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Chromosome Inversion

  What is a Chromosome Inversion? A chromosome inversion is a type of genetic variation where a segment of a chromosome is flipped and reinserted in the opposite orientation. This rearranges the order of genes within that segment. Key Points About Chromosome Inversions : Structure : Imagine a segment of DNA being cut out, flipped upside down, and placed back into the chromosome. For example: If the original sequence was A-B-C-D , after inversion, it becomes A-D-C-B . Types : Paracentric inversion : The inversion occurs outside the centromere (the central part of the chromosome). Pericentric inversion : The inversion includes the centromere. Polymorphism : Populations can be polymorphic , meaning some individuals have the inverted chromosome arrangement, while others have the "standard" arrangement. These differences can be observed in salivary gland chromosomes, where loops form during pairing (Figure 1 from the study). Recombination Issues : When...
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Temperature during developmental age dictates its resistance/tolerance

  Flies developed at low temperature (13°C) : Most cold resistant Highest abundance of Wolbachia Flies developed at high temperature (31°C) : Most heat tolerant Highest abundance of Acetobacter Source: https://pubmed.ncbi.nlm.nih.gov/29095113/
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15 mins to 2 hrs are kept for drosophila mating

Mating duration used by different research groups: 15-30 mins (https://www.sciencedirect.com/science/article/pii/S0022191012002259#s0025) 30 mins (https://www.nature.com/articles/ncomms12322) 90 minutes (https://academic.oup.com/beheco/article/22/1/184/232467?login=false) 2 hours (https://onlinelibrary.wiley.com/doi/full/10.1111/j.1420-9101.2010.01973.x) ~15 mins for mating latency + copulation time (https://academic.oup.com/jinsectscience/article/11/1/67/2492817?login=false#90814333)
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AMPs regular endosymbionts

"bacteriome highly expresses the coleoptericin A (colA) antimicrobial peptide (AMP), which was shown to prevent endosymbiont escape from the bacteriocytes." "This work provides a striking example of how a conserved immune pathway, initially described as essential in pathogen clearance, also functions in the control of mutualistic associations."  https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0397-9
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Nucleoproteins

Nucleoproteins are complex structures made up of proteins and nucleic acids, such as DNA or RNA.  Histone, protamines, ribosomes,  Spermatids are the cells which are produced from the testes as a result of spermatogenesis .  The spermatids develop into spermatozoa or sperms by the process of spermiogenesis .
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Lactobacillus plantarum and Acetobacter pomorum increases frut fly developmental pace

D. melanogaster gut microbiome, particularly Lactobacillus plantarum and Acetobacter pomorum, increases the pace of host development (Shin et al., 2011; Storelli et al., 2011).
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Lab flies have lower microbiome diverity than wild flies

Reduced Richness and Diversity : Lab-raised flies exhibit significantly lower richness and diversity of bacteria compared to wild-caught flies. Specific Strains : Laboratory flies have bacterial strains closely related to those from previous studies, with five strains being >99% identical to previously identified cultured isolates of D. melanogaster. Enterococcus, which was previously found to comprise nearly 50% of the lab bacterial microbiome, is virtually absent in current lab samples. https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002272#pgen-1002272-g002
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Immunostaining, Cytochemical staining, FISH

 Immunostaining (for Histones), Cytochemical staining (for Protamines), FISH (for lncRNA)
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PCR 20-50ng/uL template DNA

 20-50 ng/uL is the standard concentration for PCR
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spermatogenesis -> spermiogenesis

primary spermatocytes (spermatogenesis) -> meiosis -> elongating spermatids (spermiogenesis). https://www.science.org/doi/10.1126/science.adk9469
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Wolbachia is plural

 Wolbachia is plural, so use "take", not "takes"
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Wolbachia and Lactobacillus positively correlated, but negatively with Acetobacteria

Wolbachia  increased in the relative abundance of gnotobiotic fly lines with  Lb  r But no such observation with gnotobiotic with  At  replicates. source:  https://www.pnas.org/doi/10.1073/pnas.1907787116
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Symbiosis vs Symbioses

 Symbiosis = singular  Symbioses = plural
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Acetobacter tropicalis increases development rate compared to Lactobacillus brevis treatment

  Addition of the AAB species  Acetobacter tropicalis  to the food resource ( At  treatment), 2) addition of the LAB species  Lactobacillus brevis  to the food resource ( Lb  treatment), and 3) no microbial inoculation ( No-Ad  treatment).  At  and  Lb  strains were selected as representative AAB and LAB based on their different influences on  D. melanogaster  life history traits, with  At- inoculated flies displaying faster development times and shorter periods of starvation resistance than Lb-inoculated flies https://www.pnas.org/doi/10.1073/pnas.1907787116#sec-1
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Removal of the gut bacteria represses oogenesis, expedites maternal-to-zygotic-transition in the offspring

- Removal of gut bacteria (specially Acetobacter) inhibits oogenesis, accelerates maternal-to-zygotic transition in offspring, and reveals hidden phenotypic variations in mutants. - The Drosophila Aldh gene appears to mediate repressed oogenesis in flies lacking Acetobacter. https://www.nature.com/articles/ncomms11280
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Acetobacter pomorum and Acetobacter tropicalis provide thiamine (vitamin B1) to the Drosophila larva

Acetobacter pomorum and Acetobacter tropicalis strains can provide thiamine (vitamin B1) to the Drosophila larva https://journals.asm.org/doi/10.1128/mbio.00155-18
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Gut microbiome (not Wolbachia) defines mate choice in flies

" Overall, we did not find an effect of   Wolbachia   on female attractiveness or male mate choice, but we observed variable effects of naturally occurring microbiota on female attractiveness, depending on host genotype, where altering the microbiota decreased attractiveness in some lines, but increased it in others"   https://onlinelibrary.wiley.com/doi/10.1111/jeb.12788
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Microbiome functional redundancy reduces FMT efficiency

" Finally, we analyze data from two published studies of fecal microbiota transplantation (FMT), finding that high functional redundancy of the recipient’s pre-FMT microbiota raises barriers to donor microbiota engraftment." Source: https://www.nature.com/articles/s41467-020-19940-1
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Words: Hypothesis, Expect, Explore

Explore: do not use this word Hypothesis: A scientific explanation but not proven yet Expect:  Density: Relative term, for relative qPCR Titre: Exact amount, for absolute qPCR
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Gram -ve Acetobacter & Gram +ve Lactobacillus

Acetobacter are Gram -ve Lactobacillus are Gram +ve
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Forward & reverse genetics

Forward genetics: Start the research with an organism (eg. diseased or natural mutant) and then work backward to discover the genetic basis for it.  Reverse genetics, where specific genes are modified or manipulated to study their effects on a phenotype.
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Density is relative; titer is absolute

Density = realtive Titer = absolute calculation
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Propionic acid promotes larval survival

Propionic acid promotes larval survival (in low-nutrient food i.e. low yeast). Propionic acid is detected by Laravel chemoreceptors Or30a and Or94b. This propionic acid activity works on Dmel, but not on D. suzukii. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5660182/#:~:text=Propionic%20acid%20in%20the%20culture,medium%20(6.5%25%20yeast).
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CFY/fly is 10^2 to 10^8

 10^2 to 10^8 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6069112/
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Lactobacillus & Acetobacter symbiosis

  Lactobacillus produces lactate, which is used by Acetobacter to produce amino acids, which is used by Lactobacillus. https://www.nature.com/articles/s41467-020-18049-9
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Germ-free Dmel requires 3 generations since the treatment influences the first generation

1st Gen mean life is ~55 days, 2nd Gen has ~68 days, and 3rd Gen has about 72 days. CV has 60 days. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6660043/ 
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Wolbachia & microbiome load

Both a ntibiotics and  Wolbachia  significantly reduced the biodiversity of the gut microbiota without changing the total microbial load.  https://www.sciencedirect.com/science/article/pii/S0022201116302130#s0005
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Wolbachia strain wAu

Wolbachia  strain  w Au spread through Australian populations of  Drosophila simulans  despite not causing CI, [probbaly due to its antiviral effects] https://www.nature.com/articles/s42003-021-02838-z
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Wolbachia  density is not correlated with  cytoplasmic incompatibility  intensity. Wolbachia  might induce the defect in male host fertility by immunity-related pathways and thus cause an oxidative damage and cell death in male testes.
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D. sechellia & Morinda citrifolia

D. sechellia breeds poorly on laboratory food  in the absence of the fruit of its normal host plant, Morinda citrifolia ( a medicinal plant )
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Nomenclature

In bacteria, genes are lowercase italics (e.g. cifA ), while proteins are capitalized without italics (e.g., CifA)
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Dmel Dsim - Hybrid rescue

Shfr - Location of Shfr , a new gene that rescues hybrid female viability in crosses between Drosophila simulans females and D. melanogaster males
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Heterochromatin - age, sex, Y chromosome

Typically in centromeres and telomerase. Highly repetitive sequence. Have much fewer genes than euchromatin. Can silence gene expression of euchromatin. Heterochromatin increase with age and are more in males. source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7274899/
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Lactobacillus Plantarum fights off Serratia marcescens and Pseudomonas aeruginosa

Serratia marcescens and Pseudomonas aeruginosa infection was more in axenic flies. Infections were reduced when treated with Lactobacillus Plantarum. quotidian replenishment - need to replenish microbial daily If Lactobacillus is important, then why is it not maintained: Dmel gets rids its gut of most microbes to minimize the risk of acquiring and maintaining potential pathogens. The microbiome may compete with its Drosophila host for nutrients in the gut. Our evidence indicates that Drosophila seeds its food with commensal organisms by depositing fecal matter on its food source on which the bacteria grow. Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892787/#h2title
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Acetobacter (Alphaproteobacteria) & Lactobacillus (Firmicutes) - Dominant in Dmel

 Dmel microbiome is dominated by  Acetic acid bacteria (AABs), mainly genus Acetobacter (Alphaproteobacteria),  Lactic acid bacteria (LABs), mainly the genus Lactobacillus (Firmicutes) (20). And also a strong representation of other taxa, including Gammaproteobacteria (e.g., Stenotrophomonas spp.) and lactobacilli (e.g., Enterococcus spp.) (22, 23). Acetobacter fabarum, Acetobacter pomorum, Acetobacter tropicalis, Lactobacillus brevis, and Lactobacillus plantarum.
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Lhr K18, Hmr U79 - reverse evolution

 Mutations in Lhr K18 and Hmr U79 genes enable the survival of hybrids that are otherwise lethal in wild types.
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23% of genes are DEGs between Drosophila individuals

23% of genes are DEGs between Drosophila individuals due to differences in body size, weight, etc.  Hence, a pool of 5 or more replicates would yield better result. source: https://www.nature.com/articles/s41598-021-90857-5
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Different hosts respond differently to the same Wolbachia strain

Different hosts respond differently to the same Wolbachia strain. Notes: There are more than 100k Wolbachia strains Benefits to host also vary - Vitamin C to Cimex lectularius bedbugs; but virus protection to Dmel. source: https://www.nature.com/articles/s41598-021-90857-5
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44% reduction in no. of eggs when male is axenic

Axenic males produce only 66% of eggs when mated with CV females compared to CV males crossed with CV females. Also, axenic males mated with axenic females produce only 62% compared to CV couples.  Source: https://www.nature.com/articles/s41598-020-75156-9#:~:text=We%20further%20observed%20that%20the,switch%20of%20the%20female's%20transcriptome.
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crebA mediated memory increase in Drosophila by Wolbachia

In Drosophila, Wolbachia enhances learning and memory capacity (LMC) Increase in LMC by Wolbachia by decrease (miRNA) dme-miR-92b and increase crebA source: https://www.sciencedirect.com/science/article/pii/S0965174818302947
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PGM age influence CI

Image
  source: https://journals.asm.org/doi/10.1128/mBio.01879-19
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