Pouya Faridi

A repository of assays to quantify 10,000 human proteins by SWATH-MS

Mass spectrometry is the method of choice for deep and reliable exploration of the (human) proteome. Targeted mass spectrometry reliably detects and quantifies pre-determined sets of proteins in a complex biological matrix and is used in studies that rely on the quantitatively accurate and reproducible measurement of proteins across multiple samples. It requires the one-time, a priori generation of a specific measurement assay for each targeted protein. SWATH-MS is a mass spectrometric method that combines data-independent acquisition (DIA) and targeted data analysis and vastly extends the throughput of proteins that can be targeted in a sample compared to selected reaction monitoring (SRM). Here we present a compendium of highly specific assays covering more than 10,000 human proteins and enabling their targeted analysis in SWATH-MS datasets acquired from research or clinical specimens. This resource supports the confident detection and quantification of 50.9% of all human proteins annotated by UniProtKB/Swiss-Prot and is therefore expected to find wide application in basic and clinical research. Data are available via ProteomeXchange (PXD000953-954) and SWATHAtlas (SAL00016-35).

Multilayered genetic and omics dissection of mitochondrial activity in a mouse reference population

The manner by which genotype and environment affect complex phenotypes is one of the fundamental questions in biology. In this study, we quantified the transcriptome--a subset of the metabolome--and, using targeted proteomics, quantified a subset of the liver proteome from 40 strains of the BXD mouse genetic reference population on two diverse diets. We discovered dozens of transcript, protein, and metabolite QTLs, several of which linked to metabolic phenotypes. Most prominently, Dhtkd1 was identified as a primary regulator of 2-aminoadipate, explaining variance in fasted glucose and diabetes status in both mice and humans. These integrated molecular profiles also allowed further characterization of complex pathways, particularly the mitochondrial unfolded protein response (UPR(mt)). UPR(mt) shows strikingly variant responses at the transcript and protein level that are remarkably conserved among C. elegans, mice, and humans. Overall, these examples demonstrate the value of an integrated multilayered omics approach to characterize complex metabolic phenotypes.

Ferula gummosa Fruits: An Aromatic Antimicrobial Agent

Ferula gummosa Boiss. (Apiaceae) fruit volatile oil was analyzed by GC/MS. Seventy-three components (96.89%) were identified, and the major components were β-pinene (43.78%), α-pinene (27.27%), and myrcene (3.37%). The antimicrobial activity of the oil was tested on three strains of Gram positive bacteria (Staphylococcus aureus, S. epidermis, and Bacillus subtilis), three strains of Gram negative bacteria (Escherichia coli, Salmonella typhi, and Pseudomonas aeruginosa), and two strains of fungi (Candida albicans and C. kefyr). The essential oil remarkably inhibited the growth of the tested microorganisms. The results indicate that the fruits have potential for use as an aromatic antimicrobial agent.

Potential effect and mechanism of action of topical chamomile (Matricaria chammomila L.) oil on migraine headache: A medical hypothesis

Migraine is a chronic recurring headache for which no complete treatment has been found yet. Therefore, finding new treatment approaches and medicines is important. In this review, we consider the probable mechanism of action of a traditional and ethnic formulary of chamomile extract in sesame oil as a new topical medication for migraine pain relief. Chamomile oil is prepared in Traditional Persian Medicine by boiling aqueous extract of chamomile in sesame oil. To optimize the procedure, we can use a Clevenger-type apparatus to extract the essential oil and add it to the end product. The preparation includes both essential oils (chamazulene and bisabolol oxide) and polyphenols (a flavonoid such as apigenin and its derivatives). It probably possesses pain relief effects for migraines because of the following properties: (1) chamazulene and apigenin, which inhibit iNOS expression in activated macrophages and can lead to the prohibition of NO release and synthesis; (2) chamomile flavonoids, which have a strong inhibitory effect on endogenous prostaglandin E2 (PGE2) levels in RAW 264.7 macrophages and can play the role of selective COX-2 inhibitor; (3) chamomile polyphenols, which possess anti-inflammatory effects due to the inhibition of pro-inflammatory biomarkers in THP1 macrophages and which can reduce inflammation in neurovascular units (NVU) at the site of migraine pain; (4) chamomile, which has neuroprotective effects because of reduced NO levels; (5) sesamine in sesame oil, which possesses an anti-inflammatory effect. These effects are supported by main pathophysiological theories of migraine such as neural and sensitization theories. Chamomile oil is a traditional formulation still used in Iran as an ethno-medicine. Because of the mentioned mechanisms of action, it can be hypothesized that chamomile oil is a novel medicine for the relief of migraine pain.

Ibn Sina's treaties on pulsology

[5] Sackett DL. Superiority, equivalence and noninferiority trials. In: Haynes RB, Sackett DL, Guyatt GH, Tugwell P, editors. The Principles behind the tactics of performing therapeutics trials. Clinical epidemiology: how to do clinical practice research. 3rd edition. Philadelphia, PA: Lippincott Williams & Wilkins; 2006. p. 193–6. [6] Leung WC. Balancing statistical and clinical significance in evaluating treatment effects. Postgrad Med J 2001;77:201–4. [7] Coats AJ. Ethical authorship and publishing. Int J Cardiol 2009;131:149–50.

Ethnopharmacological knowledge of Shiraz and Fasa in Fars region of Iran for diabetes mellitus.

ETHNOPHARMACOLOGICAL RELEVANCE This study provides ethnopharmacological knowledge of traditional herbal healers from Shiraz and Fasa in Fars region (Iran) for treatment of diabetes mellitus. MATERIALS AND METHODS Field surveys were carried out during September 2013-February 2014 in Shiraz and Fasa. The data were collected through structured questionnaire in Persian. All plant species recorded for the treatment of diabetes mellitus were sampled. Samples were identified by a botanist and obtained a voucher specimens number and deposited in the Shiraz School of Pharmacy Herbarium. The information such as scientific name, family, local name, medicinal use(s), parts used and preparation method were provided. Literature review on available data about antidiabetic effect of the addressed plant species was done to highlight gaps in current knowledge and propose the next steps. RESULTS In total, 50 informants were interviewed. Totally 39 plant species were recommended by herbal healers, of which 28 are native to Iran. The most recommended plants for diabetes were Trigonella foenum-graecam (28 Attars), Securigera securidaca (22 Attars), Vaccinium arctostaphylos (18 Attars). The most abundant families were Fabaceae, Asteraceae, Lamiaceae and Apiaceae. Plant parts used were mainly seeds, flowers, leaves and fruits. The most usual preparation methods were decoction, powder and distillation. Around 44% of all reported plants for diabetes are also in use for obesity management CONCLUSIONS This study provided ethnopharmacological knowledge from Fars region in Iran for a specific disease and we have introduced important plant species which are recommended by local herbal healers for diabetes mellitus. For 23% of reported plants, clinical studies approved antidiabetic properties and for 61%, animal studies approved antidiabetic activity.

Analysis of Mount Atlas mastic smoke: A potential food preservative

Pistacia terebinthus L. smoke has been used traditionally in Iran as disinfectant and air purifier. Smoke was collected by a simple method, and the chemical constituents and antimicrobial activity of the smoke were analyzed. The chemical constituents of the smoke were alpha-pinene (65.1%), limonene (11.5%) and allo-ocimene (2.8%). The non polar phase of smoke noticeably inhibited the growth of different microorganisms. MIC test shows that non polar fraction of smoke can inhibit the growth of some bacteria. The results indicating that the properties of the smoke as a flavoring and preservative agent could be a potential subject for future studies.

Collection and storage of medicinal plants in The Canon of Medicine

Abstract The Canon of Medicine was the reference of medical sciences for many years in western and eastern countries. The second book of this medical encyclopedia is on pharmacology which has a chapter on collection and storage of plant materials. In this work a comparison was done on the Canon of Medicine and modern rules in this area. It seems that Ibn Sina had developed ideas on the condition of plant collection and storage which guaranteed the quality of primary materials. Overall, his rules and modern ones are alike in the most parts.

Sphygmology of Ibn Sina, a message for future

Sphygmology is a 2000-year-old method that is still used in some traditional medicine systems, mainly Iranian, Chinese and Ayurveda. Ibn Sina is one of the most popular physicians in the history of Sphygmology, who had made great contributions to this method, but few meticulous studies have been made on his concepts. In this article, his standpoints on Pulsology are studied. Ibn Sina has mentioned 10 parameters for pulse palpation, and 13 compound pulses, as well. Besides, some pulse patterns applicable for differentiating similar diseases have been introduced. Nowadays some concepts on pulse patterns, such as pulse change in sleep and pregnancy have been studied; but unfortunately many of the ideas on Pulsology have not yet been examined. Sphygmology, as an accessible and inexpensive means, having a substantial diagnosis yield, has been accepted by the people since its rise, and its development over centuries ago. Although some new instruments have been innovated, which can measure different parameters of pulse, yet sphygmology can be one of the most commonly usable diagnostic methods in future, not only applicable by cardiologists but also by all the physicians.

A review on the management of migraine in the Avicenna's Canon of Medicine.

Migraine is a common type of headache which has a deep history dating back thousands of years. Avicenna (980–1032), a Persian scholar, made a great contribution to neurology including headache and migraine. The aim of this study is to consider Avicenna’s description about migraine (Shaghighe in Persian language) including definition, etiology and intervention. Also, his definition and treatment approaches were considered based on current concepts and findings. Although Avicenna believed in humoral theory and divided migraine into two categories, hot and cold, and suggested special treatments for them as well as general considerations, most of his definitions and explained pathologies are supported by current concepts of medicine. He believed that the migraine can result from bone of skull and also intra-parenchymal; or from skull underneath membrane (dura-mater); or reaching substances from the painful side or from outer vein and arteries (extra cranial); or from brain and meninges (pia-mater). Furthermore, current findings show most medicinal plants mentioned by Avicenna for the treatment of migraine can have potentially significant effects such as remedies which stop central and peripheral sensitization [anti-neuroinflammatory agents, decreasing nitric oxide level, cyclooxygenase (COX)-2 inhibitors], as well as serotonergics, neuroprotective agents and analgesics.