Is There a Phylogenetic Signal in Prokaryote Proteins?

Using the sequence information from nine completely sequenced bacterial genomes, we extract 32 protein families that are thought to contain orthologous proteins from each genome. The alignments of these 32 families are used to construct a phylogeny with the neighbor-joining algorithm. This tree has several topological features that are different from the conventional phylogeny, yet it is highly reliable according to its bootstrap values. Upon closer study of the individual families used, it is clear that the strong phylogenetic signal comes from three families, at least two of which are good candidates for horizontal transfer. The tree from the remaining 29 families consists almost entirely of noise at the level of bacterial phylum divisions, indicating that, even with large amounts of data, it may not be possible to reconstruct the prokaryote phylogeny using standard sequence-based methods. Received: 22 November 1998 / Accepted: 17 February 1999     

Is There a Venoarterial Difference in α-Antitrypsin Levels?

Serum trypsin inhibitory capacity and α₁-antitrypsin concentrations were compared in venous and arterial bloods obtained simultaneously from patients with chronic airways obstruction. No significant venoarterial difference was observed in most patients, which was contrary to the published findings of Woolcock et al. (1972).     

Functional Traits in a Species-Rich Grassland and a Short-Term Change in Management: Is There a Competition-Colonization Trade-Off?

The species richness of grasslands generally cannot be fully restored after changes in management. Some species with small statures and basal leaf rosettes can be lost forever. The same species, however, seem to possess the traits necessary for successful re-colonization – they produce small, easily dispersable seeds, numerous seedlings and have lasting seed banks. We tested the hypothesis that plants in species-rich grasslands can be characterized by a negative correlation between their competitive ability and potential for generative regeneration, i.e. by a competition-colonization trade-off. An analysis of the traits of 95 grassland species supported this hypothesis. We then conducted a manipulative experiment in three different meadow communities in the Bílé Karpaty Mts. The experiment involved characterizing species traits during periods of different grassland management regimes in the years 1997–2000 and comparing these with the original management regime, which was restored between 2000 and 2003. We found out that the hypothesis only holds true for the pooled dataset for all three communities. When the individual meadow communities were analyzed separately, plant traits other than those responsible for the competition-colonization trade-off appear to be characteristic of responsive species, e.g. shoot lifespan or phenology. Our results imply that despite the general trade-offs found in large comparative studies, the plant response in a specific community is constrained by the local species pool.     

Is the Testis a Chemo-Privileged Site? Is There a Blood-Testis Barrier?

The incidence of testicular cancer, primarily seminoma, has been increasing in many countries, including the United States. The testis is often the site of residual cancer after adequate treatment with systemic chemotherapy. The blood-testis barrier is commonly cited as the explanation for residual tumor within the gonad after chemotherapy and as the indication for delayed orchiectomy. Conversely, complete eradication of viable tumor from the primary site is common and argues against the testis as a \"tumor sanctuary.\" Residual tumor is also demonstrated within metastatic foci, and the disparity between the histopathologic response of the primary tumor and metastatic sites may be best explained by tumor heterogeneity and multiple tumor clones. Regardless of the scientific and academic arguments, delayed radical orchiectomy remains an important part of treatment for patients undergoing primary chemotherapy.     

Neuronal Death: Is There a Role for Astrocytes?

Astrocytes are ubiquitous in the brain and have multiple functions. It is becoming increasingly clear that they play an important role in monitoring the neuromicroenvironment in CNS and in information processing or signaling in the nervous system in normal conditions and respond to CNS injuries in a gradual and varied way. It is still debated whether such reactions are beneficial or detrimental. It was believed that reactive astrogliosis observed in most neurological disorders may regulate the removal of toxic compounds produced by damaged neurons and support neuronal growth by releasing trophic factors. However it was also suggested that astrocytes contribute to a decline of neurologic function, for example by accumulation and release of excitotoxic aminoacids after ischemia and oxidative stress, formation of epileptogenic scars in response to CNS injury and metabolism of protoxins to potent toxins. In a number of metabolic diseases astrocytes, not neurons, may be the primary target. The astrocyte's role in normal and pathological conditions will be discussed in the light of recent information about their metabolism, receptor distribution and release.     

Is There a Role for the Apex in Shoot Geotropism?

Experiments with horizontal etiolated sunflower (Helianthus annuus L.) seedlings supported centrally such that both apical and basal ends are free to react to geostimulus, revealed that the apical end commences curvature 1 to 2 hours earlier than the basal end. The later curvature in the basal region is a consequence of the absence of growth in the initial period rather than merely slower growth. A comparison of zonal growth rates in a vertical and a horizontal seedling confirmed that geostimulus induces a renewal of growth in a region where growth had ceased. Removing the apical half of the hypocotyl showed that the curvature resulting from this growth initiation in the basal region is dependent on attachment to the apical region. Evidence that this dependence is unlikely to be due to energy deficiency is adduced. The prior response of the apical end to geostimulus and the apically dependent later initiation of new growth in the basal region are compatible with the delay inherent in message transport from apex to base and are considered as evidence for apical involvement in the totality of the seedling's georesponse.     

Diffusion- and Perfusion-Weighted Imaging in Acute Lacunar Infarction: Is There a Mismatch?

Purpose

Characterization of lacunar infarction (LI) by use of multimodal MRI including diffusion- and perfusion-weighted imaging (DWI, PWI) is difficult because of the small lesion size. Only a few studies evaluated PWI in LI and the results are inconsistent.

Methods

In 16 LI patients who underwent initial MRI within 6 hours after symptom onset and follow-up MRI within 1 week demographics, clinical presentation, and MRI findings were analyzed with special emphasis on DWI and PWI findings. Time to peak maps were classified as showing a normal perfusion pattern or areas of hypoperfusion which were further categorized in mismatch (PWI>DWI), inverse mismatch (PWI<DWI), and match (PWI=DWI). Quantitative perfusion maps were generated and analyzed by use of Signal Processing in NMR-Software (SPIN).

Results

Of the 16 patients (mean age 65.5±12.9 years), 14 (87.5%) were male. Clinical symptoms comprised dysarthria (50%), hemiparesis (81.3%), and hemihypaesthesia (18.8%). Intravenous thrombolysis was performed in 7 (43.8%) patients. Clinical improvement was observed in 12 patients (75 %), while 2 (12.5%) patients showed a deterioration and another 2 (12.5%) a stable course. Acute ischemic lesions (mean volume of 0.46±0.29 cm³) were located in the thalamus (n=8, 50%), internal capsule (n=4, 25%), corona Radiata (n=3, 18.8%) and the mesencephalon (n=1, 6.3%). Circumscribed hypoperfusion (mean volume 0.61±0.48 cm³) was evident in 10 (62.5%) patients. Of these, 3 patients demonstrated a match, 4 an inverse mismatch, and 3 a mismatch between DWI and PWI lesion. Mean CBF and CBV ratios were 0.65±0.28 and 0.84±0.41 respectively. Growth of DWI lesions was observed in 7 (43.8%) and reversal of DWI lesions in 3 (18.8%) patients.

Conclusions

MRI allows identification of different DWI and PWI patterns in LI, including growth and reversal of ischemic lesions. Consequently, it may serve for a better characterization of this stroke subtype and support treatment decisions in daily clinical practice.     

Different Reproductive Tactics in House Sparrows Signalled by Badge Size: Is There a Benefit to Being Average?

Sexual selection models usually predict directional selection for ornamental traits because of intra‐ as well as inter‐sexual selection. Animals frequently face reproductive trade‐offs, such as between mating and parental effort. Provided that both are essential and have opposite effects on ornament expression, we may however not necessarily expect directional selection for ornament size. The house sparrow is an ideal species to study such a trade‐off, as the size of the male ornament, the black throat badge, seems to be inversely related to mating and parental effort. It has been suggested that large‐badged males invest more in female attraction and territory defence, while small‐badged males may invest more in parental care. In a nest‐box study, we show that females started to breed earliest and produced the largest clutches when mated to males with average‐sized badges that invested in paternal care more than other males. These results are discussed in view of inter‐ as well intra‐sexual selection. Overall, average‐badged males experienced the highest hatching failures, their chicks were in the poorest physical condition and they did not fledge more chicks than other males. It is therefore unlikely that the mating advantages that we observed could by themselves lead to stabilizing selection for badge size. Our results rather suggest that badge size in male house sparrows signals different reproductive tactics, which are adapted flexibly according to their physical condition and socio‐ecological situations.     

Clinical Laboratory Personnel—Is There a Shortage in California?

In a study of vacancy rates for laboratory personnel in California to determine if there is in fact a serious or critical shortage of qualified individuals in this group of allied health professionals, it was found that while the answer is still elusive, it would appear that although the shortage may be somewhat greater than normal it is not critical in most areas of the state.For most areas, the situation seems to have improved from 1966 to 1968. There are a few geographical areas, predominantly rural, where shortages of licensed personnel are critical. Vacancy rates also are higher in hospital laboratories. Recruitment difficulties in these situations may be related to insufficient incentives, including but not necessarily limited to salaries.Training in California laboratories may facilitate recruitment in specific instances, and may assume greater importance in the future as working conditions for health professionals continue to improve in other states. And finally, the use of laboratory assistants, aides, and clerks can materially assist the laboratory work, thereby freeing the licensed professional staff to accept responsibilities commensurate with the increasing sophistication of laboratory knowledge and practice.     

Statistical Use in Clinical Studies: Is There Evidence of a Methodological Shift?

Background

Several studies indicate that the statistical education model and level in medical training fails to meet the demands of clinicians, especially when they want to understand published clinical research. We investigated how study designs and statistical methods in clinical studies have changed in the last twenty years, and we identified the current trends in study designs and statistical methods in clinical studies.

Methods

We reviewed 838 eligible clinical study articles that were published in 1990, 2000, and 2010 in four journals New England Journal of Medicine, Lancet, Journal of the American Medical Association and Nature Medicine. The study types, study designs, sample designs, data quality controls, statistical methods and statistical software were examined.

Results

Substantial changes occurred in the past twenty years. The majority of the studies focused on drug trials (61.6%, n = 516). In 1990, 2000, and 2010, there was an incremental increase in RCT studies (74.4%, 82.8%, and 84.0%, respectively, p = 0.013). Over time, there was increased attention on the details of selecting a sample and controlling bias, and there was a higher frequency of utilizing complex statistical methods. In 2010, the most common statistical methods were confidence interval for superiority and non-inferiority comparison (41.6%), survival analysis (28.5%), correction analysis for covariates (18.8%) and Logistic regression (15.3%).

Conclusions

These findings indicate that statistical measures in clinical studies are continuously developing and that the credibility of clinical study results is increasing. These findings provide information for future changes in statistical training in medical education.     

Is There a Role for the 42 Kilodalton Polypeptide in Inorganic Carbon Uptake by Cyanobacteria?

Cyanobacterial cells accumulate substantial amounts of a membrane-associated 42 kilodalton polypeptide during adaptation to low CO₂ conditions. The role of this polypeptide in the process of adaptation and in particular in the large increase in the ability to accumulate inorganic carbon (C_i), which accompanies this process, is not yet understood. We have isolated a mutant Synechococcus PCC7942 that does not accumulate the 42 kilodalton polypeptide. The mutant requires a high-CO₂ concentration for growth and exhibits a very low apparent photosynthetic affinity for extracellular C_i. The latter might be attributable to the observed defective ability of the mutant to utilize the intracellular C_i pool for photosynthesis. The 42 kilodalton polypeptide does not appear to participate directly in the active transport of C_i, since the difference between the observed capabilities for CO₂ and HCO₃⁻ uptake of the mutant and the wild type is not sufficient to account for their different growth and photosynthetic performance. Furthermore, high CO₂-grown wild-type cells, where we could not detect the 42 kilodalton polypeptide, transported CO₂ faster than the mutant. An analysis of the curves relating the rate of accumulation of C_i to the concentration of CO₂ or HCO₃⁻ supplied, in the presence or absence of carbonic anhydrase, indicated that under the experimental conditions used here, CO₂ was the preferred C_i species taken up by Synechococcus.     

Specific Lymphocyte Sensitization in Cancer: Is There a Common Antigen in Human Malignant Neoplasia?

From human cancer tissue a basic protein can be extracted by the method which yields encephalitogenic factor when applied to human brain. This tumour basic protein (obtained from several different neoplasms) acts as an antigen in the cytopherometric test for malignant neoplasia and in general gives higher results than does brain basic protein. The reverse is true when degenerative disease of the nervous system is studied. The basic protein extractable from brain and from tumours thus has some degree of specificity probably referable to its amino-acid sequence.     

Mitotic Instability in Cancer: Is There Method in the Madness?

It has been known for more than a century that neoplastic cells often exhibit disturbances of the mitotic process, but the causes have only recently been thoroughly explored. In many cancers, a combination of cell cycle checkpoint deficiency and abnormal shortening of telomeres predisposes to unbalanced chromosome segregation at cell division and the development of complex genomic rearrangements. Shortening of telomeric repeats beyond normal limits leads to fusion of chromosome ends and the formation of chromatin bridges at anaphase. In turn, these bridges may trigger at least three types of chromosomes mutation: (1) structural rearrangements of chromosomes through extensive chromatin fragmentation beyond the centromeric sequences, typically leading to the formation of isochromosomes and whole-arm translocations, (2) loss of whole chromosomes through mechanical detachment from the mitotic spindle machinery, and (3) failure of cytokinesis, leading to polyploidisation and supernumerary centrosomes, which may in turn orchestrate multipolar spindle configurations at a subsequent mitosis. Anaphase bridging rarely hinders further survival of tumour daughter cells. In contrast, multipolar mitoses may lead to extensive reshuffling of chromosome copies that compromise further clonal expansion. The telomere-dependent instability can be partly counteracted by expression of telomerase during tumour progression, but genomic stabilisation is rarely, if ever, complete.