text:
centrosomin's beautiful sister: Biological Overview | Evolutionary Homologs | Regulation | Developmental Biology | Effects of Mutation | References
Gene name - centrosomin's beautiful sister
Cytological map position- 50A9-50A9
Function - signaling
Keywords - cell cycle, centrosome cycle, centrosome maturation, Golgi complex, Golgi inheritance
Symbol - cbs
Genetic map position - 2R
Classification - GRIP domain containing golgin
cbs orthologs: Biolitmine
The eukaryotic Golgi complex is an essential organelle involved in many cellular processes, including lipid biosynthesis, protein modification and intracellular membrane trafficking. A major question and area of debate in cell biology is how the Golgi complex is inherited by daughter cells during mitosis. This has led to two different mechanistic models. One model proposes that the Golgi is a derivative of the endoplasmic reticulum (ER) and arises de novo from the ER during late telophase, whereas the other model proposes the Golgi complex is a unique organelle that arises by a template-based mechanism, requiring existing Golgi subunits for reassembly after mitosis (Eisman, 2006 and references therein).
This study examines the localization and function of a Golgi protein encoded by centrosomin's beautiful sister (cbs) during cleavage in Drosophila. Cbs contains a GRIP domain that is 57% identical to vertebrate Golgin-97. Cbs undergoes a dramatic relocalization during mitosis from the cytoplasm to an association with chromosomes from late prometaphase to early telophase, by a transport mechanism that requires the GRIP domain and Arl1, the product of the Arf72A locus. Additionally, Cbs remains independent of the endoplasmic reticulum throughout cleavage. The use of RNAi, Arf72A mutant analysis and ectopic expression of the GRIP domain, shows that cycling of Cbs during mitosis is required for the centrosome cycle. The normal cycling of Cbs is important for normal centrosome maturation, replication and spindle attachment during mitosis, and the linkage of this process to the normal nuclear cycle The effects on the centrosome cycle depend on Cbs concentration and Cbs transport from the cytoplasm to DNA. When Cbs levels are reduced centrosomes fail to mature, and when Cbs transport is impeded by ectopic expression of the GRIP domain, centrosomes undergo hypertrophy. It is proposed that, Cbs is a trans-Golgi protein that links Golgi inheritance to the cell cycle and the Drosophila Golgi is more vertebrate-like than previously recognized (Eisman, 2006).
In vertebrate cells, it is generally agreed that, during mitosis the Golgi breaks down into individual stacks at prophase, which then fragment into many mitotic Golgi vesicle clusters by prometaphase. Do clusters merge with the ER at mitosis and re-emerge at telophase to self-assemble the Golgi, or do they remain intact and independent of the ER during mitosis, acting as a template to reform the Golgi after mitosis? Persuasive evidence exists that mitotic clusters remain independent of the ER throughout mitosis, and that clusters reorganize during metaphase to associate with the mitotic spindle, centrosomes and metaphase plate during mitosis (Jesch, 2001; Jokitalo, 2001; Shima, 1998). It has also been shown that, if the Golgi is removed from cytoplasts, the Golgi complex does not form de novo from the ER. Additionally, the initiation of Golgi fragmentation and dispersal, prior to cluster formation, is required for cells to enter mitosis and may act as a Golgi-damage sensor regulating the cell cycle, which would serve to link the Golgi cycle to the centrosome cycle (Eisman, 2006 and references therein).
In Drosophila, the morphology and mitotic behavior of the Golgi is variable, based on cis-Golgi proteins and depending on the tissue type investigated. During syncytial embryogenesis maternally supplied Golgi membranes are concentrated at the embryonic cortex as several thousand punctate structures that remain unchanged during the syncytial nuclear divisions. The ER is present at the embryonic cortex and as an interconnected membrane network throughout the cytoplasm of the oocyte at fertilization. Additionally, the cortical ER and Golgi are present as a continuous network in syncytial preblastoderm embryos; this network fragments into individual units associated with nuclei following nuclear migration to the cortex in syncytial blastoderm embryos (Frescas, 2006). In cellular embryos and in Drosophila tissue culture cells the interphase Golgi exists as discrete units throughout the cytoplasm that break down and disperse during mitosis. Finally, in imaginal disc cells during pupariation, the Golgi is present as multiple stacked cisternae, which form from pre-existing Golgi units; and these cisternae have polarity (Yano, 2005), suggesting that the Drosophila Golgi has distinct functional compartments (Eisman, 2006).
Several peripheral membrane proteins called golgins have been identified that are involved in formation of the Golgi matrix and that link the Golgi to the cytoskeleton. These proteins function within specific domains of the Golgi, have a coiled-coil structure, and are regulated by small GTPases (Barr, 2003). Several cis-Golgi matrix golgins can reform a structural Golgi skeleton, in the absence of ER-derived Golgi membranes, suggesting that the matrix represents a template that gives the Golgi an autonomous identity (Seemann, 2000). Mitotic Golgi-vesicle clusters are enriched for matrix golgins and these vesicles maintain a cis to trans polarity throughout mitosis (Shima, 1997). This has led to the proposal that these vesicles are required for inheritance of the Golgi during mitosis (Seemann, 2002). In vertebrates, the golgins are clearly important for normal Golgi structure and regulation of the cell cycle. In Drosophila several cis-Golgi golgins have been investigated, but very little is known about the trans Golgi and the proteins that are specific to this compartment (Eisman, 2006).
A subset of peripheral membrane golgins contain a 42-amino-acid, functionally conserved Golgi-localization GRIP domain, which acts to localize vesicles to the trans Golgi (Barr, 1999; Kjer-Nielsen, 1999). Subsequent work has shown that this functional domain is highly conserved across the eukaryotes (Gilson, 2004; Luke, 2003; McConville, 2002). The function of GRIP proteins is still poorly understood, but ectopic expression of either the human Golgin-245 or Golgin-97 GRIP domains in HeLa cells leads to the displacement of endogenous GRIP proteins and mislocalization of other trans-Golgi proteins. This expression was also associated with a disruption of the trans-Golgi structure and interference with vesicle trafficking (Yoshino, 2003). The expression of either the Golgin-97 or Golgin-245 GRIP domains causes similar defects in Golgi structure, suggesting that the GRIP domains from both proteins share a common binding partner. However, both endogenous proteins form homodimers and thus potentially have independent functions (Luke, 2005). These findings make the GRIP domain a reliable marker of the trans Golgi in eukaryotes (Eisman, 2006).
Most GRIP proteins are regulated by the ADP-ribosylation-factor-like (ARL) GTPases (Barr, 2003). The GTP-bound form of Arl1 GTPase is required for recruitment of the GRIP domain to the trans Golgi in yeast (Behnia, 2004; Panic, 2003b) and vertebrates (Lu, 2003). The Arf72A gene, which encodes Arl1 in Drosophila has been identified and an embryonic recessive lethal allele has been recovered (Tamkun, 1991). Unfortunately, the mutant phenotype has not been investigated. Although Arl1 interacts with other, non-GRIP-containing proteins (Panic, 2003b), its interaction with most eukaryotic GRIP domains appears to be highly conserved (Eisman, 2006).
The Golgin-97 GRIP data discussed above suggests a function in maintaining Golgi structure, possibly as a component of the trans-Golgi matrix. Injection of anti-Golgin-97 antibody into cells causes the fragmentation of the entire Golgi complex, supporting a matrix function required for the global organization of this organelle (Lu, 2004). Interestingly, Golgin-97 also localizes to the centrosome throughout the cell cycle and it may act as a Golgi-nucleating protein at the centrosome, analogous to γ-tubulin nucleation of microtubules (Takatsuki, 2002). Golgin-97 is emerging as an important component of the trans Golgi in vertebrates, but has yet to be characterized in any other organism (Eisman, 2006).
This study reports the initial functional analysis of the maternal products of the Drosophila gene centrosomin's beautiful sister (cbs), during early embryogenesis. cbs encodes three isoforms, including a functional homolog of vertebrate Golgin-97. During mitosis Cbs protein undergoes a dramatic subcellular relocation, similar to the relocation described for the vertebrate Golgi matrix during mitosis. Cbs and the GRIP domain are required for maintenance of the Drosophila trans-Golgi complex during embryogenesis, and for normal centrosome maturation during the cell cycle. These results suggest that several characteristics of the Drosophila trans Golgi during the cell cycle are similar to vertebrates, making this a useful system for investigating the compartmentalization and inheritance of this complex organelle (Eisman, 2006).
The complex structure of the vertebrate Golgi, its pericentriolar location in cells and the mechanism of inheritance for this organelle appears to be a unique characteristic of vertebrates. The Drosophila Golgi complex exists as many discrete stacks during syncytial development and, on the basis of staining for the cis-Golgi proteins ßCop and p120, these stacks apparently remain unchanged during mitosis. Because of this, the embryonic Drosophila Golgi has been largely overlooked as a useful system to study this organelle during mitosis. However, this study of Cbs suggests that this is an oversight and that the inheritance and structure of the fly Golgi shares several features with the vertebrate organelle (Eisman, 2006).
This study presents the initial characterization of three golgin-like isoforms of Cbs that play a role in Golgi inheritance and the centrosome cycle in Drosophila during embryogenesis. It is proposed that two isoforms of Cbs are Golgin-97-like and, on the basis of the following, at least the GRIP-containing isoform functions at the trans Golgi. (1) The initial in silico prediction that all long isoforms of Cbs are golgin-like, suggested that Cbs is a structural protein of the relatively unknown trans-Golgi matrix in Drosophila. (2) One Cbs isoform contains a GRIP domain, which has been shown to be a functionally conserved trans-Golgi-targeting sequence in eukaryotes, making the GRIP domain a useful marker of the trans Golgi. (3) Cbs and the Drosophila Golgi protein Lva colocalize at chromosomes during congression and at the pericentriolar region during cellularization in Drosophila embryos. (4) In an Arf72A-mutant background, Cbs fails to localize to DNA during mitosis, leading to a significant reduction in Cbs and an apparent complete loss of Lva in early embryos. (5) GFP::GRIP fusion peptide is transported to the centrosomes and mitotic spindles during mitosis and interferes with the transport of endogenous Cbs protein during mitosis and normal centrosome function (Eisman, 2006).
The dramatic subcellular relocation of Cbs during mitosis at all stages of embryogenesis investigated, clearly correlates with the cell cycle and might reflect a unique mode of inheritance for a fraction of the Golgi. During embryogenesis the ER and Cbs remain independent of each other at all stages of mitosis, similar to vertebrate Golgi-matrix proteins, including Golgin-97 (Seemann, 2002; Takatsuki, 2002; Yoshimura, 2001). This supports an ER-independent mechanism for the inheritance of this fraction of the Golgi in Drosophila, whereas the association of the protein with the chromosomes argues for a chromatin-coupled mechanism for the inheritance of this Golgi component (Eisman, 2006).
Although many aspects of Cbs localization are similar to the reorganization of the animal Golgi during mitosis, the association with chromosomes from prometaphase to early telophase is unprecedented for any of the known Golgi proteins. In vertebrates, the Golgi ribbon breaks down sequentially, forming fragments around nuclei during early prophase and the mitosis entry requirement were both described by Sutterlin (Sutterlin, 2002), and the formation of mitotic vesicle clusters was described by Shima (Shima, 1998; Shima, 1997). During telophase these clusters are involved in the ATP-dependent, sequential reassembly of individual cisternae and the Golgi ribbon in vertebrates. If the embryonic Drosophila Golgi exists as individual Golgi units, the initial prophase changes in Cbs may be analogous to the initial Golgi fragmentation in vertebrates, providing a link between Golgi inheritance and the cell cycle in Drosophila. The microtubule-dependent reorganization of Cbs during late prophase and prometaphase would then correspond to the second phase of vertebrate Golgi fragmentation, when mitotic clusters associate with astral microtubules. As noted, the subsequent transport of Cbs to mitotic chromosomes may represent an efficient and reliable means of inheriting a fragmented organelle in a syncytial, rather than a cellular environment (Eisman, 2006).
The first potential interphase function of Cbs occurs during cellularization, when the approximately 6000 cortical nuclei cellularize simultaneously to form the cellular blastoderm. During cellularization, Cbs and Lva colocalize in the pericentriolar region, which is proposed to correspond to the site of the trans Golgi in Drosophila. In addition to Lva, projections from the ER colocalize with the pericentriolar Cbs region during cellularization and gastrulation, possibly for the direct transfer of new membrane from the ER to the trans Golgi. Taken together these data suggest that, at developmental stages that require large amounts of membrane production and transport, at least the trans Golgi may form a single, large continuous structure that maintains a pericentriolar location in cells and a close association with the ER, much like the vertebrate Golgi complex (Eisman, 2006).
RNAi depletion, Arf72A1-mutant analysis and GFP::GRIP ectopic expression data provide insight into the function of Cbs and the GRIP domain during embryogenesis. The RNAi depletion of the maternal pool of cbs transcript causes a significant reduction in the protein levels of Cbs, Centrosomin (Cnn) and Lva during the syncytial cleavage divisions. Additionally, Cnn fails to properly localize to mitotic centrosomes. If the loss of these proteins is excessive development fails, but if some minimal level of Cbs is present development appears to proceed normally (Pelletier, 2000), showing that after removing the Golgi in cytoplasts, the addition of 2-5% of the normal amount of Golgi restored 35% of the transport function assayed (Eisman, 2006).
Unlike RNAi-depleted embryos, in Arf72A-mutant embryos, Cbs localization during syncytial prophase is similar to wild type, but transport of Cbs to the chromosomes is completely abrogated. When Cbs is not inherited by a chromosome-based mechanism during the syncytial blastoderm stage, Cbs and Lva protein accumulation is decreased similar to RNAi depletion of Cbs, and cellularization fails, suggesting that GRIP function is required for the inheritance and maintenance of the Golgi. In Arf72A1-mutant embryos, the effect on the centrosome cycle during early syncytial blastoderm stages is less severe than RNAi but, by cellularization and early gastrulation, Cbs is nearly absent and the incidence of centrosomal defects increases, including centrosome fusions and loss of centrosomes. These data suggest that, GRIP domain function is required to maintain high levels of Cbs during late cleavage, so that normal prophase cycling of Cbs can occur. When Cbs levels are significantly reduced (similar to Cbs depletion by RNAi) Cbs fails to form aggregates during prophase and Cnn fails to localize to the centrosomes. The finding that this early relocation of Cbs might not require microtubules is similar to the finding that Cnn localization to the centrosome is by a microtubule-independent process (Eisman, 2006).
The ectopic expression of a GFP::GRIP fusion protein supports a role for this domain in the inheritance of Cbs via the chromosomes, and links Cbs to the centrosome cycle. In GFP::GRIP-expressing embryos, both the fusion protein and endogenous Cbs are transported to chromosomes but Cbs appears to bind to chromosomes more efficiently than the fusion protein. Nevertheless, large particles of Cbs accumulate in the cytoplasm during mitosis, similar to the Arf72A mutant phenotype. This block in Cbs transport also leads to an excessive accumulation of Cnn at centrosomes, causing centrosome hypertrophy and re-replication. These data suggest that, the transport of Cbs and Cnn from the cytoplasm to chromosomes and centrosomes, respectively, is linked in a time-dependent manner. The GRIP protein could interfere with Cbs transport by competing with Cbs for Arl1 binding, by affecting transport-machinery binding or a combination of the two. Alternatively, accumulation of the GRIP peptide at centrosomes might physically block transport of Cbs by directly interfering with Cnn function. Discerning between these possibilities will, of course, require further investigation. Nonetheless, it is clear that the normal cycling of Cbs is important for normal centrosome maturation, replication and spindle attachment during mitosis, and the linkage of this process to the normal nuclear cycle (Eisman, 2006).
Taken together, these results support a model that requires Cbs function for inheritance and maintenance of a subset of the Golgi complex in Drosophila, and links Golgi inheritance to the cell cycle via the centrosome cycle. During syncytial cleavage divisions, it is proposed that the initial prophase changes in Cbs are required for centrosome replication and maturation by an Arl1-independent mechanism, because both processes are normal in an Arf72A-mutant background, provided sufficient levels of cytoplasmic Cbs particles form during prophase. In RNAi-depleted animals the maternal load of cbs transcripts is reduced, resulting in an early loss of Cbs and an increase in centrosome defects. Because Cbs particles do not need to associate with centrosomes for normal replication and maturation, an indirect link is proposed between Cbs and Cnn cycles, requiring a set period of time of Cbs particle formation for sufficient Cnn localization to centrosomes. The combined data suggest that, when Cbs levels are reduced there is not sufficient time for localization of Cnn to centrosomes and, conversely, when the traffic time is extended by the ectopic expression of the GRIP domain, Cnn localization continues, resulting in centrosome hypertrophy. This mechanism functions only during prophase, because reduced centrosomes fail to mature during late mitosis in RNAi mutants and centrosome replication does not occur after prophase in embryos that express the GRIP fusion peptide (Eisman, 2006).
This characterization of Cbs suggests that many aspects of Golgi inheritance in animal cells are more similar between flies and vertebrates than previously perceived. Although the Drosophila Golgi complex is much less complex than that of the vertebrate, flies offer a powerful genetic and molecular in vivo animal system that represents an evolutionary intermediate, useful for addressing several questions regarding the animal Golgi that are difficult to address using tissue culture and in vitro systems alone. Even though many Golgi components in Drosophila remain uncharacterized, Cbs, Lva and several other cis-Golgi proteins offer a starting point for a more complete understanding of the role and regulation of golgins in Golgi structure and inheritance, how Golgi-vesicle transport is linked to the microtubule cytoskeleton and how the inheritance of this organelle is linked to the cell cycle in animals. Future work on Cbs and the Drosophila Golgi promises to be interesting and useful for reaching a more complete understanding of this fascinating organelle (Eisman, 2006).
GENE STRUCTURE
cDNA clone length - 2179bp (CG4840-RA)
Bases in 5' UTR - 161
Exons - 6
PROTEIN STRUCTURE
Amino Acids - 611 (isoform A)
Structural Domains
cbs (CG4840) was identified in studies of centrosomin (cnn). The cbs locus lies adjacent to cnn in the 50A region of the right arm of the second chromosome in Drosophila. An initial characterization included screening of cDNA libraries and expressed-sequence-tag (EST) collections to produce transcript profiles for both genes, and saturation mutagenesis screens to recover recessive lethal and sterile mutations. Multiple mutations were uncovered in cnn and other genes in this region, but no mutations were recovered cbs (Eisman, 2006).
The cbs gene is approximately 3 kb long and contains two transcription start sites located 134 and 278 base pairs distal to the most distal cnn transcription start site. The gene encodes at least five transcripts, which translate into a total of three different acidic protein isoforms. The two larger isoforms differ by the presence or absence of a functional GRIP domain and are similar to human Golgin-97. The longest isoform of Cbs is 611 amino acids long and has a predicted molecular mass of 70.8 kDa. Although the overall sequence conservation between Cbs and Golgin-97 is moderate this isoform contains a 42-amino-acid GRIP domain located near the C-terminus (aa 551-593) that is 57% identical to the GRIP domain in human Golgin-97. The alternatively spliced long Cbs isoform is missing amino acids 558 to 567, which eliminates the GRIP motif. The third short Cbs isoform is 367 amino acids long, has a predicted molecular mass of 42.7 kDa and is also similar to several golgins (Eisman, 2006).
The predicted secondary structure of Cbs is predominately coiled-coil, with short disordered regions that interrupt the coils, similar to the structure of all known golgins (Barr, 2003). There are also nine putative phosphorylation sites, consistent with the finding that several golgins undergo post-translational regulation (Dirac-Svejstrup, 2000; Preisinger, 2001) and three putative myristylation sites, necessary for post-translational modifications associated with protein-membrane interactions (Eisman, 2006).
On a western blot of 0-hours- to 2-hours-old embryos, a strong Cbs band was detected that runs just below the 77 kDa marker and a relatively weaker band that runs below the 50 kDa band of α-tubulin 84B, but well above the 34 kDa marker. The apparent molecular mass of both bands is in close agreement with the predicted sizes for the three Cbs isoforms, although both bands run slightly higher than expected. On the basis of western blot data and the isolation of both long isoforms from embryonic cDNA libraries, all three isoforms are present in early Drosophila embryos. Taken together these data suggest that Cbs produces three, potentially functionally distinct, golgin-like peripheral membrane proteins of the Drosophila trans Golgi (Eisman, 2006).
date revised: 5 March 2007


text:
Q: Javascript; unset a function? I'm pretty new to javascript. I have this function and I'd like to unset it when the screen size is less than 1024. I have two functions: a document ready function and a window resize function. When resizing the screen below 1024 I'd like the function to be unset. How to manage this?
Here is my code
<script type='text/javascript' src='//code.jquery.com/jquery-1.9.1.js'></script>
<script>
jQuery(document).ready(function($) {
    var width = (window.innerWidth > 0) ? window.innerWidth : screen.width;
    if(width > 1024) {
    setTimeout(function(){
        var lcol_height = $("#leftCol2").height() + 80; // add 80 for margin + padding
        var rcol_height = $("#rightCol2").height();

        if(rcol_height > lcol_height) $("#leftCol2").css('height',(rcol_height - 80) + 'px');
        else $("#rightCol2").css('height',lcol_height + 'px');
    }, 500);
    }
});

$(window).resize(function() { //Fires when window is resized
    var width = (window.innerWidth > 0) ? window.innerWidth : screen.width;
    if(width < 1024) {
//I'd like the margin function to be unset.
    }
    else {
        setTimeout(function(){
        var lcol_height = $("#leftCol2").height() + 80; // add 80 for margin + padding
        var rcol_height = $("#rightCol2").height();

        if(rcol_height > lcol_height) $("#leftCol2").css('height',(rcol_height - 80) + 'px');
        else $("#rightCol2").css('height',lcol_height + 'px');
    }, 500);
    }

});
</script>

Thank you so much!

A: There's no need to unset it, since you might be needing it again in case the window size increases beyond 1024px. Here is a slightly optimized version of your code:
function handleMargins() {
    var width = (window.innerWidth > 0) ? window.innerWidth : screen.width;
    if (width > 1024) {
        setTimeout(function () {
            var lcol_height = $("#leftCol2").height(); // use original margin
            var rcol_height = $("#rightCol2").height();

            if (rcol_height > lcol_height) $("#leftCol2").css('height', (rcol_height - 80) + 'px');
            else $("#rightCol2").css('height', lcol_height + 'px');
        }, 500);
    } else {
        setTimeout(function () {
            var lcol_height = $("#leftCol2").height() + 80; // add 80 for margin + padding
            var rcol_height = $("#rightCol2").height();

            if (rcol_height > lcol_height) $("#leftCol2").css('height', (rcol_height - 80) + 'px');
            else $("#rightCol2").css('height', lcol_height + 'px');
        }, 500);
    }
}

jQuery(document).ready(handleMargins);

$(window).resize(handleMargins);

Apart from being more readable, now the same code executes when you first open the page AND on resize (imagine what would happen in your original code if the window is initially smaller than 1024px).

UPDATE
See if this makes more sense (note, the boundary is set to 400px, so you need to shring that jsfiddle box to about twice the size of the divs): http://jsfiddle.net/wdey6ngf/
I've simplified your logic and everything, just wanted to show you how it works.

NOTE
Depending on how complicated your end logic is going to be, this is something you can accomplish using no JS, just plain CSS with media queries: http://jsfiddle.net/rags7zg2/ It will perform much better than the JS version.

A: If it is a global function, you can redefine it like this:
window.myFunction = function() {
  return false;
}

But you can't do it with anonymous functions obviously. So, first extract your functions:
function myResizer()
{
    var width = (window.innerWidth > 0) ? window.innerWidth : screen.width;
    if(width > 1024) {
    setTimeout(function(){
        var lcol_height = $("#leftCol2").height() + 80; // add 80 for margin + padding
        var rcol_height = $("#rightCol2").height();
        if(rcol_height > lcol_height) $("#leftCol2").css('height',(rcol_height - 80) + 'px');
        else $("#rightCol2").css('height',lcol_height + 'px');
    }, 500);
    }
}

And then use this function to set it as a ready function initially:
jQuery(document).ready(myResizer)

Later on, when you need to lose that functionality, just override it with nothing:
jQuery(document).ready(function($) { return false; }

A: Store all your code in an function, use storing settimeout in a variable, and call that in ready and onresize. Then you can use clear interval if (width < 1024).

redpajama_set_name: RedPajamaStackExchange


text:
Cubans Get One-Way Ticket, Not To Liberty, But to Cuba
By Jonathan S. Landay Staff writer of The Christian Science Monitor
February 3, 1995 | GUANTANAMO BAY, CUBA
ALBERTO LUJARDO CANELARIO had hoped that the refugee camps in Panama in which he and thousands of other Cubans languished would be stepping stones to freedom in the United States. Instead, Mr. Lujardo was returned Wednesday by US military aircraft to the same Communist-ruled island from which he fled in a raft last August, arriving with 100 compatriots at the US Naval Base at Guantanamo Bay.
There they will join 20,400 other Cubans jammed in tent cities at the base. The Cubans at Guantanamo have been there since they were intercepted last summer as they tried to reach Florida in leaky boats and homemade rafts. All remain trapped in political limbo, their fates tied to a diplomatic struggle between Washington and Cuban President Fidel Castro Ruz.
Stepping onto Guantanamo's sun-baked Tarmac, Lujardo spoke for his sullen countrymen: ``We want to go to the United States. We fled communism and we feel pain because we are political pawns. We have been betrayed by the government of the United States and the Communist government of Cuba.''
The aircraft load of Cuban refugees was among the first of 1,000 Cubans the US has begun flying under tight security from Panama to new quarters at Guantanamo. The massive operation is to be completed by March 3, when Washington must close four refugee camps that Panama had agreed to host for six months.
The refugees are being resettled in new huts of plywood walls and tent-like roofs along Guantanamo's wind-swept shores, vast improvements over the conditions in which they have been living. The new construction is the first phase of a $35-million administration plan to avert an explosion of tensions.
The hut compounds are being called ``villages'' and not camps. Electricity is to be provided and regular ``community'' bathrooms will replace portable toilets, bucket baths, and drainage ditches filled with reeking, scummy water.
Instead of the razor-wire fence that surrounds the tent cities, the hut compounds are being bounded by waist-high chain-link fences. Concrete floors are being poured for churches and libraries. Even movie theaters are planned.
But better conditions may not easily dispel the bitterness the refugees feel over their treatment and uncertain future. They remain pawns in a geopolitical contest between the US and its longtime irritant, Mr. Castro.
THE battle began with last summer's seaborne exodus that President Clinton tried to halt by ending a US policy of automatic asylum for Cuban refugees. He decided to admit just children, the elderly, and the sick into the US.
When that failed to stem the exodus, Washington negotiated a Sept. 9 accord with Castro in which it agreed to grant at least 20,000 visas per year, but only to Cubans who applied in Havana. In return, Castro stopped the exodus and agreed to accept refugees who sought repatriation.
While Washington said the refugees could remain indefinitely at Guantanamo, its visa-application rule made it clear that it preferred them to go home. Most refugees, however, are terrified of being punished if they leave the base. So, they vow to stay until US policy changes and they are allowed to immigrate.
``The cost of achieving freedom is very high,'' says Manuel Herrera Fernandez, a Havana crane operator. ``For me, I would rather wait here until I die.''
Some 200,000 Cubans, meanwhile, have applied for US visas in Havana, and there is no sign of a US policy shift on the refugees. That is because admitting them could encourage a new flight of Cubans from the penury into which their island has plunged since the demise of its former patron, the Soviet Union.
On his part, Castro seems to be hoping that the huge costs of the refugees' upkeep and their periodic violent outbursts will force Clinton into ending a more than 30-year US trade embargo on Cuba. Accordingly, US officials say, Castro has been slow in readmitting refugees who seek repatriation.
``He [Castro] has everything to gain from their being here and nothing to lose,'' says Marine Col. Douglas Hendricks, who oversees several Guantanamo refugee encampments.
Castro blames the US embargo for blocking the foreign investment he needs to shore up his crumbling economy and stabilize his regime.
Marine Brig. Gen. Raymond Ayres Jr., chief of Guantanamo's refugee operations, warns that the longer the refugees remain in limbo, the greater the potential for serious violence. ``The situation is unsatisfactory in the long-term,'' he says.
Why Castro's demand for reparations from US could backfire
Cuba's Raul Castro asks Obama to lift US trade embargo
Will Alan Gross release pave way for new US - Cuba relations?
https://www.csmonitor.com/1995/0203/03014.html

redpajama_set_name: RedPajamaCommonCrawl


text:
Q: export-csv is destroying my date-formats In powershell, I create a datatable; there's a column in the datatable, with formatted date:
SELECT RIGHT('0' + cast(day(GETDATE()) as varchar(2)),2) + '-' + CAST(DATENAME(MONTH, GETDATE()) AS VARCHAR(3)) + '-' + cast(DATEPART(year, GETDATE()) as varchar(4))

So the actual value is: dd-MMM-yyyy
Except, when I use the following, the date format is changed to dd-MMM-yy
$dtResult | export-csv $outputFile -notypeinformation

it is crucial to get the date as dd-MMM-yyyy
cheers

A: It sounds like the date is stored in the data table as a DateTime, so it will use the system default for formatting. One way around this is to convert the datatable to a collection of objects first, converting the date to a string in the process:
$dtObjects = $dtResult | Select-Object ID, Name, @{n="DateField";e={$_.DateField.ToString("dd-MMM-yyyy"}}

Replace the field names with your actual field names.


RHS: I Can Grow – Free Inspiration Pack!
The Royal Horticultural Society's 'I Can Grow' project is a chance for young people to discover and explore the benefits of gardening, not only to them, but also to their local community and the wider world.
I Can Grow is designed to empower young people, allowing them to create a campaign, using plants, to shout about the environmental and social issues they believe in.
First you need to sign up for a free inspiration pack (below) which will contain a project guide and great resources to get your class or group thinking about and eventually sharing their campaign.
This project is designed to be led by your young people as much as possible so, using the resources, encourage them to think how they could use plants to solve a problem or support a cause that means something to them.
Find out more and download your FREE inspiration pack!


text:
Napa County home price hits all-time median high, with flood of new buyers from Bay Area
This home, located at 1592 Milton Road in Napa, is listed by Rachel Mau of RE/MAX GOLD for $888,888. The current median of a Napa County home is $867,000.
Sparks Media Group
This home, located at 3541 Woodbrook Drive in Napa, is listed by Burt Polson of ACRES Real Estate Services, Inc. for $890,000. The current median of a Napa County home is $867,000.
Burt Polson photo
This home, located at 101 South Newport Drive in Napa, is listed by Suzy Anderson of Coldwell Banker Brokers of the Valley for $859,000. The current median of a Napa County home is $867,000.
Joseph Chun photo
The COVID-19 pandemic continues to impact every aspect of life in Napa County, including housing prices, with many buyers wanting to flee the big city.
The median sold price — half sold for more, half for less — of an area home hit a 30-year high in August, going from $699,000 a year ago to $867,000 this past month. That's a 24% increase, said the California Association of Realtors.
At the same time, the number of Napa County homes sold rose 52% percent, from 122 homes a year ago to 185 this August, according to Bay Area Real Estate Information Services (BAREIS).
A combination of low interest rates, a state-wide home shortage and an increased number of people now working from home means that more and more buyers are setting their sights on Napa Valley.
"People want to get out of the cities," said Realtor Suzy Anderson of Coldwell Banker Brokers of the Valley. In terms of COVID infection rates, "We're doing so much better than the cities," she said. For those looking for a "safer area," Napa fits the bill, she said.
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Realtor Rachel Mau of RE/MAX Gold.Mau said she worked with an employee from Google who recently moved to Napa County. Now telecommuting, "she can work anywhere," said Mau.
Before the move, "she was in a $5,000 a month apartment in the city," spending hours taking the daily Google shuttle back and forth to the South Bay, Mau said.
"Now she's got a home in Napa, paying $4,500 a month for her mortgage and she bought almost a million dollar property," said Mau.
"It's kind of incredible how the market has shifted," continued Mau. "Six to eight months ago, it was a seller and a buyer's market. Now we have so many buyers (combined with low interest rates) that we're seeing this craziness."
Even with Napa County's unemployment rate at historic highs, there are still many people working full time who are qualified to buy a home, she noted.
"We've created a beautiful monster here," she said.
For some listings in Napa County, especially those in the $800,000 and up range, 12 to 14 offers aren't uncommon, said Mau.
At the beginning of COVID-19, some buyers wanted more isolated properties and locations, but after the fires, "they are thinking twice about moving so far off the grid." Even something like the increased cost of fire insurance can be a deterrent, she noted.
Mau has a home listed for $888,888 at 1592 Milton Road that is quite close to the median price. To address the water problems in that area, the homeowner is having a new water tank system installed.
Mau said that her buyers from out of the area are looking for "a lifestyle that people have when they think of Napa County." Napa Valley "just has a persona of its own that is different from any other county."
Who are these new Napans? Many are younger families, younger people and those without children at home, said Anderson of Coldwell Banker Brokers of the Valley. At the same time, people are also leaving the area.
"I also had several listings which were older people moving from Napa to Arizona and Colorado," she said. Those sellers anticipate getting more for their money in other states, "so it's easier to retire."
Anderson said that the recent wildfires slowed down the market a bit, but September and October "have historically been a really good months around here."
"I don't think there will be any change until the usual holiday slowdown," which usually starts around early November, she said.
Where are these buyers looking? "All over the valley," said Anderson. "Many without kids aren't concerned about the school districts. I had one client that (wanted) an updated nice home in the million dollar range." She showed that buyer a home on Maximillian Court in north Napa. "We looked at it for 20 minutes and they made an offer, full price." That sale has since closed.
Another property on South Montgomery Street had six offers. "My buyer made an offer $25,000 higher and the house sold for $100,000 over." Looking back on it now, "We didn't have a chance," Anderson said.
"I'm waiting to hear on another" house with 12 offers, she said this past week.
The most likely buyer in such cases is usually an all-cash offer with no contingencies. "What I've been having my clients do is get preapproved with their loan so they can go in with a very clean offer," and hopefully prevail, Anderson said.
Burt Polson of ACRES Real Estate Services, Inc. primarily sells commercial real estate, but currently has a residential listing at 3541 Woodbrook Drive in Napa priced at $890,000.
The house has four bedrooms and is in the 2,000-square-foot range, which is an advantage, he said. "It's a tight market for those four bedroom homes," especially those priced under $1 million, said Polson.
As always, the challenge remains for first-time home buyers. "It's tough to find inventory, especially workforce housing. It's tough to find an entry level home in Napa," he said.
"We're not getting into the ridiculously overinflated realm," said Ted Stumpf, a Realtor with Windermere Real Estate and current chair of the Napa Valley chapter of the North Bay Association of Realtors.
Stumpf said low interest rates means that "there are more first-time home buyers than in a long time. That's a big segment of the market now that hasn't always been present" in Napa County, he said.
Even with a new record-high selling price, Stumpf isn't worried about a housing "bubble."
"It's not the same kind of environment we were in" leading up to the Great Recession, he said. "That bubble was about questionable lending practices. Folks didn't have the equity in their homes. That's not the case now. People have equity."
This price increase "is a natural result of the law of supply and demand," he said.
Regionally, the median sold price of a Bay Area home reached a new high of $1.068 million, said the California Association of Realtors. A year ago, the median was $900,000.
Watch now: Take a tour inside Napa's historic Horrell House
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Ted Stumpf
A Realtor With Windermere Real Estate
Norbar Napa Chapter President
Realtor Suzy Anderson Of Coldwell Banker Brokers Of The Valley
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Napa County Real Estate
Napa County Home For Sale
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Napa Home Prices Hit All Time High
Napa County home sales skyrocket in July; Median price also on the rise
Napa County home sales skyrocketed in July, rising 79.8% from June to July.
Historic Napa houses see major changes during COVID-19 pandemic
Which historic downtown Napa home sold for $3 million this week? Check it out.
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Napa County housing sales bounce back in June, but still historically low: sold price also on the rise
After Napa home sales fell in May, June brought better news. The number of homes sold in Napa County month-over-month rose 53%.
Napa Food Bank relocates service to New Tech parking lot
The food bank is assessing options for when Napa's schools reopen for in-person instruction on Oct. 26, staff say.
Governor signs Sen. Dodd's bill to promote home care during the pandemic
Senate Bill 214 would allow low-income seniors and people with disabilities to receive support in making the transition from skilled nursing facilities to receiving care in their homes.
Napa County home prices top $900,000
What's it cost to buy a house in Napa these days? About $900,000, according to one real estate group.
Napa County home prices rise during pandemic
The median sold price of a Napa County home in December reached $780,000. What does that mean for buyers and sellers?
Burt Polson's Real Estate in the Napa Valley: Revolutionize real estate with tokens
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Burt Polson's Real Estate in the Napa Valley: Land scams: what they're not telling you
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Burt Polson's Real Estate in the Napa Valley: Exchanges, recovery, technology and international investors
Burt Polson gives the rundown on four timely real estate topics: exchanges, recovery, technology and international investors.
Burt Polson's Real Estate in the Napa Valley: Inheriting real estate and problems
Burt Polson talks about problems when it comes to inheriting real estate.
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text:
https://www.universitypressscholarship.com/search?f_0=keywords&q_0=gene%20duplication
Keywords: gene duplication x
Biochemistry / Molecular Biology (3)
Open Section Neuroscience (1)
Page:12
The Genetics of Evolutionary Novelties
Günter P. Wagner
in Homology, Genes, and Evolutionary Innovation
This chapter examines the molecular genetics of evolutionary novelties. In particular, it investigates which molecular mechanisms might be involved in the origination of novel gene regulatory ... More
This chapter examines the molecular genetics of evolutionary novelties. In particular, it investigates which molecular mechanisms might be involved in the origination of novel gene regulatory networks (and, thus, character identity networks) and what these mechanisms imply for the origin of novel characters. The chapter begins with a discussion of the complex problem of the evolution of transcriptional regulation by focusing on the evolution of cis-regulatory elements (CREs) and the evolution of transcription factor proteins. It then asks whether novel pigment spots, such as the Drosophila wing spots, are novelties. It also explores an evolutionary novelty known as sex comb and the role of transposable elements in the origin of novel CREs. Finally, it considers the role of gene duplications, the evolution of micro-RNAs (miRNAs), and the possibility of a mechanistic difference between adaptation and innovation.Less
This chapter examines the molecular genetics of evolutionary novelties. In particular, it investigates which molecular mechanisms might be involved in the origination of novel gene regulatory networks (and, thus, character identity networks) and what these mechanisms imply for the origin of novel characters. The chapter begins with a discussion of the complex problem of the evolution of transcriptional regulation by focusing on the evolution of cis-regulatory elements (CREs) and the evolution of transcription factor proteins. It then asks whether novel pigment spots, such as the Drosophila wing spots, are novelties. It also explores an evolutionary novelty known as sex comb and the role of transposable elements in the origin of novel CREs. Finally, it considers the role of gene duplications, the evolution of micro-RNAs (miRNAs), and the possibility of a mechanistic difference between adaptation and innovation.
Keywords: molecular genetics, evolutionary novelties, gene regulatory networks, character identity network, novel characters, transcriptional regulation, cis-regulatory elements, transcription factor proteins, transposable elements, gene duplication
Expression between Duplicate Genes: Genome‐Wide Analysis
Expression divergence between duplicate genes has long been a subject of great interest to geneticists and evolutionists. Ohno proposed that expression divergence is the first step in the functional ... More
Expression divergence between duplicate genes has long been a subject of great interest to geneticists and evolutionists. Ohno proposed that expression divergence is the first step in the functional divergence between duplicate genes and thereby increases the chance of retention of duplicate genes in a genome. Further, advances in molecular biology in the 1970s and 1980s provided a much better understanding of the molecular basis of expression divergence between duplicate genes. The availability of completely sequenced genomes and microarray gene expression and other functional genomic data have stimulated many studies on these questions. This chapter introduces these results.Less
Expression divergence between duplicate genes has long been a subject of great interest to geneticists and evolutionists. Ohno proposed that expression divergence is the first step in the functional divergence between duplicate genes and thereby increases the chance of retention of duplicate genes in a genome. Further, advances in molecular biology in the 1970s and 1980s provided a much better understanding of the molecular basis of expression divergence between duplicate genes. The availability of completely sequenced genomes and microarray gene expression and other functional genomic data have stimulated many studies on these questions. This chapter introduces these results.
Keywords: expression divergence, duplicate genes, gene duplication, Ohno, functional divergence
Evolution of the DNA World and the Chance Events That Accompanied It: More about Complexity
Paul F. Lurquin and Linda Stone
in Evolution and Religious Creation Myths: How Scientists Respond
First life-forms appeared at least as early as 3.5 billion years ago in the form of prokaryotes. Some of these species developed oxygenic photosynthesis, which resulted in the presence of oxygen gas ... More
First life-forms appeared at least as early as 3.5 billion years ago in the form of prokaryotes. Some of these species developed oxygenic photosynthesis, which resulted in the presence of oxygen gas in the atmosphere. Later, eukaryotes appeared and diversified through mutation and gene duplication (including mutation and duplication of master genes), which led to the rewiring of entire gene networks. The chapter shows that there is no fundamental difference between macroevolution and microevolution. It shows that making artificial life in the lab as well as transgenic life-forms would be impossible if the Intelligent Design scenario were correct. Indeed, ID posits that living systems were holistically designed and thus cannot be constructed in a piecemeal fashion.Less
Evolution of the DNA World and the Chance Events That Accompanied It : More about Complexity
Paul F. LurquinLinda Stone
First life-forms appeared at least as early as 3.5 billion years ago in the form of prokaryotes. Some of these species developed oxygenic photosynthesis, which resulted in the presence of oxygen gas in the atmosphere. Later, eukaryotes appeared and diversified through mutation and gene duplication (including mutation and duplication of master genes), which led to the rewiring of entire gene networks. The chapter shows that there is no fundamental difference between macroevolution and microevolution. It shows that making artificial life in the lab as well as transgenic life-forms would be impossible if the Intelligent Design scenario were correct. Indeed, ID posits that living systems were holistically designed and thus cannot be constructed in a piecemeal fashion.
Keywords: eukaryotes, gene duplication, gene networks, macroevolution, master genes, microevolution, photosynthesis, prokaryotes, transgenic
Animal phylogenetics
Alessandro Minelli
in Perspectives in Animal Phylogeny and Evolution
The single main root of phylogenetics is Hennig's reformulation of the comparative method, but the empirical basis has increased enormously in recent years with the availability of an exponentially ... More
The single main root of phylogenetics is Hennig's reformulation of the comparative method, but the empirical basis has increased enormously in recent years with the availability of an exponentially increasing amount of molecular sequence data, to be analysed through increasingly sophisticated algorithms. Progress has been overcoming the pitfalls of earlier naïve hypotheses, such as the putatively uniform rate of the molecular clock across lineages, as well as problems deriving from gene duplication, gene loss, and horizontal gene transfer. However, the intrinsic limits of the resolution power of sequence comparisons are also emerging, as in the case of geologically old sequences of a series of branchings of the phylogenetic tree, which reduce in practice to multibranched star-shaped phylogenies. The single best source of data for the molecular phylogeny of the Metazoa is arguably the mitochondrial genome, in terms of gene, genome sequences, and also gene orderLess
The single main root of phylogenetics is Hennig's reformulation of the comparative method, but the empirical basis has increased enormously in recent years with the availability of an exponentially increasing amount of molecular sequence data, to be analysed through increasingly sophisticated algorithms. Progress has been overcoming the pitfalls of earlier naïve hypotheses, such as the putatively uniform rate of the molecular clock across lineages, as well as problems deriving from gene duplication, gene loss, and horizontal gene transfer. However, the intrinsic limits of the resolution power of sequence comparisons are also emerging, as in the case of geologically old sequences of a series of branchings of the phylogenetic tree, which reduce in practice to multibranched star-shaped phylogenies. The single best source of data for the molecular phylogeny of the Metazoa is arguably the mitochondrial genome, in terms of gene, genome sequences, and also gene order
Keywords: comparative method, gene duplication, gene loss, horizontal gene transfer, mitochondrial genome, molecular clock, molecular sequences, phylogenetics
Functional Divergence after Gene Duplication: Statistical Modeling
Many organisms have undergone genome-wide or local chromosome duplication events during their evolution. As a result, many genes are represented as several paralogs in the genome with related but ... More
Many organisms have undergone genome-wide or local chromosome duplication events during their evolution. As a result, many genes are represented as several paralogs in the genome with related but distinct functions (gene families). Since gene duplication is thought to have provided the raw materials for functional innovations, it is desirable to identify amino acid sites that are responsible for functional divergence from the sequence analysis of a gene family. A series of statistical models has been developed, based on the principle that functional divergence between duplicate genes is highly correlated with the change of evolutionary rate after the gene duplication. This chapter discusses these statistical and computational methods. These include the Poisson-gamma model for protein sequence evolution, the Markov chain model for type-I functional divergence, and statistical methods for type-II functional divergence.Less
Many organisms have undergone genome-wide or local chromosome duplication events during their evolution. As a result, many genes are represented as several paralogs in the genome with related but distinct functions (gene families). Since gene duplication is thought to have provided the raw materials for functional innovations, it is desirable to identify amino acid sites that are responsible for functional divergence from the sequence analysis of a gene family. A series of statistical models has been developed, based on the principle that functional divergence between duplicate genes is highly correlated with the change of evolutionary rate after the gene duplication. This chapter discusses these statistical and computational methods. These include the Poisson-gamma model for protein sequence evolution, the Markov chain model for type-I functional divergence, and statistical methods for type-II functional divergence.
Keywords: gene duplication, functional divergence, Poisson-gamma model, Markov chain model, statistical methods
Functional Divergence after Gene Duplication: Applications and Others
As most amino acid substitutions are not related to the functional divergence but only represent the neutral evolution, it becomes crucial how to distinguish statistically between these two ... More
As most amino acid substitutions are not related to the functional divergence but only represent the neutral evolution, it becomes crucial how to distinguish statistically between these two possibilities. Chapter 3 introduced the statistical methods to solve this problem, based on the principle that functional divergence between duplicate genes is highly correlated with the change of evolutionary rate. This chapter discusses several case studies for applying these methods to biological problems.Less
As most amino acid substitutions are not related to the functional divergence but only represent the neutral evolution, it becomes crucial how to distinguish statistically between these two possibilities. Chapter 3 introduced the statistical methods to solve this problem, based on the principle that functional divergence between duplicate genes is highly correlated with the change of evolutionary rate. This chapter discusses several case studies for applying these methods to biological problems.
Keywords: gene duplication, functional divergence, case studies, amino acid substituion
This chapter focuses on the developmental evolution of flowers and flower organ identity. It reviews some of the most important insights that have been gained from research on the developmental ... More
This chapter focuses on the developmental evolution of flowers and flower organ identity. It reviews some of the most important insights that have been gained from research on the developmental evolution of flowers regarding the nature of organ identity, organ integration, and the origin of evolutionary novelties. The chapter begins with a discussion of the uniqueness of flowers and the evolution of phylogeny and flower characters in angiosperms. It then examines the genetics of canonical flower development, along with the developmental genetic architecture of the flower Bauplan. It also considers flower variation and the identities of novel flower organs, the origin of the bisexual flower developmental type, perianth evolution and the origin of petals, and the realization that additional organ identities can evolve after gene duplications.Less
This chapter focuses on the developmental evolution of flowers and flower organ identity. It reviews some of the most important insights that have been gained from research on the developmental evolution of flowers regarding the nature of organ identity, organ integration, and the origin of evolutionary novelties. The chapter begins with a discussion of the uniqueness of flowers and the evolution of phylogeny and flower characters in angiosperms. It then examines the genetics of canonical flower development, along with the developmental genetic architecture of the flower Bauplan. It also considers flower variation and the identities of novel flower organs, the origin of the bisexual flower developmental type, perianth evolution and the origin of petals, and the realization that additional organ identities can evolve after gene duplications.
Keywords: flowers, flower organ identity, developmental evolution, evolutionary novelties, angiosperms, genetics, flower development, flower organs, perianth, gene duplication
in Evolution through Genetic Exchange
This chapter considers instances where the genetic exchange, in this case resulting in genomic duplications, has derived from sexual reproduction as well as other forms of recombination. It looks at ... More
This chapter considers instances where the genetic exchange, in this case resulting in genomic duplications, has derived from sexual reproduction as well as other forms of recombination. It looks at how genetic-exchange-induced duplications are seen as affecting genome evolution, gene function, adaptations and radiations of entire clades. In keeping with the tenor of the entire book, the chapter emphasizes evolutionarily creative outcomes that derive from the duplication of the genomic components of microorganisms, plants, and animals.Less
This chapter considers instances where the genetic exchange, in this case resulting in genomic duplications, has derived from sexual reproduction as well as other forms of recombination. It looks at how genetic-exchange-induced duplications are seen as affecting genome evolution, gene function, adaptations and radiations of entire clades. In keeping with the tenor of the entire book, the chapter emphasizes evolutionarily creative outcomes that derive from the duplication of the genomic components of microorganisms, plants, and animals.
Keywords: genetic exchange, gene duplication, genomic duplication, evolution
Evolution of specificity and diversity
Denis C. Shields, Catriona R. Johnston, Iain M. Wallace, and Richard J. Edwards
The divergence of proteins following gene duplication has long been recognized as an important process in the evolution of both new and specific protein functions. For functional divergence to occur, ... More
The divergence of proteins following gene duplication has long been recognized as an important process in the evolution of both new and specific protein functions. For functional divergence to occur, the duplicated gene has to survive duplication and avoid becoming a pseudogene (gene death). The mechanism by which a gene duplicates survive is still under some debate, but it is thought that maintenance of duplicate pairs can be accomplished by the evolution of novel functions, splitting ancestral functions between duplicate pairs called paralogs, or some combination of both neo- and subfunctionalization. Although no consensus has been reached as to which process plays a more dominant role in the generation and maintenance of duplicates at the genomic or protein level, the distinction is somewhat irrelevant for the bioinformatic prediction of individual specificity-determining sites; that is, those sites that are important for differences in gene function between paralogs. Instead, the evolutionary history and changing selective constraints for individual residues is important for the interpretation of results. This chapter examines the types of substitution that occur at these sites and the phylogenetic signals that they leave.Less
Denis C. ShieldsCatriona R. JohnstonIain M. WallaceRichard J. Edwards
The divergence of proteins following gene duplication has long been recognized as an important process in the evolution of both new and specific protein functions. For functional divergence to occur, the duplicated gene has to survive duplication and avoid becoming a pseudogene (gene death). The mechanism by which a gene duplicates survive is still under some debate, but it is thought that maintenance of duplicate pairs can be accomplished by the evolution of novel functions, splitting ancestral functions between duplicate pairs called paralogs, or some combination of both neo- and subfunctionalization. Although no consensus has been reached as to which process plays a more dominant role in the generation and maintenance of duplicates at the genomic or protein level, the distinction is somewhat irrelevant for the bioinformatic prediction of individual specificity-determining sites; that is, those sites that are important for differences in gene function between paralogs. Instead, the evolutionary history and changing selective constraints for individual residues is important for the interpretation of results. This chapter examines the types of substitution that occur at these sites and the phylogenetic signals that they leave.
Keywords: proteins, gene duplication, functional change, paralogs, specificity-determining sites, evolutionary change
Evolution of the vertebrate globin gene family
Jay F. Storz
in Hemoglobin: Insights into protein structure, function, and evolution
Biology, Evolutionary Biology / Genetics, Biochemistry / Molecular Biology
Chapter 5 provides an overview of the evolutionary history of the globin gene superfamily and places the evolution of vertebrate-specific globins in phylogenetic context. The duplication and ... More
Chapter 5 provides an overview of the evolutionary history of the globin gene superfamily and places the evolution of vertebrate-specific globins in phylogenetic context. The duplication and functional divergence of globin genes has promoted key physiological innovations in respiratory gas transport and other physiological functions during animal evolution. A combination of both tandem gene duplication and whole-genome duplication contributed to the diversification of vertebrate globins. Phylogenetic reconstructions arrange vertebrate globins into those that derive from vertebrate-specific duplications (cytoglobin, globin E, globin Y, and the independently derived myoglobin-like and hemoglobin-like genes of jawed vertebrates and jawless fishes [lampreys and hagfish]) and those that derive from far more ancient duplication events that predate the divergence between deuterostomes and protostomes (androglobin, globin X, and neuroglobin). Tracing the evolutionary history of deuterostome globins reveals evidence for the repeated culling of ancestral diversity, followed by lineage-specific diversification of surviving gene lineages via repeated rounds of duplication and divergence.Less
Chapter 5 provides an overview of the evolutionary history of the globin gene superfamily and places the evolution of vertebrate-specific globins in phylogenetic context. The duplication and functional divergence of globin genes has promoted key physiological innovations in respiratory gas transport and other physiological functions during animal evolution. A combination of both tandem gene duplication and whole-genome duplication contributed to the diversification of vertebrate globins. Phylogenetic reconstructions arrange vertebrate globins into those that derive from vertebrate-specific duplications (cytoglobin, globin E, globin Y, and the independently derived myoglobin-like and hemoglobin-like genes of jawed vertebrates and jawless fishes [lampreys and hagfish]) and those that derive from far more ancient duplication events that predate the divergence between deuterostomes and protostomes (androglobin, globin X, and neuroglobin). Tracing the evolutionary history of deuterostome globins reveals evidence for the repeated culling of ancestral diversity, followed by lineage-specific diversification of surviving gene lineages via repeated rounds of duplication and divergence.
Keywords: Keywords: androglobin, chimeric fusion gene, cytoglobin, gene conversion, gene duplication, gene family, genome duplication, hexacoordination, neuroglobin
Gene duplications and innovation
Andreas Wagner
in The Origins of Evolutionary Innovations: A Theory of Transformative Change in Living Systems
Gene duplications have long been thought to facilitate evolutionary innovation. This chapter highlights three dramatic classes of innovations associated with gene duplications. It then creates a ... More
Gene duplications have long been thought to facilitate evolutionary innovation. This chapter highlights three dramatic classes of innovations associated with gene duplications. It then creates a larger context for these examples, showing how gene duplications fit seamlessly into the framework it proposes here. Specifically, it points out that gene duplications are unique classes of mutations, because they systematically increase mutational robustness (which plays an important role in evolutionary innovation). Also, gene duplications increase robustness in ways that facilitate innovation. That is, they increase the size of genotype networks, and, more generally, the search space through which evolving populations can access novel phenotypic variants.Less
Gene duplications have long been thought to facilitate evolutionary innovation. This chapter highlights three dramatic classes of innovations associated with gene duplications. It then creates a larger context for these examples, showing how gene duplications fit seamlessly into the framework it proposes here. Specifically, it points out that gene duplications are unique classes of mutations, because they systematically increase mutational robustness (which plays an important role in evolutionary innovation). Also, gene duplications increase robustness in ways that facilitate innovation. That is, they increase the size of genotype networks, and, more generally, the search space through which evolving populations can access novel phenotypic variants.
Keywords: gene duplications, genotype networks, mutations, evolving populations, phenotypic variants
Evolutionary interactions between sex chromosomes and autosomes
Manyuan Long, Maria D. Vibranovski, and Yong E. Zhang
in Rapidly Evolving Genes and Genetic Systems
Investigations into the evolution of sex chromosomes and sex-determination have attracted wide attention, with voluminous literature reporting interesting findings in the evolution of individual X ... More
Investigations into the evolution of sex chromosomes and sex-determination have attracted wide attention, with voluminous literature reporting interesting findings in the evolution of individual X and Y (Z and W) chromosomes empirically and theoretically. Further examinations into the duplications involved in both sex chromosomes and autosomes have revealed a class of previously unknown processes and related mechanisms of genomic evolution: evolutionary interactions between sex chromosomes and autosomes. A plethora of data and analyses have shown that the gene traffics between the two types of chromosomes are the consequence of natural selection on the sex-related genes and may contribute to the peculiar chromosomal distribution of sex-biased genes, e.g., the dominance on the autosomes, rather than the previously predicted X chromosome, of male-biased genes. This chapter reviews the evidence for the generality of the gene traffic in different sex-determination systems and copying mechanisms of gene duplication, and discusses the underlying evolutionary mechanisms leading to the gene traffics.Less
Manyuan LongMaria D. VibranovskiYong E. Zhang
Investigations into the evolution of sex chromosomes and sex-determination have attracted wide attention, with voluminous literature reporting interesting findings in the evolution of individual X and Y (Z and W) chromosomes empirically and theoretically. Further examinations into the duplications involved in both sex chromosomes and autosomes have revealed a class of previously unknown processes and related mechanisms of genomic evolution: evolutionary interactions between sex chromosomes and autosomes. A plethora of data and analyses have shown that the gene traffics between the two types of chromosomes are the consequence of natural selection on the sex-related genes and may contribute to the peculiar chromosomal distribution of sex-biased genes, e.g., the dominance on the autosomes, rather than the previously predicted X chromosome, of male-biased genes. This chapter reviews the evidence for the generality of the gene traffic in different sex-determination systems and copying mechanisms of gene duplication, and discusses the underlying evolutionary mechanisms leading to the gene traffics.
Keywords: gene traffics, sex chromosomes, evolutionary interactions, male-biased genes, autosomes, gene duplication, retroposition, copying mechanisms, natural selection, gene evolution
Mutation, Gene Conversion, and Migration
Daniel L. Hartl
in A Primer of Population Genetics and Genomics
Biology, Biomathematics / Statistics and Data Analysis / Complexity Studies, Evolutionary Biology / Genetics
Chapter 4 focuses on forward and reverse mutation, gene duplication and functional divergence, gene conversion, and equilibrium heterozygosity. It includes an introduction to the coalescent as well ... More
Chapter 4 focuses on forward and reverse mutation, gene duplication and functional divergence, gene conversion, and equilibrium heterozygosity. It includes an introduction to the coalescent as well as the Wright–Fisher and Moran models of random genetic drift, measures of nucleotide polymorphism and diversity, and how these may be estimated from sequence data. Biased gene conversion is discussed in regard to its effects on homogeneity of nucleotide sequence across the genome. Several distinct types of effective population number are compared and contrasted including the inbreeding, variance, and coalescent effective numbers. Various models of migration are also examined including one-way migration, the island model, and stepping-stone models.Less
Chapter 4 focuses on forward and reverse mutation, gene duplication and functional divergence, gene conversion, and equilibrium heterozygosity. It includes an introduction to the coalescent as well as the Wright–Fisher and Moran models of random genetic drift, measures of nucleotide polymorphism and diversity, and how these may be estimated from sequence data. Biased gene conversion is discussed in regard to its effects on homogeneity of nucleotide sequence across the genome. Several distinct types of effective population number are compared and contrasted including the inbreeding, variance, and coalescent effective numbers. Various models of migration are also examined including one-way migration, the island model, and stepping-stone models.
Keywords: mutation, migration, gene conversion, gene duplication, subfunctionalization, allozyme polymorphism, coalescence, Wright–Fisher model, Moran model, effective population number
Mary Jane West-Eberhard
in Developmental Plasticity and Evolution
Earth Sciences and Geography, Palaeontology: Earth Sciences
Duplication occurs at all levels of phenotypic organization. It was among the first developmental phenomena to attract the attention of biologists ... More
Duplication occurs at all levels of phenotypic organization. It was among the first developmental phenomena to attract the attention of biologists interested in phenotypic transitions during evolution. Duplication and repetition of similar segments, or metamerism, appeared in the writings of Aristotle, Cuvier, Owen, and Darwin, and many early twentieth-century authors discussed it (reviewed in Lauder, 1981). More recently it has become a major theme in discussions of genetic diversification (e.g., Ohno, 1970; Weiss, 1990). Nijhout (1991a) considers iteration or redundancy of parts followed by divergence of the replicates "the major principle of morphological evolution." But it is not easy to rank modes of origin in order of their importance, because it is so easy to reclassify examples from different points of view. Just as heterochrony can be emphasized by focusing on the timing aspect of any regulatory change (as discussed in chapter 13), duplication can be emphasized by focusing on the iterative aspect of repeated expression at different times, places, or contexts. Phenotypic recombinations classified in these chapters as heterotopy, heterochrony, cross-sex transfers, or correlated shifts could be reclassified as duplications, since many are reexpressions of the same trait in a new place or context without loss of the original trait. Similarly, pleiotropy can be described as the duplicated expression of genes (Hamburger, 1980). This chapter focuses mainly on adjacent duplications that result in serial repetitions—serial homologues, or "iteration" (Nijhout, 1991a). Heterotopy, or nonadjacent duplication within the same individual and life stage, is discussed in chapter 14, even though the separation is somewhat arbitrary. The differences in position and surroundings that result in differences in phenotypic pattern are, in their effects, regulatory differences, and it is just such local differences that cause developmental processes to diverge. It is a difference in regulation, then, that causes duplicates to diverge phenotypically and ultimately renders them subject to diverging selection and divergent evolution. One could reason from this that divergence between duplicates is virtually inevitable given enough time, because the local developmental environments on all sides of duplicate parts would rarely be absolutely identical over long periods. Less
Duplication occurs at all levels of phenotypic organization. It was among the first developmental phenomena to attract the attention of biologists interested in phenotypic transitions during evolution. Duplication and repetition of similar segments, or metamerism, appeared in the writings of Aristotle, Cuvier, Owen, and Darwin, and many early twentieth-century authors discussed it (reviewed in Lauder, 1981). More recently it has become a major theme in discussions of genetic diversification (e.g., Ohno, 1970; Weiss, 1990). Nijhout (1991a) considers iteration or redundancy of parts followed by divergence of the replicates "the major principle of morphological evolution." But it is not easy to rank modes of origin in order of their importance, because it is so easy to reclassify examples from different points of view. Just as heterochrony can be emphasized by focusing on the timing aspect of any regulatory change (as discussed in chapter 13), duplication can be emphasized by focusing on the iterative aspect of repeated expression at different times, places, or contexts. Phenotypic recombinations classified in these chapters as heterotopy, heterochrony, cross-sex transfers, or correlated shifts could be reclassified as duplications, since many are reexpressions of the same trait in a new place or context without loss of the original trait. Similarly, pleiotropy can be described as the duplicated expression of genes (Hamburger, 1980). This chapter focuses mainly on adjacent duplications that result in serial repetitions—serial homologues, or "iteration" (Nijhout, 1991a). Heterotopy, or nonadjacent duplication within the same individual and life stage, is discussed in chapter 14, even though the separation is somewhat arbitrary. The differences in position and surroundings that result in differences in phenotypic pattern are, in their effects, regulatory differences, and it is just such local differences that cause developmental processes to diverge. It is a difference in regulation, then, that causes duplicates to diverge phenotypically and ultimately renders them subject to diverging selection and divergent evolution. One could reason from this that divergence between duplicates is virtually inevitable given enough time, because the local developmental environments on all sides of duplicate parts would rarely be absolutely identical over long periods.
Keywords: Alternative splicing, Bacteria, Combinatorial evolution, Diverging selection, Endosperm, Fibronectin, Gene duplication, Hemoglobins, Individuality, Mullerian mimicry
Gene duplication and hemoglobin isoform differentiation
Chapter 6 explores the physiological significance of gene duplication and hemoglobin isoform differentiation. Repeated rounds of gene duplication and divergence during the evolution of jawed ... More
Chapter 6 explores the physiological significance of gene duplication and hemoglobin isoform differentiation. Repeated rounds of gene duplication and divergence during the evolution of jawed vertebrates promoted the diversification of the subfamilies of genes that encode the different subunit chains of tetrameric hemoglobin, leading to functional differentiation between hemoglobin isoforms that are expressed during different stages of prenatal development and postnatal life. The differentiation in oxygenation properties among developmentally regulated hemoglobin isoforms has clear adaptive significance in viviparous and oviviparous vertebrates alike. In some cases, a physiological division of labor between coexpressed isoforms may also contribute to the adaptive enhancement of tissue oxygen delivery.Less
Chapter 6 explores the physiological significance of gene duplication and hemoglobin isoform differentiation. Repeated rounds of gene duplication and divergence during the evolution of jawed vertebrates promoted the diversification of the subfamilies of genes that encode the different subunit chains of tetrameric hemoglobin, leading to functional differentiation between hemoglobin isoforms that are expressed during different stages of prenatal development and postnatal life. The differentiation in oxygenation properties among developmentally regulated hemoglobin isoforms has clear adaptive significance in viviparous and oviviparous vertebrates alike. In some cases, a physiological division of labor between coexpressed isoforms may also contribute to the adaptive enhancement of tissue oxygen delivery.
Keywords: Keywords: developmental regulation, embryonic hemoglobin, fetal hemoglobin, gene duplication, isoform differentiation, isoform switching, placental gas exchange, Root effect
Fast rates of evolution in bacteria due to horizontal gene transfer
Weilong Hao
Horizontal gene transfer is recognized as a major force in shaping bacterial gene content and has gained incredible attention over the last decade, in part due to the fast growing number of sequenced ... More
Horizontal gene transfer is recognized as a major force in shaping bacterial gene content and has gained incredible attention over the last decade, in part due to the fast growing number of sequenced bacterial genomes. The genomic data have permitted an appreciation that rapid evolution in bacteria is mainly the result of the ability of almost all bacteria to horizontally acquire genes over evolutionary time. Many of these horizontal transfers can occur with multiple genes transferred per event. This chapter discusses some of the features and patterns of rapid evolution via horizontal transfer. In particular, it notes that methods which estimate rates of gene transfers, such as via parsimony or via maximum likelihood, suggest that the estimated levels of horizontal transfer are smaller than the true rates.Less
Horizontal gene transfer is recognized as a major force in shaping bacterial gene content and has gained incredible attention over the last decade, in part due to the fast growing number of sequenced bacterial genomes. The genomic data have permitted an appreciation that rapid evolution in bacteria is mainly the result of the ability of almost all bacteria to horizontally acquire genes over evolutionary time. Many of these horizontal transfers can occur with multiple genes transferred per event. This chapter discusses some of the features and patterns of rapid evolution via horizontal transfer. In particular, it notes that methods which estimate rates of gene transfers, such as via parsimony or via maximum likelihood, suggest that the estimated levels of horizontal transfer are smaller than the true rates.
Keywords: bacterial genome evolution, gene gain, gene duplication, horizontal gene transfer, bacterial genomes, maximum likelihood, multiple genes
Multiple Forms of Aromatase in Suiformes: Tissue Distribution, Regulation, and Functional Significance
Alan Conley, Veronica N. Orr, Brian C. Trainor, Trish Berger, and Austin Hughes
in Brain Aromatase, Estrogens, and Behavior
Neuroscience, Neuroendocrine and Autonomic
Pigs have three CYP19 genes encoding functional paralogues of aromatase cytochrome P450 expressed tissue specifically in the gonads/hypothalamus, placenta, and preimplantation blastocyst. Gene ... More
Pigs have three CYP19 genes encoding functional paralogues of aromatase cytochrome P450 expressed tissue specifically in the gonads/hypothalamus, placenta, and preimplantation blastocyst. Gene duplication is predicted to have relaxed selection pressure and allowed evolution of enzyme function. All isozymes catalyze estrogen synthesis. However, the "gonadal/hypothalamic" form (ghP450arom) is unique among mammalian aromatases in also synthesizing a nonaromatizable, biopotent testosterone metabolite, 1OH-testosterone (1OH-T) that is hypothesized to have promoted increased ovulation rate and litter size. High ghP450arom expression in porcine testis facilitates study of differential regulation in hypothalamus and gonads that is not possible in other species. These, the first such studies in pig brain, demonstrate unusual aspects of P450arom expression and regulation in the hypothalamus, offering promise of gaining better insight into roles of P450arom in reproductive function.Less
Alan ConleyVeronica N. OrrBrian C. TrainorTrish BergerAustin Hughes
Pigs have three CYP19 genes encoding functional paralogues of aromatase cytochrome P450 expressed tissue specifically in the gonads/hypothalamus, placenta, and preimplantation blastocyst. Gene duplication is predicted to have relaxed selection pressure and allowed evolution of enzyme function. All isozymes catalyze estrogen synthesis. However, the "gonadal/hypothalamic" form (ghP450arom) is unique among mammalian aromatases in also synthesizing a nonaromatizable, biopotent testosterone metabolite, 1OH-testosterone (1OH-T) that is hypothesized to have promoted increased ovulation rate and litter size. High ghP450arom expression in porcine testis facilitates study of differential regulation in hypothalamus and gonads that is not possible in other species. These, the first such studies in pig brain, demonstrate unusual aspects of P450arom expression and regulation in the hypothalamus, offering promise of gaining better insight into roles of P450arom in reproductive function.
Keywords: aromatase, domestic pig, evolution, gene duplication, gonads, hypothalamus, placenta, reproductive function, suiforme
Genomes and the origin of genetic variation
Glenn-Peter Sætre and Mark Ravinet
in Evolutionary Genetics: Concepts, Analysis, and Practice
Biology, Evolutionary Biology / Genetics, Biomathematics / Statistics and Data Analysis / Complexity Studies
Error and chance events, random mutations, are necessary prerequisites for evolution to happen. In a perfect world with no mutations there would be no evolution because no genetic variation would be ... More
Error and chance events, random mutations, are necessary prerequisites for evolution to happen. In a perfect world with no mutations there would be no evolution because no genetic variation would be generated that natural selection or genetic drift could work upon. This chapter first reviews how DNA is organized into genomes and genes in bacteria, archaea, and, in greater detail, eukaryotes. A surprising finding is that only a small fraction of the eukaryote genome consists of coding sequence. Evolutionary processes that can explain the presence of large amounts of noncoding DNA and the repetitive structure of the genome are reviewed, with emphasis on the roles that selfish genetic elements and unequal crossing over play. The chapter further explores the mechanisms that cause mutation and how new genes and protein functions originate.Less
Glenn-Peter SætreMark Ravinet
Error and chance events, random mutations, are necessary prerequisites for evolution to happen. In a perfect world with no mutations there would be no evolution because no genetic variation would be generated that natural selection or genetic drift could work upon. This chapter first reviews how DNA is organized into genomes and genes in bacteria, archaea, and, in greater detail, eukaryotes. A surprising finding is that only a small fraction of the eukaryote genome consists of coding sequence. Evolutionary processes that can explain the presence of large amounts of noncoding DNA and the repetitive structure of the genome are reviewed, with emphasis on the roles that selfish genetic elements and unequal crossing over play. The chapter further explores the mechanisms that cause mutation and how new genes and protein functions originate.
Keywords: genome structure, mutation, recombination, transposable elements, virus, introns, exons, RNA, concerted evolution, gene duplication
This chapter summarizes key points and provides an outlook to future challenges. It discusses how evolutionary innovations involve changes in the following three classes of biological systems: ... More
This chapter summarizes key points and provides an outlook to future challenges. It discusses how evolutionary innovations involve changes in the following three classes of biological systems: metabolic networks, regulatory circuits, and proteins and RNA molecules. It also covers the following topics: neutralism and selectionism, robustness, gene duplication, recombination, phenotypic plasticity, and changing environments and innovation.Less
This chapter summarizes key points and provides an outlook to future challenges. It discusses how evolutionary innovations involve changes in the following three classes of biological systems: metabolic networks, regulatory circuits, and proteins and RNA molecules. It also covers the following topics: neutralism and selectionism, robustness, gene duplication, recombination, phenotypic plasticity, and changing environments and innovation.
Keywords: evolution, biological systems, metabolic networks, regulatory circuits, proteins, RNA molecules, neutralism, selectionism, gene duplication, phenotypic plasticity


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Perhaps using group policy, registry editor, windows settings, and etc.
Since windows 7 configurations differ somewhat from windows 8, the settings that worked for windows 7 does not work for windows 8.


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Some may say I've been a little angsty this week, and some would be right. It's one part cabin fever and one part jittery restlessness and one part What Am I Even Doing With My Life, Episode 107. As of yesterday, it's also one part Is It Still 2017? because the Jaguars are not going to their first Super Bowl and the Patriots are going to their first Super Bowl since last year.
It's no secret that I'm not really wired for complex athletic endeavors. "Complex" meaning anything other than walking and sometimes running. However, I may have arrived at a new low over the weekend.
I've learned a thing or two in my 30 years of life, and one of those things is this: comfort > style.
I'm not exactly rolling into work in my pajamas or anything, but let's just say I've embraced a flexible definition of the word "pants." So yesterday morning, when I was deciding what to wear and I wanted to go with the Nice Black Shoe option, I came to a crossroads.
Earlier this week, after reading this post by Melanie Shankle, I realized it had been far too long since I'd posted an interesting life anecdote here. My car, as per all of the times, saw the gleaming door of opportunity and charged straight through it.
So, my headlight went out earlier this week. No big deal. I called my mechanic and he told me to bring it in anytime. Fantastic.
You now have my week in a nutshell.
I tend to be impulsive when it comes to creative things. It's not that I have an aversion to pre-planning, it's that I go from idea to action in 60 seconds or less. It's how the Pinterest wall was born. That was good.
It's also how I came to have red hair.
That was not so good.