Posted by: barn owl | January 8, 2009

Daily Nature 2009: Laughing Gull


Laughing Gull, Galveston, TX. Photograph by Dr. Jim Smith

Posted by: barn owl | January 7, 2009

Daily Nature 2009: Red Oak


Red Oak (Quercus texana) in autumn glory, Lost Maples State Natural Area, November 2008.

Posted by: barn owl | January 6, 2009

Daily Nature 2009: Red

In these redrock canyons, time creates space–an arch, an eye, this blue eye of sky. We remember why we love the desert; it is our tactile response to light, to silence, and to stillness.
Hand on stone–patience.
Hand on water–music.
Hand raised to the wind–Is this the birthplace of inspiration?

~ Terry Tempest Williams, Red

Posted by: barn owl | January 5, 2009

Daily Nature 2009: Japanese Garden Scene


Water flowing over stones and autumn leaves in the Japanese Garden, at the San Antonio Botanical Gardens (November 2008).

Posted by: barn owl | January 4, 2009

Daily Nature 2009: WPA Wildlife Poster


NYC Works Progress Administration Poster (1940)

Mixing it up a bit: here’s an image from a poster produced during the Depression era, sponsored by the WPA. The worst month for deer-motor vehicle collisions in Texas is November.

Posted by: barn owl | January 3, 2009

Daily Nature 2009: Scissor-tailed Flycatcher


Scissor-tailed Flycatcher (Tyrannus forficatus). Photo by Dr. Jim Smith.

This long-tailed flycatcher is a common sight throughout Texas and Oklahoma during the summer months. Several families nest and play in the live oak trees along the boulevard near my home.

Posted by: barn owl | January 2, 2009

Daily Nature 2009: Independence Pass


View from Independence Pass, Colorado Rocky Mountains, USA, June 2007. Some snow remaining around the scenic overlook in 2007, but not enough to prevent access. One year, there was so much snow and ice, I was unable to walk beyond the parking lot at the summit of Independence Pass. The weather in Aspen was quite chilly that year as well, even though it was early summer.

Posted by: barn owl | January 1, 2009

Daily Nature 2009: Bufflehead


Male Bufflehead (Bucephala albeola), in breeding plumage. Photo by Dr. Jim Smith.

The Bufflehead is a small, compact duck that nests in tree cavities. Winter range extends throughout much of the southern US and Mexico, as well as both east and west coasts.

Posted by: barn owl | December 18, 2008

DNA Repair During Spermatogenesis: Gimme a Break!
Although we often tend to attribute infertility to dysfunction of the female reproductive process, approximately 50% of cases are likely to result from abnormalities in spermatogenesis, or male sex cell production. After puberty, spermatogenesis continues throughout the life of a male mammal, proceeding from mitotic division of spermatogonia, through meiotic division of spermatocytes, to the transformation of haploid spermatids into mature, motile sperm (spermiogenesis). Of course, the integrity of the genome must be maintained throughout the process of spermatogenesis, as any sperm cell has the potential to contribute its DNA to the next generation. Levels of proteins involved in detection of DNA damage and in DNA repair are very high in the germ cell precursors for sperm and eggs, and remain elevated in spermatocytes up until a transition period that precedes spermiogenesis. After meiosis is completed, haploid spermatids enter a period during which they are repair-deficient, and the condensed DNA is transcriptionally inactive, and inaccessible to DNA repair enzymes. Thus, it is critical for any DNA damage, incurred during crossing over and other phases of meiosis, to be detected and repaired prior to spermiogenesis.


Sequence of events in mammalian spermatogenesis, with timeline for human and mouse. Day 0 = day of fertilization. From Marchetti and Wyrobek (2005)

Spermatogenesis in mice is very similar to that in humans, and the availability of mouse strains with targeted mutations in genes required for DNA damage detection and repair has facilitated analyses of genomic integrity maintenance during this process. In the 2007 paper I have chosen for my PLoS ONE@Two post, Paul and colleagues ( used three different strains of knockout mice, each of which harbored a targeted mutation in a different DNA repair gene, to examine the consequences of these deficiencies on male germ cell development:

1) The mismatch repair (MMR) pathway removes errors made during DNA replication that have escaped proofreading by DNA polymerase, and the MutS homologue 2 gene (Msh2) encodes a protein that is expressed at high levels in mouse spermatogonia and spermatocytes. Msh2-/- mice are more likely to develop skin cancer when exposed to UVB light, but have no known defects in spermatogenesis.

2) The nucleotide excision repair (NER) pathway takes care of UV-induced DNA damage, as well as bulky DNA lesions. The protein encoded by the Ercc1 gene (excision repair cross-complementing protein) is an essential component of NER, and is expressed at high levels in pachytene spermatocytes and round spermatids. Mice that lack this gene die of liver failure before spermatogenesis, but a transgenic “trick” allowed rescue of the liver phenotype. The rescued mice (TG-Ercc1) still lack ERCC1 in the testes, and are infertile.

3) Like ERCC1, the protein encoded by the p53 tumor suppressor gene is also involved in the homologous repair (HR) pathway. The p53 protein is expressed at high levels in the testes, and is important in recognition and repair of DNA strand breaks, as well as in mediating DNA damage-induced apoptosis. Mice that lack p53 are tumor-prone, and their mature sperm are less motile.


Double strand breaks in pachytene spermatocytes. Immunodetection of SCP3 (red) for synaptonemal complexes and γH2AX (green) for DNA DSB. The sex bodies are indicated by white arrowheads. From Paul et al. (2007)

To compare spermatogenesis and DNA damage in mice deficient for either MSH2, ERCC1, or p53, Paul and colleagues used a variety of techniques. First, they simply looked at the architecture of the seminiferous tubules in the testes, using standard histological staining methods. The TG-Ercc1-/- mice had reduced numbers of germ cell precursors, as did the Msh2-/- mice. Reduced diameters of seminiferous tubules were also observed in the testes of both these strains of knockout mice. To determine whether programmed cell death, or apoptosis, was elevated in the testes of the knockout mice, Paul and colleagues stained testicular sections for cleaved caspase-3. Increased numbers of apoptotic spermatogonia were observed in the TG-Ercc1-/- and p53-/- mice.


DNA damage detection in epididymal sperm, using the SCSA. From Paul et al. (2007)

Antibodies against the histone variant γH2AX can be used to detect unsynapsed DNA, as well as DNA double strand breaks, during meiosis. In normal pachytene spermatocytes, this variant is expected to bind to the sex body, which contains unpaired regions of the X and Y chromosomes. However, elevated numbers of γH2AX foci were detected in spermatocytes from TG-Ercc1-/-, p53-/-, and p53+/- mice. Moreover, another assay for DNA strand breaks and chromosome abnormalities, the Sperm Chromatin Structure Assay (SCSA), revealed increased DNA damage in epididymal sperm from TG-Ercc1-/- mice. Clearly, ERCC1 is critical for normal spermatogenesis, though results from other investigators indicate that the HR, rather than the NER, role of the protein is more important in this context. The functions of p53 in spermatogenesis are less clear, and confounded by the strain differences in infertility for p53-/- male mice. In the present study, on the CBA background, both DNA damage and apoptosis appeared to be elevated. The Msh2-/- mice exhibited early decreases in the number of germ cell precursors, but insignificant reductions in epididymal sperm numbers later on. Studies like this one, on the roles of DNA damage detection and repair pathway components during defined periods of spermatogenesis, are crucial to understanding how genomic integrity in the male germ line affects fertility and pregnancy outcomes. Moreover, such experiments provide a baseline for comparing the effects of environmental mutagens on reproduction and embryonic development.


Marchetti, F and Wyrobek, AJ (2005) Mechanisms and consequences of paternally-transmitted chromosomal abnormalities. Birth Defects Res. (Part C) 75, 112-129

Catriona Paul, Joanne E. Povey, Nicola J. Lawrence, Jim Selfridge, David W. Melton, Philippa T. K. Saunders (2007). Deletion of Genes Implicated in Protecting the Integrity of Male Germ Cells Has Differential Effects on the Incidence of DNA Breaks and Germ Cell Loss PLoS ONE, 2 (10) DOI: 10.1371/journal.pone.0000989

Posted by: barn owl | December 14, 2008

A meme I can live with …

… and not feel like a total boring loser. From Curiosity Killed the Cat, via Cath at VWXYNot?, an odd meme with all kinds of different experiences. I’ve emboldened the ones that I’ve done/experienced.

1. Started my own blog
2. Slept under the stars
3. Played in a band
4. Visited Hawaii
5. Watched a meteor shower
6. Given more than I can afford to charity
7. Been to Disneyland/world
8. Climbed a mountain
9. Held a praying mantis
10. Sung a solo
11. Bungee jumped
12. Visited Paris
13. Watched lightning at sea
14. Taught myself an art from scratch
15. Adopted a child
16. Had food poisoning
17. Walked to the top of the Statue of Liberty
18. Grown my own vegetables
19. Seen the Mona Lisa in France
20. Slept on an overnight train – overrated, at least if you’re tall and long-legged
21. Had a pillow fight
22. Hitchhiked
23. Taken a sick day when you’re not ill
24. Built a snow fort – didn’t expect that from a Texan, didja? Lived in Boston and Minneapolis as a child.
25. Held a lamb – squeee!
26. Gone skinny dipping
27. Run a Marathon
28. Ridden in a gondola in Venice
29. Seen a total eclipse
30. Watched a sunrise or sunset
31. Hit a home run
32. Been on a cruise
33. Seen Niagara Falls in person
34. Visited the birthplace of my ancestors – Germany and parts of the UK, but not Ireland
35. Seen an Amish community
36. Taught myself a new language
37. Had enough money to be truly satisfied – it required getting tenure, for the job security and health care coverage
38. Seen the Leaning Tower of Pisa in person
39. Gone rock climbing – With and without ropes
40. Seen Michelangelo’s David
41. Sung karaoke
42. Seen Old Faithful geyser erupt
43. Bought a stranger a meal at a restaurant
44. Visited Africa – my lifelong dream!!
45. Walked on a beach by moonlight
46. Been transported in an ambulance – rode with a friend who had been mugged, in London
47. Had my portrait painted
48. Gone deep sea fishing
49. Seen the Sistine Chapel in person
50. Been to the top of the Eiffel Tower in Paris
51. Gone scuba diving or snorkeling
52. Kissed in the rain
53. Played in the mud
54. Gone to a drive-in theater
55. Been in a movie
56. Visited the Great Wall of China
57. Started a business
58. Taken a martial arts class
59. Visited Russia
60. Served at a soup kitchen
61. Sold Girl Scout Cookies – I was a Camp Fire Girl >:-(
62. Gone whale watching
63. Got flowers for no reason
64. Donated blood, platelets or plasma – I’m O neg and CMV-free, and used to donate whole blood and platelets very regularly, until I was banned (lived in the UK for 3 years)
65. Gone sky diving
66. Visited a Nazi Concentration Camp
67. Bounced a check
68. Flown in a helicopter
69. Saved a favorite childhood toy – Are you kidding? My mom directed the play therapy programs at a large children’s hospital. I saved nothing – it all went to the playrooms.
70. Visited the Lincoln Memorial
71. Eaten caviar
72. Pieced a quilt
73. Stood in Times Square
74. Toured the Everglades
75. Been fired from a job
76. Seen the Changing of the Guards in London
77. Broken a bone – someone broke it for me, in a powderpuff football game
78. Been on a speeding motorcycle
79. Seen the Grand Canyon in person
80. Published a book
81. Visited the Vatican
82. Bought a brand new car – my current vehicle, a Honda Accord
83. Walked in Jerusalem
84. Had my picture in the newspaper
85. Read the entire Bible
86. Visited the White House
87. Killed and prepared an animal for eating – do crawfish and crabs count?
88. Had chickenpox
89. Saved someone’s life – water rescues and CPR assists, so debatable
90. Sat on a jury
91. Met someone famous
92. Joined a book club
93. Lost a loved one
94. Had a baby
95. Seen the Alamo in person – duh!
96. Swam in the Great Salt Lake
97. Been involved in a law suit
98. Owned a cell phone – but I forget to turn it on
99. Been stung by a bee
100. Ridden an elephant

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