Cooperation between humans has spawned great things in the past. This optimism is deeply rooted in the nature of collaborative work. One such opportunity has been the NORPART - Norwegian Partnership Programme for Global Academic Cooperation. Out of a total of 150 proposals that were submitted, 26 were accepted for funding, including Dr Shaper’s proposal, which aims to greatly enhance the internationalization efforts that are already underway at the Syed Babar Ali School of Science and Engineering.

The project is titled ‘Better health through partnership in higher education and bilateral student mobility: collaboration between Pakistan and Norway’. The offerings of this proposal are really exciting! Students from Norway will be offered courses at the LUMS campus. The two courses that have been selected for these international students are

Health Systems Management and Entrepreneurship and Innovation in Health Care. Alongside these courses they will also be offered a six-month internship for which the project offers two streams; Lab based Internship and Field based Internship. “To enable field based internship, we are parterning up with  Indus Hospital, Institute of Public Health (with whom LUMS had already signed an MoU), Gulab Devi Hospital and Institute of Public Health, Baluchistan.”, says Dr Saper Mirza. Speaking about additional aims of the project, Dr Shaper said that the project is to develop two courses in collaboration with  Institute of Global Health University of Bergen the courses are Disease Surveillance in low resource countries

Infection prevention and control in low resource countries.

We wish Dr Shaper Mirza and her team heartiest congratulations, and the best of luck for pulling off this promising project.

The NORPART aims to enhance the quality of higher education in Norway and selected partner countries in the Global South through academic cooperation and mutual student mobility. The programme is funded by the Ministry of Education and Research and the Ministry of Foreign Affairs of Norway.

For more information on the list of proposals, including the one selected from SBASSE, please visit: https://diku.no/en/programmes/norpart-norwegian-partnership-programme-for-global-academic-cooperation

What does not kill you makes you stronger. While not generally touted as absolute truth, the above idiom correctly sums up trends in antimicrobial resistance amongst pathogens. Like the dreaded final boss in a video game, if you do not correctly eliminate these pathogenic bacteria, they evolve into stronger, smarter versions of themselves and come right back with a vengeance. These versions, commonly known as “super bacteria,” have developed mechanisms that prove resistant against common antibiotics. Antimicrobial Resistance (AMR) is currently described by the WHO as one of the top global public health threats facing humanity. This problem is exceptionally prevalent in Pakistan, where misuse of antimicrobials has resulted in increasing AMR trends amongst common pathogens. However, through the combined efforts of Dr. Nida Javaid, Dr. Safee Ullah Chaudhary and Dr. Shaper Mirza from the Department of Biology, we can start our quest in fighting back against these pathogens and defeat them once and for all.

However, every heroic journey starts with an origin story. For this tale, our researchers described how they found their passion for Biology that began a decades-long journey that culminated in the publication of a ground-breaking research study. Dr. Nida Javaid, one of the researchers for this study, tells us how curious she found illnesses to be as a child. Inquisitive from the start, she wondered how something so microscopic that it is almost invisible could profoundly impact our lives. Thus, began her fascination with these invisible yet powerful agents leading her to choose microbiology and epidemiology as her field of interest. Equipped with a world-class education, a creative mind and a steadfast determination, our heroes understood the gravity of the threat AMR posed to Pakistan and quickly endeavored to find a solution to this problem.

 "Know your enemy." Arguably, the greatest military strategist in world history, Sun Tzu understands the importance of insight. To guarantee victory in any battle, one must have a thorough understanding of their opponent; otherwise, they will surely bite the dust. Therefore, the first step to combating rising AMR trends was to analyze the different types of soldiers in the bacterial army, their strengths, weaknesses, and attack strategies. From a scientific perspective, this means identifying the most common pathogens that cause deadly diseases, understanding their evolution to resist certain types of anti-biotics, their geographic distribution across Pakistan and what gender or age-group demographic are most susceptible to infection.

Along with their teams, the above-mentioned researchers have been working on a comprehensive analysis of long-term AMR trends in Pakistan and have published a paper identifying these trends from 2011 to 2015. Conducting a ground-breaking study on such a massive scale poses several formidable challenges, but our researchers have faced these difficulties head-on and dispatched them with ease. Dr. Nida describes how organizing such a vast dataset for this study, from so many sources, was a monumental task. They needed information on the site of isolation, demographics, and antimicrobial susceptibility profile of each isolate against over 15 antimicrobials. That’s more than 3000 separate profiles for each pathogen they have encountered. Even Sun Tzu himself would have blanched at such an onslaught of information. However, our researchers remained resolute and enjoyed the process of diligently visualizing this data. Dr. Nida fondly remembers how satisfying it was learning to utilize Circos plotting software and ultimately transforming the data into a single figure for each pathogen. After the data had been compiled, visualized and analyzed, the researchers began to draw conclusions from the results and buried under layers of increasing AMR trends for many a pathogen, they discovered something quite interesting.

The findings report a rise in antimicrobial resistance in several pathogens isolated from blood and cerebrospinal fluid cultures, such as the Acinetobacter species, which demonstrated the highest resistance rates to all antimicrobials. This, then, could be considered the Lieutenant General of the Bacterial Army, a potent threat that must be defeated, or we would suffer dire consequences. Almost all other pathogens also showcased increasing AMR trends following their leader and showcasing the might of their army. Interestingly, decreasing resistance trends were observed for Staphylococcus aureus against common antibiotics, unlike its other aggressive pathogen comrades. To that end, we would like to nominate ‘S. Aureus’ for Pathogen of the Month for being so well mannered. Truly a shining example for other microbes to follow. These findings were compiled into a research paper nearly half a decade in the making. Through this arduous journey, the researcher's preservation paid immense dividends, as Dr. Nida described her elation when this paper got accepted for publication. This data will be invaluable in planning a stellar counterattack against these pathogens. The paper highlights several actions we can take to stop the growing threat of AMR in its tracks. The public must be aware of the dangers of antibiotic misuse to resolve the problem at its source before it's too late.  

The battle lines have been drawn. As one researcher described it, AMR is a major public health challenge. The antibiotic production pipeline is drying out, and microbes are becoming increasingly resistant by the day. By 2050, every minute, a person would die due to antimicrobial-resistant infections. Considering how the COVID-19 pandemic crippled the world and its economies, it is paramount that policymakers should prioritize antimicrobial stewardship to counter the rising trends of AMR.

References:

Title: Trends In Antimicrobial Resistance Amongst Pathogens Isolated from Blood and Cerebrospinal Fluid Cultures in Pakistan (2011-2015): A Retrospective Cross-Sectional Study

Authors: Nida Javaid, Qamar Sultana, Karam Rasool, Sumanth Gandra, Fayyaz Ahmad, Safee Ullah Chaudhary, Shaper Mirza 

DOI: 10.1371/journal.pone.0250226

We are living, breathing chemical conglomerates who’ve carefully gathered knowledge over the course of centuries, to piece together clues in solving one of the greatest mysteries of our existence – the origin of life on Earth. An understanding of proteins has been a low hanging fruit of this endeavour. Decades of meticulous research on these magical molecules have revealed that much of life’s rich tapestry rests upon their complex and delicate structures. Therefore, tools and mechanisms that can zoom in on the structure of proteins and reveal the identification, are of incredible importance to scientists working on the frontier of life sciences research.

Dr. Safee Ullah Chaudhary, and his team of researchers, have developed a breakthrough tool, called PERCEPTRON, for highly efficient proteoform identification from top-down proetomics (TDP) spectral data. Their work has been published in the journal Nucleic Acids Research (NAR), a paramount achievement requiring nothing less than an outstanding team of researchers.

Reflecting on this distinction, Dr. Safee Ullah said "SBASSE at LUMS has brought together the right ingredients to undertake and sustain world-class research and development work. PERCEPTRON is one sure step to propel LUMS to the cutting edge of Proteomics and Bioinformatics research.”

Dr. Safee Ullah

PERCEPTRON, a web-based platform that outperforms all other similar tools by up to 135% in terms of reported proteins numbers and is ten times more efficient in terms of runtime.

In a technological masterstroke, Dr. Safee Ullah and his team have designed PERCEPTRON’s search pipeline to bring together algorithms for six different parameters:

1. Intact protein mass tuning
2. De novo sequence tags-based filtering
3. Characterization of terminal as well as post-translational modifications
4. Identification of truncated proteoforms,
5. In silico spectral comparison
6. Weight-based candidate protein scoring 

To meet PERCEPTRON’s heavy demand of powerful and robust technology, GPU units by NVIDIA were used, along with Microsoft ASP.NET and ANGULAR Frameworks.

Highlighting the importance of team work in this effort, Ms. Kanzal Iman, a PhD student, who is part of Dr. Safee Ullah’s team, said “Working on PERCEPTRON has instilled in me that when you believe in consistent hard work, great things happen. Team PERCEPTRON is a great example of learning from each other and growing together.”

Kanzal Iman

Another fellow co-first author of the paper, Ms Amna Ghafoor commented on the overall journey leading to the publication “The journey from a single “Hello World” to the entire GPU programming of PERCEPTRON has been a very bumpy ride. But thanks to the amazing team and blessing of Allah Almighty, we were able to pull it off Alhamdullilah.”

Amna Ghafoor

Commenting on the future support for this research, Dr. Safee Ullah said “We are looking forward to further support from the university to establish PERCEPTRON as a go-to platform for Proteome research across the globe."

PERCEPTRON aims to fill the voids in conventional protein identification software for TDP data, and make the process easier, more efficient and reliable. We congratulate Dr. Safee Ullah Chaudhary and his team for championing this multi-year effort through in-house resources at SBASSE, and pioneering Computational Biology and Bioinformatics research at the School.

Muhammad Farhan Khalid

Reference: Muhammad Farhan Khalid, Kanzal Iman, Amna Ghafoor, Mujtaba Saboor, Ahsan Ali, Urwa Muaz, Abdul Rehman Basharat, Taha Tahir, Muhammad Abubakar, Momina Amer Akhter, Waqar Nabi, Wim Vanderbauwhede, Fayyaz Ahmad, Bilal Wajid, Safee Ullah Chaudhary, PERCEPTRON: an open-source GPU-accelerated proteoform identification pipeline for top-down proteomics, Nucleic Acids Research, 2021, gkab368, https://doi.org/10.1093/nar/gkab368

More information on PERCEPTRON: https://perceptron.lums.edu.pk/index.html#/home

Notorious not only for its recurrence but also for its idiosyncratic response towards conventional treatment, cancer has held a diabolical status in the realm of health sciences for far too long. Rising up to the challenge of better understanding cancer at its biomolecular level, Dr. Safee Ullah Chaudhary was recently rewarded a grant worth Rs. 14 million, by the National Center in Big Data and Cloud Computing (NCBC), to get a panoramic understanding of how cancer works differently in different patients, by developing a cloud-based cancer modelling system along with a digital modelling library. The hope is to provide a one-of-its-kind personalized cancer treatment, that takes into account different parameters from both the disease as well as the patient.

Cancer databases comprising of gene, RNA and protein expressions will be combined with patient drug interaction information and patient profile using TISON (Theatre for In-Silico Systems Oncology), a powerful cancer modelling platform. This will be done for six clinical case study models i.e., Oral Cancer, Colorectal Cancer, Pancreatic Cancer, Neuroblastoma, Autophagy and Warburg Effect (a condition that leads to increase in the rate of glucose uptake and lactate production, even in the presence of oxygen).

Through this project, Dr. Safee Ullah intends to get a better understanding of biomolecular regulatory networks, that are rendered erroneous in the onset of cancer, and also create a model for cell responses to therapeutics. These models will then be integrated into decision circuits that can figure out the fate of each cell, leading to their import into cell lines. Eventually, a patient-specific therapeutic response can be catalogued and modelled that can help with better, more personal cancer treatments in the future.

Learn more about Dr. Safee's work here: Biomedical Informatics Research Laboratory (BIRL)

Our heartiest congratulations to Dr. Safee Ullah for getting this grant; we wish him success for this project.