Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis

Molecular profiling of single cells has advanced our knowledge of the molecular basis of development. However, current approaches mostly rely on dissociating cells from tissues, thereby losing the crucial spatial context of regulatory processes. Here, we apply an image-based single-cell transcriptomics method, sequential fluorescence in situ hybridization (seqFISH), to detect mRNAs for 387 target genes in tissue sections of mouse embryos at the 8-12 somite stage. By integrating spatial context and multiplexed transcriptional measurements with two single-cell transcriptome atlases, we characterize cell types across the embryo and demonstrate that spatially resolved expression of genes not profiled by seqFISH can be imputed. We use this high-resolution spatial map to characterize fundamental steps in the patterning of the midbrain-hindbrain boundary (MHB) and the developing gut tube. We uncover axes of cell differentiation that are not apparent from single-cell RNA-sequencing (scRNA-seq) data, such as early dorsal-ventral separation of esophageal and tracheal progenitor populations in the gut tube. Our method provides an approach for studying cell fate decisions in complex tissues and development.

Screening of plant extracts for antiprotozoal and cytotoxic activities

Methanolic and aqueous extracts derived from 43 plant species, selected either from ethnobotanical or chemotaxonomical data, were screened for their antiprotozoal activity against Leishmania donovani and Trypanosoma brucei brucei. The cytotoxic activity against KB cells was also determined. Eight extracts had IC50 values of less than 10 microg/ml against Leishmania donovani. The most active was Triclisia patens with an IC50 value of 1.5 microg/ml against Leishmania donovani. Annona purpurea and Alstonia macrophylla had IC50 values below 10 microg/ml against Trypanosoma brucei brucei. Annona purpurea was the most cytotoxic against KB cells.

Wasm: a traditional method of healing by cauterisation

Wasm or kaii is a traditional method of healing by cauterisation. This form of healing, known to the Egyptians and pre-Islamic Arabs centuries ago, is still used in the Sultanate of Oman today. In Oman, cauterisation is performed by traditional healers. It is generally thought of as a special healing system which is used for particular diseases and on occasions when modern medicine fails to cure. The instrument for cauterisation is usually a metal rod, pointed at one end or often bent at the top into a crescent shape. Different parts of the body are cauterised for different ailments and diseases.

Genetic variation of macronutrient tolerance in Drosophila melanogaster

Carbohydrates, proteins and lipids are essential nutrients to all animals; however, closely related species, populations, and individuals can display dramatic variation in diet. Here we explore the variation in macronutrient tolerance in Drosophila melanogaster using the Drosophila genetic reference panel, a collection of ~200 strains derived from a single natural population. Our study demonstrates that D. melanogaster, often considered a "dietary generalist", displays marked genetic variation in survival on different diets, notably on high-sugar diet. Our genetic analysis and functional validation identify several regulators of macronutrient tolerance, including CG10960/GLUT8, Pkn and Eip75B. We also demonstrate a role for the JNK pathway in sugar tolerance and de novo lipogenesis. Finally, we report a role for tailless, a conserved orphan nuclear hormone receptor, in regulating sugar metabolism via insulin-like peptide secretion and sugar-responsive CCHamide-2 expression. Our study provides support for the use of nutrigenomics in the development of personalized nutrition.

A terminal alkyne and disulfide functionalized agarose resin specifically enriches azidohomoalanine labeled nascent proteins

Nascent proteome presents dynamic changes in response to a certain stimulus. Thus, monitoring nascent proteome is critical to uncovering the involved biological mechanism. But the low-abundance of nascent proteome against an overwhelming pre-existing proteome limits its identification and quantification. Herein, we present a novel strategy to enrich nascent proteome from whole cell lysate for further analysis by mass spectrometry. We employed a terminal alkyne and disulfide functionalized agarose resin to capture nascent proteome which had been labeled by L-azidohomoalanine. Results from the western blot, silver staining and pulse metabolic labeling suggested that the nascent proteome could be enriched efficiently. Applied to Hela cells, the method identified about 700 nascent proteins with good correlation with previous reports. The above indicates that our strategy can be used to reveal the proteome dynamics of biological processes.

Anti-bacterial activity of essential oils against multidrug-resistant foodborne pathogens isolated from raw milk

The presence of pathogenic bacteria in food is considered as a primary cause of food-borne illness and food quality deterioration worldwide. The present study aimed to determine the effectiveness of five essential oils (EOs) against multidrug-resistant foodborne pathogens. In the current study Gram-negative bacteria (Escherichia, Enterobacter, Citrobacter, Proteus, Pseudomonas, and Klebsiella) and the Gram-positive bacteria Staphylococcus were isolated from raw milk and biochemically characterized. The anti-bacterial effect of different antibiotics and EOs (thyme, oregano, lemongrass, mint, and rosemary) was determined using the standard disc diffusion method. The antibiogram study revealed that Gram-negative bacteria were highly resistant to penicillin while Staphylococcus was resistant to streptomycin, amoxicillin, and lincomycin. Moderate resistance was observed to doxycycline, amikacin, enrofloxacin, kanamycin and cefixime. Isolates were found less resistant to gentamycin, chloramphenicol, and ciprofloxacin. EOs showed a broad range of antimicrobial activity against all bacteria except P. aeruginosa. Of these, thyme was more effective against most of the multi-drug resistant bacterial strains and formed the largest zone of inhibition (26 mm) against Escherichia followed by oregano oil (18 mm) against Staphylococcus (p<0.05). Klebsiella spp and Citrobacter spp showed resistance to mint and lemongrass oil respectively. The EOs such as lemongrass, mint and rosemary were less active against all the bacteria. The findings of the recent study suggest the use of EOs as natural antibacterial agents for food preservation.

Tracing probiotic producing bacterial species from gut of buffalo (Bubalus bubalis), South-East-Asia

Due to extensive application of antibiotics as growth promoters in animal feed, antimicrobial resistance has been increased. To overcome this challenge, rumen microbiologists search for new probiotics to improve the rate of livestock production. The present study was aimed to isolate and evaluate breed-specific lactic acid bacteria (LAB) as potential animal probiotics. The current study was conducted during 10 months from July 2020 to April 2021, in which a total of n=12 strains were isolated from different samples including milk, rumen, and feces of Nilli Ravi Buffaloes. These isolates were evaluated for their antimicrobial potential against common animal pathogens (Bacillus spp., E. coli, Staphylococcus aureus, Salmonella spp., Listeria spp.). All the isolates were identified using 16S rRNA gene sequencing and the phylogenetic analyses inferred that these strains showed close relations to the species of various genera; Enterococcus lactis, Pediococcus pentosaceus, Bacillus subtilis Weissella cibaria, Weissella soli, Bacillus tequilensis, Weissella bombi, Bacillus licheniformis, Lactococcus lactis, Bacillus megaterium, Lactobacillus ruminis, and Lactococcus lactis. NMCC-Ru2 has exhibited the enormous potential of antimicrobial activity, 28 mm, for Salmonella typhimurium;23 mm for Listeria monocytogenes 21 mm for E.coil. Highest resistance was seen in NMCC-Ru2 agasint test antbiotic, like 25.5 mm for Tetracycline. Overall results revesl that the probiotic profile of isolates was achieved using standard criteria, particularly with animal probiotic properties.

Bioinformatics based structural analysis of Cytochrome P450 genes in Candida tropicalis

Cytochrome P450 is a superfamily of enzymes that contain heme as a cofactor that functions as monooxygenases. These proteins are responsible for the oxidation of fatty acids, steroids, and xenobiotics, and the synthesis and breakdown of various hormones. Candida tropicalis has been identified as the leading cause of Candidemia, a bloodstream infection that contributes to the high mortality rate worldwide. So far, no research has reported a detailed study of the cytochrome P450 genes in the genome of Candida tropicalis. Hence, a detailed analysis involving the identification and characterisation of cytochrome P450 genes from the Candida tropicalis genome would provide valuable information about the evolutionary history and functions of the Cytochrome P450 gene family. In this study, 32 Cytochrome P450 genes were identified in Candida tropicalis, which were further grouped into four clades. The results show that most cytochrome P450 families in Candida tropicalis have a close phylogenetic relationship. And diversity might have mainly been a result of gene duplication. Clans and family groupings, alongside their putative functions and subcellular localisation, also showed the possible relationship between the genes’ cellular location and their functions. The results obtained from this study pave the way for a broader and more detailed analysis of the specific functions of each of the Cytochrome P450 genes in Candida tropicalis, as well as possible ways of altering their functions to find a way of curbing/eradicating the negative effect of Candida tropicalis and its contribution to the high rate of mortality worldwide.

Prevalence of oral HPV in the adult sample population in Sydney

BACKGROUND

Oropharyngeal squamous cell carcinomas are increasing in incidence. Risk factors include sexual behaviour, high-risk oral HPV infection and poor oral hygiene. We aimed to provide initial information on the prevalence and assess the feasibility of testing in dental settings.

METHODS

Patients ≥18 years old attending dental clinics in Sydney, Australia, were recruited, oral hygiene assessed, and 10 mL saline oral rinses obtained. Rinses were tested for HBG and HPV by PCR. Participants completed demographic and behavioural questionnaires.

RESULTS

The mean age was 48 years, of whom 131 (43.6%) were male. HPV genotypes, one each of 16, 66, 51, 35 and 58 in five participants, and 18 and 52 in one participant, were detected in six samples (2.0%), all men. Oral sex was reported by 89 (67.9%) male participants. One participant (4.3%) of the 23 with poor OH had at least one HPV genotype detected.

DISCUSSION

With dental patients willing to provide rinse samples and disclose potentially sensitive information, we found the hrHPV prevalence of 2%. Given large proportions of the general population attending dental clinics regularly, dentists may be ideally placed to screen for oropharyngeal carcinoma and contribute to the currently limited knowledge of oral HPV prevalence in Australian adults. © 2022 Australian Dental Association.

Audit of Laparoscopic Cholecystectomy: Impact of Procedure Recording on Clinical Practice

Recorded videos of laparoscopic surgery can be used to audit surgical practice with a view to improve clinical practice and surgical outcomes. The objective was to audit our own practice by reviewing video recordings of laparoscopic cholecystectomies to improve our dissection in Calot's triangle and to prevent gall bladder perforation. We used recorded videos of laparoscopic cholecystectomy. In this study initially one hundred consecutive videos were reviewed for: a) establishment of critical view of safety, b) optimization of critical view of safety by division of cystic artery before cystic duct, c) perforation of gall bladder and d) use of diathermy for cystic artery. This prospective interventional audit was performed in a Civil Hospital, Karachi and Hamdard University Hospital, Karachi, Pakistan from January 2008 to March 2010. Recommendations were made according to published literature to change the practice in these steps of procedures. These recommendations were implemented in practice and the following 100 videos were reviewed for the same criteria to see the impact on clinical practice. In the first group, critical view of safety was established in 91 patients compared with 99 patients in 2nd group (p=0.009), optimization of view was done in 54 and 83 patients respectively (p<001), perforation occurred in 32 and 19 patients respectively (p=0.035) and use of diathermy for cystic artery, which was the routine, was stopped completely in the 2nd group. Audit of recorded videos of laparoscopic cholecystectomy can be used as an effective tool to improve surgical practice for safer and better outcome.