Bacterial pili,with emphasis on Mycobacterium tuberculosis curli pili: potential biomarkers for point-of care tests and therapeutics

Context: Novel biomarkers are essential for developing rapid diagnostics and therapeutic interventions

Objective: This review aimed to highlight biomarker characterisation and assessment of unique bacterial pili.

Methods: A PubMed search for bacterial pili, diagnostics, vaccine and therapeutics was performed, with emphasis on the well characterised pili.

Results: In total, 46 papers were identified and reviewed.

Conclusion: Extensive analyses of pili enabled by advanced nanotechnology and whole genome sequencing provide evidence that they are strong biomarker candidates. Mycobacterium tuberculosis curli pili are emphasised as important epitopes for the development of much needed point-of-care diagnostics and therapeutics.     

Recent advances in proteomic applications for schistosomiasis research: potential clinical impact

Introduction: Schistosomiasis is a neglected tropical disease affecting hundreds of millions of people worldwide. Recent advances in the field of proteomics and the development of new and highly sensitive mass spectrometers and quantitative techniques have provided new tools for advancing the molecular biology, cell biology, diagnosis and vaccine development for public health threats such as schistosomiasis.

Areas covered: In this review we describe the latest advances in research that utilizes proteomics-based tools to address some of the key challenges to developing effective interventions against schistosomiasis. We also provide information about the potential of extracellular vesicles to advance the fight against this devastating disease.

Expert commentary: Different proteins are already being tested as vaccines against schistosomiasis with promising results. The re-analysis of the Schistosoma spp. proteomes using new and more sensitive mass spectrometers as well as better separation approaches will help identify more vaccine targets in a rational and informed manner. In addition, the recent development of new proteome microarrays will facilitate characterisation of novel markers of infection as well as new vaccine and diagnostic candidate antigens.     

Exploring dengue proteome to design an effective epitope-based vaccine against dengue virus

Dengue, a mosquito-borne disease, is caused by four known dengue serotypes. This infection causes a range of symptoms from a mild fever to a sever homorganic fever and death. It is a serious public health problem in subtropical and tropical countries. There is no specific vaccine currently available for clinical use and study on this issue is ongoing. In this study, bioinformatics approaches were used to predict antigenic, immunogenic, non-allergenic, and conserved B and T-cell epitopes as promising targets to design an effective peptide-based vaccine against dengue virus. Molecular docking analysis indicated the deep binding of the identified epitopes in the binding groove of the most popular human MHC I allele (human leukocyte antigens [HLA] A*0201). The final vaccine construct was created by conjugating the B and T-cell identified epitopes using proper linkers and adding an appropriate adjuvant at the N-terminal. The characteristics of the new subunit vaccine demonstrated that the epitope-based vaccine was antigenic, non-toxic, stable, and soluble. Other physicochemical properties of the new designed construct including isoelectric point value, aliphatic index, and grand average of hydropathicity were biologically considerable. Molecular docking of the engineered vaccine with Toll-like receptor 2 (TLR2) model revealed the hydrophobic interaction between the adjuvant and the ligand binding regions in the hydrophobic channel of TLR2. The study results indicated the high potential capability of the new multi-epitope vaccine to induce cellular and humoral immune responses against the dengue virus. Further experimental tests are required to investigate the immune protection capacity of the new vaccine construct in animal models.

Communicated by Ramaswamy H. Sarma     

Circulating adiponectin as a biomarker in renal cell carcinoma: a systematic review and meta-analysis

Context: Metabolic imbalance in renal cell carcinoma (RCC) can lead to abnormal adiponectin levels.

Objective: To evaluate circulating adiponectin as a detection or predictive marker for RCC.

Methods: A comprehensive literature search and meta-analysis was performed on studies reporting circulating adiponectin levels and RCC. The meta-analysis was performed using RevMan.

Results: Seven studies compared the circulating adiponection levels between RCC cases and controls. Adiponectin level was significantly lower in RCC cases compared to controls at pre-diagnosis and pre-operative time-points. RCC stage, grade and subtype did not affect adiponectin levels.

Conclusion: Low circulating adiponectin could be a predictive or risk factor for RCC.     

PTD modified paclitaxel anti-resistant liposomes for treatment of drug-resistant non-small cell lung cancer

Context: Non-small cell lung carcinoma (NSCLC) is a type of epithelial lung cancer that accounts for approximately 80–85% of lung carcinoma cases. Chemotherapy for the NSCLC is unsatisfactory due to multidrug resistance, nonselectively distributions and the accompanying side effects.

Objective: The objective of this study was to develop a kind of PTD modified paclitaxel anti-resistant liposomes to overcome these chemotherapy limitations.

Method: The studies were performed on LLT cells and resistant LLT cells in vitro and on NSCLC xenograft mice in vivo, respectively.

Results and discussion: In vitro results showed that the liposomes with suitable physicochemical characteristics could significantly increase intracellular uptake in both LLT cells and resistant LLT cells, evidently inhibit the growth of cancer cells, and clearly induce the apoptosis of resistant LLT cells. Studies on resistant LLT cells xenograft mice demonstrated that the liposomes magnificently enhanced the anticancer efficacy in vivo. Involved action mechanisms were down-regulation of adenosine triphosphate binding cassette transporters on resistant LLT cells, and activation of the apoptotic enzymes (caspase 8/9/3).

Conclusion: The PTD modified paclitaxel anti-resistant liposomes may provide a promising strategy for treatment of the drug-resistant non-small cell lung cancer.     

Yap overexpression attenuates septic cardiomyopathy by inhibiting DRP1-related mitochondrial fission and activating the ERK signaling pathway

Context: Yes-associated protein (Yap) has been linked to several cardiovascular disorders, but the role of this protein in septic cardiomyocytes is not fully understood.

Objective: The aim of our study was to explore the influence of Yap in septic cardiomyopathy in vivo and in vitro.

Materials and methods: In the current study, Yap transgenic mice and Yap adenovirus-mediated gain-of-function assays were used in an LPS-established septic cardiomyopathy model. Mitochondrial function and mitochondrial fission were determined through western blotting, immunofluorescence analysis and ELISA.

Results: Our results demonstrated that Yap expression was downregulated by LPS, whereas Yap overexpression sustained cardiac function and attenuated cardiomyocyte death. The functional exploration revealed that LPS treatment induced cardiomyocyte mitochondrial stress, as manifested by mitochondrial superoxide overproduction, cardiomyocyte ATP deprivation, and caspase-9 apoptosis activation. Furthermore, we demonstrated that LPS-mediated mitochondrial damage was controlled by mitochondrial fission. However, Yap overexpression reduced mitochondrial fission and therefore improved mitochondrial function. A molecular investigation revealed that Yap overexpression inhibited mitochondrial fission by reversing ERK activity, and the inhibition of the ERK pathway promoted DRP1 upregulation and thereby mediated mitochondrial fission activation in the presence of Yap overexpression.

Conclusions: Overall, our results suggest that the cause of septic cardiomyopathy appears to be connected with Yap downregulation. The overexpression of Yap can attenuate myocardial inflammation injury through the reduction of DRP1-related mitochondrial fission in an ERK pathway activation-dependent manner.     

Editorial Retraction

Upon a thorough investigation, it has been determined that the paper titled “Integrating Microbial Composting and Vermicomposting for Effective Utilization of By-Products of Sugar Cane-Processing Industries” by Shweta, Rahul Kumar, B.L. Singh, and Verma Deepshikha published in the Bioremediation Journal, 2010, Volume 14, pages 158–167, was simultaneously submitted and published in two journals. The same study with minor textual variations titled “Composting of sugar-cane waste by-products through treatment with microorganisms and subsequent vermicomposting” also written by Shweta, Rahul Kumar, B.L. Singh, and Verma Deepshikha published in the Elsevier publication, Bioresource Technology, 2010, 6707–6711, three months prior to publishing in Bioremedation Journal.

As a result the article published in Bioremediation Journal has been retracted and should not be cited in the electronic or print version of the journal.

Dr. Hanadi S. Rifai

Editor-in-Chief

Bioremediation Journal

Please click here to view the article to which this statement of retraction relates.     

H19 non-coding RNA in urine cells detects urothelial carcinoma: a pilot study

Context: Urothelial carcinoma (UC) is common and highly recurrent. Diagnosis and follow-up involve invasive cystoscopies.

Objective: To evaluate H19 RNA in urine cells as diagnostic tool for UC.

Materials and methods: RT-PCR analysis of urine samples from healthy volunteers and UC patients.

Results: H19 RNA was unequivocally detected in the urine of 90.5% of patients and 25.9% of controls. H19 copies were three orders of magnitude higher in patients. Receiver operating characteristic analysis showed an area under the curve of 0.933.

Conclusions: This pilot study shows that urinary cell H19 is a highly sensitive test for UC and pending verification could transform patient management.     

Association between polymorphisms in IL21 gene and risk for sepsis

Context: Sepsis is now the leading cause of death in the noncardiovascular intensive care unit (ICU).

Objective: To investigate whether polymorphisms in IL21 gene contribute to sepsis susceptibility.

Materials and methods: Three single-nucleotide polymorphisms of IL21 (rs907715, rs2055979, rs12508721) were genotyped by TaqMan assay in patients with sepsis and control subjects.

Results: Polymorphisms rs2055979 and rs12508721 in IL21 were more frequent in sepsis patients compared to general population. But allele frequency of rs907715 was not significantly different between sepsis patients and control subjects.

Conclusion: Polymorphisms in IL21 may be associated with sepsis risk.     

Evaluation of genetic diversity and population structure of Macqueen’s Bustard Chlamydotis macqueenii in Iran

Capsule: There is low genetic diversity in the Macqueen’s Bustard Chlamydotis macqueenii in Iran.

Aims: To investigate the genetic diversity and population structure of Macqueen’s Bustard in Iran, using two mitochondrial DNA loci.

Methods: Molecular diversity of the mitochondrial cytochrome oxidase c subunit I (COI) gene and part of the mitochondrial control region D-loop (in total 1183 base pairs) were analysed from 26 individual Macqueen’s Bustards from three regions of Iran.

Results: There was little variation in nucleotides and haplotypes in the populations for genes of both CR and COI. The population had free breeding and gene flow between the three study regions in Iran: Petregan, Ferdows and Yazd.

Conclusion: The use of molecular and genetic studies is essential to strengthen the protection of genetic diversity of the Macqueen’s Bustard.     

Application of proteomics to the study of Helicobacter pylori and implications for the clinic

Introduction: Helicobacter pylori (H. pylori) is a gram-negative bacterium that colonizes the gastric epithelium and mucous layer of more than half the world’s population. H. pylori is a primary human pathogen, responsible for the development of chronic gastritis, peptic ulceration and gastric cancer. Proteomics is impacting several aspects of medical research: understanding the molecular basis of infection and disease manifestation, identification of therapeutic targets and discovery of clinically relevant biomarkers.

Areas covered: The main aim of the present review is to provide a comprehensive overview of the contribution of proteomics to the study of H. pylori infection pathophysiology. In particular, we focused on the role of the bacterium and its most important virulence factor, CagA, in the progression of gastric cells transformation and cancer progression. We also discussed the proteomic approaches aimed at the investigation of the host response to bacterial infection.

Expert commentary: In the field of proteomics of H. pylori, comprehensive analysis of clinically relevant proteins (functional proteomics) rather than entire proteomes will result in important medical outcomes. Finally, we provided an outlook on the potential development of proteomics in H. pylori research.     

Big endothelin-1 level is a useful marker for predicting the presence of isolated coronary artery ectasia

Context: Endothelin-1(ET-1) has been implicated in coronary artery disease (CAD) and may be associated with coronary artery ectasia (CAE).

Objective: To clarify the relationship between big ET-1 and isolated CAE.

Methods: We measured big ET-1 with ELISA in 216 patients (CAE, n?=?72; CAD, n?=?72; normal, n?=?72) and evaluated the link with isolated CAE.

Results: The level of plasma big ET-1 was significantly higher in patients with isolated CAE (p?<?0.001). Big ET-1 was strongly and independently associated with CAE by multivariate analysis (OR 95%CI: 1.026 (1.018–1.034), p?=?0.000).

Conclusions: Big ET-1 may be a useful predictor for the presence of isolated CAE.     

Plant sex and phenological stage affect interactions with rhizosphere nematode communities

Background: In dioecious plants, females and males associate differently with mycorrhizal fungi, but interactions with other rhizosphere organisms are less well studied.

Aims: We investigated the effect of plant sex on rhizosphere nematode communities associated with Corema album, a dioecious shrub occurring in coastal habitats.

Methods: Rhizosphere samples were collected from males and females in three populations (150 plants), during fruiting and flowering. Nematode communities were characterised and compared between plant sexes through statistical analyses of the abundance of trophic groups, plant parasitic nematode (PPN) genera and ecological indices.

Results: Free-living nematodes showed no statistically significant differences owing to plant sex. Conversely, PPN community composition was significantly different between plant sexes during fruiting but not flowering, suggesting that physiological requirements over the annual phenological cycle of the plant influence ecological interactions with the rhizosphere.

Of the 13 PPN genera identified, the ectoparasitic Criconema and Hemicriconemellawere more abundant in the rhizosphere of males during fruiting, whereas the endoparasitic Meloidogyne associated more frequently with females, suggesting that plant host suitability is related to PPN feeding strategy.

Conclusions: It appears that interactions of individuals of different sexes of C. album with the rhizosphere nematode community vary with phenological stage, especially for PPN.     

Effect of shoulder stability exercises on hand grip strength in patients with shoulder impingement syndrome

Background: Shoulder impingement syndrome (SIS) is the second most common musculoskeletal condition that causes shoulder pain in the general population. Shoulder girdle muscle imbalance and posterior capsule tightness have been implicated as contributing factors.

Objective: The purpose of this study was to investigate the effect of shoulder stability exercises (SSEs) on hand grip strength in patients with unilateral SIS.

Methods: A total of 16 patients with a mean age of 32?±?9.3?years diagnosed with stage II unilateral SIS participated in this study. A standardized SSE programme was conducted in the clinic under the direct 1-to-1 supervision of a physical therapist thrice weekly for 4?weeks for a total of 12 sessions on the affected and non-affected shoulders. The effect of the SSE programme on isometric hand grip strength was analysed.

Results: A significant difference (p?=?.016) was observed in the hand grip strength of the affected shoulder side before and after the intervention, but no significant difference (p?=?1.0) was found in the hand grip strength of the non-affected shoulder side post-intervention.

Conclusion: The reduction in isometric hand grip strength of the affected shoulder side compared to that of the non-affected shoulder side in the same subject before the intervention shows that SIS significantly affects the hand grip strength of the affected side. SSEs significantly affect the isometric hand grip strength of SIS patients.     

European Turtle Dove Streptopelia turtur diet composition in Southern Spain: the role of wild seeds in Mediterranean forest areas

Capsule: The diet of European Turtle Doves Streptopelia turtur in Mediterranean forest contained a large volume of wild plant seed but from a small number of key species.

Aims: To determine which seed species are consumed by Turtle Doves in Mediterranean forest areas.

Methods: Digestive tract contents were identified and evaluated for 222 Turtle Doves shot by hunters during three consecutive years.

Results: Thirty seed species were identified in the diet, but only a few species represented most of the volume and frequency. Wild plant seeds appeared in 65.8% of digestive tracts and showed significant variation between years. Although the main wild seed species consumed each year varied annually, certain species were found in the diet every year in high volume and frequency. Adults showed a more diverse and numerous consumption of wild seeds than did juveniles. Plastic granules were also found in 3.8% of individuals.

Conclusion: A greater number of wild seed species was found in the diet in contrast to previous studies performed in farmland. Echium plantagineum and Amaranthus deflexus could be important seed sources for Turtle Doves in Mediterranean forest. Additionally, the herbaceous species found in the diet whose seeds ripen earlier in the season might play an important role in Turtle Dove reproductive performance, since they are frequently the only available food in the first half of the breeding season.     

Morphological and sexual traits in Atlas and Iberian Pied Flycatchers Ficedula hypoleuca speculigera and F. h. iberiae: a comparison

Capsule: There are significant biometric differences between Pied Flycatchers from Iberian and north African populations which are consistent with proposals to classify the two forms into separate species.

Aims: To determine the similarities and differences in the main biometrical and plumage sex traits between populations of the Iberian Pied Flycatcher Ficedula hypoleuca iberiae and the Atlas Flycatcher Ficedula hypoleuca speculigera.

Methods: Biometric and plumage traits of 193 breeding individuals of Iberian Pied Flycatchers and 43 Atlas Flycatchers were measured in 2014 with standardized protocols.

Results: Both sexes of Atlas Flycatchers were larger than Iberian Pied Flycatchers in skeletal (tarsus) and wing size and also differed in bill morphology, which was wider but shallower in speculigera than iberiae, with females (but not males) having shorter bills than iberiae females. Males differed in mantle colour and forehead patch size, with speculigera males being darker and displaying larger forehead patches than iberiae males. As in populations of iberiae, some speculigera females also expressed a white forehead patch.

Conclusion: We demonstrate significant phenotypic differences between Iberian Pied Flycatchers and Atlas Flycatchers with respect to size and traits of ecological and evolutionary relevance, supporting the recently proposed scenarios on their independent evolution.     

The role of recruitment and dispersal limitation in tree community assembly in Amazonian forests

Background: Species composition of plant communities is shaped by the interplay between dispersal limitation, environmental filters and stochastic events.

Aims: The aim of this work was to investigate the effects of dispersal limitation and environmental filtering on tree recruitment. To accomplish this, we employed the unified neutral theory of biodiversity and biogeography to examine migration within the metacommunity, defined as a set of interacting local communities linked by the dispersal of multiple potentially interacting species.

Methods: We sampled 12,975 individuals with dbh ≥ 1 cm in 26 1-ha permanent plots, including habitats of terra firme, transitional forests, várzea and campinarana, on the upper Madeira River, Brazilian Amazon.

Results: Campinarana drew individuals from outside the metacommunity species pool at a mean probability of recruitment of 0.06, a much lower probability than terra firme (0.31), transitional (0.21) and várzea forests (0.22). Environmental variables, such as water table depth, soil texture and fertility, were related to differences in community assembly.

Conclusions: Species abundance distribution and diversity patterns of plant assemblages in a large river landscape in the Amazon highlight the importance of environmental heterogeneity that conditions beta-diversity. The high variation in recruitment probabilities from the metacommunity species pool to local communities suggests high habitat variability in the process of maintaining patterns of local diversity.     

Changes in upland bird abundances show associations with moorland management

Capsule: Changes in abundance of six bird species showed associations with moorland management.

Aims: To assess responses of breeding birds to moorland management over a 14-year period.

Methods: Vegetation and birds were surveyed at 2–3-year intervals and changes examined in relation to sheep and cattle grazing, vegetation burning and cutting.

Results: Seven correlations between change in management and change in bird abundance were detected, and six between change in vegetation and change in bird abundance. On plots where sheep numbers declined, Golden Plover Pluvialis apricaria and Northern Wheatear Oenanthe oenanthe declined. Where a greater area was burned, Golden Plover increased in the initial post-burning period but Red Grouse Lagopus lagopus scotica declined. Eurasian Curlew Numenius arquata and Sky Lark Alauda arvensis increased where a greater area of moorland vegetation was cut. Whinchat Saxicola rubetra declined with increasing cattle numbers on a plot.

Conclusions: Bird populations respond to changes in moorland management, but these changes are not always associated with detectable changes in vegetation. These responses of moorland breeding birds to management could help refine agri-environment options and other conservation interventions on moorland. Responses differed between bird species, ideally requiring site-specific planning where managing for multiple species is a goal.     

Riboflavin as an independent and accurate biomarker for adherence in a randomized double-blind and placebo-controlled clinical trial

Background: Medication adherence is critical for success of clinical trials.

Objective: To assess oral riboflavin is an adherence marker.

Methods: Riboflavin was incorporated into active treatment and placebo pills for a clinical trial lasting for 2 years.

Results: The accuracy (area under the receiver operating curve) of urinary riboflavin was 0.91 as a binary classifier of adherence, and was similar or better than for two active study ingredients daidzein (0.92) and genistein (0.87) (all p?<?0.0001). Decreased adherence over time was similar in the two study groups.

Conclusion: Riboflavin is an accurate and useful biomarker for study pill ingestion.