1,059 Matching Annotations
  1. Nov 2017
    1. It has been found a conserved relationship among dsx/tra/tra-2 across dipterans so that this axis represents the ancestral state of the sex determination cascade,

      The conserved relationship among all dipterans suggests that this form of relationship evolved to be long ago. Part A of Figure 1 explains the cascade of how sex is determined among drosophila. This serves an example of a mechanism that works efficiently in determining sex. Through evolution and natural selection, the mechanisms that would perform most efficiently would be passed on (as can be expressed in Part A of Figure 1), while the other inefficient mechanisms would be removed from the population. -Elder

  2. Oct 2017
    1. To answer the second part of the question, we studied the specific protein positions targeted by selection in SXL. Significant evidence of adaptive selection was found at 15 codons (p ≤ 0.05) predominantly located at N- and C-terminal regions (Fig. 4a). These results are consistent with functional studies showing that the sex-specific properties of extant Drosophila SXL depend on its global structure, and that modifications at N- and C-terminal domains of SXL in the drosophilid lineage represented coevolutionary changes determining the appropriate folding of SXL to carry out its sex-specific function (Ruiz et al. 2013)

      The SXL protein controls sex determination and dosage compensation in the Drosophilla. This protein is said to depend on its global structure rather than on a specific domain. In this way, it implies, that these modifications represent co-evolutionary changes that determine the folding of SXL proteins to carry out its sex-determination and dosage compensation. - Jake Barbee

    2. Two major conclusions can be drawn from these results: first, the diversification of Sxl in dipterans seems to have been driven by episodes of adaptive selection involving amino acid replacements at specific codons in terminal protein domains. Second, the recruitment of Sxl into sex-specific roles required bursts of adaptive selection during the evolution of dipterans and most importantly in the common ancestor of drosophilids, probably taking advantage of its preexisting role as a general splicing factor (Ruiz et al. 2003; Serna et al. 2004).

      Bursts of natural selection is what lead to evolution of Sxl which replaced amino acids in the final proteins in the complex. This was required for the progression of the dipterans because this change early on is what caused the consistency of Sxl today. -Elder

    3. SXL (the top component of the Drosophila sex determination cascade) constitutes the slowest evolving sex determining protein in drosophilids (Fig. 2b) as well as a slow evolving protein in other insect species (see Table 2 for details). However, there is still the possibility that such a high degree of conservation is a result of the lack of sex-specific functions in insects other than Drosophila (Cline et al. 2010; Sánchez 2008). Two approaches were followed in order to explore this scenario: first, the analysis of SXL in non-drosophilid insects revealed an evolutionary rate of 0.95 × 10−3 substitutions/site per MY (Table 2), constituting a much lower rate than the one estimated for Drosophila (2.80 × 10−3 substitutions/site per MY)

      This slow rate suggests the success of this SXL gene, since the evolving rate is slow, the need for change is limited and very slim. The continual success of this gene is selected by nature to continue with very little changes made to the sequencing. -Elder

    4. Additional tests for the presence of local molecular clocks were carried out in the case of SXL (insects) by using the program HyPhy

      HyPhy stands for hypothesis testing using phylogenies. Hyphy is a software package that serves many purposes as well as multiple audiences. It is used primarily for the analysis of genetic sequences using techniques in phylogenetics (studies of evolutionary history). Though it is also commonly used in molecular evolution, and to study rates and patterns of sequence evolution. It can also be compiled as a shared library and called upon by other programming environments, thus making HyPhy great for group work. To learn more, click here https://academic.oup.com/bioinformatics/article/21/5/676/220389/HyPhy-hypothesis-testing-using-phylogenies -Jake Barbee

    5. To fill this gap, the present work investigates the levels of variation displayed by five sex-determining proteins across 59 insect species, finding high rates of evolution at basal components of the cascade.

      The author’s goal for this article is to find high rates of evolution at the basal components of the cascade. The author does this by examining the displayed variations of five sex-determining proteins in a sample of fifty-nine insect species. To see a simple example of what the author is trying to determine click here. https://www.youtube.com/watch?v=7usaaiggDgw -Jake Barbee

    6. The study of the epistatic relationships between Sxl and the other genes involved in sex determination [i.e., transformer (tra), transformer-2 (tra-2), fruitless (fru), and doublesex (dsx)] has revealed a hierarchical interaction among them during development (Baker and Ridge 1980), with the product of one gene controlling the sex-specific splicing of the primary transcript of the gene immediately downstream [reviewed in (Sánchez 2008)] (Fig. 1a).

      Splicing refers to the process of joining or inserting genes or fragments of genes. This excerpt refers to the phenotypic and genotypic relationship between Sxl and other sex determinants that contain a hierarchy and produce a "suppressor" that controls the transcription of the gene downstream. Where downstream refers to the final level of the cascade. -Elder

    7. epistatic

      The phenomenon in which one gene is affected by the presence of other genes. The phenotypic effect of one gene is being masked by another gene. -Elder

    8. the program committing the embryo to either the male or the female pathway is under the control of the gene Sex lethal (Sxl)

      The "Sex lethal" gene is the sex determining gene of the sexually reproducing Drosophilia Melanogaster, During embryonic development, an XX embryo would have the Sxl gene expressed or active, while the XY embryo would have the Sxl gene suppressed or dormant to ensure the development of a male Drosophilia. -Elder

    9. Fig 1. Schematic representation of the hierarchical epistatic interactions constituting the sex determination cascade in Drosophila [adapted from (Sánchez 2008)] evolving from bottomto top (DSX doublesex, FRU fruitless, TRA-2 transformer-2, TRA transformer, SXL Sex-lethal). a In the absence of X/A signal in males, truncated SXL and TRA proteins will be produced leading to the synthesis of male-specific FRU and DSX that will eventually result in maleness. The major components of the cascade analyzed in the present work are indicated in gray background. b Under the bottom-up hypothesis, genes more recently recruited into sex determining pathways are expected to cause divergence toward the top of the cascade. c According to the developmental constraint hypothesis, genes involved in early aspects of development would be more constrained due to the large deleterious pleiotropic effects of mutations

      The author is using the chart to display sex-determining proteins of the Drosophila species. He does this to better describe how proteins play an important role in sex determination. The author also displays how Drosophila evolved bottom-up to create a higher divergence towards the top of the cascade. This would thus explain why genes evolved earlier would be more restricted than those evolved later down the cascade. To better explain sex-determination please watch this video. https://www.youtube.com/watch?v=NQ4Mh_CU15E -Jake Barbee

    10. protein divergence

      The process by which genes after duplication shift in function. -Eri-Ray

    11. homologous

      A homologous gene is a gene inherited from a common ancestor. Homo- is a prefix for "same", implying that the genes are similar in sequence and may have similar functions. -Eri-Ray

    12. regulatory cascade

      A regulatory cascade is a system of signal-transducer proteins that relay signals from receptors to the proteins that carry out cellular responses. -Eri-Ray

    13. pleiotropic

      pleiotropy can be defined as the production by a single gene of two or more unrelated effects. -Eri-Ray

    14. dipterans

      Dipterans are insects of the order diptera. They are considered "true" flies, as they can undergo rapid and radical metamorphosis. Flies are commonly used for experiments due to their availability and ease to breed. -Eri-Ray

    15. Most part of the molecular evolutionary analyses was carried out using the program MEGA version 6 (Tamura et al. 2013)

      MEGA which stands for: Molecular Evolutionary Genetics Analysis is a software in which the user can create DNA sequence alignments, look at phylogenetic histories, and conduct molecular evolutionary analysis (tamura et al. 2013). The MEGA can estimate the divergences of the phylogenetic tree as well as building a phylogenetic tree with time as a scale. -Elder Learn more at: MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

    16. adaptive selection

      The mechanism of choosing the most beneficial trait for survival in an environment, the other traits that are not needed are kept in small reserves, but not wiped out. The rest die off due to having less relative fitness. -Elder

    17. diversifying selection

      Changes in the population's genome based on the traits that are being favored by the environment. -Elder

    18. evolutionary constraints

      restraints on adaptive evolution, a.k.a. restraints on natural selection. -Elder

    19. genetic switches

      The mechanism in which genes are regulated to be expressed or not expressed. (to be "turned on" or "turned off") -Elder

    20. trans-regulatory elements

      Specific genes that regulate distant genes, also known as DNA sequences that code for transcription factors. - Elder

    21. Sxl in Diptera

      From previous articles, the testing IN Drosophila melanogaster, the gene Sex-lethal (Sxl) controls the processes of sex determination, sexual behavior, and dosage compensation (the products of the X-linked genes are present in equal amounts in males and females. Sxl produces two temporally distinct sets of transcripts corresponding to the function of the female-specific early and non-sex-specific late promoters, respectively -Melanie Learn more: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448812/

    22. splicing regulation

      join or insert (a gene or gene fragment). -Melanie

    23. basal

      forming or belonging to a bottom layer or base -Melanie

    24. TRA

      represents the fastest evolving protein in the sex determination cascade -Melanie

    25. epistatic

      the interaction of genes that are not alleles, in particular the suppression of the effect of one such gene by another -Melanie

    26. phylogeny

      is the branch of biology that deals with phylogenesis; the evolutionary development and diversification of a species or group of organisms, or of a particular feature of an organism -Melanie

    1. Receivers were attached with shackles and heavy duty plastic cable-ties to a length of polyurethane braided rope

      Polyester rope is used because it has extreme resistance to abrasion and sunlight. -Sindy

    2. elliptical transect

      The orbital path along which the species is studied. -Sindy

    3. Externally mounted transmitters were fitted to these individuals instead of performing intracoelomic insertion because of inclement weather and rough sea conditions.

      The presence of reef sharks with external transmitters as well as internal transmitters further validates the results obtained. Despite the turbulence of weather conditions, all sharks were accounted for, providing an accurately measured population pool. -Sindy

    4. precludes

      To prevent from occuring -Sindy

    5. cayes

      Also known as a key, a caye is a low level island topical to a reef. -Sindy

    6. geographically discrete nursery areas

      A nursery area is a location in which a large subset of the species is populated. For example, a swamp is a nursery area for many types of mosquitoes. The idea that reef sharks do not have a "geographically discrete nursery area" simply means that one can spot a population of reef sharks rather easily in this habitat. -Sindy

    7. endemic

      Native or confined to a certain area -Sindy

    8. Caribbean reef shark populations can benefit from no-take marine reserves and increase in abundance in these areas

      The author expects the well being and population of reef sharks living in no-take marine reserves to be beneficial and higher respectively than those living elsewhere. No-take marine reserves are protected areas of a marine habitat that prohibit human activity. This makes sense because the disastrous effects that human actions have on marine environments is common knowledge. Reef sharks would thrive in a location where adequate amounts of supply are met due to natural resources and the fact that a no-take reserve are essentially a no-fishing area. This prevents sharks from being hunted for their fins, meat etc. In a fiji no-take marine reserve, there was observed to be four times as many sharks than in an areas where fishing was allowed.



    9. Acoustic monitoring of several individuals revealed year round residency to small home ranges within the reserve, indicating that this protected area reduced the exposure of these individuals to fisheries

      Acoustic monitoring is the use of hydrophones (much like a microphone or recorder) to detect the presence of marine animals via sound waves produced by the noises they make. In this case, it was noted that several marine animals continued to inhabit marine reserves for year round periods thus reducing their exposure to fisheries and their potential dangers. -Sindy

    10. ) Lognormal

      A distribution of normally displayed logarithms. A logarithm is a mathematical formulation. -Mohammad

    11. coelom.

      A body cavity that is lined on one side by the body wall and the other by a main body system such as the intestinal tract. -Mohammad

    12. monofilament gillnets

      A type of fishing gear that is harmful to species that are supposed to be protected. -Mohammad

    13. Akaike's Information Criterion (AIC)

      Determines the Quality of a set of data. -Alejandro

    14. sporadically

      Irregularly occurring -Mohammad

    15. gill-nets

      A net that traps fish in it by their gills. -Emily

    16. relative abundance

      How common or rare a species is compared to other species in its community. -Emily

    17. catch-per-unit effort

      Index of fish abundance. -Emily

    18. respite

      A period of rest, usually during or after an action requiring maximal effort. -Alejandro

    19. telemetry

      The recordings of information gathered by a particular machine. -Alejandro

    20. ontogenetic

      Having to do with the development from initial location to final location. -Alejandro

    21. fauna

      Inhabitants. in this case animals, belonging to a specific area. -Alejandro

    22. Linear regression

      Linear Regression is a statistical way to determine the relationship between the independent and dependent variable displayed as a straight line on a graph to indicate a set of real data values. -Sindy

    23. spurious

      Not being what it claims or appears to be. -Sindy

    24. inclement

      Undesirable -Sindy

    25. congeners

      Organisms that share the same genus -Sindy

    26. no-take marine reserves

      Reserves that restrict human activity. -Sindy

  3. Sep 2017
    1. Calliphoridae

      Calliphoridae is the scientific name for "blow flies". -Jake Barbee

    2. truncated

      To truncate something means to cut off a piece of in order to shorten it. In this case the SXL and TRA proteins have been cut short. - Jake Barbee

    3. Drosophila melanogaster

      Drosophila melanogaster is the scientific name for the common fruit fly. -Jake Barbee

    4. cascade

      Cascade is a series of events that occur subsequently to one another. -Jake Barbee

    5. deleterious pleiotropic effects

      You can break this down into two main parts: deleterious, and pleiotropic. "Deleterious" meaning something that is harmful or causes damage, while "pleiotropic" means one gene is adversely affecting other phenotypic traits . In this way we can conclude that a "deleterious pleiotropic effect" is when one gene causes harm or damage to phenotypic traits. -Jake Barbee