A Synthesis of Literature on the Nuclear Lamina: Molecular mechanisms leading to laminopathic diseases [Science. Why not?]

Perkins BP, LSU Biological Sciences Undergraduate
May 9, 2008

The nuclear envelope is the double membrane that surrounds the nucleus and separates the genetic material and nucleoplasm from the cytosol in eukaryotic cells. It is composed of the inner and outer nuclear membranes (each consisting of a lipid bilayer), nuclear pore complexes, and the nuclear lamina. The nuclear envelope is also known to have some associations with chromatid. The space between the inner and outer nuclear membranes is called the perinuclear space (Mounkes et al., 2003). The outer membrane is covered in ribosomes and is continuous with the rough endoplasmic reticulum. The inner membrane is associated with the nuclear lamina (Wehnert and Bonne, 2002).

The major components of the nuclear lamina, the nuclear lamins, are Type V intermediate filaments (Mounkes et al., 2003). Lamins are evolutionarily conserved nuclear-specific intermediate filaments that support many nuclear functions that include maintaining nuclear shape, DNA replication, regulation of gene expression, transcription elongation by RNA Polymerase II, nuclear positioning, segregation of chromosomes, meiosis, and apoptosis (Wiesel et al., 2008). In metazoan cells there are four major lamin proteins encoded by three genes. The A-type lamins (lamins A and C) are different splice variants of the same gene, LMNA. The B-type lamins (lamins B1 and B2) are the products of two separate genes, LMNB1 and LMNB2 respectively (Meshorer and Gruenbaum, 2008).

All B-type lamins and lamin A (not lamin C) are synthesized with a conserved CaaX (Cysteine – aliphatic amino acid – aliphatic amino acid ‑ any amino acid) motif in their carboxyl tails that is subject to post-translational modifications (Liu and Zhou, 2008). The maturation of the prelamin begins with the farnesylation of the cysteine in the CaaX motif by a farnesyl transferase. Next, the last three residues on the carboxyl tail (aaX) are cleaved off by either Ras-converting enzyme (Rce1) or Zinc metalloproteases related to Ste24p (Zmpste24). As a result, the cysteine undergoes methylation by the isoprenylcysteine carboxyl methyltransferase. Prelamin A then undergoes a final processing step in which the 15 amino acids of the carboxyl tail, including the farnesyl group, are cleaved off by Zmpste24 (Fig. 1; Meshorer and Gruenbaum, 2008). The second cleavage of 15 amino acids at the carboxyl tail of prelamin A results in the removal of the farnesyl residue and subsequent dissociation of mature lamin A from the nuclear membrane (Mattioli et al., 2008). B‑type lamin, however, does not go through a second cleavage by Zmpste24 leaving B-type lamin constitutively farnesylated and associated with the nuclear membrane.

A-type and B-type lamins also differ based on the types of cells tin which they are expressed. All cell types express at least one of the B-type lamins, whereas some cells simply do not express, or express at significantly lower levels, the A-type lamins (e.g. cells of the early embryo, embryonic stem cells, stem cells in the immune and haematopoietic systems, and cells in the neuroendocrine system). The birth of mice with null mutations in their LMNA genes which were phenotypically indistinguishable from their wild type siblings during their first two weeks of postnatal development supported the hypothesis that A-type lamins are not essential to the overall development process (Mounkes et al., 2003). However, mutations in the human LMNA gene are the cause of at least 11 different heritable diseases that are commonly known as laminopathies (Wiesel et al., 2008).

The Laminopathies

One of the laminopathies that has drawn a great deal of attention from researchers is Hutchison‑Gilford progeria syndrome (HGPS). Hutchison-Gilford progeria syndrome is a disease in which the physical aspects of aging are accelerated (Fig. 2; Scaffidi et al., 2005). Most of the patients who suffer from Hutchison-Gilford progeria syndrome have a point mutation in the LMNA gene. This mutation results in the translation of a lamin A lacking 50 amino acids, including the second cleavage site in prelamin A. (Figure 1; Meshorer and Gruenbaum, 2008). The mutant protein (Called LAD50) is therefore constitutively farnesylated and incorporates abnormally into the nuclear lamina. This grouping of LAD50 proteins leads to mechanical defects, thickening of the lamina, loss of peripheral heterochromatin, and increased DNA damage, among other things. If farnesyl transferase inhibitors are administered, the cellular phenotypes can be treated. Also, mutations in the protein that performs the second cleavage (Zmpste24) lead to similar cellular phenotypes. This gives evidence for the hypothesis that the permanent farnesylation of the LAD50 protein is what leads to the diseases associated with this lamin A mutant. (Meshorer and Gruenbaum, 2008).

Unlike the pluripotent and rapidly growing embryonic stem cells, that do not express A-type lamins, somatic (adult) stem cells are tissue specific and highly dependent on their niche, from which they receive signals that influence the stem cells’ fates. The signaling mechanisms that are used by the different stem cell niches converge on four main pathways (Notch, Wnt, TGFβ, and Sonic hedgehog; Meshorer and Gruenbaum, 2008). The Notch signaling pathway is a major regulator of stem cell fate that has been implicated in premature aging. To study the molecular mechanisms that make the LAD50 mutant produce progeroid phenotypes, two separate stable cell lines, one with the LAD50 protein and the other with the wild type protein, were created and the gene expression of the two cell lines was compared. In the cells expressing LAD50, downstream signaling via the Notch pathway was induced by the Notch co‑activator Ski‑interacting protein which loses its grip due to the progerinated lamina produced by the LAD50 proteins. Because Notch is a major regulator of stem cell fate, and because they are the main tissue group that is affected by progeria, the mesenchymal stem cells were chosen to be studied in this experiment. In addition to activation of the Notch pathway, the mesenchymal cells responded to the mutant LAD50 protein by displaying sporadic, undirected differentiation along all three germ layers. This result shows the involvement of mesenchymal stem cell regulation in the pathology of Hutchison-Gilford progeria syndrome through the downstream activation of Notch signaling (Meshorer and Gruenbaum, 2008).

Emery-Dreifuss muscular dystrophy (EDMD) is another laminopathy which is usually inherited as either an X‑linked form of muscular dystrophy or an autosomal-dominant form. However, rare cases of autosomal recessive transmission have been reported (Wehnert and Bonne, 2002). Emery-Dreifuss muscular dystrophy is generally characterized by three symptoms which include early onset contractures (chronic loss of joint motion typically in elbows or achilles tendon), very slow progressive muscle weakness and degeneration involving the upper arms and lower legs, and cardiac disease in adult life (Wehnert and Bonne, 2002). It is caused by mutations in the STA gene which encodes emerin. Mutations in the STA gene almost always lead to the displacement of emerin from the nuclear envelope. (Mounkes et al., 2003). Emerin is anchored to the inner nuclear membrane by its carboxy-terminal tail, the remainder of the molecule resides in the nucleoplasm. It has several serine protein kinase sites and seems to have a role in the organization of the nuclear membrane during cell division (Fig. 3; Wehnert and Bonne, 2002). Emerin is known to interact with nuclear lamins and many of the lamin associated proteins including Barrier-to-autointegration factor (BAF) and Btf, a death promoting transcriptional repressor. The exact consequences of a loss of emerin from the nuclear envelope on the activities of these emerin-binding proteins remains to be established but it is clear that a lack of emerin due to a mutation in the STA gene is the cause of Emery‑Dreifuss muscular dystrophy (Mounkes et al., 2003).

Disease Causing Mechanisms

It has been sufficiently demonstrated in the above examples that mutations in nuclear lamin can lead to a diverse array of diseases. These laminopathies are a group of heritable diseases that are the product of mutations in genes that code for A‑type lamin and lamina-associated proteins. They include Emery-Dreifuss muscular dystrophy, Pelger-Huet anomaly, Limb girdle muscular dystrophy type 1B, dilated cardiomyopathy, Dunnigan’s familial partial lipodystrophy, mandibuloacral dysplaysia, Hutchison‑Gilford progeria syndrome, and more (Mounkes et al., 2003). The laminopathies show a wide variety of inheritance patterns and mechanisms of causing laminopathies. Some of the diseases resulting from mutations in laminal genes are tissue specific while others are harmful to multiple tissue types, all leading to the question: Why is it that mutations affecting the nuclear lamina give rise to such a diverse group of diseases? (Worman and Courvalin, 2004).

One hypothesis for the disease causing mechanism of these mutations involves defects in lamin synthesis caused by mutations in genes encoding the lamins. Although in metazoan cells B-type lamins are the products of two separate genes, in Caenorhabditis elegans B-type lamins are the product of a single gene. Most biological roles of mammalian lamins are evolutionarily conserved in C. elegans. In addition, the single C. elegans lamin probably functions both as A-type and B-type lamin. Recently, it has been shown that the B-type C. elegans lamin (Ce-lamin) is able to form stable intermediate filaments in vitro. Therefore, by inserting mutations into conserved residues in Ce-lamin that cause diseases when mutated in human lamin A, it can be investigated how mutations in specific residues of Ce-lamin corresponding to laminopathic disease causing mutations in the human LMNA gene affect filament and paracrystal assembly in vitro and lamin organization and dynamics in vivo. The assembly of the filaments and paracrystals can be seen using negative staining electron microscopy techniques. Fourteen laminopathic disease causing mutations were studied in this way; of the fourteen studied, only six of them showed evidence of disruption to the assembly of Ce-lamin filaments or paracrystals. This finding suggests that although defects in filament assembly may be one of the mechanisms that leads to laminopathies, it cannot be the only mechanism involved in causing these diseases (Wiesel et al., 2008).

The “mechanical stress” hypothesis of laminopathic disease diversity states that abnormalities in nuclear structure that are caused by mutations in lamin encoding genes can make the cell more susceptible to cellular damage that is caused by physical stress (Worman and Courvalin, 2004). Mutated cells under such conditions of stress show a significant redistribution of the proteins that are associated with the nuclear envelope and an increased fragility of the nucleus. In effect, cells that undergo large amounts of mechanical stress begin to function improperly. It would follow from the same line of reasoning, however, that the mechanical stress model is less likely to account for the defects in white adipose tissues that are associated with the diseases mandibuloacral dysplasia and Dunnigan’s familial partial lipodystrophy because of the lack of mechanical stress that is placed on these tissues on a consistant basis (Mounkes et al., 2003). Therefore, there must be yet another mechanism for the causal agent of these laminopathies.

The “gene expression” hypothesis on the diversity of laminopathic diseases suggests that LMNA mutations may affect the structure and function of the nucleus which can in turn have an effect on gene expression (Worman and Courvalin, 2004). A class of proteins known as the Nespirins localize to the nuclear envelope and interact with emirin and A-type lamins. These Nespirins appear to be integral to anchoring the nucleus to the interphase cytoskeleton. Such an interaction may be important to the correct transmission of mechanically induced signaling from the cell surface to the nucleus that could be potentially disrupted at many levels, including at the level of a nuclear envelope that is functioning improperly because of mutations in genes encoding laminal proteins (Mounkes et al., 2003).

Although there is not a common molecular mechanism for disease causing that unites all of the laminopathies, the models that we have thus far discovered and suggested are nonexclusive to each other, giving us room for models that can be used together to help find treatments for laminopathic diseases. Even without a single common mechanism of action among the laminopathies, many scientists are coming up with ideas on how to treat cells with LMNA mutations and people who suffer from crippling laminopathies. As was illustrated above, prelamin A processing is altered in some LMNA‑linked diseases, including Hutchison‑Gilford progeria syndrome, which leads to permanent farnesylation of the mutated lamin A protein. Permanently farnesylated lamin A is toxic to the cell and leads to cell dysfunction and diseased phenotypes (Meshorer and Gruenbaum, 2008). Accumulation of prelamin A in laminopathic cells causes severe heterochromatin defects, but chromatin organization and function can be recovered by treatment with mevinolin, an inhibitor of the hydromethyl–glutaryl-synthase which is indirectly impairing prelamin A farnesylation, in combination with the inhibitor of histone deacethylases trichostatin A (Mattioli et al., 2008). The cellular phenotypes of LMNA mutations can also be reversed through the use of farnesyl transferase inhibitors preventing the permanent farnesylation of the mutated lamin A. This again showcases the toxicity of the constitutively farnesylated LAD50 mutant (Meshorer and Gruenbaum, 2008).

In Conclusion

Whith all of the papers written about the nuclear envelope in general and the nuclear lamina and laminopathies it seems as though we have a grasp of much of the information dealing with mutations in laminal genes and laminopathies caused by them. But, the nuclear lamina is a complicated network that likely plays a role in DNA replication, chromatin organization, spatial arrangement of nuclear pore complexes, nuclear growth, mechanical stabilization of the nucleus, anchorage of the nuclear envelope proteins (Wehnert and Bonne, 2002), and many other things. There is such a plethora of protein-protein interactions, protein-nucleic acid interactions, protein‑enzyme interactions, activator and supressor relationships to genes that can possibly get mutated and produce proteins that interact inderictly with almost every other organelle in the cell that finding the exact purpose and reason for every protein interaction or the molecular mechanism of disease causing for all the laminopathies will take a long time to come. But, as long as people are suffering from degenerative laminopathic diseases, and as long as scientist continue to search for the answers to life’s questions and people’s problems, we will be making new discoveries about the cell, the nucleus, the nuclear envelope, the lamina, laminopathies for years to come.

Figures (Click Thumbnails for a Clearer Image):

Figure 1. Processing of lamin A in normal and HGPS cells. (left) The process of maturation of prelamin A. The first three steps are common to all CAAX proteins, including all B-type lamins. Inhibition of the second or third steps results in toxic lamin A accumulation, causing HGPS, restricted dermopathy (RD), or mandibuloacral dysplasia (MAD). The fourth step involves cleavage of 15 amino acids away from the terminal cysteine by Zmpste24. (right) The processing of prelamin A in the most common HGPS mutation, which deletes amino acids 607 – 656 (progerin / LAD50), including the second cleavage site of lamin A by Zmpste24 (Meshorer and Gruenbaum, 2008).

Figure 2. Hutchinson-Gilford Progeria Syndrome. HGPS is a childhood disorder caused by mutations in one of the major architectural proteins of the cell nucleus. (bottom, right) In HGPS patients the cell nucleus has dramatically aberrant morphology. (top, right) The uniform cell nucleus shape typically found in healthy individuals (Scaffidi et al., 2005).

Figure 3. Schematic view of the nuclear envelope. The nuclear envelope is composed of two lipid bilayer membranes, the nuclear pore complexes and the nuclear lamina. The outer nuclear membrane is continuous with the endoplasmic reticulum. The inner nuclear membrane is separated from the outer nuclear membrane by the perinuclear space, except at the nuclear pore complexes, where the outer and the inner nuclear membrane are connected. Underlying the inner membrane is the fibrous nuclear lamina. It is composed of two types of lamin proteins: A-type lamins (lamins A/C) and B-type lamins (B1 and B2). They interact with chromatin, BAF, and HP1 as well as with other proteins of the inner nuclear membrane as lamin B receptor LBR), lamina-associated proteins (LAPs), emerin, MAN1, and nurim. (Wehnert and Bonne, 2002).

Citations:

Liu B, & Zhou Z (2008). Lamin A/C, laminopathies and premature ageing. Histology and Histopathology, 23, 747-763

Mattioli E, Columbaro M, Capanni C, Santi S, Maraldi NM, D’Apice MR, Novelli G, Riccio M, Squarzoni S, Foisner R, & Lattanzi G. (2008). Drugs affecting prelamin A processing: effects on heterochromatin organization. Experimental. Cell Research., 314, 453-462

Meshorer E, & Gruenbaum Y. (2008). Gone with the Wnt/Notch: stem cells in laminopathies, progeria, and aging. Journal of Cell Biology, 181, 9-13

Mounkes L, Kozlov S, Burke B, & Stewart CL. (2003). The laminopathies: nuclear structure meets disease. Current Opinion in Genetics & Development, 13, 223-230

Scaffidi P, Gordon L, & Misteli T. PLoS Biol 3(11):e395. (2005). http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pbio.0030395 PLoS BiolWehnert MS, & Bonne G. (2002). The nuclear muscular dystrophies. Seminars in Pediatric Neurology., 9 (2), 100-107

Wiesel N, Mattout A, Melcer S, Melamed-Book N, Herrmann H, Medalia O, Aebi U, & Gruenbaum Y. (2008). Laminopathic mutations interfere with the assembly, localization, and dynamics of nuclear lamins. Proceedings of the National Academy of Sciences U.S.A., 105, 180-185

Worman HJ, & Courvalin JC. (2004). How do mutations in lamins A and C cause disease? The Journal of Clinical Investigation, 113, 349-351

 

Niche partitioning in orb-weaver spiders of Louisiana.

B. P. Perkins, LSU Biology Undergrad

Introduction

The competitive exclusion principle can be paraphrased in four words: Complete competitors cannot coexist (Hardin, 1960). Although some find this to be an over-simplified maxim that may cause some ecologists to overlook more important underlying evidence, it does raise some interesting questions in the curious mind (Cole, 1960). The principle states that if two distinct populations use the same resources, live sympatrically, and if one population is even slightly better at translating energy to reproductive success than the other; then the fitter population will eventually drive the less fit population to extinction (Hardin, 1960). However, there is another option for the less fit population. Character displacement is an evolutionary process that involves a directional selection toward niche divergence. Sympatric species whose niches originally overlap will have selective pressures on them that cause reduced niche overlap and allow the species to coexist (Molles, 2007).

This experiment looks at the apparent coexistence of three orb-weaver spider species in Louisiana: Gasteracantha cancriformis, Nephila clavipes, and Leucauge sp. Based on the exclusion principle explained above, if the three species inhabit the same ecological niche, the most successful species of spider should drive the others to extinction. Because there is more than one species of spider living sympatrically, it must be assumed that they partition the resources in some way that reduces niche overlap and allows for coexistence. The only question that remains is that of how the spiders actually divide the resources amongst themselves.

Enders (1974) showed that coexisting spider species can partition their niches by building webs at different heights in the forest to catch different types of prey. To test if the orb-weaver spiders that are being studied use this method of niche partitioning, the average web height of each species will be compared. If the spiders being tested use this method of vertical stratification for reducing niche overlap we will expect to see a significant difference in the web heights measured. Craig (1989) lumps understory orb-weaver spiders in Panama into two alternative foraging modes. Large spiders build one large web per feeding period whereas small spiders build a few smaller webs. To test if the orb-weavers in Louisiana use these alternative methods of foraging we will compare the average web area of each species. A significant difference in web area among species would be evidence supporting this method of niche partitioning. Barghusen et al. (1997) showed that the web of the common house spider is more efficient at capturing flies when the strand density is increased. Although orb weaver spiders are being studied, it can still be determined if they use alternative strand densities as a method of reducing niche overlap. To test this we will compare the strand and radii density of the spider webs measured to look for a significant difference among the species. A significant difference supports the hypothesis that they use this method of niche partitioning.

Methods

Field work.—Random samples of orb-weaver spiders were taken at two locations in Baton Rouge, Louisiana (Ben Hur Experimental Forest and Bluebonnet Swamp) over a two year time. One sample was taken during the fall semester of 2006 and the other was taken during the fall semester of 2008. Measurements were taken of the spider size (as measured by length), the height of the center of the web off of the ground, the longest length across a diameter of the web, the length of the diameter perpendicular to the longest diameter, the number of strands per five centimeters of web (strand density), and the number of radii around the web. Data was collected on three species of orb-weaver spiders (Gasteracantha cancriformis, Nephila clavipes, and Leucauge sp.).

Data analyses.—First the data was compiled from the measurements taken in the fall of 2006 and the fall of 2008. The web area was then calculated by multiplying together the two diameter lengths. The radii density was found by dividing the number of radii per web by the area of the web. Bar graphs were made showing the average spider length (to be used as a reference point for comparing spiders), average web height, average web area, strand density, and radii density with 95% confidence intervals. Finally, ANOVA and T-tests were performed on each group of data (spider length, web height, web area, strand density, and radii density) to determine if there are in fact any significant differences among the three species of spider.

Results (Boring and Technical, feel free to skip to the Discussion)

Figure 1 is a representation of the average sizes of the spiders measured. There is a significant difference in size among the three orb-weaver species (F_2,318 = 145.11, P = 1.66*10 ⁴⁵). Nephila clavipes is significantly larger than both Gasteracantha cancriformis (t₂₉₃ = 15.51, t_crit = 1.97, P = 4.86*10^-40) and Leucauge sp. (t₁₅₁ = 7.14, t_crit = 1.98, P = 3.66*10^-11). Leucauge sp. is significantly smaller than Gasteracantha cancriformis (t₁₉₂ = -6.14, t_crit = 1.97, P = 4.73*10^-9).

The average web heights for each species of spider measured are presented in Figure 2. There is a significant difference in the web height among the three species of orb-weaver spiders (F_2,318 = 40.17, P = 2.79*10^-16). Nephila clavipes have significantly higher webs off of the ground than both Gasteracantha cancriformis (t₂₉₃ = 5.06, t_crit = 1.97, P = 7.33*10^-7) and Leucauge sp. (t₁₅₁ = 7.83, t_crit = 1.98, P = 7.81*10 ¹³). Leucauge sp. have significantly lower webs to the ground than Gasteracantha cancriformis (t₁₉₂ = -6.40, t_crit = 1.97, P = 1.16*10^-9).

Figure 3 is a representation of the average web areas of the spiders. There is a significant difference in web area among the three species of orb-weaver spiders (F_2,318 = 19.10, P = 1.47*10^-8). Nephila clavipes have significantly larger web area than both Gasteracantha cancriformis (t₂₉₃ = 5.38, t_crit = 1.97, P = 1.54*10^-7) and Leucauge sp. (t₁₅₁ = 3.44, t_crit = 1.98, P = 0.0007). There is not a significant difference between the web areas of Gasteracantha cancriformis and Leucauge sp. (t₁₉₂ = 1.74, t_crit = 1.97, P = 0.08).

There is no significant difference among the strand densities (Figure 4; F_2,318 = 2.49, F_crit = 3.02, P = 0.08), but there is a significant difference in the radii densities among the three species of orb weaver spiders (Figure 5; F_2,318 = 45.04, F_crit = 3.02, P = 6.00*10^-18). Gasteracantha cancriformis and Nephila clavipes do not have a significant difference in radii density (t₂₉₃ = 0.27, t_crit = 1.97, P = 0.79). Leucauge sp. has a significantly larger radii density than both Gasteracantha cancriformis (t₁₉₂ = 7.94, t_crit = 1.97, P = 1.66*10^-13) and Nephila clavipes (t₁₅₁ = 6.94, t_crit = 1.98, P = 1.11*10^-10).

Discussion

The analysis of web heights shows that each species does build webs at different heights. The largest species (Nephila clavipes) had the highest webs and as spider size decreases (Gasteracantha cancriformis then Leucauge sp.) so does web height (Figure 1 & 2). This evidence supports the hypothesis that orb-weaver spiders use the vertical stratification method of niche partitioning. The spiders likely build their webs at different heights to catch different types of bugs, affectively reducing niche overlap and promoting coexistence. However, the web height could also be a function of web area. Larger webs will naturally need to be higher off of the ground than smaller webs; therefore, we must also take into consideration the analysis of web area to determine the method of niche partitioning for these spiders.

The web area analysis shows that Nephila clavipes have significantly larger webs than both Gasteracantha cancriformis and Leucauge sp., but there is not a difference between the web areas of the latter two species (Figure 3). This supports Craig’s (1989) observation of two alternative foraging modes in orb weaver spiders. The larger Nephila clavipes builds a larger web whereas the other two species build smaller webs. This allows the spiders to divide the resources and not drive one another to extinction. Because we did not count the number of webs each spider built there is more research that must be done to determine if the spiders use these exact two methods, but this is a step in that direction.

Finally, there was no difference between strand densities of the spiders (Figure 4), and only Leucauge sp. had a different radii density (Figure 5). This does not support the hypothesis that orb-weaver spiders use strand density as a method of niche partitioning. If web thread density was a factor used to decrease niche overlap then we would expect to see each species with a different strand or radii density, but that is not the case. The spiders must use some other method of promoting niche divergence in order to coexist in the same environment.

These data suggest a combination of methods that spiders use to minimize niche overlap. While, to the untrained observer, it seems that the spiders all use the same resources and thus must drive one another to extinction, upon closer observation they are not actually complete competitors . A combination of web height and size is seen to be used by the orb-weavers to divide resources, but the strand and radii densities did not seem to play a role. This all suggests a complicated relationship between many different factors that allow multiple species to live in the same environment. Further research into alternative foraging modes in spiders from different places could shed light on the orb weavers. It would also be interesting to compare these data with data from spiders of the same species from different locations. The methods found to be used by the spiders studied in this experiment could have come about solely as a function of the local fauna. The same species compared from a different location could give a different order in the stratification of the webs, or a whole new method of niche partitioning altogether. Whether, like Cole (1960) said, the competitive exclusion principle is a trite maxim or not; it opens the door for some interesting research in the field of Ecology.

Citations

BARGHUSEN, L., CLAUSSEN, D., ANDERSON, M., & BAILER, A. (1997). The effects of temperature on the web-building behaviour of the common house spider, Achaearanea tepidariorum Functional Ecology, 11 (1), 4-10 DOI: 10.1046/j.1365-2435.1997.00040.x

Cole, L. (1960). Competitive Exclusion Science, 132 (3423), 348-349 DOI: 10.1126/science.132.3423.348

Craig CL. (1989). Alternative foraging modes of orb weaving spiders. Biotropica, 21 (3), 257-264

Enders, F. (1974). Vertical Stratification in Orb-Web Spiders (Araneidae, Araneae) and a Consideration of Other Methods of Coexistence Ecology, 55 (2) DOI: 10.2307/1935219

Hardin, G. (1960). The Competitive Exclusion Principle Science, 131 (3409), 1292-1297 DOI: 10.1126/science.131.3409.1292

Molles M. 2007. Ecology: Concepts and Applications. 4th ed. McGraw Hill. NY. 309-317.

(Pictures thanks to Wikipedia)

 

Microbial Genetics (2): Genetic Nomenclature

Genetic Nomenclature

The phenotype of an organism consists of the observable traits of that organism. The genotype is the actual genetic composition of the organism, its genes and alleles. There are commonly accepted rules followed when naming the phenotypes and genotypes in bacteria, although notations can vary. The phenotype is designated using a three letter code with the first letter capitalized. Superscripts are used to distinguish mutant (-) from wild-type (+) phenotypes. A particular bacteria’s ability to synthesize tryptophan, for example, would be written Trp⁺. However, when describing an organism’s phenotype, the mutant traits, such as the inability to synthesize tryptophan (Trp^–), and not the wild type traits are listed. Antibiotic resistance is written using a similar three letter code, but instead of ‘+’ or ‘-‘ superscripts an ‘r’ is used for resistance and an ‘s’ for sensitivity. E. coli‘s resistance to the antibiotic Eryhtromycin would be written Erm^r.

Genotypic descriptions are written using a three letter code related to the phenotypic designation. For the genotypic designation, however, all three letters are lower case and either italicized or underlined. Also different for genotypic designations is that by simply mentioning a gene it is assumed that it is a mutant. Take the following genotype and respective phenotype for example:

• genotype: trp, met, lys
• phenotype: Trp^–, Met^–, Lys^–

The ‘-‘ mutant superscript is assumed in the phenotype by simply designating the gene in the genotype. It is possible for one protein to be encoded by more than one gene. In such a case an upper case letter (which is also italicized) is added to the end of the three letter gene description. Tryptophan synthetase, the enzyme which catalyzes the final step in the biosynthesis of tryptophan, is encoded by both the trpA gene and the trpB gene. It is even possible to have different mutations in the same gene. In that case a number is added to the end of the gene designation. Mutations in different alleles of the trpA gene could be written trpA1 or trpA32. Finally, a specific nucleotide deletion can be represented using a ‘Δ’ before the gene and the designation for the particular nucleotide after.

• genotype: recA1, thi, trpB2, Δ(lacZ)m15
• phenotype: RecA^–, Thi^–, TrpB^–, LacZ^–

And here are some links to pages about genetic nomenclature used for specific organisms:

E. coli genome project:

‘The E. coli Genome Project at the University of Wisconsin-Madison had its genesis in an editorial by Frederick R. Blattner in the November 18, 1983 issue of Science, in which he raised the idea of completely sequencing the E. coli (and human) genomes:’

“At present the worldwide accomplishment in DNA sequence amounts to 2.3 x 10e6 base pairs, representing 2500 individual sequences. It is now becoming more or less routine to sequence completely the DNA of whole genetic entities ranging from single genes through multigene families to simple life forms such as viruses and phage. Currently the largest single DNA molecule to have been sequenced is the phage lambda genome (48502 base pairs). We are beginning to recognize that determination of the total genetic specification of more advanced life forms may be a possibility in the relatively near future. Extension of this principle to bacteria (genome size 5 x 10e6 base pairs) — the simplest free living forms — would require an increase of the worldwide technical effort by only a factor of 2. Some three orders of magnitude more would be needed to progress to the total human genome.”

— F. R. Blattner (1983) “Biological Frontiers” Science 222(4625), 719-720. [not indexed in PubMed]

‘In that same year we began isolation of an overlapping lambda clonebank of E. coli K-12 strain MG1655. Those clones served as the starting material in our initial efforts to sequence the whole genome. Improvements in sequencing technology have since reached the point where whole-genome sequencing of microbial genomes is routine, and the human genome has in fact been completed. But in those early years of radioactive sequencing reactions and manual reading of autoradiographs, it was a daunting undertaking…’

Mouse Nomenclature Home Page:

‘The Mouse Genome Informatics Database is the authoritative source of official names for mouse genes, alleles, and strains. Nomenclature follows the rules and guidelines established by the International Committee on Standardized Genetic Nomenclature for Mice.’

Genetic nomenclature for Drosophila melanogaster:

‘The nomenclature guidelines below explain how FlyBase assigns canonical symbols and names to its genetic objects (genes, alleles, transposons, insertions, aberrations and balancers). We encourage the community and journals to adhere to FlyBase-approved symbols/names for consistency in published datasets. While these guidelines cover most circumstances, there may be exceptional cases not clearly covered here. Please contact FlyBase to discuss such cases or any other aspect of the nomenclature.’

Guidlines for Human Gene Nomenclature:

‘Guidelines for human gene nomenclature were first published in 1979 [1], when the Human Gene Nomenclature Committee was first given the authority to approve and implement human gene names and symbols. Updates of these guidelines were published in 1987 [2],1995 [3], and 1997 [4].  With the recent publications of the complete human genome sequence there is an estimated total of 26,000-40,000 genes, as suggested by the International Human Genome Sequencing Consortium [5] and Venter et al. [6].  Thus, the guidelines have been updated to accommodate their application to this wealth of information, although symbols are still only assigned when required for communication. These updates were derived with input from the HUGO Gene Nomenclature Committee (HGNC) International Advisory Committee and attendees of the ASHG01NW Gene Nomenclature Workshop.  All approved human gene symbols can be found in the HGNC database [7].’

‘The philosophy of the HGNC remains “that gene nomenclature should evolve with new technology rather than be restrictive as sometimes occurs when historical and single gene nomenclature systems are applied” [2].’

‘A summary of the guidelines is presented here:
1. Each approved gene symbol must be unique.
2. Symbols are short-form representations (or abbreviations) of the descriptive gene name.
3. Symbols should only contain Latin letters and Arabic numerals.
4. Symbols should not contain punctuation.
5. Symbols should not contain “G” for gene.
6. Symbols do not contain any reference to species, for example “H/h” for human.’

(Header Image: Petri Dish Art)

 

Why Texas? Why!?!?!

‘WHITEHOUSE, TX (KLTV) – The school year is almost here, and if literature of the Bible is not already offered in your child’s school, it will be this fall.’

‘Books are a common sight in classrooms around the nation,  but the Bible is one book that is not. Come this fall, a Texas law says all public schools must offer information relating to the Bible in their curriculum.’

The law was actually passed in 2007 but first goes into effect for the 2009-2010 school year. Here you can find a copy of it to read over yourself. Take special notice of the part that lays out the required curriculum:

Of course they have the obligatory ‘a course offered under this law shall not endorse, favor, or promote, or disfavor or show hostility toward any particular religion or nonreligious faith or religious perspective.’ But I imagine Texas schools wont be requiring classes on the Talmud, Q’uran, Tao Te Ching, LaVey’s Satanic Bible, Dianetics, Eastern Orthodox Bible, Wicca, or Militant Atheist texts any time soon.

(Header Image: The Great Desecration)

 

Microbial Genetics (1)

A Basic Introduction

All of the organisms on earth have been classified into one of three major divisions.

1. eubacteria
2. archaea
3. eukaryotes

Most of the genetic diversity on Earth is represented by microbes. Recent data have shown that humans differ from chimpanzees by only 1.5% of their DNA sequences. Eukaryotic DNA sequences are so similar that the genome of one species can be used to predict the genome of others. In a typical bacterium, however,  25-50% of the genes are unique to that species.

Archaea

Archaea (formerly known as the archaebacteria) are single-celled microbes mostly represented by extremophiles, organisms that live under conditions where other types of organisms cannot survive. Until recently the archaea were classified in the same group as eubacteria; however, comparisons of transcription factors and membrane ATPases suggest that archaea are more closely related to eukaryotes than eubacteria. Substantially less is known about the archaea than about the eubacteria which are thus often referred to as just ‘bacteria’.

True Bacteria

The eubacteria consist of a wide variety of single- and multi-cellular species, some with complex developmental cycles. They are divided into two subgroups based on the results of a Gram stain test.

1. gram-negative cells (stain pink)
2. gram-positive cells (stain purple)

There are four basic steps of the Gram stain. A primary stain (crystal violet) is applied to a heat-fixed smear of a bacterial culture, followed by the addition of a mordant (Gram’s iodine), rapid decolorization with alcohol or acetone, and counterstaining with safranin or basic fuchsin. Gram-negative bacteria are surrounded by thin inner and outer membranes which retain little of the dye resulting in a pink cell. Gram positive bacteria have a thick cell wall made of peptidoglycan which retains much of the dye resulting in a deep blue or purple cell.

Gram stained cerebrospinal fluid showing gram-positive anthrax baccilli (purple rods).

Eubacteria Examples

The genus Myxococcus consists of gram-negative bacterium that exist as free-living single-celled organisms during part of their lifecycle and can aggregate and self-organize to form fruiting bodies in response to environmental cues. Epulopiscium fishelsoni is one of the largest bacterium known, and because of this it has evolved some curious adaptations. The gram-positive Epulopiscium reproduces exclusively through an unusual form of sporulation reminiscent of vivipary. Anywhere from one to twelve daughter cells are grown inside of the parent cell until the cell eventually lyses and the new bacteria burst through the cell wall. Another member of the eubacteria, the actinomycetes, are used by the Attine tribe of ants for the antibiotics produced by the fungus-like bacteria. The actinomycete-produced antibiotics protect the ants’ fungal gardens from infection by a parasitic fungus (Escovopsis).

Chloroplasts and Mitochondria

Current evidence indicates that eukaryotic mitochondria and chloroplasts are descended from free-living eubacteria that formed a symbiosis with eukaryotes. Comparisons of highly conserved ribosomal RNA (rRNA) gene seuences suggest mitochondria are descended from the proteobacteria and chloroplasts are descended from the cyanobacteria. In fact, some dinoflagellates (eukaryotes) are known to engulf cyanobacteria when it is light out, allowing the dinoflagellates to photosynthesize, then discard the cyanobacteria at night when they have no use for them.

Why more is known about some bacteria than is known about any other type of organism.

What is currently know about the basic molecular mechanisms in cells is a result of studies of bacteria. This is because bacteria are relatively easy to manipulate genetically. Bacteria are haploid organisms. In diploid organisms most mutations are recessive making them difficult to identify. Mutations in haploid organisms usually have an immediate, easily identifiable effect. Bacteria also hav short generation times. The shorter the generation time the more experiments that can be done. Some strains of Escherichia coli (E. coli) can reproduce every 20 minutes under ideal conditions. The asexual reproduction used by bacteria makes it is easy to obtain a large number of identical organisms to perform experiments on. Every daughter cell is a clone of the mother. With bacteria there is no sex to complicate genetic experiments. The ability to grow colonies on agar plates allows researchersto produce a large number of organisms in a small place, and no matter how crowded the bacteria are on the original agar plate, it is possible to isolate a pure strain of the bacterium in one or a few steps of colony purification. Using serial dilutions a measurable number of discrete colonies can easily be obtained from a densely concentrated culture. One of the major advantages of bacterial genetics is the opportunity to isolate rare mutants or other strains of bacterium. Using the proper selective growth conditions a single bacterium can be seleted from among billions placed on an agar plate. Finally, the three methods of genetic exchange between bacteria (transformation, conjugation, and transduction) allow for the possibility of all the genetic exepriments performed on microbes.

(Header Image: Epulopiscium)

 

Brilliant

 

Scientia pro publica # Seven

Scientia pro publica is a blog carnival dedicated to bringing together in one place links to the best of science blogging that would be of general interest. The new Scientia pro publica is up over at Greg Laden’s Blog and yours truly has an article featured. Go check out some of the other articles and see what you like.

(Header Image)

 

The Pseudoscience Chronicles Volume 3:Girls will be girls and boys will be boys.

Perusing our friend Timberwraith’s blog, Haunted Timber, I came across an amazing story I had to share. It is about two 24 year old Swedish parents who are raising their child not as a boy or a girl, but as a child. I recommend reading what Timberwraith had to say here. You can go here to read the story in english, or here for some Swedish.

Let me start by saying that this was not intended to be a Pseudoscience Chronicles post (I just enjoyed the story) until I read what one of the interviewees had to say ten paragraphs in. I was shocked at first by what Susan Pinker said (in the english version of the story), but then was not surprised to find out that she is a psychologist and journalist:

‘“Ignoring children’s natures simply doesn’t work,” says Susan Pinker, a psychologist and newspaper columnist from Toronto, Canada, who wrote the book The Sexual Paradox, which focuses on sex differences in the workplace.’

‘“Child-rearing should not be about providing an opportunity to prove an ideological point, but about responding to each child’s needs as an individual,” Pinker tells The Local.’

It’s ironic how she claims that raising a child should be about responding to each child’s individual needs, then goes on to say we should force children into preconceived gender-roles. If anything, keeping the child’s sex a secret allows the parents to respond to their child’s actual needs rather than the artificial needs implanted by a cultural construction that attempts to fit every single person in the world into one of two restricted categories. So I guess what she was actually trying to say was that child-rearing should only be about providing an opportunity to prove an ideological point if that ideological point is ‘gender exists get used to it’.

Pinker goes on to make some more crazy claims:

‘“I don’t think that trying to keep a child’s sex a secret will fool anyone, nor do I think it’s wise or ethical,” says Pinker. “As with any family secret, when we try to keep an elemental truth from children, it usually blows up in the parent’s face, via psychosomatic illness or rebellious behaviour.”’

Of course, the parents are not keeping any truth from the child (I don’t even know how they would do that). They are simply allowing the child to grow into what it wants to be.  They are responding to their child’s needs as an individual. They are being good parents.

With that, I would like to welcome Susan Pinker to the Pseudoscience Chronicles.

-Bryan Perkins

(Header Image: Hijras India’s Third Gender)

 

It’s a Wonderful Day for Anthropology

Sophie, an author from the old Science. Why not?, has a shiny new wordpress blog as well. She calls it A Wonderful Day for Anthropology. Here is a little from the About page:

‘Originally interested in Psychology and Sociology, I finally found my calling in the holistic field of Anthropology.  Although I haven’t declared a concentration, I anticipate this blog will be a helpful resource. I hope to explore Archaeological, Biological, Cultural, and Linguistic Anthropology to the fullest extent and learn from others who share my passion for the field.’

You can find her first post here. Read it, leave comments, and enjoy. I know I will.

-Bryan Perkins

 

The Pseudoscience Chronicles Volume 2: Spirituality is about as good for your health as sugar pills.

I don’t read Time Magazine much, but I recently acquired some old issues and I found one I would like to share with everyone. On February 23 Time printed the ‘Mind & Body Special Issue: How Faith Can Heal’, and I had a few problems with the article entitled ‘The Biology of Belief‘ by Jeffrey Kluger.

The article begins with a subtitle that sets the stage for the rest of the piece:

‘Science and religion argue all the time, but they increasingly agree on one thing: a little spirituality may be very good for your health.’

From the start we can smell the agenda behind Kluger’s words. ‘Scientists increasingly agree’ likely means that there have been a couple of new studies published attempting to convince us that any correlation between spirituality, in the broadest sense of the word, and health absolutely proves causation. ‘A little spirituality is good for your health’ will likely be transformed into ‘religion heals ills when medicine just can’t do it’. But let’s try not to make too many presumptions yet.

In the first two paragraphs Kluger claims that the parietal lobe makes ‘your brain the spiritual amusement park it can be.’ He obviously knows the names and locations of some brain regions, but he gives no clear description of what each lobe does and how they produce a ‘spiritual amusement park’ in your brain. Either he hopes to explain it to us later, or we just have to take his word for it.

Five paragraphs into the article we finally get to it. ‘A growing body of scientific evidence suggest that faith may indeed bring us health.’ Boom! ‘People who attend religious services have a lower risk of dying in any one year than people who don’t attend.’ Boom! ‘People who believe in a loving God fare better after a diagnosis of illness than people who believe in a punitive God.’ Boom!?!

Kluger does the arguing for me in the very next paragraph:

‘You live longer if you go to church because you’re there for the cholesterol-screening drive and nurse visiting service. Your viral load goes down when you include spirituality in your fight against [disease] because your levels of cortisol–a stress hormone–go down first.’

Faith and religion are not what is causing an increase in life expectancy, there is nothing supernatural about it. There is no reason to use spirituality and religion to explain coincidental correlation.

But Bryan, didn’t you read? ‘People who believe in a loving God fare better after a diagnosis of illness than people who believe in a punitive God.’ Who cares? This tells me nothing. Do people who believe in a loving God live longer than those who believe in a punitive God, or do they simply take the news better when they are told that they are going to die? If they don’t survive longer, then this has nothing to do with the effect of spirituality on physical health. This evidence simply compares two subsets of spiritual people who believe in different types of God. On the one hand spirituality is good for you but on the other it isn’t good for you. Faith can heal, but only the right faith. All this does is underle the subjectivity of religion. I wonder how atheists fare after being diagnosed with an illness, but I am sure that didn’t fit with the intended message of Kluger’s article.

IT’S ALL IN YOUR HEAD

Kluger then goes on to discuss the work of Dr. Andrew Newberg a professor of radiology, psychology, and religious studies at the University of Pennsylvania. ‘Newberg and his team have come to recognize just which parts of the brain light up during just which experiences.’ (By this I assume that Kluger means they took brain scans of individuals performing particular activities and determined which areas were in use when). Yet again this holds no support for the idea that faith and spirituality will give you good health. We merely see that for every activity that we as humans perform, there is some region of our brain that is involved.

Not only did Newberg and Team determine which areas are involved in each task, they also scanned the brains of people before and after meditation training. What they found was that meditation training increased the size of certain lobes of the brain, and as the lobes bulked up memory improved. In other words, intense mind training increases the size and functionality of a person’s brain. (No $&!# Sherlock?)

Of course there was no comparison between the improvement of a person who was subjected to calculus training or learned how to play a musical instrument, I am sure they too would have an increase in brain size and memory capacity. But who cares about finding all of the evidence when the evidence you have now supports the hypothesis that you want to be correct?

Kluger goes on to describe ‘one of the staples of traditional wellness protocols and traditional religious rituals the cleansing fast, which is said to purge toxins in the first case and purge sins or serve other pious ends in the second.’ And again, in the very next paragraph, he explains and then immediately dismisses science that counters his claim that spirituality (in this instance fasting) is healthful:

‘The brain is a very energy-intensive organ, one that requires a lot of calories to keep running. When food intake is cut, the liver steps into the breach, producing glucose and sending it throughout the body — always making sure the brain gets a particularly generous helping. The liver’s reserve lasts only about 24 hours, after which, cells begin breaking down the body’s fats and proteins — essentially living off the land. As this happens, the composition of the blood — including hormones, neurotransmitters and metabolic by-products — changes. Throw this much loopy chemistry at a sensitive machine like the brain and it’s likely to go on the blink. “There are very real changes that occur in the body very rapidly that might explain the clarity during fasting,” says Dr. Catherine Gordon, an endocrinologist at Children’s Hospital in Boston. “The brain is in a different state even during a short-term fast.” Biologically, that’s not good…’

Biologically fasting is not good for your health; even if the ‘light-headed sense of peace, albeit brief, that comes with it reinforces the fast and [seemingly] rewards you for engaging in it all the same.’ So far that is the most revelatory news I have read in this article. Not because it wasn’t obvious that fasting is not good for your health in the first place. Rather because the most concrete evidence that Kluger has presented thus far is the exact opposite of what he is trying to claim. He as shown only that spirituality (particularly fasting) is not good for your health.

HOW POWERFUL IS PRAYER

This is one of my favorite sections in this article. Kluger begins by telling us that most believers and very serious theologians ‘believe in the power of so-called intercessory prayer to heal the sick.’ Plus, Kluger tells us, some very serious scientists have ‘looked at’ this question as well. More than 6,000 studies have been published on the topic since 2000. I wonder which of these 6,000 studies Kluger will use to support the idea that prayer will help your health, let’s see:

‘As long ago as 1872, Francis Galton, the man behind eugenics and fingerprinting, reckoned that monarchs should live longer than the rest of us, since millions of people pray for the health of their King or Queen every day. His research showed just the opposite — no surprise, perhaps, given the rich diet and extensive leisure that royal families enjoy. An oft discussed 1988 study by cardiologist Randolph Byrd of San Francisco General Hospital found that heart patients who were prayed for fared better than those who were not. But a larger study in 2005 by cardiologist Herbert Benson at Harvard University challenged that finding, reporting that complications occurred in 52% of heart-bypass patients who received intercessory prayer and 51% of those who didn’t. Sloan says even attempting to find a scientific basis for a link between prayer and healing is a “fool’s errand” — and for the most basic methodological reason. “It’s impossible to know how much prayer is received,” he says, “and since you don’t know that, you can’t determine dose.”‘

Wait. So your saying the widely excepted research suggests that 52% of patients who did receive prayer suffered complications and 51% of people who did not receive prayer suffered complications. Meaning there is no significant difference between patients who recieve prayer and patients who don’t. So, again, spirituality is not helping.

Finally, Kluger goes on to discuss his only relevant scientific claim in this whole article, that of the placebo effect. If I opened up this issue and read a four page article about the placebo effect I would have no problem with it. They could mention that prayer, religion, faith, and spirituality can all have a placebo effect, but also that the placebo effect can be produced by much more. They would tell us that it can also be produced by sugar tablets, sham surgery, or belief in any false information (including that of faith and religion already discussed). They would not exaggerate the affectiveness of spirituality to undermine the truth that evidence supports. The fact that spirituality is about as good for your health as sugar pills.

In conclusion, welcome to The Pseudoscience Chronicles Jeffrey Kluger.

-Bryan Perkins

(Header Image: ‘Gris-gris‘ by: Charles M. Gandolfo; New Orleans Historic VooDoo Museum)