The expression pattern and regulatory functions of microRNAs (miRNAs) are intensively investigated in various tissues, cell types and disorders. Differential miRNA expression signatures have been revealed in healthy and unhealthy tissues using high-throughput profiling methods. For further analyses of miRNA signatures in biological samples, we describe here a simple and efficient method to detect multiple miRNAs simultaneously in total RNA. The size-coded ligation-mediated polymerase chain reaction (SL-PCR) method is based on size-coded DNA probe hybridization in solution, followed-by ligation, PCR amplification and gel fractionation. The new method shows quantitative and specific detection of miRNAs. We profiled miRNAs of the let-7 family in a number of organisms, tissues and cell types and the results correspond with their incidence in the genome and reported expression levels. Finally, SL-PCR detected let-7 expression changes in human embryonic stem cells as they differentiate to neuron and also in young and aged mice brain and bone marrow. We conclude that the method can efficiently reveal miRNA signatures in a range of biological samples.

There are no mucosal adjuvant formulations licensed for human use, despite protection against many mucosally-transmitted infections probably requiring immunity at the site of pathogen entry1. Polyethyleneimines (PEI) are organic polycations used as nucleic acid transfection reagents in vitro, and gene and DNA vaccine delivery vehicles in vivo2, 3. Here we show that PEI has unexpected and unusually potent mucosal adjuvant activity in conjunction with viral subunit glycoprotein antigens. Single intranasal administration of influenza HA or HSV-2 gD with PEI elicited robust protection from otherwise lethal infection, and was superior to existing experimental mucosal adjuvants. PEI formed nanoscale complexes with antigen that were taken up by antigen presenting cells in vitro and in vivo, promoted DC trafficking to draining lymph nodes and induced non-proinflammatory cytokine responses. PEI adjuvanticity required release of host dsDNA that triggered Irf-3-dependent signaling. PEI therefore merits further investigation as a mucosal adjuvant for human use.

The present study was undertaken to test the efficacy of immunization with the native major outer membrane protein (nMOMP) of C. trachomatis mouse pneumonitis (MoPn) serovar in combination with a novel immunostimulatory adjuvant consisting of CpG oligodeoxynucleotide (ODN) linked to the nontoxic B subunit of cholera toxin (CTB-CpG) to elicit a protective immune response to C. trachomatis. High levels of Chlamydia specific IgG antibodies were detected in the sera from BALB/c mice immunized intramuscularly and subcutaneously (i.m.+s.c.) with the nMOMP/CTB-CpG vaccine or with nMOMP adjuvanted with a mixture of CT and CpG ODN (CT + CpG). Further, these immunization schemes gave rise to significant T-cell mediated Chlamydia-specific immune responses. No Chlamydia-specific humoral or cell-mediated immune responses were detected in the control mice vaccinated with ovalbumin together with either CTB-CpG or CT + CpG. Following an intranasal challenge with C. trachomatis the groups of mice immunized with nMOMP plus CTB-CpG, CT + CpG or live C. trachomatis were found to be protected based on their change in body weight and lung weight as well as number of inclusion forming unit recovered from the lungs, as compared with control groups immunized with ovalbumin plus either adjuvants. Interestingly, IFN-γ-producing CD4+, but not CD8+, T-cells showed a significant correlation with the outcomes of the challenge. In conclusion, nMOMP in combination with the novel adjuvant CTB-CpG elicited a significant antigen specific antibody and cell-mediated immune responses as well as protection against a pulmonary challenge with C. trachomatis.

The extra demand imposed upon the Libyan health services during and after the Libyan revolution in 2011 led the ailing health systems to collapse. To start the planning process to re-engineer the health sector, the Libyan Ministry of Health in collaboration with the World Health Organisation (WHO) and other international experts in the field sponsored the National Health Systems Conference in Tripoli, Libya, between the 26th and the 30th of August 2012. The aim of this conference was to study how health systems function at the international arena and to facilitate a consultative process between 500 Libyan health experts in order to identify the problems within the Libyan health system and propose potential solutions. The scientific programme adopted the WHO health care system framework and used its six system building blocks: i) Health Governance; ii) Health Care Finance; iii) Health Service Delivery; iv) Human Resources for Health; v) Pharmaceuticals and Health Technology; and vi) Health Information System. The experts used a structured approach starting with clarifying the concepts, evaluating the current status of that health system block in Libya, thereby identifying the strengths, weaknesses, and major deficiencies. This article summarises the 500 health expert recommendations that seized the opportunity to map a modern health systems to take the Libyan health sector into the 21st century.

Background

Plasmodium vivax is the prevalent malarial species accounting for 70% of malaria burden in Pakistan; however, there is no baseline data on the circulating genotypes. Studies have shown that polymorphic loci of gene encoding antigens pvcsp and pvmsp1 can be used reliably for conducting molecular epidemiological studies. Therefore, this study aimed to bridge the existing knowledge gap on population structure on P. vivax from Pakistan using these two polymorphic genes.

Methods

During the period January 2008 to May 2009, a total of 250 blood samples were collected from patients tested slide positive for P. vivax, at the Aga Khan University Hospital, Karachi, or its collection units located in Baluchistan and Sindh Province. Nested PCR/RFLP was performed, using pvcsp and pvmsp1 markers to detect the extent of genetic diversity in clinical isolates of P. vivax from southern Pakistan.

Results

A total of 227/250 (91%) isolates were included in the analysis while the remainder were excluded due to negative PCR outcome for P.vivax. Pvcsp analysis showed that both VK 210 (85.5%, 194/227) and VK 247 type (14.5%, 33/227) were found to be circulating in P. vivax isolates from southern Pakistan. A total of sixteen and eighty-seven genotypes of pvcsp and pvmsp-1 were detected respectively.

Conclusion

This is the first report from southern Pakistan on characterization of P. vivax isolates confirming that extensively diverse pvcsp and pvmsp1 variants are present within this region. Results from this study provide valuable data on genetic diversity of P. vivax that will be helpful for further epidemiological studies.

The envelope glycoproteins of herpes simplex virus 1 (HSV-1) and HSV-2, with the exception of glycoprotein G, elicit cross-reactive B- and T-cell responses. Human vaccine trials, using the cross-reactive glycoproteins B and D, have shown no protection against genital HSV-2 infection or disease. In this study, the mature form of glycoprotein G (mgG-2) of HSV-2 was used for immunization of mice, either alone or in combination with adjuvant CpG, followed by an intravaginal challenge with a lethal dose of a fully virulent HSV-2 strain. Mice immunized with mgG-2 plus CpG showed low disease scores and a significantly higher survival rate (73%) than mice immunized with mgG-2 alone (20%) or controls (0%). Accordingly, limited numbers of infectious HSV-2 particles were detected in the spinal cord of mice immunized with mgG-2 plus CpG. The observed protection was associated with a gamma interferon (IFN-γ) response by splenic CD4+ T cells upon antigen restimulation in vitro and in vaginal washes 1 day postinfection. The majority of sera collected from mice immunized with mgG-2 plus CpG showed macrophage-mediated antibody-dependent cellular cytotoxicity and antibody-dependent complement-mediated cytolysis, while no neutralization activity was observed. In conclusion, we have shown that immunization with the type-specific mgG-2 protein in combination with CpG could elicit protective immunity against an otherwise lethal vaginal HSV-2 challenge. The mgG-2 protein may therefore constitute a promising HSV-2 vaccine antigen to be considered for future human trials.

ABSTRACT

A new human coronavirus (hCoV-EMC) has emerged very recently in the Middle East. The clinical presentation resembled that of the severe acute respiratory syndrome (SARS) as encountered during the epidemic in 2002/2003. In both cases, acute renal failure was observed in humans. HCoV-EMC is a member of the same virus genus as SARS-CoV but constitutes a sister species. Here we investigated whether it might utilize angiotensin-converting enzyme 2 (ACE2), the SARS-CoV receptor. Knowledge of the receptor is highly critical because the restriction of the SARS receptor to deep compartments of the human respiratory tract limited the spread of SARS. In baby hamster kidney (BHK) cells, lentiviral transduction of human ACE2 (hACE2) conferred permissiveness and replication for SARS-CoV but not for hCoV-EMC. Monkey and human kidney cells (LLC-MK2, Vero, and 769-P) and swine kidney cells were permissive for both viruses, but only SARS-CoV infection could be blocked by anti-hACE2 antibody and could be neutralized by preincubation of virus with soluble ACE2. Our data show that ACE2 is neither necessary nor sufficient for hCoV-EMC replication. Moreover, hCoV-EMC, but not SARS-CoV, replicated in cell lines from Rousettus, Rhinolophus, Pipistrellus, Myotis, and Carollia bats, representing four major chiropteran families from both suborders. As human CoV normally cannot replicate in bat cells from different families, this suggests that hCoV-EMC might use a receptor molecule that is conserved in bats, pigs, and humans, implicating a low barrier against cross-host transmission.

IMPORTANCE

A new human coronavirus (hCoV) emerged recently in the Middle East. The disease resembled SARS (severe acute respiratory syndrome), causing a fatal epidemic in 2002/2003. Coronaviruses have a reservoir in bats and because this novel virus is related to SARS-CoV, we investigated whether it might replicate in bat cells and use the same receptor (angiotensin-converting enzyme 2 [ACE2]). This knowledge is highly critical, because the SARS-CoV receptor influenced pathology, and its localization in the deep respiratory tract is thought to have restricted the transmissibility of SARS. Our data show that hCoV-EMC does not need the SARS-CoV receptor to infect human cells. Moreover, the virus is capable of infecting human, pig, and bat cells. This is remarkable, as human CoVs normally cannot replicate in bat cells as a consequence of host adaptation. Our results implicate that the new virus might use a receptor that is conserved between bats, pigs and humans suggesting a low barrier against cross-host transmission.

While airway exchange catheters (AEC) are designed to safely maintain a secure airway and sometimes allow for ventilation while exchanging an endotracheal tube or performing a trial tracheal extubation, their use is sometimes associated with devastating complications. Pneumothorax is an underappreciated complication with AECs that can occur even in the absence of high pressure ventilation with quick clinical deterioration. The development of a pneumothorax can be difficult to distinguish from other potential causes of clinical deterioration and the clinician should maintain a high level of suspicion for quick diagnosis and treatment. Here we report a case of tension pneumothorax leading to cardiovascular collapse that occurred very suddenly with the introduction of an AEC. This pneumothorax presented in an atypical manner by all monitors available except for blood pressure monitoring. Therefore this case highlights the need for strong clinical suspicion of pneumothorax with the use of AECs.

YAP2 transcriptional regulator mediates a plethora of cellular functions, including the newly discovered Hippo tumor suppressor pathway, by virtue of its ability to recognize WBP1 and WBP2 signaling adaptors among a wide variety of other ligands. Herein, using isothermal titration calorimery (ITC) and circular dichroism (CD) in combination with molecular modeling (MM) and molecular dynamics (MD), we provide evidence that the WW1 and WW2 domains of YAP2 recognize various PPXY motifs within WBP1 and WBP2 in a highly promiscuous and subtle manner. Thus, although both WW domains strictly require the integrity of the consensus PPXY sequence, non-consensus residues within and flanking this motif are not critical for high-affinity binding, implying that they most likely play a role in stabilizing the polyproline type II (PPII) helical conformation of the PPXY ligands. Of particular interest is the observation that both WW domains bind to a PPXYXG motif with highest affinity, implicating a preference for a non-bulky and flexible glycine one-residue C-terminal to the consensus tyrosine. Importantly, a large set of residues within both WW domains and the PPXY motifs appear to undergo rapid fluctuations on a nanosecond time scale, arguing that WW-ligand interactions are highly dynamic and that such conformational entropy may be an integral part of the reversible and temporal nature of cellular signaling cascades. Collectively, our study sheds light on the molecular determinants of a key WW-ligand interaction pertinent to cellular functions in health and disease.

The absence of the palmaris longus (PL) has been shown to vary based on body side, gender, and ethnicity. In prior studies, homogenous ethnic populations have been shown to have differences in rates of absence. However, no study thus far has analyzed the differences in palmaris longus prevalence in a multiethnic population. We prospectively collected data on 516 patients visiting the outpatient hand clinics at LAC+USC Medical Center and Keck Medical Center. Analysis of the data was then performed for variables including ethnicity, laterality, and gender. There were no differences in the absence of the PL based on laterality or gender. Ethnically, there was no difference between white (non-Hispanic) and white (Hispanic) patients, with prevalence of 14.9% and 13.1%, respectively. However, African American (4.5%) and Asian (2.9%) patients had significantly fewer absences of the PL than the Caucasian, Hispanic reference group (P = 0.005 and P = 0.008, resp.). African Americans and Asians have a decreased prevalence of an absent PL. The Caucasian population has a relatively greater prevalence of an absence of the PL. This epidemiological study demonstrates the anatomic variation in this tendon and may be taken into account when planning an operation using tendon grafts.

Impairment of vascular growth is a hallmark of diabetic complications, but the progression and mechanisms are poorly understood. To determine whether obesity and early diabetes impair endothelium-dependent vasodilatation and vascular response to ischemia, microvascular function as well as angiogenic responses to ischemia were assessed in young (C57) and 6-month-old lean mice (old C57), in obese (db-C57) mice, and in mice suffering an early (db-KsJ) and sustained type 2 diabetes (old db-KsJ). Glycemia gradually increased from the db-C57 to the old db-KsJ. Early and established type II diabetes significantly reduced the level of insulin that was significantly increased in obese mice. Endothelial function was assessed in isolated resistance arteries while the angiogenic response induced by unilateral hindlimb ischemia was analyzed, after 28 days, with a laser Doppler flowmeter and angiography. Aging (−21%), obesity (−45%), as well as early (−58%) and sustained type II diabetes (−69%) induced a progressive impairment of the endothelium-dependent relaxation of the gracilis artery. Laser Doppler measurements demonstrated that only early and sustained type II diabetes impaired skin blood flow recovery. Vascular collateralization was reduced with aging and severely impaired in older db-KsJ mice, the two strains of mice in which ischemia reduced eNOS expression. These results demonstrate that endothelial dysfunction induced by obesity is insufficient to alter the angiogenic response to ischemia. Furthermore, the development of frank type II diabetes or increasing age is required to impair the vascular response to hindlimb ischemia. We conclude that additional risk factors or severe endothelial dysfunction may be requisite to impede the angiogenic response to ischemia.

Stimulating, and some blocking, antibodies to the TSH receptor (TSHR) have conformation-dependent epitopes reported to involve primarily the leucine rich repeat region of the ectodomain (LRD). However, successful crystallization of TSHR residues 22–260 has omitted important extracellular non-LRD residues including the hinge region which connects the TSHR ectodomain to the transmembrane domain and which is involved in ligand induced signal transduction. The aim of the present study, therefore, was to determine if TSHR antibodies (TSHR-Abs) have non-LRD binding sites outside the LRD. To obtain this information we employed the method of epitope protection in which we first protected TSHR residues 1–412 with intact TSHR antibodies and then enzymatically digested the unprotected residues. Those peptides remaining were subsequently delineated by mass spectrometry. Fourteen out of 23 of the reported stimulating monoclonal TSHR-Ab crystal contact residues were protected by this technique which may reflect the higher binding energies of certain residues detected in this approach. Comparing the protected epitopes of two stimulating TSHR-Abs we found both similarities and differences but both antibodies also contacted the hinge region and the amino terminus of the TSHR following the signal peptide and encompassing cysteine box 1 which has previously been shown to be important for TSH binding and activation. A monoclonal blocking TSHR antibody revealed a similar pattern of binding regions but the residues that it contacted on the LRD were again distinct. These data demonstrated that conformationally dependent TSHR-Abs had epitopes not confined to the LRDs but also incorporated epitopes not revealed in the available crystal structure. Furthermore, the data also indicated that in addition to overlapping contact regions within the LRD, there are unique epitope patterns for each of the antibodies which may contribute to their functional heterogeneity.

Castleman and Towne described a disease presenting as a mediastinal mass resembling thymoma. It is also known as "giant lymph node hyperplasia", "lymph node hamartoma", "angiofollicular mediastinal lymph node hyperplasia", and "angiomatous lymphoid hyperplasia". The pathogenesis is unknown, but the bulk of evidence points toward faulty immune regulation, resulting in excessive B-lymphocyte and plasma-cell proliferation in lymphatic tissue. In addition to the mediastinal presentation, extrathoracic involvement in the neck, axilla, mesentery, pelvis, pancreas, adrenal gland, and retroperitoneum also have been described. There are 2 major pathologic variations of Castleman disease: (1) hyaline-vascular variant, the most frequent, characterized by small hyaline-vascular follicles and capillary proliferation; and (2) the plasma-cell variant, in which large lymphoid follicles are separated by sheets of plasma cells. The hyaline-vascular cases usually are largely asymptomatic, whereas the less common plasma-cell variant may present with fever, anemia, weight loss, and night sweats, along with polyclonal hypergamma-globulinemia. Castleman disease is a rare lymphoproliferative disorders. Few cases have been described world widely. In this article we reviewed the classification, pathogenesis, pathology, radiological features and up to date treatment with special emphasis on the role of viral stimulation, recent therapeutic modalities and the HIV-associated disease.

Background

Although hypertrophic scar (HTS) formation following cleft lip repair is relatively common, published rates vary widely, from 1% to nearly 50%. The risk factors associated with HTS formation in cleft patients are not well characterized. The primary aim of this retrospective study of 180 cleft lip repairs is to evaluate the frequency of postoperative HTS among various ethnic groups following cleft lip repair.

Methods

A retrospective chart view of patients undergoing primary cleft lip repair over a 16-year period (1990–2005) by the senior surgeon was performed. The primary outcome was the presence of HTS at 1 year postoperatively. Bivariate analysis and multivariable logistic regression were used to evaluate potential risk factors for HTS, including ethnicity, type and laterality of cleft, and gender.

Results

One hundred and eighty patients who underwent cleft lip repair were included in the study. The overall rate of postoperative HTS formation was 25%. Ethnicity alone was found to be an independent predictor of HTS formation. Caucasian patients had the lowest rate of HTS formation (11.8%) and were used as the reference group. HTS rates were significantly higher in the other ethnicities, 32.2% in Hispanic patients (odds ratio [OR]: 3.51; 95% confidence interval [CI]: 1.53–8.85), and 36.3% for Asian patients (OR 4.27; 95% CI: 1.36–13.70). Sex, cleft type, and cleft laterality were not associated with increased rates of HTS.

Conclusions

Differences in ethnic makeup of respective patient populations may be a major factor influencing the wide variability of reported HTS rates. Consideration should be given to potential prophylactic treatments for HTS in susceptible ethnic populations.

Fusidic acid is a common therapy for staphylococcal infections in Saudi Arabia, but reports have suggested high rates of resistance among clinical isolates. Susceptibility testing of S. aureus to fusidic acid is further complicated by the lack of consensus on mean inhibitory concentrations (MIC) and disk diffusion cutoffs to determine resistance. The purpose of this study was to determine the correlation between disk diffusion and Etest determined MIC susceptibility results in clinical isolates of S. aureus from a large academic hospital in Riyadh, Saudi Arabia. Our data demonstrate excellent correlation between Etest determined MIC and disk diffusion susceptibility data, using either previously proposed zone sizes of ≥21 mm as susceptible and ≤18 mm as resistant or the EUCAST recommended zone size of ≤24 mm for resistance, in an area with relatively high rates of fusidic acid resistance.

Characterization of toxicogenomic signatures of carcinogen exposure holds significant promise for mechanistic and predictive toxicology. In vitro transcriptomic studies allow the comparison of the response to chemicals with diverse mode of actions under controlled experimental conditions. We conducted an in vitro study in TK6 cells to characterize gene expression signatures of exposure to 15 genotoxic carcinogens frequently used in European industries. We also examined the dose-responsive changes in gene expression, and perturbation of biochemical pathways in response to these carcinogens. TK6 cells were exposed at 3 dose levels for 24 h with and without S9 human metabolic mix. Since S9 had an impact on gene expression (885 genes), we analyzed the gene expression data from cells cultures incubated with S9 and without S9 independently. The ribosome pathway was affected by all chemical-dose combinations. However in general, no similar gene expression was observed among carcinogens. Further, pathways, i.e. cell cycle, DNA repair mechanisms, RNA degradation, that were common within sets of chemical-dose combination were suggested by clustergram. Linear trends in dose–response of gene expression were observed for Trichloroethylene, Benz[a]anthracene, Epichlorohydrin, Benzene, and Hydroquinone. The significantly altered genes were involved in the regulation of (anti-) apoptosis, maintenance of cell survival, tumor necrosis factor-related pathways and immune response, in agreement with several other studies. Similarly in S9+ cultures, Benz[a]pyrene, Styrene and Trichloroethylene each modified over 1000 genes at high concentrations. Our findings expand our understanding of the transcriptomic response to genotoxic carcinogens, revealing the alteration of diverse sets of genes and pathways involved in cellular homeostasis and cell cycle control.

Purpose. To compare treatment outcome (survival rate, condition of hard and soft peri-implant tissues) and prosthodontic maintenance requirements of two versus three narrow-diameter bone level implants with Locator attachments supporting mandibular overdentures. Materials and Methods. Twenty completely edentulous patients with atrophic mandibles were treated. Ten patients (Group A) were treated with overdentures supported by two narrow (3.3-mm diameter) implants (Straumann AG, Basel, Switzerland) and ten patients (Group B) were treated with overdentures supported by three narrow implants. Locator (Zest Anchors, USA) attachments were used for prosthetic anchorage. Standardized clinical and radiographic parameters (survival rate, plaque index, calculus index, gingival index, bleeding index, probing depth and marginal bone loss) were evaluated at the time of the completion of the prosthetic treatment (baseline) and after 6, 12 and 24 months of functional loading. Prosthodontic maintenance requirements were also scored. Results. Only one implant was lost (Group B) during the healing period. There were no significant differences with regards to any of the studied clinical and radiographic parameters between the two groups (P > 0.05). Few prosthetic complications were recorded. Conclusions. No need to insert more than two narrow-diameter bone level implants with Locator attachments in cases of atrophic mandible to support an overdenture, however, long-term prospective studies are required to support this notion.

Women in developing countries experience postnatal depression at rates that are comparable with or higher than those in developed countries. However, their personal experiences during pregnancy and childbirth have received little attention in relation to postnatal depression. In particular, the contribution of obstetric complications to their emotional well-being during the postpartum period is still not clearly understood. This study aimed to (a) describe the pregnancy and childbirth experiences among women in Bangladesh during normal childbirth or obstetric complications and (b) examine the relationship between these experiences and their psychological well-being during the postpartum period. Two groups of women—one group with obstetric complications (n=173) and the other with no obstetric complications (n=373)—were selected from a sample of women enrolled in a community-based study in Matlab, Bangladesh. The experiences during pregnancy and childbirth were assessed in terms of a five-point rating scale from ‘severely uncomfortable=1’ to ‘not uncomfortable at all=5’. The psychological status of the women was assessed using a validated local version of the Edinburgh Postnatal Depression Scale (EPDS) at six weeks postpartum. Categorical data were analyzed using the chi-square test and continuous data by analysis of variance. Women with obstetric complications reported significantly more negative experiences during their recent childbirth [95% confidence interval (CI) 1.36-1.61, p<0.001] compared to those with normal childbirth. There was a significant main effect on emotional well-being due to experiences of pregnancy [F (4,536)=4.96, p=0.001] and experiences of childbirth [F (4,536)=3.29, p=0.01]. The EPDS mean scores for women reporting severe uncomfortable pregnancy and childbirth experiences were significantly higher than those reporting no such problems. After controlling for the background characteristics, postpartum depression was significantly associated with women reporting a negative childbirth experience. Childbirth experiences of women can provide important information on possible cases of postnatal depression.

Outbreaks linked to food-borne and hospital-acquired pathogens account for millions of deaths and hospitalizations as well as colossal economic losses each and every year. Prevention of such outbreaks and minimization of the impact of an ongoing epidemic place an ever-increasing demand for analytical methods that can accurately identify culprit pathogens at the earliest stage. Although there is a large array of effective methods for pathogen detection, none of them can satisfy all the following five premier requirements embodied for an ideal detection method: high specificity (detecting only the bacterium of interest), high sensitivity (capable of detecting as low as a single live bacterial cell), short time-to-results (minutes to hours), great operational simplicity (no need for lengthy sampling procedures and the use of specialized equipment), and cost effectiveness. For example, classical microbiological methods are highly specific but require a long time (days to weeks) to acquire a definitive result.1 PCR- and antibody-based techniques offer shorter waiting times (hours to days), but they require the use of expensive reagents and/or sophisticated equipment.2-4 Consequently, there is still a great demand for scientific research towards developing innovative bacterial detection methods that offer improved characteristics in one or more of the aforementioned requirements. Our laboratory is interested in examining the potential of DNAzymes as a novel class of molecular probes for biosensing applications including bacterial detection.5

DNAzymes (also known as deoxyribozymes or DNA enzymes) are man-made single-stranded DNA molecules with the capability of catalyzing chemical reactions.6-8 These molecules can be isolated from a vast random-sequence DNA pool (which contains as many as 1016 individual sequences) by a process known as "in vitro selection" or "SELEX" (systematic evolution of ligands by exponential enrichment).9-16 These special DNA molecules have been widely examined in recent years as molecular tools for biosensing applications.6-8

Our laboratory has established in vitro selection procedures for isolating RNA-cleaving fluorescent DNAzymes (RFDs; Fig. 1) and investigated the use of RFDs as analytical tools.17-29 RFDs catalyze the cleavage of a DNA-RNA chimeric substrate at a single ribonucleotide junction (R) that is flanked by a fluorophore (F) and a quencher (Q). The close proximity of F and Q renders the uncleaved substrate minimal fluorescence. However, the cleavage event leads to the separation of F and Q, which is accompanied by significant increase of fluorescence intensity.

More recently, we developed a method of isolating RFDs for bacterial detection.5 These special RFDs were isolated to "light up" in the presence of the crude extracellular mixture (CEM) left behind by a specific type of bacteria in their environment or in the media they are cultured (Fig. 1). The use of crude mixture circumvents the tedious process of purifying and identifying a suitable target from the microbe of interest for biosensor development (which could take months or years to complete). The use of extracellular targets means the assaying procedure is simple because there is no need for steps to obtain intracellular targets.

Using the above approach, we derived an RFD that cleaves its substrate (FS1; Fig. 2A) only in the presence of the CEM produced by E. coli (CEM-EC).5 This E. coli-sensing RFD, named RFD-EC1 (Fig. 2A), was found to be strictly responsive to CEM-EC but nonresponsive to CEMs from a host of other bacteria (Fig. 3).

Here we present the key experimental procedures for setting up E. coli detection assays using RFD-EC1 and representative results.

Extracts from eleven different plant species such as jute (Corchorus capsularis L.), cheerota (Swertia chiraita Ham.), chatim (Alstonia scholaris L.), mander (Erythrina variegata), bael (Aegle marmelos L.), marigold (Tagetes erecta), onion (Allium cepa), garlic (Allium sativum L.), neem (Azadiracta indica), lime (Citrus aurantifolia), and turmeric (Curcuma longa L.) were tested for antibacterial activity against potato soft rot bacteria, E. carotovora subsp. carotovora (Ecc) P-138, under in vitro and storage conditions. Previously, Ecc P-138 was identified as the most aggressive soft rot bacterium in Bangladeshi potatoes. Of the 11 different plant extracts, only extracts from dried jute leaves and cheerota significantly inhibited growth of Ecc P-138 in vitro. Finally, both plant extracts were tested to control the soft rot disease of potato tuber under storage conditions. In a 22-week storage condition, the treated potatoes were significantly more protected against the soft rot infection than those of untreated samples in terms of infection rate and weight loss. The jute leaf extracts showed more pronounced inhibitory effects on Ecc-138 growth both in in vitro and storage experiments.

A total of 91 isolates of probable antagonistic bacteria of potato soft rot bacterium Erwinia carotovora subsp. carotovora (Ecc) were extracted from rhizospheres and endophytes of various crop plants, different soil varieties, and atmospheres in the potato farming areas of Bangladesh. Antibacterial activity of the isolated probable antagonistic bacteria was tested in vitro against the previously identified most common and most virulent soft rot causing bacterial strain Ecc P-138. Only two isolates E-45 and E-65 significantly inhibited the in vitro growth of Ecc P-138. Physiological, biochemical, and carbon source utilization tests identified isolate E-65 as a member of the genus Bacillus and the isolate E-45 as Lactobacillus sp. The stronger antagonistic activity against Ecc P-138 was found in E-65 in vitro screening and storage potatoes. E-65 reduced the soft rot infection to 22-week storage potatoes of different varieties by 32.5–62.5% in model experiment, demonstrating its strong potential to be used as an effective biological control agent for the major pectolytic bacteria Ecc. The highest (62.5%) antagonistic effect of E-65 was observed in the Granola and the lowest (32.7%) of that was found in the Cardinal varieties of the Bangladeshi potatoes. The findings suggest that isolate E-65 could be exploited as a biocontrol agent for potato tubers.