor FcgammaRIIIB. Binding was inhibited by a synthetic version of the peptide, whereas neither human IgG nor the FcgammaRI-specific monoclonal antibodies (mAb) mAb22 and 32.2 interfered. Flow-cytometry analysis and internalization studies showed that a synthetic biotin-conjugated peptide ADGACLRSGRGCGAAK-bio was able to target U937 cells and FcgammaRI transfected IIA1.6 cells, and further to promote internalization and vesicular degradation of streptavidin coupled to 1 microm magnetic beads. These peptides may have potential as FcgammaRI targeting reagents.

Wortmannin-sensitive trafficking steps in the endocytic pathway in rat liver endothelial cells

Liver endothelial cells (LECs) play an important homoeostatic role by removing potentially harmful macromolecules from blood. The extremely efficient endocytosis in LECs makes these cells an interesting model for the study of the involvement of phosphoinositides in the different steps of the endocytic process. In the present investigation we have studied the effect of wortmannin, an inhibitor of phosphatidylinositol kinases, on uptake, recycling and intracellular transport of (125)I-labelled ovalbumin, which is taken up in LECs via mannose-receptor-mediated endocytosis. Wortmannin was found to inhibit both uptake and degradation of ovalbumin. Further studies indicated that the reduced uptake via the mannose receptor was due both to a reduction of the number of surface receptors and a reduction in the rate of receptor-ligand internalization. Transport of ligand from endosomes to lysosomes was prevented, leading to increased recycling of internalized ligand. Wortmannin treatment released the Rab5 effector EEA1 from the endosomes and caused reduced size of early endosomes.

Fluid phase endocytosis of [125I]iodixanol in rat liver parenchymal, endothelial and Kupffer cells

Endocytosis of [125I]iodixanol was studied in vivo and in vitro in rat liver cells to determine fluid phase endocytic activity in different liver cells (hepatocytes, Kupffer cells and endothelial cells). The Kupffer cells were more active in the uptake of [l25I]iodixanol than parenchymal cells or endothelial cells. Inhibition of endocytic uptake via clathrin-coated pits (by potassium depletion and hypertonic medium) reduced uptake of [125I]iodixanol much more in Kupffer cells and endothelial cells than in hepatocytes. To gain further information about the importance of clathrin-mediated fluid phase endocytosis, the expression of proteins known to be components of the endocytic machinery was investigated. Using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblotting, endothelial cells and Kupffer cells were found to express approximately fourfold more rab4, rab5 and rab7 than parenchymal cells, while clathrin was expressed at a higher level in endothelial cells than in Kupffer cells and hepatocytes. Using electron microscopy it was shown that liver endothelial cells contained approximately twice as many coated pits per membrane unit than the parenchymal and Kupffer cells, thus confirming the immunoblotting results concerning clathrin expression. Electron microscopy on isolated liver cells following fluid phase uptake of horseradish peroxidase (HRP) showed that HRP-containing organelles had a different morphology in the different cell types: In the liver endothelial cells HRP was in small, tubular endosomes, while in Kupffer cells HRP was mainly found in larger structures, reminiscent of macropinosomes. Parenchymal cells contained HRP in small vacuolar endosomes with a punctuated distribution. In conclusion, we find that the Kupffer cells and the endothelial cells have a higher pinocytic activity than the hepatocytes. The hepatocytes do, however, account for most of the total hepatic uptake. The fluid phase endocytosis in liver endothelial cells depends mainly on clathrin-mediated endocytosis, while the parenchymal cells have additional clathrin-independent mechanisms that may play an important role in the uptake of plasma membrane components. In the Kupffer cells the major uptake of fluid phase markers seems to take place via a macropinocytic mechanism.

Effects of inhibitors of the vacuolar proton pump on hepatic heterophagy and autophagy

Bafilomycin A(1) (BAF) and concanamycin A (ConcA) are selective inhibitors of the H(+)-ATPases of the vacuolar system. We have examined the effects of these inhibitors on different steps in endocytic pathways in rat hepatocytes, using [(125)I]tyramine-cellobiose-labeled asialoorosomucoid ([(125)I]TC-AOM) and [(125)I]tyramine-cellobiose-labeled bovine serum albumin ([(125)I]TC-BSA) as probes for respectively receptor-mediated endocytosis and pinocytosis (here defined as fluid phase endocytosis). The effects of BAF and ConcA were in principle identical, although ConcA was more effective than BAF. The main findings were as follows. (1) BAF/ConcA reduced the rate of uptake of both [(125)I]TC-AOM and [(125)I]TC-BSA. The reduced uptake of [(125)I]TC-AOM was partly due to a redistribution of the asialoglycoprotein receptors (ASGPR) such that the number of surface receptors was reduced approximately 40% without a change in the total number of receptors. (2) BAF/ConcA at the same time increased retroendocytosis (recycling) of both probes. The increased recycling of the ligand ([(125)I]TC-AOM) is partly a consequence of the enhanced pH in endosomes, which prevents dissociation of ligand. (3) It was furthermore found that the ligand remained bound to the receptor in presence of BAF/ConcA and that the total amount of ligand molecules internalized in BAF/ConcA-treated cells was only slightly in excess of the total number of receptors. These data indicate that reduced pH in endosomes is the prime cause of receptor inactivation and release of ligand in early endosomes. (4) Subcellular fractionation experiments showed that [(125)I]TC-AOM remained in early endosomes, well separated from lysosomes in sucrose gradients. The fluid phase marker, [(125)I]TC-BSA, on the other hand, seemed to reach a later endosome in the BAF/ConcA-treated cells. This organelle coincided with lysosomes in the gradient, but hypotonic medium was found to selectively release a lysosomal enzyme (beta-acetylglucosaminidase), indicating that even [(125)I]TC-BSA remained in a prelysosomal compartment in the BAF/ConcA-treated cells. (5) Electron microscopy using horseradish peroxidase (HRP) as a fluid phase marker verified that BAF/ConcA inhibited transfer of material from late endosomes ('multivesicular bodies'). (6) BAF/ConcA led to accumulation of lactate dehydrogenase (LDH) in autophagic vacuoles, but although the drugs partly inhibited fusion between autophagosomes and lysosomes a number of autolysosomes was formed in the presence of BAF/ConcA. This observation explains the reduced buoyant density of lysosomes (revealed in sucrose density gradients). In conclusion, BAF/ConcA inhibit transfer of endocytosed material from late endosomes to lysosomes, but do not at the same time prevent fusion between autophagosomes and lysosomes.