Computational Design of Auxotrophy-Dependent Microbial Biosensors for Combinatorial Metabolic Engineering Experiments

Combinatorial approaches in metabolic engineering work by generating genetic diversity in a microbial population followed by screening for strains with improved phenotypes. One of the most common goals in this field is the generation of a high rate chemical producing strain. A major hurdle with this approach is that many chemicals do not have easy to recognize attributes, making their screening expensive and time consuming. To address this problem, it was previously suggested to use microbial biosensors to facilitate the detection and quantification of chemicals of interest. Here, we present novel computational methods to: (i) rationally design microbial biosensors for chemicals of interest based on substrate auxotrophy that would enable their high-throughput screening; (ii) predict engineering strategies for coupling the synthesis of a chemical of interest with the production of a proxy metabolite for which high-throughput screening is possible via a designed bio-sensor. The biosensor design method is validated based on known genetic modifications in an array of E. coli strains auxotrophic to various amino-acids. Predicted chemical production rates achievable via the biosensor-based approach are shown to potentially improve upon those predicted by current rational strain design approaches. (A Matlab implementation of the biosensor design method is available via http://www.cs.technion.ac.il/~tomersh/tools)

TRPA1 is essential for the vascular response to environmental cold exposure

This work was supported by the British Heart Foundation and a Capacity Building Award in Integrative Mammalian Biology. It was also supported by Arthritis Research UK and XK is supported by a British Pharmacological Society AJ Clark studentship

Patterns of violence in Karachi, Pakistan

Objectives: Government reports on violence in developing countries are almost universally based upon police data, which are typically incomplete and unreliable. Violence in Karachi was evaluated using ambulance service, not police, records. Setting: Karachi, Pakistan. Methodology: The study was based on a case series of persons suffering from intentional injuries and transported by Edhi, the largest emergency service in Karachi, between October 1993 and January 1996. Main outcome variables were injury and death rates. Results: Edhi Ambulance Service transported 4091 intentionally injured persons during the 29 month period from October 1993 to January 1996. Ninety five per cent (n=3864) were males; 74% (n=2823) were 20 to 40 years of age, and 2400 (58%) died before reaching the hospital. Firearms were the most common mode of injury (n=3396, 83%). Forty six per cent (n=1828) of violent injuries occurred in four neighborhoods of Karachi—22% in Korangi (n= 884) and 8% each in Orangi (n=337), Malir Colony (n=307), and Nazimabad (n=300). On the 32 days when a political strike was called, more people were injured (mean = 10.4 v 5.0 persons, p=0.01) and killed (mean 6.6 v 3.9 persons, p<0.01) compared with days without a political strike. Conclusion: Violence is a major public health problem in Karachi, affecting predominantly wage earners. At least some of the violence is rooted within the political system. Detailed study of the causes of violence that explains the role that political and ethnic tensions play, may suggest strategies to lessen the toll of violence

Risky behavior of bus commuters and bus drivers in Karachi, Pakistan

Buses account for a disproportionate number of road traffic accident fatalities in Karachi, Pakistan and other developing countries. Potentially dangerous bus driving and commuting practices that increase risk of road accidents and the effect of traffic police on bus behavior are evaluated. A total of 250 episodes each of disembarking and embarking commuters, buses stopping and moving on the road at ten of Karachi\u27s highest risk intersections for traffic injuries were observed. Of the disembarking passengers, 33% did not wait for the bus to stop; 54% stepped off in the center of the road and 84% did not look out for traffic. Among the embarking commuters, 38% got on moving buses; 73% climbed on buses filled to their outer foot boards and 83% waited for buses on the street. Males were more likely than females to jump off a moving bus (43% versus 1.6%, P \u3c 0.001), get on a moving bus (49% versus 12%, P \u3c 0.001), and run to catch a bus (45% versus 8%, P \u3c 0.001). At the bus stops, 30% of the buses did not stop completely; 46% stopped away from the stop and 79% stopped in the center of the road. Where traffic police were present buses were more likely to race (9% versus 3%, P = 0.05) and to cut off other vehicles (13% versus 2%, P = 0.001) than where police were absent. Risky behavior is common among both Karachi bus drivers and bus commuters. The traditional efforts to regulate bus traffic through traffic police is ineffective

Pedestrian environment and behavior in Karachi, Pakistan

Pedestrian road traffic accidents (RTAs) are responsible for a substantial number of injuries and deaths in Karachi. To better understand the situations facing pedestrians we selected ten of Karachi\u27s highest risk locations for pedestrian RTAs and observed 250 pedestrians for each of three activities--crossing the street, walking on the street, and walking on the sidewalk. We also observed the extent and effect of street and sidewalk encroachments. A total of 35% of the pedestrians crossing the street caused traffic to swerve to avoid them. Pedestrians crossing one lane at a time were 2.9 times more likely to cause the traffic to swerve than pedestrians who crossed the whole street at once (53 vs. 18%, RR = 2.9, 95% CI = 1.9-4.3). Pedestrians crossing in a group were 1.8 times more likely to cause traffic to swerve compared to those crossing singly (49 vs. 28%, RR = 1.8, 95% CI = 1.3-2.5, P = 0.001). A total of 36% ran while crossing and were 1.8 times more likely to cause traffic to swerve than those who walked (48 vs. 27%, RR = 1.8, 95% CI = 1.3-2.5). An average of 77% of the sidewalk width was blocked by encroachments which forced pedestrians to step on the road resulting in vehicles swerving. An average 33% of the street width was blocked by illegally parked vehicles. Pedestrians in Karachi indulge in risky behaviors. Encroachments on streets and sidewalks compound the problem. Piloting efforts to modify pedestrian behavior and the environment they negotiate should be considered to reduce pedestrian deaths

Vulnerability to homicide in Karachi: political activity as a risk factor

BACKGROUND: Previous studies analysing Karachi ambulance data from 1993 to 1995 identified neighbourhoods in Karachi disproportionately affected by homicide. As a step toward developing intervention programmes to curb violence, we conducted a study to identify risk factors for becoming a homicide victim in a high violence area of Karachi. METHODS: We interviewed families of 35 cases, individuals intentionally killed through acts of violence between January 1994 and January 1997, and 85 community-based controls frequency matched by sex, from Orangi, a high violence area of Karachi. RESULTS: Most of our cases and controls were male (97% and 92%, respectively) and had similar socioeconomic and ethnic backgrounds. All the victims were killed by firearms; 4 (11%) had been tortured prior to death. Most of the victims were killed in the streets (n = 25, 71%). Of these, 7 (36%) had been killed by law-enforcement officers, while 6 (24%) died from indiscriminate firing. People who were killed were 34 times more likely to have attended all political processions (29% versus 1%, odds ratio [OR] = 34; 95% CI: 4-749, P \u3c 0.001), 19 times more likely to have attended political meetings (31% versus 2%, OR = 19; 95% CI: 4-136, P \u3c 0.001), and 17 times more likely to have held an important position in a political party (29% versus 2%, OR = 17; 95% CI: 3-120, P \u3c 0.001) than controls. CONCLUSIONS: Homicide in Orangi was political. Efforts to improve trust between ethnic groups and to build legitimacy for non-violent forms of conflict resolution are important steps to limit future violence

The Biological Agents of Concern, Historical Epidemics, and Current Outbreaks: Assessing the Level of Prior Preparedness in the European Region

Khan MI, Khan S, Chotani R, Hornberg C, Laaser U. The Biological Agents of Concern, Historical Epidemics, and Current Outbreaks: Assessing the Level of Prior Preparedness in the European Region. The Internet Journal of Infectious Diseases. 2003;3(1)

Addicted schoolchildren: prevalence and characteristics of areca nut chewers among primary school children in Karachi, Pakistan

Objectives: To evaluate the habits of betel quid use and areca nut chewing among school-aged children in Karachi, Pakistan. Areca nut (betel nut) is chewed by itself, in various scented preparations, and in betel quid (containing betel leaf, areca nut, slaked lime, condiments, sweeteners and sometimes tobacco) in various parts of Pakistan and India. It is associated with carcinogenesis, foreign body aspiration in children and oral submucous fibrosis, and may aggravate asthma.Methods: We selected a stratified random sample of 160 primary school children between 4 and 16 years of age in Baba Island, Karachi.Results: Seventy-four per cent of the children (118/159) used areca nut and 35% (55/159) used betel quid daily. More boys chewed areca nut than girls (72% vs 30%). The proportion of areca nut users increased by grade (from 48% in first grade to 90% in fifth grade). Most areca users first tried it with a family member (42%) or a friend (26%), and most (68%) consumed three or more packets a day. Children with fathers with three or fewer years of education were more likely to use areca nut (OR 3.2; 95% CI 1.2-8.4), and children whose mothers helped with homework less likely (OR 0.5; 95% CI 0.2-0.91; P = 0.027) to use it. Boys (OR 6.6; 95% CI 2.3-18.7) and areca nut users (OR 8.8; 95% CI2.8-27.0) were more likely to use betel quid.CONCLUSION: To reduce the use of areca nut, the Pakistan Government should consider imposing taxes on it, limiting advertising and actively communicating its health risks to the public