Reservoir Dogs

The cockerels were exuberantly sounding the alarm, proclaiming the ascent of the Far Eastern sun as though the new day offered potential to every desire in these spiritual lands. Cock-a-doodle-doo!!!! Cock-a-doodle-doo!!!!

The other vacationers, which included my English father and Filipino mother with a collage of cousins, uncles and aunties, had voyaged from the polluted megalopolis of Manila to this tranquil paradise in the northern Philippines. At this early hour they were still snoozing, refusing the cockerel’s unease. My Tita (Auntie) Pearl, however, had been awake for at least a few hours, being both the local and acting host to our gathering. She had busied herself with deliberations over her preparations for the forthcoming midday breakfast and later banquet.

My nose followed the source of the distinct aromatic scent of squid adobo; my favourite native dish and my early activities surprised her and her helpers. Although the teasing smell could easily be one excuse, I was really awake this early to face the challenge of a run with my Tito (Uncle), who holds a military background. His name was Lucero, or Lou for short, but everyone called him Bubut. At least I could bank on delicious food as reward for my upcoming torment in the tropical heat.

I walked beyond the cooking area towards the back of the house, taking advantage of a few free minutes whilst my Tito readied himself. I made my way past the empty hammocks and magnificent coconut trees, with intent towards the safe haven for the house’s guardian canines, all-the-while keeping a watchful eye for those silent masters of the undergrowth. The thought of snakes sent shivers down my Mother’s spine, although I kept to myself a longing wish to see one in the wild. The Northern Philippine Cobra marshalled these lands and I was not about to allow my physiology to fight with the venom of this earthly creature. At last, I had made it to the dog-pen, greeted by my good friend Brownie with warmth greater than the Philippine air. I fussed his brown coat, provoking such violent outbursts of howling from his rancorous companions to make you think they were rabid. I only hoped these bullies would not later physicalize their frustrations on my soft-hearted friend. The rancour eventually settled down, allowing one final handshake in peace before I duly negotiated my way to the front black gates of the house, decorated with golden spires and camber, to meet my Uncle.

The hobbled road ran alongside the Cagayan River, the provincial name which covers our home in Solana and the neighbouring city of Tuguegarao. At seven-thirty in the morning there was little activity but for the clunking of a caribou’s hooves and the cuck-kooing of unruly cockerels, although our temperature had registered a humid twenty centigrade. Tito and I ran in rhythmic silence, battling the salt in our eyes as much as the heaviness of the air. These early experiences in life have been embedded in my memory ever since, inspiring me stay fit and active and push the limits to my own physical capabilities. I owe much to these runs through roads surrounded with towering tropical trees in the tranquillity of my family’s provincial lands.

Solana, Cagayan

Twenty minutes of running had passed by the time we had reached the end of the road. We stretched for a few minutes, looking out towards the mudded banks of the Cagayan River, contemplating the dangers of deforesting and logging to both the birds and our waters. When we turned our heads to home we were startled to realise a small group of observers had assembled no more than 150 metres ahead. Our efforts of stealth this dawn had unmistakably failed. There stood seven canine guardians, eyeing us in disbelief as if to question the audacity of our trespass through their sacred territory. Although a few were slim, this only meant they were overdue a next meal and their snarls and barks served as a potent warning. The Alpha-male stood at the apex of the pack and, contrary to the rest, eyed us in cold, petrifying silence.

“Don’t look at them, just straight ahead and never in the eyes. Keep running, nice and steady. Wouldn’t want to get rabies!” My veteran Uncle whispered his orders

RABIES. This maddening virus, shaped to resemble a bullet and peppered with glycoprotein spikes, is capable of transforming the human mind-set to one of fury; sending their hosts into distress at the allusion of water, light or even a gentle breeze. Once such symptoms develop, death is almost inevitable. In the Philippines, Rabies virus is prevalent within canines who may act as a viral reservoir, and sadly killed 202 people in 2011. Such a disease is referred to as ‘enzootic’.

Sam, in cooler English climates. His territorial attitude might be mistakenly described as 'rabid' behaviour. He certainly isn't.
Sam, in cooler English climates. His territorial attitude might be mistakenly described as ‘rabid’ behaviour. He certainly isn’t.

It falls within Class V of the seven Baltimore Classifications for viruses, respecting its single strand of ‘negative’ sense RNA which encodes just five genes. If untreated, rabies will voyage to the central nervous system, resulting in either ‘Furious’ rabies or the lesser known ‘Paralytic’ rabies which accounts for 30% of all human cases. In such cases of ‘Paralytic’ rabies, muscles will weaken and paralyse at the initial site of the scratch mark before the victim is slowly enveloped by a coma as a prelude to eventual death. Immediate wound cleaning and immunization via post-exposure-prophylaxis can prevent such occurrences and each year, over 15 million people receive such immunizations to prevent the disease, which is estimated to prevent hundreds of thousands of deaths.

Map of Rabies Endemic Areas
Map of Rabies Endemic Areas

Statistically and geographically, I was in the right place for a bad outcome; as a young kid just wanting to play I was a sitting duck for a rabid brute. At 12 years old I knew little better and, to worsen the situation the closest facility with vaccine therapy or rabies immunoglobulin was hours away.

Against my inhibitions, my Uncle and I picked up the pace, entering a charge towards the rowdy pack on patrol. I was soaked to the skin in sweat from the humidity but wished for the guardians not to see nor sense it, fearing they would acknowledge my fear through my perspirations. I transfixed my eyes transfixed upon a mango tree far in the distance. I continued to run but against my better judgement I caught glimpse of the Alpha’s stare, and so began the pack’s charge to us.

“Keep running, look straight ahead and nowhere else” came the orders. My Tito’s coolness gave me the confidence I inherently lacked. The gang powered towards us, the cacophony of growls and barks getting louder. 40 metres away….My heart was thumping so hard in my chest I feared they would see this too. 30 metres and closing…. I suddenly preferred England. 20 metres…. My numbers were up, and so young.

To my astonishment the pack started to slow. I continued to focus my eyes on the forgiving Mango tree trying hard to contain my relief. 10 metres…. The Alpha decelerated to a light trot, the others in lax pursuit. They parted to our right and jogged by our side, with all evidence of anger dissolved.

Our companions flanked us to the black iron gates where safety was once again assured, with the reward in sight as I spied through the windows of our Auntie’s dining room. I turned to see the pack disperse, uninterested and wandering. My first ‘real’ run in the tropics had tested me more than I could have anticipated, encouraging a sense of exaltation. I felt calmed after the ordeal, and would make sure to spend some time with my soft-natured friend Brownie as soon as I had enjoyed a cool, refreshing shower and the fine Filipino cuisine offered by my Tita.

With Brownie in Solana
With Brownie in Solana

Viral Attitudes: A Conference Apart

What a difference a day makes? Try two hundred and forty-five.

Exactly that many days lay between the attitudes observed to the Ebola virus research updates from the annual Médecins Sans Frontières (MSF) Scientific Day held in May of 2014, to the ‘Topics in Infection’ conference held by the Royal Society of Tropical Medicine & Hygiene at the end of last month. On both occasions I felt a comforting warmth of familiarity humbled by a dose of realism and inadequacy, seated amongst academic and clinical kingpins, barely visible from my rung of the ladder despite our agreed passions.

At the first conference I was officially on representative duties for an NGO – First Aid Africa – who aims to provide sustainable skills in emergency life-saving skills across rural East Africa.  That didn’t matter in this auditorium. Here, I was invisible.

There were two updates dedicated to the thread-like virus that day, carefully scheduled at the point of reawakening from the graveyard shift; the contagion of yawns reaching their conclusion. A strong-jawed and dark-haired American man took the stage and began by depicting the operational difficulties facing MSF in rural West Africa. Here, communities viewed the white Doctors in their protective glory with nothing but apprehension. The facts and figures were laid bare, and they weren’t particularly big. He offered a little of that American ‘Hoo-ha!’ in his rhetoric, as if to condemn us of our own disinterest as much as the suffering caused by this virus in remote regions of Gueckedou in Guinea.

I silently observed my fellow tropical disease enthusiasts as the second of the speakers prepared himself, fumbling with his pointer (not remotely a euphemism) and some sheets of important paper. I could hear the dissenters stirring, questioning the need for two talks on a disease which had barely registered a hiccup in the endeavours of MSF over the past 12 months, inclusive of operations in Syria and Sudan. He spoke of the ongoing clinical research and the analysis of transmission dynamics, carrying the drama well through his youth and bouncy rhetoric which most likely declared itself out of the pride and enjoyment he felt in sharing his work.

His final graph appeared, and his charisma was equalled by a gruff of indifference from the audience.

“Why is he even allowed to show us this? It’s a sample size of 16!” came a whisper with little intent for secrecy from behind me. I turned, only to meet the raised eyebrows of an olive-skinned, thirty-something woman with L’Oreal-Ad-worthy brunette hair.

The sniggers spread across our troop in an outbreak of their own. The voices of rebellion roused to grind down the bold naivety of the charismatic stage performer. Clearly there were other, more pertinent subjects to focus on. As the second speaker wound down his spiel, we – the crowd – offered our obligatory applause and little else.

As expected, the talks closed by the formation of a panel consisting of our speakers and other relevant personnel, ready to face our questioning. The crowd returned with an onslaught of cynicism, broken only by the laughter drawn when the American banged his fists defiantly to declare “The International community sat around and watched while we, MSF, stepped up to the plate!”

This is, of-course, true. The work of MSF throughout the current outbreak has been exemplary and it is testing to imagine that the progress being made to curb the outbreak, including the influx of experimental vaccines to Sierra Leone, could have been achieved without their leadership and co-ordination. The World Health Organisation have been caught out by the co-discover of the virus, Professor Peter Piot, indicating a failure to act in earnestness to the first official lab confirmation in back in March 2014. On the 23rd May, the day of this MSF Scientific update, there had been less than 500 confirmed cases of Ebola across Guinea, Sierra Leone and Liberia. Exactly 8 months later that figure had magnified to 21,797 across six countries.

Accordingly, the RSMTH conference last month ‘Topics in Infection’ opened with gusto. Three talks contextualised the Ebola Virus through a need for ongoing research in outbreak scenarios, to understand its’ clinical and pathological profile and to map its’ zoonotic niche. The crowd were drawn in from the start. For many, this update was everything they had come for.

It is undoubtedly a shame that our attitudes have taken so long to alter. As an international community of self-professed ‘do-gooders’, we have been humbled. We have learned much along the way to delivering an experimental Ebola vaccine to Liberia which is due to be tested in roughly 30,000 people. The first speaker encouraged us to listen in on further movements and consider research ventures with Plasmapheresis; testing Ebola convalescent blood for post-exposure prophylaxis. There is still much to learn before the next conference I attend.

Border Cross

International borders are meaningless to infectious diseases such as Yellow Fever

Date of Event: July 19th 2014

The tatty card with its leaden yellow shade lay submerged under various other travel documents at the bottom of my rugged rucksack, falling within eyeshot as the Impala brought us closer to the border of Kenya and the United Republic of Tanzania. Through the dust-laden windshield I could make out the anticipating ‘Rolex’ and ‘D&G’ floggers surrounding the white block-buildings of the Immigration Offices dominating the horizon.

I had made few acquaintances on this corrosive leg from the bustling centre of Nairobi; my temporary companions preferring the solace of internal reflections on earlier travels, taking time out only to frown disapprovingly at the radio’s irregular chirrups, stubbornly camouflaging their frustrations through tight lips.

Finally, I surfaced the Yellow Fever certificate, feeling it appropriate to exclaim to my neighbour with an “Aha – got it!” as if to drive the achievement home with raised eyebrows.

She turned leftwards towards me, her eyes distracted for a fraction on what I imagined to be one of the many hopeful junk-food sellers beginning to stir around our slowing, battered grey shuttle-bus.

I am not entirely certain but perhaps my neighbour was called ‘Helen’, with a heavy interest in architecture having spent most of the preceding journey engrossed in a tome of odd archaeological digs, using the rest of the time to muse on her dreams for her PhD in the subject, due to start soon in the United Kingdom. If the friends I have made in recent years are anything to go by, her PhD ambitions have probably altered more times than the Daily Mail has ran an absurd, fear-mongering piece on Ebola, since we had said our goodbyes.

Staring at the yellow document, wedged between the finger and thumb of my right hand, neither she nor I knew exactly its’ importance in our fate for the upcoming border-cross.

“I’m not even sure we need it” doubted Helen, as she fumbled to stash her book away in a rucksack in far better condition than mine.

On the converse I positioned myself on the ‘would need it’ camp, albeit without much confidence. My tentative response, however, made me feel ashamed given my education in microbiology. I bullied myself into thinking I should know the significance of this virus in all countries.

We eventually stepped out of the vehicle to join our equally hesitant fellow travellers, hovering awkwardly on the hardened mud amongst a littering of Fanta and Coca-Cola labels which can be found in even the most rural places of east Africa, before donning a strut of self-importance towards the arches of the Immigration Office.

A short wait later, lengthened only by the sweat induced moaning of our foreign congregation, I dutifully presented my passport and thumb to the Official; a smartly dressed Tanzanian woman whose soft spoken voice was all the more difficult to hear on the other side of the glass shield. I expected my yellow fever certificate to be summoned from the safety of my left pocket at any moment.

It never came.

“The Yellow Fever Certificate. Do you want to check it?” I asked in a regretfully, almost offensive, toiled manner.

She smiled back at me as I began to move my left hand towards my pocket. “OK, thank you, next please!”

I stood for a moment, feeling the glare of other travellers through the back of my head to get a move on.

“Why the indifference?” I wondered.

As I trudged onwards, placing the passport in safe retreat, I recalled the significance of the Yellow Fever Virus, a single strand of ribonucleic acids capable of manipulating the cells its’ human hosts to cause a blood bursting fever, or a discolouration of the skin and eyes, giving credence to its’ name. Some people know it as “Yellow Jack” from the days where yellow flags on ships signified a quarantine status, disrupting the trade between the Western hemisphere and coastal regions of West Africa at the close of the 19th century.

Back then, nobody knew exactly what caused the disease, although it was noted how recovery conferred with long lasting defence; from what we now understand to be the result of our adaptive immune response.

Sir Patrick Manson, in his Manual of Diseases of Warm Climates, referred only to a “germ or virus” but based on observations considered an external period from a human host for the agent to be infectious. This ‘transmission’ proved to come at the mercy of Aedes aegypti mosquitos, who live their ephemeral existence seeking constant replenishment from the crimson blood of tree-top monkeys or unsuspecting humans, occasionally spreading the virus between these hosts.

Our awareness covers only a snapshot of the scourges the virus has caused. Philadelphia, the once capital of the United States, lost almost 10% of its population at the hands of Yellow Fever Virus in 1793. It’s victims, since the first days of the virus’ discovery, across endemic regions of Middle – and South – America, and sub-Saharan African countries such as Kenya and Tanzania, will measure in multitudes of millions.

Scientists and health workers are heavily reliant on numbers. Our infatuation with statistics and percentages helps to reduce death and illness to a mere succession of digits, void of humanistic value. Just one year before I was born to a nurse and engineer in a modern and well equipped City-hospital in the middle of England, 5 million people, primarily across the tropics, faced a showdown with Yellow Fever Virus and its’ offering of doom. Supportive care is the only way to aid the human body to overcome this infectious agent’s inclination to wreak havoc on liver and blood cells. Today, people are still vulnerable, albeit in much lesser numbers. My arrival into a country of seasons and widely accessible vaccines placed my life at an almost negligible risk of dying from Yellow Fever. Serendipity and the ingrained habits of a mosquito will mean that approximately 270,000 inhabitants of the continent I had flown into, would not be so lucky within the next 12 months.

It makes perfect sense to contextualise this dramatic reduction in global deaths from Yellow Fever, with the knowledge that vaccine coverage since 1998 has increased by 46%. Such a public health feat owes much to the Nobel Prize winning efforts of Max Theiler, for his development of what was to be named vaccine ‘17D’. Derivatives of this universal standard encompass the world-wide available vaccines today, and has aided scientists to understand more about other viruses such as Dengue Virus and Japanese Encephalitis Virus, which belong to the same ‘family’ of viruses (flaviviridae). The molecular ‘backbone’ to 17D has aided the development of ‘chimeric’ vaccines, which could be useful in tackling Dengue fever. The principles behind the inception of the Yellow Fever vaccine are as important now as 80 years ago.

And yet the Immigration Official, protected by her glass pane and armed, but admittedly day-dreaming security personnel, couldn’t give two winks as to whether I had bothered to reduce mine and others’ chances of falling victim to Yellow Fever or not. Perhaps she spent too long looking at my pathetic and anxious expression, like all the other Caucasian (or in my case – a little Asian) border-hoppers whom she had already spent her energy on that day. Maybe it was my unnerving Kamikaze-like passport photo that cheered her to shoe me on without further interrogation. Or maybe Yellow Fever simply was not a big deal any more, to her or to her country.

I traipsed closer to the chugging, undulating engine of the Impala shuttle bus as if to announce a readiness to leave, in what was geographically now the United Republic of Tanzania. I turned my head towards Helen who followed in close pursuit and gestured my vaccine certificate towards her, its’ colour in forgiving contrast to that of the mid-day African sun.

“She didn’t even ask me….” I mumbled disappointedly.

I set myself up for part two of the voyage, headed towards the mountains of Arusha in northern Tanzania. As I watched the brown-haze of dust kick from alternating convoys and nodded without retention to Helen’s architectural reflections, my thoughts fell back to the smart Official; hoping she might pay an indirect tribute to Max Theiler and global vaccination efforts by summoning the card of another traveller, intending to cross the border that day.

aedes aegypti mosquito
The vector of Yellow Fever Virus: Aedes aegypti mosquito

Topics in Infection 2015

The Annual RSTMH Conference ‘Topics in Infection’ happened yesterday in London, and I was lucky enough to join in on the action. At a later date I will write on some of the exciting ongoing work and historical perspectives discussed in yesterday’s meeting, including a surprisingly entertaining talk on Imported Cases of Malaria from Professor Chris Whitty of the London School of Hygiene and Tropical Medicine.

But for now – Aren’t I happy that it was agreed yesterday that there is absolutely no evidence for the involvement in Dogs for Ebola transmission to humans! 


Ebola: The Hidden Thread

The family, filoviridae, of which the virus in question belongs, allows us to conjure up an image of the perpetrator; after all, the Latin filum alludes to its’ filamentous structure. A hidden threadlike set of molecules indeed. All filoviruses that have caused disease in humans have been endemic to sub-Saharan Africa only and it is here, in West Africa to be more specific, where the story of the biggest Ebola virus outbreak on record continues to unfold.

Image: Ebolavirus. Credit: Frederick A Murphy

The virus was discovered less than 40 years ago in Zaire, by a team of Belgian scientists including The London School of Hygiene and Tropical Medicine’s current Director Professor Peter Piot, and was named after the nearby ‘Ebola’ river from where the scientists were investigating. The initial outbreaks were small in nature but the clinical features were devastating enough to spread fear across affected communities to wherever their stories reached.

To learn that a few strands of RNA transmitted by human contact, or possibly through the saliva or excreta of Rousettus aegyotiacus; or even the whole mammal on your dinner plate, can cause a visibly harrowing haemorrhagic fever with the capacity to kill within the space of twenty-one days, is enough to make the calmest of physicians exhibit cutis anserina. This is goose-bumps for the non medically adept layperson (myself included).

On September 9th, the World Health Organisation tallied 4,293 cases and 2,296 deaths across five West African countries which obliterates the previous record of 425 cases in Uganda during the 2000 – 2001 outbreak. Liberia is one of the worst affected countries, with the capital Monrovia so under-resourced to controlling the transmissions they are having to turn away up to 30 infected patients per day, according to Medecins sans Frontiers. The health systems in the affected countries are, quite clearly, struggling. Whilst the intermittent stories of recovery trickle through to offer the compulsory hope in any situation where it feels it does not belong, it is the realistic urgency from clinicians and scientists that has to be acted on to counter the frightening statistics on offer.

Esoteric as the virus may be, currently localised to an area of the world many of us will never venture, there holds a great degree of encouragement through seeing medical science funding bodies, such as the Wellcome Trust and Bill & Melinda Gates foundation, release emergency funds to help contain the Ebola epidemic. The experimental treatment ZMapp which was used to treat British Ebola patient and humanitarian nurse Will Pooley, alongside vector based vaccines, are considered promising prospects.

It is possible to download the full Manson’s Tropical Medicine chapter on Viral Haemorrhagic Fevers here, free, courtesy of The Wellcome Trust.

My Cushy Pooch

Her name was Poppy – my first ever pooch whom guided me from my pre-Mexican bandit facial hair days, through to a completely new era in my life, as she bid me her final farewell during my first week of Edinburgh University.  Half German Shepherd – Half Total Fluffpot, my fondest memories of her include her attempt to bite a douchey fella who walked in that douchey way whilst giving some douchey agro to my Dad on a walk… and her devout company throughout that 5 set Wimbledon Epic between Federer and Nadal (I think she wanted the tennis balls…..). A wonderful dog, with a golden mane, golden heart..and an exquisite talent for delicately unwrapping chocolate bars from underneath the Christmas tree (True story!).


“She has Cushing’s Disease” came the weighted words of the Dog Doctor, or Vet if you will, towards her final days of duty as our ultimate guard dog. Poppy had been through a few veterinary scraps throughout her time with us…but her old age and progression of the condition would not allow us to see her through this one. The time to rest had come.

Cushing’s syndrome itself is the name given to the signs and symptoms attributed to prolonged and inappropriate exposure to elevated glucocorticoids such as the stress hormone – Cortisol. Our dear Pops was believed to have had a corticotroph adenoma, which results in excessive levels of secreted Adrenocorticotropic hormone (ACTH) and stimulates, down the line, the adrenal cortex, which is embedded in endocrine glands situated at the top of our kidneys, to produce ridiculously high levels of cortisol.

The long term results of exposure to this stress hormone are Weight gain & Obesity, high blood sugar levels (Hyperglycaemia) and loss of skeletal muscle mass. We humans get it too! Additional things more obvious in homo sapiens include the development of ‘buffalo hump’ – fat depots over the thoracocervical spine (about mid-way down on the back) – as well as bright red-purple striae (stripes/bands/lines) over 1 cm in width, around the abdomen. Given that the hyperglycaemia persists and continually stimulates the secretion of that all important hormone insulin from the pancreas to help control blood sugar levels, you might describe this aspect of the condition as a type of Type 2 Diabetes Mellitus. However, the rise in insulin levels do not effectively reduce the blood sugar levels because the skeletal muscle and fatty (adipose) tissues don’t take up the glucose, which is in higher availability in the blood, as much as they should.

Dear ol’ Pops passed the Dexamethasone suppression test, by showing no suppression of ACTH and cortisol secretion upon administration of external, supraphysiological doses of glucocorticoids….thus confirming her condition. Whilst the removal of the adrenal adenomas would have fixed the high cortisol level issue, her overall condition and age hindered the certainty of cure over further risk.

At least a few times a month, she’ll trot into my dreams, roll onto her back and beg for a tummy tickle though! Silly Pops…. Happy Christmas and New Years in doggy heaven…which I imagine to be some sort of wood with trees that grow Bonios.

Model Mayhem

Never mind the glorious Victoria Secret types (well….). There are other kinds of wonderful models in this world. StatisticalModels, Public Health Efficacy models and low and behold….Animal Models. Often the target issue of animal right activists against the world of dirty pharma (and rightly so), animal models do and have played an insightful role into how medicines work before giving them a go in us human likes. A couple of success stories from this website gives a very brief insight into new-found treatments for PTSD, Memory problems and Polio for example. Animals have also helped recently in our understanding of Rheumatoid Arthritis pathophysiology.

In 2012 I took it upon myself to investigate Animal Models and their use in a specific area of neurophysiology – looking at the movement disorder ‘Parkinson’s diseaseor PD. I knew from the start it would be tricky business, for example – does the Substantia Nigra (one of the warzones in the PD brain) of a glorified rat really represent the human Substantia Nigra? But still, I knew a good bunch of reasons for animal research to help understand important conditions such as PD.

I wanted to investigate how animal research has helped in our understanding of the relationship between genetic causes and environmental causes in the origin and progression of this movement disorder. Under the guidance of some statistical wizards and a Professor who always had to put his feet up on something when he talked, I was led to the epicentre of a scientific nightmare.

Out of 23 animal research studies I analysed with rigorous statistical methods and several Pick ‘n’ Mixes from the downstairs WH Smiths, a grand total of zero bothered to ensure the person investigating the results of their experiment were ‘not in the know’ of the experimental animals and the control groups. This of-course increases bias and bias is the very thing any clinical trial would want to avoid. And so why should a pre-clinical study, in animals, which require trillions of hours of the sharpest brain-work and a fair amount of funding, be any different? Save time and money at the start in this animal research, and quicker we may be onto the path to success in finding the answer to BIG questions such as the Origin of Parkinson’s disease, or how it progresses, or how best to treat it. Sure yes, I’m picky on the one point here but it’s a big point, and other parameters in these studies were poorly controlled to.

Nonetheless – some physiological considerations to ponder upon did crop up. Namely, a mutation (A53T) in a gene called alpha-synuclein appears to be enhance the negative effects of one potent environmental toxin that causes PD symptoms – a molecule called MPTP. As with many areas of Parkinson’s disease research, the energy factories of our cells – Mitochondria – appear to hold the link here too.

Whilst the picture is of PD causality and pathophysiology is  building, a slicker methodology shouldn’t be overlooked in the next round of audits. Only then can the masterpiece truly take shape. Only then can we be certain to find real answers (a cure, perhaps?) to real problems. Only then, can we hope to replace, reduce and refine animal models in medical research. 

Sounds good if you ask me!


English: Horizontal MRI (T1 weighted) slice wi...
English: Horizontal MRI (T1 weighted) slice with highlighting indicating location of the substantia nigra. (Photo credit: Wikipedia)

Feeling old? Telomere about it…..

2 months on from turning 24, I’m still finding it difficult to come to terms with the ordeal. It feels like yesterday when a younger friend turned to me and said “Jeees Phil tomorrow you’re seventeen! Gettin’ old man….” and now after a quick head-to-toe examination in the mirror, I take in the battle-wounds accumulated since; A freckle on my nose from when I squeezed a spot in earnest (probably a little too hard); A couple of shaving scars from whenever I obliterate my admirable attempt of a Confucius beard; A lower left leg scar gifted from the door of a deluded Taxi driver……..and a pair of ‘not-quite-fully-recovered’ ankles from when I battered the streets of London in the Marathon of 2009. Not a great deal to report on the exteriors to be honest. But deep inside the cells of the tissues of the organs of the Phil….things are going nutz!

Inside a cell, it’s virtually a whirlwind Blockbuster day-in and day-out. The genetic components in each of our cells, which provide the necessary information to produce proteins so you appear the way you do, are packed densely within chromosomes. Each of our chromosomes have “end-caps”, called telomeres, that play an important role in stabilising the end of chromosomes, because the ends of chromosomes tend to be a bit vulnerable you see (just like the outer penguins in a colony to the bitter cold). These telomere ends do not contain any active genes themselves but instead contain a variety of highly repeated DNA sequences and special proteins which form a unique structure at the end of a chromosome.

In my somatic cells, or more particularly – most cells other than my germ cells, circulating stem cell populations (haematopoetic cells for example) and my highly proliferative skin cells –  my telomeres have gradually been getting shorter and shorter upon each division. As these cells divide throughout ageing, the ‘end-caps’ erode away causing the cells to malfunction or die. Only in those highly proliferative cell types are telomeres able to not only maintain their length but extend it, courtesy of a unique RNA transcriptase enzyme called telomerase.

Don’t get me wrong, there are perks to being 24 as opposed to 17 regardless of my depleting telomere lengths. Not having to put my hand up to go to the toilet is one of them! But there’s serious stuff to this business. Research leads us to believe that the telomere shortening mechanism sets a limit on the lifespan of a cell, thus heavily contributing to the process of ageing at a cellular level. Also, abnormalities in telomere regulation can lead to cancer – typically down to missed checkpoints on the path to senescence (limited replicative potential) as telomeres become shorter, and an overactivation of the enzyme telomerase.

So can we avoid cancers and keep our telomeres long?

A small pilot study published in The Lancet Onocology earlier this year suggests that making positive changes in our diet, stress management and social management may result in longer telomeres. Sounds optimistic, but worthy of our attention.

And so here’s to a long and happy life and a bright future full of youthful codgers……unless our Telomeres go AWOL.

Elizabeth Blackburn, Carol Greider, and Jack Szostak were awarded the 2009 Nobel Prize in Physiology or Medicine for the discovery of how chromosomes are protected by telomeres and the enzyme telomerase.

I will certainly get around to that Will Smith & Ali post some-time soon!

A General Analysis of An In-Depth Analysis of a Piece of….Erm…

A general analysis of….An In-Depth Analysis of a Piece of Shit: Distribution of Schistosoma mansoni and Hookwork Eggs in Human Stool.

While the game of patience, CV-rewrites, recruitment calls and casual “I’m a solid team-player” line-drops continue – I’ve had a chance to read this bad-boy, along with Animal Farm and a layered spy novel by Ian McEwan (thoroughly enjoyable!).

A Bit of Background

My analysis of one of the most socially networked open access articles (from PLoS) is fairly vague (no false advertisement here), but the paper made me laugh and the title, like it did me, probably had most people in disbelief on first glance. Now, Open Access Journals (OAJs) often come under fire for their quality, by which I mean the scientific rigour of the research within a publication and to what level the submissions are actually screened, known as the peer review process. Indeed, only a few days ago we have witnessed the results of a brilliantly crafted Sting Operation which highlighted the desperately worrying trend of novel OAJs appearing with fictional editors and fabricated institutions along with miserable peer review performances. I mean – truly dismal performances. Well done John Bohannon! Despite this, PLoS faired well in the Sting Operation despite more general concerns from academics over the quality of scientific papers that PLoS typically publish. All the more reason to give this ‘In depth analysis of a piece of …….’ paper a read and see personally whether its’ conclusions have any grounding.

A hilarious title is not completely novel in academic research – take this one about coked up honeybees for example, or any on this list compiled by WIRED magazine. Either way, the concept of this actual study is well within reason and there are some interesting and important implications to come out of the sound findings, such as how Doctors determine the diagnosis of a helminth (parasitic worms) infection and potentially how future studies, which determine the effect of medicines designed to act against these worms (antihelmintic drugs), are designed.

I made a friend in Vietnam who wanted to focus her PhD on intestinal worms. She had this cool hypothesis (that was still a growing idea) about immune system and worm ecology, which made me scratch my head for struggling to understand better, but she never told me just how big of a worldwide issue they pose. The WHO reckons that about 24% of the World’s human population is infected with a soil-transmitted helminth. Now this doesn’t have to mean it’s an issue – but it can be. Especially if you’ve been infected with a relatively big load of them, which can lead to diarrhoea, stomach pains, neural impairments and blood loss. Epidemiological surveys, which typically investigate stool samples for evidence of parasitic worm eggs, show the highest burden lies in the tropics and sub-tropics. However despite knowing this and having drugs available to control helminth infections, public health researchers and clinicians commonly share the concern that helminth infections represent, with immensity, a neglected tropical disease.

Hence the study holds two ultimate aims, 1) to determine whether the eggs of helminths Schistosoma mansoni and Hookworms exhibit any particular spatial distribution in the piece of, erm…ahem….faecal matter… and 2) to understand what might constitute a more accurate diagnosis. Sounds like a perfectly reasonable endeavour for the advancement of medical knowledge for such a high burden disease right? Yes (say yes).

The Study’s Execution

222 individuals from Ivory Coast were invited to participate in this study. For the ‘field collection’, the instructions as presented in the ‘INSTRUCTIONS’ figure below, were given to all participants. Notice that the timing is recorded, which is particularly important as the time delay from the stool production appears to influence diagnostic sensitivity – especially for hookworm.

There is such a thing as the Bristol Stool Chart (BSC; nice one Bristol!) which is a medical aid to distinguish human stools into categories. Here, the authors place specimens into 5 distinct categories:

1) Sausage-shaped (equivalent to type 3 on the BSC)

2) Sausage-shaped but lumpy (type 2 BSC)

3) Sausage-shaped but soft (type 3 BSC)

4) Lumpy (Type 1 BSC)

5) Mushy (Types 5-7 BSC).

…and then (randomly) either underwent whole-stool homogenisation (high frequency mushing, often performed with tiny silicon beads) or underwent direct helminth egg spatial disbtribution examination by drawing lots. Regardless, fecal egg counts (FECs) were taken before and after homogenization.

The authors are very thorough in explaining what they did, giving details of how deep the cut into the faecal samples and the tools they used throughout. They also give a solid account for time as a confounding factor and therefore, randomly allocate the times of stool sample analysis, with each examination time point lasting 2 hours. No qualms here – brilliant stuff. However, what exactly are the four distinctive examination time points that these researchers claimed to have established? Why not mention what they are at least once throughout the paper? Wouldn’t future researchers / diagnostic teams want to know???? Bizarre. Also, the researchers follow WHO guidelines for the Kato-Katz ‘thick smear’ preparation and examination which is common practice, despite the authors indicating shortcomings of this method from the start-off (see below).

Regardless of the processing schemes, an approximate third of all samples were stored in the following manners to determine their effect on egg degradation, with the obvious aim to determine how best to store stool samples in the future for accurate helminth diagnosis:

1) Stored in a box on ice

2) Stored covered with a tissue soaked with tap water

3) Placed in shade outside of the laboratory without any additional preservation effects.


We are never convincingly told exactly why the above storage methods were chosen. I suppose we are meant to assume that these are typical storage procedures during helminth diagnosis. However, because of relative uncertainty of how best to go about storing these stool samples, it makes for interesting commentary in the results.

Incredible Details


This is how to do it – Field Workers: Watch and Learn! This is what I want to see in every set of instructions I see from now on. Something I can relate to. Direct. Clear. Scientifically astute. Makes me laugh.

Sausage and the Kato-Katz
Sausage and the Kato-Katz

So, prior to homogenisation, the researchers chopped the ‘sausage shaped’ faecal samples into four pieces and performed the Kato-Katz procedure on central and surface areas, in preparation for the search of parasitic worm eggs.


The investigators are using the Kato-Katz method to process the stool samples in preparation for the search of eggs. This is still a common procedure however, even the authors state problems of reliability in the detection for parasitic eggs in faecal samples. So if the intent of study is to get to the bottom of helminth distribution in faeces, why not go one step further by utilising other tests to strengthen the validity of results, such as this.

Shit Results

Not really! They’re quite cool actually. Of the 222 participants, 125 were positive for helminth infection, but only 116 had enough stool for analysis (52.3%). There’s an approximate third split for the storage method, followed by categorising the samples into ‘suitability of assessment’ for

– egg location along the length axis (n = 45)

– egg location along a cross-sectional axis (n = 35)

And then, OF THESE, also…..

– homogenisation of stool parts (n = 62)

Note: 53 ‘whole stools’ (i.e. they are not cut up into tidy pieces) undergo direct homogenisation.

By then performing Kato-Katz thick smear preparation and microscopy examination, the investigators identified five different helminth infections under varying prevalences and infection intensities. Amazingly, 5.6% of infected samples showed evidence for TRIPLE worm infection, with 20% showing DOUBLE worm infection. They sure do get about…. It’s important to note that for the rest of the statistical anaylses, the investigators only ever really focus on S. mansoni and Hookworm.

SPATIAL DISTRIBUTION: No clear pattern was observed although in hookworm infected individuals, higher egg counts were significantly noticeable in the front-ermost piece of stool sample than the back-ermost piece.


– For Schistosoma mansoni the egg count results did not differ between the different time points regardless of how they were stored.

– For Hookworm positive samples, it’s a different story. The egg counts do decay over time UNLESS if samples were stored on ice or ‘kept humid’ they say – which I assume means ‘covered with water soaked tissue’???


No reporting of a blinded assessment of outcome. This is a shame really, considering the investigators were on a good roll (concerning laboratory practice) by stating randomised allocation of the 5 different categories of stool samples into either full stool homogenization or ‘piece’ homogenization.

Even though the statistical analyses back up their findings, we’re only dealing with one immediate population from Ivory Coast here. However, it has to start somewhere and this is a step in the right direction towards a deeper, more universal understanding of helminth diagnosis and how to conduct parasitic worm epidemiological surveys.

5 Point Conclusion

– Solid piece of necessary work with the aim of improving diagnostic procedures for this high burden, neglected tropical disease.

– Hookworm eggs exhibit time-dependant decay, unlike Schistosoma mansoni eggs. This can be avoided if samples are kept on ice. However, I would still love to know what the ‘4 distinctive time points’ were that they established – surely this is useful and necessary diagnostic information? Either way, a good general rule of thumb to take away from this would be to store stool samples on ice (if possible, within the sweltering heat of the tropics) and don’t dither about the examination process for accurate diagnosis. Both of the aims of the study I set out at the beginning of this piece, are generally well met.

– Why question the Kato-Katz method and then stick with it without adding more for validity of testing?? A few laboratory procedures could be improved – such as blinded (or double blinded) assessment of outcome, which in this case is faecal egg count.

– The direct results are only relevant to Ivory Coast. However, it paves the way for more in-depth analyses  throughout the rest of the tropics / sub-tropics and does provide useful, novel and researched information for the conduction of future surveillance studies.

And perhaps of most interest…..

– The Title is well chosen. It made you read it. It made this article one of the most widely circulated Open Access papers among social networks. The authors even poked some light-hearted fun at it in their conclusion by quotation marking piece of shit as if to say….”yeah, that’s right – we did that!” Great stuff, and it brought a smile to my face. Schistosomiasis and helminth infections in general really are what we define a ‘neglected tropical disease’ and given that many top-level researchers devote their time to addressing this, I can fully understand their desire to share their findings in the hope it inspires more people to rally against this burden of momentous proportions. Good on ’em.

Thank you for reading my fairly vague analysis on an in-depth analysis of a piece of youknowwhat.



Next time on Philandtropical:

How Will Smith turned from this…… 

Fresh Prince
Fresh Prince

…. to this…..

Will Smith Ali

New Journeys, New Friends and New Discoveries

This is sort of an “all in one” miniramble, but nonetheless, let me update you on an eventful week.

At the research unit I’ve been working at this summer for my MSc project – a couple of groups have formed. Namely, a desert club, of which Jackie, a Princeton PhD student, is clearly in-charge of through her relentless dictating of which new Vietnamese desert to indulge in with her co-workers every week. Also, this past weekend saw the assembly of a new entourage – who would brave the disease vessel that is the ‘night sleeper bus’, at the expense of my health, to a coastal city of promised fresh air. After an 11 hour overnight bus journey, our 11 souls, confined to the rear bunks of the shuttle, stepped foot in Nha Trang.


The sea breeze provided fuel for rejuvenation, and Nha Trang – the home to the discoverer of Yersinia pestis (the agent for causing bubonic plague) in a time long ago – provided pure respite from the incessant buzz of motorbikes in Ho Chi Minh City.

Equipped with nothing but each others company (and a couple of snorkles), we swam, speedboated, lounged, laughed, ate, motorbiked (sorry Mum and Dad – won’t happen again), sunbathed, ate, photographed, mudbathed, played cards, ATE, beach partied, walked the coastline, explored an aquarium, and many other things. And of-course – I cannot forget to mention the sheer diversity and deliciousness of the food we had eaten! Sea-food is in the main here and although we sampled a number of restaurants, the real highlight came when we cooked for ourselves and ate together in the comfort of our own rented Villa. Barbecue grilled beef, shrimp and aubergine were courtesy of mine and Uyen’s efforts (a PhD student at OUCRU)…..some yummy noodle dishes thanks to Mi Phan, the mastermind behind the weekend’s excursions….. and a number of other goodies from everyone else in the group.


It has been an absolute pleasure to be part of Oxford University life in Viet Nam this summer – and it’s all going by at an eye-watering rate. My project has been engaging, the academics I’ve met – encouraging, and the new friends I’ve made – brilliant and inspiring. Each of them have their own incredible story to tell, with distinct passions and visions but a combined goal of making advances in science and medicine – in the broadest sense of these terms. One new friend and PhD student from Princeton, Ruthie (who happens to be a former LSHTMer too), is currently on a plane away from Viet Nam. As a mathematical / statistical modeller with a focus on HIV, I know she’s off to make big news, even if it is in humble steps. She’s the first of our Summer researchers to go – and I can’t help but think how grateful I am for the time spent here so far. Good luck Ruthie – we’ll miss you!Image

And as for New Discoveries — well, let’s just say the ball is rolling in the science park. It looks as if I have discovered three new strains of Bat Coronaviruses in Viet Nam – with all current evidence pointing towards this. Now, this is exciting for a number of reasons…. but on a personal level my thoughts are “bloody hell this is cool!”. Next week I’ll be going to the heart of the forest in which some of these bats belong – It’ll soon be time to embrace the mystery of nature in one of Viet Nam’s most forested areas of land.

For my next few posts (coming soon) – I promise to explain the A to Z of my project, the findings, the implications and the science behind it all.

Stay with me friends….


Get every new post delivered to your Inbox.

Join 1,208 other followers