ISSN 1556-6757







Volume 1, Issue 1, 2007


The Handedness of Z-DNA

C. S. Delmonte


Many medical research teams continue to study the wide range of human conditions influenced by the structure and function of Z-DNA, for example, the differentiation of fibre cells in the adult lens1, a pox virus which complexes with Z-DNA2, the inhibition of transcriptional activation3, a conserved family of Z-DNA binding proteins4, the rle of Z-DNA in the activity of the hippocampus in the Alzheimer Brain5, an RNA deaminase has a binding site for Z-DNA6, 7, and a human gene codes for the protein dlm-1 which has a Z-DNA binding domain8.  Z-DNA-forming sites have been reported within the human genome9.  New Z-DNA duplexes are being currently reported10. While the Z form has been assigned a left-handed helical sense11, a central difficulty about the crystallographic identification of Z‑form oligodeoxyribonucleotides and Z-DNA as being uniformly left‑handed is the creation of a crucial paradox. Highly regarded crystallographers, for example Sasisekharan & Brahmachari12 , and Leslie et al.13, record the complete conversion of the B to the Z form inside semi-crystalline fibres under the very mild conditions of humidity change alone.  Likewise, Mahendrasingham et al.14 studied the transition of the B to the D form under similarly mild conditions using time-lapse data recording. These crystallographers argue strongly from the direct experimental evidence of a clear change in well-defined diffraction patterns that the B, D and Z forms must have the same helical handedness to effect such changes from one polymorph to another inside semi-crystalline fibres with high conversions, since only small structural changes are conceivable in these circumstances. Much earlier, Franklin & Gosling15 had reported the complete interconversion of the A to and from the B form, and likewise Marvin et al.16 had reported the conversion of form B to C inside fibres with humidity change alone.  Therefore, if they have a uniform helical handedness along their whole molecular lengths, A, B, C, D and Z‑DNA would all have the same uniform helical handedness because these polymorphs are all variously interconvertible inside solid fibres.  Now, Dickerson's group17,18 claims, from a study of a true oligodeoxyribonucleotide crystal, that B‑DNA is right‑handed.  Rich's group11 have studied a crystalline fragment, designated Z‑DNA, which they claim is left‑handed.  If the DNA polymorphs are claimed to each have a uniform helical handedness along their whole molecular lengths, and if the Z form fibre in vivo is claimed to have the same handedness as the crystalline Z-DNA fragment (a proposition which has never been directly established), it would seem that at least one team of crystallographers must be wrong.  Either DNA fibres of the forms A, B, C, D & Z have the same helical handedness as suggested by their various, ready interconversions inside fibres, or the B and Z polymorphs have opposite handedness as deduced from the structural solutions derived from X-ray diffraction from true crystals of their respective oligodeoxyribonucleotides which are then extended to the structure of the high polymer. Full Article

The Effects of culture Conditions on biosurfactant activity of Pseudomonas aeruginosa 181 using response surface methodology
AL-Araji Laith, R.N.Z.A. Rahman,, M. Basri, A.B. Salleh

Response surface methodology (RSM) was used to study interactive effects of the parameters (pH, stirring rate, casamino acid concentration and incubation period) on the biosurfactants activity. It was implied that the effect of any one parameter could not, on its own, explain the outcome of the reaction without considering the input of the other parameters. For this reason, experiments in this following were performed to gain some insight into their combined interactive effects. Within the experimental range studied, optimal conditions for the biosurfactant

activity were predicted using the optimization function of the Design Expert software. The actual biosurfactant activities by Pseudomonas aeruginosa 181 were 28.43 dyne / cm for surface tension and 85% Emulsification Index (E24).  Full Article

Manora Island Project: a model primary care project in Pakistan

Amin A. Muhammad Gadit


This community based project which was established in an island of Karachi-Pakistan is a unique example of health care to a deprived community on a voluntary basis. It involves a group of  dedicated medical doctors and social workers who surveyed a local community in the island with a population of n=5000, administered a questionnaire to assess their current health status along with the demographic information, provided on-site health services and reassessed their health status twice with a yearly interval and found that there was a significant decline in the morbidity of the local residents. It was concluded that if such projects are replicated nation-wide, the country’s health services will have tremendous improvement. Full Article


Using TreeNet for Identifying Management Thresholds of Mantled Howling Monkeys' Habitat Preferences on Ometepe Island, Nicaragua, on a Tree and Home Range Scale
Jesse N. Popp, Denise Neubauer, Lisa M. Paciulli, Falk Huettmann


Numerous studies have been conducted on mantled howling monkeys (Alouatta palliata). However, very few of the studies have dealt with explicitly quantifying spatial and habitat preferences. Thus, the exact used and unused habitats of howling monkeys remain neither fully investigated nor quantified. Thus, crucial thresholds for science-based sustainable management programs continue to be unknown. Therefore, in this paper, the presence and absence of two howling monkey groups in different forest types on the island of Ometepe, Nicaragua were examined. Data were collected onseveral variables including the focal animal's tree location and measurements of that tree. Thesedata were linked with landscape features such as proximity to man-made and natural edges. In orderto assess the generalizability and robustness of the findings, the data were analyzed on two scales: (i) the trees the monkeys used were compared to random (pseudo-absence) trees and (ii) home rangeswere estimated based on the animals locations and compared to unused (‘absence’) areas.Resource Selection Functions (RSFs), which are widely utilized for comparing localities used by wildlife to unused locations, were employed. The powerful TreeNet (Salford Systems Ltd.) algorithm wasapplied to obtain the resource functions and thresholds. The results indicate that tree Diameter at Breast Height (DBH) and its derivatives were the most relevant variable explaining where the howling monkeys occurred in the island forest habitats.This study uses a powerful TreeNet algorithm to determine resource selection functions and thresholds of the mantled howling monkey on two habitat scales in order to contribute to their conservation. Full Article


Absence of Mirror Self-Referential Behavior in Two Asian Elephants

Moti Nissani, Donna Hoefler-Nissani



To date, one investigation failed to find mirror self-referential behavior in Asian elephants while two others reported positive results, a contradiction which could, among other things, be ascribed to the poor visual acuity of elephants.  To throw additional light on these contradictory reports, the present study of mirror self-referential behavior in two captive Asian elephants bypasses the traditional mark test, relying instead on the elephants’ response to a far more visually conspicuous object, and on prior habituation to the presence of this object in their enclosure.  In this study, neither elephant engaged in self-referential behavior in front of a mirror.  Our simple experimental paradigm could serve as a more convenient alternative to the widely used traditional mark test, could meet some methodological objections which have been raised against the traditional mark test, and could profitably augment the traditional test in difficult or controversial cases. Full Article 


Antimicrobial activity and micropropagation of Peperomia tetraphylla
Ingelia White, Lora Oshima, Nelly D. Leswara


Peperomia tetraphylla (G. Forst.) Hook. & Arn. (Piperaceae) or ala ala wai nui kane is a fleshy native Hawaiian herb reputed to cure feminine ailments in traditional Hawaiian medicine. A preliminary study on its antimicrobial activity, palatability and micropropagation techniques was conducted at the University of Hawaii – Windward Community College from May to December 2003. The entire plant, including stems, leaves and spikes was ground in 99.9% methanol with mortar and pestle, and centrifuged for 10 minutes at maximum speed to obtain its supernatant. Various concentrations in duplicates of crude methanolic extract of P. tetraphylla were prepared for pour plate and agar diffusion tests against Candida albicans, Escherichia coli and Staphylococcus aureus. Extract concentrations of 125 mg/mL (1.25 mg /10 L) and 250 mg/mL (2.5 mg /10 L) influenced the microbial growth. A highly significant colony reduction (72%) was shown in pour plates containing 125 mg/mL of extract for C. albicans, 57% for E. coli and 30% for S. aureus. The disks containing 2.5 mg /10 L extract in agar diffusion plates yielded a 33 mm inhibition zone for C. albicans, 9 mm for E. coli and 10 mm for S. aureus. This study suggests the possible use of P. tetraphylla for treatment of vaginitis, cystitis and skin infections caused by those microorganisms. The plant can be safely ingested as a food medicine. In vitro culture of leaves, stems and seeds produced plantlets within 28 to 30 days.  Full Article

Possible deletion of a 245 bps polymorphic marker in breast cancer cells (MCF-7)
AKM A. Hussain, Brian H. Crawford, Nathan M. Jideama

A polymorphic biomarker gene with a nucleotide sequence of 245 bps was isolated from normal human mammary epithelial cells (MCF-10A) by using the DNA amplification fingerprinting (DAF) technique. This marker was absent in human breast cancer cells (MCF-7).  A Genbank database search with this gene sequence revealed it had 100% homology with the nucleotide sequence of human chromosome 4 (BAC RP11-451F20) (bps 1613220-161564) (Genbank account: AC093844.3).  The nucleotide sequence of the biomarker was translated using Genbank CDS (account gi |11387274 |sp |P55782| PPNK_BUCAI), and revealed that this gene codes for a probable inorganic polyphosphate/ATP-NAD kinase. In order to evaluate the effects that the 245 bps biomarker would have on the morphology of MCF-7 cells, the MCF-7 cells were transfected with the 245 bps biomarker.  There were observable changes in the morphology of the transfected cells.  These changes included an increase in cell elongation and a decrease in cell aggregation.  Full Article


Effect of Ovariectomy, Labisia pumila var alata Treatment and Estrogen Replacement Therapy on the Morphology of Adipose Tissue in Ovariectomized Sprague DawleyRats
Ayida Al-Wahabi, Wan Nazaimoon WM, Farihah HS, Azian AL



Introduction:Labisia pumila var alata or as known among Malay women as Kacip Fatimah (KF), has long being recognized for its medicinal value. Recently, researches have demonstrated its estrogenic activity.  Ovariectomy (surgical menopause) is known to cause weight gain and increase adiposity due to estrogen deficiency. Objective: This study was aimed to investigate the effect of Labisia pumila consumption and Estrogen Replacement Therapy (ERT) on the morphology of adipose tissue following ovariectomy. Methodology: 6 months old female (Sprague Dawley) rats were ovariectomized (bilaterally) under anesthesia using the ventral approach and randomly divided into OVXC (ovariectomized control), KF and ERT. KF and ERT received daily oral treatment of water extract of Labisia pumila (17.5 mg/kg/day), and ERT (64.5 g/kg/day) respectively for a period of three months. A group of 9 normal rats was left intact and used as normal control (NOR). Rats were sacrificed by cervical dislocation and tissue samples from abdominal fat were collected and fixed immediately either in 4% paraformaldehyde for electron microscopy or in 10% formalin for light microscopy. Results: Light microscopy revealed hypertrophic growth (increase in the size of adipocytes) as well as increasing vasculature of adipose tissue in the OVX rats compared to the normal rats. Transmission electron microscopy (TEM) revealed thickening of the adipocyte membrane of the OVXC rats. KF and ERT-treatment were demonstrated to cause adipocytes membranes' breakage as shown by the fragmentation of the collagen bands. Conclusion: Results implied a possible role for Labisia pumila var alata in modulating postmenopausal adiposity through the initiation of the lipolysis process in adipose tissue. Full Article|


Neuropsychological Generation of Source Amnesia: An Episodic Memory Disorder of the
Frontal Brain   
Shaheen Emmanuel Lakhan



Source amnesia is an explicit memory (declarative) disorder, particularly episodic, where source or contextual information concerning facts is severely distorted and/or unable to be recalled.  This paper reviews the literature on source amnesia, including memory distrust syndrome, and its accepted correlation with the medial diencephalic system and the temporal lobes, and the suggested linkage between the frontal lobes, including special interest with the prefrontal cortex.  Posthypnotic induction was the first presentation of source amnesia identified in the literature.  The Wisconsin Cart Sorting Test (WCST), Positron Emission Topography (PET), Phonemic Verbal Fluency Test, Stroop Color Word Interference Test, and explicit and implicit memory tests are defined and linked to empirical research on amnesiacs. Full Article


Mental Health Model: Comparison Between a Developed and a Developing Country

Amin A. Muhammad Gadit



There has been an alarming increase in the incidence of mental illness the world over. Individual countries are struggling to address this issue in terms of professional resources, available facilities and economic burden. Both the developing and the developed countries are facing the dilemma under the current scenario of increasing mental health morbidity.In order to assess the situation a comparison is made between a developed and a developing country in terms of the population, number of psychiatric beds, morbidity patterns, number of psychiatrists, GDP, average annual income, health care expenditures, waiting times for consultation and nature of services. Data  related to population, number of psychiatric beds, morbidity patterns, number of psychiatrists, GDP, average annual income, health care expenditures, waiting times for consultation and nature of services was gathered systematically from literature search using PubMed, Google, Medline and publications from the W.H.O., UNICEF, Canadian Medical Association, Pakistan Medical and Dental Council, Government of Newfoundland and Labrador and local monographs for both cities in the developing and developed countries. Two cities from different worlds in terms of population, St. John’s, Canada with a significantly low population and Karachi, Pakistan where majority of the people are rural-based giving a picture of low population vs. high population. Number of psychiatric beds is much smaller compared to the population of Karachi, prevalence of mental illnesses is of higher magnitude, low average annual income, there is no established model for mental health care and general health care expenditure is from out of pocket. St. John’s has a full-fledged model with some community and specialized services, which are government sponsored, but the striking feature of this is the long waiting time hindering the health care benefits to the local population. Karachi with all its problems has practically zero to one week’s waiting time despite low number of psychiatrists. There are problems in service delivery for mental health both in the developing and the developed world and therefore, there is a room for improvement by mutual learning and modification of available resources. Full Article  


Phenotypic, molecular and antibiotic resistance profiling of nosocomial Pseudomonas aeruginosa strains isolated from two Irish Hospitals

Ferguson D, Cahill O.J, Quilty B



P.aeruginosa is a significant pathogen associated with nosocomial and community-acquired chronic infection. Presumptive P.aeruginosa isolates were obtained from two Irish hospitals. The aim of this study was to phenotypically and genotypically characterise the isolates, and assess their innate virulence in response to antibiotic treatment. The clinical strains were characterised biochemically by API NE and Biolog GN systems, and subsequently confirmed as P.aeruginosa by 16s rRNA sequence analysis. Their genetic relationship was established by Phylogenetic analysis of the 16s rRNA, which confirmed individuality amongst the strains but more significantly, genetic similarity to known clinical isolates of P.aeruginosa and Burkholderia cepacia, the cystic fibrosis pathogen. Antibiotic resistance profiles were completed on all the isolates to obtain MIC values for numerous antibiotics.  Extrapolation of the MIC profiles identified one multi-resistant strain, characterised by high-level resistance to gentamicin, the topically administered treatment for invasive P.aeruginosa infection. This strain was chosen for further study. Biochemical tests identified all the clinical isolates as P.aeruginosa, which with the exception of subtle metabolic differences were indistinguishable from each other. Phenotypic differences were confirmed by 16s rRNA sequencing which identified genetic relationship with other clinical pathogens. MIC profiling identified one multi-resistant clinical isolate, P.aeruginosa PA13, resistant to all classes of antibiotic, specifically aminoglycosides. This study demonstrated that the occurrence of chronic P.aeruginosa infection is not restricted to one genotype, as confirmed by phylogenetic and molecular epidemiology. It also illustrates the potential for cross-resistance between clinical isolates in nosocomial environments, confirming the need for more rigorous infection control protocols. Full Article


Quantification of Plasmatic Thrombin Generation byTrypsin
Thomas W. Stief


Active trypsin in blood could severely modulate hemostasis. In the present study citrated blood or plasma of healthy donors was pre-incubated with trypsin. The plasma was recalcified and specific thrombin generation was measured. 1-10 ng/ml trypsin enhances intrinsic thrombin generation > 2fold. Trypsin might activate intrinsic coagulation factors or prothrombin (100 ng/ml trypsin generates within 60 min 15 mIU/ml thrombin from 100 4g/ml prothrombin), causing a pathologic disseminated intravascular coagulation. The recalcified coagulation

activity assay (RECA) allows to investigate the action of trypsin on intrinsic thrombin generation. The RECA is a very sensitive method to detect prothrombotic changes of blood. Full Article