Genomic comparisons of Rhizobium species using in silico AFLP-PCR, endonuclease restriction, and AMPylating enzymes

Background: The whole-genome sequences of nine Rhizobium species were evaluated using different in silico molecular techniques such as AFLP-PCR, restriction digest, and AMPylating enzymes. The entire genome sequences were aligned with progressiveMauve and visualized by reconstructing phylogenetic tree using NTSYS pc 2.11X. The "insilico.ehu.es" was used to carry out in silico AFLP-PCR and in silico restriction digest of the selected genomes. Post-translational modification (PTM) and AMPylating enzyme diversity between the proteome of Rhizobium species were determined by novPTMenzy. Results: Slight variations were observed in the phylogeny based on AFLP-PCR and PFGE and the tree based on whole genome. Results clearly demonstrated the presence of PTMs, i.e., AMPylation with the GS-ATasE (GlnE), Hydroxylation, Sulfation with their domain, and Deamidation with their specific domains (AMPylating enzymes) GS-ATasE (GlnE), Fic, and Doc (Phosphorylation); Asparagine_hydroxylase and Collagen_prolyl_lysyl_hydroxylase; Sulfotransferase; and CNF (Cytotoxic Necrotizing Factors), respectively. The results pertaining to PTMs are discussed with regard to functional diversities reported in these species. Conclusions: The phylogenetic tree based on AFLP-PCR was slightly different from restriction endonuclease- and PFGE-based trees. Different PTMs were observed in the Rhizobium species, and the most prevailing type of PTM was AMPylation with the domain GS-ATasE (GlnE). Another type of PTM was also observed, i.e., Hydroxylation and Sulfation, with the domains Asparagine_hydroxylase and Collagen_prolyl_lysyl_hydroxylase and Sulfotransferase, respectively. The deamidation type of PTM was present only in Rhizobium sp. NGR234. How to cite: Qureshi MA, Pervez MT, Babar ME, et al. Genomic comparisons of Rhizobium species using in silico AFLP-PCR, endonuclease restrictions and ampylating enzymes.

Diagnosis of hydatid cyst parotid gland by fine needle aspiration cytology [FNAC]

Fine Needle aspiration of parotid gland swellings is commonly done as a first line investigation. Fine needle aspiration of one such cystic lesion in a 45 years old female was performed. The cytopathological appearance of the aspirate turned out to be typical of Hydatid Cyst. The case is reported with review of literature

Transabdominal and transvaginal repair of vesicovaginal fistula

Objective: To evaluate the results of surgical repair of VVF through transabdominal and transvaginal routes

Study Design: Prospective study

Place and Duration of Study: This study was carried out in Teaching Hospital, Ghazi Khan Medical College, DG Khan from June 2009 to May 2014

Patients and Methods: Total 26 patients of VVF with age range of 22-60years were included in the study.Fistulas had two types, simple and complex, according to site, size and aetiology . Simple VVFs were repaired through the vaginal route and complex ones through abdominal route. Patients were assessed at an interval of twoto three weeks to start with, twice after three-months and thereafter depending oncomplaints

Results: Sixteen [61%] patients had simple fistulas, while 10 [38%] patients had complex fistulas and one of the patients had complex fistula associated with rectal communication who was excluded . The most common cause was trauma during obstructed labour in 12[47%] patients, whereas the other common cause was hysterectomy. Sixteen [61%] patients were approached through transvaginal route, out of them 9 had supratrigonal and 7 trigonal fistulas. Ten [38%] patients with complex fistulas were approached by abdominal route. Duration of the surgery, blood loss, pain after surgery and stay in hospital was found to be shorter in transvaginal surgery. Two patients have failed repair with significant complications, a success rate of 92% was achieved. At a follow-up of one year 24 women had uneventful, active sexual life while 2 of them had some degree of pain during sexual intercourse

Conclusion: It's concluded that both the routes of VVF repair has a similar successrate

Burns in pediatric population admitted in two tertiary care hospitals

Burns in Pediatric population accounts for almost 77% of total burn cases in developing countries including Pakistan. To calculate the frequency and causes of burns in pediatric population. Prospective cross sectional survey done in the emergency departments of pediatric units of Mayo Hospital Lahore and Pakistan Institute of Medical Sciences, Islamabad over 6 months from July to December 2012. Subjects and All new cases of burns presenting to the emergency departments of these hospital were included in the study while those who were previously admitted with burns and were undergoing some reconstructive surgery or treated for complications were excluded. A questionnaire was completed by the duty doctor while interviewing the parents or care givers. The frequency of all variables was measured in percentage. A total of 600 children were enrolled in the study. Their ages ranged from 0-12 years with 270[45%] constituting toddlers between the ages of 1-2 years. Gender showed female predominance in 372[62%] cases. Place of injury was home in 80% cases [480]. Mothers were illiterate in 60% cases [370]. Commonest causes of burns were scalds [43.6%], followed by flame burns [20.6%], electrical burns [15.3%], chemical burns [10.2%] and other causes [10.3%]. Single multipurpose room of poor socioeconomic homes and maternal ignorance about burn prevention were common contributing factors. Burns were more in toddlers and in female gender. Creating awareness in mothers can reduce the injury Manifold

Increasing tendency of rape with females in Pakistan

To study the increasing tendency of rape with females in Pakistan. Observational study. This study was conducted at the Emergency Departments of Gangaram Hospital Lahore, Mayo Hospital Lahore, Services Hospital Lahore., Shahina Jamil Hospital Abbottabad from 1[st] January 2012 to 31[st] May 2013. The cases of rape were selected from Services hospital Lahore, Mayo hospital Lahore, Shahina Jamil leaching hospital Abbottabad and Gangaram Hospital Lahore. The data of rape with female was collected on proforma and analyzed for results. The incidence of rape was maximum at the age range 21 30 years [39%] as compared to age range 60 and above [1 2%]. It was seen that incidence of rape was maximum in labor class of women as compared to house wives and business man wives 5-9% which was minimum. In this study the incidence of rape with women was 55% [55 cases] it] lower class, 30% in middle class [30 cases] but the victim of rape in high gentry was IS% [15 cases]. The Rape victims were 64 o [64 cases] in unmarried women and 36% [36 cases] in married women. The incidence of rape was 41% in urban area [4! cases] and 59% [59 cases] in rural area. In this study 37% [37 cases] were semen positive and 63% [63 cases] were of semen negative. The injuries of private parts and rest of the body were present in 83% victims of rape [83 cases] and 17% [17 cases] were those victims in which the injuries were absent. At the last 91% [9lcases] were brought by the police for medico legal examination / certification and 9% [9 cases] were come on their self request. The tendency of rape with females is a global problem/sex assault due to, 1] internet use for sex stimulation, 2] Indian sexy movies. 3] the female mixing with males, 4] Co education, 5] Joint possession of offices, 6] Sexy Movies on cable, 7] Non religious gatherings and 8] Unawareness of Islamic teaching

Causes of childhood unintentional injuries in urban cities of Pakistan

Unintentional childhood injuries are the leading cause of death and disability worldwide and its incidence is higher in low to middle income countries. To determine the frequency of childhood unintentional injuries in pediatric units of two tertiary care hospitals. Prospective cross sectional study in pediatric surgical unit of Mayo Hospital, Lahore [01 July, 2012 to 30 September, 2012] and Children's Hospital, PIMS, Islamabad [01 October, 2012 to 31 December, 2012] July to December 2012. All children presenting with unintentional injuries to the pediatric surgical emergency of above two hospitals were included in study. Unintentional Injuries were [burns, RTAs, falls, piercing sharps etc.] are accidental injuries that occur without any planned intention of someone to harm children. Children who were previously treated for unintentional injuries, unexplained injuries, medico-legal cases were excluded from the study. An informed consent was taken [from the parents or care-givers] and the questionnaire was filled by the duty doctor through interview. The demographic data was taken. Age, Gender and maternal educational status were measured Frequency of all variables was measured and simple frequency was measured. The data was analyzed in SPSS 11 version. A total of 600 patients [300 from each selected hospital] were included in the study. The predominant cause of unintentional injury was burn [37.2%] followed by fall [21.5%] and pedestrian hit [16.1%]. Maximum unintentional injuries were noted in 6-10 years [45%] and minimum in 0-1 years [1%]. Male children were affected more [62%] as compared to females. Maternal education was low or nil in 40% cases with majority [46.6%] belonging to poor socioeconomic group. Home was the most frequent place of injury [58.7%]. This study showed that 37% of the unintentional injuries were due to burning and the most common place of injury was the home which may be reduced by creating awareness in public and especially by educating the mothers

Increasing tendency of "target killing" in Pakistan

To determine the increasing tendency of target killing in Pakistan. Retrospective study. This study was conducted at the Emergency Departments of Services Hospital Lahore, Gangaram Hospital Lahore, Mayo Hospital Lahore and Shahina Jamil Hospital Abbottabad from 01-01-2012 to 31-05-2013. 100 cases of Target Killing were selected from Emergency Deptt of services Hospital Lahore, Emergency Deptt of Gangaram Hospital Lahore, Emergency Deptt of Mayo Hospital Lahore and Emergency Deptt of Shahina Jamil Hospital Abbottabad. The data was collected from above said hospitals on proforma and analyzed for results. In our study the incidence of target killing was maximum at the age of 21-30 years [33%] and minimum at the age of 71-80 years as show in Table No.1. The incidence of target killing was 20% in lower class, 34% in middle class, 56% in upper class as shown in Table No 2. Addict people had 83% incidence of target killing and 17% in non addict people as shown in Table No 3. The incidence of target killing was 83% in people having mental / physical sickness has compared to healthy people [17%] as shown in Table No 4. The incidence of target killing was 37% in literate people and 63% in illiterate people as shown in Table No 5. The incidence of target killing was high 67% in people living in non joint family system as compared to people living in joint families [33%] as shown in Table No 6. The incidence of target killing was 37% in literate people as compared to illiterate people [63%] as shown in Table No 7. The trend of target killing was 67% in rural area and 33% in urban area as shown in table No. 8. Target Killing is a global problem. This problem is due to 1]Mental /physical or both Sickness of the people, 2] Frustration of people due to economical/ political/ sectarian disputes, 3] Far Away from Islamic teachings, 4] Out spread of addiction in Pakistan

Stercolith Perforation

A 62-year-old diabetic bed ridden woman, presented to the emergency department with symptoms suggestive of peritonitis. She had been taking oral laxatives and enemas to relieve her chronic constipation for last 6 years. Hard impacted stools and pelvic tenderness were found on digital rectal examination. Her X-ray abdomen showed soft tissue shadows in the colon but there was no gas under the diaphragm on chest X-ray. Sonography found free fluid in pelvis. She was resuscitated, and her hyperglycemia was controlled by use of regular insulin as per sliding scale. Operative findings revealed free fluid in pelvis and very hard faecalomas lying free in peritoneal cavity. There was a 2 x 3 cm perforation at the anterior wall of the recto-sigmoid junction. Peritoneal toilet was carried out followed by Hartmann's procedure. Histopathology of perforation side showed no evidence of malignancy

Comparison of microleakage in resin modified glass ionomer cements and poly acids modified composites [compomers]

Microleakage of oral fluids and microbial components is a dynamic factor occurring at the tooth-restoration interface. Different restorative materials show different values of micro-leakage depending upon their composition, setting reaction and nature of physical and/or chemical bonds with the dental tissues. The aim of this study was to compare the microleakage of Resin modified Glass lonomer [Fuji II.LC] and Polyacid modified Composite Resins [Dyract]. It was a comparative cross sectional study which was carried out in the Department of Dentistry, Pakistan Institite of Medical Sciences [PIMS] Islamabad. Fifty healthy, unrestored extracted premolar teeth allocated randomly in to two groups. Class V cavities were prepared at the cemento-enamel junction in all fifty teeth, and restored with Fuji II.LC [GC America] and Dyract [Dentsply], 25 teeth in each group. All the teeth were placed in 2% basic fuchsin dye for 24 hrs at37C. Teeth were then embedded in cold cure acrylic resin, resectioned longitudinally in - ISOMETA, and the dye penetration at the enamel and cementum margin were scored at 10 X magnification stereo microscope and distinct leakage patterns were recorded. Data was analyzed using SPSS version 10.0. The resin-modified glass ionomers showed less microleakage than the polyacid modified composite resin especially at gingival margins

Role of Topical Glyceryl Trinitrate in the Management of Anal Fissure

1] To evaluate the effectiveness of topical 0.2% Glyceryl Trinitrate [GTN] ointment in symptomatic relief and healing of anal fissure. 2] To establish the role of GTN as a first line treatment for both acute and chronic anal fissure. 3] To elaborate the safety profile of GTN with respect to its side effects. Prospective, randomized case control study. Surgical unit II, Jinnah Hospital, Lahore. 1 year from 1-2-2005 to 31-2-2006. Fifty patients of all ages and either sex with a clinical diagnosis of fissure in ano [both acute and chronic] were included in the study. Patients were randomly divided into two groups. The treatment group [Group-A] was advised 0.2% GTN ointment whereas the control group [Group-B] was prescribed a local anesthetic ointment [Lignocaine Compound [R] Knoll]. Both groups applied the given drugs twice daily for a period of 8 weeks and follow-up at the end of first, second and eighth week was carried out. A long-term follow-up at the end of 6 months was undertaken to look for any recurrence of the disease. 18 patients out of 50 patients presented with acute anal fissure while 32 presented with chronic anal fissure. 77% of patients with acute fissure in Group A showed fissure healing while 44% of patients with acute fissure were benefited in Group B. When the failures of group B were subjected to GTN, 80% of the patients showed healing of their fissures. 81% of patients suffering from chronic anal fissure were cured in Group A while 25% of patients showed improvement in Group B. Nonbenefited patients in group B when subjected to GTN, 66% showed fissure healing. Recurrence was seen in 8 patients in group A [24%] and 3 patients in group [38%] at long term follow-up. Anal fissure is a common general surgical problem associated with severe anal pain. Regarding conservative treatment, the advent of GTN is a healing hope for patients with anal fissure. It has revolutionized the non-surgical treatment, as it is effective, safe and economical in terms of cure of both acute and chronic anal fissures

study of sperm morphology in a Pakistani population

The aim of this study was to determine the sperm morphology of proven fertile males and to compare the same with that of infertile males. This study was carried out at International Medical College Rawalpindi and its attached Railway hospital and Islamabad Clinic Serving Infertile Couples Islamabad, from June 2005 to July 2006. 50 healthy fertile males were selected and their semen morphology was determined according to Tygerberg's strict criteria, while another 50 infertile males were recruited as controls Proven fertile group showed significantly higher morphologically normal forms of sperms [3.04 +/- 1.63] than the infertile group. Sperm morphology assessed by strict criteria is of value in the in-vivo situation to identify a group with greater chance of having an infertility problem and strict criteria sperm morphology analysis should be used to minimize variations in intra and inter-individual and inter-laboratory sperm morphology assessment

Contemporary clinical features of cholesteatoma

Chronic Otitis media with Cholesteatoma is a destructive lesion of middle ear and mastoid region. In a series of 122 patients with established diagnosis of atticoantral disease, clinical characteristics of consecutive 74 patients with cholesteatoma otitis media were compared with 48 patients with chronic otitis media without cholesteatoma [Controls]. The patients answered a questionnaire, preoperative and perioperative clinical observations were recorded. There were no specific presenting symptoms or clinical signs that could distinguished the cholesteatoma patients. However, these patients had a significantly higher incidence [32%] of previous middle ear surgery than the control patients [18%]. Aural bleeding was reported in higher number in controlled cases [8.5%] as compare to cholesteatoma cases [1.3%]. Pars flaccida perforation was noted in 94% [80% isolated] in cholesteatoma patients. Extracranial complications e.g. mastoid abscess, postaural fistula, mastoiditis and otitis externa was note in 6.7% and 4% respectively in cholesteatoma and control group. The percentage of labyrinthitis and facial nerve affection was 11% and 4.1% in cholesteatoma cases respectively against 6% and 2% in control group. The cholsteatoma was not evident until the time of surgical exploration in as many as 28% of cases. Therefore surgical exploration appears to be the reliable and safest way to identify cholesteatoma

Anemia in surgical patients

To find out prevalence of surgery related anemia in the patients routinely admitted in a general surgical ward. Prospective Cohort Study. Surgical Unit II, Jinnah Hospital, Lahore. 100 studied patients included males and females of all age groups from 13 years to 70 years. They were assessed for the effect of surgery on the preoperative hemoglobin levels and causes of anemia in relation to socioeconomic status. Total of 100 patients were randomly selected for the study but after applying exclusion principles, 95 patients were left with mean age of 33 years, mean hemoglobin concentration of 8.66 in all and 8.79 after excluding the patients with massive blood losses post trauma/gunshot. Mean postoperative hemoglobin excluding trauma patients was 8.71. 52% of patients had anemia due to nutritional deficiency, of which 82% were females; followed by 31% related to chronic diseases and the rest due to acute blood loss. Anemia is still one the major co-morbidities in preoperative patients and we found that surgical procedures did not cause significant difference to hemoglobin levels postoperatively. Almost all the patients followed by chronic diseases. They are more prevalent in people from socioeconomically deprived groups of society

Physiological basis and clinical utility of erythrocyte sedimentation rate

The erythrocyte sedimentation rate [ESR] determination is a commonly performed laboratory test with a time-honored role. However, the usefulness of this test has decreased as new methods of evaluating disease have been developed. The test remains helpful in the specific diagnosis of a few conditions, including temporal arteritis, polymyalgia rheumatica and, possibly, rheumatoid arthritis. It is useful in monitoring these conditions and may predict relapse in patients with Hodgkin's disease. Use of the ESR as a screening test to identify patients who have serious disease is not supported by the literature. Some studies suggest that the test may be useful as a "sickness index" in the elderly or as a screening tool for a few specific infections in certain settings. An extreme elevation of the ESR is strongly associated with serious underlying disease, most often infection, collagen vascular disease or metastatic malignancy. When an increased rate is encountered with no obvious clinical explanation, the physician should repeat the test after an appropriate interval rather than pursue an exhaustive search for occult disease

Spectrum of precipitating factors of hepatic encephalopathy in liver cirrhosis

To ascertain the spectrum of precipitating factors of hepatic encephalopathy in patients with liver cirrhosis. descriptive study. The study was conducted in the department of medicine, medical B unit of Postgraduate Medical Institute, Lady Reading Hospital, Peshawar over six months. All patients with cirrhosis of liver[CL] of more than 12 years of age, manifesting signs of hepatic encephalopathy [HE] were included and those who had acute fulminant hepatitis or had noncirrhotic portal hypertension were excluded from the study. Detailed history, clinical examination and thorough investigations were done to look for any precipitating factor and the findings were recorded on a proforma. Fifty patients [32 males and 18 females] were enrolled. 47 patients had hepatitis B, C or both positive. 64% were in the age group of 45-60 years and 76% were having either grade III or IV coma. Thirty three [66%] patients had asterixis which was found to be a sensitive index for the diagnosis of HE in patients who were not in coma. Jaundice and Ascites were other common presenting features. Electrolytes imbalance in 28[56%] patients, diarrhea in 20[40%], constipation in 16[32%], infections in 12[24%] and gastrointestinal bleed in 11[22%] patients were amongst the commonest precipitating factors. None gave the history of alcoholism or recent surgery Occurrence of precipitating factors for HE in patients with CL is a common phenomenon and all such patients must be hospitalized to ascertain and manage such factors

foreign body in the ventricle of larynx

A case in which 6 cm long chicken bone was impacted in the vertical of larynx is reported. The patient presented to us after 3 months with throat discomfort and hoarseness of voice

Aetiological factors in epistaxis

This is a study of one hundred patients of epistaxis who reported to the Department of ENT at Services Hospital, Lahore during the year 1993-1994. A thorough evaluation of these patients for a possible cause revealed "trauma" to be the commonest [45%]. Next in frequency was the idiopathic group [24%]. Other aetiological factors like hypertension [9%], neoplasia [9%], acute nasal infection [7%], bleeding disorders [4%] and miscellaneous [2%] formed the rest of this bulk

Prevalence of various symptoms in adenoids

One hundred cases of adenoids were studied at Mayo Hospital, Lahore during 1990-91. A detailed history was taken from each patient to know the frequency of various symptoms apart from the main presenting complaint. The commonest symptom thus detected, was nasal obstruction in 84% of patients. Amongst the least common symptoms were episodes of apnea in 3% of cases and cephalgia or morning headache in 8% of patients

Microflora in chronic suppurative otitis media

To elucidate relative proportion of various bacteria falling in two major conventional groups of chronic suppurative otitis media namely tubotympanic and atticoantral. Design: Study of 150 patients in OPD involving 82 cases of atticoantral type of chronic suppurative otitis media and 68 cases of tubotympanic disease. Setting: Department of E.N.T. Services Hospital, Allama Iqbal Medical College, Lahore. 150 consecutive cases of chronic suppurative otitis media. Main outcome measures: Categorization of chronic suppurative otitis media into atticoantral or tubotympanic type in view of clinical features, examination under microscope and investigations. Processing of swab from each case for aerobic and an aerobic culture. Various strains of microflora found in 82 cases of atticoantral type of chronic suppurative otitis media were pseudomonas aeruginosa in 37 cases [45.3%] proteus in 18 [12.2%] staphylococci in 10 [12.1%], E. Coli in 03 [3.6%], Klebsiella in 03 [3.6%] and Anaerobes in 11 [13.3%]. On the other hand the commonest micro-organism in 68 cases of tubotympanic variety was staphylococcus in 28 patients [41.1%]. The other strains isolated in this group were pseudomonas in 21 cases [30.9%1, proteus 08 [11.8%], E.Coli 05 [7.4%], Klebsiella 04 [5.9%] and anaerobes 02 [2.9%]. Conclusions: The commonest infecting organism in atticoantral type of suppurative otitis media are gram negative rods with pseudomonas dominating the picture while staphylococci are the most commonly found organisms in tubotympanic pathology with gram negative organisms and few anaerobes forming the rest of main bulk in this infective process