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Joined: Jul 2009
Location: Tacoma
Oddometer: 94
Great write-up Doc, glad you made it back home and congrats on the adventure. Originally from the Adirondacks, so interested in your perspective of that part of the world - - sounds like a fantastic effort.
The Pacific Northwest awaits. . .
Joined: Aug 2009
Location: S.E. PA
Oddometer: 204
Glad you are finally back in NM....looking forward to wrap up...no hurry...rest up.
Tryin' to get home..
Joined: Nov 2005
Location: ABQ, New Mexico
Oddometer: 1,227
Some replies...
Before I start wrapping this RR up, let me wrap up the replies...
P.S. Will thoroughly document the flat tire in the wrapup...
Thanks to all for following. This was---for me---a great ride. And I very much appreciated all your comments and encouragement.
Final wrap-up and thoughts coming in a couple hours...
Isa. 58:14 (KJV)
2013 BMW GSW (traveler)
1992 Ducati 900SS (looker)
1991 Honda Hawk NT650 (commuter)
Tryin' to get home..
Joined: Nov 2005
Location: ABQ, New Mexico
Oddometer: 1,227
Sunday, August 3: Guymon, Oklahoma --> Albuquerque, New Mexico (HOME)
This update will chronicle the last day of my nearly one-month trip from New Mexico back to Vermont, then back home. A subsequent update will include some final comments, observations, complaints, rants, well, you ought to be familiar with me by now...
Leaving Guymon, OK...
There are really two main routes from Guymon, OK back to Albuquerque, NM. Route (1) follows US 64/412 W thru Boise City to Clayton and Springer, thence S on I-25. Route (2) follows US 54 SW thru the Texas panhandle (lotta "panhandles" in these parts; of course Missouri has a "bootheel"...) and onward into New Mexico, where it joins I-40 at Tucumcari. I selected route (1)---as I did on the outbound leg---because the section of I-40 between Tucumcari and ABQ is pretty dismal. Flat, lotta trucks...WAY WAY below the caliber of, say, the "Wendell H. Ford Parkway" (did I get that correct?) in Kentucky.
BTW, just as I was getting to sleep the night before, the rumble of you-know-what awoke me...darn those things! In the morning while loading Wotan I saw that it was labeled "EXPERIMENTAL PANHEAD"...now there's an oxymoron...why are those things always so darn loud?
It was fairly early Sunday morning, and I had US 64 between Guymon and Boise City pretty much all to myself. So I set the cruise control on 60 mph (the speed limit, BTW) and looked forward to a very relaxing day...
Heading W on US 64 between Guymon and Boise City, OK...
How often these days does one get to truly relax like I was doing now? Relatively good road surface, NO traffic, pretty country (as I've said, IMHO there ain't no flyover country), a mellow bike (the GSW hadn't missed a beat)...what could possibly go wrong?
And my mind was wandering...PA RIDER and I had a discussion about the pioneers who initially populated the west. A hardy breed. Way tougher than we. My maternal ancestors homesteaded 160 acres in northern Wisconsin (grandfather emigrated from Germany, picked up my grandmother while passing thru Ohio...as a fetching 16-YO she caught his eye and that was that...) and raised 11 boys plus my mother. My paternal ancestors were "small town" folks, but ended up in Oklahoma...oh yeah, the Picher lead & zinc mines...
Stopped at a "Travel Center" in Boise City just to take a toilet break. Always figure I should buy something, so I wandered around: maybe a NASCAR T-shirt? How 'bout a "biker" T-shirt? Or a studded wallet? I settled for a small bottle of "spicy hot" V-8 juice (it WAS pretty hot).
Back in Nuevo Mexico...
After passing thru Boise City, OK, it's just a hop, skip, and carve (well, no curves to carve) into New Mexico...the "Land of Enchantment." Note the bullet holes...also, the state question is RED or GREEN?...as in the color of chile (with an "e"...with an "i" it's Texas chili...whole diff'rent thing).
Entering New Mexico---watch for stray rounds...
BTW, entering New Mexico is often an interesting experience. Entering from the north, one leaves Colorado and enters New Mexico. The landscape goes from green to brown, and---all of a sudden---it seems like most houses have a junked car parked in the front yard
Entering NM from the NE (like I'm doing) is pretty harmless; the transition is hardly noticeable. That may be a comment on western Oklahoma...I'll leave it up to you to puzzle it out.
The Santa Fe Trail.
Time for some education (you DO know that "DUCATI" is embedded within education, no?). At the eastern edge of Clayton, New Mexico there was a little display about the Santa Fe Trail, so I stopped and took a few fotos...first Wotan and the main three-cornered sign:
Wotan and the main Santa Fe Trail trifold...
As the sign says..."one of the great overland trade routes of the 19th century..."
Pioneered in 1821, it ran for 900 miles.
Yeah, some of you "Iron Butt" guys can do 900-mile days; heck, that's nothing, right? The SS 1000 is only the starting point...then what's next, the "Bun Burner 1500"...I forgot the whole genre; I admire those guys, but not my cup of tea.
Here's how they did the 900 miles "back in the day"...
If you're not the lead dog, the view never changes...
This pane of the trifold described some of the travelers of the Santa Fe Trail.
American & Mexican traders, Indians, fur trappers, buffalo hunters, adventurers (that's us)...
The woman at lower right, Susan Shelby Magoffin, was one of the few white women who made the trip (in fact, the FIRST white woman to make the trip). She wrote a memoir: Down the Santa Fe Trail and into Mexico...I've read it; VERY interesting, and highly recommended.
Susan Shelby Magoffin had some amazing experiences, written about in her memoir.
Here are a couple signs about the Santa Fe Trail:
Some information about the Santa Fe Trail...
And the Cimarron Cutoff...some of those "cutoffs" (short cuts) turned out to be disastrous...in fact, I read a book about one within the last year, but can't recall the nam (the "Meek" cutoff, on the Oregon Trail?)
The Cimarron Cutoff.
Welcome to Clayton, New Mexico...
Just a short piece W of the Santa Fe Trail exhibit is the thriving metropolis of Clayton, New Mexico:
Some statistics on Clayton, New Mexico. More people than I thought...
At this time on Sunday morning, ain't much happenin' in Clayton. Saw the convenience store/gas station coming up, so I slowed to pull in for fuel and a break. WHUMPPP! Man, I'm glad I'm on a bike...that dip (more like a ditch) in the road just about got me...ouch.
Filled up Wotan (it was 83 miles of NUTHIN' between Clayton and Springer, so definitely wanna gas up here) and took a little break myself. Lovely morning, calm and cloudless. Probably spent 15 minutes in Clayton, before leaving for Springer (and I-25) 83 miles to the west.
Thank DOG for Tire Pressure Sensors...
So I was about 10 miles west of Clayton, ridin' along fat, dumb, and happy. Well, happy anyway
All of sudden...a RED WARNING came up on the dashboard...definitely gets your attention! Uh-oh...rear tire deflating! Unfortunately, I've seen it before---last Fall near Capitan, NM.
OK, what to do? The rear tire pressure indicated was 31 psi, and the TPS reads about 5 psi low. And it wasn't deflating rapidly at all. Should be able to make it back to Clayton (although there's nothing there of any assistance), so I turned around and rode back.
Actually, there WAS something of assistance back in Clayton: a wider road across from the convenience store, and it was in the shade. So unload the bike (not strictly necessary, but easier to maneuver, and you know how big & strong I am).
Park in the shade, and get to work...
I've "shimmed" the side stand on Wotan, so he prefers to be on a surface leaning to the left; hence I parked facing the "wrong way"---no problem, wide shoulder. But...I couldn't easily get him up on the center stand (bein' a 98-pound weakling). That's OK, just roll until I find the leak. AHA!! There it is...
Found the puncture...
Hmm, what the Sam Hill was it? Not very big...got it out; a little shard of metal:
Nasty little metal shard...
Hmmm, I'll bet I know what happened. Y'know that "ditch" I went through? Well, lotsa folks with overloaded trailers and housecars come thru that thing, and SCRAPE like crazy. I'll betcha lots pieces of steel get peeled off. And I just happened to run over one that was pointed up JUST SO... Oh well, my bad luck. But good luck to have the TPS notify me of it before I was in the middle of nowhere. Yeah, still coulda fixed it out there, but man, cars whizzin' by while I'm working---my hair would be completely gray after that...
If the TPS hadn't alerted me, I'd have been 40 miles further along out there...
The Rest of the Story...
Got back on US 64 towards Springer---checked the tire pressure every 10 miles (with the TPS, not stopping w/my gauge) and it was holding just fine. Those string plugs work great. And I have a 12V "tire inflator" (all the plastic housing stripped of so the gears are exposed, etc.) I was riding at a conservative speed (60 mph) for a while, though...
Stopped for lunch (at 1500 hours) at Las Vegas, NM (hadn't eaten since breakfast at 0615), but nothing to photograph there. Did a quick RR update indicating I'd had a puncture (yeah, not that big a deal, but a delay nonetheless, and kind of a hassle).
Rounding the southern spur of the Sangre de Cristo Mountains (pretty much the first mountains I'd seen in dangnere a month) I saw a pretty view and tried to capture it...not very successfully.
Southern spur of the Sangre de Cristo mountains, east of Santa Fe, New Mexico.
Back in my Beautiful Garage Again!
The miles from Springer to ABQ seemed to pass quickly, and at 1700 hours (right on the GPS prediction) I rolled into the garage. Mrs. Greg was there to greet me with a smile...and also some good Mexican food (had been a month since that, too).
A big hug for Mrs. Greg...
And this morning, I thought I'd take a look at my tire plugging job...couldn't even find it! Finally with great diligence I found it...it's that little light "smudge"...what a great job!
Tire plug hardly visible.
Since that tire (Michelin Pilot Road 4 "Trail") has lotsa wear left, I'll remove it, and repair it from inside with a "patch/plug" combination. Not today, though.
So that's it. Home after 5,637 miles. I'll write up my "final thoughts" in a subsequent posting (later this afternoon). My eyes are kinda tired right now.
Isa. 58:14 (KJV)
2013 BMW GSW (traveler)
1992 Ducati 900SS (looker)
1991 Honda Hawk NT650 (commuter)
Tryin' to get home..
Joined: Nov 2005
Location: ABQ, New Mexico
Oddometer: 1,227
Final Wrapup: misc. thoughts, observations, etc.
Decided to separate out this posting from the "main" final day ride report...I'm just gonna list a few random things that occurred to me.
1. The BMW R1200GSW. This was my first "long trip" on the GSW; I owned it since June 2013. Test-ridden '08 and '10 GS's, but didn't like 'em that much. This bike was quite different. I'd encourage anyone who felt the same about "older" GS's to try the new one. Of course, Mrs. Greg taught me that motorcycles are like food: they're not good or bad, it's whether YOU like 'em that matters. And I've been riding since 1957; ridden almost everything 'cept Harleys and big touring bikes.
2. ADVers are kinda Snobby. Neither one of the ones I encountered (in almost a month) waved to me. Of course I don't wave to anyone else, either
3. Dr. Greg considers VEGETARIANISM. In Woodward, Oklahoma...I pulled up next to a "cattle hauler." Y'know, the big "perforated" trailers. Was full of cattle. They're two-tiered: upper & lower. I looked over and a cow looked over at me; he was on the lower level, and his head was just plastered with cow dung. His "upper level" buddy just had to go. Now, heading for your execution is bad enough...doing so in such ignominy is just too much. I like steaks and burgers, but...made me so sad.
4. Shacking up with ADV inmates is the best. I've known this before; done it on previous trips. But everyone I stayed with was SO hospitable...I'm very grateful. Met some folks who will be lifelong friends. I don't want to name names, cuz I'd leave someone out. But you all were SO KIND to me...kinda restores one's faith in humanity.
5. Always take a SPARE PAIR of GLASSES. After sitting on my glasses and breaking them in Vermont...if I hadn't brought a spare pair with me (a little old, but still usable) I'd still be back in Vermont trying to find my way...
6. So far so good on "active retirement." Neither my father nor his father lived very long post-retirement. They both had "lots of hobbies" they were going to pursue, but instead JUST SAT AROUND. It's in my genes. My natural tendency is to just sit around. But so far, so good...gotta just keep ridin'...
7. Camping sure has changed. I know that, you know that, but...I still remember when camping meant a sleeping bag, (optional) tent, etc. Now it's a 60-foot RV... I do enjoy camping in more primitive sites, typically in the west.
8. Big ATV's. Man, what's up with all the BIG ATV's. Y'know, the Polaris RAZ-R type? I saw SCADS of those things heading out everywhere. Most people have a lot more money than I do...back when I grew up you had to build your own...mine was a dune buggy with a VW front end, '63 Corvair Spyder (turbo) transaxle, chrome-molybdenum tube frame...I've got a pic, I should post it.
9. Motorcycle Cruise Control. Don't leave home without it! Just MHO. I have small, weak hands, and cruise control is wonderful. Even though Ducati omitted it from the Multi 1200S (despite being TBW, and a "touring" model), Tuneboy (Oz company) developed one, and I flashed it into the ECM. Not tuned quite right, BMW engineers got it perfect. Love it.
10. "Live" Ride Report. Early on, wasn't sure if I was up to doing "live" updates. Turns out I really got into it. iPad Mini, external keyboard...piece of cake. In fact I'm at home now, and prefer that combo to my MacBook Pro (Apple user since 1981; DEC before that).
11. An American Tragedy. Was very satisfying to actually track down the location where this thing occurred. Have lunch in the Glenmore Hotel, where Grace Brown and Chester Gillette stayed (unmarried!) That was the entire rationale for this trip, and I am very satisfied.
12. Roadside Tire Repair. Yeah, plugging tubeless tires is no big deal, but sure glad I found a nice spot to work, it wasn't raining, etc. I know, "...the adventure begins when things stop going as planned..." Maybe I'll peel that ADV sticker off the pannier
13. Nice to have Encouragement. When I had my "crisis of spirit" back in northern Kentucky, I got numerous "hang in there" comments, including Mrs. Greg of course. Very helpful. Thanks to all.
14. Where's the bathroom? Awoke about 0315 this morning (yes, I'm an old man), asked Mrs. Greg "...where's the bathroom?" Then it occured to me, "this is MY house!" I'd been on the road long enough. It was time to come home.
Isa. 58:14 (KJV)
2013 BMW GSW (traveler)
1992 Ducati 900SS (looker)
1991 Honda Hawk NT650 (commuter)
Chasin' the Serb
Joined: Apr 2009
Location: NC
Oddometer: 285
The Best of the Best! . Thanks Dr. G! . BTW - you definitely married up! . But I bet you already knew that.
Thanks for the effort. We enjoyed riding along with you.
Forever Noob
Joined: Jul 2007
Location: PNW
Oddometer: 186
Thank You!
I followed along and enjoyed the report and am glad you made home safe and sound.
Where to next?
Joined: Aug 2007
Location: Jo.burg, South Africa
Oddometer: 16
Thanks for making the effort to do the report - thoughts, museums, signposts and all ....
Gnarly Adventurer
Joined: Feb 2013
Location: Not really New, not really Mexico, by Taos
Oddometer: 258
Great RR
Welcome back to the land of green chiles... It was fun tagging along. Great summary!
'15 Freeride 250r
'07 Ural GearUp
Baja Survivor: http://advrider.com/forums/showthread.php?t=1046271
the road less traveled...
Joined: Aug 2006
Location: Plano, Texas
Oddometer: 87
... as usual. Thank you for sharing your adventures. Those of us that don't have the time for a month long trip can enjoy your ride. Also, a couple of times you reference that the picture doesn't do the scene justice; cameras just can't capture what the human eye can capture and the brain put into a picture. At best, pictures are a reminder of what we saw and allow us to recall how beautiful (or not, depending on perspective and subject) it was in person. That said, thank you for all the photos because if your camera can capture a picture that intrigues me, as yours did, then it makes me want to visit and ride the same places.
Again, thanks for sharing and looking forward to your PNW escapades.
2012 Super Tenere
Tryin' to get home..
Joined: Nov 2005
Location: ABQ, New Mexico
Oddometer: 1,227
Nice comments, guys. I know I left off a couple "observations"...if I remember I'll start with number (15).
Isa. 58:14 (KJV)
2013 BMW GSW (traveler)
1992 Ducati 900SS (looker)
1991 Honda Hawk NT650 (commuter)
Joined: Jun 2009
Location: San Diego
Oddometer: 98
I know your preference is to travel solo. Traveling with others can be problematic for many reasons.
For the last five years I have saved money and built up vacation for a 3 week ride around the United States. Have seen so much and had so much fun. Traveling on a motorcycle is such a rich, organic way to travel.
I've lucky to have had a riding partner for those years that is great to travel with. No big personality conflicts and we share the same general travel philosophy (we like to stay off interstates, make no firm plans and are both cheap)!
I think sharing experiences with somebody enriches the experience and lessens the "Horse To The Barn" syndrome after a couple weeks. There have been countless times where one of us has exclaimed to the other "Did you see what I just saw? Two memories are better than one. Just my two cents.
That being said, if it came down to going on trips alone or not going at all, I would set out solo in a heartbeat.
Thanks, again, Doc, for taking us along!
Joined: Aug 2009
Location: S.E. PA
Oddometer: 204
+1..thanks a lot.
Rocket Engineer
Joined: May 2008
Location: New Mexico
Oddometer: 83
Glad to see you're enjoying "active retirement!" Thanks for sharing your adventure. I made a couple rides back east this summer, but alas now college is back in session.
Thought I'd share my favorite route from Guymon to Abq. Met a herd of burros while doing the 325 stretch on the ST1300 last summer.
krishl IBA10823 DL650 KLR650 R1200GSAdv ST1300A Trek4900 Tuono
Tryin' to get home..
Joined: Nov 2005
Location: ABQ, New Mexico
Oddometer: 1,227
Thanks VERY MUCH for your response...
P.S. Off soon to the North Rim; delayed RR in "Day Trippin"...
Isa. 58:14 (KJV)
2013 BMW GSW (traveler)
1992 Ducati 900SS (looker)
1991 Honda Hawk NT650 (commuter)
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In humans, cleft palate (CP) accounts for one of the largest number of birth defects with a complex genetic and environmental etiology. TGFβ3 has been established as an important regulator of palatal fusion in mice and it has been shown that TGFβ3-null mice exhibit CP without any other major deformities. However, the genes that regulate cellular decisions and molecular mechanisms maintained by the TGFβ3 pathway throughout palatogenesis are predominantly unexplored. Our objective in this study was to analyze global transcriptome changes within the palate during different gestational ages within TGFβ3 knockout mice to identify TGFβ3-associated genes previously unknown to be associated with the development of cleft palate. We used deep sequencing technology, RNA-Seq, to analyze the transcriptome of TGFβ3 knockout mice at crucial stages of palatogenesis, including palatal growth (E14.5), adhesion (E15.5), and fusion (E16.5).
The overall transcriptome analysis of TGFβ3 wildtype mice (C57BL/6) reveals that almost 6000 genes were upregulated during the transition from E14.5 to E15.5 and more than 2000 were downregulated from E15.5 to E16.5. Using bioinformatics tools and databases, we identified the most comprehensive list of CP genes (n = 322) in which mutations cause CP either in humans or mice, and analyzed their expression patterns. The expression motifs of CP genes between TGFβ3+/− and TGFβ3−/− were not significantly different from each other, and the expression of the majority of CP genes remained unchanged from E14.5 to E16.5. Using these patterns, we identified 8 unique genes within TGFβ3−/− mice (Chrng, Foxc2, H19, Kcnj13, Lhx8, Meox2, Shh, and Six3), which may function as the primary contributors to the development of cleft palate in TGFβ3−/− mice. When the significantly altered CP genes were overlaid with TGFβ signaling, all of these genes followed the Smad-dependent pathway.
Our study represents the first analysis of the palatal transcriptome of the mouse, as well as TGFβ3 knockout mice, using deep sequencing methods. In this study, we characterized the critical regulation of palatal transcripts that may play key regulatory roles through crucial stages of palatal development. We identified potential causative CP genes in a TGFβ3 knockout model, which may lead to a better understanding of the genetic mechanisms of palatogenesis and provide novel potential targets for gene therapy approaches to treat cleft palate.
Keywords:RNA-Seq; Next-generation sequencing; TGFβ3; Knockout; Transcriptome; Cleft palate; Palatogenesis; Palate; Craniofacial
Cleft palate (CP) is the second most common birth defect (1/800 live births) in humans, and is caused by the lack of fusion of the embryonic palatal shelves early in gestation (6–10 weeks) [1]. The formation of a continuous palate is a complex process involving multiple steps, including: palatal shelf growth, elevation, attachment, and fusion. The stages of palatogenesis are regulated by numerous genes that are essential for normal palate development. Our laboratory has a long-standing interest in identifying the genetic and molecular mechanisms that regulate palatogenesis in order to understand the factors involved in the development of orofacial clefts [2-11]. It has been shown that both genetic and environmental elements contribute to the development of cleft palate [12,13]. We previously presented that Transforming Growth Factor (TGF)-β isoforms play essential roles in the regulation of palatal morphogenesis, including the finding that TGFβ3 mediates palatal fusion both in primary cells and organ culture [5,14,15]. According to several population-based mutation screening studies, TGFβ3 is considered a candidate gene for non-syndromic CP in humans [16-22]. Furthermore, TGFβ3 knockout mice are born with CP but lack other major defects [23-25].
In our earlier studies [26], we examined gene expression during palatal fusion in normal mice using microarray analysis and detected several genes essential for completion of palatal development. As genome sequencing technologies advanced, it has become feasible to systematically analyze global transcriptomal changes and identify the key molecular components in the developing palate during crucial stages of palatogenesis. Failure to regulate functional or structural genes during these stages may result in cleft palate. Next-generation sequencing (NGS) technologies, or RNA-Seq, have recently emerged as a revolutionary tool of transcriptomics [27] by revealing the complex landscape of the transcriptome with high-throughput at an incomparable level of sensitivity and accuracy [27,28]. The results of RNA-Seq demonstrate high levels of reproducibility for both technical and biological replicates [29,30]. The analysis of TGFβ3 knockout mice by RNA-Seq provides a valuable resource to facilitate our understanding of the complex genetic and molecular mechanisms of palatogenesis. This technology also allows us to detect allelic and splice variants of some of the genes involved in palate development in TGFβ3 knockout mice, which is currently beyond the scope of this article.
Evidence suggests that TGFβ3 is essential to palato-genesis, especially during embryonic days (E) E14.5 to E16.5. However, the cellular mechanisms maintained and regulated by TGFβ3 signaling have not been extensively explored to enable an understanding of those genes functionally regulated by TGFβ3 during normal palatogenesis or those genes deregulated in TGFβ3-null mice. Our objective in this study was to analyze transcriptome changes and their contribution to the development of CP among different gestational ages and TGFβ3 knockout alleles. In this study, we analyzed the transcriptome of TGFβ3 mice by RNA-Seq at crucial stages of palatogenesis, including: palatal convergence, adhesion, and fusion; and we characterized some crucial transcripts that may play key regulatory roles throughout palatal development. We used palatal shelves extracted from E14.5, E15.5 and E16.5 allelic mice to analyze differential expression patterns of their transcriptome throughout the palatal developmental process. The overall transcriptome analysis of TGFβ3 WT mice revealed that almost 6000 genes were upregulated during the transition from E14.5 to E15.5 and more than 2000 were downregulated from E15.5 to E16.5, which suggests that regulation of these transcripts is essential during the stages of palate development. In order to streamline the analysis of the high number of transcripts, we downsized the list of genes to CP genes only. Using biological databases, we categorized a comprehensive inventory of CP genes both in human and mouse genomes and focused on their differential expressions and biological interpretations. Unexpectedly, the expression patterns of CP genes between TGFβ3+/− and TGFβ3−/− were not significantly different from each other, and the expression of the majority of CP genes remained unchanged from E14.5 to E16.5. Using this data, we identified 8 unique genes (Chrng, Foxc2, H19, Kcnj13, Lhx8, Meox2, Shh, and Six3), which may regulate cleft palate formation in TGFβ3−/− mice. We used Ingenuity Pathway Analysis (IPA) software to analyze downstream effects of these genes on biological functions, molecular networks, and regulatory pathways- particularly TGFβ signaling. This is the first genome scale analysis of the palatal transcriptome of mice generated by RNA-Seq technology during critical stages of palatogenesis. This data will allow the comprehensive analysis of TGFβ signaling during palatogenesis and provide information on the chronological regulation of downstream TGFβ-activated transcription factors that function to induce cellular differentiation, transformation, and apoptosis.
Analysis of RNA-seq data
As outlined in the experimental workflow of our study (Figure 1), RNA samples were extracted from mouse palatal tissues of TGFβ3 knockout mice (homozygous (−/−), heterozygous (+/−), and wildtype (+/+)) at three developmental stages (E14.5, E15.5, and E16.5); libraries were prepared, converted to cDNA, and sequenced by using the Illumina HiSeq2000 next generation sequencer. The bioinformatics analysis of RNA-Seq data was processed using the Tuxedo protocol [31], which includes TopHat, Cufflinks and CummeRbund packages from R. The CP genes were identified from OMIM and MGI databases and downstream effects were analyzed using IPA.
Figure 1. Experimental workflow of the study. RNA samples were extracted from mouse palatal tissues of TGFβ3 knockout mice (homozygous, heterozygous, and wildtype) at three developmental stages (E14.5, E15.5, and E16.5); libraries were prepared, converted to cDNA, and sequenced by using the Illumina HiSeq2000 next generation sequencer. Fastq files were uploaded to the server for quality control analysis of sequence reads using FastQC. There were no sequence manipulation processes performed for any fastq file, given that the quality score was high at both the 3′ and 5′ ends. All of the reads were mapped to the reference genome (mm9, built name NCBIM37) by using TopHat. Quantification of transcripts, statistics tests for differential expression, and detection of splice variants were performed using Cufflinks; quality assessments of biological and technical replicates were performed using CummeRbund; and pairwise comparisons of samples and differential expression of transcripts were analyzed using CuffDiff. Venn diagrams of all significantly altered (FC ≥ 2.0) transcripts were drawn using the R VennDiagram package [75]. CP related genes (n = 322) were extracted from human (OMIM) and mouse (MGI) genome databases. CP genes were classified based on their patterns of expression (n = 9) for each genotype and their heatmaps were generated using the R pheatmap package. Expression pattern groups of CP genes were uploaded to IPA software as datasets and core analyses were run to detect downstream effects: canonical pathways and biological functions relevant to sample datasets.
Our data clearly demonstrate that TGFβ3 wildtype (+/+) palates from E15.5 expressed increased TGFβ3 protein, double the expression of heterozygous (+/−) and as expected the homozygous (−/−) palates were completely devoid of any TGFβ3 expression (Additional file 1). Extracted RNA samples were evaluated by RNA integrity numbers (RIN) to monitor quality and degradation with BioAnalyzer (Agilent Technologies, Palo Alto, CA). We confirmed that all of the palatal RNA samples had an RIN ≥ 8.4, indicating the high quality and low degradation of our experimental samples (Additional file 2). The RNA libraries were prepared for cDNA conversion and the samples were sequenced by Illumina techniques using HiSeq 2000. We obtained total reads from the RNA-Seq samples ranging from 14 million to 96 million (Additional file 3). Among all samples, only 4 samples have less than 40 million reads. We did not apply sequence manipulations on either 3′ or 5′ ends because the RNA-Seq sequencing quality was high across all samples based on our FastQC data quality control analysis. The relative abundance of transcripts was normalized to the total read number and shown as fragments per kilobase per million (FPKM) and mapped via Cufflinks.
Additional file 1. TGFβ3 protein expression in the alleles of TGFβ3 knockout mice. Western blot analysis show that while homozygous (HM; −/−) palates did not show any expression TGFβ3 protein in the palate collected at E15.5 heterozygous (HT; +/−) palates expressed limited levels of the TGFβ3 protein while the wild-type (WT; +/+) palates expressed higher level of TGFβ3 protein.
Format: TIFF Size: 390KB Download file
Additional file 2. Table listing RNA integrity numbers (RIN) to monitor quality and degradation of RNA samples.
Format: XLSX Size: 13KB Download file
Additional file 3. Table showing the number of reads per replicate of RNA samples.
Format: XLSX Size: 14KB Download file
In order to evaluate the reproducibility of our experimental samples and procedures, two independent biological and technical replicates for each gestational age and each allele resulting in 36 (n = 9 × 2 × 2) paired-end samples were assayed [32]. Using the scatter plots generated by CummeRbund, biological and technical replicates of our samples were validated based on the comparison of their read numbers per transcript. We detected a high correlation among both the biological and technical replicates of each gestational age and allele (Figure 2) (r = 0.98, Pearson's correlation; p < 0.001). The replicates of E14.5 of TGFβ3−/− mice are presented in Figure 2. Additional scatter plots for all of the other samples with their replicates are shown in Additional file 4. Because the expression values (FPKM) of certain CP related genes differed significantly among the gestational ages, we transformed the FPKM value of each gene into log10 (FPKM + 1), rounded up to 2 decimal places, and used transformed values for further analysis.
Figure 2. Validation of biological and technical replicates using CummeRbund. The read numbers per transcript between the (A) biological and (B) technical replicates were compared. Since the read number per transcript (FPKM value) ranged from 0 to >10,000, the read number + 1 was transformed by log10. Each dot represents data from one transcript. There was a high correlation between the two sequencing results (r = 0.98, Pearson's correlation; p < 0.001 two tail). Additional scatter plots for the other samples are shown in the Additional file 4.
Additional file 4. Validation of biological and technical replicates using CummeRbund. The read numbers per transcript between the biological replicates were compared. Since the read number per transcript (FPKM value) ranged from 0 to >10,000, the read number + 1 was transformed by log10. Each dot represents data from one transcript. There was a high correlation between the two sequencing results (r = 0.98, Pearson's correlation; p < 0.001 two tail).
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Overall transcriptome expression profile
Using the R VennDiagram package, we created Venn diagrams to illustrate the number of transcripts in each experimental group that passed the significance and fold change (FC ≥ 2.0) thresholds designated by Cufflinks (Additional file 5). From our overall transcriptome analyses of TGFβ3 knockout mice alleles (Table 1), in all genotypic groups, the majority of the differentially expressed transcripts between E14.5 and E15.5 were upregulated: 62% for TGFΒ3−/− (n = 1721), 53% for TGFΒ3+/− (n = 1063), and 80% for WT (n = 5946). Out of 1721 transcripts upregulated in TGFΒ3−/−, 1030 (60%) were shared with WT. Interestingly, a significant portion of the upregulated genes in WT (30%, n = 1792) were downregulated between E15.5 and E16.5, but not in TGFΒ3−/−'s E15.5 to E16.5 (Table 1). The names of the genes significantly increased from E14.5 to E15.5 followed by downregulation in E16.5 and their corresponding Venn Diagrams are presented in Additional file 6. This first-up-then-down pattern of expression suggests that these transcripts may be crucial at E15.5, which corresponds to the stage of midline epithelial seam (MES) degradation and palatal fusion. Since it was not feasible to analyze all significantly altered genes during palatal stages, we have shortlisted the genes to be analyzed to CP-causing genes only.
Additional file 5. Venn diagrams of all significantly differentially expressed genes. Differential expression of transcripts within TGFβ3 alleles (TGFΒ3−/−, TGFΒ3+/−, and WT) were compared using Venn diagrams. Lists of differentially expressed genes with their EntrezIDs were uploaded to the R VennDiagram package [75], the query was run, and the detected numbers and gene lists were exported to MS Excel. Relationships among the lists of differentially expressed genes within TGFβ3 allelic mice are depicted as intersections or uniqueness and grouped with their corresponding gestational age (E14.5, E15.5, and E16.5). A significant overlap of differentially expressed genes was observed among the allelic variants at each gestational age. Venn diagrams were not drawn per scale.
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Additional file 6. Table listing the names of the genes significantly increased from E14.5 to E15.5 followed by downregulation in E16.5 and their.
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Table 1. Number of transcript changes among TGFβ3 alleles
Identification of CP related genes and their expression patterns
Following the identification of genes causing CP in humans and mice, as described in the methods, we generated a Venn diagram to detect common genes between humans and mice that cause CP after becoming dysfunctional (Additional file 7). We identified 37 common genes that cause CP in both species. Within the human CP list, there were 194 transcripts that share orthologous copies with mice. We approached these genes as putative CP genes, considering that their KO models have not been generated yet. Overall, the CP gene list we developed includes 322 genes: 128 genes derived from mouse and 230 genes derived from human databases (Table 2). For an enhanced visualization of the expression values (FPKM) of all CP genes (n = 322), a Circos image was drawn based on the circular composition of CP genes located on human chromosomes [33] (Additional file 8).
Additional file 7. Venn diagram of cleft palate (CP) related genes acquired from OMIM and MGI Using the OMIM (Online Mendelian Inheritance in Man) database, we identified 280 genes and loci involved in genetic diseases associated with CP syndromes in humans. Several studies have developed knockout mouse models which exhibit CP [77]. We used the Mouse Genome Informatics (MGI) international database resource for laboratory mice to identify 128 genes (out of 223 genotypes) that cause CP in mice. The mouse genes were filtered based on gene names only, because some of the same genes were either studied by different labs or have splice variants, and as a result they were listed several times as genotypes in the MGI database. The human and mouse CP-associated genes were compared to find common genes, and the Homologene tool of NCBI [78] was used to compare and detect the orthologs of human and mouse CP related genes. We determined that 50 (out of 280) human CP related genes and loci were not represented, i.e. non-orthologs, within the mouse genome.
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Additional file 8. Ideogram of CP genes on chromosomes. A zoomable Circos image is drawn based on circular composition of CP genes on chromosomes. Data tracks appear inside and/or outside the circular layout. When the PDF file is magnified, tracks include FPKM values of CP genes as histograms and labeled from the outer circle to inner circle as "gene name, 14.5HM, 15.5HM, 15.5HM, 14.5HT, 15.5HT, 16.5HT, 14.5WT, 15.5WT, and 16.5WT".
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Table 2. List of genes causing CP according to MGI and OMIM databases (n = 322)
On the basis of our differential expression profile data between genotypes and gestational ages (Table 1), we decided to group and analyze the potential CP genes based on their expression patterns throughout different stages of palatogenesis. We categorized the 322 CP genes identified above into 9 possible expression patterns based on the comparison of their expression values (upregulated, downregulated, or unchanged) across the 3 different gestational age groups analyzed by RNA-seq (E14.5, E15.5, and E16.5) (Figure 3). The patterns (p) represent the change in expression value of the transcript first from E14.5 to E15.5, and second from E15.5 to E16.5, which is explained in detail in Figure 3. The genes in each expression pattern group are listed and common genes among them are diagrammed in Additional file 9.
Figure 3. Expression patterns of CP genes through palatal stages: FPKM values of each CP gene were transformed into log10 (FPKM + 1) and rounded up to 2 decimal places. These 322 CP genes were categorized into 9 possible expression patterns (p) based on the comparison of the transformed FPKM values with FC ≥ 2.0 across 3 different gestational groups for each genotype (n = 3). The patterns represent the expression value of the transcript first from E14.5 to E15.5, then from E15.5 to E16.5. Each pattern is color-coded to differentiate patterns for further analysis. p1 unchanged-unchanged (remain unchanged); p2 upregulated-unchanged; p3 unchanged-upregulated; p4 upregulated-downregulated; p5 upregulated-upregulated; p6 downregulated-unchanged; p7 downregulated-upregulated; p8 unchanged-downregulated; and p9 downregulated-downregulated.
Additional file 9. Table listing the all the CP genes sorted according to their pattern.
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Considering the differential expression of CP genes throughout palatogenesis, we generated individual heatmaps according to the expression patterns of CP related genes and grouped them into corresponding genotypes (Figure 4). In TGFΒ3−/−, the majority of transcripts (n = 294; 92%) were placed in p1, which denotes unchanged expression of genes throughout gestation. Similarly, in TGFΒ3+/− samples, the majority of transcripts were in p1 (n = 293; 91%). Surprisingly, the list of genes in p1 from TGFΒ3−/− and TGFΒ3+/− were highly comparable (92%) (Additional file 9). The genes clustered in p1 unique to TGFΒ3−/−, but not in TGFΒ3+/−, were Chrng, Foxc2, H19, Kcnj13, Lhx8, Meox2, Shh, and Six3 (Table 3). We concluded that these 8 genes demand additional attention due to their unchanged level of expression during crucial stages of palatogenesis.
Figure 4. CP genes represented in pattern-oriented heatmaps. Transcripts were clustered based on expression patterns (n = 9) and heatmaps were constructed using the R pheatmap package. Each column corresponds to the transformed FPKM value of transcripts in duplicate, and each row corresponds to a gene. None of the genotypes had transcripts clustered in p9. Additionally, p4 in TGFΒ3−/− and p5 in TGFΒ3+/− did not contain transcripts. Therefore, the total number of CP gene patterns/genotype groups is 22. The increasing intensity of red to yellow signifies a higher level of expression (FPKM) in the given sample of a specific transcript. The list of genes for each particular pattern and genotype are shown in Additional file 9.
Table 3. Unique TGFβ3−/− genes following the p1 pattern
Finally, in WT samples, the transcripts were more equally dispersed into p1, p2 and p4 as 29%, 32%, and 23% respectively. These results suggest that in normal mice, the majority of CP transcripts are required to be upregulated between E14.5 and E15.5 (denoted as p2 and p4), which corresponds to the most crucial stages of palatogenesis- the adhesion and the fusion stages [34]. Some of these upregulated genes were eventually downregulated (p4) or remained at the same expression levels (p2), which suggest that they may contribute to the final phase of palate development.
Downstream pathway analysis of CP genes
We used the IPA software to determine how the expression pattern-clustered CP genes interconnected with each other to facilitate cellular biofunctions and signaling. According to the core analysis of all CP genes (n = 322) using the IPA, the most significant top 5 cellular functions were cellular development, gene expression, cellular growth and proliferation, cell signaling and cell morphology (Table 4). Although the numbers of molecules were higher in some cellular functions, the ranking was based on p-values calculated by IPA according to relevance of datasets with IKB. Differentially expressed molecules clustered into GO of these cellular biofunctions are tabulated in Additional file 10. The pattern-oriented distribution of the top cellular biofunctions (n = 8) in relation to the TGFβ pathway are illustrated with a color coded matrix with the darker color representing higher relevance between cellular functions and uploaded CP gene pattern datasets (Figure 5).
Figure 5. Downstream effects analysis of CP gene patterns using IPA. The effects of TGFβ3 alleles on CP genes during palatogenesis were examined in the context of differentially expressed human and mouse genes using Ingenuity Pathway Analysis (IPA). Entrez IDs of each CP gene pattern/genotype group (n = 22) were uploaded to IPA as individual datasets. Each identifier was mapped to its corresponding gene object in the Ingenuity Knowledge Base (IKB). Interactions were then queried between these datasets and all other gene objects stored within IPA to generate a set of overlapping direct interaction networks. The significant genes were categorized, compared to functional categories in the IPA database, and ranked according to their p-values. The cellular processes that are most significantly altered in our datasets were: gene expression, cellular development, cellular growth and proliferation, cell signaling, cell morphology, cell death and survival, cellular movement, and cell cycle. The pattern-oriented distribution of the top cellular biofunctions were ranked and illustrated in a color coded matrix: the darker color represents greater relevance between cellular function and CP gene datasets.
Additional file 10. Table showing differentially expressed molecules clustered into GO of cellular biofunctions.
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Table 4. Differentially expressed molecules clustered into GO of cellular biofunctions
The CP genes unique to p1 of TGFΒ3−/− (n = 8) may have necessary functions for the complete development of palatal shelves. Therefore, we analyzed the interaction of these genes with each other, as well as with key biofunctions and TGFβ signaling using IPA (Figure 6). We found that 5 of these genes (Shh, Foxc2, Six3, Meox2, and H19) are closely related to each other, with Tnf (tumor necrosis factor) and Ccnd1 (Cyclin d1) being their intersecting molecules. These genes were mostly associated with cell morphology and cell death biofunctions, and were indirectly associated with TGFβ signaling through Pias4 (protein inhibitor of activated STAT, 4).
Figure 6. Cellular biofunction and pathway analysis of CP genes unique to p1 of TGFΒ3−/− (n = 8). Entrez IDs of CP genes unique to p1 of TGFΒ3−/− were identified using the Venn diagram and uploaded to IPA as an individual dataset. Core analysis was run by default settings on IPA, and the top cellular biofunctions, diseases, and canonical pathways were detected. IPA Path Designer was used to generate the network of these genes through an overlay of the biofunctions and pathways. Genes belonging to the Unique TGFΒ3−/− p1 list were merged into a network (Foxc2, H19, Meox2, Six3, Shh) and gray-shaded. Relationships are shown with colored arrows for easy gene identification.
According to IPA core analysis, there were 19 molecules associated with TGFβ signaling [Ratio: 19/89 (21%)] among all of the CP genes (n = 322). TGFβ signaling molecules along the pathway and their cellular locations are illustrated in Figure 7. TGFβ signaling transcripts expressed in both TGFΒ3−/− and TGFΒ3+/− were (n = 18): Acvr1, Bmp2, Bmp4, Bmp7, Crebbp, Grb2, Inhba, Inhbb, Kras, Map2k1, Map2k2, Nkx2-5, Runx2, Smad3, TGFβ2, TGFβ3, TGFβr1, TGFβr2 (Table 3). All of these molecules followed the p1 expression pattern, which represents a uniform level of expression throughout all time points. However, within WT transcripts, TGFβ-associated molecules were almost equally distributed among p1, p2, p4, and p8. All represented TGFβ pathway molecules (n = 19) were grouped into genotypes according to their expression patterns (Table 5). When the significantly altered CP genes were overlaid with TGFβ signaling, all of these genes followed the Smad-dependent pathway (Figure 7).
Figure 7. Characterization of CP genes in relation to the canonical TGFβ signaling pathway. The cellular localization of CP genes which function in the canonical TGFβ pathway was illustrated using IPA Path Designer. CP gene datasets uploaded to IPA were analyzed using default settings for the core analysis. A total of 19 CP transcripts from these datasets were associated with the TGFβ canonical pathway: ACVR1, BMP2, BMP4, BMP7, CREBBP, GRB2, INHBA, INHBB, KRAS, MAP2K1, MAP2K2, NKX2-5, RUNX2, SMAD3, TGFβ2, TGFβ3, TGFβR1, and TGFβR2. These datasets (n = 7) were selected and overlaid with each other using the IPA Path Designer. Color codes reflect the genotype and expression pattern of CP genes as follows: Orange lines: both TGFβ3−/−p1 and TGFΒβ3+/−p1; green filled: WTp1; light blue filled: WTp2; orange filled: WTp4; and purple filled: WTp8. The types of molecules are annotated in the legend.
Table 5. TGFβ pathway molecules grouped into genotypes with patterns
Global transcriptome of TGFβ3 alleles
Palatogenesis is a complex process involving multiple steps, including: palatal shelf growth, elevation, adhesion and fusion (Additional file 11). It requires the orchestration of several key cellular functions (such as cellular proliferation, differentiation, movement, communication, and death) regulated by numerous genes and signaling pathways. It has been well documented that disruption of structural and regulatory genes involved in any stage of palatogenesis, which occurs between E11.5 and E16.5 in mice, contributes to the formation of cleft palate [34]. On the basis of our studies and others [5,6,35], the stages from E14.5 to E16.5 have been identified as the most critical phases. During these stages, the palatal shelves adhere to each other with a seam and the seam begins to disintegrate in order to complete fusion, resulting in a confluent palate. Therefore, we anticipated that the majority of the genes contributing to physiological palatogenesis would be progressively regulated during these phases. In this study, we took advantage of high-throughput sequencing technology, RNA-Seq, to quantitatively analyze the expression of transcripts in mouse embryonic palatal tissues at three developmental stages.
Additional file 11. Stages of palatogenesis in the mouse. (A) Time-course of palate development in mice. (B-F) Scanning electron micrographs showing oral views of the secondary palate at representative developmental stages [reprinted from Kaufman (Kaufman, 1992) with permission]. Orange lines mark sites of fusion between the medial nasal processes and maxillary processes, white arrowheads point to initial outgrowths of the primary palate, white arrows point to the initial outgrowth of the secondary palatal shelves, red arrowheads mark the initial site of palatal adhesion and fusion, and the yellow arrowhead points to the gap between the primary and secondary palates that will disappear following fusion between these tissues. (G-U) Representative histological frontal sections from anterior (G-K), middle (L-P), and posterior (Q-U) regions of the developing palate at each indicated stage. The middle palate region is flanked by the developing upper molar tooth germs (black arrows in M-P) and corresponds to the palatine region of the future hard palate. The posterior palate region corresponds to the future soft palate. At E11.5 (G,L,Q), the palatal shelf outgrowths arise from the oral surface of the maxillary processes. At E13.5 (H,M,R), the palatal shelves exhibit distinct shapes along the AP axis. By E14.5 (I,N,S), the palatal shelves have elevated to the horizontal position. At ~ E15.0 (J,O,T), the palatal shelves make contact at the midline and initiate fusion by formation of the midline epithelial seam (MES) in the mid-anterior region (arrowhead in O). By E15.5 (K,P,U), palatal shelf fusion is evident in the middle and posterior regions, with complete removal of the MES (black arrowheads in P,U). Remnants of the MES can still be seen in the anterior region (K) at this stage and the palatal shelves also fuse superiorly with the nasal septum. Magnification is not equivalent between stages. MdbP, mandibular process; MNP, medial nasal process; MxP, maxillary process; NS, nasal septum; PP, primary palate; PS, palatal shelf; SP, secondary palate; T, tongue. Adapted from Bush J O and Jiang R. Development 139, 231–243 (2012).
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The integrity and quality of the isolated RNA are the primary factors contributing to successful RNA-Seq studies [36], therefore we ensured that our palatal RNA samples were of high quality based on their RIN (>8.4). In our study, we used the "paired end" approach for RNA-Seq, wherein a single 100bp-long read is sequenced at both ends, which allows the tracking of alternate splice junctions, as well as further analysis of SNPs, insertions and deletions; thus providing more accurate and informative sequencing results from our samples [37,38]. We submitted the raw reads of RNA-Seq data (fastq files) to SRA and the assembly data to the Transcriptome Shotgun Assembly Database.
Our global transcriptome analyses of TGFβ3 alleles showed that significant numbers of transcripts (~6000 genes) were differentially expressed between E14.5 and E15.5, particularly within the WT fetuses, indicating functional roles of these genes during this time period of palatogenesis (Table 1). Interestingly, we found lower numbers of transcriptome alterations between the same time points within the TGFβ3−/− mice (n = 2770), which can be explained by the consequential suppression of gene clusters due to inactivation of the TGFβ3 gene. However it was surprising to observe that the lowest number of transcriptome changes were in TGFβ3+/− mice, n = 1993, which are phenotypically identical to WT mice [25]. This may suggest that only this number of gene alterations is sufficient to enhance the palatal growth and fusion.
Furthermore, in normal mice (WT) the majority of transcripts were upregulated during the early transition of palatogenesis (E14.5 - E15.5) and downregulated during the later transitions (E15.5 - E16.5), suggesting that these are critical stages of palatogenesis requiring extensive gene regulation. This pattern of upregulated-downregulated expression suggests that particular CP genes may follow the same expression pattern to stimulate disintegration of the palatal seam, resulting in a confluent palate.
Understanding the expression of CP genes
The OMIM and MGI databases provide up-to-date and adequately classified information about genetic diseases in humans and mice, respectively; therefore, the identification of CP related genes from either species was uncomplicated. However the merger of the information from these databases required further computer analysis to identify common and individual CP genes between the two species (Additional file 7). To our knowledge, our list of CP genes (Table 2) covers the most comprehensive number of genes (n = 322), which cause CP when mutated in either species alone or both species [39,40].
It was expected that TGFβ3 allelic mice follow 9 different expression pattern combinations during the E14.5-E15.5 and the E15.5-E16.5 transitions (Figure 3). Interestingly, none of the genes followed pattern 9, which represents the continuous downregulation of the transcript throughout all palatal stages. We observed that the majority of the CP genes were equally clustered into p2, p4, and p8 in WT samples (WT), representing normal palate development (Figure 4). Conversely, in both the TGFΒ3−/− and TGFΒ3+/− samples, almost all CP transcripts (91%) were accumulated in p1, and demonstrated high similarity between datasets (92%) (Additional file 9). This suggests that expression regulation of CP genes in both of these allelic mice was either delayed or abandoned.
Unique TGFΒ3−/− genes following the p1 pattern
Although the pattern of transcriptional expression between TGFΒ3−/− and TGFΒ3+/− are unexpectedly similar, phenotypic expression of CP occurs only in TGFΒ3−/− and not in TGFΒ3+/− pups [24,25]. This suggests that the unique p1 genes of TGFΒ3−/− (n = 8; Chrng, Foxc2, H19, Kcnj13, Lhx8, Meox2, Shh, and Six3) may play crucial roles in the completion of palatogenesis. Therefore, we analyzed their specific functions within the cell, their roles in palatogenesis, and their interactions with the TGFβ signaling pathway using IPA and GeneCards [41].
Chrng (Cholinergic receptor, nicotinic, gamma) is a transmembrane glycoprotein and has been shown to play a role in neuromuscular organogenesis and ligand binding [42]. Mutation of Chrng causes the developmental disorder multiple pterygium syndrome in humans, exhibited by isolated CP, short stature, vertebral (spine) defects, joint contractures, and webbing of the neck, armpit, elbow, and knee [42,43]. Pterygium is also associated with Irf6 and p63 mutations in humans [44], and both Irf6 and p63 are known to be closely associated with TGFβ signaling. Nevertheless, according to current literature, we could not find any relationships between Chrng and other molecules of the TGFΒ3−/− unique p1 list (Figure 6), or the TGFβ pathway.
Foxc2 (Forkhead box C2) is a member of the forkhead box (FOX) family of transcription factors and has been shown to be functional during development of mesenchymal tissues [45]. Mutations in Foxc2 are responsible for the hereditary lymphedema-distichiasis syndrome with CP observed in some patients [46]. In addition, Foxc2 is also involved in cancer metastases. In particular, expression of Foxc2 is induced when epithelial cells undergo epithelial-mesenchymal transition (EMT) [47]. Recently, Lindley at al. (2010) showed that Foxc2 may play a role in EMT maintenance when human mammary epithelial cells are treated with TGFβ [45]. (The Foxc2 knockout mouse is not available, according to KOMP). Overall, these relationships suggest that Foxc2 could be a vital element of palatal confluency through facilitation of EMT. Furthermore, failure of proper Foxc2 transcript regulation may result in CP in TGFβ3−/− fetus.
H19 is an imprinted maternally expressed transcript and expresses a long noncoding RNA. It has been shown that an enhancer deletion affects the expression of both H19 and Insulin-like growth factor 2 (Igf2), thus the Igf2 and the H19 genes are proposed to utilize a set of common enhancers [48,49]. When Thomas et al. (1997) produced transgenic mice that express the Igf2 gene under the control of the H19 enhancers, a large fraction of homozygous mice developed CP [44]. In our network analysis (Figure 6), we found that H19 is indirectly related with TGFβ signaling through TNF, which suggests that it may play a crucial role during palatogenesis under regulation of TGFβ.
The Kcnj13 gene encodes a member of the inwardly rectifying potassium channel family of proteins and regulates ion transmembrane transport and mutations in Kcnj1 are associated with snowflake vitreoretinal degeneration [50]. There were no significant relationships found between Kcnj12 and other molecules of the TGFΒ3−/− unique p1 list (Figure 6), or the TGFβ pathway. However, this does not rule out its potential regulatory interaction with TGFβ signaling, and therefore demands additional studies to determine its role during palate development.
Lhx8 is a member of the LIM homeobox family of transcription factor proteins, which are involved in patterning and differentiation of various tissue types. Lhx8 is expressed in the mesenchyme of the mouse palatal structures throughout their development [11]. Zhao et al. (1999) showed that in Lhx8 homozygous mutant embryos, the bilateral primordial palatal shelves formed and elevated normally, but they often failed to make contact and to fuse properly, resulting in a cleft secondary palate [51]. Inoue M et al. (2006) proposed that the L3/Lhx8 gene contributes to epithelial mesenchymal interactions during facial morphogenesis and that Fgf-8b and Tgfβ3 were responsible for Lhx8 expression in the maxillary process [52]. Our RNA-Seq study of TGFβ3 −/− fetuses further confirmed the requirement of upregulated expression of Lhx8 throughout palatal morphogenesis.
The Meox2 gene (mesenchyme homeobox 2) encodes a member of a subfamily of non-clustered, diverged, antennapedia-like homeobox-containing genes [53,54]. Jin et al. (2006) found that Meox2 is highly expressed in the posterior region of the developing palate, and the reduction of Meox2 gene levels increased the susceptibility of mice to cleft palate through a novel post-fusion mechanism [53]. The posterior cleft in E15.5 Meox2 −/− mice contained no epithelial cells, therefore they proposed that Meox2 may function to strengthen the fusing zone of palatal shelves. The lack of strong fusion of epithelial cells during stable expression of Meox2 may explain why the palatal shelves of TGFβ3−/− mice attach to each other, but fail to fuse [25]. Recently, Valcourt et al. (2007) showed that ectopic Meox2 suppressed epithelial cell proliferation in cooperation with Tgfβ1, and mediated induction of the cell cycle inhibitor gene p21 [54]. Furthermore, they showed that Meox2 failed to promote EMT and partially blocked Tgfβ1-induced EMT [54]. Considering the requirement of EMT during palatal fusion, Meox2 expression needs to be downregulated at the later stages of palatogenesis, as observed in both WT and TGFβ3+/− mice in our study.
Sonic hedgehog, Shh, is a member of the hedgehog family of secreted proteins and has been implicated as the key inductive morphogen in patterning of vertebrates during organogenesis; particularly the ventral neural tube, the anterior-posterior limb axis, and the ventral somites [55]. Shh signaling plays essential roles in craniofacial development by regulating a number of transcription factors and signaling interactions that take place between the epithelium and mesenchyme during normal palatogenesis [56]. Lan et al. (2009) showed that Shh is predominantly expressed in palatal epithelia and signals directly to the palatal mesenchyme to regulate palatal mesenchyme cell proliferation through maintenance of cyclin D1 and D2 (Ccnd1 and Ccnd2) expression [56]. Recently, Sasaki et al. (2007) showed that Shh expression in the palates of Tgfβ3-null mice was reduced throughout E12.5–E15.5, and thereby proposed that Shh may be involved in TGFβ3 regulation of normal palatal fusion [57]. Our results further support that upregulated expression of Shh is necessary for the successful completion of palatogenesis, as observed in the TGFβ3+/− and WT mice, but not in TGFβ3−/−.
SIX homeobox 3 (Six3) is a transcription factor crucial to embryonic development by providing the necessary instructions for the formation of the forebrain and eye development [58]. Similar to Shh [59], mutations in the homeodomain of the human Six3 gene cause holoprosencephaly and are associated with midline facial cleft - tessier cleft 14 [60]. In mice, it has been shown that Six3 protein increases expression of Ccnd1 protein [61], which is directly related to TGFβ signaling (Figure 6). Our results indicate that Six3 expression has to be upregulated after E14.5 for the precise progression of palate development. Therefore, the interaction of Six3 with TGFβ3 and their mechanism of activation deserve further analysis using biological techniques.
Cellular biofunctions and TGFβ pathway molecules
The expression pattern-clustered CP genes interconnect each other to facilitate cellular biofunctions and canonical pathways. The relevance of these groups of gene datasets was detected using IPA core analysis (Figure 5).
Our primary objective in this study was to analyze the transcriptomal differences among the alleles of TGFβ3 knockout mice. Thus, it was critical to find the relationship of CP genes with the TGFβ signaling pathway, which encompasses 89 molecules (Figure 7). TGFβ3 controls the fusion of palatal shelves by EMT and apoptosis [5,14,62]. Furthermore, TGFβ1 and TGFβ2 regulate mesenchymal cell proliferation and extracellular matrix synthesis in the palate [63]. Although not all of the molecules of the TGFβ signaling pathway are associated with CP genes, it is noteworthy that all of the related CP genes followed the Smad-dependent pathway. This may indicate that TGFβ3 regulates the CP genes through Smad-signaling, with ancillary involvement of ERK, PI3K, JNK, MAPK, etc. Thus, the promoter regions of these CP genes should be analyzed for Smad-binding elements using ChIP-PCR or ChIP-Seq. The majority of these CP genes followed the p8 expression pattern in WT mice, which represents the unchanged-downregulated expression pattern. This suggests that TGFβ molecules are required during E14.5 and E15.5, but are less necessary during E16.5, which correlates with our previous findings demonstrating the sequential function of TGFβ3 throughout the degradation of the palatal seam [5].
Overall, these sequencing and bioinformatics analysis studies are used as gene identification tools for future experiments to further understand the detailed mechanism of palate development. The 8 putative CP causing genes and Smad-dependent TGFβ signaling molecules will be analyzed in detail using gene and protein expression studies, as well transcription factor and promoter binding assays.
As a result of the complexity of TGFβ signaling, apparently simple but highly important questions regarding the development of cleft palate remain unanswered, including: what is the genetic footprint of TGFβ3 in normal palatogenesis and how does the deregulation of TGFβ3 signaling cause cleft palate? In this study, we have attempted to answer these questions through the extensive quantitative transcriptome analysis of the palates of TGFβ3 knockout mice through RNA sequencing technology. Our study represents the first detailed analysis of palatal transcriptomes generated by RNA-Seq technology during critical stages of palatogenesis. The dataset described here will provide an enriched resource for searching transcripts that may play key regulatory roles at different stages of palatal development. Furthermore, we identified 8 key genes which may play fundamental roles in the development of cleft palate in TGFβ3−/− mice. Our combined results provide an initial understanding of the complex genetic mechanism of TGFβ3-mediated palatogenesis, and may lead to the identification of genes for the targeted prenatal treatment of cleft palate.
Mouse breeding and genotyping
The generation and genotyping of TGFβ3−/− mice have been described previously [25]. TGFβ3 heterozygous (+/−) C57BL/6J male and female mice were provided by Tom Doetschman (BIO5 Institute, University of Arizona, AZ). Mice were housed in accredited animal facilities at the University of Nebraska Medical Center (UNMC). All procedures were approved by the IACUC (Institutional Animal Care and Use Committee) of UNMC. Homozygous (−/−) embryos were obtained by mating TGFβ3+/− male and female mice. The morning that the vaginal plug was pulled was considered embryonic day (E) 0.5. Tissue samples were individually labeled and embryonic tails were used for genotyping by PCR. Genomic DNA was prepared using the Wizard Genomic DNA Purification Kit (Promega – A1120). The primers used for TGFβ3 were as follows:
TGFβ3 Forward 5′ TGGGAGTCATGGCTGTAACT 3′
TGFβ3 Reverse 5′ CACTCACACTGGCAAGTAGT 3′
pMC1-Neo 5′ GCCGAGAAAGTATCCATCAT 3′
These primers amplified 600 bp and 400 bp fragments for the mutated and WT alleles, respectively. PCR conditions were 30 cycles of 95°C for 30 seconds, 57°C for 45 seconds, 72°C for 1 minute, followed by one cycle of 72°C for 10 minutes.
Typically, 8 fetuses were obtained from each pregnancy in a Mendelian-fashion 3 allelic-genotype (1:2:1) as 2 TGFβ3−/−, 4 TGFβ3+/−, and 2 WT. Palates were extracted from fetuses as described earlier [2] at 3 time points (E14.5, E15.5, and E16.5) as duplicates and the tissues were stored in RNAlater RNA Stabilization Reagent (QIAGEN, CA) to preserve transcript integrity. In order to evaluate the reproducibility of our experimental samples and procedures, two independent biological and technical replicates were assayed for each gestational age and each allele resulting in 36 (n = 3 × 3 × 2 × 2) samples for sequencing.
Protein, RNA extraction, construction of small RNA libraries, and RNA-Seq
Total proteins were extracted from the palatal shelves collected from embryonic (E) 15.5 and western blot was performed as previously done in our lab and described in [9,10] using antibody against TGFβ3 (R & D Systems, MN). We extracted the RNA using the RNeasy Kit (QIAGEN, CA) and evaluated the RNA for purity and concentration by ultraviolet spectroscopy (NanoDrop, Wilmington, DE). RNA integrity numbers (RIN) [64,65], based on an algorithm for judging the integrity of RNA samples, were evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). Libraries were prepared using the Illumina mRNA-Seq Sample Preparation Kit (San Diego, CA) according to the manufacturer's instructions. Briefly, poly(A) + RNA was recovered from 1 μg of total RNA using two rounds of isolation with oligo-dT-coated Sera-Mag magnetic beads. The recovered poly (A) + RNA was then chemically fragmented. RNA fragments were converted to cDNA using SuperScript II and random primers. The second strands were synthesized using RNaseH and DNA Pol I. The ends of the cDNA were repaired using T4 DNA polymerase, T4 polynucleotide kinase, and Klenow DNA polymerase. A single adenosine was added to the 3′ end using Klenow fragment (3′ to 5′ exo minus). Adaptors were attached to both ends of the cDNA using T4 DNA ligase. RNA fragments were extracted from a 2% low range ultra agarose sizing gel. The fragments were amplified by 15 cycles of PCR using Phusion DNA polymerase. Libraries were validated with Agilent Bioanalyzer (Palo Alto, CA). Libraries were diluted to 10 pM and applied to an Illumina flow cell using the Illumina Cluster Station. Sequencing was performed on Illumina HiSeq 2000 according to the manufacturer's instructions [66,67].
Mapping and quantification of transcripts
RNA-Seq datasets were analyzed by following the recently published RNA-Seq protocol [31]. The 36 samples (paired-end reads, including biological replicates and technical replicates; n = 3 × 3 × 2 × 2) were individually mapped onto the mouse genome (mm9, build name NCBIM37) by using TopHat v1.4.1 [68-70]. Preprocessing steps were not applied to the raw data (fastq) files because the sequencing quality was very high in both 3′ and 5′ ends according to the FastQC reports [71]. The relative abundance of reads was normalized to the total read number and shown as fragments per kilobase per million mapped (FPKM) [71]. After the alignment, Cufflinks v1.3.0 [72-74] was used to estimate the abundances of transcripts. Cuffdiff from Cufflinks repository was used to perform pairwise comparisons between different genotypes and gestational groups. The dispersion between each biological replicate was also tested by Cuffdiff, as well as the dispersion between each technical replicate. CummeRbund ( http://compbio.mit.edu/cummeRbund/ webcite) software [31] provides functions for creating commonly used expression plots, such as: volcano, scatter and box plots, using processed data from Cuffdiff. We used CummeRbund to generate scatter plots to use for quality assessments of both biological and technical replicates.
We used the VennDiagram [75], an R package that enables the automated generation of highly-customizable, high-resolution Venn diagrams, to illustrate the number of transcripts in each experimental group which passed the significance and fold change (FC ≥ 2.0) filtrations through Cufflinks. Pattern-oriented listings of CP genes were illustrated with GeneVenn, a web application for comparing gene lists (Additional file 5).
Identification of cleft palate genes
We used the OMIM (Online Mendelian Inheritance in Man) database to retrieve 280 genes and loci involved in genetic diseases associated with CP syndromes in humans. We used information from developmental biology studies demonstrating CP in knockout mouse models and the Mouse Genome Informatics (MGI) website with the mammalian phenotype browser, the international database resource for the laboratory mice, to retrieve 128 genes (out of 223 genotypes) causing CP in mice. The pattern-oriented heatmaps of CP genes were illustrated by using R pheatmap package
Biological interpretation and pathway analysis
The effects of TGFβ alleles on CP genes during palatogenesis were examined in the context of differentially expressed human and mouse genes using Ingenuity Pathway Analysis (IPA), (Ingenuity Systems, CA), a web-delivered application used to discover, visualize, and explore relevant networks. After performing statistical analysis and filtering of the RNA-Seq data, the Entrez IDs and FPKM values of each group were uploaded to IPA as a dataset. Each identifier was mapped to its corresponding gene object in the IKB. Interactions were then queried between these datasets and all other gene objects stored within IPA to generate a set of direct interaction networks that were overlapped. The significant genes were categorized, compared to functional categories in the IPA database, and ranked according to their p-values. P-values less than 0.05 indicate a statistically significant, nonrandom association between a set of significant genes and a set of all genes related to a given function in the IKB [76]. Through the assessment of differentially expressed genes, cellular processes that were most significantly altered in our dataset were: gene expression, cellular development, cellular growth and proliferation, cell signaling, cell morphology, cell death and survival, cellular movement, and cell cycle. Based on these IPA analyses, the cellular biofunction categories mentioned above and the TGFβ pathway were filtered among other cellular processes and canonical pathways; then ranked according to their p-values and represented as a color coded matrix. Datasets associated with the TGFβ pathway were overlaid using the IPA Pathway Designer.
TGFβ3: Transforming growth factor β 3; NGS: Next generation sequencing; RNA-Seq: RNA Sequencing; FC: Fold change; IPA: Ingenuity pathway analysis; E: Embryonic day; CP: Cleft palate; TGFΒ3−/−: Homozygous; WT: Wild-type; TGFΒ3+/−: Heterozygous; FPKM: Fragments per kilo base per million mapped.
Competing interests
The authors declare that they have no competing interests.
Authors' contributions
FO carried out the study design, animal breeding, sample collection, RNA extraction, identification of CP genes, IPA analyses, and drafted the manuscript. YL undertook RNA-Seq data quality control, processing, alignment, visualization, bioinformatics analyses, and helped to draft the manuscript. XZ performed animal breeding, collected palatal tissues and extract RNA CG and AN supervised the design and coordination of the study, and edited the manuscript. All authors read and approved the final manuscript.
Authors' information
FO is a postdoctoral research associate in AN's group and has a strong background in cell biology and bioinformatics. He designed the research, identified CP genes, and analyzed the transcriptome. YL is a graduate student in CG's group with training in computer science. He performed all RNA-Seq data processing and several bioinformatics studies. XZ is a graduate student in AN's group studying palatal signaling. CG (Associate professor) has an interdisciplinary background both in molecular and computational biology. He has published a number of computational prediction methods on protein subcellular localization since 2004. AN (Associate professor) is a craniofacial developmental biologist and has extensive experience in cell signaling that governs palate development in TGFβ3 mice.
This research is supported by NIDCR, NIH grant (R01DE017986) to Dr. Ali Nawshad. The UNMC DNA Sequencing Core receives partial support from the NCRR (1S10RR027754-01, 5P20RR016469, RR018788-08) and the NIGMS (8P20GM103427, GM103471-09). This publication's contents are the sole responsibility of the authors and do not necessarily represent the official views of the NIH or NIGMS.
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Williams LJ, Tabbaa DG, Li N, Berlin AM, Shea TP, Maccallum I, Lawrence MS, Drier Y, Getz G, Young SK: Paired-end sequencing of Fosmid libraries by Illumina.
Sengupta S, Bolin JM, Ruotti V, Nguyen BK, Thomson JA, Elwell AL, Stewart R: Single read and paired end mRNA-Seq Illumina libraries from 10 nanograms total RNA.
Gritli-Linde A: p63 and IRF6: brothers in arms against cleft palate.
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Lindley LE, Briegel KJ: Molecular characterization of TGFbeta-induced epithelial-mesenchymal transition in normal finite lifespan human mammary epithelial cells.
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Hader C, Marlier A, Cantley L: Mesenchymal-epithelial transition in epithelial response to injury: the role of Foxc2.
Leighton PA, Saam JR, Ingram RS, Stewart CL, Tilghman SM: An enhancer deletion affects both H19 and Igf2 expression.
Bartolomei MS, Zemel S, Tilghman SM: Parental imprinting of the mouse H19 gene.
Hejtmancik JF, Jiao X, Li A, Sergeev YV, Ding X, Sharma AK, Chan CC, Medina I, Edwards AO: Mutations in KCNJ13 cause autosomal-dominant snowflake vitreoretinal degeneration.
Zhao Y, Guo YJ, Tomac AC, Taylor NR, Grinberg A, Lee EJ, Huang S, Westphal H: Isolated cleft palate in mice with a targeted mutation of the LIM homeobox gene lhx8.
Inoue M, Kawakami M, Tatsumi K, Manabe T, Makinodan M, Matsuyoshi H, Kirita T, Wanaka A: Expression and regulation of the LIM homeodomain gene L3/Lhx8 suggests a role in upper lip development of the chick embryo.
Jin JZ, Ding J: Analysis of Meox-2 mutant mice reveals a novel postfusion-based cleft palate.
Valcourt U, Thuault S, Pardali K, Heldin CH, Moustakas A: Functional role of Meox2 during the epithelial cytostatic response to TGF-beta.
Cobourne MT, Green JB: Hedgehog signalling in development of the secondary palate.
Lan Y, Jiang R: Sonic hedgehog signaling regulates reciprocal epithelial-mesenchymal interactions controlling palatal outgrowth.
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subset: commoncrawl


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Kingery joined by Kevin Newman and Bobby Dalbec on All-Conference team.
The meet will take place on May 28-30 in Austin, Texas.
On Monday, the fifth-ranked Wildcats finished fifth in stroke play to advance to match play.
Fifth-seeded Arizona will face fourth-seeded Stanford at 7:50 a.m. ET on Tuesday.
The 33-year coaching veteran took three schools to five total College World Series, winning twice, including at Arizona in 2012.
No. 5 Arizona will tee at 12:10 p.m. ET for round four on Monday.
Baseball Closes 2015 Season With 8-1 Victory
Arizona's Season Comes to an End at LSU
No. 5 Arizona will tee at 1 p.m. ET on Sunday for round three.
There was a multitude of quality marks put up on Saturday night at the Tucson Elite Classic.
Bannister's Gem Gives Cats Senior Night Win
Cats Blanked in Super Regional Opener


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General Manager: Bryan Lane
Bryan Lane is the General Manager of WNHU. He oversees all activities at WNHU, and is a faculty advisor for all student-run management & programming. Bryan Lane has had a career in the Radio Industry for over 30 years. He graduated with a B.A. Mass Communication/Broadcasting, from Mansfield University, Mansfield, PA & a M.S. Ed., from St. Joseph's College of Maine, Standish, ME. Some of Bryan's favorites are-Stevie Wonder, Nirvana, Paul Simon, Shelby Lynne, & Led Zeppelin.
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Head Engineer: John Ramsey
John Ramsey is Chief Engineer of WNHU. He oversees the technical aspects of the station's operations, including the FM station as well as the three internet streams. He joined the station's staff in 2014 and his first job was to move WNHU into their new home on Ruden St in W. Haven. He has been a broadcast engineer since 1978 and runs his own broadcast engineering consulting firm, Ramsey Communications. He is the author of the book "Hartford Radio", webmaster ofhttp://hartfordradiohistory.com and http://coldwar-ct.com and founder of the Connecticut Radio Alliance (ctradioalliance.org) that represents the state's college and non-commercial radio stations.


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Report: Bruins looking to trade Tomas Kaberle's rights
|06.28.11 at 10:38 pm ET
According to a tweet from TSN's Darren Dreger, the Bruins sent out an email Tuesday offering Tomas Kaberle's negotiating rights to other teams. Any team that acquired Kaberle would, as the Bruins do now, be able to negotiate with the defenseman exclusively leading up to the opening of free agency on Friday.
Kaberle, 33, is one of only two unrestricted free agents from the Bruins' Stanley Cup champion lineup. Acquired on Feb. 18 in exchange for center Joe Colborne, a 2011 first-round pick and a 2012 second-rounder, he had one goal and eight assists for nine points in 24 regular-season games with the B's. He and Dennis Seidenberg tied for lead among Bruins' defenseman in postseason points with 11.
Rights to free-agents-to-be can be moved by the teams with which they last played, as the Flyers traded for the rights to goalie Ilya Bryzgalov before locking him up last week. The Canucks traded the rights to defenseman Christian Ehrhoff to the Islanders on Tuesday.
Latest from Bleacher Report
- Brad Marchand's Hot Streak a Big Reason for the Boston Bruins' Recent...
- Prospect Depth Allows BOS to Not Rush Pastrnak
- Seth Griffith Fitting in on the First Line with the Boston Bruins
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- Bruins' Patrice Bergeron Records 500th Career Point
- Bruins Players Dress Up as 'Frozen' Characters
- Looking at Bruins Defensive Pairings Without Chara


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Grid Connect Solar Power Systems
Why invest in solar?
- Do you want to save money on your next electricity bill?
- Do you want to power your home or business with clean energy?
- Do you want to be less dependent on the big energy retailers?
- Do you want to add value to your property?
If you answered yes to any of these questions you may want to consider a grid connect solar power system. Over 1 million Australian households and businesses have already joined the green revolution and installed solar on their rooftops. It is not too late, you too can save and reduce your environmental footprint.
A grid connected solar power system will supply your household with energy and, if you consume less than you produce, feed the surplus to the electricity grid. Surplus energy is usually metered and credited to your power bill (depending on what State you are in and what retailer you are with). Some electricity providers install a bidirectional meter that runs backwards when you feed electricity to the grid. Compare energy retailers on Energy made Easy website. In NSW, feed-in tariffs are "voluntary" and only a few retailers offer them to non Solar-Bonus-Scheme customers.
Grid Connect Solar Components
A grid connect solar system is not very complex. It essentially consists of solar panels and an inverter. The inverter converts the DC electricity from the solar panels into 240V AC for the grid. Inverters are small and can be mounted on the inside or outside of your house. The solar panels are ideally mounted on a north facing roof. You could also mount the panels on a pole or ground frame if your roof is facing 'the wrong way'.
View our Grid Feed Photo Gallery.
Solar panels and inverters require minimum maintenance as they do not have any moving parts. Rain will usually keep the panels clean. Today's solar panels come with a 25-year performance warranty, but are designed to last 50 years or more. View the components that we use.
System Size and Cost
To determine an appropriate system size please read our residential use and business use section which includes system examples and prices. You could also use our grid connect solar calculator for a rough but instant quote (you will need a recent and typical electricity bill).
The amounts quoted (for grid connect solar systems) include solar panels, inverter, basic frame (not tilted), cabling, fuses, labels and labour.
Contact us for prices on other systems, or
Our Grid Input Today
At 17:10:48


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Jim Motavalli
New York Times contributor blogs about cars and other interesting ways of getting around.
The Volt convertible (and other exciting cars coming our way)
A seasonal cornucopia from carmakers includes an affordable Ferrari, an electric Mazda, a hybrid Bug and the return of the timeless Chrysler Cordoba.
Fri, Apr 01, 2011 at 01:05 PM
BUDGET-MINDED: The Ferrari Californano, with 50 mpg and India-sourced power, is an instant classic. (Photo: Tina Barker/Flickr)
I hung on every word from General Motors spokesman Taylor Wildwood, who revealed to the world in the virtual pages of Road & Track that Chevrolet would show a ragtop Volt at the upcoming New York International Auto Show, and bring it to market this summer at a remarkable $43,000 (just $2,000 more than the sedan).
This is a Volt, so of course there are green touches, including a manual top to save electricity and an ultra-thin transparent photovoltaic skin covering two-thirds of the roof and powering interior cooling fans. I was all set to put in my order when the extravagantly named Mr. Wildwood was shown to be fictional, and the whole thing an April Fools' joke. But the prank was played straight enough that I'm sure some people called their Chevy dealers.
This whole thing led me to think about cars I could invent for seasonal levity, with the calendar as an excuse. Here are a few:
The collector Cordoba: The actor Ricardo Montalbán had many accomplishments, including the famous television series "Fantasy Island." But it was his 1975 commercials for the Chrysler Cordoba and its "rich Corinthian leather" that were closest to his heart. At his death, Montalbán left funds to create a special, limited-edition Cordoba, recreating the personal coupe he loved so much. Every detail is preserved, including its tasteful accent lighting, vinyl roof and 400-cubic-inch V-8 with an optional four-barrel carburetor. A tape cassette of Spanish guitar music is included.
VW Beetle Hybrid. VW has caught the green bug in a big way, and its latest manifestation is an ultra-fuel efficient 45-mpg combined hybrid. The car has been long rumored, and now it's here, with a 177-horsepower drivetrain borrowed from the New Compact Coupe concept car. VW promises to plant a tree in the Black Forest for every hybrid sold. In a separate development, the Autostadt theme park next to the company's Wolfsburg factory is now 100 percent wind and solar powered. Company-trained craftsmen draw on that renewable power to make hand-sewn lederhosen that are sold in the Autostadt gift shop.
An affordable Ferrari: It had to happen. The recession has so shrunken the pool of millionaire playboys that a number of Italian automakers, including Lamborghini (with the Honda Civic-engined EconoSportiva) and Bugatti (that's Jetta power in the BudgetFire), have been forced to respond. Ferrari was the last holdout, but its partnership with Tata has at last born fruit in the form of the Californano. All the classic Ferrari styling cues are preserved, but the Californano also achieves 50 mpg through its two-cylinder 624-cc rear-mounted engine. Because this is a Ferrari, Italian tuners "breathed" on the power plant to achieve 54 horsepower, allowing 15-second zero-to-60 times and a top speed approaching 60 mph. Ferraris are known as "ticket magnets," but the Californano is guaranteed never to have a day in court.
The Mazda2 EV: The lightweight $14,000 subcompact Mazda, with 35 mpg on the highway, is a hit in the U.S., so it's not that surprising that the automaker would turn it into a battery EV (the cells are from Panasonic) with 110-mile range. Expect the Mazda2 EV to hit these shores as a competitor for the Honda Fit battery car in late summer of 2012. The price is unknown, but it could slot in at $30,000 to undercut the Nissan Leaf. Asked why Mazda was so long a holdout in building an EV, spokesman Grant Miatan said that company engineers lost valuable time in an internal debate on which side to locate the charger port. In a compromise, it has them on both sides.
The opinions expressed by MNN Bloggers and those providing comments are theirs alone, and do not reflect the opinions of MNN.com. While we have reviewed their content to make sure it complies with our Terms and Conditions, MNN is not responsible for the accuracy of any of their information.


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Metal Mafia Spider Web Cupcake Navel Bar
(approx. $3.18 or €2.35)
- Product Type: Body Jewellery
- Ships in 1-2 days
- UK & Worldwide Delivery
- StockID: 156385
- One Size Fits All
Unleash your inner gothic goddess with this awesome Metal Mafia belly bar! Featuring a unique spider web cupcake design in red and white hanging from a black metal bar with red gems for a sublime finish.


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One thing is clear—just as Attorney General Kamala Harris took the lead in privacy efforts and is leading state attorneys general in their own investigation of the Neiman Marcus, Target, and Michaels Stores breaches, she is taking the lead in cyber. Watch this space.
DISCLAIMER: Because of the generality of this update, the information provided herein may not be applicable in all situations and should not be acted upon without specific legal advice based on particular situations.
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