Economic valuation of selected ecosystem services in Islamabad Capital Territory (ICT), Pakistan

Abstract Payment for ecosystem services (PES) is a mechanism where a consumer is able and ready to pay for the protection of the precise ecosystem service and there must be a provider such as local societies receiving an economic resource, who in return, must have the ability to maintain that ecosystem service. Economic valuation provides basis for payment for ecosystem services. Therefore, objective of this study was to evaluate tourism and carbon stock services of the Islamabad Capital Territory (ICT), Pakistan. Two forest zones (Chirpine and Scrub) of Islamabad capital territory (ICT) were selected for estimation of carbon stock and their carbon credits and carbon worth, a questionnaire-based survey was conducted for tourism as a payment for ecosystem services. The method for carbon stock assessment was systematic sampling for Chirpine forest whereas random sampling was done for scrub forest. The size of sampling plot was 17.84 m radius, and a total of 93 plots (49 Scrub zone and 44 Chirpine zone) was taken in the study area. The carbon stock of both zones (Chirpine and Scrub zone) is 22556.75 ton/ha (Chirpine 20105.79, Scrub 2450.96) and total carbon dioxide sequestered by both zone is 82557.72 ton/ha (Chirpine 73587.2, Scrub 8970.52), total carbon credits of both zone is 302160.87 (Chirpine 269328.97, Scrub 32831.9) and the carbon worth of both Chirpine and scrub zone is 4532418.92 $ (Chirpine 4039937.09$, Scrub 492481.83$). Similarly, from tourism point of view, in Shakar Parian, 94% tourists were agreed for PES whereas 6% were disagreed for the PES (the 6% tourist were disagreed to contribute for PES, 40% were agreed for Rs.5 contribution and 54% for Rs.10.). moreover, in Lake view Park, 97% tourists were agreed and 3% are disagreed (In Lake View Park 5% tourists were disagreed for the PES contribution whereas 32% were agreed for Rs.5 and 63% were for Rs.10). In Damen e Koh, around 87% tourist were agreed and 13% were disagreed, (24% were agreed for the contribution of Rs.5 and 63% tourists were agreed for the contribution of Rs.10). In Marghazar Zoo, 93% tourists were agreed (22% were agreed for contribution of Rs.5 and 71% tourist were agreed for contribution of Rs.10) and 7% are disagreed for PES whereas 7% tourists were not agreed for contribution. PES may implement to compensate forest and parks manager to ensure better management of the forests and parks. Due to prime location and scenic beauty of the ICT, it has huge potential for implementation of PES mechanism for sustainable forest management and conservation. Therefore, it is recommended that Capital Development Authority (CDA) Islamabad should devise a plan for implementation of PES in forests and parks of ICT for its sustainable management of recreational and forest resources.

Yield, carbon stock, and price dynamics of agroforestry tree species in district Mardan, Khyber Pakhtunkhwa, Pakistan

Abstract A socio-economic study was conducted in district Mardan of the Khyber Pakhtunkhwa (KP) province of Pakistan to get a comprehensive knowledge of the agroforestry tree species grown on the farmlands, their yield, and carbon stock. For yield and carbon stock estimation, data were collected from 59 sample plots by measuring the diameter, height, volume, and biomass of selected agroforestry tree species through D-tape and Haga altimeter. A total of 59 sample plots were inventoried using 2.5 percent sampling intensity. Each sample plot has an area of 0.5 ha, where each tree with a Diameter at Breast Height (DBH) ≥ 5 cm was inventoried. The calculated amount of volume of each tree species was then converted to biomass by multiplying it by the density of wood and the Biomass Expansion Factor (BEF). Total yield and C stock for the selected agroforestry tree species were 11535.2 metric tons and 2102.2 metric tons, respectively. Populus euroamericana is classified as the main tree with 28% growing stock prior to Morus alba by 21%, while Melia azedarach, Eucalyptus camaldulensis, Dalbergia sissoo, Acacia nilotica, Salix tetrasperma, and Bombax ceiba consist of 15%, 12%, 8%, 6%,7% and 3% growing stock respectively. Among the species found in different sampling plots the yield of Populus euroamericana was found to be 4747.5 metric tons and it was followed by the species Morus alba found at 2027.3 metric tons. Similarly, the volume for Melia azedarach, Eucalyptus camaldulensis, Dalbergia sissoo, Salix spp, Boombox ceiba, and Acacia nilotica was 1532.2 tons,1503 ton,745.7,203.5ton, 555.4ton and 220.5ton, respectively. The carbon stock for Populus euroamericana was calculated as 777.8 ton/ha, while for Eucalyptus camaldulensis, Melia azedarach, Morus alba, Dalbergia sissoo, Acacia nilotica, Salix species, and Bombax ceiba it was calculated as 312.3ton/ha, 272.1ton/ha, 363ton/ha, 245.1ton/ha, 51.4ton/ha, 27.3ton/ha and 53.2ton/ha, respectively. The questionnaire survey conducted for price dynamics showed that the majority of respondents purchase timber from the market for construction. But they use farm trees with low-quality city construction. They dislike using local timber in the conventional building as timber from farm trees is liable to insect attack. Rs. 50,000-100000, (33.33%) of daily sales was concluded from 50% of the trader while (16.7%) of the traders have their sales between Rs.150,000-200,000. Therefore, it is concluded by the authors that both provincial and federal government should promote agroforestry in Pakistan through different incentives because it has the potential to cope with dilemma of deforestation of natural forests and improve the livelihood of local peoples. It is strongly recommended that special projects just like the Ten Billion Tree Afforestation Project (T-BTTP) should be launched for agroforestry plantation and promotion in the country to sustain the ecological harmony and uplift the socio-economic condition of the peoples of Pakistan.

P-735 Exploring representation and inclusivity in fertility and reproductive health societies’ leadership

Study question

How diverse is the board-level executive leadership of the leading fertility and reproductive health societies in Europe, Australia and North America?

Summary answer

There is good gender diversity among the reproductive health societies included in the study, with limited ethnic diversity.

What is known already

Reproductive health societies promote understanding and interest in reproductive biology and medicine. They are leading authorities, providing guidelines, opinions, and direction to practitioners, policy makers and the public. Membership on these societies’ board is a marker of influence and prestige. Many societies have clear Equality and Diversity Statement on their website, suggesting that they value representation of members from whom they obtain fees. This study presents a quantification of the executive leadership demographic diversity of major fertility and reproductive health societies in Europe, Australia and North America to evaluate diversity in governance.

Study design, size, duration

We conducted a review of the websites of ten leading fertility and reproductive health societies in the Europe, Australia and North America to quantity gender and ethnic diversity. Data analysis was conducted on the information obtained in January 2022. We included the executive leadership team /governing board members but excluded subgroup leaders or special interest group coordinators.

Participants/materials, setting, methods

Organisations reviewed include: American College of Obstetricians and Gynaecologists(ACOG), American Society for Reproductive Medicine(ASRM), British Fertility Society(BFS), Canadian Fertility and Andrology Society(CFAS), European Society of Human Reproduction and Embryology(ESHRE), The Fertility Society of Australia and New Zealand(FSA), International Federation of Obstetrics and Gynaecology(FIGO), The Royal Australian and New Zealand College of Obstetricians and Gynaecologists(RANZCOG), Royal College of Obstetricians and Gynaecologists (RCOG), and The Society of Obstetricians and Gynaecologists of Canada(SOGC).

Main results and the role of chance

Proportion for each demographic group at the time of the study are summarised below; where n = total number of board members; Gender: W= women, M= Men; ethnicity: Wh = White, B = Black and A = Asian.

In total, the number of board level/executive leadership members, responsible for governance in the societies reviewed were 112. Gender diversity was 41% Men, 59% Women, while ethnic diversity was 82% White, 3% Black and 15% Asian. It is encouraging to see the gender parity in the executive leadership of the organisations review, there remains an important need to improve ethnic diversity in order to better represent the membership and wider community  they serve. This has implications for role-modelling, equity, minimising the negative impact of groupthink and reaching/giving underrepresented group a voice.

Limitations, reasons for caution

Results presented are based on a snapshot at the time of review. Organisations periodically change leadership. Additionally, gender identification is based on self-identification in individual’s profile biography.

Wider implications of the findings

As reproductive health organisations continue make extensive contributions to the field, it is important for their leadership to represent the diversity of members and wider population they serve. There remains a need to move beyond diversity and equality statement to actively deploy policies and processes to improve and monitor representation.

Trial registration number

not applicable

Assessment of particulate matter (PM) in ambient air of different settings and its associated health risk in Haripur city, Pakistan

Particulate matter (PM) is a major air pollutant causing serious health problems. The aim of the present study was to find out concentration of PM in ambient air and its associated health risk in Haripur city, Pakistan. Twenty-three samples were taken at various educational institutes, hospitals, recreational areas and industries in Haripur city. Concentration of PM2.5 (µg/m3) and PM10 (µg/m3) was measured with Youngteng YT-HPC 3000A portable PM counter. The results revealed that values of both PM2.5 and PM10 were above the permissible limits (35 µg/m3 for PM2.5 and 150 µg/m3 for PM10) set by Environmental Protection Agency Pakistan (Pak-EPA) in all the educational institutes, hospitals, recreational areas and industries investigated. Furthermore, significant (p<0.05) variation was found in the concentration of both PM2.5 and PM10 in all the educational institutes, hospitals, recreational areas, and industries studied. The concentration of PM2.5 was positively correlated with the concentration of PM10 in all the sampling sites. Therefore, from 1-14 scale standard of health index, the values of PM2.5 and PM10 exhibited that the ambient air quality of Haripur city Pakistan is under high risk. If the regulatory authorities such as Environmental Protection Agency, Health Department and Local Government monitor PM pollution in different settings of Haripur city, then a decrease can be possible in the pollution level. The remedies that can be taken to overcome the problem of ambient air pollution such as PM are plantation of trees at the sites where there are higher levels of air pollutants and use of masks on personal protection basis along with implementation of pollution control system in industries of Hattar Industrial Estate Haripur city, Pakistan.

Hospital malnutrition in northeast and southeast Asia: A systematic literature review

BACKGROUND & AIMS

Hospital malnutrition is a prevalent yet frequently under-recognised condition that is associated with adverse clinical and economic consequences. Systematic reviews from various regions of the world have provided regional estimates of the prevalence of malnutrition and the magnitude of the associated health and economic burden; however, a systematic assessment of the prevalence and consequences of hospital malnutrition in northeast and southeast Asia has not been conducted.

METHODS

We performed a systematic literature search for articles on hospital malnutrition in 11 Asian countries published in English between January 1, 1997 and January 15, 2018. Studies reporting data on the prevalence, clinical consequences, or economic impact of hospital malnutrition in an adult inpatient population with a sample size ≥30 were eligible for inclusion.

RESULTS

The literature search identified 3207 citations; of these, 92 studies (N = 62,280) met the criteria for inclusion. There was substantial variability in study populations and assessment methods; however, a majority of studies reported a malnutrition prevalence of >40%. Malnutrition was associated with an increase in clinical complications, mortality, length of hospitalisation, hospital readmissions, and healthcare costs.

CONCLUSIONS

Hospital malnutrition is a highly prevalent condition among hospitalised patients in northeast and southeast Asia. Additionally, poor nutritional status is associated with increased morbidity and mortality and increased healthcare costs. Further research aimed at improving the identification and proactive management of hospitalised patients at risk for malnutrition is necessary to improve patient outcomes and alleviate the burden on local healthcare budgets.

Biodegradation Studies of Benzene, Toluene, Ethylbenzene and Xylene (BTEX) Compounds by Gliocladium sp. and Aspergillus terreus

Benzene, toluene, ethylbenzene and xylene (BTEX) are monoaromatic hydrocarbons found frequently in petroleum and its derivatives; and they are among the most important pollutants of soil and groundwater. This study focused on harnessing the enzymatic capabilities of filamentous fungi Gliocladium sp. and Aspergillus terreus, dwelling in a petroleum-contaminated soil to degrade benzene, toluene, ethylbenzene and xylene (BTEX) compounds. The biodegradation experiment was carried out using the fungi individually and in consortium in a batch culture containing mineral salts medium supplemented with 1% v/v BTEX. The experiments were carried out in triplicates at room temperature on a rotary shaker (180rpm) for twenty five days and aliquots were taken on a five day interval to determine the hydrocarbon utilizing fungal (HUF) count and residual BTEX in order to monitor the rate of biodegradation. The hydrocarbon utilizing fungal counts were determined by direct counting using a Neubauer  Haemocytometer while, the residual BTEX was determined using absorbance values measured using a spectrophotometer and the corresponding concentrations determined from a standard curve. The highest percentage degradation of BTEX was observed with Aspergillus terreus (89.1%) while, the least was observed with Gliocladium sp. (84.4%). The growth peak was attained on the 15th day in all treatments after which the HUF counts declined. Statistical analysis showed no significant difference (P>0.05) in the mean amounts of BTEX degraded and hydrocarbon-utilizing fungal counts between the treatments. The strains of Gliocladium sp. and Aspergillus terreus used in this study showed high ability for BTEX degradation thus, they are potential candidates for bioremediation of soils contaminated with monoaromatic hydrocarbons. Keywords: Biodegradation, BTEX, Gliocladium sp., Aspergillus terreus, Monoaromatic hydrocarbons

Clinical Practice Guidelines in Complicated Intra-Abdominal Infection 2018: An Indonesian Perspective

BACKGROUND

The occurrence of complicated intra-abdominal infections (cIAI) remains high despite system improvement in accordance with Joint Commission International because of heterogeneity of management. However, published clinical practice guidelines (CPGs) were not feasible to be implemented because these guidelines were not specific to Indonesian characteristics. Thus, a national CPG should be developed to minimize heterogeneity in the management of cIAI in Indonesia.

METHODS

We developed a CPG on cIAI through the adaptation of published CPGs. The process proceeded in steps recommended by ADAPTE. Published CPGs were critically appraised using Appraisal of Guidelines for Research and Evaluation (AGREE) II critical appraisal tools. For a specific updated CPG, the analysis was performed using Checklist for the Reporting of Updated Guidelines (CheckUp). Appropriate statements and recommendations in selected CPGs were adapted into our CPG with consideration of Indonesian characteristics. The recommendations were established by the hierarchy of evidence on Grading of Recommendations Assessment, Development and Evaluation (GRADE). The approval of the recommendation draft was performed using the Delphi method.

RESULTS

Sixty-eight full-text guidelines were downloaded from several sites. Thirty-three CPGs were related to intra-abdominal infection and 18 others were specific on CPG on intra-abdominal infection and cIAI. On review of these 18 CPGs, 13 were strongly recommended, three were recommended, and two were not recommended. On review updated CPGs, five updated CPGs were found, all with the same score. Two of the strongly recommended updated CPGs had been published in 2016 and 2017, i.e. recommendations by the World Society of Emergency Surgery 2016 consensus conference and revised CPG of the Surgical Site Infection Society. There were a total of 84 statements and recommendations developed and approved by the task force through using the Delphi method.

CONCLUSIONS

This guideline summarizes the definition, classification, pathophysiology, etiology, risk factors, assessments, and management of cIAI. Evidence-based recommendations have been developed with consideration of Indonesian-specific characteristics.

Antibiotic management of complicated intra-abdominal infections in adults: The Asian perspective

Regional epidemiological data and resistance profiles are essential for selecting appropriate antibiotic therapy for intra-abdominal infections (IAIs). However, such information may not be readily available in many areas of Asia and current international guidelines on antibiotic therapy for IAIs are for Western countries, with the most recent guidance for the Asian region dating from 2007. Therefore, the Asian Consensus Taskforce on Complicated Intra-Abdominal Infections (ACT-cIAI) was convened to develop updated recommendations for antibiotic management of complicated IAIs (cIAIs) in Asia. This review article is based on a thorough literature review of Asian and international publications related to clinical management, epidemiology, microbiology, and bacterial resistance patterns in cIAIs, combined with the expert consensus of the Taskforce members. The microbiological profiles of IAIs in the Asian region are outlined and compared with Western data, and the latest available data on antimicrobial resistance in key pathogens causing IAIs in Asia is presented. From this information, antimicrobial therapies suitable for treating cIAIs in patients in Asian settings are proposed in the hope that guidance relevant to Asian practices will prove beneficial to local physicians managing IAIs.

Clinical and prognostic significance of RhoA and RhoC gene expression in esophageal squamous cell carcinoma

BACKGROUND

Rho GTPases are involved in the organization of a microfilament network, cell-to-cell interaction, and malignant transformation. To elucidate the role of Rho GTPases in esophageal squamous cell carcinoma (ESCC), we compared the levels of RhoA and RhoC mRNA from ESCC with the corresponding normal tissue originating from the same patients.

METHODS

Real-time reverse transcriptase-polymerase chain reaction was performed to observe rhoA and rhoC in esophageal cell lines. Next, the mRNA levels of rhoA and rhoC were evaluated from 50 patients.

RESULTS

The rhoA and rhoC were higher in ESCC cell lines than in noncancerous esophageal cell. rhoC was overexpressed in TTn, which was obtained directly from a surgical specimen of a metastatic lesion of ESCC in the mandible. rhoA and rhoC were significantly higher in ESCC patient than in the normal counterparts (P = .0022 and P < .0001, respectively). rhoA correlated with tumor differentiation and rhoC correlated with an advanced tumor, node, metastasis system classifications. rhoA and rhoC in ESCC showed a positive correlation (P = .008). Patients with rhoA overexpression showed a significantly poorer prognosis than those with rhoA underexpression (P = .044).

CONCLUSIONS

To our knowledge, this study is the first in which the expression of RhoA and RhoC at the mRNA level in ESCC was examined and compared with its normal counterpart. Our results suggest that rhoA and rhoC are involved in ESCC progression and useful as prognostic markers. Further study will be needed to examine the therapeutic potential of the Rho GTPase inhibitor as a promising anticancer therapy, especially in ESCC.

Chemically synthesized sugar-cholestanols possess a preferential anticancer activity involving promising therapeutic potential against human esophageal cancer

The understanding of the cell signaling pathways and the molecular events leading to cell death of cancer cells will provide in-depth perspective into the identification and development of potent anticancer agents. A balance between cell proliferation and cell death has been raised as a rational target for the management of malignant tumors. In the present study, the authors demonstrated that chemically synthesized sugar-cholestanols consisting of GlcNAcbeta-, Galbeta- and GlcNAcbeta1,3Galbeta-cholestanols exerted a strong inhibiting activity against cell proliferation of esophageal cancer cells, but cholestanol itself did not show such an activity against the same cancer cells at all. In addition to their predominant role as an antiproliferation agent, evidence based on the molecular analyses suggested that sugar-cholestanols played a regulatory role in multiple signal transduction pathways inducing apoptosis through both the death signal-extrinsic and the mitochondria-intrinsic pathways. Sugar-cholestanols seemed to be more susceptible to esophageal cancer cells than to non-cancerous esophageal cells at the very early event of their exposure and, further, to suppress specifically the expression of vascular endothelial growth factor. Taken together, these novel functions of sugar-cholestanols indicate that they could have promising therapeutic potential against human esophageal cancer.

Anticancer effects of gallic acid isolated from Indonesian herbal medicine, Phaleria macrocarpa (Scheff.) Boerl, on human cancer cell lines

The natural antioxidant gallic acid (GA) was isolated from fruits of a medicinal Indonesian plant, Phaleria macrocarpa (Scheff.) Boerl. The structure was identified on the basis of spectroscopic analysis and comparison with authentic compound. GA demonstrated a significant inhibition of cell proliferation in a series of cancer cell lines and induced apoptosis in esophageal cancer cells (TE-2) but not in non-cancerous cells (CHEK-1). Observation of the molecular mechanism of apoptosis showed that GA up-regulated the pro-apoptosis protein, Bax, and induced caspase-cascade activity in cancer cells. On the other hand, GA down-regulated anti-apoptosis proteins such as Bcl-2 and Xiap. In addition, GA also induced down-regulation of the survival Akt/mTOR pathway. In non-cancerous cells, we observed delayed expression of pro-apoptosis related proteins. Our results suggest that GA might be a potential anticancer compound. However, in depth in vivo studies are needed to elucidate the exact mechanism.

Expression of carbohydrate antigens in human esophageal squamous cell carcinoma: prognostic application and its diagnostic implications

BACKGROUND

Tumor markers whose antigenic determinants have been demonstrated to consist of carbohydrates are probably one of the most extensive tools that have been used in routine cancer diagnosis. In this study, the relevance of carbohydrate antigen expression profile was examined in esophageal squamous cell carcinoma together with prognosis in 130 patients.

METHODS

The expression of carbohydrate antigens was estimated immunohistochemically by anti-sialyl Lewis a (sialyl Le(a)) and anti-sialyl Lewis x (sialyl Le(x)) monoclonal antibodies, and correlation between their staining and clinicopathological status was examined. In addition, the correlation of both carbohydrate antigens expression was evaluated with microvessel density (MVD).

RESULTS

Expressions of sialyl Lewis antigens and MVD were associated with several clinicopathological features that reflect the tumor aggressiveness in esophageal cancer. The 5-year survival rate of patients was found to be associated with expression of sialyl Le(a) and sialyl Le(x) antigens and with MVD; thus, all of them were revealed to be independent prognostic factors.

CONCLUSIONS

Combination of these factors offered a better prediction of prognosis of esophageal squamous cell carcinoma. Further, carbohydrate antigens represent a promising target for therapeutic approaches against the disease.

RhoA and RhoC proteins promote both cell proliferation and cell invasion of human oesophageal squamous cell carcinoma cell lines in vitro and in vivo

There is growing evidence that Rho proteins are deregulated by overexpression in tumours; and according to some reports, this correlates with disease progression. Our previous clinical study had demonstrated a correlation between RhoA expression and tumour progression in oesophageal squamous cell carcinoma (ESCC). These findings prompted us to study, using nude mice, pathological roles of Rho proteins in human ESCC cells. Western blot analysis in ESCC cell lines, in addition to cell proliferation and in vitro migration assays, were performed to observe the malignant potential of RhoA and RhoC in untransfected and transfected cells. Constitutively active RhoA, RhoC and dominant negative RhoA (dnRhoA) proteins were transfected to ESCC (TE-1 and TE-2) cells. The stably transfected cells were injected into nude mice, and the growth and metastasis of these cells to the lungs were analysed. Tumour tissues were then examined using immunohistochemical methods for proteins Ki-67 (MIB-1), FAK, MMP-1, MMP-9 and TIMP-3. Protein levels of RhoA and RhoC in ESCC cell lines were visualised by Western blotting, and showed highest expression in TE-2 cells. Results from the migration assay illustrated that both RhoA and RhoC play a role in migration of ESCC cells. In TE-2 transfected cells, RhoC showed greater migration compared to RhoA. By using an experimental metastasis model in nude mice, RhoA was found to promote more tumour growth than RhoC, whereas RhoC induced lung metastasis in comparison to RhoA. Ki-67 labelling index was used to evaluate the proliferation potential of tumour tissue inoculated from nude mice. In TE-2 cells RhoA gave a proliferation capacity of 24.8+/-0.5, which was significantly higher than those of TE-2 RhoC 10+/-0.4 (P<0.01). Strong immunoreactivity for FAK, MMP-1 and MMP-9 proteins was present in all tumour cells. By contrast, loss of TIMP-3 expression was observed in all tumour cells. In conclusion, our results indicate that pro-oncogenic Rho proteins are involved in promoting tumour growth, cell migration and metastasis in human ESCC cells in nude mice. The results from this study suggest that active Rho proteins may induce a transforming effect that leads to a malignant phenotype.

Perceptions of influenza and influenza vaccination in patients attending hospital outpatient clinics

Influenza remains a major cause of morbidity and disruption to health services during winter. Annual vaccination of risk groups is the mainstay of influenza management policy. Despite much national publicity, vaccine uptake remains below desired levels. We investigated the perceptions of influenzal illness and opinions on vaccination in hospital outpatients attending clinics associated with risk and non-risk (i.e. control) morbidities. There were 270 recruited patients in risk groups: 90 each from diabetic, respiratory and cardiac clinics and equal numbers in three age groups (40-49, 50-59, 60-69 years). Equal numbers of controls were recruited from colorectal, fracture and dermatology clinics. The perceptions of influenza and knowledge of the preventive value of vaccination were fairly accurate in both groups. Fewer people in both groups had been vaccinated than had been specifically advised to be vaccinated. Advice for vaccination had been received by fewer people attending the cardiac clinic than the other two risk associated clinics. More use could be made of the health education opportunity afforded by attendance at hospital outpatient clinics.

Cortical upper layer neurons derive from the subventricular zone as indicated bySvet1gene expression

The cerebral cortex is composed of a large variety of different neuron types. All cortical neurons, except some interneurons, are born in two proliferative zones, the cortical ventricular (VZ) and subventricular (SVZ) zones. The relative contribution of both proliferative zones to the generation of the diversity of the cortical neurons is not well understood. To further dissect the underlying mechanism, molecular markers specific for the SVZ are required. Towards this end we performed a subtraction of cDNA libraries, generated from E15.5 and E18.5 mouse cerebral cortex. A novel cDNA, Svet1, was cloned which was specifically expressed in the proliferating cells of the SVZ but not the VZ. The VZ is marked by the expression of the Otx1 gene. Later in development, Svet1 and Otx1 were expressed in subsets of cells of upper (II-IV) and deep (V-VI) layers, respectively. In the reeler cortex, where the layers are inverted, Svet1 and Otx1 label precursors of the upper and deeper layers, respectively, in their new location. Interestingly, in the Pax6/small eye mutant, Svet1 activity was abolished in the SVZ and in the upper part of the cortical plate while the Otx1 expression domain remained unchanged. Therefore, using Svet1 and Otx1 as cell-type-specific molecular markers for the upper and deep cortical layers we conclude that the Sey mutation affects predominantly the differentiation of the SVZ cells that fail to migrate into the cortical plate. The abnormality of the SVZ coincides with the absence of upper layer cells in the cortex. Taken together our data suggest that while the specification of deep cortical layers occurs in the ventricular zone, the SVZ is important for the proper specification of upper layers.

Angiozyme: a novel angiogenesis inhibitor

Several inhibitors of angiogenesis are being developed for the treatment of cancer. One dominant strategy involves disruption of the vascular endothelial growth factor (VEGF) pathway by inhibition of the receptors for VEGF. Inhibition of the VEGF receptor activity can be accomplished using catalytic RNA molecules known as ribozymes, which downregulate VEGF receptor function by specifically cleaving the mRNAs for the primary VEGF receptors, Flt-1 and KDR. Significant inhibition of angiogenesis using ribozymes against both receptors has been demonstrated. In animal tumor models, antitumor effects are most pronounced with the anti-Flt-1 ribozyme known as Angiozyme (Ribozyme Pharmaceuticals, Boulder, CO). Extensive preclinical studies have demonstrated no significant toxicities. Clinical trials of Angiozyme are currently in progress for patients with advanced malignancy. Preliminary results demonstrate Angiozyme to be well tolerated, without significant side effects. Several phase II trials are underway for patients with advanced malignancy to test therapeutic efficacy.

X-ray crystallographic observation of "in-line" and "adjacent" conformations in a bulged self-cleaving RNA/DNA hybrid

The RNA strand in an RNA/DNA duplex with unpaired ribonucleotides can undergo self-cleavage at bulge sites in the presence of a variety of divalent metal ions (Hüsken et al., Biochemistry, 1996, 35:16591-16600). Transesterification proceeds via an in-line mechanism, with the 2'-OH of the bulged nucleotide attacking the 3'-adjacent phosphate group. The site-specificity of the reaction is most likely a consequence of the greater local conformational freedom of the RNA backbone in the bulge region. A standard A-form backbone geometry prohibits formation of an in-line arrangement between 2'-oxygen and phosphate. However, the backbone in the region of an unpaired nucleotide appears to be conducive to an in-line approach. Therefore, the bulge-mediated phosphoryl transfer reaction represents one of the simplest RNA self-cleavage systems. Here we focus on the conformational features of the RNA that underlie site-specific cleavage. The structures of an RNA/DNA duplex with single ribo-adenosyl bulges were analyzed in two crystal forms, permitting observation of 10 individual conformations of the RNA bulge moiety. The bulge geometries cover a range of relative arrangements between the 2'-oxygen of the bulged nucleotide and the P-O5' bond (including adjacent and near in-line) and give a detailed picture of the conformational changes necessary to line up the 2'-OH nucleophile and scissile bond. Although metal ions are of crucial importance in the catalysis of analogous cleavage reactions by ribozymes, it is clear that local strain or conformational flexibility in the RNA also affect cleavage selectivity and rate (Soukup & Breaker, RNA, 1999, 5:1308-1325). The geometries of the RNA bulges frozen out in the crystals provide snapshots along the reaction pathway prior to the transition state of the phosphoryl transfer reaction.

Pharmacokinetics and tolerability of an antiangiogenic ribozyme (ANGIOZYME) in healthy volunteers

The pharmacokinetics and tolerability of a chemically stabilized synthetic ribozyme (ANGIOZYME) targeting the Flt-1 VEGF receptor mRNA were evaluated in healthy volunteers. In a placebo-controlled, single-dose escalation study, ribozyme was administered as a 4-hour i.v. infusion of 10 or 30 mg/m2 or as a s.c. bolus of 20 mg/m2. Peak ribozyme plasma concentrations of 1.5 and 3.8 micrograms/mL were observed after the 10 and 30 mg/m2 i.v. infusions, respectively. When normalized to dose, AUC values as well as peak concentrations increased proportionally as the dose was increased from 10 to 30 mg/m2. Peak concentrations of 0.9 microgram/mL were observed approximately 3.25 hours after a 20 mg/m2 s.c. bolus of ribozyme. The dose-normalized AUCs obtained after s.c. dosing were compared to the mean dose-normalized AUC after i.v. dosing to estimate an absolute s.c. bioavailability (f) of approximately 69%. An average elimination half-life of 28 to 40 minutes was observed after i.v. administration, which increased to 209 minutes after s.c. administration. Only 4 of 12 reported adverse events were possibly related to administration of ribozyme (headache and somnolence). Thus, ribozyme administration was well tolerated after a single 4-hour i.v. infusion of up to 30 mg/m2 or a single s.c. bolus of 20 mg/m2.

Crystal structure of an RNA duplex containing phenyl-ribonucleotides, hydrophobic isosteres of the natural pyrimidines

Chemically modified nucleotide analogs have gained widespread popularity for probing structure-function relationships. Among the modifications that were incorporated into RNAs for assessing the role of individual functional groups, the phenyl nucleotide has displayed surprising effects both in the contexts of the hammerhead ribozyme and pre-mRNA splicing. To examine the conformational properties of this hydrophobic base analog, we determined the crystal structure of an RNA double helix with incorporated phenyl ribonucleotides at 1.97 A resolution. In the structure, phenyl residues are engaged in self-pairing and their arrangements suggest energetically favorable stacking interactions with 3'-adjacent guanines. The presence of the phenyl rings in the center of the duplex results in only moderate changes of the helical geometry. This finding is in line with those of earlier experiments that showed the phenyl analog to be a remarkably good mimetic of natural base function. Because the stacking interactions displayed by phenyl residues appear to be similar to those for natural bases, reduced conformational restriction due to the lack of hydrogen bonds with phenyl as well as alterations in its solvent structure may be the main causes of the activity changes with phenyl-modified RNAs.

The novel PCR-based technique of genotyping applied to identification of scrambler mutation in mice

For a wide range of research purposes it is necessary to perform genotyping, i.e. to test which alleles, each corresponding to a particular locus, are present in the individual genome. Here we suggest a protocol of genotyping for mice with scrambler (scm) mutation. This mutation results in the aberrant splicing of the corresponding mRNA and affects the expression of mdab1 protein. Traditional approaches using genomic Southern hybridization or PCR with specific primers are not suitable for the genotyping of scm because of the lack of comprehensive information on the organization of the gene and on the presence of repetitive sequences in the known region. Here we propose a quick and highly reproducible method for genotyping scm mutant mice. The protocol consists of the following steps: isolation of genomic DNA, digestion with the restriction endonuclease, anchoring of resulting fragments with the adapter, and PCR amplification using adapter-specific primers. The final product of PCR amplification has a characteristic length which is different for the wt (wild type) and scm alleles. Thus, the characteristic pattern of bands obtained for each individual mouse specimen serves as criteria for the presence of wild type and/or scm allele. We believe that this approach could have wider application. The protocol can be easily modified and used as a convenient tool for identification of other genomic defects including those artificially introduced into genome by knockout or gene-trap techniques.

Structural variation induced by different nucleotides at the cleavage site of the hammerhead ribozyme

The hammerhead ribozyme is capable of cleaving RNA substrates at 5' UX 3' sequences (where the cleavage site, X, can be A, C, or U). Hammerhead complexes containing dC, dA, dI, or rG nucleotides at the cleavage site have been studied by NMR. The rG at the cleavage site forms a Watson-Crick base pair with C3 in the conserved core of the hammerhead, indicating that rG substrates inhibit the cleavage reaction by stabilizing an inactive conformation of the molecule. Isotope-edited NMR experiments on the hammerhead complexes show that there are different short proton-proton distances between neighboring residues depending upon whether there is a dC or dA at the cleavage site. These NMR data demonstrate that there are significant differences in the structure and/or dynamics of the active-site residues in these hammerhead complexes. Molecular dynamics calculations were used to model the conformations of the cleavage-site variants consistent with the NMR data. The solution conformations of the hammerhead ribozyme-substrate complexes are compared with the X-ray structure of the hammerhead ribozyme and are used to help understand the thermodynamic and kinetic differences among the cleavage-site variants.

The structural basis of hammerhead ribozyme self-cleavage

We have captured an 8.7 A conformational change that takes place in the cleavage site of the hammerhead ribozyme during self-cleavage, using X-ray crystallography combined with physical and chemical trapping techniques. This rearrangement brings the hammerhead ribozyme from the ground state into a conformation that is poised to form the transition state geometry required for hammerhead RNA self-cleavage. Use of a 5'-C-methylated ribose adjacent to the cleavage site permits this ordinarily transient conformational change to be kinetically trapped and observed crystallographically after initiating the hammerhead ribozyme reaction in the crystal. Cleavage of the corresponding unmodified hammerhead ribozyme in the crystal under otherwise identical conditions is faster than in solution, indicating that we have indeed trapped a catalytically relevant intermediate form of this RNA enzyme.

Inductive interactions regulating body patterning in planarian, revealed by analysis of expression of novel gene scarf

Subtractive hybridization was used to search for the early difference in gene expression between anteriorly and posteriorly regenerating tissues of the same region of the planarian body. A sequence (named scarf) specific for posteriorly regenerating tissue was isolated, encoding a soluble C-type lectin consisting of two slightly different carbohydrate-recognition domains. Such an unusual bivalent structure allows attribution of the protein to a novel subfamily of C-type lectins. scarf expression in intact planarian is rather abundant and follows a characteristic pattern not linked to any known morphological structure. We performed a series of experiments using scarf as a molecular marker. Its expression was monitored during different types of regeneration by whole-mount in situ hybridization and reverse-transcription polymerase chain reaction. The obtained data suggest that scarf expression is positively regulated by anterior tissues closely adjacent to the scarf-expressing region, so that their surgical removal results in rapid scarf switch-off. In turn, tissues expressing scarf seem to inhibit its activation anteriorly. This indicates that at least some of the body patterning events in planarians are based on a system of reciprocal inductive interactions rather than on a global morphogen gradient.

1-Deazaadenosine: synthesis and activity of base-modified hammerhead ribozymes

The incorporation of 1-deazaadenosine (c1A, 1b) into a hammerhead ribozyme and the resulting catalytic activity is described. For this purpose the phosphoramidite 2a and the 3'-phosphonate 2b as well as Fractosil-linked 1-deazaadenosine (3b) were prepared. The methoxyacetyl group was used for the 6-amino group protection and the triisopropylsilyl residue was introduced as the 2'-OH protecting group. Replacement of residues A14and A15.1 of the hammerhead ribozyme by 1-deazaadenosine resulted in a significantly reduced catalytic activity. Substitution of the A6, A9 and A13 residues has only a minor influence. The findings observed on ribozymes modified with 1-deazaadenosine were compared with those containing other adenosine analogues.

Endoscopic ultrasound miniprobe-guided steroid injection for treatment of refractory esophageal strictures

Local injection of corticosteroids into refractory esophageal strictures to decrease the restenosis rate has been reported. Here we report our efforts in three patients to render the delivery of steroids more precise, by injecting them in the thickest segment of the stricture with the guidance of a high frequency ultrasound miniprobe passed through a regular upper endoscope. Steroid injection under ultrasound miniprobe guidance may be indicated for patients who do not respond to a "blind" steroid injection without miniprobe guidance.

Cellular uptake properties of a 2'-amino/2'-O-methyl-modified chimeric hammerhead ribozyme targeted to the epidermal growth factor receptor mRNA

Catalytic RNA or ribozymes have important potential applications as molecular biological tools in the study of gene expression and as therapeutic inhibitors of disease-causing genes. Very little is known, however, about the cellular uptake mechanisms of exogenously delivered synthetic ribozymes. In this study, we have characterized the uptake properties of a synthetic, 2'-O-methyl-modified ribozyme containing U4/U7 amino groups within the catalytic core of the hammerhead motif. The cellular uptake of the internally [32P]-radiolabeled hammerhead ribozyme in U87-MG glioma cells was temperature, energy, and pH dependent and involved an active process that could be competed with cold ribozyme of the same chemistry and sequence, an all 2'-O-methyl-modified ribozyme of the same sequence, antisense PS-ODNs, and a variety of other polyanions (salmon sperm DNA, spermidine, dextran sulfate, and heparin). Subcellular distribution studies of fluorescently labeled ribozymes confirmed an extranuclear, punctate localization similar to that observed for an endosomal marker, dextran. Our study highlights that hammerhead ribozymes, despite exhibiting a defined secondary structure, enter cells by an endocytic mechanism that appears to be similar to that reported for a variety of antisense ODNs. These observations should facilitate the development of more efficient delivery systems.

Ordered differential display: a simple method for systematic comparison of gene expression profiles

A method for display of 3'-end restriction fragments of cDNAs is proposed, extending the idea reported recently. First, representative pools of such fragments are selectively amplified using PCR suppression effect. Then, simplified subsets of these fragments suitable for comparison by PAGE are amplified by adapter-specific primers extended by two randomly picked bases at their 3'ends. By testing all possible combinations of extended primers the whole mRNA pool may be systematically investigated. The method was applied to search for molecular regional markers of freshwater planarian Dugesia tigrina .

Effect of structural modifications on the activity of the leadzyme

The structure/function properties of functional groups in the leadzyme have been studied by assaying the activity of analog ribozymes generated by the systematic substitution of modified nucleotides in the internal loop region of the ribozyme. Guanosine analogs introduced at positions 4 and 7 occupied by guanosine in the wild-type molecule severely diminished cleavage. The substitution of deoxycytidine for cytidine at the cleavage site completely eliminated the activity of the leadzyme, as expected if the adjacent 2'-OH were the nucleophile in the cleavage reaction. On the other hand, substitution of an abasic nucleotide for adenosine at position 8 did not affect the activity of the ribozyme. An analysis of the activity of these analogs gives rise to the proposal of a triple-base pair motif implicating C1, G4, and G7.

Quantitating tertiary binding energies of 2' OH groups on the P1 duplex of the Tetrahymena ribozyme: intrinsic binding energy in an RNA enzyme

Binding of the Tetrahymena ribozyme's oligonucleotide substrate (S) involves P1 duplex formation with the ribozyme's internal guide sequence (IGS) to give an open complex, followed by docking of the P1 duplex into the catalytic core via tertiary interactions to give a closed complex. The overall binding energies provided by 2' OH groups on S and IGS have been measured previously. To obtain the energetic contribution of each of these 2' OH groups in the docking step, we have separately measured their contribution to the stability of a model P1 duplex using "substrate inhibition". This new approach allows measurement of duplex stabilities under conditions identical to those used for ribozyme binding measurements. The tertiary binding energies from the individual 2' OH groups include a small destabilizing contribution of 0.7 kcal/mol and stabilizing contributions of up to -2.9 kcal/mol. The energetic contributions of specific 2' OH groups are discussed in the context of considerable previous work that has characterized the tertiary interactions of the P1 duplex. A "threshold" model for the open and closed complexes is presented that provides a framework to interpret the energetic effects of functional group substitutions on the P1 duplex. The sum of the tertiary stabilization provided by the conserved G x U wobble at the cleavage site and the individual 2' OH groups on the P1 duplex is significantly greater than the observed tertiary stabilization of S (11.0 vs 2.2 kcal/mol). It is suggested that there is an energetic cost for docking the P1 duplex into the active site that is paid for by the "intrinsic binding energy" of groups on the P1 duplex. Substrates that lack sufficient tertiary binding energy to overcome this energetic barrier exhibit reduced reactivities. Thus, the ribozyme appears to use the intrinsic binding energy of groups on the P1 duplex for catalysis. This intrinsic binding energy may be used to position reactants within the active site and to induce electrostatic destabilization of the substrate, relative to its interactions in solution.

Construction of cDNA libraries from small amounts of total RNA using the suppression PCR effect

Here we describe a method for preparing high-quality cDNA libraries from total RNA. By this method, double-stranded (ds) cDNA ligated with a specially designed ds adaptor is amplified by PCR using a modified T-primer and another primer corresponding to the outer part of the adaptor. The suppression PCR effect strongly inhibits the amplification of poly(A) RNA, thereby reducing background. This method leads to amplification of high-quality cDNA, facilitating the construction of representative cDNA libraries from as little as 10-100 ng of total RNA.

Optimizing the cell efficacy of synthetic ribozymes. Site selection and chemical modifications of ribozymes targeting the proto-oncogene c-myb

Expression of the proto-oncogene c-myb is necessary for proliferation of vascular smooth muscle cells. We have developed synthetic hammerhead ribozymes that recognize and cleave c-myb RNA, thereby inhibiting cell proliferation. Herein, we describe a method for the selection of hammerhead ribozyme cleavage sites and optimization of chemical modifications that maximize cell efficacy. In vitro assays were used to determine the relative accessibility of the ribozyme target sites for binding and cleavage. Several ribozymes thus identified showed efficacy in inhibiting smooth muscle cell proliferation relative to catalytically inactive controls. A combination of modifications including several phosphorothioate linkages at the 5'-end of the ribozyme and an extensively modified catalytic core resulted in substantially increased cell efficacy. A variety of different 2'-modifications at positions U4 and U7 that confer nuclease resistance gave comparable levels of cell efficacy. The lengths of the ribozyme binding arms were varied; optimal cell efficacy was observed with relatively short sequences (13-15 total nucleotides). These synthetic ribozymes have potential as therapeutics for hyperproliferative disorders such as restenosis and cancer. The chemical motifs that give optimal ribozyme activity in smooth muscle cell assays may be applicable to other cell types and other molecular targets.

Chemically modified hammerhead ribozymes with improved catalytic rates

A site-specific chemical modification strategy has been employed to elucidate structure-function relationships at the only phylogenetically nonconserved position within the core of the hammerhead ribozyme (N7). Four different base substitutions at position 7 resulted in increased catalytic rates. A pyridin-4-one base substitution increased the rate of the chemical step up to 12-fold. These results are the first examples of chemical modifications within a catalytic RNA that enhance the rate of the chemical step. Four base substitutions resulted in decreased catalytic rates. The results do not correlate with proposed hydrogen bond interactions (Pley et al., 1994; Scott et al., 1995). This study demonstrates the utility of using unnatural nucleotide analogs-rather than mutagenesis with the four standard nucleotides alone-to elucidate structure-function relationships of small RNAs.

Rescue of abasic hammerhead ribozymes by exogenous addition of specific bases

We have synthesized 13 hammerhead ribozyme variants, each containing an abasic residue at a specific position of the catalytic core. The activity of each of the variants is significantly reduced. In four cases, however, activity can be rescued by exogenous addition of the missing base. For one variant, the rescue is 300-fold; for another, the rescue is to the wild-type level. This latter abasic variant (G10.1X) has been characterized in detail. Activation is specific for guanine, the base initially removed. In addition, the specificity for guanine versus adenine is substantially altered by replacing C with U in the opposite strand of the ribozyme. These results show that a binding site for a small, noncharged ligand can be created in a preexisting ribozyme structure. This has implications for structure-function analysis of RNA, and leads to speculations about evolution in an "RNA world" and about the potential therapeutic use of ribozymes.

Hammerhead ribozyme engineering

Of all the catalytic RNAs the hammerhead ribozyme is the most chemically modified and structurally studied. Such studies have resulted in improvements in the nuclease resistance of ribozymes, reductions in their size, and improvements in their catalytic efficiency. These improvements have facilitated the use of ribozymes for therapeutic applications, and have allowed us to study how the three-dimensional structure of the enzyme and its array of functional groups interact to create a catalytic site where a phosphodiester bond is cleaved.

RNA hydration: a detailed look

The crystal structure of the RNA duplex [r(CCCCGGGG)]2 has been refined to 1.46 A resolution with room temperature synchrotron diffraction data. This represents the highest resolution reported to date for an all-RNA oligonucleotide and is well beyond the best resolution ever achieved with an A-form DNA duplex. The analysis of the ordered hydration around the octamer duplex reveals conserved regular arrangements of water molecules in both grooves. In the major groove, all located first shell water molecules can be fitted into a pattern that is repeated through all eight base pairs, involves half the phosphate oxygens, and joins the two strands. In the minor groove, roughly across its narrowest dimension, tandem water molecules link the 2'-hydroxyl groups of adjacent nucleotides in base-pair steps in a similarly regular fashion. The structure provides evidence for an important role of the 2'-hydroxyl groups in the thermodynamic stabilization of RNA, beyond their known functions of locking the sugar pucker and mediating 3' --> 5' intrastrand O2'...O4' hydrogen bonds. The ribose 2'-hydroxyls lay the foundation for the enthalpic stability of the RNA relative to the DNA duplex, both as a scaffold for the water network in the minor groove and through their extensive individual hydration.

Inhibition of vascular smooth muscle cell proliferation by ribozymes that cleave c-myb mRNA

Proliferation of injured smooth muscle cells contributes to the reocclusion or restenosis of coronary arteries that often occurs following angioplasty procedures. We have identified and optimized nuclease-resistant ribozymes that efficiently cleave c-myb RNA. Three ribozymes targeting different sites in the c-myb mRNA were synthesized chemically and delivered to rat aortic smooth muscle cells with cationic lipids; all three inhibited serum-stimulated cell proliferation significantly. RNA molecules with two base substitutions in the catalytic core that render the ribozyme catalytically inactive had little effect on smooth muscle cell proliferation. Ribozymes with scrambled binding arm sequences also failed to affect cell cycle progression of vascular smooth muscle cells. Furthermore, inhibition of rat smooth muscle cell proliferation correlated with a reduction in intact c-myb mRNA. Efficacy of the chemically-modified ribozyme was compared directly to phosphorothioate antisense oligodeoxynucleotides targeting the same site in the c-myb RNA; the ribozyme had superior efficacy and showed greater specificity than the antisense molecules. Exogenously delivered ribozymes also inhibited porcine and human smooth muscle cell proliferation effectively. Ribozymes targeting c-myb or other regulators of smooth muscle cell proliferation may represent novel therapeutics for the treatment of restenosis after coronary angioplasty.

Crystal structures of an A-form duplex with single-adenosine bulges and a conformational basis for site-specific RNA self-cleavage

BACKGROUND

Bulged nucleotides are common secondary structural motifs in RNA molecules and are often involved in RNA-RNA and RNA-protein interactions. RNA is selectively cleaved at bulge sites (when compared to other sites within stems) in the presence of divalent metal cations. The effects of bulge nucleotides on duplex stability and topology have been extensively investigated, but no detailed X-ray structures of bulge-containing RNA fragments have been available.

RESULTS

We have crystallized a self-complementary RNA-DNA chimeric 11-nucleotide sequence containing single-adenosine bulges under two different conditions, giving two distinct crystal forms. In both lattices the adenosines are looped out, leaving the stacking interactions in the duplex virtually unaffected. The bulges cause the duplex to kink in both cases. In one of the structures, the conformation of the bulged nucleotide places its modeled 2'-oxygen in line with the adjacent phosphate on the 3' side, where it is poised for nucleophilic attack.

CONCLUSIONS

Single adenosine bulges cause a marked opening of the normally narrow RNA major groove in both crystal structures, rendering the bases more accessible to interacting molecules compared with an intact stem. The geometries around the looped-out adenosines are different in the two crystal forms, indicating that bulges can confer considerable local plasticity on the usually rigid RNA double helix. The results provide a conformational basis for the preferential, metal-assisted self-cleavage of RNA at bulged sites.

Base and sugar requirements for RNA cleavage of essential nucleoside residues in internal loop B of the hairpin ribozyme: implications for secondary structure

The hairpin ribozyme is a small self-cleaving RNA that can be engineered for RNA cleavage in trans and has potential as a therapeutic agent. We have used a chemical synthesis approach to study the requirements of hairpin RNA cleavage for sugar and base moieties in residues of internal loop B, an essential region in one of the two ribozyme domains. Individual nucleosides were substituted by either a 2'-deoxy-nucleoside, an abasic residue, or a C3-spacer (propyl linker) and the abilities of the modified ribozymes to cleave an RNA substrate were studied in comparison with the wild-type ribozyme. From these results, together with previous studies, we propose a new model for the potential secondary structure of internal loop B of the hairpin ribozyme.