text:
Chat with Michael DiRocco
Welcome to SportsNation! On Friday, ESPN NFL Nation Jacksonville Jaguars reporter Michael DiRocco drops by to chat and answer all of your Jaguars questions.
DiRocco covered the University of Florida for 13 years, including 10 with the Florida Times-Union, before moving to the Jaguars beat with ESPN.com. A graduate of Jacksonville University and a multi-APSE aware winner, DiRocco lives in Middleburg, Fla. with his wife and two sons.
Send your questions now and join DiRocco Friday at 3 p.m. ET!
More Michael DiRocco: Jaguars blog | Chats | @ESPNDiRocco | NFL index
Michael DiRocco (2:58 PM)
Hello everyone. Let's get started. Before we do, a quick note: This will be the last chat until July 24. I'm going on vacation and we're not going to have one on July 17.
James (KY)
So we've hit a "Dead Zone" until July so i wanted to pose some "what if" questions. IF Blackmon had never gotten into trouble this past season and stayed clean and active how much different do you think that would have changed Caldwell and the Jag's draft plans? Do you think they still would have drafted Lee in the 2nd? and if not who else do you think they may have drafted there if not a WR? If they would have drafted an O-Lineman in the 2nd do you think they still move back into the 2nd for Robinson or do you think they may have gone WR in the 3rd?
Michael DiRocco (3:02 PM)
James: That's a good question. I think they still may have taken Lee in the second because I know they liked him a lot and were surprised he was not taken in the first round. They didn't think they'd be able to get him at all but when he fell into their lap they couldn't resist. But I don't think they then would have traded back into the second round to get Robinson. Then they take Linder in the third ...
Kyle (CA)
Should the Jaguars sign Tebow to take the reigns while Bortles learns from the bench?
Michael DiRocco (3:02 PM)
Kyle: No.
Chris Fiegler (Latham,NY)
When do you think that the Jacksonville Jaguars will see Blake Bortles Starting Games in 2014?
Michael DiRocco (3:02 PM)
Chris: I think he'll be on the field sometime in December, after the Jags have been eliminated from the playoff picture.
Dirk (Jax, Fl)
I find it encouraging and shows just how tough these players are to go through what they do. Take D Rob with nerve damage to where he had no feeling, and than take all that criticism without ever blaming the injury. Austin Pastor with playing with one shoulder, and Josh Evans with bone spurs are a couple more examples. It makes me wonder what other players might have had a deli-bating injury. Maybe Zane Beadles having been a pro bowler the year before might have had a bad injury this past year that resulted in a down year. Do you know of any other players and or specifically why Beadles had a down year?
Michael DiRocco (3:04 PM)
Dirk: I know Roy Miller also had a bad shoulder that really limited his effectiveness. Geno Hayes had a bad knee. And don't forget Cecil played through a shoulder joint injury and the sports hernia for a while. I have not heard, from outside the organization or inside, that Beadles had an injury last year. It may have just been a down year for him. That happens. But even if he only plays marginally better than he did last year it's still an upgrade for the Jags at that position.
Otto (CA)
Is Marqise Lee's ankle OK?
Michael DiRocco (3:05 PM)
Otto: He was out the boot by the end of minicamp and he is expected to be cleared completely for the start of training camp.
Wayne Dawson (Richmond Heights)
No question this week. Just wanted to tell you that we hope you have a great vacation. Thanks for the chats.
Michael DiRocco (3:06 PM)
Wayne: Thank you. I'm not sure what I'm going to do with myself at 3 p.m. the next three Fridays -- other than be on the 15th hole, putting a line in the water, or enjoying an ice-cold ... drink.
Dirk (Jax, Fl)
When watching Henne last year it seemed he would look really good a couple games than have a couple bad games. Is this due to the mental part of the game, and just Henne being not yet being comfortable in the system. Is it more about reading defenses or something else? He seems to have all the physical tools to succeed, whats missing?
Michael DiRocco (3:09 PM)
Dirk: It's a little bit of everything that you mentioned. He has not been in an offensive system for back-to-back years, so that impacts his decision-making on the field. He's making quicker decisions now and that was evident in the way he looked during OTAs and minicamp. He's a pretty bright guy and didn't put the Jags into very bad situations. I don't recall a pass last year in which I went, "What the heck was he thinking?" I'm sure there were a few but the fact that none stick out -- unlike Gabbert's intercepted screen pass in the opener -- is a good sign. That being said, he's not an elite QB. He can be a solid QB and one that can lead a team to the playoffs if he's got a good cast surrounding him.
Brian (Cville, VA )
Based on what you've heard from scouts about Bortles, how was he viewed historically agaisnt QB prospects? Obviously he wasn't a Luck/RG3/Elway caliber, but surely he wasn't a Gabbert/Locker/Ponder either. Have most scouts (especially non-Jaguars) given you the impression they see him as a top 10 QB 5 years from now?
Michael DiRocco (3:12 PM)
Brian: Bortles wasn't viewed as a player who could come in and start right away. He needed some fundamental work and a few other minor tweaks. I'd say he was closer to an E.J. Manuel, Christian Ponder. Not comparing them, but closer to that end of the spectrum rather than the Andrew Luck/Cam Newton end. As for 5 years from now, that's way too early to speculate.
Brian (Cville, VA )
At the end of the year ________ will have caught the most balls for the Jaguars out of the backfield? (i.e. Gerhart, Robinson, Sanders)
Michael DiRocco (3:13 PM)
Brian: Gerhart. He's a better pass catcher than people think.
Brian (Cville, VA)
Blake Bortles has a (better, worse, too close to call) arm than Blaine Gabbert.
Michael DiRocco (3:14 PM)
Brian: worse. Gabbert did have a pretty strong arm. That being said, it's not like Bortles is throwing lollipops. He's got a good arm. It's just not as strong as Gabbert's.
Tyler (Louisville, KY)
Mike, what do you think the future is for Chris Prosinski?
Michael DiRocco (3:15 PM)
Tyler: It's going to be tough for him to make the roster. He's a good special teams player and can really run but the Jags brought in several safeties, including Sherrod Martin, who started 36 games for Carolina. I don't think he makes the roster this year.
Damian Moody-Smith [via mobile]
Too early prediction time: Superbowl winner? Outsider to watch for Superbowl? Jags record? Keep up the good work!
Michael DiRocco (3:15 PM)
Damian: As long as I'm not held to these picks -- San Francisco, Cincinnati, 6-10/7-9.
Brian (Cville, VA)
The most talented RB currently on the Jaguars roster is ___________.
Michael DiRocco (3:16 PM)
Brian: Toby Gerhart. He's the most talented as far as being a RB. But the most physically talented of the group may be Denard Robinson.
Jason (Jax, FL)
Is all the Denard Robinson hype real? Could this be breakout year for him? Can we expect OW to play like a o-weapon?
Michael DiRocco (3:17 PM)
Jason: I'm beginning to think it is. He's looked great catching the ball and we know what he can do in the open field. If he's able to prove he can be a reliable pass catcher than he will have a breakout year.
Jason (Jax, FL)
Best FA acquisition this offseason so far, in your opinion>
Michael DiRocco (3:19 PM)
Jason: Gerhart. I know I said I want to see him do it on the field to prove he can, but I like what I've seen from him in OTAs and minicamp.
Brian (Cville, VA)
Which Marqise Lee do you think the Jaguars drafted? The one that looked like a top 5 pick in 2011 & 2012 or the one that stayed dinged up in 2013 and will have trouble staying on the field in the NFL?
Michael DiRocco (3:20 PM)
Brian: I would have told you the first one after the draft, but now I'm not sure. It's not good that he hurt his ankle in one of his first workouts. But lets give him the benefit of the doubt. If he gets banged up in training camp then that's a legitimate concern.
Brian (Cville, VA)
I've heard you say that Henne is looking great in camp. Do you think he just struggled with not being named the starting QB in year's past or....
Michael DiRocco (3:21 PM)
Brian: I think he just wasn't comfortable completely with the offense. He had a new one to learn each year. This is his second year in Fisch's offense and I think that's a huge deal for him.
Damian Moody-Smith [via mobile]
Which Jags players are entering the last year of their contracts this coming season?
Michael DiRocco (3:24 PM)
Damian: Ricky Stanzi, Cecil Shorts, Tyson Alualu, Roy Miller, Geno Hayes, Alan Ball, Chris Prosinski, and Sherrod Martin will be unrestricted free agents after 2014. Jordan Todman, Will Ta'ufo'ou, Jacques McClendon and Mike Brewster will be restricted free agents after 2014.
Brian (Cville, VA)
In Alualu's second offseason, there was a buzz that he was ready to be a world-beater (8+ sack guy at DT). Then he hurt his knee and he's been a JAG (just another guy) since. Have you heard this story and gotten any info on it?
Michael DiRocco (3:26 PM)
Brian: From what I understand, Alualu actually hurt his knee during one of his first training camp practices and played through it his rookie season. I heard that it occurred during an Oklahoma drill, which is something that Jack Del Rio liked to have. Other teams don't do it because of injury risk and it really serves no purpose.
Brian (Cville, VA)
I'm a UVA fan. I loved watching Pasztor play a very solid RT for us last year. (In case you were wondering he didn't start a game at OT at UVA). What do you think his ceiling is in the NFL?
Michael DiRocco (3:28 PM)
Brian: I know David Caldwell likes him and believes he can be a very good right tackle. I don't see him being an elite player but there aren't many right tackles that are. As he gets more comfortable at that spot he'll get better.
Ryan (Las Vegas, NV)
What will the strength of this Jaguars team be?
Michael DiRocco (3:30 PM)
Ryan: The defensive line should be better. There's more depth and the addition of Clemons and Bryant give the Jags two top-flight defensive ends. A healthy Roy Miller and the addition of Ziggy Hood will help against the run.
Michael DiRocco (3:30 PM)
Brian: Nope. He'll eventually have to change.
Michael DiRocco (3:31 PM)
Ed: I can see Chad Henne doing that. When he goes back to Michigan in the summer he works with a high school football team so he can stay sharp throwing. He is essentially the receivers and QBs coach for a while.
Michael DiRocco (3:32 PM)
Yankees: I'm sorry, I didn't understand your question because I was too busy polishing my 2013 World Series ring.
Brian (Cville, VA)
Blake Bortles one trait that will most help him succeed in the NFL is _________________________.
Michael DiRocco (3:34 PM)
Brian: He's a gym rat and loves football. Don't under-estimate how important that is. The great ones live football and he does, too.
Brian (Cville, VA)
Give me a player drafted rounds 4 or later in last year's draft and this year's draft that we'll look back on in 3 years and think "man, what good value they got considering where he was drafted".
Michael DiRocco (3:35 PM)
Brian: That's easy for this year. CB Aaron Colvin. Were it not for a torn ACL he would have been likely a second-round pick. If Denard Robinson (fifth round) has solved his pass-catching issues then he could be a playmaker.
Brian (Cville, VA)
Marcedes Lewis will catch over/under 7.5 TDs this year? Over/under 64.5 receptions?
Michael DiRocco (3:36 PM)
Brian: Under on both. I don't think 50 catches and 5 TDs are out of the question, though.
Dave (Miami)
How hands-on or hands-off is Shad Khan?
Michael DiRocco (3:37 PM)
Dave: He's pretty hands off. He lets the people he hires do their job. As far as owners go, he's the anti-Jerry Jones.
Brian (Cville, VA)
Look into your crystal ball.....Justin Blackmon will be the next Cris Carter or the next R Jay Soward?
Michael DiRocco (3:38 PM)
Brian: At this point I'm leaning more toward R. Jay Soward. I haven't seen any indication that he is moving forward to solve his issues, as Gene Frenette wrote about last weekend.
Chris Fiegler (Latham,NY)
Where does the Jacksonville Jaguars have their Summer Training Camp?
Michael DiRocco (3:42 PM)
Chris: At the practice fields adjacent to EverBank Field.
Damian Moody-Smith [via mobile]
Would you agree linebacker appears so far to be the position of weakness? What do you expect from this group this season?
Michael DiRocco (3:54 PM)
Damian: I'd agree with that on defense. The group has to make more plays and has to get faster. I think the addition of Dekoda Watson is going to be a big help provided he's healthy. Telvin Smith won't make a huge impact this year but I can see him being a regular playmaker in 2-3 years. I'm expecting the group this year to make a few more big plays than it did last year but my expectations overall are for the unit to not be worse than 2013.
Dave (Miami)
So where you vacationing?
Michael DiRocco (3:55 PM)
Dave: We are going whitewater rafting and camping in the mountains. Then I'm gonna play a lot of golf.
Damian [via mobile]
Whats your offensive weakness then? Interior o line probably biggest concern?
Michael DiRocco (3:58 PM)
Damian: That and what the receivers will look like after Cecil and Ace. Plus, will Ace be able to duplicate the success he had last year? How much can the two rookies contribute?
Bert (Zumbrota, MN)
The "highlights" of Storm Johnson look more like a prototypical running back than any other in the draft. I know that there are some negative factors as well, but how are things looking for him at the moment?
Michael DiRocco (4:01 PM)
Bert: He was impressive in OTAs and minicamp. Caught the ball well and looked strong running with it. But it wasn't in pads. His two biggest areas of improvement, according to Gus Bradley, are pass protection and ball security. We'll see how much work he has to do in those areas in training camp.
Michael DiRocco (4:02 PM)
OK everyone, that's it for this week -- and until July 24. I want to thank you all for participating. There were a lot of people that doubted there would be anyone in this chat when I first started it and the number of participants has exceeded my expectations. Thanks again and I'll talk to you again on July 24.
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We have characterized a newly identified 16.6 kb deletion which removes a significant proportion of the human α-globin cluster including the ψζ1, α D , ψα1 and α2-globin genes but leaves the duplicated α1 gene intact. This complicated rearrangement results from a combination of slippage and strand switching at sites of microhomology during replication. Functional analysis shows that expression of the remaining α1 gene is increased, rather than down-regulated by this deletion. This could be related to its proximity to the remote upstream α-globin regulatory elements or reduced competition for these elements in the absence of the dominant α2-globin gene. The finding of a very mild phenotype associated with such an extensive deletion in the α-globin cluster implies that much of the DNA removed by the deletion is likely to be functionally unimportant. These findings suggest that other than the upstream regulatory elements and promoter proximal elements there are unlikely to be additional positive cis -acting sequences in the α-globin cluster.
The human α-globin cluster lies close to the telomere of chromosome 16 (16p13.3) and includes an embryonic gene (ζ2), two fetal/adult α genes (α2 and α1), two minor globin-like genes (α D , θ) and two pseudo genes (ψζ1 and ψα1) arranged in the order; telomere-ζ2−ψζ1−α D −ψα1−α2− α1−θ-centromere (Fig. 1 A). Expression of the α-like globin genes is controlled by remote sequences (multispecies conserved regulatory elements, MCS-R1 to 4) lying 10–48 kb upstream of the α-globin genes, of which MCS-R2 appears to be the major regulatory element ( 1 ).
Natural mutations of the human α-globin cluster and their regulatory elements have provided important insights into the general mechanisms by which mutations may arise and influence gene regulation ( 2–9 ). These chromosome rearrangements in turn provide important information relating genome structure to function. Normal individuals have two α-globin genes (αα) on each copy of chromosome 16 (αα/αα) producing sufficient α-globin chains to balance the β-like globin chains encoded on chromosome 11, thus making the predominant adult (HbA, α 2 β 2 ) and fetal (HbF, α 2 γ 2 ) hemoglobin tetramers. Variant chromosomes with no (- -), or one (-α) α-globin gene are common causes of α-thalassemia, associated with tetramers of excess β [HbH (hemoglobin H), β 4 ] and γ (Hb Bart's, γ 4 ) globin chains. Typically, individuals with α-thalassemia are anemic, with small red cells (reduced mean corpuscular volume, MCV) containing reduced amounts of Hb (reduced mean corpuscular hemoglobin, MCH). The α-thalassemias are amongst the most common of all human genetic diseases ( 10 ). Rare cases of α-thalassemia result from deletions removing one or more of the regulatory elements ( 1 ).
In addition to mutations that cause thalassemia there are many naturally occurring SNPs (single nucleotide polymorphisms) and CNVs (copy number variations) at the α-globin cluster that do not cause thalassemia or any red cell changes. These mutations either cause only minor changes in α-globin expression or no significant change at all. Such point mutations and rearrangements are useful because they define regions of the chromosome that have no influence on α-globin expression, thus complementing and validating experiments designed to understand how the α-globin cluster is normally regulated within its natural chromosomal context in vivo ( 11 ).
Here we describe a deletion which removes 16.6 kb from the human α-globin cluster, including the ψζ1, α D , ψα1 and α2 genes together with a substantial amount of intergenic non-coding DNA, but leaving the α1 gene intact. Detailed analysis of the breakpoints of the deletion revealed a complex rearrangement in which the 5′ and 3′ breakpoints are joined by an inverted segment of DNA derived from the ψζ1 gene. It seems most likely that this has arisen via the process of slippage and strand switching during replication, a mechanism recently highlighted by Chen et al . ( 12 ) and Lee et al . ( 13 ). We show that this extensive deletion from the α-globin cluster does not down-regulate expression of the remaining α1 gene. The mutation adds significantly to data from previously reported rearrangements of the α-globin cluster and transgenic experiments, demonstrating that (other than the upstream MCS-R elements) there are no additional positive cis -acting elements in the 20 kb containing this multigene family other than those in the immediate vicinity of the globin genes themselves.
Identification of a family with a novel rearrangement of the α-globin cluster
In neonates with α-thalassemia, the imbalance in globin chain synthesis results in an excess of free γ-globin chains which form Hb Bart's. During switching (γ to β), an elevated level of Hb Bart's at birth can be detected and provides a sensitive indicator of α-thalassemia ( 11 ). The propositus (EN), of Vietnamese origin, was first identified via a cord blood survey of an ethnically diverse UK population ( 14 ). The level of Hb Bart's in the cord blood was 4.9%, which lies at the upper end of the levels seen in individuals missing a single α-globin gene (-α/αα).
Using multiplex ligation-dependent probe amplification (MLPA) as an initial screen for DNA deletions, we identified reduction in gene copy number at probes: HBZP, HBAP2, HBAP1 and ψα1−α2 indicating a deletion of at least 8 kb from the α-globin cluster (Fig. 1 A and B). Southern blot analysis of DNA from the propositus demonstrated an abnormal pattern consistent with a deletion. This was confirmed by analyzing an interspecific hybrid containing the abnormal copy of chromosome 16 in a mouse erythroleukemia (MEL) cell background. The most informative results were derived from digests using Bgl II, Hin dIII and Spe I analyzed with ζ and α probes (Fig. 1 A and C). The 5′ breakpoint of the deletion was localized to a region of 5.8 kb between ζ2 and ψζ1 flanked by Hin dIII (co-ordinate 147782) and Bgl II (co-ordinate 153170) restriction sites while the 3′ breakpoint was delimited to a 0.78 kb region between α2 and α1 flanked by Bgl II (co-ordinate 165301) and Spe I sites (co-ordinate 166073) (Fig. 1 A and C). The position of the breakpoints was further refined by designing various primers throughout these breakpoint regions which were tested (in combination) until a specific and reproducible amplification product spanning the breakpoint was obtained (Fig. 1 D). A family study showed that this rearrangement was carried by both the propositus (EN) and the mother (BV), who have very mild hematological defects (Table 1 ). The red cell indices are at the mild end of the range observed with a single α-globin gene deletion (-α/αα) and are bordering the normal range (Table 1 ). The mild phenotype of EN at age nine contrasts with the high level of Hb Bart's (indicative of a more severe phenotype) detected at birth, suggesting that this defect may have somewhat different effects during fetal and adult life. As a result of the very mild adult phenotype, we would anticipate that had this patient not been detected in a neonatal screen for Hb Bart's at birth, she would have most likely evaded detection by conventional screening strategies in later life.
|BV (mother)
|EN (propositus)
|TN (father)
|Age (at testing)
|Hb (g/dl)
|MCV (fl)
|MCH (pg)
|HbA 2
|HbH inclusions
|Not tested
|-α 16.6 /αα
|-α 16.6 /αα
|BV (mother)
|EN (propositus)
|TN (father)
|Age (at testing)
|Hb (g/dl)
|MCV (fl)
|MCH (pg)
|HbA 2
|HbH inclusions
|Not tested
|-α 16.6 /αα
|-α 16.6 /αα
The data show the hematological results detected in the propositus (EN, at age 9), her mother (BV, at age 31) and her father (TN, at age 26). The mother (BV) and the propositus (EN) are mildly anemic and lie within the ranges observed in individuals with the -α/αα genotype (frequently referred to as silent α-thalassemia) which also overlaps the normal range ( 33 ).
Sequence analysis across the deletion breakpoints
The PCR product, which specifically amplifies this rearrangement (Fig. 1 D), was sequenced. Comparison with the wild-type sequence shows that the 5′ deletion breakpoint lies between 148978 and 148982 and the 3′ breakpoint between 165614 and 165622. Surprisingly, the breakpoints were found to be joined by an insertion of unknown sequence of ∼360 bp. Subsequent analysis showed the insertion to contain a series of imperfect tandemly repetitive elements with high homology (99%) to a region in the ψζ1 gene (co-ordinates 153221–153582) which contains a 248 bp simple tandem repeat (GGGGA) n (Fig. 2 ). The insertion is also related to a similar region in the ζ2 gene (89% homology). It is of interest that the insert at the breakpoint lies in the opposite orientation to that seen in the wild-type ψζ1 pseudogene. Close inspection of the 5′ and 3′ breakpoints revealed some ambiguity; the extent of the deletion is between 16632 and 16644 bp and the insertion is between 361 and 373 bp (Fig. 2 A). It was not possible to define these sizes more precisely because of microhomology between sequences flanking the deletion and sequences flanking the repeat elements of the inserted DNA (Fig. 2 A and B). It seems most likely that this rearrangement (designated -α 16.6 ) arose via an error in replication repaired by switching of DNA strands as described in Discussion.
To ensure that the phenotype resulted solely from this rearrangement, the remaining α-globin genes and the major upstream regulatory element (MCS-R2) were also sequenced and found to be wild-type, as were the β-globin genes.
Functional analysis of the -α 16.6 chromosome
Although the 16.6 kb deletion removes a significant portion of the α-globin cluster (including ψζ1, α D , ψα1 and α2 genes) it leaves the α1 gene intact. The hematological data in the two family members who carry this deletion (Table 1 ) are consistent with the mild type of α-thalassemia which occurs in individuals with three functional α-globin genes (-α/αα) rather than four (αα/αα) ( 11 ) implying that the remaining α1-globin gene on the abnormal chromosome (-α 16.6 ) is expressed normally.
To investigate expression from the α1 gene directly we established interspecific (MEL × chromosome 16) hybrids containing single copies of either the normal (αα) or abnormal (-α 16.6 ) chromosome 16 from the patient, BV. Such hybrids were induced into terminal erythroid maturation (and globin gene transcription). Since some hybrid cells may lose a whole or partial copy of chromosome 16 during cell division, Southern blot analysis was used to estimate human α-globin gene copy numbers at the time of harvesting each culture (data not shown).
An RNA protection assay (RPA) identifying human and mouse specific transcripts was used to estimate the relative amounts of human and mouse α-globin in each hybrid culture ( 15 ). These values were then corrected for the estimated human and mouse gene copy numbers per cell. Abundant amounts of human α-globin RNA were detected in hybrids containing the -α 16.6 chromosome, confirming that the remaining α1 gene on this chromosome was active (Fig. 3 A). Quantitation of these data (Fig. 3 B) provisionally suggested that this α1 gene was expressed at higher levels than the normal α1- and α2-globin genes. More importantly, finding no significant down-regulation of the remaining α1 gene is consistent with the mild phenotype observed in adults (Table 1 ).
Chromatin structure and recruitment of RNA polymerase II at the -α 16.6 chromosome α1 gene
To investigate the functional status of the remaining α1 gene in more detail, we looked for markers of gene activation across the α-globin cluster on the mutant -α 16.6 chromosome.
Gene activation is usually associated with histone acetylation (H3ac and H4ac) at the promoter of the gene in question ( 16 ). We therefore determined the pattern and quantified the relative levels of histone acetylation across both normal (αα) and abnormal (-α 16.6 ) chromosomes in induced MEL hybrids at specific points of interest by chromatin immunoprecipitation (ChIP) (Fig. 4 A). In general, the pattern of H3ac and H4ac over the intact α-globin gene and the surrounding region on the -α 16.6 chromosome was very similar to that observed on the normal chromosome (αα) (Fig. 4 B and C). These patterns of histone modification were also consistent with our previous analyses of histone acetylation across the human α-globin cluster in primary erythroid cells, with H3ac primarily occurring at the promoter and body of the gene and H4ac occurring at both the gene and the upstream regulatory elements ( 17 ). The bodies of the nearby, ubiquitously expressed housekeeping genes ( c16orf8 and LUC7L ) demonstrated relatively low levels of acetylation (serving as a negative control) whereas the promoter of one such gene ( c16orf35 ; probe HS-14 on Fig. 4 ) was acetylated (serving as a positive control).
We next analyzed the recruitment of RNA polymerase II (Pol II) at the α-globin cluster by ChIP. Pol II was present at the α-globin promoter on the -α 16.6 chromosome. Furthermore, the level of enrichment was significantly higher than on the normal chromosome 16 (Fig. 4 D) consistent with the higher level of RNA expression per gene seen from this chromosome. As expected, comparatively low levels of enrichment were observed at the other points of interest across the entire α-globin gene cluster, upstream regulatory elements and surrounding genes of both wild-type and mutant chromosomes (Fig. 4 D). These results therefore confirm that Pol II is recruited to the activated, single, intact α1 gene on the -α 16.6 chromosome and may be increased with respect to each of the two α genes on a normal chromosome (αα).
Although the globin gene clusters are amongst the most intensively studied of all loci, the details of their tissue-specific and developmentally regulated expression are still not clear. This underscores the complexity and consequent difficulties in establishing the general principles underlying mammalian gene regulation. This problem is compounded by observations demonstrating that some of the mechanisms (both in cis and trans ) by which specific genes are regulated differ between human and experimental models, such as mouse ( 18 , 19 ). Furthermore, the interpretation of transgenic models may be compromised by factors such as chromosomal position effects and variation in gene copy numbers. Careful analysis of natural variants in human populations therefore continues to provide an invaluable and essential approach to complement experimental systems.
Superficially the human α-globin cluster, which spans ∼30 kb comprising five genes and two pseudogenes, appears complex and yet here we have shown that removal of 16.6 kb including the ψζ1, α D , ψα1 and α2 gene does not down-regulate the remaining α1 gene suggesting that this region contains no positive cis -acting elements. This observation prompted us to review previously published deletions that either have no discernible effect on α-globin expression, or remove one of the duplicated α-globin genes but have no effect on the remaining gene (Fig. 5 A). Together these mutations suggest that the only critical regulatory sequences in this region are those spanning the structural gene and its promoter (∼3.5 kb of the 30 kb).
The other critical cis -acting sequences lie outside the multigene family. These are the four highly conserved non-coding sequences referred to as upstream regulatory elements (MCS-R1 to 4). Natural deletions of these elements which cause α-thalassemia all remove MCS-R1 and R2 ( 20 ), and experimental data suggest that MCS-R2 is the major regulatory element ( 1 ). None of the other elements has enhancer activity on their own or in combination and their role (if any) is not yet clear.
It has recently been shown that during erythropoiesis, the upstream elements and the α-globin promoters become progressively bound by key transcription factors to form multiprotein/DNA complexes which eventually physically interact as Pol II is recruited to the α-globin promoters ( 21 ). A similar interaction has also been observed at the β-globin cluster ( 22 ); in this case between the upstream elements (referred to as the β-globin locus control region, β-LCR) and the promoters of the five β-like genes. It has been proposed that the β-LCR can only interact with a single promoter at any time, creating competition between multiprotein complexes at each promoter for access to the β-LCR. If such competition for the α-globin upstream elements occurred between the different adult α-globin promoters (α2, α1) this could explain why we observed increased loading of Pol II and RNA transcription (per gene copy) from the single α-globin gene in the -α 16.6 chromosome: in this case, all of the activity of the upstream elements would be directed to one gene rather than two (Fig. 5 B). In support of this, it has been previously suggested that removal of a single α-globin gene in the common deletions that cause α-thalassemia (-α 3.7 and -α 4.2 ) may be associated with a compensatory increase in the expression of the remaining α1 gene ( 23 ). Although this scenario is most likely we cannot exclude the possibility of the deletion removing repressive cis -acting elements. This might be resolved in the future by performing similar analysis using chromosomes carrying the common -α 4.2 deletion.
Natural mutations may also help to elucidate other nuclear processes including replication and recombination. Most frequently α-thalassemia results from deletion of one (-α) or both (- -) of the duplicated α-globin genes. Such chromosomes occur at high frequencies in all tropical and subtropical regions of the world because heterozygotes (-α/αα, -α/-α and - -/αα) are thought to be at an advantage in the presence of endemic falciparum malaria ( 24 ). This is balanced by the severe phenotypes of compound heterozygotes (- -/-α, HbH disease) and homozygotes (- -/- -, Hb Bart's hydrops fetalis). To date >50 deletions associated with α-thalassemia have been described and they provided amongst the first examples of non-allelic homologous recombination, and illegitimate recombination in the human genome. The -α 16.6 chromosome described here provides an example of a complex rearrangement in which a region between two breakpoints has been repaired by an inverted sequence derived from the ψζ1 gene (Fig. 2 ). The structure of this rearrangement is very similar to that found in the breakpoint of the - - MED deletion, first described almost 20 years ago ( 6 ). At that time we proposed that the - - MED deletion had arisen by repairing a double strand break (arising during replication) with an Okazaki fragment from the lagging strand of a closely opposed replication loop. This mechanism has more recently been set out in greater detail ( 13 ). In Lee et al . ( 13 ), it was proposed that a replication Fork Stalling and Template Switching (FoSTeS) event can occur when the nature of the sequence causes a replication fork to stall or pause such that the lagging strand disengages and switches to a nearby template at another active replication fork where there is a region of microhomology. It therefore seems likely that the -α 16.6 rearrangement has arisen by a similar mechanism as illustrated in Figure 6 and that this may be a common mechanism underlying deletions, insertions, transpositions and duplications in the human genome.
Over the past few years, in the field of human genetics, there has been considerable interest in understanding the origins and influence of CNV on gene expression. The detailed analysis of a single locus continues to shed new light on such effects and gives some insight into the potential complexity associated with this phenomenon.
Hematological studies
Patient consent was obtained in accordance with standard ethics approval guidelines. Full blood counts, examination of peripheral blood films, high performance liquid chromatography (Biorad Variant™, Biorad, Hercules, USA) analysis of hemoglobin and identification of HbH inclusions were performed as previously described ( 14 , 25 ).
Cell culture
Epstein-Barr virus (EBV)-transformed B-lymphocyte cell lines were established from the mother of the propositus (BV) and a number of normal individuals. Interspecific hybrids containing the abnormal chromosome -α 16.6 were established by fusing EBV-transformed lymphocytes from the patient and normal to MEL cells as previously described ( 26 ). These cells were induced for 3 days to undergo terminal differentiation using HMBA (25 m m ) and Hemin (0.3M) as previously described ( 15 ).
DNA analysis
Characterization of -α 16.6 deletion breakpoints
DNA was extracted with phenol and chloroform using standard methods. The α-globin genotypes were determined as previously described ( 27 ). MLPA (Service XS, Leiden, The Netherlands) was performed as described previously ( 28 ). Further mapping of the -α 16.6 breakpoint by Southern blot analysis was performed with a variety of restriction enzymes (including Bgl II, Hin dIII and Spe I) using α and ζ probes. Known DNA sequences around the 5′ and 3′ breakpoints were used to design forward 506 (5′-CTCATCCAGACTCTCCAGCTG-3′) and reverse 507 (5′-CAAGTACACACAGAGGTGC-3′) PCR primers which amplified across the deletion. The 1091 bp breakpoint fragment generated was sequenced directly using the same primers, in addition to a nested primer, 505 (5′-CCATCTATCAACAGAAGCAA-3′). The patient's remaining α-globin genes and the major upstream regulatory element (MCS-R2) were also amplified and directly sequenced. The primers and DNA sequence are available on request.
Determination of human α-globin gene copy number
Southern blot analysis was performed to calculate the ratio of human α-globin gene to mouse α-globin gene in the cultures ( 15 ). DNA from MEL hybrids was digested with Pst I and the subsequent blot was hybridized concurrently with probes specific for the human α- and mouse α-globin genes ( 15 ). The intensities of the human α and mouse α signals were measured using the Storm™ Phosphorimager (GE Healthcare Life Sciences, Amersham, UK) and a ratio of human α:mouse α signal was determined for each culture.
RNA analysis
Total RNA from induced MEL hybrid cells was prepared with TRI reagent (Sigma, St Louis, USA). RPA was performed using 32 P-labeled mouse and human α-globin Sp6-derived cDNA probes (SP6/T7 transcription kit; Roche, Basel, Switzerland) as described previously ( 15 , 29 ). The products were resolved by polyacrylamide electrophoresis, and the specific 'protected' fragments were quantitated using the Storm™ Phosphorimager (GE Healthcare Life Sciences). Human α-globin expression was calculated as a ratio of human α to mouse α RNA signal, after correction for the number of labeled nucleotides in each probe. The values obtained were adjusted for human α-globin content using Southern blot data.
Chromatin immunoprecipitation
ChIP was performed as previously described ( 21 ) using the ChIP assay kit (Upstate/Millipore, Billerica, USA). Each ChIP was performed on 1.0 × 10 7 MEL hybrid cells. Immunoprecipitation of the DNA/protein complexes was performed directly on fresh sonicated chromatin overnight at 4°C with antibodies against the protein of interest ( 21 , 30 ). Antibodies used were: anti-diacetylated histone 3 (Upstate 06-599) anti-tetra-acetylated histone 4 (Upstate 06-866) and anti-Pol II (H-224) (Santa Cruz Biotechnology, Santa Cruz, USA sc-9001). Quantitative PCR (q-PCR) of immunoprecipitated DNA was performed by Real Time on the ABI 7000 Sequence detection system (Applied Biosystems, Foster City, USA) using forward and reverse primers and FAM-TAMRA modified probes (manufactured by Eurogentec, Liege, Belgium) ( 21 , 30 ). The quantitative data from q-PCR analysis were expressed as fold enrichment of bound material over input (relative to endogenous mouse Gapdh ). Fold enrichments were calculated by a modification of the comparative C T method (ΔΔCT) described by Applied Biosystems.
This work was supported by the Medical Research Council, The National Health Service (UK) and the Oxford Biomedical Research Centre.
The authors would like to thank Dr Adrian Stephens, Dr Roger Amos and Dr M. Beekes for providing blood samples for the study; Sue Butler for technical assistance; and Liz Rose and Nicki Gray for their help in preparing the manuscript. They are also grateful to Professor Bill Wood and Dr Richard Gibbons for their comments on the manuscript.
Conflict of Interest statement . None declared.


text:
The Spatial Allocator (SA) is a set of tools that helps users manipulate and generate data files related to emissions and air quality modeling. The tools perform functions similar to Geographic Information Systems, but are provided to the modeling community free of charge. In addition, the tools are designed to support some of the unique aspects of the file formats used for Community Multiscale Air Quality (CMAQ), Sparse Matrix Operator Kernel Emissions (SMOKE), and Weather Research and Forecasting (WRF) modeling. The MIMS Spatial Allocator is licensed as open-source software and provided at no cost because its development was sponsored by EPA. The Spatial Allocator uses GIS industry standard ESRI shapefiles, image files supported by GDAL, netCDF files and plain text data files as input and output data. The SA system includes three components developed for specific applications: Vector, Raster, and Surrogate Tools.
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For Raster Tools:
|All needed Spatial Allocator components are contained in the installation package.
SA was first developed for surrogate computation and vector data processing to support some of the unique aspects of the file formats used for CMAQ and SMOKE. Those tools are specifically used to process shapefiles (or vector data) and are now stored under the Vector Tools. Later on, we developed Java-based Surrogate Tools which allow users to compute multiple surrogates and perform QA on the computed surrogates. During the last few years, we have been focused on the development of the Raster Tools which are used to process land use data and satellite images for WRF and CMAQ modeling. The tools which integrate the WRF/CMAQ with the EPIC for the FEST-C system were also developed under the Raster Tools. The development of the SA system is mainly supported by the U.S. EPA and the development of satellite image processing tools is supported by NASA ROSE projects.


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Teams, Markets and Systems
Business Innovation and Information Technology
By (author) Claudio U. Ciborra
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Teams, Markets and Systems by Claudio U. Ciborra
Book DescriptionDespite the waves of re-engineering, there is still a gap between the opportunities offered by information technology and the progress of business transformation. New forms of information technology offer an increasing variety of network-based applications that range from groupware to electronic commerce, but its applications lack a sound understanding of the link between organizational processes, information and technology. This book provides a new set of concepts and methods to design new forms of business organizations around the latest network infrastructures. Professor Ciborra uses the principles of institutional economics to propose reforms of the relationships with suppliers, customers, strategic partners, and internal work organisation, based on a different mix of three basic organizational forms: teams, markets and hierarchies. Information technology can indeed be harnessed to shape businesses and markets so as to increase the transparency of markets, the agility of hierarchies, and the effectiveness and quality of the working life of teams.
Buy Teams, Markets and Systems book by Claudio U. Ciborra from Australia's Online Bookstore, Boomerang Books.
Book DetailsISBN: 9780521574655
(228mm x 152mm x 16mm)
Pages: 272
Imprint: Cambridge University Press
Publisher: Cambridge University Press
Publish Date: 28-Nov-1996
Country of Publication: United Kingdom
Books By Author Claudio U. Ciborra
From Control to Drift, Paperback (June 2001)» View all books by Claudio U. Ciborra
An insight into the issues surrounding information infrastructure implementation in global corporations. The author suggests that the economics of standards and increasing returns be joined with the perspectives from the social studies of science and technology to provide a fresh view of the management of IT in global corporations.
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A riveting new play that swept Broadway last season will open the Maltz Jupiter Theatre's 2016/17 season, Let Us Entertain You! (more...)
For more than sixty years, Queen Elizabeth II has held private weekly meetings with each Prime Minister, from Churchill to Cameron. In these intimate and sometimes explosive conversations, we see glimpses of the woman who wears the crown and witness the moments that shaped a monarch. Go behind the walls of Buckingham Palace and into the private chambers of Queen Elizabeth II for the audience in Peter Morgan's riveting new play that swept Broadway last season. Sponsored by the John McDonald Company. Learn More (more...)
The Lincoln Center drama is a riveting depiction of a historical moment in diplomacy, leavened with whisky, waffles and a lot of furniture moving. (more...)
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J.T. Rogers' emotional and darkly comic drama tells of the negotiations that led to the Oslo Accords. (more...)
Commissioned by Lincoln Center Theater, J.T. Rogers' Oslo officially opens tonight, July 11, at the Mitzi E. Newhouse Theater (150 West 65 Street). Let's see what the critics had to say... (more...)
BroadwayWorld.com's Upcoming Events calendar for the week - updated on 7/9/2016.
How did the 1993 Middle East peace talks come to be held secretly in a
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Commissioned byLincoln Center Theater,J.T. Rogers' Oslo is currently in previews ahead of an official opening night of Monday, July 11 at the Mitzi E. Newhouse Theater (150 West 65 Street). Check out a first look below! (more...)
Commissioned by Lincoln Center Theater, J.T. Rogers' Oslo begins performances today, Thursday, June 16 and will open Monday, July 11 at the Mitzi E. Newhouse Theater (150 West 65 Street). (more...)
BroadwayWorld.com's Upcoming Events calendar for the week - updated on 6/11/2016.
Lincoln Center Theater will welcome Michael Aronov, Adam Dannheisser, Jennifer Ehle, Daniel Jenkins, Dariush Kashani, Jefferson Mays, Daniel Oreskes, Henny Russell, Joseph Siravo, and T. Ryder Smith in the cast of its upcoming production of OSLO, a new play by J.T. Rogers, directed by Bartlett Sher. (more...)
Peter Morgan's The Audience, starring Helen Mirren and directed by Stephen Daldry, began previews on February 14 and opened on March 8 at Broadway's Gerald Schoenfeld Theatre (236 West 45th Street). The production closes today, June 28, and below, BroadwayWorld takes you back to the play's beginning on the Great White Way! (more...)
Sara Ramirez picked the right night to attend THE AUDIENCE. (more...)
Helen Mirren stopped by last night's LATE NIGHT to talk about being the Queen of Broadway in the critically acclaimed play THE AUDIENCE. Check out clips from the performance below! (more...)
Peter Morgan's play THE AUDIENCE, which opened on Broadway on March 8th, has recouped the $3.4 million spent on production costs. (more...)
THE AUDIENCE's Helen Mirren stopped by LIVE today and talked about meeting the Queen of England (and getting "Queenitis") with Kelly Ripa and co-host Mark Cuban. (more...)
Helen Mirren stopped by this morning's TODAY to talk about her new film 'Woman in Gold' and her starring role as Queen Elizabeth II in Broadway's THE AUDIENCE. Check out the appearance below! (more...)
Helen talks to Jimmy about her adventures traveling on New York City trains while commuting to her Broadway play, THE AUDIENCE. (more...)
Helen Mirren, currently starring in Peter Morgan's The Audience on Broadway, will visit LIVE WITH KELLY AND MICHAEL today, March 31, 2015. (more...)
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